├── .gitignore ├── .gitmodules ├── LICENSE ├── README.md ├── assets └── SDE-harness-logo_00.png ├── config ├── credentials.template.yaml └── models.template.yaml ├── docs └── Quick_Integration_Guide.md ├── environment.yml ├── examples ├── EXAMPLES_OVERVIEW.md ├── README.md ├── advanced_usage │ ├── 01_custom_metrics.py │ └── README.md ├── basic_usage │ ├── 01_generation_basics.py │ ├── 02_oracle_basics.py │ ├── 03_prompt_basics.py │ ├── 04_workflow_basics.py │ ├── 04_workflow_basics_mock.py │ └── README.md ├── generation_examples.py ├── history_workflow_examples.py ├── integration_examples │ ├── 01_cli_integration.py │ └── README.md └── project_examples │ ├── README.md │ ├── run_llmeo_example.py │ └── simple_optimization │ ├── README.md │ ├── config.yaml │ ├── run_optimization.py │ └── sample_data.json ├── projects ├── bio-discovery-agent │ ├── .gitignore │ ├── CEGv2.txt │ ├── LICENSE │ ├── README.md │ ├── README_REFACTORING.md │ ├── _archive │ │ ├── ARCHIVE_SUMMARY.md │ │ ├── analyze.py │ │ ├── analyze_new.py │ │ ├── analyze_predictions.py │ │ ├── baseline.py │ │ ├── get_gene_summary.py │ │ ├── research_assistant.py │ │ ├── research_assistant_new.py │ │ ├── src │ │ │ └── modes │ │ │ │ ├── perturb_genes_backup.py │ │ │ │ ├── perturb_genes_fixed.py │ │ │ │ └── perturb_genes_with_scores.py │ │ ├── test_refactor.py │ │ └── tools.py │ ├── assets │ │ ├── icon.jpg │ │ └── simple_outline.png │ ├── cli.py │ ├── data │ │ ├── README.md │ │ ├── schmidt.py │ │ ├── schmidt_ifng_d1.gene_summary.txt │ │ ├── schmidt_ifng_d2.gene_summary.txt │ │ └── screen.py │ ├── datasets │ │ ├── ground_truth_Carnevale22_Adenosine.csv │ │ ├── ground_truth_Horlbeck.csv │ │ ├── ground_truth_IFNG.csv │ │ ├── ground_truth_IL2.csv │ │ ├── ground_truth_Sanchez21.csv │ │ ├── ground_truth_Sanchez21_down.csv │ │ ├── ground_truth_Scharenberg22.csv │ │ ├── ground_truth_Steinhart_crispra_GD2_D22.csv │ │ ├── task_prompts │ │ │ ├── Carnevale22_Adenosine.json │ │ │ ├── Horlbeck.json │ │ │ ├── IFNG.json │ │ │ ├── IL2.json │ │ │ ├── Sanchez21.json │ │ │ ├── Sanchez21_down.json │ │ │ ├── Scharenberg22.json │ │ │ └── Steinhart_crispra_GD2_D22.json │ │ ├── topmovers_Carnevale22_Adenosine.npy │ │ ├── topmovers_Horlbeck.npy │ │ ├── topmovers_IFNG.npy │ │ ├── topmovers_IL2.npy │ │ ├── topmovers_Sanchez21.npy │ │ ├── topmovers_Sanchez21_down.npy │ │ ├── topmovers_Scharenberg22.npy │ │ └── topmovers_Steinhart_crispra_GD2_D22.npy │ ├── pytest.ini │ ├── requirements.txt │ ├── src │ │ ├── __init__.py │ │ ├── evaluators │ │ │ ├── __init__.py │ │ │ ├── bio_metrics.py │ │ │ └── oracle_evaluator.py │ │ ├── modes │ │ │ ├── __init__.py │ │ │ ├── analyze.py │ │ │ ├── baseline.py │ │ │ └── perturb_genes.py │ │ ├── tools │ │ │ ├── LLM.py │ │ │ ├── README.md │ │ │ ├── __init__.py │ │ │ ├── achilles.py │ │ │ ├── gene.py │ │ │ └── get_lit_review.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── data_loader.py │ │ │ ├── gene_utils.py │ │ │ ├── llm_interface.py │ │ │ ├── prompts.py │ │ │ └── tools.py │ └── tests │ │ ├── README.md │ │ ├── __init__.py │ │ ├── run_tests.py │ │ ├── test_bio_metrics.py │ │ ├── test_data_loader.py │ │ ├── test_llm_interface.py │ │ ├── test_modes.py │ │ ├── test_oracle_evaluator.py │ │ └── test_oracle_integration.py ├── chat-mof │ ├── .gitignore │ ├── README.md │ ├── cli_generate_verify.py │ ├── data │ │ └── coremof.xlsx │ ├── requirements.txt │ └── src │ │ ├── __init__.py │ │ ├── generation.py │ │ ├── mof_name_generator.py │ │ ├── oracle.py │ │ ├── prompt.py │ │ └── workflow.py ├── llmeo │ ├── README.md │ ├── cli.py │ ├── data │ │ └── 1M-space_50-ligands-full.csv │ ├── environment.yml │ ├── pytest.ini │ ├── src │ │ ├── __init__.py │ │ ├── modes │ │ │ ├── __init__.py │ │ │ ├── few_shot.py │ │ │ ├── multi_prop.py │ │ │ └── single_prop.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── _utils.py │ │ │ ├── data_loader.py │ │ │ └── prompt.py │ ├── test.py │ └── tests │ │ ├── README.md │ │ ├── __init__.py │ │ ├── conftest.py │ │ ├── run_tests.py │ │ ├── test_cli.py │ │ ├── test_data_loader.py │ │ ├── test_modes.py │ │ ├── test_prompts.py │ │ └── test_utils.py ├── llmsr │ ├── README.md │ ├── assets │ │ └── img.png │ ├── cli.py │ ├── data │ │ ├── __init__.py │ │ └── dataset.py │ ├── requirements.txt │ └── src │ │ ├── __init__.py │ │ ├── core │ │ ├── __init__.py │ │ ├── buffer.py │ │ ├── generation.py │ │ ├── oracle.py │ │ └── prompt.py │ │ └── modes │ │ ├── __init__.py │ │ ├── evol.py │ │ └── iter.py ├── matllmsearch │ ├── .gitignore │ ├── README.md │ ├── cli.py │ ├── logs │ │ └── analyze_generation │ │ │ ├── evaluated_results.json │ │ │ ├── generations.csv │ │ │ └── metrics.csv │ ├── requirements.txt │ └── src │ │ ├── __init__.py │ │ ├── evaluators │ │ ├── __init__.py │ │ └── materials_oracle.py │ │ ├── modes │ │ ├── __init__.py │ │ ├── analyze.py │ │ ├── csg.py │ │ └── csp.py │ │ └── utils │ │ ├── __init__.py │ │ ├── config.py │ │ ├── data_loader.py │ │ ├── e_hull_calculator.py │ │ ├── evaluate_structures.py │ │ ├── stability_calculator.py │ │ └── structure_generator.py ├── molleo │ ├── README.md │ ├── README_RESTRUCTURED.md │ ├── _archive │ │ ├── MoleculeSTM │ │ │ ├── downstream_molecule_edit_utils.py │ │ │ ├── models │ │ │ │ ├── GA │ │ │ │ │ ├── ZINC_first_1000.smi │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── crossover.py │ │ │ │ │ └── mutate.py │ │ │ │ ├── MLP.py │ │ │ │ ├── __init__.py │ │ │ │ ├── mega_molbart │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── decoder.py │ │ │ │ │ ├── mega_mol_bart.py │ │ │ │ │ ├── megatron_bart.py │ │ │ │ │ ├── tokenizer.py │ │ │ │ │ └── util.py │ │ │ │ └── molecule_gnn_model.py │ │ │ └── scripts │ │ │ │ ├── README.md │ │ │ │ ├── downstream_01_retrieval_ATC.py │ │ │ │ ├── downstream_01_retrieval_ATC_KV-PLM.py │ │ │ │ ├── downstream_01_retrieval_ATC_Retrieval.py │ │ │ │ ├── downstream_01_retrieval_Description_Pharmacodynamics.py │ │ │ │ ├── downstream_01_retrieval_Description_Pharmacodynamics_KV-PLM.py │ │ │ │ ├── downstream_01_retrieval_Description_Pharmacodynamics_Retrieval.py │ │ │ │ ├── downstream_02_molecule_edit_step_01_MoleculeSTM_Space_Alignment.py │ │ │ │ ├── downstream_02_molecule_edit_step_02_GA.py │ │ │ │ ├── downstream_02_molecule_edit_step_02_High_Variance.py │ │ │ │ ├── downstream_02_molecule_edit_step_02_MoleculeSTM_Latent_Optimization.py │ │ │ │ ├── downstream_02_molecule_edit_step_02_PCA.py │ │ │ │ ├── downstream_02_molecule_edit_step_02_Random_Perturbation.py │ │ │ │ ├── downstream_03_property_prediction.py │ │ │ │ ├── downstream_03_property_prediction_KV-PLM.py │ │ │ │ ├── pretrain.py │ │ │ │ ├── run_train_molecule_edit_model.sh │ │ │ │ ├── slurm_files │ │ │ │ ├── 12303811.error │ │ │ │ └── 12303811.out │ │ │ │ ├── temp │ │ │ │ ├── accuracy.npz │ │ │ │ └── edited_SMILES.tsv │ │ │ │ ├── temp2 │ │ │ │ ├── accuracy.npz │ │ │ │ └── edited_SMILES.tsv │ │ │ │ ├── temp3 │ │ │ │ ├── accuracy.npz │ │ │ │ └── edited_SMILES.tsv │ │ │ │ └── temp6 │ │ │ │ ├── accuracy.npz │ │ │ │ └── edited_SMILES.tsv │ │ ├── multi_objective │ │ │ ├── main │ │ │ │ ├── molleo_multi │ │ │ │ │ ├── GPT4.py │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── biot5.py │ │ │ │ │ ├── crossover.py │ │ │ │ │ ├── features.py │ │ │ │ │ ├── hparams_default.yaml │ │ │ │ │ ├── hparams_tune.yaml │ │ │ │ │ ├── mol_lm.py │ │ │ │ │ ├── mol_lm_utils.py │ │ │ │ │ ├── mutate.py │ │ │ │ │ ├── network.py │ │ │ │ │ ├── oracle │ │ │ │ │ │ └── jnk3.pkl │ │ │ │ │ ├── results │ │ │ │ │ │ ├── results_BioT5_['jnk3', 'qed']_['sa']0.yaml │ │ │ │ │ │ └── results_GPT-4_['jnk3', 'qed']_['sa']0.yaml │ │ │ │ │ ├── run.py │ │ │ │ │ └── utils.py │ │ │ │ ├── molleo_multi_pareto │ │ │ │ │ ├── GPT4.py │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── biot5.py │ │ │ │ │ ├── crossover.py │ │ │ │ │ ├── features.py │ │ │ │ │ ├── hparams_default.yaml │ │ │ │ │ ├── hparams_tune.yaml │ │ │ │ │ ├── mol_lm.py │ │ │ │ │ ├── mol_lm_utils.py │ │ │ │ │ ├── mutate.py │ │ │ │ │ ├── network.py │ │ │ │ │ ├── oracle │ │ │ │ │ │ └── jnk3.pkl │ │ │ │ │ ├── results │ │ │ │ │ │ ├── results_BioT5_['jnk3', 'qed']_['sa']0.yaml │ │ │ │ │ │ └── results_GPT-4_['jnk3', 'qed']_['sa']0.yaml │ │ │ │ │ ├── run.py │ │ │ │ │ └── utils.py │ │ │ │ ├── optimizer.py │ │ │ │ ├── pareto_optimizer.py │ │ │ │ └── utils │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── chem.py │ │ │ │ │ ├── chem_utils.py │ │ │ │ │ ├── eval_utils.py │ │ │ │ │ ├── jtvae_data_utils.py │ │ │ │ │ ├── nn_utils.py │ │ │ │ │ ├── preprocess.py │ │ │ │ │ ├── script_utils.py │ │ │ │ │ ├── smiles_data_utils.py │ │ │ │ │ └── vocab.py │ │ │ ├── oracle │ │ │ │ ├── fpscores.pkl │ │ │ │ └── jnk3_current.pkl │ │ │ └── run.py │ │ └── single_objective │ │ │ ├── data │ │ │ └── zinc.tab │ │ │ ├── main │ │ │ ├── molleo │ │ │ │ ├── GPT4.py │ │ │ │ ├── __init__.py │ │ │ │ ├── biot5.py │ │ │ │ ├── crossover.py │ │ │ │ ├── features.py │ │ │ │ ├── hparams_default.yaml │ │ │ │ ├── hparams_tune.yaml │ │ │ │ ├── mol_lm.py │ │ │ │ ├── mol_lm_utils.py │ │ │ │ ├── mutate.py │ │ │ │ ├── network.py │ │ │ │ ├── oracle │ │ │ │ │ └── jnk3.pkl │ │ │ │ ├── results │ │ │ │ │ ├── results_BioT5_qed_15.yaml │ │ │ │ │ ├── results_GPT-4_qed_15.yaml │ │ │ │ │ └── results_molleo_qed_15.yaml │ │ │ │ ├── run.py │ │ │ │ └── utils.py │ │ │ ├── optimizer.py │ │ │ └── utils │ │ │ │ ├── __init__.py │ │ │ │ ├── chem.py │ │ │ │ ├── chem_utils.py │ │ │ │ ├── eval_utils.py │ │ │ │ ├── jtvae_data_utils.py │ │ │ │ ├── nn_utils.py │ │ │ │ ├── preprocess.py │ │ │ │ ├── script_utils.py │ │ │ │ ├── smiles_data_utils.py │ │ │ │ └── vocab.py │ │ │ ├── oracle │ │ │ └── fpscores.pkl │ │ │ └── run.py │ ├── cli.py │ ├── example_usage.py │ ├── images │ │ └── README │ │ │ ├── lgga_overview.png │ │ │ └── molleo_overview.gif │ ├── requirements.txt │ ├── src │ │ ├── __init__.py │ │ ├── core │ │ │ ├── __init__.py │ │ │ ├── molleo_optimizer.py │ │ │ └── prompts.py │ │ ├── ga │ │ │ ├── __init__.py │ │ │ ├── crossover.py │ │ │ └── mutations.py │ │ ├── generation.py │ │ ├── modes │ │ │ ├── __init__.py │ │ │ ├── multi_objective.py │ │ │ └── single_objective.py │ │ ├── oracles │ │ │ ├── __init__.py │ │ │ ├── base.py │ │ │ └── tdc_oracles.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── evolutionary_ops.py │ │ │ └── mol_utils.py │ └── tests │ │ ├── example_comprehensive.py │ │ ├── example_no_llm.py │ │ └── example_with_llm.py ├── proteinoptimizer │ ├── README.md │ ├── assets │ │ ├── hold │ │ ├── protein_main.pdf │ │ └── protein_main.png │ ├── cli.py │ ├── data │ │ ├── AAV │ │ │ ├── AAV_wild_type.csv │ │ │ ├── ground_truth.csv │ │ │ ├── gt_medium_range.csv │ │ │ └── mutation_analysis.csv │ │ ├── GB1 │ │ │ └── fitness.csv │ │ ├── GFP │ │ │ ├── FPG_position_analysis.csv │ │ │ ├── GFP_wild_type.csv │ │ │ ├── ground_truth.csv │ │ │ ├── gt_medium_range.csv │ │ │ ├── mutation_analysis.csv │ │ │ └── mutation_point.csv │ │ ├── Syn-3bfo │ │ │ ├── 3bfo_1_A_model_state_dict.npz │ │ │ └── fitness.csv │ │ └── TrpB │ │ │ └── fitness.csv │ ├── requirements.txt │ ├── results │ │ ├── results_multi_aav_0_baseline.json │ │ ├── results_multi_aav_0_gpt-5-mini.json │ │ ├── results_multi_gb1_0_baseline.json │ │ ├── results_multi_gb1_0_gpt-5-mini.json │ │ ├── results_multi_gfp_0_baseline.json │ │ ├── results_multi_gfp_0_gpt-5-mini.json │ │ ├── results_multi_syn-3bfo_0_baseline.json │ │ ├── results_multi_syn-3bfo_0_gpt-5-mini.json │ │ ├── results_multi_trpb_0_baseline.json │ │ ├── results_multi_trpb_0_gpt-5-mini.json │ │ ├── results_single_aav_0_baseline.json │ │ ├── results_single_aav_0_gpt-5-mini.json │ │ ├── results_single_gb1_0_baseline.json │ │ ├── results_single_gb1_0_gpt-5-mini.json │ │ ├── results_single_gfp_0_baseline.json │ │ ├── results_single_gfp_0_gpt-5-mini.json │ │ ├── results_single_syn-3bfo_0_baseline.json │ │ ├── results_single_syn-3bfo_0_gpt-5-mini.json │ │ ├── results_single_trpb_0_baseline.json │ │ └── results_single_trpb_0_gpt-5-mini.json │ ├── run_all.sh │ └── src │ │ ├── __init__.py │ │ ├── analyze.py │ │ ├── core │ │ ├── __init__.py │ │ ├── multiobjective.py │ │ ├── pareto.py │ │ ├── pareto_optimizer.py │ │ └── protein_optimizer.py │ │ ├── generation.py │ │ ├── modes │ │ ├── __init__.py │ │ ├── multi_objective_protein.py │ │ ├── multi_pareto_protein.py │ │ └── single_objective.py │ │ ├── oracles │ │ ├── __init__.py │ │ ├── base.py │ │ ├── fitness_oracles.py │ │ ├── ml_oracles.py │ │ └── multi_objective_oracles.py │ │ ├── utils │ │ ├── GGS_utils │ │ │ └── __init__.py │ │ ├── __init__.py │ │ ├── ckpt │ │ │ ├── AAV │ │ │ │ ├── mutations_0 │ │ │ │ │ └── percentile_0.0_1.0 │ │ │ │ │ │ ├── cnn_oracle.ckpt │ │ │ │ │ │ └── config.yaml │ │ │ │ ├── mutations_6 │ │ │ │ │ └── percentile_0.2_0.4 │ │ │ │ │ │ ├── tik-gamma-1_smoothed │ │ │ │ │ │ └── ham1_n-250K │ │ │ │ │ │ │ ├── config.yaml │ │ │ │ │ │ │ └── predictor.ckpt │ │ │ │ │ │ └── unsmoothed │ │ │ │ │ │ └── predictor │ │ │ │ │ │ ├── config.yaml │ │ │ │ │ │ └── predictor.ckpt │ │ │ │ └── mutations_7 │ │ │ │ │ └── percentile_0.0_0.3 │ │ │ │ │ ├── tik-gamma-1_smoothed │ │ │ │ │ └── ham1_n-250K │ │ │ │ │ │ ├── config.yaml │ │ │ │ │ │ └── predictor.ckpt │ │ │ │ │ ├── unsmoothed │ │ │ │ │ └── predictor │ │ │ │ │ │ ├── config.yaml │ │ │ │ │ │ └── predictor.ckpt │ │ │ │ │ └── unsmoothed_smoothed │ │ │ │ │ ├── 01_04_2025_03_11 │ │ │ │ │ ├── config.yaml │ │ │ │ │ ├── epoch_099.ckpt │ │ │ │ │ └── last.ckpt │ │ │ │ │ └── 01_05_2025_18_25 │ │ │ │ │ ├── config.yaml │ │ │ │ │ ├── epoch_099.ckpt │ │ │ │ │ └── last.ckpt │ │ │ └── GFP │ │ │ │ ├── mutations_0 │ │ │ │ └── percentile_0.0_1.0 │ │ │ │ │ ├── cnn_oracle.ckpt │ │ │ │ │ ├── config.yaml │ │ │ │ │ └── samples │ │ │ │ │ └── temp-0.01-ngibbs-1000-epochs-10 │ │ │ │ │ └── config.yaml │ │ │ │ ├── mutations_6 │ │ │ │ └── percentile_0.2_0.4 │ │ │ │ │ ├── tik-gamma-1_smoothed │ │ │ │ │ └── ham1_n-250K │ │ │ │ │ │ ├── config.yaml │ │ │ │ │ │ └── predictor.ckpt │ │ │ │ │ └── unsmoothed │ │ │ │ │ └── predictor │ │ │ │ │ ├── config.yaml │ │ │ │ │ └── predictor.ckpt │ │ │ │ └── mutations_7 │ │ │ │ └── percentile_0.0_0.3 │ │ │ │ ├── tik-gamma-1_smoothed │ │ │ │ └── ham1_n-250K │ │ │ │ │ ├── config.yaml │ │ │ │ │ └── predictor.ckpt │ │ │ │ ├── unsmoothed │ │ │ │ └── predictor │ │ │ │ │ ├── config.yaml │ │ │ │ │ └── predictor.ckpt │ │ │ │ └── unsmoothed_smoothed │ │ │ │ ├── 01_03_2025_23_36 │ │ │ │ └── config.yaml │ │ │ │ ├── 01_03_2025_23_56 │ │ │ │ ├── config.yaml │ │ │ │ ├── epoch_079.ckpt │ │ │ │ ├── last.ckpt │ │ │ │ └── samples │ │ │ │ │ └── temp-0.01-ngibbs-1000-epochs-10 │ │ │ │ │ ├── config.yaml │ │ │ │ │ ├── eval_run_new │ │ │ │ │ └── epoch_filter_last │ │ │ │ │ │ ├── acceptance_rates.npy │ │ │ │ │ │ ├── metrics_oracle_cnn_sampling_greedy.csv │ │ │ │ │ │ ├── metrics_predictor_sampling_greedy.csv │ │ │ │ │ │ ├── results_oracle_cnn_sampling_greedy.csv │ │ │ │ │ │ └── results_predictor_sampling_greedy.csv │ │ │ │ │ ├── seed_1.csv │ │ │ │ │ ├── seed_1_acceptance_rates.pkl │ │ │ │ │ └── seed_1_cluster_centers.csv │ │ │ │ ├── 01_04_2025_01_22 │ │ │ │ └── config.yaml │ │ │ │ └── samples │ │ │ │ └── temp-0.01-ngibbs-1000-epochs-10 │ │ │ │ └── config.yaml │ │ ├── evolutionary_ops.py │ │ ├── potts_model.py │ │ ├── predictors.py │ │ └── tokenize.py │ │ └── workflow.py └── synplanner │ ├── README.md │ ├── assets │ └── llm-retro-overview.png │ ├── cli.py │ ├── env_setup.sh │ ├── src │ ├── hparams_default.yaml │ ├── optimizer │ │ ├── base_optimizer.py │ │ ├── route.py │ │ └── route_optimizer.py │ ├── oracle │ │ └── oracle.py │ ├── rag │ │ ├── generate_retro_templates.py │ │ └── sim_based_rag.py │ ├── sascore │ │ ├── fpscores.pkl.gz │ │ └── sascorer.py │ ├── scscore │ │ ├── LICENSE │ │ ├── README.md │ │ ├── models │ │ │ └── model.ckpt-10654.as_numpy.json.gz │ │ ├── notebooks │ │ │ └── __init__.py │ │ ├── scripts │ │ │ ├── get_reaxys_data.py │ │ │ ├── get_sa_scores_interactive.py │ │ │ ├── get_uspto_50k.py │ │ │ └── make_h5_file.py │ │ ├── scscore │ │ │ ├── __init__.py │ │ │ ├── nntrain_fingerprint.py │ │ │ ├── standalone_model_numpy.py │ │ │ └── standalone_model_tf.py │ │ └── utils │ │ │ ├── SA_Score │ │ │ ├── README │ │ │ ├── UnitTestSAScore.py │ │ │ ├── __init__.py │ │ │ ├── data │ │ │ │ └── zim.100.txt │ │ │ ├── fpscores.pkl.gz │ │ │ └── sascorer.py │ │ │ ├── __init__.py │ │ │ └── nn.py │ └── utils │ │ ├── chemistry_utils.py │ │ ├── prompt.py │ │ └── utils.py │ └── test_smiles.smi ├── pyproject.toml ├── pytest.ini ├── requirements.txt ├── sde_harness ├── __init__.py ├── base │ ├── __init__.py │ ├── cli_base.py │ ├── evaluator_base.py │ └── project_base.py └── core │ ├── __info__.py │ ├── __init__.py │ ├── generation.py │ ├── oracle.py │ ├── prompt.py │ ├── utils.py │ └── workflow.py ├── setup.py └── tests ├── README.md ├── __init__.py ├── conftest.py ├── run_tests.py ├── test_base_classes.py ├── test_core_generation.py ├── test_core_oracle.py ├── test_core_prompt.py └── test_core_workflow.