From ae55acfeca98acfd3b281074968c02c0e0849ce2 Mon Sep 17 00:00:00 2001
From: windr00 <imrwz@icloud.com>
Date: Mon, 15 Apr 2024 03:32:14 +0000
Subject: [PATCH] remove macOS thumb files, and add .gitignore to ignore
 furthuer ones

---
 .DS_Store                                     | Bin 6148 -> 0 bytes
 ._.DS_Store                                   | Bin 4096 -> 0 bytes
 ._LICENSE                                     | Bin 4096 -> 0 bytes
 ._README.md                                   | Bin 4096 -> 0 bytes
 ._utrlm_requirements.txt                      | Bin 4096 -> 0 bytes
 .gitignore                                    |  37 ++++++++++++++++++
 Model/.DS_Store                               | Bin 6148 -> 0 bytes
 Model/._.DS_Store                             | Bin 4096 -> 0 bytes
 ...6batchToks_lr1e-05_MLMLossMin_epoch201.pkl | Bin 4096 -> 0 bytes
 ...6batchToks_lr1e-05_MLMLossMin_epoch200.pkl | Bin 4096 -> 0 bytes
 ...structureweight1.0_MLMLossMin_epoch103.pkl | Bin 4096 -> 0 bytes
 ..._structureweight1.0_MLMLossMin_epoch91.pkl | Bin 4096 -> 0 bytes
 ...structureweight1.0_MLMLossMin_epoch109.pkl | Bin 4096 -> 0 bytes
 ...structureweight1.0_MLMLossMin_epoch115.pkl | Bin 4096 -> 0 bytes
 ..._structureweight1.0_MLMLossMin_epoch93.pkl | Bin 4096 -> 0 bytes
 ...structureweight1.0_MLMLossMin_epoch115.pkl | Bin 4096 -> 0 bytes
 ...structureweight1.0_MLMLossMin_epoch100.pkl | Bin 4096 -> 0 bytes
 ..._structureweight1.0_MLMLossMin_epoch79.pkl | Bin 4096 -> 0 bytes
 ..._128embedsize_4096batchToks_MLMLossMin.pkl | Bin 4096 -> 0 bytes
 ...upervisedweight1.0_MLMLossMin_epoch200.pkl | Bin 4096 -> 0 bytes
 ...supervisedweight1.0_MLMLossMin_epoch93.pkl | Bin 4096 -> 0 bytes
 ...upervisedweight1.0_MLMLossMin_epoch127.pkl | Bin 4096 -> 0 bytes
 ...structureweight1.0_MLMLossMin_epoch200.pkl | Bin 4096 -> 0 bytes
 ...ers_16heads_128embedsize_4096batchToks.pkl | Bin 4096 -> 0 bytes
 Model/Downstream/.DS_Store                    | Bin 6148 -> 0 bytes
 Scripts/.DS_Store                             | Bin 8196 -> 0 bytes
 Scripts/._.DS_Store                           | Bin 4096 -> 0 bytes
 Scripts/In-Housing/.DS_Store                  | Bin 6148 -> 0 bytes
 Scripts/In-Housing/._.DS_Store                | Bin 4096 -> 0 bytes
 .../In-Housing/._6_unFinetune_results.ipynb   | Bin 4096 -> 0 bytes
 .../In-Housing/._7_Optimus_retrained.ipynb    | Bin 4096 -> 0 bytes
 Scripts/In-Housing/._8_finetune_results.ipynb | Bin 4096 -> 0 bytes
 .../In-Housing/._Hypothesis_PairedTtest.ipynb | Bin 4096 -> 0 bytes
 Scripts/In-Housing/._results                  | Bin 4096 -> 0 bytes
 Scripts/In-Housing/results/.DS_Store          | Bin 6148 -> 0 bytes
 Scripts/In-Housing/results/._.DS_Store        | Bin 4096 -> 0 bytes
 Scripts/Results/.DS_Store                     | Bin 6148 -> 0 bytes
 Scripts/Results/._.DS_Store                   | Bin 4096 -> 0 bytes
 Scripts/Results/._EightLibrary_results.ipynb  | Bin 4096 -> 0 bytes
 Scripts/Results/._Independent_10foldCV.ipynb  | Bin 4096 -> 0 bytes
 .../._Independent_BenchmarkSplit.ipynb        | Bin 4096 -> 0 bytes
 Scripts/Results/._ThreeCellLine_results.ipynb | Bin 4096 -> 0 bytes
 .../AttentionBased_Interpretation/.DS_Store   | Bin 6148 -> 0 bytes
 .../AttentionBased_Interpretation/._.DS_Store | Bin 4096 -> 0 bytes
 ...tionalOperation_Attention_KmerMotifs.ipynb | Bin 4096 -> 0 bytes
