├── .gitignore ├── DREAMNets_BuildModel_Train_and_Predict.ipynb ├── LICENSE ├── README.md ├── Test_Your_NN_In_Prix_Fixe.ipynb ├── benchmarks ├── atac-seq │ ├── README.MD │ ├── dream_cnn.py │ ├── dream_cnn_with_bias_model.py │ ├── dream_rnn.py │ ├── dream_rnn_with_bias_model.py │ ├── train_dream_cnn.py │ ├── train_dream_rnn.py │ └── train_modified.py ├── drosophila │ ├── DREAMNets_buildModel_Train_Predict.ipynb │ ├── data │ │ ├── sample_test.txt │ │ ├── sample_train.txt │ │ └── sample_val.txt │ ├── prixfixe │ │ ├── __init__.py │ │ ├── autosome │ │ │ ├── __init__.py │ │ │ ├── add_blocks.py │ │ │ ├── coreblock.py │ │ │ ├── dataprocessor.py │ │ │ ├── dataset.py │ │ │ ├── final_layers_block.py │ │ │ ├── first_layers_block.py │ │ │ ├── predictor.py │ │ │ ├── trainer.py │ │ │ └── utils.py │ │ ├── bhi │ │ │ ├── __init__.py │ │ │ ├── add_blocks.py │ │ │ ├── coreblock.py │ │ │ ├── first_layers_block.py │ │ │ └── utils.py │ │ ├── prixfixe │ │ │ ├── __init__.py │ │ │ ├── coreblock.py │ │ │ ├── dataprocessor.py │ │ │ ├── final_layers_block.py │ │ │ ├── first_layers_block.py │ │ │ ├── predictor.py │ │ │ ├── prix_fixe_net.py │ │ │ └── trainer.py │ │ └── unlockdna │ │ │ ├── __init__.py │ │ │ ├── add_blocks.py │ │ │ ├── coreblock.py │ │ │ └── utils.py │ └── readme.MD └── human │ ├── DREAMNets_buildModel_Train_Predict.ipynb │ ├── data │ ├── sample_test.txt │ ├── sample_train.txt │ └── sample_valid.txt │ ├── prixfixe │ ├── __init__.py │ ├── autosome │ │ ├── __init__.py │ │ ├── add_blocks.py │ │ ├── coreblock.py │ │ ├── dataprocessor.py │ │ ├── dataset.py │ │ ├── final_layers_block.py │ │ ├── first_layers_block.py │ │ ├── trainer.py │ │ └── utils.py │ ├── bhi │ │ ├── __init__.py │ │ ├── add_blocks.py │ │ ├── coreblock.py │ │ ├── first_layers_block.py │ │ └── utils.py │ ├── prixfixe │ │ ├── __init__.py │ │ ├── coreblock.py │ │ ├── dataprocessor.py │ │ ├── final_layers_block.py │ │ ├── first_layers_block.py │ │ ├── predictor.py │ │ ├── prix_fixe_net.py │ │ └── trainer.py │ └── unlockdna │ │ ├── __init__.py │ │ ├── add_blocks.py │ │ ├── coreblock.py │ │ └── utils.py │ └── readme.MD ├── data ├── demo_train.txt ├── demo_val.txt ├── filtered_test_data_with_MAUDE_expression.txt ├── plasmid.json ├── public_leaderboard_ids │ ├── SNVs_exp_indices.json │ ├── challenging_exp_indices.json │ ├── ground.json │ ├── high_exp_indices.json │ ├── low_exp_indices.json │ ├── motif_perturbation_exp_indices.json │ ├── motif_tiling_exp_indices.json │ ├── random_exp_indices.json │ ├── sample_submission.json │ └── yeast_exp_indices.json ├── sample_submission.txt └── test_subset_ids │ ├── all_SNVs_seqs.csv │ ├── all_random_seqs.csv │ ├── challenging_seqs.csv │ ├── high_exp_seqs.csv │ ├── low_exp_seqs.csv │ ├── motif_perturbation_seqs.csv │ ├── motif_tiling_seqs.csv │ └── yeast_seqs.csv ├── dream_submissions ├── BHI - dream challenge │ ├── code │ │ ├── .gitignore │ │ ├── README.md │ │ ├── environment.yaml │ │ └── src │ │ │ ├── data.py │ │ │ ├── infer.py │ │ │ ├── infer_txt.py │ │ │ ├── net.py │ │ │ ├── postprocess.py │ │ │ ├── postprocess_9045.py │ │ │ ├── postprocess_txt.py │ │ │ ├── train.py │ │ │ ├── train_full.py │ │ │ └── util.py │ └── report.pdf ├── BUGF │ ├── code │ │ ├── LICENSE │ │ ├── README.md │ │ ├── focal_loss.py │ │ ├── nndef_exp_alibi.py │ │ ├── pytorch_challenge.py │ │ └── pytorch_xla_train.py │ └── report.pdf ├── BioNML │ ├── code │ │ ├── .gitignore │ │ ├── Instruction.docx │ │ ├── architecture │ │ │ └── new_BioNML_CrossAtt_v3.py │ │ ├── configs │ │ │ └── config39v3.yaml │ │ ├── run.bat │ │ ├── run_config_v1.py │ │ └── utils │ │ │ ├── layers.py │ │ │ ├── train_utils.py │ │ │ └── utils.py │ └── report.docx ├── Camformers │ ├── code │ │ ├── LICENSE │ │ ├── README.md │ │ ├── python_package_versions.txt │ │ └── script │ │ │ ├── README.txt │ │ │ ├── camformers_submission.py │ │ │ └── predict_test.py │ └── report.pdf ├── Davuluri lab │ ├── code │ │ ├── README.md │ │ ├── customized_models.py │ │ ├── make_prediction.py │ │ ├── requirements.txt │ │ ├── run.py │ │ ├── setup.cfg │ │ ├── setup.py │ │ ├── src │ │ │ ├── transformers.egg-info │ │ │ │ ├── PKG-INFO │ │ │ │ ├── SOURCES.txt │ │ │ │ ├── dependency_links.txt │ │ │ │ ├── entry_points.txt │ │ │ │ ├── requires.txt │ │ │ │ └── top_level.txt │ │ │ └── transformers │ │ │ │ ├── __init__.py │ │ │ │ ├── activations.py │ │ │ │ ├── activations_tf.py │ │ │ │ ├── benchmark │ │ │ │ ├── __init__.py │ │ │ │ ├── benchmark.py │ │ │ │ ├── benchmark_args.py │ │ │ │ ├── benchmark_args_tf.py │ │ │ │ ├── benchmark_args_utils.py │ │ │ │ ├── benchmark_tf.py │ │ │ │ └── benchmark_utils.py │ │ │ │ ├── commands │ │ │ │ ├── __init__.py │ │ │ │ ├── add_new_model.py │ │ │ │ ├── convert.py │ │ │ │ ├── download.py │ │ │ │ ├── env.py │ │ │ │ ├── lfs.py │ │ │ │ ├── run.py │ │ │ │ ├── serving.py │ │ │ │ ├── train.py │ │ │ │ ├── transformers_cli.py │ │ │ │ └── user.py │ │ │ │ ├── configuration_utils.py │ │ │ │ ├── convert_graph_to_onnx.py │ │ │ │ ├── convert_pytorch_checkpoint_to_tf2.py │ │ │ │ ├── convert_slow_tokenizer.py │ │ │ │ ├── convert_slow_tokenizers_checkpoints_to_fast.py │ │ │ │ ├── convert_tf_hub_seq_to_seq_bert_to_pytorch.py │ │ │ │ ├── data │ │ │ │ ├── __init__.py │ │ │ │ ├── data_collator.py │ │ │ │ ├── datasets │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── glue.py │ │ │ │ │ ├── language_modeling.py │ │ │ │ │ └── squad.py │ │ │ │ ├── metrics │ │ │ │ │ ├── __init__.py │ │ │ │ │ └── squad_metrics.py │ │ │ │ ├── processors │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── glue.py │ │ │ │ │ ├── squad.py │ │ │ │ │ ├── utils.py │ │ │ │ │ └── xnli.py │ │ │ │ └── test_generation_utils.py │ │ │ │ ├── dependency_versions_check.py │ │ │ │ ├── dependency_versions_table.py │ │ │ │ ├── file_utils.py │ │ │ │ ├── generation_beam_search.py │ │ │ │ ├── generation_logits_process.py │ │ │ │ ├── generation_tf_utils.py │ │ │ │ ├── generation_utils.py │ │ │ │ ├── hf_api.py │ │ │ │ ├── hf_argparser.py │ │ │ │ ├── integrations.py │ │ │ │ ├── modelcard.py │ │ │ │ ├── modeling_flax_utils.py │ │ │ │ ├── modeling_outputs.py │ │ │ │ ├── modeling_tf_outputs.py │ │ │ │ ├── modeling_tf_pytorch_utils.py │ │ │ │ ├── modeling_tf_utils.py │ │ │ │ ├── modeling_utils.py │ │ │ │ ├── models │ │ │ │ ├── __init__.py │ │ │ │ ├── albert │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_albert.py │ │ │ │ │ ├── convert_albert_original_tf_checkpoint_to_pytorch.py │ │ │ │ │ ├── modeling_albert.py │ │ │ │ │ ├── modeling_tf_albert.py │ │ │ │ │ ├── tokenization_albert.py │ │ │ │ │ └── tokenization_albert_fast.py │ │ │ │ ├── auto │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── auto_factory.py │ │ │ │ │ ├── configuration_auto.py │ │ │ │ │ ├── feature_extraction_auto.py │ │ │ │ │ ├── modeling_auto.py │ │ │ │ │ ├── modeling_flax_auto.py │ │ │ │ │ ├── modeling_tf_auto.py │ │ │ │ │ └── tokenization_auto.py │ │ │ │ ├── bart │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_bart.py │ │ │ │ │ ├── convert_bart_original_pytorch_checkpoint_to_pytorch.py │ │ │ │ │ ├── modeling_bart.py │ │ │ │ │ ├── modeling_tf_bart.py │ │ │ │ │ ├── tokenization_bart.py │ │ │ │ │ └── tokenization_bart_fast.py │ │ │ │ ├── barthez │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── tokenization_barthez.py │ │ │ │ │ └── tokenization_barthez_fast.py │ │ │ │ ├── bert │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_bert.py │ │ │ │ │ ├── convert_bert_original_tf2_checkpoint_to_pytorch.py │ │ │ │ │ ├── convert_bert_original_tf_checkpoint_to_pytorch.py │ │ │ │ │ ├── convert_bert_pytorch_checkpoint_to_original_tf.py │ │ │ │ │ ├── modeling_bert.py │ │ │ │ │ ├── modeling_flax_bert.py │ │ │ │ │ ├── modeling_tf_bert.py │ │ │ │ │ ├── tokenization_bert.py │ │ │ │ │ └── tokenization_bert_fast.py │ │ │ │ ├── bert_generation │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_bert_generation.py │ │ │ │ │ ├── modeling_bert_generation.py │ │ │ │ │ └── tokenization_bert_generation.py │ │ │ │ ├── bert_japanese │ │ │ │ │ ├── __init__.py │ │ │ │ │ └── tokenization_bert_japanese.py │ │ │ │ ├── bertweet │ │ │ │ │ ├── __init__.py │ │ │ │ │ └── tokenization_bertweet.py │ │ │ │ ├── big_bird │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_big_bird.py │ │ │ │ │ ├── convert_bigbird_original_tf_checkpoint_to_pytorch.py │ │ │ │ │ ├── modeling_big_bird.py │ │ │ │ │ └── tokenization_big_bird.py │ │ │ │ ├── blenderbot │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_blenderbot.py │ │ │ │ │ ├── convert_blenderbot_original_pytorch_checkpoint_to_pytorch.py │ │ │ │ │ ├── modeling_blenderbot.py │ │ │ │ │ ├── modeling_tf_blenderbot.py │ │ │ │ │ └── tokenization_blenderbot.py │ │ │ │ ├── blenderbot_small │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_blenderbot_small.py │ │ │ │ │ ├── modeling_blenderbot_small.py │ │ │ │ │ ├── modeling_tf_blenderbot_small.py │ │ │ │ │ ├── tokenization_blenderbot_small.py │ │ │ │ │ └── tokenization_blenderbot_small_fast.py │ │ │ │ ├── bort │ │ │ │ │ └── convert_bort_original_gluonnlp_checkpoint_to_pytorch.py │ │ │ │ ├── camembert │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_camembert.py │ │ │ │ │ ├── modeling_camembert.py │ │ │ │ │ ├── modeling_tf_camembert.py │ │ │ │ │ ├── tokenization_camembert.py │ │ │ │ │ └── tokenization_camembert_fast.py │ │ │ │ ├── convbert │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_convbert.py │ │ │ │ │ ├── convert_convbert_original_tf1_checkpoint_to_pytorch.py │ │ │ │ │ ├── convert_convbert_original_tf1_checkpoint_to_pytorch_and_tf2.py │ │ │ │ │ ├── modeling_convbert.py │ │ │ │ │ ├── modeling_tf_convbert.py │ │ │ │ │ ├── tokenization_convbert.py │ │ │ │ │ └── tokenization_convbert_fast.py │ │ │ │ ├── cpm │ │ │ │ │ ├── __init__.py │ │ │ │ │ └── tokenization_cpm.py │ │ │ │ ├── ctrl │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_ctrl.py │ │ │ │ │ ├── modeling_ctrl.py │ │ │ │ │ ├── modeling_tf_ctrl.py │ │ │ │ │ └── tokenization_ctrl.py │ │ │ │ ├── deberta │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_deberta.py │ │ │ │ │ ├── modeling_deberta.py │ │ │ │ │ └── tokenization_deberta.py │ │ │ │ ├── deberta_v2 │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_deberta_v2.py │ │ │ │ │ ├── modeling_deberta_v2.py │ │ │ │ │ └── tokenization_deberta_v2.py │ │ │ │ ├── deit │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_deit.py │ │ │ │ │ ├── convert_deit_timm_to_pytorch.py │ │ │ │ │ ├── feature_extraction_deit.py │ │ │ │ │ └── modeling_deit.py │ │ │ │ ├── dialogpt │ │ │ │ │ ├── __init__.py │ │ │ │ │ └── convert_dialogpt_original_pytorch_checkpoint_to_pytorch.py │ │ │ │ ├── distilbert │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_distilbert.py │ │ │ │ │ ├── modeling_distilbert.py │ │ │ │ │ ├── modeling_tf_distilbert.py │ │ │ │ │ ├── tokenization_distilbert.py │ │ │ │ │ └── tokenization_distilbert_fast.py │ │ │ │ ├── dna_kmer │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_dna_kmer.py │ │ │ │ │ ├── tokenization_dna_kmer.py │ │ │ │ │ └── tokenization_dna_kmer_fast.py │ │ │ │ ├── dna_sub │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_dna_sub.py │ │ │ │ │ ├── tokenization_dna_sub.py │ │ │ │ │ ├── tokenization_dna_sub_fast.py │ │ │ │ │ └── tokenizer │ │ │ │ │ │ ├── 5000 │ │ │ │ │ │ └── m.model │ │ │ │ │ │ ├── 10000 │ │ │ │ │ │ ├── m.model │ │ │ │ │ │ └── tokenizer.json │ │ │ │ │ │ └── tokenizer.json │ │ │ │ ├── dpr │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_dpr.py │ │ │ │ │ ├── convert_dpr_original_checkpoint_to_pytorch.py │ │ │ │ │ ├── modeling_dpr.py │ │ │ │ │ ├── modeling_tf_dpr.py │ │ │ │ │ ├── tokenization_dpr.py │ │ │ │ │ └── tokenization_dpr_fast.py │ │ │ │ ├── electra │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_electra.py │ │ │ │ │ ├── convert_electra_original_tf_checkpoint_to_pytorch.py │ │ │ │ │ ├── modeling_electra.py │ │ │ │ │ ├── modeling_tf_electra.py │ │ │ │ │ ├── tokenization_electra.py │ │ │ │ │ └── tokenization_electra_fast.py │ │ │ │ ├── encoder_decoder │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_encoder_decoder.py │ │ │ │ │ └── modeling_encoder_decoder.py │ │ │ │ ├── flaubert │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_flaubert.py │ │ │ │ │ ├── modeling_flaubert.py │ │ │ │ │ ├── modeling_tf_flaubert.py │ │ │ │ │ └── tokenization_flaubert.py │ │ │ │ ├── fsmt │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_fsmt.py │ │ │ │ │ ├── convert_fsmt_original_pytorch_checkpoint_to_pytorch.py │ │ │ │ │ ├── modeling_fsmt.py │ │ │ │ │ └── tokenization_fsmt.py │ │ │ │ ├── funnel │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_funnel.py │ │ │ │ │ ├── convert_funnel_original_tf_checkpoint_to_pytorch.py │ │ │ │ │ ├── modeling_funnel.py │ │ │ │ │ ├── modeling_tf_funnel.py │ │ │ │ │ ├── tokenization_funnel.py │ │ │ │ │ └── tokenization_funnel_fast.py │ │ │ │ ├── gpt2 │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_gpt2.py │ │ │ │ │ ├── convert_gpt2_original_tf_checkpoint_to_pytorch.py │ │ │ │ │ ├── modeling_gpt2.py │ │ │ │ │ ├── modeling_tf_gpt2.py │ │ │ │ │ ├── tokenization_gpt2.py │ │ │ │ │ └── tokenization_gpt2_fast.py │ │ │ │ ├── gpt_neo │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_gpt_neo.py │ │ │ │ │ ├── convert_gpt_neo_mesh_tf_to_pytorch.py │ │ │ │ │ └── modeling_gpt_neo.py │ │ │ │ ├── herbert │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── tokenization_herbert.py │ │ │ │ │ └── tokenization_herbert_fast.py │ │ │ │ ├── ibert │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_ibert.py │ │ │ │ │ ├── modeling_ibert.py │ │ │ │ │ └── quant_modules.py │ │ │ │ ├── layoutlm │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_layoutlm.py │ │ │ │ │ ├── modeling_layoutlm.py │ │ │ │ │ ├── modeling_tf_layoutlm.py │ │ │ │ │ ├── tokenization_layoutlm.py │ │ │ │ │ └── tokenization_layoutlm_fast.py │ │ │ │ ├── led │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_led.py │ │ │ │ │ ├── modeling_led.py │ │ │ │ │ ├── modeling_tf_led.py │ │ │ │ │ ├── tokenization_led.py │ │ │ │ │ └── tokenization_led_fast.py │ │ │ │ ├── longformer │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_longformer.py │ │ │ │ │ ├── convert_longformer_original_pytorch_lightning_to_pytorch.py │ │ │ │ │ ├── modeling_longformer.py │ │ │ │ │ ├── modeling_tf_longformer.py │ │ │ │ │ ├── tokenization_longformer.py │ │ │ │ │ └── tokenization_longformer_fast.py │ │ │ │ ├── lxmert │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_lxmert.py │ │ │ │ │ ├── convert_lxmert_original_tf_checkpoint_to_pytorch.py │ │ │ │ │ ├── modeling_lxmert.py │ │ │ │ │ ├── modeling_tf_lxmert.py │ │ │ │ │ ├── tokenization_lxmert.py │ │ │ │ │ └── tokenization_lxmert_fast.py │ │ │ │ ├── m2m_100 │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_m2m_100.py │ │ │ │ │ ├── convert_m2m100_original_checkpoint_to_pytorch.py │ │ │ │ │ ├── modeling_m2m_100.py │ │ │ │ │ └── tokenization_m2m_100.py │ │ │ │ ├── marian │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_marian.py │ │ │ │ │ ├── convert_marian_tatoeba_to_pytorch.py │ │ │ │ │ ├── convert_marian_to_pytorch.py │ │ │ │ │ ├── modeling_marian.py │ │ │ │ │ ├── modeling_tf_marian.py │ │ │ │ │ └── tokenization_marian.py │ │ │ │ ├── mbart │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_mbart.py │ │ │ │ │ ├── convert_mbart_original_checkpoint_to_pytorch.py │ │ │ │ │ ├── modeling_mbart.py │ │ │ │ │ ├── modeling_tf_mbart.py │ │ │ │ │ ├── tokenization_mbart.py │ │ │ │ │ ├── tokenization_mbart50.py │ │ │ │ │ ├── tokenization_mbart50_fast.py │ │ │ │ │ └── tokenization_mbart_fast.py │ │ │ │ ├── megatron_bert │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_megatron_bert.py │ │ │ │ │ ├── convert_megatron_bert_checkpoint.py │ │ │ │ │ └── modeling_megatron_bert.py │ │ │ │ ├── megatron_gpt2 │ │ │ │ │ └── convert_megatron_gpt2_checkpoint.py │ │ │ │ ├── mmbt │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_mmbt.py │ │ │ │ │ └── modeling_mmbt.py │ │ │ │ ├── mobilebert │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_mobilebert.py │ │ │ │ │ ├── convert_mobilebert_original_tf_checkpoint_to_pytorch.py │ │ │ │ │ ├── modeling_mobilebert.py │ │ │ │ │ ├── modeling_tf_mobilebert.py │ │ │ │ │ ├── tokenization_mobilebert.py │ │ │ │ │ └── tokenization_mobilebert_fast.py │ │ │ │ ├── mpnet │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_mpnet.py │ │ │ │ │ ├── modeling_mpnet.py │ │ │ │ │ ├── modeling_tf_mpnet.py │ │ │ │ │ ├── tokenization_mpnet.py │ │ │ │ │ └── tokenization_mpnet_fast.py │ │ │ │ ├── mt5 │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_mt5.py │ │ │ │ │ ├── modeling_mt5.py │ │ │ │ │ └── modeling_tf_mt5.py │ │ │ │ ├── openai │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_openai.py │ │ │ │ │ ├── convert_openai_original_tf_checkpoint_to_pytorch.py │ │ │ │ │ ├── modeling_openai.py │ │ │ │ │ ├── modeling_tf_openai.py │ │ │ │ │ ├── tokenization_openai.py │ │ │ │ │ └── tokenization_openai_fast.py │ │ │ │ ├── pegasus │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_pegasus.py │ │ │ │ │ ├── convert_pegasus_tf_to_pytorch.py │ │ │ │ │ ├── modeling_pegasus.py │ │ │ │ │ ├── modeling_tf_pegasus.py │ │ │ │ │ ├── tokenization_pegasus.py │ │ │ │ │ └── tokenization_pegasus_fast.py │ │ │ │ ├── phobert │ │ │ │ │ ├── __init__.py │ │ │ │ │ └── tokenization_phobert.py │ │ │ │ ├── prophetnet │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_prophetnet.py │ │ │ │ │ ├── convert_prophetnet_original_pytorch_checkpoint_to_pytorch.py │ │ │ │ │ ├── modeling_prophetnet.py │ │ │ │ │ └── tokenization_prophetnet.py │ │ │ │ ├── rag │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_rag.py │ │ │ │ │ ├── modeling_rag.py │ │ │ │ │ ├── modeling_tf_rag.py │ │ │ │ │ ├── retrieval_rag.py │ │ │ │ │ └── tokenization_rag.py │ │ │ │ ├── reformer │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_reformer.py │ │ │ │ │ ├── convert_reformer_trax_checkpoint_to_pytorch.py │ │ │ │ │ ├── modeling_reformer.py │ │ │ │ │ ├── tokenization_reformer.py │ │ │ │ │ └── tokenization_reformer_fast.py │ │ │ │ ├── retribert │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_retribert.py │ │ │ │ │ ├── modeling_retribert.py │ │ │ │ │ ├── tokenization_retribert.py │ │ │ │ │ └── tokenization_retribert_fast.py │ │ │ │ ├── roberta │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_roberta.py │ │ │ │ │ ├── convert_roberta_original_pytorch_checkpoint_to_pytorch.py │ │ │ │ │ ├── modeling_flax_roberta.py │ │ │ │ │ ├── modeling_roberta.py │ │ │ │ │ ├── modeling_tf_roberta.py │ │ │ │ │ ├── tokenization_roberta.py │ │ │ │ │ └── tokenization_roberta_fast.py │ │ │ │ ├── speech_to_text │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_speech_to_text.py │ │ │ │ │ ├── convert_s2t_fairseq_to_tfms.py │ │ │ │ │ ├── feature_extraction_speech_to_text.py │ │ │ │ │ ├── modeling_speech_to_text.py │ │ │ │ │ ├── processing_speech_to_text.py │ │ │ │ │ └── tokenization_speech_to_text.py │ │ │ │ ├── squeezebert │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_squeezebert.py │ │ │ │ │ ├── modeling_squeezebert.py │ │ │ │ │ ├── tokenization_squeezebert.py │ │ │ │ │ └── tokenization_squeezebert_fast.py │ │ │ │ ├── t5 │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_t5.py │ │ │ │ │ ├── convert_t5_original_tf_checkpoint_to_pytorch.py │ │ │ │ │ ├── modeling_t5.py │ │ │ │ │ ├── modeling_tf_t5.py │ │ │ │ │ ├── tokenization_t5.py │ │ │ │ │ └── tokenization_t5_fast.py │ │ │ │ ├── tapas │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_tapas.py │ │ │ │ │ ├── convert_tapas_original_tf_checkpoint_to_pytorch.py │ │ │ │ │ ├── modeling_tapas.py │ │ │ │ │ └── tokenization_tapas.py │ │ │ │ ├── transfo_xl │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_transfo_xl.py │ │ │ │ │ ├── convert_transfo_xl_original_tf_checkpoint_to_pytorch.py │ │ │ │ │ ├── modeling_tf_transfo_xl.py │ │ │ │ │ ├── modeling_tf_transfo_xl_utilities.py │ │ │ │ │ ├── modeling_transfo_xl.py │ │ │ │ │ ├── modeling_transfo_xl_utilities.py │ │ │ │ │ └── tokenization_transfo_xl.py │ │ │ │ ├── vit │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_vit.py │ │ │ │ │ ├── convert_vit_timm_to_pytorch.py │ │ │ │ │ ├── feature_extraction_vit.py │ │ │ │ │ └── modeling_vit.py │ │ │ │ ├── wav2vec2 │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_wav2vec2.py │ │ │ │ │ ├── convert_wav2vec2_original_pytorch_checkpoint_to_pytorch.py │ │ │ │ │ ├── feature_extraction_wav2vec2.py │ │ │ │ │ ├── modeling_wav2vec2.py │ │ │ │ │ ├── processing_wav2vec2.py │ │ │ │ │ └── tokenization_wav2vec2.py │ │ │ │ ├── xlm │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_xlm.py │ │ │ │ │ ├── convert_xlm_original_pytorch_checkpoint_to_pytorch.py │ │ │ │ │ ├── modeling_tf_xlm.py │ │ │ │ │ ├── modeling_xlm.py │ │ │ │ │ └── tokenization_xlm.py │ │ │ │ ├── xlm_prophetnet │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_xlm_prophetnet.py │ │ │ │ │ ├── modeling_xlm_prophetnet.py │ │ │ │ │ └── tokenization_xlm_prophetnet.py │ │ │ │ ├── xlm_roberta │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_xlm_roberta.py │ │ │ │ │ ├── modeling_tf_xlm_roberta.py │ │ │ │ │ ├── modeling_xlm_roberta.py │ │ │ │ │ ├── tokenization_xlm_roberta.py │ │ │ │ │ └── tokenization_xlm_roberta_fast.py │ │ │ │ └── xlnet │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── configuration_xlnet.py │ │ │ │ │ ├── convert_xlnet_original_tf_checkpoint_to_pytorch.py │ │ │ │ │ ├── modeling_tf_xlnet.py │ │ │ │ │ ├── modeling_xlnet.py │ │ │ │ │ ├── tokenization_xlnet.py │ │ │ │ │ └── tokenization_xlnet_fast.py │ │ │ │ ├── optimization.py │ │ │ │ ├── optimization_tf.py │ │ │ │ ├── pipelines │ │ │ │ ├── __init__.py │ │ │ │ ├── base.py │ │ │ │ ├── conversational.py │ │ │ │ ├── feature_extraction.py │ │ │ │ ├── fill_mask.py │ │ │ │ ├── question_answering.py │ │ │ │ ├── table_question_answering.py │ │ │ │ ├── text2text_generation.py │ │ │ │ ├── text_classification.py │ │ │ │ ├── text_generation.py │ │ │ │ ├── token_classification.py │ │ │ │ └── zero_shot_classification.py │ │ │ │ ├── testing_utils.py │ │ │ │ ├── tokenization_utils.py │ │ │ │ ├── tokenization_utils_base.py │ │ │ │ ├── tokenization_utils_fast.py │ │ │ │ ├── trainer.py │ │ │ │ ├── trainer_callback.py │ │ │ │ ├── trainer_pt_utils.py │ │ │ │ ├── trainer_seq2seq.py │ │ │ │ ├── trainer_tf.py │ │ │ │ ├── trainer_utils.py │ │ │ │ ├── training_args.py │ │ │ │ ├── training_args_seq2seq.py │ │ │ │ ├── training_args_tf.py │ │ │ │ └── utils │ │ │ │ ├── __init__.py │ │ │ │ ├── dummy_flax_objects.py │ │ │ │ ├── dummy_pt_objects.py │ │ │ │ ├── dummy_sentencepiece_and_speech_objects.py │ │ │ │ ├── dummy_sentencepiece_and_tokenizers_objects.py │ │ │ │ ├── dummy_sentencepiece_objects.py │ │ │ │ ├── dummy_speech_objects.py │ │ │ │ ├── dummy_tf_objects.py │ │ │ │ ├── dummy_tokenizers_objects.py │ │ │ │ ├── dummy_vision_objects.py │ │ │ │ ├── hp_naming.py │ │ │ │ ├── imagenet_classes.py │ │ │ │ ├── logging.py │ │ │ │ ├── model_parallel_utils.py │ │ │ │ ├── modeling_auto_mapping.py │ │ │ │ ├── notebook.py │ │ │ │ ├── sentencepiece_model_pb2.py │ │ │ │ └── versions.py │ │ └── utils │ │ │ ├── check_copies.py │ │ │ ├── check_dummies.py │ │ │ ├── check_repo.py │ │ │ ├── check_table.py │ │ │ ├── download_glue_data.py │ │ │ ├── get_modified_files.py │ │ │ ├── link_tester.py │ │ │ └── style_doc.py │ └── report.pdf ├── DrAshokAndFriends │ ├── code │ │ ├── Code.py │ │ ├── LICENSE │ │ └── README.md │ └── report.docx ├── High Schoolers Are All You Need │ ├── code │ │ ├── .gitignore │ │ ├── README.md │ │ ├── Testing Code │ │ │ └── GetPredictions.py │ │ └── Training Code │ │ │ ├── DataProcessing.py │ │ │ └── ModelTraining.py │ └── report.pdf ├── KircherLab │ ├── code │ │ ├── .editorconfig │ │ ├── .gitattributes │ │ ├── .gitignore │ │ ├── LICENSE │ │ ├── README.md │ │ ├── config │ │ │ └── config.yaml │ │ ├── environment.yaml │ │ ├── resources │ │ │ ├── README.md │ │ │ └── sample_submission.json │ │ ├── src │ │ │ ├── __init__.py │ │ │ ├── correlation.py │ │ │ ├── create_submission.py │ │ │ ├── model.py │ │ │ ├── predict.py │ │ │ ├── prediction.py │ │ │ ├── sequence.py │ │ │ └── train.py │ │ └── workflow │ │ │ ├── Snakefile │ │ │ ├── envs │ │ │ ├── default.yml │ │ │ └── tensorflow.yml │ │ │ ├── rules │ │ │ ├── common.smk │ │ │ └── main.smk │ │ │ ├── schemas │ │ │ └── config.schema.yaml │ │ │ └── scripts │ │ │ ├── bucket_callibration.py │ │ │ └── input_data.py │ └── report.pdf ├── MadLab │ ├── code │ │ ├── Data_preprocessing_final.ipynb │ │ ├── README.md │ │ └── Train_test_code.ipynb │ └── report.pdf ├── Metformin-121 │ ├── code │ │ ├── LICENSE │ │ ├── Metformin-121.ipynb │ │ └── README.md │ └── report.pdf ├── NAD │ ├── code │ │ ├── .gitignore │ │ ├── Fig.jpeg │ │ ├── README.md │ │ ├── README.pdf │ │ ├── Step0.sh │ │ ├── Step1.sh │ │ ├── Step2.sh │ │ ├── Util │ │ │ ├── SimpleViTModel.py │ │ │ ├── Utils.py │ │ │ └── sam.py │ │ ├── data │ │ │ └── vectors.txt │ │ ├── glove │ │ │ ├── LICENSE │ │ │ ├── Makefile │ │ │ ├── README.md │ │ │ ├── build │ │ │ │ ├── cooccur │ │ │ │ ├── shuffle │ │ │ │ └── vocab_count │ │ │ ├── demo.sh │ │ │ ├── eval │ │ │ │ ├── matlab │ │ │ │ │ ├── WordLookup.m │ │ │ │ │ ├── evaluate_vectors.m │ │ │ │ │ └── read_and_evaluate.m │ │ │ │ ├── octave │ │ │ │ │ ├── WordLookup_octave.m │ │ │ │ │ ├── evaluate_vectors_octave.m │ │ │ │ │ └── read_and_evaluate_octave.m │ │ │ │ ├── python │ │ │ │ │ ├── distance.py │ │ │ │ │ ├── evaluate.py │ │ │ │ │ └── word_analogy.py │ │ │ │ └── question-data │ │ │ │ │ ├── capital-common-countries.txt │ │ │ │ │ ├── capital-world.txt │ │ │ │ │ ├── city-in-state.txt │ │ │ │ │ ├── currency.txt │ │ │ │ │ ├── family.txt │ │ │ │ │ ├── gram1-adjective-to-adverb.txt │ │ │ │ │ ├── gram2-opposite.txt │ │ │ │ │ ├── gram3-comparative.txt │ │ │ │ │ ├── gram4-superlative.txt │ │ │ │ │ ├── gram5-present-participle.txt │ │ │ │ │ ├── gram6-nationality-adjective.txt │ │ │ │ │ ├── gram7-past-tense.txt │ │ │ │ │ ├── gram8-plural.txt │ │ │ │ │ └── gram9-plural-verbs.txt │ │ │ ├── randomization.test.sh │ │ │ └── src │ │ │ │ ├── README.md │ │ │ │ ├── common.c │ │ │ │ ├── common.h │ │ │ │ ├── cooccur.c │ │ │ │ ├── glove.c │ │ │ │ ├── shuffle.c │ │ │ │ └── vocab_count.c │ │ ├── glove_embedding.py │ │ ├── main.py │ │ ├── prediction.txt │ │ ├── requirements.txt │ │ └── test_predict.py │ └── report.pdf ├── NGT4 │ ├── code │ │ ├── correction.py │ │ ├── function.py │ │ ├── model.py │ │ ├── one_hot.py │ │ ├── submission.py │ │ └── training.py │ └── report.pdf ├── Noisy-Chardonnay │ ├── code │ │ ├── .DS_Store │ │ ├── README.md │ │ ├── predict.py │ │ ├── utils.py │ │ └── wandb.py │ └── report.pdf ├── Peppa │ ├── code │ │ ├── .gitignore │ │ ├── LICENSE │ │ ├── README.md │ │ ├── Step1_generate_DNA_matrix.py │ │ ├── Step2_train_eval.py │ │ ├── attention_module.py │ │ ├── enform_XS.png │ │ ├── enformer5.py │ │ └── final_submission.py │ └── report.pdf ├── QUT_seq2exp │ ├── code │ │ ├── DataPrep.ipynb │ │ ├── GenerateTestPreds.ipynb │ │ ├── ModelandTraining.ipynb │ │ └── utils.py │ └── report.pdf ├── SYSU-SAIL-2022 │ ├── code │ │ ├── README.md │ │ ├── pretrain_expr.py │ │ ├── run_pretrain.sh │ │ ├── run_submit.sh │ │ ├── run_test.sh │ │ ├── run_train.sh │ │ ├── submit.py │ │ ├── test_expr.py │ │ ├── train_expr_group.py │ │ └── train_utils.py │ └── report.pdf ├── The Dream Team │ ├── code │ │ ├── README.md │ │ ├── default_variables.py │ │ ├── final.json │ │ └── training_and_testing_official.ipynb │ └── report.pdf ├── UTKbioinformatics │ ├── code │ │ ├── DREAM_NLP_Regression_Finetune.ipynb │ │ ├── DREAM_NLP_Regression_Train.ipynb │ │ └── README.md │ └── report.pdf ├── Unlock_DNA │ ├── code │ │ ├── README.md │ │ ├── mode_training.ipynb │ │ ├── prepare_tfdatasets.ipynb │ │ └── tf26_py37_a100.yml │ └── report.pdf ├── Wan&Barton_BBK │ ├── code │ │ ├── LICENSE │ │ ├── README.md │ │ ├── figures │ │ │ ├── bins.jpg │ │ │ └── training_curve.jpeg │ │ ├── requirements.txt │ │ └── src │ │ │ ├── Final_submission.py │ │ │ └── train.py │ └── report.pdf ├── Wen Group │ ├── code │ │ ├── .gitattributes │ │ ├── README.md │ │ ├── dream_competition_2022.py │ │ ├── model.py │ │ ├── prediction.py │ │ ├── prediction_notebook │ │ │ └── DREAM2022-Prediction-on-Test-V0.54.ipynb │ │ └── requirements.txt │ └── report.pdf ├── Yuanfang Guan │ ├── code │ │ ├── README.md │ │ ├── cnn_sigmoid_1024.py │ │ ├── predict_deeplearning.py │ │ └── train_deeplearning.py │ └── report.pdf ├── Zeta │ ├── code │ │ ├── model.jpg │ │ └── train_test_code.ipynb │ └── report.docx ├── auth │ ├── code │ │ ├── README.md │ │ ├── edited.py │ │ ├── test.py │ │ ├── test_edited.py │ │ └── train.py │ └── report.pdf ├── autosome.org │ ├── code │ │ ├── README.md │ │ ├── environment.yml │ │ ├── model.py │ │ ├── test.py │ │ ├── test.sh │ │ ├── train.py │ │ └── train.sh │ └── report.pdf ├── mt │ ├── code │ │ ├── 250_pandas_final_1_bis_bc-0.745-Copy1.nbconvert.ipynb │ │ ├── README.md │ │ ├── banner.png │ │ └── environment.yml │ └── report.docx └── wztr │ ├── code │ ├── .gitignore │ ├── README.md │ ├── environment.yaml │ ├── scripts │ │ └── train_model.py │ ├── seq2exp │ │ ├── __init__.py │ │ ├── data.py │ │ ├── layers.py │ │ ├── models.py │ │ ├── tools.py │ │ ├── trainner.py │ │ └── visualization.py │ └── setup.py │ └── report.pdf ├── environment.yml ├── images └── random_promoter_dream_challenge_2022.png └── prixfixe ├── __init__.py ├── autosome ├── __init__.py ├── add_blocks.py ├── coreblock.py ├── dataprocessor.py ├── dataset.py ├── final_layers_block.py ├── first_layers_block.py ├── predictor.py ├── trainer.py └── utils.py ├── bhi ├── __init__.py ├── add_blocks.py ├── coreblock.py ├── dataprocessor.py ├── dataset.py ├── final_layers_block.py ├── first_layers_block.py ├── predictor.py ├── trainer.py └── utils.py ├── evaluation.py ├── prixfixe ├── __init__.py ├── coreblock.py ├── dataprocessor.py ├── final_layers_block.py ├── first_layers_block.py ├── predictor.py ├── prix_fixe_net.py └── trainer.py ├── readme.MD └── unlockdna ├── __init__.py ├── add_blocks.py ├── coreblock.py ├── dataprocessor.py ├── dataset.py ├── final_layers_block.py ├── first_layers_block.py ├── predictor.py ├── trainer.py └── utils.py /.gitignore: -------------------------------------------------------------------------------- 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