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/.gitignore -------------------------------------------------------------------------------- /.gitmodules: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/README.md -------------------------------------------------------------------------------- /assets/SDE-harness-logo_00.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/assets/SDE-harness-logo_00.png -------------------------------------------------------------------------------- /config/credentials.template.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/config/credentials.template.yaml -------------------------------------------------------------------------------- /config/models.template.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/config/models.template.yaml -------------------------------------------------------------------------------- /docs/Quick_Integration_Guide.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/docs/Quick_Integration_Guide.md -------------------------------------------------------------------------------- /environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/environment.yml -------------------------------------------------------------------------------- /examples/EXAMPLES_OVERVIEW.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/examples/EXAMPLES_OVERVIEW.md -------------------------------------------------------------------------------- /examples/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/examples/README.md -------------------------------------------------------------------------------- /examples/advanced_usage/01_custom_metrics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/examples/advanced_usage/01_custom_metrics.py -------------------------------------------------------------------------------- /examples/advanced_usage/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/examples/advanced_usage/README.md -------------------------------------------------------------------------------- /examples/basic_usage/01_generation_basics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/examples/basic_usage/01_generation_basics.py -------------------------------------------------------------------------------- /examples/basic_usage/02_oracle_basics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/examples/basic_usage/02_oracle_basics.py -------------------------------------------------------------------------------- /examples/basic_usage/03_prompt_basics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/examples/basic_usage/03_prompt_basics.py -------------------------------------------------------------------------------- /examples/basic_usage/04_workflow_basics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/examples/basic_usage/04_workflow_basics.py -------------------------------------------------------------------------------- /examples/basic_usage/04_workflow_basics_mock.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/examples/basic_usage/04_workflow_basics_mock.py -------------------------------------------------------------------------------- /examples/basic_usage/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/examples/basic_usage/README.md -------------------------------------------------------------------------------- /examples/generation_examples.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/examples/generation_examples.py -------------------------------------------------------------------------------- /examples/history_workflow_examples.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/examples/history_workflow_examples.py -------------------------------------------------------------------------------- /examples/integration_examples/01_cli_integration.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/examples/integration_examples/01_cli_integration.py -------------------------------------------------------------------------------- /examples/integration_examples/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/examples/integration_examples/README.md -------------------------------------------------------------------------------- /examples/project_examples/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/examples/project_examples/README.md -------------------------------------------------------------------------------- /examples/project_examples/run_llmeo_example.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/examples/project_examples/run_llmeo_example.py -------------------------------------------------------------------------------- /examples/project_examples/simple_optimization/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/examples/project_examples/simple_optimization/README.md -------------------------------------------------------------------------------- /examples/project_examples/simple_optimization/config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/examples/project_examples/simple_optimization/config.yaml -------------------------------------------------------------------------------- /examples/project_examples/simple_optimization/run_optimization.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/examples/project_examples/simple_optimization/run_optimization.py -------------------------------------------------------------------------------- /examples/project_examples/simple_optimization/sample_data.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/examples/project_examples/simple_optimization/sample_data.json -------------------------------------------------------------------------------- /projects/bio-discovery-agent/.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/.gitignore -------------------------------------------------------------------------------- /projects/bio-discovery-agent/CEGv2.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/CEGv2.txt -------------------------------------------------------------------------------- /projects/bio-discovery-agent/LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/LICENSE -------------------------------------------------------------------------------- /projects/bio-discovery-agent/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/README.md -------------------------------------------------------------------------------- /projects/bio-discovery-agent/README_REFACTORING.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/README_REFACTORING.md -------------------------------------------------------------------------------- /projects/bio-discovery-agent/_archive/ARCHIVE_SUMMARY.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/_archive/ARCHIVE_SUMMARY.md -------------------------------------------------------------------------------- /projects/bio-discovery-agent/_archive/analyze.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/_archive/analyze.py -------------------------------------------------------------------------------- /projects/bio-discovery-agent/_archive/analyze_new.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/_archive/analyze_new.py -------------------------------------------------------------------------------- /projects/bio-discovery-agent/_archive/analyze_predictions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/_archive/analyze_predictions.py -------------------------------------------------------------------------------- /projects/bio-discovery-agent/_archive/baseline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/_archive/baseline.py -------------------------------------------------------------------------------- /projects/bio-discovery-agent/_archive/get_gene_summary.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/_archive/get_gene_summary.py -------------------------------------------------------------------------------- /projects/bio-discovery-agent/_archive/research_assistant.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/_archive/research_assistant.py -------------------------------------------------------------------------------- /projects/bio-discovery-agent/_archive/research_assistant_new.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/_archive/research_assistant_new.py -------------------------------------------------------------------------------- /projects/bio-discovery-agent/_archive/src/modes/perturb_genes_backup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/_archive/src/modes/perturb_genes_backup.py -------------------------------------------------------------------------------- /projects/bio-discovery-agent/_archive/src/modes/perturb_genes_fixed.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/_archive/src/modes/perturb_genes_fixed.py -------------------------------------------------------------------------------- /projects/bio-discovery-agent/_archive/src/modes/perturb_genes_with_scores.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/_archive/src/modes/perturb_genes_with_scores.py -------------------------------------------------------------------------------- /projects/bio-discovery-agent/_archive/test_refactor.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/_archive/test_refactor.py -------------------------------------------------------------------------------- /projects/bio-discovery-agent/_archive/tools.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/_archive/tools.py -------------------------------------------------------------------------------- /projects/bio-discovery-agent/assets/icon.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/assets/icon.jpg -------------------------------------------------------------------------------- /projects/bio-discovery-agent/assets/simple_outline.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/assets/simple_outline.png -------------------------------------------------------------------------------- /projects/bio-discovery-agent/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/cli.py -------------------------------------------------------------------------------- /projects/bio-discovery-agent/data/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/data/README.md -------------------------------------------------------------------------------- /projects/bio-discovery-agent/data/schmidt.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/data/schmidt.py -------------------------------------------------------------------------------- /projects/bio-discovery-agent/data/schmidt_ifng_d1.gene_summary.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/data/schmidt_ifng_d1.gene_summary.txt -------------------------------------------------------------------------------- /projects/bio-discovery-agent/data/schmidt_ifng_d2.gene_summary.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/data/schmidt_ifng_d2.gene_summary.txt -------------------------------------------------------------------------------- /projects/bio-discovery-agent/data/screen.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/data/screen.py -------------------------------------------------------------------------------- /projects/bio-discovery-agent/datasets/ground_truth_Carnevale22_Adenosine.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/datasets/ground_truth_Carnevale22_Adenosine.csv -------------------------------------------------------------------------------- /projects/bio-discovery-agent/datasets/ground_truth_Horlbeck.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/datasets/ground_truth_Horlbeck.csv -------------------------------------------------------------------------------- /projects/bio-discovery-agent/datasets/ground_truth_IFNG.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/datasets/ground_truth_IFNG.csv -------------------------------------------------------------------------------- /projects/bio-discovery-agent/datasets/ground_truth_IL2.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/datasets/ground_truth_IL2.csv -------------------------------------------------------------------------------- /projects/bio-discovery-agent/datasets/ground_truth_Sanchez21.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/datasets/ground_truth_Sanchez21.csv -------------------------------------------------------------------------------- /projects/bio-discovery-agent/datasets/ground_truth_Sanchez21_down.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/datasets/ground_truth_Sanchez21_down.csv -------------------------------------------------------------------------------- /projects/bio-discovery-agent/datasets/ground_truth_Scharenberg22.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/datasets/ground_truth_Scharenberg22.csv -------------------------------------------------------------------------------- /projects/bio-discovery-agent/datasets/ground_truth_Steinhart_crispra_GD2_D22.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/datasets/ground_truth_Steinhart_crispra_GD2_D22.csv -------------------------------------------------------------------------------- /projects/bio-discovery-agent/datasets/task_prompts/Carnevale22_Adenosine.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/datasets/task_prompts/Carnevale22_Adenosine.json -------------------------------------------------------------------------------- /projects/bio-discovery-agent/datasets/task_prompts/Horlbeck.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/datasets/task_prompts/Horlbeck.json -------------------------------------------------------------------------------- /projects/bio-discovery-agent/datasets/task_prompts/IFNG.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/datasets/task_prompts/IFNG.json -------------------------------------------------------------------------------- /projects/bio-discovery-agent/datasets/task_prompts/IL2.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/datasets/task_prompts/IL2.json -------------------------------------------------------------------------------- /projects/bio-discovery-agent/datasets/task_prompts/Sanchez21.