a96123155 · windr00 · Apr 15, 2024
diff --git a/.DS_Store b/.DS_Store
diff --git a/._.DS_Store b/._.DS_Store
diff --git a/._LICENSE b/._LICENSE
diff --git a/._README.md b/._README.md
diff --git a/._utrlm_requirements.txt b/._utrlm_requirements.txt
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,37 @@
+# Created by https://www.toptal.com/developers/gitignore/api/macos
+# Edit at https://www.toptal.com/developers/gitignore?templates=macos
+
+### macOS ###
+# General
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Icon must end with two \r
+Icon
+
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+
+### macOS Patch ###
+# iCloud generated files
+*.icloud
+
+# End of https://www.toptal.com/developers/gitignore/api/macos
diff --git a/Model/.DS_Store b/Model/.DS_Store
diff --git a/Model/._.DS_Store b/Model/._.DS_Store
diff --git a/...fiveSpeciesCao_6layers_16heads_128embedsize_4096batchToks_lr1e-05_MLMLossMin_epoch201.pkl b/...fiveSpeciesCao_6layers_16heads_128embedsize_4096batchToks_lr1e-05_MLMLossMin_epoch201.pkl
diff --git a/...fiveSpeciesCao_6layers_16heads_128embedsize_4096batchToks_lr1e-05_MLMLossMin_epoch200.pkl b/...fiveSpeciesCao_6layers_16heads_128embedsize_4096batchToks_lr1e-05_MLMLossMin_epoch200.pkl
diff --git a/...size_4096batchToks_lr1e-05_supervisedweight1.0_structureweight1.0_MLMLossMin_epoch103.pkl b/...size_4096batchToks_lr1e-05_supervisedweight1.0_structureweight1.0_MLMLossMin_epoch103.pkl
diff --git a/...dsize_4096batchToks_lr1e-05_supervisedweight1.0_structureweight1.0_MLMLossMin_epoch91.pkl b/...dsize_4096batchToks_lr1e-05_supervisedweight1.0_structureweight1.0_MLMLossMin_epoch91.pkl
diff --git a/...size_4096batchToks_lr1e-05_supervisedweight1.0_structureweight1.0_MLMLossMin_epoch109.pkl b/...size_4096batchToks_lr1e-05_supervisedweight1.0_structureweight1.0_MLMLossMin_epoch109.pkl
diff --git a/...size_4096batchToks_lr1e-05_supervisedweight1.0_structureweight1.0_MLMLossMin_epoch115.pkl b/...size_4096batchToks_lr1e-05_supervisedweight1.0_structureweight1.0_MLMLossMin_epoch115.pkl
diff --git a/...dsize_4096batchToks_lr1e-05_supervisedweight1.0_structureweight1.0_MLMLossMin_epoch93.pkl b/...dsize_4096batchToks_lr1e-05_supervisedweight1.0_structureweight1.0_MLMLossMin_epoch93.pkl
diff --git a/...size_4096batchToks_lr1e-05_supervisedweight1.0_structureweight1.0_MLMLossMin_epoch115.pkl b/...size_4096batchToks_lr1e-05_supervisedweight1.0_structureweight1.0_MLMLossMin_epoch115.pkl
diff --git a/...size_4096batchToks_lr1e-05_supervisedweight1.0_structureweight1.0_MLMLossMin_epoch100.pkl b/...size_4096batchToks_lr1e-05_supervisedweight1.0_structureweight1.0_MLMLossMin_epoch100.pkl
diff --git a/...dsize_4096batchToks_lr1e-05_supervisedweight1.0_structureweight1.0_MLMLossMin_epoch79.pkl b/...dsize_4096batchToks_lr1e-05_supervisedweight1.0_structureweight1.0_MLMLossMin_epoch79.pkl
diff --git a/Model/._ESM2SI_3.1_fiveSpeciesCao_6layers_16heads_128embedsize_4096batchToks_MLMLossMin.pkl b/Model/._ESM2SI_3.1_fiveSpeciesCao_6layers_16heads_128embedsize_4096batchToks_MLMLossMin.pkl
diff --git a/...rs_16heads_128embedsize_4096batchToks_lr1e-05_supervisedweight1.0_MLMLossMin_epoch200.pkl b/...rs_16heads_128embedsize_4096batchToks_lr1e-05_supervisedweight1.0_MLMLossMin_epoch200.pkl
diff --git a/...ers_16heads_128embedsize_4096batchToks_lr1e-05_supervisedweight1.0_MLMLossMin_epoch93.pkl b/...ers_16heads_128embedsize_4096batchToks_lr1e-05_supervisedweight1.0_MLMLossMin_epoch93.pkl
diff --git a/...rs_16heads_128embedsize_4096batchToks_lr1e-05_supervisedweight1.0_MLMLossMin_epoch127.pkl b/...rs_16heads_128embedsize_4096batchToks_lr1e-05_supervisedweight1.0_MLMLossMin_epoch127.pkl
diff --git a/...ers_16heads_128embedsize_4096batchToks_lr1e-05_structureweight1.0_MLMLossMin_epoch200.pkl b/...ers_16heads_128embedsize_4096batchToks_lr1e-05_structureweight1.0_MLMLossMin_epoch200.pkl
diff --git a/Model/._ESM2_1.4_five_species_TrainLossMin_6layers_16heads_128embedsize_4096batchToks.pkl b/Model/._ESM2_1.4_five_species_TrainLossMin_6layers_16heads_128embedsize_4096batchToks.pkl
diff --git a/Model/Downstream/.DS_Store b/Model/Downstream/.DS_Store
