Added additional example scripts for finetuning on Absolut data.

jlparkI · Nov 17, 2024 · d78c184 · d78c184
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diff --git a/config/__pycache__/__init__.cpython-38.pyc b/config/__pycache__/__init__.cpython-38.pyc
diff --git a/dataset_loaders/__pycache__/__init__.cpython-38.pyc b/dataset_loaders/__pycache__/__init__.cpython-38.pyc
diff --git a/dataset_loaders/__pycache__/textfile_loader.cpython-38.pyc b/dataset_loaders/__pycache__/textfile_loader.cpython-38.pyc
diff --git a/evodiff/__pycache__/__init__.cpython-38.pyc b/evodiff/__pycache__/__init__.cpython-38.pyc
diff --git a/evodiff/__pycache__/collaters.cpython-38.pyc b/evodiff/__pycache__/collaters.cpython-38.pyc
diff --git a/evodiff/__pycache__/constants.cpython-38.pyc b/evodiff/__pycache__/constants.cpython-38.pyc
diff --git a/evodiff/__pycache__/data.cpython-38.pyc b/evodiff/__pycache__/data.cpython-38.pyc
diff --git a/evodiff/__pycache__/losses.cpython-38.pyc b/evodiff/__pycache__/losses.cpython-38.pyc
diff --git a/evodiff/__pycache__/metrics.cpython-38.pyc b/evodiff/__pycache__/metrics.cpython-38.pyc
diff --git a/evodiff/__pycache__/model.cpython-38.pyc b/evodiff/__pycache__/model.cpython-38.pyc
diff --git a/evodiff/__pycache__/plot.cpython-38.pyc b/evodiff/__pycache__/plot.cpython-38.pyc
diff --git a/evodiff/__pycache__/pretrained.cpython-38.pyc b/evodiff/__pycache__/pretrained.cpython-38.pyc
diff --git a/evodiff/__pycache__/utils.cpython-38.pyc b/evodiff/__pycache__/utils.cpython-38.pyc
diff --git a/example_finetune_script.sh b/example_finetune_script.sh
@@ -19,9 +19,9 @@ conda activate evodiff
 # and to update the other lines as appropriate.
 
 python fine_tune.py --config_fpath /stg3/data3/Jonathan/jonathan2/pdl1_evodiff_tuning/evodiff/config/config38M.json \
-	--out_fpath /stg3/data3/Jonathan/jonathan2/pdl1_evodiff_tuning/evodiff_results/ \
-	--train_fpath /stg3/data3/Jonathan/jonathan2/pdl1_evodiff_tuning/train_pdl1.txt \
-	--valid_fpath /stg3/data3/Jonathan/jonathan2/pdl1_evodiff_tuning/test_pdl1.txt \
+	--out_fpath /stg3/data3/Jonathan/jonathan2/resp2_absolut/fine_tuning/ \
+	--train_fpath /stg3/data3/Jonathan/jonathan2/resp2_absolut/fine_tuning/il2_80_genAI_seqs.txt \
+	--valid_fpath /stg3/data3/Jonathan/jonathan2/resp2_absolut/fine_tuning/ \
         --checkpoint_freq 60 \
         --LoRA 16
 #	--large_model
diff --git a/il2_evodiff b/il2_evodiff
diff --git a/il2_finetuning.sh b/il2_finetuning.sh
@@ -0,0 +1,30 @@
+#!/bin/bash
+
+#SBATCH -p gpu
+#SBATCH --job-name il2_evodiff
+#SBATCH --output il2_evodiff
+#SBATCH -w gpu-2
+#SBATCH --gres=gpu:1
+#SBATCH --mem=50G
+
+
+module load cuda
+
+source /stg3/data3/Jonathan/.bashrc
+source /stg3/data3/Jonathan/.bash_profile
+
+conda activate evodiff
+
+
+python fine_tune.py --config_fpath /stg3/data3/Jonathan/jonathan2/resp2_absolut/evodiff_ft/config/config640M.json \
+	--out_fpath /stg3/data3/Jonathan/jonathan2/resp2_absolut/fine_tuning/il2_90/ \
+	--train_fpath /stg3/data3/Jonathan/jonathan2/resp2_absolut/fine_tuning/il2_90/il2_90_genAI_train.txt \
+	--valid_fpath /stg3/data3/Jonathan/jonathan2/resp2_absolut/fine_tuning/il2_90/il2_90_genAI_test.txt \
+    --large_model
+
+
+python fine_tune.py --config_fpath /stg3/data3/Jonathan/jonathan2/resp2_absolut/evodiff_ft/config/config640M.json \
+	--out_fpath /stg3/data3/Jonathan/jonathan2/resp2_absolut/fine_tuning/il2_80/ \
+	--train_fpath /stg3/data3/Jonathan/jonathan2/resp2_absolut/fine_tuning/il2_80/il2_80_genAI_train.txt \
+	--valid_fpath /stg3/data3/Jonathan/jonathan2/resp2_absolut/fine_tuning/il2_80/il2_80_genAI_test.txt \
+    --large_model
diff --git a/l1evodiff b/l1evodiff
diff --git a/neura_evodiff b/neura_evodiff
diff --git a/neura_finetuning.sh b/neura_finetuning.sh
@@ -0,0 +1,28 @@
+#!/bin/bash
+
+#SBATCH -p gpu
+#SBATCH --job-name neura_evodiff
+#SBATCH --output neura_evodiff
+#SBATCH -w gpu-2
+#SBATCH --gres=gpu:1
+#SBATCH --mem=50G
+
+module load cuda
+
+source /stg3/data3/Jonathan/.bashrc
+source /stg3/data3/Jonathan/.bash_profile
+
+conda activate evodiff
+
+
+python fine_tune.py --config_fpath /stg3/data3/Jonathan/jonathan2/resp2_absolut/evodiff_ft/config/config640M.json \
+	--out_fpath /stg3/data3/Jonathan/jonathan2/resp2_absolut/fine_tuning/neura_80/ \
+	--train_fpath /stg3/data3/Jonathan/jonathan2/resp2_absolut/fine_tuning/neura_80/neuraminidase_80_genAI_train.txt \
+	--valid_fpath /stg3/data3/Jonathan/jonathan2/resp2_absolut/fine_tuning/neura_80/neuraminidase_80_genAI_test.txt \
+    --large_model
+
+python fine_tune.py --config_fpath /stg3/data3/Jonathan/jonathan2/resp2_absolut/evodiff_ft/config/config640M.json \
+	--out_fpath /stg3/data3/Jonathan/jonathan2/resp2_absolut/fine_tuning/neura_90/ \
+	--train_fpath /stg3/data3/Jonathan/jonathan2/resp2_absolut/fine_tuning/neura_90/neuraminidase_90_genAI_train.txt \
+	--valid_fpath /stg3/data3/Jonathan/jonathan2/resp2_absolut/fine_tuning/neura_90/neuraminidase_90_genAI_test.txt \
+    --large_model