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/datasets/task_prompts/Sanchez21.json -------------------------------------------------------------------------------- /projects/bio-discovery-agent/datasets/task_prompts/Sanchez21_down.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/datasets/task_prompts/Sanchez21_down.json -------------------------------------------------------------------------------- /projects/bio-discovery-agent/datasets/task_prompts/Scharenberg22.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/datasets/task_prompts/Scharenberg22.json -------------------------------------------------------------------------------- /projects/bio-discovery-agent/datasets/task_prompts/Steinhart_crispra_GD2_D22.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/datasets/task_prompts/Steinhart_crispra_GD2_D22.json -------------------------------------------------------------------------------- /projects/bio-discovery-agent/datasets/topmovers_Carnevale22_Adenosine.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/datasets/topmovers_Carnevale22_Adenosine.npy -------------------------------------------------------------------------------- /projects/bio-discovery-agent/datasets/topmovers_Horlbeck.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/datasets/topmovers_Horlbeck.npy -------------------------------------------------------------------------------- /projects/bio-discovery-agent/datasets/topmovers_IFNG.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/datasets/topmovers_IFNG.npy -------------------------------------------------------------------------------- /projects/bio-discovery-agent/datasets/topmovers_IL2.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/datasets/topmovers_IL2.npy -------------------------------------------------------------------------------- /projects/bio-discovery-agent/datasets/topmovers_Sanchez21.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/datasets/topmovers_Sanchez21.npy -------------------------------------------------------------------------------- /projects/bio-discovery-agent/datasets/topmovers_Sanchez21_down.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/datasets/topmovers_Sanchez21_down.npy -------------------------------------------------------------------------------- /projects/bio-discovery-agent/datasets/topmovers_Scharenberg22.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/datasets/topmovers_Scharenberg22.npy -------------------------------------------------------------------------------- /projects/bio-discovery-agent/datasets/topmovers_Steinhart_crispra_GD2_D22.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/datasets/topmovers_Steinhart_crispra_GD2_D22.npy -------------------------------------------------------------------------------- /projects/bio-discovery-agent/pytest.ini: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/pytest.ini -------------------------------------------------------------------------------- /projects/bio-discovery-agent/requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/requirements.txt -------------------------------------------------------------------------------- /projects/bio-discovery-agent/src/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/src/__init__.py -------------------------------------------------------------------------------- /projects/bio-discovery-agent/src/evaluators/__init__.py: -------------------------------------------------------------------------------- 1 | """BioDiscoveryAgent evaluators module.""" -------------------------------------------------------------------------------- /projects/bio-discovery-agent/src/evaluators/bio_metrics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/src/evaluators/bio_metrics.py -------------------------------------------------------------------------------- /projects/bio-discovery-agent/src/evaluators/oracle_evaluator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/src/evaluators/oracle_evaluator.py -------------------------------------------------------------------------------- /projects/bio-discovery-agent/src/modes/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/src/modes/__init__.py -------------------------------------------------------------------------------- /projects/bio-discovery-agent/src/modes/analyze.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/src/modes/analyze.py -------------------------------------------------------------------------------- /projects/bio-discovery-agent/src/modes/baseline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/src/modes/baseline.py -------------------------------------------------------------------------------- /projects/bio-discovery-agent/src/modes/perturb_genes.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/src/modes/perturb_genes.py -------------------------------------------------------------------------------- /projects/bio-discovery-agent/src/tools/LLM.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/src/tools/LLM.py -------------------------------------------------------------------------------- /projects/bio-discovery-agent/src/tools/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/src/tools/README.md -------------------------------------------------------------------------------- /projects/bio-discovery-agent/src/tools/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/src/tools/__init__.py -------------------------------------------------------------------------------- /projects/bio-discovery-agent/src/tools/achilles.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/src/tools/achilles.py -------------------------------------------------------------------------------- /projects/bio-discovery-agent/src/tools/gene.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/src/tools/gene.py -------------------------------------------------------------------------------- /projects/bio-discovery-agent/src/tools/get_lit_review.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/src/tools/get_lit_review.py -------------------------------------------------------------------------------- /projects/bio-discovery-agent/src/utils/__init__.py: -------------------------------------------------------------------------------- 1 | """BioDiscoveryAgent utilities module.""" -------------------------------------------------------------------------------- /projects/bio-discovery-agent/src/utils/data_loader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/src/utils/data_loader.py -------------------------------------------------------------------------------- /projects/bio-discovery-agent/src/utils/gene_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/src/utils/gene_utils.py -------------------------------------------------------------------------------- /projects/bio-discovery-agent/src/utils/llm_interface.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/src/utils/llm_interface.py -------------------------------------------------------------------------------- /projects/bio-discovery-agent/src/utils/prompts.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/src/utils/prompts.py -------------------------------------------------------------------------------- /projects/bio-discovery-agent/src/utils/tools.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/src/utils/tools.py -------------------------------------------------------------------------------- /projects/bio-discovery-agent/tests/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/tests/README.md -------------------------------------------------------------------------------- /projects/bio-discovery-agent/tests/__init__.py: -------------------------------------------------------------------------------- 1 | """Unit tests for BioDiscoveryAgent.""" -------------------------------------------------------------------------------- /projects/bio-discovery-agent/tests/run_tests.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/tests/run_tests.py -------------------------------------------------------------------------------- /projects/bio-discovery-agent/tests/test_bio_metrics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/tests/test_bio_metrics.py -------------------------------------------------------------------------------- /projects/bio-discovery-agent/tests/test_data_loader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/tests/test_data_loader.py -------------------------------------------------------------------------------- /projects/bio-discovery-agent/tests/test_llm_interface.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/tests/test_llm_interface.py -------------------------------------------------------------------------------- /projects/bio-discovery-agent/tests/test_modes.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/tests/test_modes.py -------------------------------------------------------------------------------- /projects/bio-discovery-agent/tests/test_oracle_evaluator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/tests/test_oracle_evaluator.py -------------------------------------------------------------------------------- /projects/bio-discovery-agent/tests/test_oracle_integration.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/bio-discovery-agent/tests/test_oracle_integration.py -------------------------------------------------------------------------------- /projects/chat-mof/.gitignore: -------------------------------------------------------------------------------- 1 | results/ 2 | *.json 3 | 4 | -------------------------------------------------------------------------------- /projects/chat-mof/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/chat-mof/README.md -------------------------------------------------------------------------------- /projects/chat-mof/cli_generate_verify.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/chat-mof/cli_generate_verify.py -------------------------------------------------------------------------------- /projects/chat-mof/data/coremof.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/chat-mof/data/coremof.xlsx -------------------------------------------------------------------------------- /projects/chat-mof/requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/chat-mof/requirements.txt -------------------------------------------------------------------------------- /projects/chat-mof/src/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/chat-mof/src/__init__.py -------------------------------------------------------------------------------- /projects/chat-mof/src/generation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/chat-mof/src/generation.py -------------------------------------------------------------------------------- /projects/chat-mof/src/mof_name_generator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/chat-mof/src/mof_name_generator.py -------------------------------------------------------------------------------- /projects/chat-mof/src/oracle.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/chat-mof/src/oracle.py -------------------------------------------------------------------------------- /projects/chat-mof/src/prompt.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/chat-mof/src/prompt.py -------------------------------------------------------------------------------- /projects/chat-mof/src/workflow.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/chat-mof/src/workflow.py -------------------------------------------------------------------------------- /projects/llmeo/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/llmeo/README.md -------------------------------------------------------------------------------- /projects/llmeo/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/llmeo/cli.py -------------------------------------------------------------------------------- /projects/llmeo/data/1M-space_50-ligands-full.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/llmeo/data/1M-space_50-ligands-full.csv -------------------------------------------------------------------------------- /projects/llmeo/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/llmeo/environment.yml -------------------------------------------------------------------------------- /projects/llmeo/pytest.ini: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/llmeo/pytest.ini -------------------------------------------------------------------------------- /projects/llmeo/src/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/llmeo/src/__init__.py -------------------------------------------------------------------------------- /projects/llmeo/src/modes/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/llmeo/src/modes/__init__.py -------------------------------------------------------------------------------- /projects/llmeo/src/modes/few_shot.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/llmeo/src/modes/few_shot.py -------------------------------------------------------------------------------- /projects/llmeo/src/modes/multi_prop.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/llmeo/src/modes/multi_prop.py -------------------------------------------------------------------------------- /projects/llmeo/src/modes/single_prop.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/llmeo/src/modes/single_prop.py -------------------------------------------------------------------------------- /projects/llmeo/src/utils/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/llmeo/src/utils/__init__.py -------------------------------------------------------------------------------- /projects/llmeo/src/utils/_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/llmeo/src/utils/_utils.py -------------------------------------------------------------------------------- /projects/llmeo/src/utils/data_loader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/llmeo/src/utils/data_loader.py -------------------------------------------------------------------------------- /projects/llmeo/src/utils/prompt.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/llmeo/src/utils/prompt.py -------------------------------------------------------------------------------- /projects/llmeo/test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/llmeo/test.py -------------------------------------------------------------------------------- /projects/llmeo/tests/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/llmeo/tests/README.md -------------------------------------------------------------------------------- /projects/llmeo/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/llmeo/tests/__init__.py -------------------------------------------------------------------------------- /projects/llmeo/tests/conftest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/llmeo/tests/conftest.py -------------------------------------------------------------------------------- /projects/llmeo/tests/run_tests.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/llmeo/tests/run_tests.py -------------------------------------------------------------------------------- /projects/llmeo/tests/test_cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/llmeo/tests/test_cli.py -------------------------------------------------------------------------------- /projects/llmeo/tests/test_data_loader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/llmeo/tests/test_data_loader.py -------------------------------------------------------------------------------- /projects/llmeo/tests/test_modes.