diff --git a/Scripts/.DS_Store b/Scripts/.DS_Store
diff --git a/Scripts/._.DS_Store b/Scripts/._.DS_Store
diff --git a/Scripts/In-Housing/.DS_Store b/Scripts/In-Housing/.DS_Store
diff --git a/Scripts/In-Housing/._.DS_Store b/Scripts/In-Housing/._.DS_Store
diff --git a/Scripts/In-Housing/._6_unFinetune_results.ipynb b/Scripts/In-Housing/._6_unFinetune_results.ipynb
diff --git a/Scripts/In-Housing/._7_Optimus_retrained.ipynb b/Scripts/In-Housing/._7_Optimus_retrained.ipynb
diff --git a/Scripts/In-Housing/._8_finetune_results.ipynb b/Scripts/In-Housing/._8_finetune_results.ipynb
diff --git a/Scripts/In-Housing/._Hypothesis_PairedTtest.ipynb b/Scripts/In-Housing/._Hypothesis_PairedTtest.ipynb
diff --git a/Scripts/In-Housing/._results b/Scripts/In-Housing/._results
diff --git a/Scripts/In-Housing/results/.DS_Store b/Scripts/In-Housing/results/.DS_Store
diff --git a/Scripts/In-Housing/results/._.DS_Store b/Scripts/In-Housing/results/._.DS_Store
diff --git a/Scripts/Results/.DS_Store b/Scripts/Results/.DS_Store
diff --git a/Scripts/Results/._.DS_Store b/Scripts/Results/._.DS_Store
diff --git a/Scripts/Results/._EightLibrary_results.ipynb b/Scripts/Results/._EightLibrary_results.ipynb
diff --git a/Scripts/Results/._Independent_10foldCV.ipynb b/Scripts/Results/._Independent_10foldCV.ipynb
diff --git a/Scripts/Results/._Independent_BenchmarkSplit.ipynb b/Scripts/Results/._Independent_BenchmarkSplit.ipynb
diff --git a/Scripts/Results/._ThreeCellLine_results.ipynb b/Scripts/Results/._ThreeCellLine_results.ipynb
diff --git a/Scripts/Results/AttentionBased_Interpretation/.DS_Store b/Scripts/Results/AttentionBased_Interpretation/.DS_Store
diff --git a/Scripts/Results/AttentionBased_Interpretation/._.DS_Store b/Scripts/Results/AttentionBased_Interpretation/._.DS_Store
diff --git a/...rpretation/._IndependentHuman_PushLen50_ConvolutionalOperation_Attention_KmerMotifs.ipynb b/...rpretation/._IndependentHuman_PushLen50_ConvolutionalOperation_Attention_KmerMotifs.ipynb
diff --git a/...ults/AttentionBased_Interpretation/._U1_ConvolutionalOperation_Attention_KmerMotifs.ipynb b/...ults/AttentionBased_Interpretation/._U1_ConvolutionalOperation_Attention_KmerMotifs.ipynb
diff --git a/...pts/Results/AttentionBased_Interpretation/._fivespecies_representation-PCA-KNN-UMAP.ipynb b/...pts/Results/AttentionBased_Interpretation/._fivespecies_representation-PCA-KNN-UMAP.ipynb
diff --git a/Scripts/Results/AttentionBased_Interpretation/._unmod1_representation-PCA-KNN-UMAP.ipynb b/Scripts/Results/AttentionBased_Interpretation/._unmod1_representation-PCA-KNN-UMAP.ipynb
diff --git a/Scripts/UTRLM_downstream/._Finetune_extract_append_predictor_Sample_10fold-lr-huber-DDP.py b/Scripts/UTRLM_downstream/._Finetune_extract_append_predictor_Sample_10fold-lr-huber-DDP.py
diff --git a/...RLM_downstream/._Finetune_extract_append_predictor_VaryLength_10fold-lr-huber-DDP-Adam.py b/...RLM_downstream/._Finetune_extract_append_predictor_VaryLength_10fold-lr-huber-DDP-Adam.py
diff --git a/Scripts/UTRLM_pretraining/._ESM2_alldata_全部层训练.py b/Scripts/UTRLM_pretraining/._ESM2_alldata_全部层训练.py
diff --git a/Scripts/UTRLM_pretraining/._v2_ESM2_alldata_SupervisedInfo.py b/Scripts/UTRLM_pretraining/._v2_ESM2_alldata_SupervisedInfo.py
diff --git a/Scripts/UTRLM_pretraining/._v2_Extract_ESM2_embedding_attention.py b/Scripts/UTRLM_pretraining/._v2_Extract_ESM2_embedding_attention.py
diff --git a/Scripts/UTRLM_pretraining/._v3DDP_ESM2_alldata_SupervisedInfo_SecondaryStructure.py b/Scripts/UTRLM_pretraining/._v3DDP_ESM2_alldata_SupervisedInfo_SecondaryStructure.py
diff --git a/Scripts/UTRLM_pretraining/._v5DDP_ESM2_alldata_DownStreamData.py b/Scripts/UTRLM_pretraining/._v5DDP_ESM2_alldata_DownStreamData.py
diff --git a/Scripts/esm/.DS_Store b/Scripts/esm/.DS_Store
diff --git a/Scripts/esm/._.DS_Store b/Scripts/esm/._.DS_Store
diff --git a/Scripts/esm/._multihead_attention.py b/Scripts/esm/._multihead_attention.py
diff --git a/Scripts/esm/._pretrained.py b/Scripts/esm/._pretrained.py
diff --git a/Scripts/esm/model/._esm2_secondarystructure.py b/Scripts/esm/model/._esm2_secondarystructure.py