├── LICENSE ├── MolBART ├── __init__.py ├── csv_data_retrieval.py ├── csv_data_retrieval_chembl.py ├── eval_megatron_retrieval.sh ├── eval_megatron_retrieval_controlled.sh ├── megatron_molbart │ ├── LICENSE_MOLBART │ ├── Megatron-LM-v1.1.5-3D_parallelism │ │ ├── LICENSE │ │ ├── MANIFEST.in │ │ ├── README.md │ │ ├── build │ │ │ └── lib │ │ │ │ └── megatron │ │ │ │ ├── __init__.py │ │ │ │ ├── arguments.py │ │ │ │ ├── checkpointing.py │ │ │ │ ├── data │ │ │ │ ├── Makefile │ │ │ │ ├── __init__.py │ │ │ │ ├── bert_dataset.py │ │ │ │ ├── dataset_utils.py │ │ │ │ ├── gpt2_dataset.py │ │ │ │ ├── helpers.cpp │ │ │ │ ├── ict_dataset.py │ │ │ │ ├── indexed_dataset.py │ │ │ │ ├── realm_dataset_utils.py │ │ │ │ ├── realm_index.py │ │ │ │ └── samplers.py │ │ │ │ ├── deprecated_data_utils │ │ │ │ ├── __init__.py │ │ │ │ ├── configure_data.py │ │ │ │ ├── corpora.py │ │ │ │ ├── datasets.py │ │ │ │ ├── file_utils.py │ │ │ │ ├── lazy_loader.py │ │ │ │ ├── samplers.py │ │ │ │ ├── tf_dl.py │ │ │ │ ├── tokenization.py │ │ │ │ ├── tokenization_gpt2.py │ │ │ │ └── wordpiece.py │ │ │ │ ├── fp16 │ │ │ │ ├── __init__.py │ │ │ │ ├── fp16.py │ │ │ │ ├── fp16util.py │ │ │ │ └── loss_scaler.py │ │ │ │ ├── fused_kernels │ │ │ │ └── __init__.py │ │ │ │ ├── global_vars.py │ │ │ │ ├── indexer.py │ │ │ │ ├── initialize.py │ │ │ │ ├── learning_rates.py │ │ │ │ ├── memory.py │ │ │ │ ├── model │ │ │ │ ├── __init__.py │ │ │ │ ├── bert_model.py │ │ │ │ ├── classification.py │ │ │ │ ├── distributed.py │ │ │ │ ├── fused_bias_gelu.py │ │ │ │ ├── fused_softmax.py │ │ │ │ ├── gpt2_model.py │ │ │ │ ├── language_model.py │ │ │ │ ├── multiple_choice.py │ │ │ │ ├── realm_model.py │ │ │ │ ├── transformer.py │ │ │ │ └── utils.py │ │ │ │ ├── module.py │ │ │ │ ├── mpu │ │ │ │ ├── __init__.py │ │ │ │ ├── cross_entropy.py │ │ │ │ ├── data.py │ │ │ │ ├── grads.py │ │ │ │ ├── initialize.py │ │ │ │ ├── layers.py │ │ │ │ ├── mappings.py │ │ │ │ ├── random.py │ │ │ │ ├── tests │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── commons.py │ │ │ │ │ ├── test_cross_entropy.py │ │ │ │ │ ├── test_data.py │ │ │ │ │ ├── test_initialize.py │ │ │ │ │ ├── test_layers.py │ │ │ │ │ └── test_random.py │ │ │ │ └── utils.py │ │ │ │ ├── package_info.py │ │ │ │ ├── text_generation_utils.py │ │ │ │ ├── tokenizer │ │ │ │ ├── __init__.py │ │ │ │ ├── bert_tokenization.py │ │ │ │ ├── gpt2_tokenization.py │ │ │ │ └── tokenizer.py │ │ │ │ ├── training.py │ │ │ │ └── utils.py │ │ ├── changes.md │ │ ├── dist │ │ │ ├── megatron_lm-1.1.5-py3.6.egg │ │ │ └── megatron_lm-1.1.5-py3.7.egg │ │ ├── examples │ │ │ ├── ds_config.json │ │ │ ├── ds_pretrain_gpt2.sh │ │ │ ├── ds_pretrain_gpt2_pipe.sh │ │ │ ├── ds_zero_stage_2_config.json │ │ │ ├── evaluate_zeroshot_gpt2.sh │ │ │ ├── finetune_mnli_distributed.sh │ │ │ ├── finetune_race_distributed.sh │ │ │ ├── generate_text.sh │ │ │ ├── merge_mp_bert.sh │ │ │ ├── pretrain_bert.sh │ │ │ ├── pretrain_bert_distributed.sh │ │ │ ├── pretrain_gpt2.sh │ │ │ └── pretrain_gpt2_distributed.sh │ │ ├── images │ │ │ ├── Makefile │ │ │ ├── cases.png │ │ │ ├── scaling-dp.png │ │ │ ├── scaling-mp.png │ │ │ └── tables.tex │ │ ├── megatron │ │ │ ├── __init__.py │ │ │ ├── arguments.py │ │ │ ├── checkpointing.py │ │ │ ├── data │ │ │ │ ├── Makefile │ │ │ │ ├── __init__.py │ │ │ │ ├── bert_dataset.py │ │ │ │ ├── dataset_utils.py │ │ │ │ ├── gpt2_dataset.py │ │ │ │ ├── helpers.cpp │ │ │ │ ├── ict_dataset.py │ │ │ │ ├── indexed_dataset.py │ │ │ │ ├── realm_dataset_utils.py │ │ │ │ ├── realm_index.py │ │ │ │ ├── samplers.py │ │ │ │ └── test │ │ │ │ │ ├── test_indexed_dataset.py │ │ │ │ │ └── test_preprocess_data.sh │ │ │ ├── deprecated_data_utils │ │ │ │ ├── __init__.py │ │ │ │ ├── configure_data.py │ │ │ │ ├── corpora.py │ │ │ │ ├── datasets.py │ │ │ │ ├── file_utils.py │ │ │ │ ├── lazy_loader.py │ │ │ │ ├── samplers.py │ │ │ │ ├── scripts │ │ │ │ │ ├── presplit_sentences_json.py │ │ │ │ │ ├── split_gpt2_json.py │ │ │ │ │ └── split_json.py │ │ │ │ ├── tf_dl.py │ │ │ │ ├── tokenization.py │ │ │ │ ├── tokenization_gpt2.py │ │ │ │ └── wordpiece.py │ │ │ ├── fp16 │ │ │ │ ├── __init__.py │ │ │ │ ├── fp16.py │ │ │ │ ├── fp16util.py │ │ │ │ └── loss_scaler.py │ │ │ ├── fused_kernels │ │ │ │ ├── __init__.py │ │ │ │ ├── scaled_masked_softmax.cpp │ │ │ │ ├── scaled_masked_softmax.h │ │ │ │ ├── scaled_masked_softmax_cuda.cu │ │ │ │ ├── scaled_upper_triang_masked_softmax.cpp │ │ │ │ ├── scaled_upper_triang_masked_softmax.h │ │ │ │ └── scaled_upper_triang_masked_softmax_cuda.cu │ │ │ ├── global_vars.py │ │ │ ├── indexer.py │ │ │ ├── initialize.py │ │ │ ├── learning_rates.py │ │ │ ├── memory.py │ │ │ ├── model │ │ │ │ ├── __init__.py │ │ │ │ ├── bert_model.py │ │ │ │ ├── classification.py │ │ │ │ ├── distributed.py │ │ │ │ ├── fused_bias_gelu.py │ │ │ │ ├── fused_softmax.py │ │ │ │ ├── gpt2_model.py │ │ │ │ ├── language_model.py │ │ │ │ ├── multiple_choice.py │ │ │ │ ├── realm_model.py │ │ │ │ ├── transformer.py │ │ │ │ └── utils.py │ │ │ ├── module.py │ │ │ ├── mpu │ │ │ │ ├── __init__.py │ │ │ │ ├── cross_entropy.py │ │ │ │ ├── data.py │ │ │ │ ├── grads.py │ │ │ │ ├── initialize.py │ │ │ │ ├── layers.py │ │ │ │ ├── mappings.py │ │ │ │ ├── random.py │ │ │ │ ├── tests │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── commons.py │ │ │ │ │ ├── test_cross_entropy.py │ │ │ │ │ ├── test_data.py │ │ │ │ │ ├── test_initialize.py │ │ │ │ │ ├── test_layers.py │ │ │ │ │ └── test_random.py │ │ │ │ └── utils.py │ │ │ ├── package_info.py │ │ │ ├── text_generation_utils.py │ │ │ ├── tokenizer │ │ │ │ ├── __init__.py │ │ │ │ ├── bert_tokenization.py │ │ │ │ ├── gpt2_tokenization.py │ │ │ │ └── tokenizer.py │ │ │ ├── training.py │ │ │ └── utils.py │ │ ├── megatron_lm.egg-info │ │ │ ├── PKG-INFO │ │ │ ├── SOURCES.txt │ │ │ ├── dependency_links.txt │ │ │ ├── not-zip-safe │ │ │ ├── requires.txt │ │ │ └── top_level.txt │ │ ├── pretrain_bert.py │ │ ├── pretrain_gpt2.py │ │ ├── pretrain_ict.py │ │ ├── requirements.txt │ │ ├── setup.py │ │ ├── tasks │ │ │ ├── data_utils.py │ │ │ ├── ensemble_classifier.py │ │ │ ├── eval_utils.py │ │ │ ├── finetune_utils.py │ │ │ ├── glue │ │ │ │ ├── data.py │ │ │ │ ├── finetune.py │ │ │ │ ├── mnli.py │ │ │ │ └── qqp.py │ │ │ ├── main.py │ │ │ ├── race │ │ │ │ ├── data.py │ │ │ │ └── finetune.py │ │ │ └── zeroshot_gpt2 │ │ │ │ ├── datasets.py │ │ │ │ ├── detokenizer.py │ │ │ │ └── evaluate.py │ │ └── tools │ │ │ ├── create_doc_index.py │ │ │ ├── generate_samples_gpt2.py │ │ │ ├── linter.py │ │ │ ├── merge_mp_partitions.py │ │ │ ├── openwebtext │ │ │ ├── README.md │ │ │ ├── blacklist_urls.py │ │ │ ├── cleanup_dataset.py │ │ │ ├── find_duplicates.py │ │ │ ├── group_duplicates_url.py │ │ │ ├── merge_jsons.py │ │ │ └── remove_group_duplicates.py │ │ │ └── preprocess_data.py │ ├── __init__.py │ ├── checkpointing.py │ ├── csv_data.py │ ├── decoder.py │ ├── ds_config.json │ ├── megatron_bart.py │ └── util.py ├── train_megatron_retrieval.sh ├── train_megatron_retrieval_chembl.sh ├── train_retrieval.py ├── train_retrieval_chembl.py └── utils │ ├── LICENSE_MEGAMOLBART │ ├── __init__.py │ └── tokenizer.py ├── README.md ├── assets ├── model.jpg └── vis.jpg ├── download_scripts ├── download_data_cov.sh ├── download_data_exp.sh ├── download_data_guacamol.sh ├── download_data_ret_precompute.sh ├── download_models.sh └── download_results_reproduce.sh ├── eval_notebooks ├── ablation_gsk3jnk3.ipynb ├── ablation_qedlogp_distribution.ipynb └── visualization_guacamol.ipynb ├── guacamol ├── guacamol │ ├── __init__.py │ ├── guacamol │ │ ├── LICENSE_GUACAMOL │ │ ├── __init__.py │ │ ├── assess_distribution_learning.py │ │ ├── assess_goal_directed_generation.py │ │ ├── benchmark_suites.py │ │ ├── common_scoring_functions.py │ │ ├── distribution_learning_benchmark.py │ │ ├── distribution_matching_generator.py │ │ ├── frechet_benchmark.py │ │ ├── goal_directed_benchmark.py │ │ ├── goal_directed_generator.py │ │ ├── goal_directed_score_contributions.py │ │ ├── score_modifier.py │ │ ├── scoring_function.py │ │ ├── standard_benchmarks.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── chemistry.py │ │ │ ├── data.py │ │ │ ├── descriptors.py │ │ │ ├── fingerprints.py │ │ │ ├── helpers.py │ │ │ ├── math.py │ │ │ └── sampling_helpers.py │ └── guacamol_baseline │ │ ├── LICENSE_GUACAMOL_BASELINE │ │ ├── crossover.py │ │ └── mutate.py ├── retrieval_ga_generator.py └── run_retrieval_ga.py └── inference ├── cheminformatics ├── LICENSE_CHEMINFORMATICS ├── __init__.py ├── common │ ├── cuchemcommon │ │ ├── __init__.py │ │ ├── context.py │ │ ├── data │ │ │ ├── __init__.py │ │ │ ├── cluster_wf.py │ │ │ ├── generative_wf.py │ │ │ └── helper │ │ │ │ ├── __init__.py │ │ │ │ └── chembldata.py │ │ ├── fingerprint.py │ │ ├── utils │ │ │ ├── __init__.py │ │ │ ├── logger.py │ │ │ ├── singleton.py │ │ │ └── sysinfo.py │ │ └── workflow.py │ ├── generated │ │ ├── generativesampler_pb2.py │ │ └── generativesampler_pb2_grpc.py │ └── grpc │ │ └── generativesampler.proto └── utils │ ├── fpscores.pkl.gz │ └── inference_original.py ├── inference.py ├── 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