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/llmeo/tests/test_modes.py -------------------------------------------------------------------------------- /projects/llmeo/tests/test_prompts.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/llmeo/tests/test_prompts.py -------------------------------------------------------------------------------- /projects/llmeo/tests/test_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/llmeo/tests/test_utils.py -------------------------------------------------------------------------------- /projects/llmsr/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/llmsr/README.md -------------------------------------------------------------------------------- /projects/llmsr/assets/img.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/llmsr/assets/img.png -------------------------------------------------------------------------------- /projects/llmsr/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/llmsr/cli.py -------------------------------------------------------------------------------- /projects/llmsr/data/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/llmsr/data/__init__.py -------------------------------------------------------------------------------- /projects/llmsr/data/dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/llmsr/data/dataset.py -------------------------------------------------------------------------------- /projects/llmsr/requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/llmsr/requirements.txt -------------------------------------------------------------------------------- /projects/llmsr/src/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/llmsr/src/__init__.py -------------------------------------------------------------------------------- /projects/llmsr/src/core/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/llmsr/src/core/__init__.py -------------------------------------------------------------------------------- /projects/llmsr/src/core/buffer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/llmsr/src/core/buffer.py -------------------------------------------------------------------------------- /projects/llmsr/src/core/generation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/llmsr/src/core/generation.py -------------------------------------------------------------------------------- /projects/llmsr/src/core/oracle.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/llmsr/src/core/oracle.py -------------------------------------------------------------------------------- /projects/llmsr/src/core/prompt.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/llmsr/src/core/prompt.py -------------------------------------------------------------------------------- /projects/llmsr/src/modes/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/llmsr/src/modes/__init__.py -------------------------------------------------------------------------------- /projects/llmsr/src/modes/evol.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/llmsr/src/modes/evol.py -------------------------------------------------------------------------------- /projects/llmsr/src/modes/iter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/llmsr/src/modes/iter.py -------------------------------------------------------------------------------- /projects/matllmsearch/.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/matllmsearch/.gitignore -------------------------------------------------------------------------------- /projects/matllmsearch/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/matllmsearch/README.md -------------------------------------------------------------------------------- /projects/matllmsearch/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/matllmsearch/cli.py -------------------------------------------------------------------------------- /projects/matllmsearch/logs/analyze_generation/evaluated_results.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/matllmsearch/logs/analyze_generation/evaluated_results.json -------------------------------------------------------------------------------- /projects/matllmsearch/logs/analyze_generation/generations.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/matllmsearch/logs/analyze_generation/generations.csv -------------------------------------------------------------------------------- /projects/matllmsearch/logs/analyze_generation/metrics.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/matllmsearch/logs/analyze_generation/metrics.csv -------------------------------------------------------------------------------- /projects/matllmsearch/requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/matllmsearch/requirements.txt -------------------------------------------------------------------------------- /projects/matllmsearch/src/__init__.py: -------------------------------------------------------------------------------- 1 | """MatLLMSearch - Crystal Structure Generation using LLMs""" -------------------------------------------------------------------------------- /projects/matllmsearch/src/evaluators/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/matllmsearch/src/evaluators/__init__.py -------------------------------------------------------------------------------- /projects/matllmsearch/src/evaluators/materials_oracle.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/matllmsearch/src/evaluators/materials_oracle.py -------------------------------------------------------------------------------- /projects/matllmsearch/src/modes/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/matllmsearch/src/modes/__init__.py -------------------------------------------------------------------------------- /projects/matllmsearch/src/modes/analyze.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/matllmsearch/src/modes/analyze.py -------------------------------------------------------------------------------- /projects/matllmsearch/src/modes/csg.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/matllmsearch/src/modes/csg.py -------------------------------------------------------------------------------- /projects/matllmsearch/src/modes/csp.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/matllmsearch/src/modes/csp.py -------------------------------------------------------------------------------- /projects/matllmsearch/src/utils/__init__.py: -------------------------------------------------------------------------------- 1 | """Utility modules for MatLLMSearch""" -------------------------------------------------------------------------------- /projects/matllmsearch/src/utils/config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/matllmsearch/src/utils/config.py -------------------------------------------------------------------------------- /projects/matllmsearch/src/utils/data_loader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/matllmsearch/src/utils/data_loader.py -------------------------------------------------------------------------------- /projects/matllmsearch/src/utils/e_hull_calculator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/matllmsearch/src/utils/e_hull_calculator.py -------------------------------------------------------------------------------- /projects/matllmsearch/src/utils/evaluate_structures.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/matllmsearch/src/utils/evaluate_structures.py -------------------------------------------------------------------------------- /projects/matllmsearch/src/utils/stability_calculator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/matllmsearch/src/utils/stability_calculator.py -------------------------------------------------------------------------------- /projects/matllmsearch/src/utils/structure_generator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/matllmsearch/src/utils/structure_generator.py -------------------------------------------------------------------------------- /projects/molleo/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/README.md -------------------------------------------------------------------------------- /projects/molleo/README_RESTRUCTURED.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/README_RESTRUCTURED.md -------------------------------------------------------------------------------- /projects/molleo/_archive/MoleculeSTM/downstream_molecule_edit_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/MoleculeSTM/downstream_molecule_edit_utils.py -------------------------------------------------------------------------------- /projects/molleo/_archive/MoleculeSTM/models/GA/ZINC_first_1000.smi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/MoleculeSTM/models/GA/ZINC_first_1000.smi -------------------------------------------------------------------------------- /projects/molleo/_archive/MoleculeSTM/models/GA/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /projects/molleo/_archive/MoleculeSTM/models/GA/crossover.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/MoleculeSTM/models/GA/crossover.py -------------------------------------------------------------------------------- /projects/molleo/_archive/MoleculeSTM/models/GA/mutate.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/MoleculeSTM/models/GA/mutate.py -------------------------------------------------------------------------------- /projects/molleo/_archive/MoleculeSTM/models/MLP.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/MoleculeSTM/models/MLP.py -------------------------------------------------------------------------------- /projects/molleo/_archive/MoleculeSTM/models/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/MoleculeSTM/models/__init__.py -------------------------------------------------------------------------------- /projects/molleo/_archive/MoleculeSTM/models/mega_molbart/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/MoleculeSTM/models/mega_molbart/__init__.py -------------------------------------------------------------------------------- /projects/molleo/_archive/MoleculeSTM/models/mega_molbart/decoder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/MoleculeSTM/models/mega_molbart/decoder.py -------------------------------------------------------------------------------- /projects/molleo/_archive/MoleculeSTM/models/mega_molbart/mega_mol_bart.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/MoleculeSTM/models/mega_molbart/mega_mol_bart.py -------------------------------------------------------------------------------- /projects/molleo/_archive/MoleculeSTM/models/mega_molbart/megatron_bart.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/MoleculeSTM/models/mega_molbart/megatron_bart.py -------------------------------------------------------------------------------- /projects/molleo/_archive/MoleculeSTM/models/mega_molbart/tokenizer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/MoleculeSTM/models/mega_molbart/tokenizer.py -------------------------------------------------------------------------------- /projects/molleo/_archive/MoleculeSTM/models/mega_molbart/util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/MoleculeSTM/models/mega_molbart/util.py -------------------------------------------------------------------------------- /projects/molleo/_archive/MoleculeSTM/models/molecule_gnn_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/MoleculeSTM/models/molecule_gnn_model.py -------------------------------------------------------------------------------- /projects/molleo/_archive/MoleculeSTM/scripts/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/MoleculeSTM/scripts/README.md -------------------------------------------------------------------------------- /projects/molleo/_archive/MoleculeSTM/scripts/downstream_01_retrieval_ATC.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/MoleculeSTM/scripts/downstream_01_retrieval_ATC.py -------------------------------------------------------------------------------- /projects/molleo/_archive/MoleculeSTM/scripts/downstream_01_retrieval_ATC_KV-PLM.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/MoleculeSTM/scripts/downstream_01_retrieval_ATC_KV-PLM.py -------------------------------------------------------------------------------- /projects/molleo/_archive/MoleculeSTM/scripts/downstream_01_retrieval_ATC_Retrieval.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/MoleculeSTM/scripts/downstream_01_retrieval_ATC_Retrieval.py -------------------------------------------------------------------------------- /projects/molleo/_archive/MoleculeSTM/scripts/downstream_01_retrieval_Description_Pharmacodynamics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/MoleculeSTM/scripts/downstream_01_retrieval_Description_Pharmacodynamics.py -------------------------------------------------------------------------------- /projects/molleo/_archive/MoleculeSTM/scripts/downstream_01_retrieval_Description_Pharmacodynamics_KV-PLM.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/MoleculeSTM/scripts/downstream_01_retrieval_Description_Pharmacodynamics_KV-PLM.py -------------------------------------------------------------------------------- /projects/molleo/_archive/MoleculeSTM/scripts/downstream_01_retrieval_Description_Pharmacodynamics_Retrieval.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/MoleculeSTM/scripts/downstream_01_retrieval_Description_Pharmacodynamics_Retrieval.py -------------------------------------------------------------------------------- /projects/molleo/_archive/MoleculeSTM/scripts/downstream_02_molecule_edit_step_01_MoleculeSTM_Space_Alignment.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/MoleculeSTM/scripts/downstream_02_molecule_edit_step_01_MoleculeSTM_Space_Alignment.py -------------------------------------------------------------------------------- /projects/molleo/_archive/MoleculeSTM/scripts/downstream_02_molecule_edit_step_02_GA.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/MoleculeSTM/scripts/downstream_02_molecule_edit_step_02_GA.py -------------------------------------------------------------------------------- /projects/molleo/_archive/MoleculeSTM/scripts/downstream_02_molecule_edit_step_02_High_Variance.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/MoleculeSTM/scripts/downstream_02_molecule_edit_step_02_High_Variance.py -------------------------------------------------------------------------------- /projects/molleo/_archive/MoleculeSTM/scripts/downstream_02_molecule_edit_step_02_MoleculeSTM_Latent_Optimization.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/MoleculeSTM/scripts/downstream_02_molecule_edit_step_02_MoleculeSTM_Latent_Optimization.py -------------------------------------------------------------------------------- /projects/molleo/_archive/MoleculeSTM/scripts/downstream_02_molecule_edit_step_02_PCA.