 ...tionalOperation_Attention_KmerMotifs.ipynb | Bin 4096 -> 0 bytes
 ...especies_representation-PCA-KNN-UMAP.ipynb | Bin 4096 -> 0 bytes
 ...._unmod1_representation-PCA-KNN-UMAP.ipynb | Bin 4096 -> 0 bytes
 ...nd_predictor_Sample_10fold-lr-huber-DDP.py | Bin 4096 -> 0 bytes
 ...tor_VaryLength_10fold-lr-huber-DDP-Adam.py | Bin 4096 -> 0 bytes
 ...50\345\261\202\350\256\255\347\273\203.py" | Bin 4096 -> 0 bytes
 .../._v2_ESM2_alldata_SupervisedInfo.py       | Bin 4096 -> 0 bytes
 .../._v2_Extract_ESM2_embedding_attention.py  | Bin 4096 -> 0 bytes
 ...ldata_SupervisedInfo_SecondaryStructure.py | Bin 4096 -> 0 bytes
 .../._v5DDP_ESM2_alldata_DownStreamData.py    | Bin 4096 -> 0 bytes
 Scripts/esm/.DS_Store                         | Bin 6148 -> 0 bytes
 Scripts/esm/._.DS_Store                       | Bin 4096 -> 0 bytes
 Scripts/esm/._multihead_attention.py          | Bin 4096 -> 0 bytes
 Scripts/esm/._pretrained.py                   | Bin 4096 -> 0 bytes
 .../esm/model/._esm2_secondarystructure.py    | Bin 4096 -> 0 bytes
 60 files changed, 37 insertions(+)
 delete mode 100644 .DS_Store
 delete mode 100644 ._.DS_Store
 delete mode 100644 ._LICENSE
 delete mode 100644 ._README.md
 delete mode 100644 ._utrlm_requirements.txt
 create mode 100644 .gitignore
 delete mode 100644 Model/.DS_Store
 delete mode 100644 Model/._.DS_Store
 delete mode 100644 Model/._ESM2DSD_FC3.1_fiveSpeciesCao_6layers_16heads_128embedsize_4096batchToks_lr1e-05_MLMLossMin_epoch201.pkl
 delete mode 100644 Model/._ESM2DSD_FS4.1_fiveSpeciesCao_6layers_16heads_128embedsize_4096batchToks_lr1e-05_MLMLossMin_epoch200.pkl
 delete mode 100644 Model/._ESM2SISS_FS4.10_fiveSpeciesCao_6layers_16heads_128embedsize_4096batchToks_lr1e-05_supervisedweight1.0_structureweight1.0_MLMLossMin_epoch103.pkl
 delete mode 100644 Model/._ESM2SISS_FS4.13_fiveSpeciesCao_6layers_16heads_128embedsize_4096batchToks_lr1e-05_supervisedweight1.0_structureweight1.0_MLMLossMin_epoch91.pkl
 delete mode 100644 Model/._ESM2SISS_FS4.16_fiveSpeciesCao_6layers_16heads_128embedsize_4096batchToks_lr1e-05_supervisedweight1.0_structureweight1.0_MLMLossMin_epoch109.pkl
 delete mode 100644 Model/._ESM2SISS_FS4.19_fiveSpeciesCao_6layers_16heads_128embedsize_4096batchToks_lr1e-05_supervisedweight1.0_structureweight1.0_MLMLossMin_epoch115.pkl
 delete mode 100644 Model/._ESM2SISS_FS4.1_fiveSpeciesCao_6layers_16heads_128embedsize_4096batchToks_lr1e-05_supervisedweight1.0_structureweight1.0_MLMLossMin_epoch93.pkl
 delete mode 100644 Model/._ESM2SISS_FS4.22_fiveSpeciesCao_6layers_16heads_128embedsize_4096batchToks_lr1e-05_supervisedweight1.0_structureweight1.0_MLMLossMin_epoch115.pkl
 delete mode 100644 Model/._ESM2SISS_FS4.4_fiveSpeciesCao_6layers_16heads_128embedsize_4096batchToks_lr1e-05_supervisedweight1.0_structureweight1.0_MLMLossMin_epoch100.pkl
 delete mode 100644 Model/._ESM2SISS_FS4.7_fiveSpeciesCao_6layers_16heads_128embedsize_4096batchToks_lr1e-05_supervisedweight1.0_structureweight1.0_MLMLossMin_epoch79.pkl
 delete mode 100644 Model/._ESM2SI_3.1_fiveSpeciesCao_6layers_16heads_128embedsize_4096batchToks_MLMLossMin.pkl
 delete mode 100644 Model/._ESM2SI_FS4.1_fiveSpeciesCao_6layers_16heads_128embedsize_4096batchToks_lr1e-05_supervisedweight1.0_MLMLossMin_epoch200.pkl
 delete mode 100644 Model/._ESM2SI_FS4.4_fiveSpeciesCao_6layers_16heads_128embedsize_4096batchToks_lr1e-05_supervisedweight1.0_MLMLossMin_epoch93.pkl
