├── .github └── workflows │ └── install.yaml ├── .gitignore ├── .pre-commit-config.yaml ├── LICENSE ├── README.md ├── assets └── logo │ ├── LLcheD.png │ ├── LLcheD.svg │ ├── LLcheM.png │ ├── LLcheM.svg │ ├── chemnlp.png │ └── chemnlp.svg ├── code_of_conduct.md ├── conda.yaml ├── data ├── check_pandas.py ├── check_smiles_split.py ├── kg │ ├── chebi_chebi │ │ └── meta.yaml │ ├── chembl33_preprocessed_filtered_bioactivity_dataset_w_fullprotnames_smiles │ │ └── meta.yaml │ ├── compound_chebi │ │ └── meta.yaml │ ├── compound_chebi_chebi │ │ └── meta.yaml │ ├── compound_chebi_chebi_chebi_1 │ │ └── meta.yaml │ ├── compound_chebi_chebi_chebi_2 │ │ └── meta.yaml │ ├── compound_protein │ │ └── meta.yaml │ ├── compound_protein_compound_1 │ │ └── meta.yaml │ ├── compound_protein_compound_2 │ │ └── meta.yaml │ ├── compound_protein_compound_3 │ │ └── meta.yaml │ ├── compound_protein_disease │ │ └── meta.yaml │ ├── compound_protein_domain │ │ └── meta.yaml │ ├── compound_protein_ec_number │ │ └── meta.yaml │ ├── compound_protein_go_term_1 │ │ └── meta.yaml │ ├── compound_protein_go_term_2 │ │ └── meta.yaml │ ├── compound_protein_go_term_3 │ │ └── meta.yaml │ ├── compound_protein_go_term_4 │ │ └── meta.yaml │ ├── compound_protein_hpo │ │ └── meta.yaml │ ├── compound_protein_hpo_disease_1 │ │ └── meta.yaml │ ├── compound_protein_hpo_disease_2 │ │ └── meta.yaml │ ├── compound_protein_pathway │ │ └── meta.yaml │ ├── compound_protein_pathway_disease_1 │ │ └── meta.yaml │ ├── compound_protein_pathway_disease_2 │ │ └── meta.yaml │ ├── compound_protein_pathway_disease_3 │ │ └── meta.yaml │ ├── compound_protein_protein │ │ └── meta.yaml │ ├── drug_chebi │ │ └── meta.yaml │ ├── drug_chebi_chebi │ │ └── meta.yaml │ ├── drug_chebi_chebi_chebi │ │ └── meta.yaml │ ├── drug_disease_pathway │ │ └── meta.yaml │ ├── drug_disease_pathway_protein │ │ └── meta.yaml │ ├── drug_protein │ │ └── meta.yaml │ ├── drug_protein_disease │ │ └── meta.yaml │ ├── drug_protein_domain │ │ └── meta.yaml │ ├── drug_protein_drug │ │ └── meta.yaml │ ├── drug_protein_ec_number │ │ └── meta.yaml │ ├── drug_protein_go_term │ │ └── meta.yaml │ ├── drug_protein_hpo │ │ └── meta.yaml │ ├── drug_protein_hpo_disease │ │ └── meta.yaml │ ├── drug_protein_pathway │ │ └── meta.yaml │ ├── drug_protein_pathway_disease │ │ └── meta.yaml │ └── drug_protein_protein │ │ └── meta.yaml ├── natural │ ├── preprocess_europepmc.py │ ├── preprocess_msds.py │ ├── preprocess_nougat.py │ └── preprocess_nougat.sh ├── postprocess_split.py ├── tabular │ ├── BACE │ │ ├── meta.yaml │ │ └── transform.py │ ├── BBBP │ │ ├── meta.yaml │ │ └── transform.py │ ├── MUV_466 │ │ ├── meta.yaml │ │ └── transform.py │ ├── MUV_548 │ │ ├── meta.yaml │ │ └── transform.py │ ├── MUV_600 │ │ ├── meta.yaml │ │ └── transform.py │ ├── MUV_644 │ │ ├── meta.yaml │ │ └── transform.py │ ├── MUV_652 │ │ ├── meta.yaml │ │ └── transform.py │ ├── MUV_689 │ │ ├── meta.yaml │ │ └── transform.py │ ├── MUV_692 │ │ ├── meta.yaml │ │ └── transform.py │ ├── MUV_712 │ │ ├── meta.yaml │ │ └── transform.py │ ├── MUV_713 │ │ ├── meta.yaml │ │ └── transform.py │ ├── MUV_733 │ │ ├── meta.yaml │ │ └── transform.py │ ├── MUV_737 │ │ ├── meta.yaml │ │ └── transform.py │ ├── MUV_810 │ │ ├── meta.yaml │ │ └── transform.py │ ├── MUV_832 │ │ ├── meta.yaml │ │ └── transform.py │ ├── MUV_846 │ │ ├── meta.yaml │ │ └── transform.py │ ├── MUV_852 │ │ ├── meta.yaml │ │ └── transform.py │ ├── MUV_858 │ │ ├── meta.yaml │ │ └── transform.py │ ├── MUV_859 │ │ ├── meta.yaml │ │ └── transform.py │ ├── RedDB │ │ ├── meta.yaml │ │ └── transform.py │ ├── SIDER │ │ ├── meta.yaml │ │ └── transform.py │ ├── ames_mutagenicity │ │ ├── meta.yaml │ │ └── transform.py │ ├── aminoacids │ │ ├── meta.yaml │ │ └── transform.py │ ├── bc5chem │ │ ├── meta.yaml │ │ └── transform.py │ ├── bc5disease │ │ ├── meta.yaml │ │ └── transform.py │ ├── bicerano_dataset │ │ ├── meta.yaml │ │ └── transform.py │ ├── bio_ner │ │ ├── meta.yaml │ │ └── transform.py │ ├── bioavailability_ma_et_al │ │ ├── meta.yaml │ │ └── transform.py │ ├── block_polymers_morphology │ │ ├── meta.yaml │ │ └── transform.py │ ├── blood_brain_barrier_martins_et_al │ │ └── transform.py │ ├── buchwald_hartwig │ │ ├── meta.yaml │ │ └── transform.py │ ├── caco2_wang │ │ ├── meta.yaml │ │ └── transform.py │ ├── carcinogens │ │ ├── meta.yaml │ │ └── transform.py │ ├── cav3_t-type_calcium_channels_butkiewicz │ │ ├── meta.yaml │ │ └── transform.py │ ├── chebi_20 │ │ ├── meta.yaml │ │ └── transform.py │ ├── check_pandas.py │ ├── check_smiles_split.py │ ├── chem_caption_smarts │ │ ├── meta.yaml │ │ ├── preprocess.py │ │ └── transform.py │ ├── chembl_v29 │ │ ├── meta.yaml │ │ └── transform.py │ ├── chemcaption_fragments │ │ ├── meta.yaml │ │ └── transform.py │ ├── chemcaption_rdkit │ │ ├── meta.yaml │ │ ├── preprocess.py │ │ └── transform.py │ ├── chemdner │ │ ├── meta.yaml │ │ └── transform.py │ ├── chemistry_stackexchange │ │ ├── meta.yaml │ │ └── transform.py │ ├── choline_transporter_butkiewicz │ │ ├── meta.yaml │ │ └── transform.py │ ├── clearance_astrazeneca │ │ ├── meta.yaml │ │ └── transform.py │ ├── clintox │ │ ├── meta.yaml │ │ └── transform.py │ ├── core_mof_no_topo │ │ ├── meta.yaml │ │ └── transform.py │ ├── cyp2c9_substrate_carbonmangels │ │ ├── meta.yaml │ │ └── transform.py │ ├── cyp2d6_substrate_carbonmangels │ │ ├── meta.yaml │ │ └── transform.py │ ├── cyp3a4_substrate_carbonmangels │ │ ├── meta.yaml │ │ └── transform.py │ ├── cyp_p450_1a2_inhibition_veith_et_al │ │ ├── meta.yaml │ │ └── transform.py │ ├── cyp_p450_2c19_inhibition_veith_et_al │ │ ├── meta.yaml │ │ └── transform.py │ ├── cyp_p450_2c9_inhibition_veith_et_al │ │ ├── meta.yaml │ │ └── transform.py │ ├── cyp_p450_2d6_inhibition_veith_et_al │ │ ├── meta.yaml │ │ └── transform.py │ ├── cyp_p450_3a4_inhibition_veith_et_al │ │ ├── meta.yaml │ │ └── transform.py │ ├── drug_induced_liver_injury │ │ ├── meta.yaml │ │ └── transform.py │ ├── drugchat_liang_zhang_et_al │ │ ├── meta.yaml │ │ └── transform.py │ ├── fda_adverse_reactions │ │ ├── meta.yaml │ │ └── transform.py │ ├── flashpoint │ │ ├── meta.yaml │ │ └── transform.py │ ├── formation_energies │ │ ├── meta.yaml │ │ └── transform.py │ ├── freesolv │ │ ├── meta.yaml │ │ └── transform.py │ ├── h2_storage_materials │ │ ├── LICENSE │ │ ├── meta.yaml │ │ ├── processing.ipynb │ │ └── transform.py │ ├── half_life_obach │ │ ├── meta.yaml │ │ └── transform.py │ ├── herg_blockers │ │ ├── meta.yaml │ │ └── transform.py │ ├── herg_central_at_10uM │ │ ├── meta.yaml │ │ └── transform.py │ ├── herg_central_at_1uM │ │ ├── meta.yaml │ │ └── transform.py │ ├── herg_central_inhib │ │ ├── meta.yaml │ │ └── transform.py │ ├── herg_karim_et_al │ │ ├── meta.yaml │ │ └── transform.py │ ├── hiv │ │ ├── meta.yaml │ │ └── transform.py │ ├── human_intestinal_absorption │ │ ├── meta.yaml │ │ └── transform.py │ ├── inverse_1 │ │ ├── meta.yaml │ │ └── transform.py │ ├── inverse_2 │ │ ├── meta.yaml │ │ └── transform.py │ ├── inverse_3 │ │ ├── meta.yaml │ │ └── transform.py │ ├── iupac_goldbook │ │ ├── meta.yaml │ │ └── transform.py │ ├── iupac_smiles │ │ ├── meta.yaml │ │ └── transform.py │ ├── kcnq2_potassium_channel_butkiewicz │ │ ├── meta.yaml │ │ └── transform.py │ ├── ld50_catmos │ │ ├── meta.yaml │ │ └── transform.py │ ├── ld50_zhu │ │ ├── example_processing_and_templates.ipynb │ │ ├── meta.yaml │ │ └── transform.py │ ├── lipophilicity │ │ ├── data_original.txt │ │ ├── meta.yaml │ │ └── transform.py │ ├── m1_muscarinic_receptor_agonists_butkiewicz │ │ ├── meta.yaml │ │ └── transform.py │ ├── m1_muscarinic_receptor_antagonists_butkiewicz │ │ ├── meta.yaml │ │ └── transform.py │ ├── mattermodeling_stackexchange │ │ ├── meta.yaml │ │ └── transform.py │ ├── melting_points │ │ ├── meta.yaml │ │ └── transform.py │ ├── merge.py │ ├── mofdscribe │ │ ├── meta.yaml │ │ └── transform.py │ ├── mol2svg │ │ ├── meta.yaml │ │ └── transform.py │ ├── mol_repr_transl │ │ └── transform.py │ ├── mona │ │ ├── example_processing_and_templates.ipynb │ │ ├── meta.yaml │ │ └── transform.py │ ├── moses │ │ ├── meta.yaml │ │ └── transform.py │ ├── mp_anisotropy │ │ ├── meta.yaml │ │ └── transform.py │ ├── mp_bulk_modulus │ │ ├── meta.yaml │ │ └── transform.py │ ├── mp_descriptions │ │ ├── meta.yaml │ │ └── transform.py │ ├── mp_self_supervised │ │ ├── meta.yaml │ │ ├── prepare_data.py │ │ └── transform.py │ ├── mp_shear_modulus │ │ ├── meta.yaml │ │ └── transform.py │ ├── ncbi_disease │ │ ├── meta.yaml │ │ └── transform.py │ ├── nlmchem │ │ ├── meta.yaml │ │ └── transform.py │ ├── nomad_structure │ │ ├── meta.yaml │ │ └── transform.py │ ├── nr_ahr_tox21 │ │ ├── meta.yaml │ │ └── transform.py │ ├── nr_ar_lbd_tox21 │ │ ├── meta.yaml │ │ └── transform.py │ ├── nr_ar_tox21 │ │ ├── meta.yaml │ │ └── transform.py │ ├── nr_aromatase_tox21 │ │ ├── meta.yaml │ │ └── transform.py │ ├── nr_er_lbd_tox21 │ │ ├── meta.yaml │ │ └── transform.py │ ├── nr_er_tox21 │ │ ├── meta.yaml │ │ └── transform.py │ ├── nr_ppar_gamma_tox21 │ │ ├── meta.yaml │ │ └── transform.py │ ├── ocp │ │ ├── meta.yaml │ │ └── transform.py │ ├── odd_one_out │ │ ├── meta.yaml │ │ └── transform.py │ ├── opv │ │ ├── meta.yaml │ │ └── transform.py │ ├── oqmd │ │ ├── meta.yaml │ │ └── transform.py │ ├── orbnet_denali │ │ ├── develop_transform.ipynb │ │ ├── meta.yaml │ │ └── transform.py │ ├── ord_masked │ │ ├── meta.yaml │ │ └── transform.py │ ├── ord_predictions │ │ ├── meta.yaml │ │ └── transform.py │ ├── ord_procedure_steps │ │ ├── meta.yaml │ │ └── transform.py │ ├── ord_rxn_smiles_procedure │ │ ├── meta.yaml │ │ └── transform.py │ ├── ord_rxn_smiles_yield_pred │ │ ├── meta.yaml │ │ └── transform.py │ ├── ord_steps_yield │ │ ├── meta.yaml │ │ └── transform.py │ ├── orexin1_receptor_butkiewicz │ │ ├── meta.yaml │ │ └── transform.py │ ├── p_glycoprotein_inhibition_broccatelli_et_al │ │ ├── meta.yaml │ │ └── transform.py │ ├── pampa_ncats │ │ ├── example_processing_and_templates.ipynb │ │ ├── meta.yaml │ │ └── transform.py │ ├── peptides_hemolytic │ │ ├── meta.yaml │ │ └── transform.py │ ├── peptides_nonfouling │ │ ├── meta.yaml │ │ └── transform.py │ ├── peptides_soluble │ │ ├── meta.yaml │ │ └── transform.py │ ├── perovskite_db │ │ ├── meta.yaml │ │ └── transform.py │ ├── physics_stackexchange │ │ ├── explore.ipynb │ │ ├── meta.yaml │ │ └── transform.py │ ├── potassium_ion_channel_kir2_1_butkiewicz │ │ ├── meta.yaml │ │ └── transform.py │ ├── qm8 │ │ ├── meta.yaml │ │ └── transform.py │ ├── qm9 │ │ ├── meta.yaml │ │ ├── prep_csv.py │ │ └── transform.py │ ├── qmof_gcmc │ │ ├── meta.yaml │ │ └── transform.py │ ├── qmof_quantum │ │ ├── meta.yaml │ │ └── transform.py │ ├── rdkit_features │ │ ├── meta.yaml │ │ └── transform.py │ ├── rhea_db_masked │ │ ├── meta.yaml │ │ └── transform.py │ ├── rhea_db_predictions │ │ ├── meta.yaml │ │ └── transform.py │ ├── run_all_transform.sh │ ├── sarscov2_3clpro_diamond │ │ ├── meta.yaml │ │ └── transform.py │ ├── sarscov2_vitro_touret │ │ ├── meta.yaml │ │ └── transform.py │ ├── serine_threonine_kinase_33_butkiewicz │ │ ├── meta.yaml │ │ └── transform.py │ ├── sigma_aldrich_safety_data │ │ ├── meta.yaml │ │ └── transform.py │ ├── skin_reaction │ │ ├── meta.yaml │ │ └── transform.py │ ├── smiles_to_3d │ │ ├── meta.yaml │ │ └── transform.py │ ├── solubility_aqsoldb │ │ ├── meta.yaml │ │ └── transform.py │ ├── sr_are_tox21 │ │ ├── meta.yaml │ │ └── transform.py │ ├── sr_atad5_tox21 │ │ ├── meta.yaml │ │ └── transform.py │ ├── sr_hse_tox21 │ │ ├── meta.yaml │ │ └── transform.py │ ├── sr_mmp_tox21 │ │ ├── meta.yaml │ │ └── transform.py │ ├── sr_p53_tox21 │ │ ├── meta.yaml │ │ └── transform.py │ ├── suzuki_miyaura_sach │ │ ├── meta.yaml │ │ └── transform.py │ ├── thermosol │ │ ├── meta.yaml │ │ └── transform.py │ ├── train_test_split.py │ ├── tyrosyl-dna_phosphodiesterase_butkiewicz │ │ ├── meta.yaml │ │ └── transform.py │ ├── uniprot_binding_single │ │ ├── meta.yaml │ │ └── transform.py │ ├── uniprot_binding_sites_multiple │ │ ├── meta.yaml │ │ └── transform.py │ ├── uniprot_organisms │ │ ├── meta.yaml │ │ └── transform.py │ ├── uniprot_reactions │ │ ├── meta.yaml │ │ └── transform.py │ ├── uniprot_sentences │ │ ├── meta.yaml │ │ └── transform.py │ ├── uspto │ │ ├── meta.yaml │ │ └── transform.py │ ├── uspto_yield │ │ ├── meta.yaml │ │ └── transform.py │ ├── volume_of_distribution_at_steady_state_lombardo_et_al │ │ ├── meta.yaml │ │ └── transform.py │ └── zinc │ │ ├── meta.yaml │ │ └── transform.py ├── text_sampling │ ├── extend_tabular.py │ ├── extend_tabular_processed.py │ ├── get_dataset_overlap.py │ ├── preprocess_kg.py │ ├── text_sampling.py │ └── utils.py └── train_test_split.py ├── docs ├── CONTRIBUTING.md ├── api │ ├── meta_yaml_augmentor.md │ ├── meta_yaml_generator.md │ ├── sampler.md │ └── sampler_cli.md └── index.md ├── experiments ├── README.md ├── ablations │ ├── 20240814_sample_data.bash │ └── continued_pretrain.py ├── configs │ ├── data_configs │ │ ├── data_mixing.yml │ │ ├── hf_data.yml │ │ ├── hf_data_wiki.yml │ │ ├── prep_lm_eval_data.yml │ │ └── prep_smiles_data.yml │ ├── deepspeed │ │ ├── deepspeed_S1.json │ │ ├── deepspeed_S2.json │ │ ├── deepspeed_offload_S2.json │ │ └── deepspeed_offload_S3.json │ ├── eval_configs │ │ ├── default_eval_config.yaml │ │ ├── nlp_eval_config.yaml │ │ ├── safety_eval_config.yaml │ │ └── stem_eval_config.yaml │ ├── gpt-neox │ │ ├── 160M.yml │ │ ├── cluster_setup.yml │ │ └── soft_prompt.yml │ └── hugging-face │ │ ├── 160M_full.yml │ │ ├── 160M_ptune.yml │ │ ├── 1B_fine_tune.yml │ │ ├── 3B_fine_tune.yml │ │ ├── 410M_fine_tune.yml │ │ └── 7B_fine_tune.yml ├── data │ ├── merge_epmc_to_jsonl.py │ ├── prepare_gptneox_chemrxiv.py │ ├── prepare_hf_dataset.py │ ├── prepare_lm_eval_dataset.py │ ├── prepare_mixed_data.py │ ├── prepare_smiles_dataset.py │ ├── prepare_xyz_denali_data.py │ ├── sbatch_hf_dataset.sh │ ├── sbatch_hf_split.sh │ ├── sbatch_merge_epmc_jsonl.sh │ └── split_data.py ├── scripts │ ├── env_creation_hf.sh │ ├── env_creation_neox.sh │ ├── eval_create_batch_configs.py │ ├── miniconda_install.sh │ ├── run_eval.sh │ ├── run_eval_batch.sh │ ├── run_grid_search.py │ ├── run_n_shot_benchmarks_eval.py │ ├── run_tune.py │ ├── sbatch_train_hf.sh │ ├── sbatch_train_hf_multinode.sh │ ├── sbatch_train_neox.sh │ ├── transfer_all_checkpoint_to_s3.sh │ ├── transfer_checkpoint_to_s3.sh │ └── transfer_hf_cache.sh └── working │ └── calculate_nll.py ├── mkdocs.yml ├── pyproject.toml ├── src └── chemnlp │ ├── __init__.py │ ├── data │ ├── constants.py │ ├── convert.py │ ├── hf_datasets.py │ ├── meta.yaml │ ├── meta_yaml_augmentor.py │ ├── meta_yaml_generator.py │ ├── ner.py │ ├── random_variable.py │ ├── reprs.py │ ├── sampler.py │ ├── sampler_cli.py │ ├── split.py │ └── utils.py │ ├── data_val │ ├── __init__.py │ ├── config.py │ ├── model.py │ └── validate.py │ └── utils.py └── tests ├── __init__.py ├── data ├── __init__.py ├── test_sampler.py └── test_sampler_cli.py ├── test_ner.py └── test_reprs.py /.github/workflows/install.yaml: 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