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/MoleculeSTM/scripts/downstream_02_molecule_edit_step_02_PCA.py -------------------------------------------------------------------------------- /projects/molleo/_archive/MoleculeSTM/scripts/downstream_02_molecule_edit_step_02_Random_Perturbation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/MoleculeSTM/scripts/downstream_02_molecule_edit_step_02_Random_Perturbation.py -------------------------------------------------------------------------------- /projects/molleo/_archive/MoleculeSTM/scripts/downstream_03_property_prediction.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/MoleculeSTM/scripts/downstream_03_property_prediction.py -------------------------------------------------------------------------------- /projects/molleo/_archive/MoleculeSTM/scripts/downstream_03_property_prediction_KV-PLM.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/MoleculeSTM/scripts/downstream_03_property_prediction_KV-PLM.py -------------------------------------------------------------------------------- /projects/molleo/_archive/MoleculeSTM/scripts/pretrain.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/MoleculeSTM/scripts/pretrain.py -------------------------------------------------------------------------------- /projects/molleo/_archive/MoleculeSTM/scripts/run_train_molecule_edit_model.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/MoleculeSTM/scripts/run_train_molecule_edit_model.sh -------------------------------------------------------------------------------- /projects/molleo/_archive/MoleculeSTM/scripts/slurm_files/12303811.error: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/MoleculeSTM/scripts/slurm_files/12303811.error -------------------------------------------------------------------------------- /projects/molleo/_archive/MoleculeSTM/scripts/slurm_files/12303811.out: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/MoleculeSTM/scripts/slurm_files/12303811.out -------------------------------------------------------------------------------- /projects/molleo/_archive/MoleculeSTM/scripts/temp/accuracy.npz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/MoleculeSTM/scripts/temp/accuracy.npz -------------------------------------------------------------------------------- /projects/molleo/_archive/MoleculeSTM/scripts/temp/edited_SMILES.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/MoleculeSTM/scripts/temp/edited_SMILES.tsv -------------------------------------------------------------------------------- /projects/molleo/_archive/MoleculeSTM/scripts/temp2/accuracy.npz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/MoleculeSTM/scripts/temp2/accuracy.npz -------------------------------------------------------------------------------- /projects/molleo/_archive/MoleculeSTM/scripts/temp2/edited_SMILES.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/MoleculeSTM/scripts/temp2/edited_SMILES.tsv -------------------------------------------------------------------------------- /projects/molleo/_archive/MoleculeSTM/scripts/temp3/accuracy.npz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/MoleculeSTM/scripts/temp3/accuracy.npz -------------------------------------------------------------------------------- /projects/molleo/_archive/MoleculeSTM/scripts/temp3/edited_SMILES.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/MoleculeSTM/scripts/temp3/edited_SMILES.tsv -------------------------------------------------------------------------------- /projects/molleo/_archive/MoleculeSTM/scripts/temp6/accuracy.npz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/MoleculeSTM/scripts/temp6/accuracy.npz -------------------------------------------------------------------------------- /projects/molleo/_archive/MoleculeSTM/scripts/temp6/edited_SMILES.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/MoleculeSTM/scripts/temp6/edited_SMILES.tsv -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/main/molleo_multi/GPT4.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/multi_objective/main/molleo_multi/GPT4.py -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/main/molleo_multi/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/main/molleo_multi/biot5.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/multi_objective/main/molleo_multi/biot5.py -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/main/molleo_multi/crossover.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/multi_objective/main/molleo_multi/crossover.py -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/main/molleo_multi/features.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/multi_objective/main/molleo_multi/features.py -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/main/molleo_multi/hparams_default.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/multi_objective/main/molleo_multi/hparams_default.yaml -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/main/molleo_multi/hparams_tune.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/multi_objective/main/molleo_multi/hparams_tune.yaml -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/main/molleo_multi/mol_lm.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/multi_objective/main/molleo_multi/mol_lm.py -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/main/molleo_multi/mol_lm_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/multi_objective/main/molleo_multi/mol_lm_utils.py -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/main/molleo_multi/mutate.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/multi_objective/main/molleo_multi/mutate.py -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/main/molleo_multi/network.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/multi_objective/main/molleo_multi/network.py -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/main/molleo_multi/oracle/jnk3.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/multi_objective/main/molleo_multi/oracle/jnk3.pkl -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/main/molleo_multi/results/results_BioT5_['jnk3', 'qed']_['sa']0.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/multi_objective/main/molleo_multi/results/results_BioT5_['jnk3', 'qed']_['sa']0.yaml -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/main/molleo_multi/results/results_GPT-4_['jnk3', 'qed']_['sa']0.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/multi_objective/main/molleo_multi/results/results_GPT-4_['jnk3', 'qed']_['sa']0.yaml -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/main/molleo_multi/run.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/multi_objective/main/molleo_multi/run.py -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/main/molleo_multi/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/multi_objective/main/molleo_multi/utils.py -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/main/molleo_multi_pareto/GPT4.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/multi_objective/main/molleo_multi_pareto/GPT4.py -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/main/molleo_multi_pareto/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/main/molleo_multi_pareto/biot5.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/multi_objective/main/molleo_multi_pareto/biot5.py -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/main/molleo_multi_pareto/crossover.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/multi_objective/main/molleo_multi_pareto/crossover.py -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/main/molleo_multi_pareto/features.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/multi_objective/main/molleo_multi_pareto/features.py -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/main/molleo_multi_pareto/hparams_default.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/multi_objective/main/molleo_multi_pareto/hparams_default.yaml -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/main/molleo_multi_pareto/hparams_tune.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/multi_objective/main/molleo_multi_pareto/hparams_tune.yaml -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/main/molleo_multi_pareto/mol_lm.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/multi_objective/main/molleo_multi_pareto/mol_lm.py -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/main/molleo_multi_pareto/mol_lm_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/multi_objective/main/molleo_multi_pareto/mol_lm_utils.py -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/main/molleo_multi_pareto/mutate.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/multi_objective/main/molleo_multi_pareto/mutate.py -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/main/molleo_multi_pareto/network.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/multi_objective/main/molleo_multi_pareto/network.py -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/main/molleo_multi_pareto/oracle/jnk3.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/multi_objective/main/molleo_multi_pareto/oracle/jnk3.pkl -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/main/molleo_multi_pareto/results/results_BioT5_['jnk3', 'qed']_['sa']0.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/multi_objective/main/molleo_multi_pareto/results/results_BioT5_['jnk3', 'qed']_['sa']0.yaml -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/main/molleo_multi_pareto/results/results_GPT-4_['jnk3', 'qed']_['sa']0.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/multi_objective/main/molleo_multi_pareto/results/results_GPT-4_['jnk3', 'qed']_['sa']0.yaml -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/main/molleo_multi_pareto/run.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/multi_objective/main/molleo_multi_pareto/run.py -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/main/molleo_multi_pareto/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/multi_objective/main/molleo_multi_pareto/utils.py -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/main/optimizer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/multi_objective/main/optimizer.py -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/main/pareto_optimizer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/multi_objective/main/pareto_optimizer.py -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/main/utils/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/main/utils/chem.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/multi_objective/main/utils/chem.py -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/main/utils/chem_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/multi_objective/main/utils/chem_utils.py -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/main/utils/eval_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/multi_objective/main/utils/eval_utils.py -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/main/utils/jtvae_data_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/multi_objective/main/utils/jtvae_data_utils.py -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/main/utils/nn_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/multi_objective/main/utils/nn_utils.py -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/main/utils/preprocess.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/multi_objective/main/utils/preprocess.py -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/main/utils/script_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/multi_objective/main/utils/script_utils.py -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/main/utils/smiles_data_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/multi_objective/main/utils/smiles_data_utils.py -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/main/utils/vocab.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/multi_objective/main/utils/vocab.py -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/oracle/fpscores.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/multi_objective/oracle/fpscores.pkl -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/oracle/jnk3_current.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/multi_objective/oracle/jnk3_current.pkl -------------------------------------------------------------------------------- /projects/molleo/_archive/multi_objective/run.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/multi_objective/run.py -------------------------------------------------------------------------------- /projects/molleo/_archive/single_objective/data/zinc.tab: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/single_objective/data/zinc.tab -------------------------------------------------------------------------------- /projects/molleo/_archive/single_objective/main/molleo/GPT4.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/single_objective/main/molleo/GPT4.py -------------------------------------------------------------------------------- /projects/molleo/_archive/single_objective/main/molleo/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /projects/molleo/_archive/single_objective/main/molleo/biot5.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/single_objective/main/molleo/biot5.py -------------------------------------------------------------------------------- /projects/molleo/_archive/single_objective/main/molleo/crossover.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/single_objective/main/molleo/crossover.py -------------------------------------------------------------------------------- /projects/molleo/_archive/single_objective/main/molleo/features.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/single_objective/main/molleo/features.py -------------------------------------------------------------------------------- /projects/molleo/_archive/single_objective/main/molleo/hparams_default.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/single_objective/main/molleo/hparams_default.yaml -------------------------------------------------------------------------------- /projects/molleo/_archive/single_objective/main/molleo/hparams_tune.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/single_objective/main/molleo/hparams_tune.yaml -------------------------------------------------------------------------------- /projects/molleo/_archive/single_objective/main/molleo/mol_lm.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/single_objective/main/molleo/mol_lm.py -------------------------------------------------------------------------------- /projects/molleo/_archive/single_objective/main/molleo/mol_lm_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/single_objective/main/molleo/mol_lm_utils.py -------------------------------------------------------------------------------- /projects/molleo/_archive/single_objective/main/molleo/mutate.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/single_objective/main/molleo/mutate.py -------------------------------------------------------------------------------- /projects/molleo/_archive/single_objective/main/molleo/network.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/single_objective/main/molleo/network.py -------------------------------------------------------------------------------- /projects/molleo/_archive/single_objective/main/molleo/oracle/jnk3.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/single_objective/main/molleo/oracle/jnk3.pkl -------------------------------------------------------------------------------- /projects/molleo/_archive/single_objective/main/molleo/results/results_BioT5_qed_15.