 delete mode 100644 Model/._ESM2SI_FS4.7_fiveSpeciesCao_6layers_16heads_128embedsize_4096batchToks_lr1e-05_supervisedweight1.0_MLMLossMin_epoch127.pkl
 delete mode 100644 Model/._ESM2SS_FS4.1_fiveSpeciesCao_6layers_16heads_128embedsize_4096batchToks_lr1e-05_structureweight1.0_MLMLossMin_epoch200.pkl
 delete mode 100644 Model/._ESM2_1.4_five_species_TrainLossMin_6layers_16heads_128embedsize_4096batchToks.pkl
 delete mode 100644 Model/Downstream/.DS_Store
 delete mode 100644 Scripts/.DS_Store
 delete mode 100644 Scripts/._.DS_Store
 delete mode 100644 Scripts/In-Housing/.DS_Store
 delete mode 100644 Scripts/In-Housing/._.DS_Store
 delete mode 100644 Scripts/In-Housing/._6_unFinetune_results.ipynb
 delete mode 100644 Scripts/In-Housing/._7_Optimus_retrained.ipynb
 delete mode 100644 Scripts/In-Housing/._8_finetune_results.ipynb
 delete mode 100644 Scripts/In-Housing/._Hypothesis_PairedTtest.ipynb
 delete mode 100644 Scripts/In-Housing/._results
 delete mode 100644 Scripts/In-Housing/results/.DS_Store
 delete mode 100644 Scripts/In-Housing/results/._.DS_Store
 delete mode 100644 Scripts/Results/.DS_Store
 delete mode 100644 Scripts/Results/._.DS_Store
 delete mode 100644 Scripts/Results/._EightLibrary_results.ipynb
 delete mode 100644 Scripts/Results/._Independent_10foldCV.ipynb
 delete mode 100644 Scripts/Results/._Independent_BenchmarkSplit.ipynb
 delete mode 100644 Scripts/Results/._ThreeCellLine_results.ipynb
 delete mode 100644 Scripts/Results/AttentionBased_Interpretation/.DS_Store
 delete mode 100644 Scripts/Results/AttentionBased_Interpretation/._.DS_Store
 delete mode 100644 Scripts/Results/AttentionBased_Interpretation/._IndependentHuman_PushLen50_ConvolutionalOperation_Attention_KmerMotifs.ipynb
 delete mode 100644 Scripts/Results/AttentionBased_Interpretation/._U1_ConvolutionalOperation_Attention_KmerMotifs.ipynb
 delete mode 100644 Scripts/Results/AttentionBased_Interpretation/._fivespecies_representation-PCA-KNN-UMAP.ipynb
 delete mode 100644 Scripts/Results/AttentionBased_Interpretation/._unmod1_representation-PCA-KNN-UMAP.ipynb
 delete mode 100644 Scripts/UTRLM_downstream/._Finetune_extract_append_predictor_Sample_10fold-lr-huber-DDP.py
 delete mode 100644 Scripts/UTRLM_downstream/._Finetune_extract_append_predictor_VaryLength_10fold-lr-huber-DDP-Adam.py
 delete mode 100644 "Scripts/UTRLM_pretraining/._ESM2_alldata_\345\205\250\351\203\250\345\261\202\350\256\255\347\273\203.py"
 delete mode 100644 Scripts/UTRLM_pretraining/._v2_ESM2_alldata_SupervisedInfo.py
 delete mode 100644 Scripts/UTRLM_pretraining/._v2_Extract_ESM2_embedding_attention.py
 delete mode 100644 Scripts/UTRLM_pretraining/._v3DDP_ESM2_alldata_SupervisedInfo_SecondaryStructure.py
 delete mode 100644 Scripts/UTRLM_pretraining/._v5DDP_ESM2_alldata_DownStreamData.py
 delete mode 100644 Scripts/esm/.DS_Store
 delete mode 100644 Scripts/esm/._.DS_Store
 delete mode 100644 Scripts/esm/._multihead_attention.py
 delete mode 100644 Scripts/esm/._pretrained.py
 delete mode 100644 Scripts/esm/model/._esm2_secondarystructure.py

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diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..314044f
--- /dev/null
+++ 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
\ No newline at end of file
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