├── .gitignore ├── .gitmodules ├── .vscode └── launch.json ├── Dockerfile ├── LICENSE ├── README.md ├── assets ├── DNABERT-2.pdf ├── GENA-LM.pdf ├── HyenaDNA.pdf ├── Nucleotide Transformer.pdf ├── architecture.png ├── bert2_val_negative.jpg ├── bert2_val_positive.jpg ├── clusters_tsne.pdf ├── dna_clustering.png ├── genbench.webp ├── genomic_structure_h1esc.pdf ├── genomic_structure_h1esc.png ├── genomic_structure_hff.pdf ├── genomic_structure_hff.png ├── hyena_val_negative.jpg ├── hyena_val_positive.jpg ├── image_process.ipynb ├── orca_val_negative.jpg ├── orca_val_positive.jpg └── pipeline.png ├── configs ├── callbacks │ ├── base.yaml │ ├── checkpoint.yaml │ ├── gpu_affinity.yaml │ ├── rich.yaml │ └── wandb.yaml ├── config.yaml ├── dataset │ ├── EMP.yaml │ ├── chromatin_profile.yaml │ ├── drosophila_enhancer_activity.yaml │ ├── genomic_benchmark.yaml │ ├── genomic_benchmark_regression.yaml │ ├── genomic_long_range_benchmark.yaml │ ├── genomic_structure_dataset.yaml │ ├── genomic_structure_dataset_orca.yaml │ ├── hg38.yaml │ ├── hg38_fixed_test.yaml │ ├── icl_hg38.yaml │ ├── mouse.yaml │ ├── nucleotide_transformer.yaml │ ├── plant_genomic_benchmark.yaml │ ├── prom.yaml │ ├── promoter_prediction.yaml │ ├── species.yaml │ ├── splice.yaml │ ├── splicing_prediction.yaml │ ├── tf.yaml │ └── virus.yaml ├── evals │ ├── hg38.yaml │ ├── hg38_decoder.yaml │ ├── hyena_dna_512ksl.yaml │ ├── icl_genomics.yaml │ ├── instruction_tuned_genomics.yaml │ └── soft_prompting_genomics.yaml ├── experiment │ ├── base.yaml │ └── hg38 │ │ ├── Bulk_expression.yaml │ │ ├── EMP.yaml │ │ ├── EMP_CNN.yaml │ │ ├── GUE.yaml │ │ ├── cage_prediction.yaml │ │ ├── chromatin_profile.yaml │ │ ├── drosophila_enhancer_activity.yaml │ │ ├── genomic_benchmark.yaml │ │ ├── genomic_benchmark_BERT2.yaml │ │ ├── genomic_benchmark_CNN.yaml │ │ ├── genomic_benchmark_Genalm.yaml │ │ ├── genomic_benchmark_Genalm_large.yaml │ │ ├── genomic_benchmark_Genslm.yaml │ │ ├── genomic_benchmark_NT.yaml │ │ ├── genomic_benchmark_bert.yaml │ │ ├── genomic_benchmark_evo.yaml │ │ ├── genomic_benchmark_hyena_Tiny.yaml │ │ ├── genomic_benchmark_hyena_small.yaml │ │ ├── genomic_benchmark_mamba.yaml │ │ ├── genomic_structure.yaml │ │ ├── genomic_structure_orca.yaml │ │ ├── hg38.yaml │ │ ├── hg38_CNN.yaml │ │ ├── hg38_attention.yaml │ │ ├── hg38_attention_3_mer.yaml │ │ ├── hg38_fixed_test.yaml │ │ ├── hg38_fixed_test_attention.yaml │ │ ├── hg38_hyena.yaml │ │ ├── hg38_hyena_3_mer.yaml │ │ ├── hg38_hyena_icl.yaml │ │ ├── hg38_hyena_seqlen_warmup_reload.yaml │ │ ├── mouse.yaml │ │ ├── mouse_3_mer.yaml │ │ ├── mouse_3_mer_attention.yaml │ │ ├── mouse_CNN.yaml │ │ ├── mouse_attention.yaml │ │ ├── nucleotide_transformer.yaml │ │ ├── plant_genomic_benchmark_3_mer.yaml │ │ ├── plant_genomic_benchmark_3_mer_attention.yaml │ │ ├── plant_genomic_benchmark_CNN.yaml │ │ ├── plant_genomic_benchmark_scratch.yaml │ │ ├── plant_genomic_benchmark_scratch_attention.yaml │ │ ├── prom.yaml │ │ ├── prom_3_mer.yaml │ │ ├── prom_3_mer_attention.yaml │ │ ├── prom_CNN.yaml │ │ ├── prom_attention.yaml │ │ ├── species.yaml │ │ ├── species_attention.yaml │ │ ├── splice.yaml │ │ ├── splice_CNN.yaml │ │ ├── splice_attention.yaml │ │ ├── splicing_prediction.yaml │ │ ├── tf.yaml │ │ ├── tf_CNN.yaml │ │ ├── tf_attention.yaml │ │ ├── virus.yaml │ │ ├── virus_CNN.yaml │ │ └── virus_attention.yaml ├── loader │ └── default.yaml ├── model │ ├── layer │ │ ├── ff.yaml │ │ ├── h3-conv.yaml │ │ ├── hyena-filter.yaml │ │ ├── hyena.yaml │ │ ├── hyena_dna.yaml │ │ ├── id.yaml │ │ ├── mha.yaml │ │ └── mha_dna.yaml │ └── transformer.yaml ├── optimizer │ ├── adam.yaml │ ├── adamw.yaml │ └── sgd.yaml ├── pipeline │ ├── EMP.yaml │ ├── EMP_CNN.yaml │ ├── GUE.yaml │ ├── chromatin_profile.yaml │ ├── drosophila_enhancer_activity.yaml │ ├── genomic_benchmark.yaml │ ├── genomic_benchmark_CNN.yaml │ ├── genomic_benchmark_bert.yaml │ ├── genomic_benchmark_regression.yaml │ ├── genomic_long_range_benchmark.yaml │ ├── genomic_structure_dataset.yaml │ ├── genomic_structure_dataset_orca.yaml │ ├── hg38.yaml │ ├── hg38_CNN.yaml │ ├── mouse.yaml │ ├── mouse_CNN.yaml │ ├── nucleotide_transformer.yaml │ ├── plant_genomic_benchmark.yaml │ ├── plant_genomic_benchmark_cnn.yaml │ ├── prom.yaml │ ├── prom_CNN.yaml │ ├── species.yaml │ ├── splice.yaml │ ├── splice_CNN.yaml │ ├── splicing_prediction.yaml │ ├── tf.yaml │ ├── tf_CNN.yaml │ ├── virus.yaml │ └── virus_CNN.yaml ├── scheduler │ ├── constant.yaml │ ├── constant_warmup.yaml │ ├── cosine.yaml │ ├── cosine_warmup.yaml │ ├── cosine_warmup_timm.yaml │ ├── linear_warmup.yaml │ ├── multistep.yaml │ ├── plateau.yaml │ └── step.yaml ├── task │ ├── genomic_structure_prediction.yaml │ ├── lm.yaml │ ├── masked_multiclass_classification.yaml │ ├── multiclass_classification.yaml │ ├── multilabel_classification.yaml │ ├── multilabel_regression.yaml │ └── regression.yaml └── trainer │ ├── debug.yaml │ ├── default.yaml │ ├── full.yaml │ └── lm.yaml ├── convert_csv_to_txt.ipynb ├── count_data_size.ipynb ├── environment.yml ├── experiment ├── Bulk_expression │ ├── Bulk_expression_Enformer.sh │ ├── Bulk_expression_NT.sh │ ├── Bulk_expression_bert2.sh │ ├── Bulk_expression_gena_lm.sh │ ├── Bulk_expression_hyena.sh │ └── Bulk_expression_mamba.sh ├── GUE │ ├── GUE_CNN.sh │ ├── GUE_NT.sh │ ├── GUE_dnabert.sh │ ├── GUE_dnabert_2.sh │ ├── GUE_genalm.sh │ ├── GUE_hyena.sh │ └── GUE_mamba.sh ├── Promoter_prediction │ ├── promoter_prediction_NT.sh │ ├── promoter_prediction_bert.sh │ ├── promoter_prediction_bert2.sh │ ├── promoter_prediction_genalm.sh │ ├── promoter_prediction_hyena.sh │ └── promoter_prediction_mamba.sh ├── Splicing_prediction │ ├── splicing_prediction_NT.sh │ ├── splicing_prediction_bert.sh │ ├── splicing_prediction_bert2.sh │ ├── splicing_prediction_genalm.sh │ ├── splicing_prediction_hyena.sh │ ├── splicing_prediction_mamba.sh │ └── splicing_prediction_spliceai.sh ├── cage_prediction │ ├── cage_prediction_NT.sh │ ├── cage_prediction_bert2.sh │ ├── cage_prediction_genalm.sh │ ├── cage_prediction_hyena.sh │ └── cage_prediction_mamba.sh ├── drosophila_enhancer_activity │ ├── drosophila_enhancer_activity_NT.sh │ ├── drosophila_enhancer_activity_bert.sh │ ├── drosophila_enhancer_activity_bert2.sh │ ├── drosophila_enhancer_activity_deepstar.sh │ ├── drosophila_enhancer_activity_genalm.sh │ ├── drosophila_enhancer_activity_hyena.sh │ └── drosophila_enhancer_activity_mamba.sh ├── experiment.MD ├── genomic_benchmark │ ├── genomic_benchmark_CNN.sh │ ├── genomic_benchmark_NT.sh │ ├── genomic_benchmark_dnabert.sh │ ├── genomic_benchmark_dnabert_2.sh │ ├── genomic_benchmark_genalm.sh │ ├── genomic_benchmark_hyena.sh │ └── genomic_benchmark_mamba.sh ├── genomic_structure │ ├── genomic_structure_bert2.sh │ ├── genomic_structure_bert2_h1sec.sh │ ├── genomic_structure_genalm.sh │ ├── genomic_structure_genalm_h1sec.sh │ ├── genomic_structure_hyena_h1sec.sh │ ├── genomic_structure_hyena_hff.sh │ ├── genomic_structure_mamba.sh │ ├── genomic_structure_mamba_h1sec.sh │ └── genomic_structure_orca_h1esc.sh ├── genomic_structure_prediction │ └── genomic_structure_prediction.sh ├── run_central dogma.sh └── species │ ├── species_NT.sh │ ├── species_bert.sh │ ├── species_bert2.sh │ ├── species_genalm.sh │ ├── species_hyena.sh │ └── species_mamba.sh ├── huggingface.py ├── notebook ├── 4.broken_xaxis.png ├── Bulk_RNA_Expression.pdf ├── Bulk_RNA_Expression.png ├── Bulk_prediction_spearman.ipynb ├── Bulk_prediction_spearman.pdf ├── DNABERT-2.pdf ├── Drosophila_Enhancers_Prediction.pdf ├── Drosophila_Enhancers_Prediction.png ├── GENA-LM.pdf ├── HyenaDNA.pdf ├── NT_parameter_size_impact.pdf ├── Nucleotide Transformer.pdf ├── cage_prediction_pearsonr.ipynb ├── count_flops.ipynb ├── drosophila_pearsonr.ipynb ├── gene_cluster.ipynb ├── macs_bert2.txt ├── macs_genalm.txt ├── macs_hyena.txt ├── macs_nt.txt ├── mcc.ipynb ├── notebook.md ├── parameter_size.ipynb ├── performance_length.ipynb ├── performance_length_promoter.pdf ├── performance_length_species.pdf ├── plot_Drosophil_Enhancer.ipynb ├── plot_genomic_structure.ipynb ├── plot_genomic_structure_h1esc.ipynb ├── plot_genomic_structure_hff.ipynb ├── plot_splice_site_prediction.ipynb ├── sequence_embedding.pdf ├── splicing_prauc.ipynb └── test.ipynb ├── read_fa.ipynb ├── requirements.txt ├── requirements_central dogma.txt ├── selene_utils2.py ├── src ├── callbacks │ ├── gpu_affinity.py │ ├── norms.py │ ├── params.py │ ├── progressive_resizing.py │ ├── seqlen_warmup_reload.py │ ├── timer.py │ └── wandb.py ├── dataloaders │ ├── __init__.py │ ├── base.py │ ├── datasets │ │ ├── chromatin_profile_dataset.py │ │ ├── drosophila_enhancer_activity_dataset.py │ │ ├── file_utils.py │ │ ├── genomic_bench_dataset.py │ │ ├── genomic_bench_regression_dataset.py │ │ ├── genomic_long_range_benchmark.py │ │ ├── genomic_structure_dataset.py │ │ ├── genomic_structure_dataset_orca.py │ │ ├── genslm_tokenizer.py │ │ ├── lm_dataset.py │ │ ├── nucleotide_transformer_dataset.py │ │ ├── plant_genomic_bench_dataset.py │ │ ├── species_dataset.py │ │ ├── splicing_dataset.py │ │ ├── splicing_prediction_dataset.py │ │ └── tokenization_utils.py │ ├── et.py │ ├── fault_tolerant_sampler.py │ ├── genomics.py │ ├── selene_utils2.py │ └── utils │ │ └── vocabulary.py ├── models │ ├── nn │ │ ├── __init__.py │ │ ├── adaptive_softmax.py │ │ ├── components.py │ │ ├── dxt.py │ │ ├── gate.py │ │ ├── residual.py │ │ └── utils.py │ └── sequence │ │ ├── CNN.py │ │ ├── Enformer.py │ │ ├── NT.py │ │ ├── SpliceAI.py │ │ ├── __init__.py │ │ ├── base.py │ │ ├── block.py │ │ ├── block_fft.py │ │ ├── deepSTAR.py │ │ ├── dna_embedding.py │ │ ├── dnabert.py │ │ ├── dnabert_2.py │ │ ├── ff.py │ │ ├── genalm.py │ │ ├── genslm.py │ │ ├── hyena.py │ │ ├── long_conv.py │ │ ├── long_conv_kernel.py │ │ ├── long_conv_lm.py │ │ ├── mha.py │ │ ├── model.py │ │ ├── orca.py │ │ ├── pool.py │ │ ├── simple_lm.py │ │ └── src │ │ └── transformers │ │ ├── __init__.py │ │ ├── activations.py │ │ ├── commands │ │ ├── __init__.py │ │ ├── convert.py │ │ ├── download.py │ │ ├── env.py │ │ ├── run.py │ │ ├── serving.py │ │ ├── train.py │ │ └── user.py │ │ ├── configuration_albert.py │ │ ├── configuration_auto.py │ │ ├── configuration_bart.py │ │ ├── configuration_bert.py │ │ ├── configuration_camembert.py │ │ ├── configuration_ctrl.py │ │ ├── configuration_distilbert.py │ │ ├── configuration_flaubert.py │ │ ├── configuration_gpt2.py │ │ ├── configuration_mmbt.py │ │ ├── configuration_openai.py │ │ ├── configuration_roberta.py │ │ ├── configuration_t5.py │ │ ├── configuration_transfo_xl.py │ │ ├── configuration_utils.py │ │ ├── configuration_xlm.py │ │ ├── configuration_xlm_roberta.py │ │ ├── configuration_xlnet.py │ │ ├── convert_albert_original_tf_checkpoint_to_pytorch.py │ │ ├── convert_bart_original_pytorch_checkpoint_to_pytorch.py │ │ ├── convert_bert_original_tf_checkpoint_to_pytorch.py │ │ ├── convert_bert_pytorch_checkpoint_to_original_tf.py │ │ ├── convert_gpt2_original_tf_checkpoint_to_pytorch.py │ │ ├── convert_openai_original_tf_checkpoint_to_pytorch.py │ │ ├── convert_pytorch_checkpoint_to_tf2.py │ │ ├── convert_roberta_original_pytorch_checkpoint_to_pytorch.py │ │ ├── convert_t5_original_tf_checkpoint_to_pytorch.py │ │ ├── convert_transfo_xl_original_tf_checkpoint_to_pytorch.py │ │ ├── convert_xlm_original_pytorch_checkpoint_to_pytorch.py │ │ ├── convert_xlnet_original_tf_checkpoint_to_pytorch.py │ │ ├── dnabert-config │ │ ├── bert-config-3 │ │ │ ├── config.json │ │ │ ├── special_tokens_map.json │ │ │ ├── tokenizer_config.json │ │ │ └── vocab.txt │ │ ├── bert-config-4 │ │ │ ├── config.json │ │ │ ├── special_tokens_map.json │ │ │ ├── tokenizer_config.json │ │ │ └── vocab.txt │ │ ├── bert-config-5 │ │ │ ├── config.json │ │ │ ├── special_tokens_map.json │ │ │ ├── tokenizer_config.json │ │ │ └── vocab.txt │ │ └── bert-config-6 │ │ │ ├── config.json │ │ │ ├── special_tokens_map.json │ │ │ ├── tokenizer_config.json │ │ │ └── vocab.txt │ │ ├── file_utils.py │ │ ├── hf_api.py │ │ ├── modelcard.py │ │ ├── modeling_albert.py │ │ ├── modeling_auto.py │ │ ├── modeling_bart.py │ │ ├── modeling_bert.py │ │ ├── modeling_camembert.py │ │ ├── modeling_ctrl.py │ │ ├── modeling_distilbert.py │ │ ├── modeling_encoder_decoder.py │ │ ├── modeling_flaubert.py │ │ ├── modeling_gpt2.py │ │ ├── modeling_mmbt.py │ │ ├── modeling_openai.py │ │ ├── modeling_roberta.py │ │ ├── modeling_t5.py │ │ ├── modeling_tf_albert.py │ │ ├── modeling_tf_auto.py │ │ ├── modeling_tf_bert.py │ │ ├── modeling_tf_camembert.py │ │ ├── modeling_tf_ctrl.py │ │ ├── modeling_tf_distilbert.py │ │ ├── modeling_tf_gpt2.py │ │ ├── modeling_tf_openai.py │ │ ├── modeling_tf_pytorch_utils.py │ │ ├── modeling_tf_roberta.py │ │ ├── modeling_tf_t5.py │ │ ├── modeling_tf_transfo_xl.py │ │ ├── modeling_tf_transfo_xl_utilities.py │ │ ├── modeling_tf_utils.py │ │ ├── modeling_tf_xlm.py │ │ ├── modeling_tf_xlm_roberta.py │ │ ├── modeling_tf_xlnet.py │ │ ├── modeling_transfo_xl.py │ │ ├── modeling_transfo_xl_utilities.py │ │ ├── modeling_utils.py │ │ ├── modeling_xlm.py │ │ ├── modeling_xlm_roberta.py │ │ ├── modeling_xlnet.py │ │ ├── optimization.py │ │ ├── optimization_tf.py │ │ ├── pipelines.py │ │ ├── tokenization_albert.py │ │ ├── tokenization_auto.py │ │ ├── tokenization_bart.py │ │ ├── tokenization_bert.py │ │ ├── tokenization_bert_japanese.py │ │ ├── tokenization_camembert.py │ │ ├── tokenization_ctrl.py │ │ ├── tokenization_distilbert.py │ │ ├── tokenization_dna.py │ │ ├── tokenization_flaubert.py │ │ ├── tokenization_gpt2.py │ │ ├── tokenization_openai.py │ │ ├── tokenization_roberta.py │ │ ├── tokenization_t5.py │ │ ├── tokenization_transfo_xl.py │ │ ├── tokenization_utils.py │ │ ├── tokenization_xlm.py │ │ ├── tokenization_xlm_roberta.py │ │ ├── tokenization_xlnet.py │ │ └── utils_encoder_decoder.py ├── ops │ ├── fftconv.py │ ├── krylov.py │ ├── toeplitz.py │ ├── unroll.py │ └── vandermonde.py ├── tasks │ ├── decoders.py │ ├── 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