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/single_objective/main/molleo/results/results_BioT5_qed_15.yaml -------------------------------------------------------------------------------- /projects/molleo/_archive/single_objective/main/molleo/results/results_GPT-4_qed_15.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/single_objective/main/molleo/results/results_GPT-4_qed_15.yaml -------------------------------------------------------------------------------- /projects/molleo/_archive/single_objective/main/molleo/results/results_molleo_qed_15.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/single_objective/main/molleo/results/results_molleo_qed_15.yaml -------------------------------------------------------------------------------- /projects/molleo/_archive/single_objective/main/molleo/run.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/single_objective/main/molleo/run.py -------------------------------------------------------------------------------- /projects/molleo/_archive/single_objective/main/molleo/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/single_objective/main/molleo/utils.py -------------------------------------------------------------------------------- /projects/molleo/_archive/single_objective/main/optimizer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/single_objective/main/optimizer.py -------------------------------------------------------------------------------- /projects/molleo/_archive/single_objective/main/utils/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /projects/molleo/_archive/single_objective/main/utils/chem.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/single_objective/main/utils/chem.py -------------------------------------------------------------------------------- /projects/molleo/_archive/single_objective/main/utils/chem_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/single_objective/main/utils/chem_utils.py -------------------------------------------------------------------------------- /projects/molleo/_archive/single_objective/main/utils/eval_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/single_objective/main/utils/eval_utils.py -------------------------------------------------------------------------------- /projects/molleo/_archive/single_objective/main/utils/jtvae_data_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/single_objective/main/utils/jtvae_data_utils.py -------------------------------------------------------------------------------- /projects/molleo/_archive/single_objective/main/utils/nn_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/single_objective/main/utils/nn_utils.py -------------------------------------------------------------------------------- /projects/molleo/_archive/single_objective/main/utils/preprocess.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/single_objective/main/utils/preprocess.py -------------------------------------------------------------------------------- /projects/molleo/_archive/single_objective/main/utils/script_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/single_objective/main/utils/script_utils.py -------------------------------------------------------------------------------- /projects/molleo/_archive/single_objective/main/utils/smiles_data_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/single_objective/main/utils/smiles_data_utils.py -------------------------------------------------------------------------------- /projects/molleo/_archive/single_objective/main/utils/vocab.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/single_objective/main/utils/vocab.py -------------------------------------------------------------------------------- /projects/molleo/_archive/single_objective/oracle/fpscores.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/single_objective/oracle/fpscores.pkl -------------------------------------------------------------------------------- /projects/molleo/_archive/single_objective/run.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/_archive/single_objective/run.py -------------------------------------------------------------------------------- /projects/molleo/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/cli.py -------------------------------------------------------------------------------- /projects/molleo/example_usage.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/example_usage.py -------------------------------------------------------------------------------- /projects/molleo/images/README/lgga_overview.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/images/README/lgga_overview.png -------------------------------------------------------------------------------- /projects/molleo/images/README/molleo_overview.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/images/README/molleo_overview.gif -------------------------------------------------------------------------------- /projects/molleo/requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/requirements.txt -------------------------------------------------------------------------------- /projects/molleo/src/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/src/__init__.py -------------------------------------------------------------------------------- /projects/molleo/src/core/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/src/core/__init__.py -------------------------------------------------------------------------------- /projects/molleo/src/core/molleo_optimizer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/src/core/molleo_optimizer.py -------------------------------------------------------------------------------- /projects/molleo/src/core/prompts.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/src/core/prompts.py -------------------------------------------------------------------------------- /projects/molleo/src/ga/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/src/ga/__init__.py -------------------------------------------------------------------------------- /projects/molleo/src/ga/crossover.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/src/ga/crossover.py -------------------------------------------------------------------------------- /projects/molleo/src/ga/mutations.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/src/ga/mutations.py -------------------------------------------------------------------------------- /projects/molleo/src/generation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/src/generation.py -------------------------------------------------------------------------------- /projects/molleo/src/modes/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/src/modes/__init__.py -------------------------------------------------------------------------------- /projects/molleo/src/modes/multi_objective.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/src/modes/multi_objective.py -------------------------------------------------------------------------------- /projects/molleo/src/modes/single_objective.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/src/modes/single_objective.py -------------------------------------------------------------------------------- /projects/molleo/src/oracles/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/src/oracles/__init__.py -------------------------------------------------------------------------------- /projects/molleo/src/oracles/base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/src/oracles/base.py -------------------------------------------------------------------------------- /projects/molleo/src/oracles/tdc_oracles.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/src/oracles/tdc_oracles.py -------------------------------------------------------------------------------- /projects/molleo/src/utils/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/src/utils/__init__.py -------------------------------------------------------------------------------- /projects/molleo/src/utils/evolutionary_ops.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/src/utils/evolutionary_ops.py -------------------------------------------------------------------------------- /projects/molleo/src/utils/mol_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/src/utils/mol_utils.py -------------------------------------------------------------------------------- /projects/molleo/tests/example_comprehensive.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/tests/example_comprehensive.py -------------------------------------------------------------------------------- /projects/molleo/tests/example_no_llm.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/tests/example_no_llm.py -------------------------------------------------------------------------------- /projects/molleo/tests/example_with_llm.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/molleo/tests/example_with_llm.py -------------------------------------------------------------------------------- /projects/proteinoptimizer/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/README.md -------------------------------------------------------------------------------- /projects/proteinoptimizer/assets/hold: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /projects/proteinoptimizer/assets/protein_main.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/assets/protein_main.pdf -------------------------------------------------------------------------------- /projects/proteinoptimizer/assets/protein_main.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/assets/protein_main.png -------------------------------------------------------------------------------- /projects/proteinoptimizer/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/cli.py -------------------------------------------------------------------------------- /projects/proteinoptimizer/data/AAV/AAV_wild_type.csv: -------------------------------------------------------------------------------- 1 | wild_type_sequence 2 | DEEEIRTTNPVATEQYGSVSTNLQRGNR 3 | -------------------------------------------------------------------------------- /projects/proteinoptimizer/data/AAV/ground_truth.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/data/AAV/ground_truth.csv -------------------------------------------------------------------------------- /projects/proteinoptimizer/data/AAV/gt_medium_range.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/data/AAV/gt_medium_range.csv -------------------------------------------------------------------------------- /projects/proteinoptimizer/data/AAV/mutation_analysis.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/data/AAV/mutation_analysis.csv -------------------------------------------------------------------------------- /projects/proteinoptimizer/data/GB1/fitness.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/data/GB1/fitness.csv -------------------------------------------------------------------------------- /projects/proteinoptimizer/data/GFP/FPG_position_analysis.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/data/GFP/FPG_position_analysis.csv -------------------------------------------------------------------------------- /projects/proteinoptimizer/data/GFP/GFP_wild_type.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/data/GFP/GFP_wild_type.csv -------------------------------------------------------------------------------- /projects/proteinoptimizer/data/GFP/ground_truth.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/data/GFP/ground_truth.csv -------------------------------------------------------------------------------- /projects/proteinoptimizer/data/GFP/gt_medium_range.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/data/GFP/gt_medium_range.csv -------------------------------------------------------------------------------- /projects/proteinoptimizer/data/GFP/mutation_analysis.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/data/GFP/mutation_analysis.csv -------------------------------------------------------------------------------- /projects/proteinoptimizer/data/GFP/mutation_point.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/data/GFP/mutation_point.csv -------------------------------------------------------------------------------- /projects/proteinoptimizer/data/Syn-3bfo/3bfo_1_A_model_state_dict.npz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/data/Syn-3bfo/3bfo_1_A_model_state_dict.npz -------------------------------------------------------------------------------- /projects/proteinoptimizer/data/Syn-3bfo/fitness.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/data/Syn-3bfo/fitness.csv -------------------------------------------------------------------------------- /projects/proteinoptimizer/data/TrpB/fitness.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/data/TrpB/fitness.csv -------------------------------------------------------------------------------- /projects/proteinoptimizer/requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/requirements.txt -------------------------------------------------------------------------------- /projects/proteinoptimizer/results/results_multi_aav_0_baseline.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/results/results_multi_aav_0_baseline.json -------------------------------------------------------------------------------- /projects/proteinoptimizer/results/results_multi_aav_0_gpt-5-mini.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/results/results_multi_aav_0_gpt-5-mini.json -------------------------------------------------------------------------------- /projects/proteinoptimizer/results/results_multi_gb1_0_baseline.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/results/results_multi_gb1_0_baseline.json -------------------------------------------------------------------------------- /projects/proteinoptimizer/results/results_multi_gb1_0_gpt-5-mini.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/results/results_multi_gb1_0_gpt-5-mini.json -------------------------------------------------------------------------------- /projects/proteinoptimizer/results/results_multi_gfp_0_baseline.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/results/results_multi_gfp_0_baseline.json -------------------------------------------------------------------------------- /projects/proteinoptimizer/results/results_multi_gfp_0_gpt-5-mini.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/results/results_multi_gfp_0_gpt-5-mini.json -------------------------------------------------------------------------------- /projects/proteinoptimizer/results/results_multi_syn-3bfo_0_baseline.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/results/results_multi_syn-3bfo_0_baseline.json -------------------------------------------------------------------------------- /projects/proteinoptimizer/results/results_multi_syn-3bfo_0_gpt-5-mini.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/results/results_multi_syn-3bfo_0_gpt-5-mini.json -------------------------------------------------------------------------------- /projects/proteinoptimizer/results/results_multi_trpb_0_baseline.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/results/results_multi_trpb_0_baseline.json -------------------------------------------------------------------------------- /projects/proteinoptimizer/results/results_multi_trpb_0_gpt-5-mini.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/results/results_multi_trpb_0_gpt-5-mini.json -------------------------------------------------------------------------------- /projects/proteinoptimizer/results/results_single_aav_0_baseline.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/results/results_single_aav_0_baseline.json -------------------------------------------------------------------------------- /projects/proteinoptimizer/results/results_single_aav_0_gpt-5-mini.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/results/results_single_aav_0_gpt-5-mini.json -------------------------------------------------------------------------------- /projects/proteinoptimizer/results/results_single_gb1_0_baseline.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/results/results_single_gb1_0_baseline.json -------------------------------------------------------------------------------- /projects/proteinoptimizer/results/results_single_gb1_0_gpt-5-mini.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/results/results_single_gb1_0_gpt-5-mini.json -------------------------------------------------------------------------------- /projects/proteinoptimizer/results/results_single_gfp_0_baseline.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/results/results_single_gfp_0_baseline.json -------------------------------------------------------------------------------- /projects/proteinoptimizer/results/results_single_gfp_0_gpt-5-mini.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/results/results_single_gfp_0_gpt-5-mini.json -------------------------------------------------------------------------------- /projects/proteinoptimizer/results/results_single_syn-3bfo_0_baseline.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/results/results_single_syn-3bfo_0_baseline.json -------------------------------------------------------------------------------- /projects/proteinoptimizer/results/results_single_syn-3bfo_0_gpt-5-mini.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/results/results_single_syn-3bfo_0_gpt-5-mini.json -------------------------------------------------------------------------------- /projects/proteinoptimizer/results/results_single_trpb_0_baseline.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/results/results_single_trpb_0_baseline.json -------------------------------------------------------------------------------- /projects/proteinoptimizer/results/results_single_trpb_0_gpt-5-mini.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/results/results_single_trpb_0_gpt-5-mini.json -------------------------------------------------------------------------------- /projects/proteinoptimizer/run_all.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/run_all.sh -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/__init__.py: -------------------------------------------------------------------------------- 1 | """ProteinOptimizer Project Root""" 2 | 3 | __version__ = "0.1.0" -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/analyze.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/analyze.py -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/core/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/core/__init__.py -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/core/multiobjective.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/core/multiobjective.py -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/core/pareto.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/core/pareto.py -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/core/pareto_optimizer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/core/pareto_optimizer.py -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/core/protein_optimizer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/core/protein_optimizer.py -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/generation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/generation.py -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/modes/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/modes/__init__.py -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/modes/multi_objective_protein.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/modes/multi_objective_protein.py -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/modes/multi_pareto_protein.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/modes/multi_pareto_protein.py -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/modes/single_objective.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/modes/single_objective.py -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/oracles/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/oracles/__init__.py -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/oracles/base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/oracles/base.py -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/oracles/fitness_oracles.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/oracles/fitness_oracles.py -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/oracles/ml_oracles.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/oracles/ml_oracles.py -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/oracles/multi_objective_oracles.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/oracles/multi_objective_oracles.py -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/GGS_utils/__init__.py: -------------------------------------------------------------------------------- 1 | # This file makes the GGS_utils directory a Python package. -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/__init__.py: -------------------------------------------------------------------------------- 1 | # This file makes the GGS_utils directory a Python package. -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/ckpt/AAV/mutations_0/percentile_0.0_1.0/cnn_oracle.ckpt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/ckpt/AAV/mutations_0/percentile_0.0_1.0/cnn_oracle.ckpt -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/ckpt/AAV/mutations_0/percentile_0.0_1.0/config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/ckpt/AAV/mutations_0/percentile_0.0_1.0/config.yaml -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/ckpt/AAV/mutations_6/percentile_0.2_0.4/tik-gamma-1_smoothed/ham1_n-250K/config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/ckpt/AAV/mutations_6/percentile_0.2_0.4/tik-gamma-1_smoothed/ham1_n-250K/config.yaml -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/ckpt/AAV/mutations_6/percentile_0.2_0.4/tik-gamma-1_smoothed/ham1_n-250K/predictor.ckpt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/ckpt/AAV/mutations_6/percentile_0.2_0.4/tik-gamma-1_smoothed/ham1_n-250K/predictor.ckpt -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/ckpt/AAV/mutations_6/percentile_0.2_0.4/unsmoothed/predictor/config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/ckpt/AAV/mutations_6/percentile_0.2_0.4/unsmoothed/predictor/config.yaml -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/ckpt/AAV/mutations_6/percentile_0.2_0.4/unsmoothed/predictor/predictor.ckpt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/ckpt/AAV/mutations_6/percentile_0.2_0.4/unsmoothed/predictor/predictor.ckpt -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/ckpt/AAV/mutations_7/percentile_0.0_0.3/tik-gamma-1_smoothed/ham1_n-250K/config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/ckpt/AAV/mutations_7/percentile_0.0_0.3/tik-gamma-1_smoothed/ham1_n-250K/config.yaml -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/ckpt/AAV/mutations_7/percentile_0.0_0.3/tik-gamma-1_smoothed/ham1_n-250K/predictor.ckpt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/ckpt/AAV/mutations_7/percentile_0.0_0.3/tik-gamma-1_smoothed/ham1_n-250K/predictor.ckpt -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/ckpt/AAV/mutations_7/percentile_0.0_0.3/unsmoothed/predictor/config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/ckpt/AAV/mutations_7/percentile_0.0_0.3/unsmoothed/predictor/config.yaml -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/ckpt/AAV/mutations_7/percentile_0.0_0.3/unsmoothed/predictor/predictor.ckpt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/ckpt/AAV/mutations_7/percentile_0.0_0.3/unsmoothed/predictor/predictor.ckpt -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/ckpt/AAV/mutations_7/percentile_0.0_0.3/unsmoothed_smoothed/01_04_2025_03_11/config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/ckpt/AAV/mutations_7/percentile_0.0_0.3/unsmoothed_smoothed/01_04_2025_03_11/config.yaml -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/ckpt/AAV/mutations_7/percentile_0.0_0.3/unsmoothed_smoothed/01_04_2025_03_11/epoch_099.ckpt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/ckpt/AAV/mutations_7/percentile_0.0_0.3/unsmoothed_smoothed/01_04_2025_03_11/epoch_099.ckpt -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/ckpt/AAV/mutations_7/percentile_0.0_0.3/unsmoothed_smoothed/01_04_2025_03_11/last.ckpt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/ckpt/AAV/mutations_7/percentile_0.0_0.3/unsmoothed_smoothed/01_04_2025_03_11/last.ckpt -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/ckpt/AAV/mutations_7/percentile_0.0_0.3/unsmoothed_smoothed/01_05_2025_18_25/config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/ckpt/AAV/mutations_7/percentile_0.0_0.3/unsmoothed_smoothed/01_05_2025_18_25/config.yaml -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/ckpt/AAV/mutations_7/percentile_0.0_0.3/unsmoothed_smoothed/01_05_2025_18_25/epoch_099.ckpt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/ckpt/AAV/mutations_7/percentile_0.0_0.3/unsmoothed_smoothed/01_05_2025_18_25/epoch_099.ckpt -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/ckpt/AAV/mutations_7/percentile_0.0_0.3/unsmoothed_smoothed/01_05_2025_18_25/last.ckpt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/ckpt/AAV/mutations_7/percentile_0.0_0.3/unsmoothed_smoothed/01_05_2025_18_25/last.ckpt -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_0/percentile_0.0_1.0/cnn_oracle.ckpt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_0/percentile_0.0_1.0/cnn_oracle.ckpt -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_0/percentile_0.0_1.0/config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_0/percentile_0.0_1.0/config.yaml -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_0/percentile_0.0_1.0/samples/temp-0.01-ngibbs-1000-epochs-10/config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_0/percentile_0.0_1.0/samples/temp-0.01-ngibbs-1000-epochs-10/config.yaml -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_6/percentile_0.2_0.4/tik-gamma-1_smoothed/ham1_n-250K/config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_6/percentile_0.2_0.4/tik-gamma-1_smoothed/ham1_n-250K/config.yaml -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_6/percentile_0.2_0.4/tik-gamma-1_smoothed/ham1_n-250K/predictor.ckpt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_6/percentile_0.2_0.4/tik-gamma-1_smoothed/ham1_n-250K/predictor.ckpt -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_6/percentile_0.2_0.4/unsmoothed/predictor/config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_6/percentile_0.2_0.4/unsmoothed/predictor/config.yaml -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_6/percentile_0.2_0.4/unsmoothed/predictor/predictor.ckpt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_6/percentile_0.2_0.4/unsmoothed/predictor/predictor.ckpt -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_7/percentile_0.0_0.3/tik-gamma-1_smoothed/ham1_n-250K/config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_7/percentile_0.0_0.3/tik-gamma-1_smoothed/ham1_n-250K/config.yaml -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_7/percentile_0.0_0.3/tik-gamma-1_smoothed/ham1_n-250K/predictor.ckpt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_7/percentile_0.0_0.3/tik-gamma-1_smoothed/ham1_n-250K/predictor.ckpt -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_7/percentile_0.0_0.3/unsmoothed/predictor/config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_7/percentile_0.0_0.3/unsmoothed/predictor/config.yaml -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_7/percentile_0.0_0.3/unsmoothed/predictor/predictor.ckpt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_7/percentile_0.0_0.3/unsmoothed/predictor/predictor.ckpt -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_7/percentile_0.0_0.3/unsmoothed_smoothed/01_03_2025_23_36/config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_7/percentile_0.0_0.3/unsmoothed_smoothed/01_03_2025_23_36/config.yaml -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_7/percentile_0.0_0.3/unsmoothed_smoothed/01_03_2025_23_56/config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_7/percentile_0.0_0.3/unsmoothed_smoothed/01_03_2025_23_56/config.yaml -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_7/percentile_0.0_0.3/unsmoothed_smoothed/01_03_2025_23_56/epoch_079.ckpt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_7/percentile_0.0_0.3/unsmoothed_smoothed/01_03_2025_23_56/epoch_079.ckpt -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_7/percentile_0.0_0.3/unsmoothed_smoothed/01_03_2025_23_56/last.ckpt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_7/percentile_0.0_0.3/unsmoothed_smoothed/01_03_2025_23_56/last.ckpt -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_7/percentile_0.0_0.3/unsmoothed_smoothed/01_03_2025_23_56/samples/temp-0.01-ngibbs-1000-epochs-10/config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_7/percentile_0.0_0.3/unsmoothed_smoothed/01_03_2025_23_56/samples/temp-0.01-ngibbs-1000-epochs-10/config.yaml -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_7/percentile_0.0_0.3/unsmoothed_smoothed/01_03_2025_23_56/samples/temp-0.01-ngibbs-1000-epochs-10/eval_run_new/epoch_filter_last/acceptance_rates.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_7/percentile_0.0_0.3/unsmoothed_smoothed/01_03_2025_23_56/samples/temp-0.01-ngibbs-1000-epochs-10/eval_run_new/epoch_filter_last/acceptance_rates.npy -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_7/percentile_0.0_0.3/unsmoothed_smoothed/01_03_2025_23_56/samples/temp-0.01-ngibbs-1000-epochs-10/eval_run_new/epoch_filter_last/metrics_oracle_cnn_sampling_greedy.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_7/percentile_0.0_0.3/unsmoothed_smoothed/01_03_2025_23_56/samples/temp-0.01-ngibbs-1000-epochs-10/eval_run_new/epoch_filter_last/metrics_oracle_cnn_sampling_greedy.csv -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_7/percentile_0.0_0.3/unsmoothed_smoothed/01_03_2025_23_56/samples/temp-0.01-ngibbs-1000-epochs-10/eval_run_new/epoch_filter_last/metrics_predictor_sampling_greedy.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_7/percentile_0.0_0.3/unsmoothed_smoothed/01_03_2025_23_56/samples/temp-0.01-ngibbs-1000-epochs-10/eval_run_new/epoch_filter_last/metrics_predictor_sampling_greedy.csv -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_7/percentile_0.0_0.3/unsmoothed_smoothed/01_03_2025_23_56/samples/temp-0.01-ngibbs-1000-epochs-10/eval_run_new/epoch_filter_last/results_oracle_cnn_sampling_greedy.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_7/percentile_0.0_0.3/unsmoothed_smoothed/01_03_2025_23_56/samples/temp-0.01-ngibbs-1000-epochs-10/eval_run_new/epoch_filter_last/results_oracle_cnn_sampling_greedy.csv -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_7/percentile_0.0_0.3/unsmoothed_smoothed/01_03_2025_23_56/samples/temp-0.01-ngibbs-1000-epochs-10/eval_run_new/epoch_filter_last/results_predictor_sampling_greedy.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_7/percentile_0.0_0.3/unsmoothed_smoothed/01_03_2025_23_56/samples/temp-0.01-ngibbs-1000-epochs-10/eval_run_new/epoch_filter_last/results_predictor_sampling_greedy.csv -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_7/percentile_0.0_0.3/unsmoothed_smoothed/01_03_2025_23_56/samples/temp-0.01-ngibbs-1000-epochs-10/seed_1.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_7/percentile_0.0_0.3/unsmoothed_smoothed/01_03_2025_23_56/samples/temp-0.01-ngibbs-1000-epochs-10/seed_1.csv -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_7/percentile_0.0_0.3/unsmoothed_smoothed/01_03_2025_23_56/samples/temp-0.01-ngibbs-1000-epochs-10/seed_1_acceptance_rates.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_7/percentile_0.0_0.3/unsmoothed_smoothed/01_03_2025_23_56/samples/temp-0.01-ngibbs-1000-epochs-10/seed_1_acceptance_rates.pkl -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_7/percentile_0.0_0.3/unsmoothed_smoothed/01_03_2025_23_56/samples/temp-0.01-ngibbs-1000-epochs-10/seed_1_cluster_centers.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_7/percentile_0.0_0.3/unsmoothed_smoothed/01_03_2025_23_56/samples/temp-0.01-ngibbs-1000-epochs-10/seed_1_cluster_centers.csv -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_7/percentile_0.0_0.3/unsmoothed_smoothed/01_04_2025_01_22/config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_7/percentile_0.0_0.3/unsmoothed_smoothed/01_04_2025_01_22/config.yaml -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_7/percentile_0.0_0.3/unsmoothed_smoothed/samples/temp-0.01-ngibbs-1000-epochs-10/config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/ckpt/GFP/mutations_7/percentile_0.0_0.3/unsmoothed_smoothed/samples/temp-0.01-ngibbs-1000-epochs-10/config.yaml -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/evolutionary_ops.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/evolutionary_ops.py -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/potts_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/potts_model.py -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/predictors.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/predictors.py -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/utils/tokenize.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/utils/tokenize.py -------------------------------------------------------------------------------- /projects/proteinoptimizer/src/workflow.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/proteinoptimizer/src/workflow.py -------------------------------------------------------------------------------- /projects/synplanner/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/synplanner/README.md -------------------------------------------------------------------------------- /projects/synplanner/assets/llm-retro-overview.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/synplanner/assets/llm-retro-overview.png -------------------------------------------------------------------------------- /projects/synplanner/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/synplanner/cli.py -------------------------------------------------------------------------------- /projects/synplanner/env_setup.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/synplanner/env_setup.sh -------------------------------------------------------------------------------- /projects/synplanner/src/hparams_default.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/synplanner/src/hparams_default.yaml -------------------------------------------------------------------------------- /projects/synplanner/src/optimizer/base_optimizer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/synplanner/src/optimizer/base_optimizer.py -------------------------------------------------------------------------------- /projects/synplanner/src/optimizer/route.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/synplanner/src/optimizer/route.py -------------------------------------------------------------------------------- /projects/synplanner/src/optimizer/route_optimizer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/synplanner/src/optimizer/route_optimizer.py -------------------------------------------------------------------------------- /projects/synplanner/src/oracle/oracle.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/synplanner/src/oracle/oracle.py -------------------------------------------------------------------------------- /projects/synplanner/src/rag/generate_retro_templates.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/synplanner/src/rag/generate_retro_templates.py -------------------------------------------------------------------------------- /projects/synplanner/src/rag/sim_based_rag.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/synplanner/src/rag/sim_based_rag.py -------------------------------------------------------------------------------- /projects/synplanner/src/sascore/fpscores.pkl.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/synplanner/src/sascore/fpscores.pkl.gz -------------------------------------------------------------------------------- /projects/synplanner/src/sascore/sascorer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/synplanner/src/sascore/sascorer.py -------------------------------------------------------------------------------- /projects/synplanner/src/scscore/LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/synplanner/src/scscore/LICENSE -------------------------------------------------------------------------------- /projects/synplanner/src/scscore/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/synplanner/src/scscore/README.md -------------------------------------------------------------------------------- /projects/synplanner/src/scscore/models/model.ckpt-10654.as_numpy.json.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/synplanner/src/scscore/models/model.ckpt-10654.as_numpy.json.gz -------------------------------------------------------------------------------- /projects/synplanner/src/scscore/notebooks/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /projects/synplanner/src/scscore/scripts/get_reaxys_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/synplanner/src/scscore/scripts/get_reaxys_data.py -------------------------------------------------------------------------------- /projects/synplanner/src/scscore/scripts/get_sa_scores_interactive.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/synplanner/src/scscore/scripts/get_sa_scores_interactive.py -------------------------------------------------------------------------------- /projects/synplanner/src/scscore/scripts/get_uspto_50k.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/synplanner/src/scscore/scripts/get_uspto_50k.py -------------------------------------------------------------------------------- /projects/synplanner/src/scscore/scripts/make_h5_file.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/synplanner/src/scscore/scripts/make_h5_file.py -------------------------------------------------------------------------------- /projects/synplanner/src/scscore/scscore/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /projects/synplanner/src/scscore/scscore/nntrain_fingerprint.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/synplanner/src/scscore/scscore/nntrain_fingerprint.py -------------------------------------------------------------------------------- /projects/synplanner/src/scscore/scscore/standalone_model_numpy.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/synplanner/src/scscore/scscore/standalone_model_numpy.py -------------------------------------------------------------------------------- /projects/synplanner/src/scscore/scscore/standalone_model_tf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/synplanner/src/scscore/scscore/standalone_model_tf.py -------------------------------------------------------------------------------- /projects/synplanner/src/scscore/utils/SA_Score/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/synplanner/src/scscore/utils/SA_Score/README -------------------------------------------------------------------------------- /projects/synplanner/src/scscore/utils/SA_Score/UnitTestSAScore.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/synplanner/src/scscore/utils/SA_Score/UnitTestSAScore.py -------------------------------------------------------------------------------- /projects/synplanner/src/scscore/utils/SA_Score/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /projects/synplanner/src/scscore/utils/SA_Score/data/zim.100.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/synplanner/src/scscore/utils/SA_Score/data/zim.100.txt -------------------------------------------------------------------------------- /projects/synplanner/src/scscore/utils/SA_Score/fpscores.pkl.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/synplanner/src/scscore/utils/SA_Score/fpscores.pkl.gz -------------------------------------------------------------------------------- /projects/synplanner/src/scscore/utils/SA_Score/sascorer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/synplanner/src/scscore/utils/SA_Score/sascorer.py -------------------------------------------------------------------------------- /projects/synplanner/src/scscore/utils/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /projects/synplanner/src/scscore/utils/nn.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/synplanner/src/scscore/utils/nn.py -------------------------------------------------------------------------------- /projects/synplanner/src/utils/chemistry_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/synplanner/src/utils/chemistry_utils.py -------------------------------------------------------------------------------- /projects/synplanner/src/utils/prompt.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/synplanner/src/utils/prompt.py -------------------------------------------------------------------------------- /projects/synplanner/src/utils/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/synplanner/src/utils/utils.py -------------------------------------------------------------------------------- /projects/synplanner/test_smiles.smi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/projects/synplanner/test_smiles.smi -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/pyproject.toml -------------------------------------------------------------------------------- /pytest.ini: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/pytest.ini -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/requirements.txt -------------------------------------------------------------------------------- /sde_harness/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/sde_harness/__init__.py -------------------------------------------------------------------------------- /sde_harness/base/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/sde_harness/base/__init__.py -------------------------------------------------------------------------------- /sde_harness/base/cli_base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/sde_harness/base/cli_base.py -------------------------------------------------------------------------------- /sde_harness/base/evaluator_base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/sde_harness/base/evaluator_base.py -------------------------------------------------------------------------------- /sde_harness/base/project_base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/sde_harness/base/project_base.py -------------------------------------------------------------------------------- /sde_harness/core/__info__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/sde_harness/core/__info__.py -------------------------------------------------------------------------------- /sde_harness/core/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/sde_harness/core/__init__.py -------------------------------------------------------------------------------- /sde_harness/core/generation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/sde_harness/core/generation.py -------------------------------------------------------------------------------- /sde_harness/core/oracle.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/sde_harness/core/oracle.py -------------------------------------------------------------------------------- /sde_harness/core/prompt.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/sde_harness/core/prompt.py -------------------------------------------------------------------------------- /sde_harness/core/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/sde_harness/core/utils.py -------------------------------------------------------------------------------- /sde_harness/core/workflow.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/sde_harness/core/workflow.py -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/setup.py -------------------------------------------------------------------------------- /tests/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/tests/README.md -------------------------------------------------------------------------------- /tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/tests/__init__.py -------------------------------------------------------------------------------- /tests/conftest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/tests/conftest.py -------------------------------------------------------------------------------- /tests/run_tests.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/tests/run_tests.py -------------------------------------------------------------------------------- /tests/test_base_classes.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/tests/test_base_classes.py -------------------------------------------------------------------------------- /tests/test_core_generation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/tests/test_core_generation.py -------------------------------------------------------------------------------- /tests/test_core_oracle.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/tests/test_core_oracle.py -------------------------------------------------------------------------------- /tests/test_core_prompt.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/tests/test_core_prompt.py -------------------------------------------------------------------------------- /tests/test_core_workflow.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HowieHwong/sde-harness/HEAD/tests/test_core_workflow.py --------------------------------------------------------------------------------