XMerge branch 'regression-dilshana' of github.com:yigbt/deepFPlearn i…

…nto regression-dilshana
yigbt · Nov 20, 2024 · 27a3c9b · 27a3c9b
2 parents a3d5ac6 + 21cc2cd
commit 27a3c9b
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diff --git a/example/dilshana-sweep-trial/train_dilshana.json b/example/dilshana-sweep-trial/train_dilshana.json
@@ -0,0 +1,25 @@
+{
+"py/object": "dfpl.options.Options",
+"inputFile": "/home/shanavas/PycharmProjects/deepFPlearn/example/data/herg_10uM_NN_sliced_minus2to2.csv",
+"outputDir": "/data/bioinf/projects/data/2024_invitrodb_data/dilshana/home/PyCharm/sweep/trial",
+"ecModelDir": "/home/shanavas/PycharmProjects/deepFPlearn/example/models/generic_encoder/",
+"type": "smiles",
+"fpType": "topological",
+"fpSize": 2048,
+"encFPSize": 256,
+"enableMultiLabel": false,
+"verbose": 2,
+"trainAC": false,
+"trainFNN": true,
+"compressFeatures": true,
+"kFolds": 1,
+"testSize": 0.2,
+"optimizer": "Adam",
+"batchSize": 128,
+"lossFunction": "mse",
+"epochs": 5000,
+"activationFunction": "tanh",
+"fnnType": "REG",
+"wabTracking": true
+}
+
diff --git a/example/herg10uM_sliced.json b/example/herg10uM_sliced.json
@@ -1,8 +1,8 @@
 {
   "py/object": "dfpl.options.Options",
-  "inputFile": "example/data/herg_10uM_NN_sliced_minus2to2.csv",
-  "outputDir": "example/herg_10uM/train/comp_sliced",
-  "ecModelDir": "example/models/generic_encoder/",
+  "inputFile": "PycharmProjects/deepFPlearn/example/data/herg_10uM_NN_sliced_minus2to2.csv",
+  "outputDir": "PycharmProjects/generate_dfpl_regression_data/example/herg_10/train/",
+  "ecModelDir": "PycharmProjects/deepFPlearn/example/models/generic_encoder/",
   "type": "smiles",
   "fpType": "topological",
   "fpSize": 2048,

diff --git a/example/train_dilshana.json b/example/train_dilshana.json
@@ -0,0 +1,26 @@
+{
+  "py/object": "dfpl.options.Options",
+  "inputFile": "PycharmProjects/deepFPlearn/example/data/herg_10uM_NN_sliced_minus2to2.csv",
+  "outputDir": "/data/bioinf/projects/data/2024_invitrodb_data/dilshana/home/PyCharm/sweep",
+  "ecModelDir": "Pycharm/example/models/generic_encoder/",
+  "type": "smiles",
+  "fpType": "topological",
+  "fpSize": 2048,
+  "encFPSize": 256,
+  "enableMultiLabel": false,
+  "verbose": 2,
+  "trainAC": false,
+  "trainFNN": true,
+  "compressFeatures": false,
+  "kFolds": 1,
+  "testSize": 0.2,
+  "optimizer": "Adam",
+  "batchSize": 128,
+  "lossFunction": "mse",
+  "epochs": 5000,
+  "activationFunction": "tanh",
+  "fnnType": "REG",
+  "wabTracking": true
+}
+
+
diff --git a/sweep_initial.yaml b/sweep_initial.yaml
@@ -5,7 +5,7 @@ command:
   - "source /home/shanavas/miniforge3/bin/activate /home/shanavas/miniforge3/envs/dfpl_env"
   - "/home/shanavas/miniforge3/envs/dfpl_env/bin/python" 
   -  ${program} 
-  -  "train-good1"
+  -  "train"
   -  "-f" 
   -  "/home/shanavas/PycharmProjects/deepFPlearn/example/dilshana-sweep-trial/train_dilshana.json"
   -  ${args}

diff --git a/sweep_trial.yaml b/sweep_trial.yaml
@@ -0,0 +1,32 @@
+program: dfpl 
+command:
+  - ${env}
+  - "/home/shanavas/miniforge3/envs/dfpl_env/bin/python" 
+  - "-m"  
+  -  ${program} 
+  -  "train"
+  -  "-f" 
+  -  "/home/shanavas/PycharmProjects/deepFPlearn/example/dilshana-sweep-trial/train_dilshana.json"
+  -  ${args}
+method: random
+metric:
+  name: val_loss
+  goal: minimize
+parameters:
+  dropout:
+    distribution: uniform
+    min: 0.00001
+    max: 0.5
+  l2reg:
+    distribution: uniform
+    min: 0.00001
+    max: 0.1
+  batchSize:
+    values: [64, 128, 256, 512]
+  learningRate:
+    distribution: uniform
+    min: 0.00001
+    max: 0.01  
+  wabTarget:
+    value: AR
+
diff --git a/wandb/debug-internal.log b/wandb/debug-internal.log
@@ -1 +1 @@
-run-20241113_115750-eo5mov7c/logs/debug-internal.log
+run-20241120_154315-7i2068pl/logs/debug-internal.log
diff --git a/wandb/debug.log b/wandb/debug.log
@@ -1 +1 @@
-run-20241113_115750-eo5mov7c/logs/debug.log
+run-20241120_154315-7i2068pl/logs/debug.log
diff --git a/wandb/latest-run b/wandb/latest-run
@@ -1 +1 @@
-run-20241113_115750-eo5mov7c
+run-20241120_154315-7i2068pl
diff --git a/wandb_new.sh b/wandb_new.sh
@@ -0,0 +1,19 @@
+#!/bin/bash -l
+# Standard output and error:
+#SBATCH --chdir=/home/shanavas              # Set the working directory
+#SBATCH --output=/home/%u/%x-%j.out           # Standard output log
+#SBATCH --error=/home/%u/%x-%j.err            # Standard error log
+#SBATCH --mem-per-cpu=2G                       # Memory per CPU
+#SBATCH -G 1                                  # Request 1 GPU if needed, change as necessary
+#SBATCH --time=0-12:00:00                      # Maximum runtime (2 hours)
+
+
+module purge
+#module load cuda/12.0
+
+source ~/miniforge3/etc/profile.d/conda.sh
+conda activate dfpl_env
+# Run the program:
+#srun wandb agent Pycharm/deepFPlearn/81yqknwm &> dfpl_run.log
+
+srun wandb agent --count 50 dilshana-ufz/deepFPlearn/o5rkx4co &> dfpl_run.log
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		run-20241113_115750-eo5mov7c/logs/debug-internal.log
		run-20241120_154315-7i2068pl/logs/debug-internal.log
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		@@ -1 +1 @@
		run-20241113_115750-eo5mov7c/logs/debug.log
		run-20241120_154315-7i2068pl/logs/debug.log
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		@@ -1 +1 @@
		run-20241113_115750-eo5mov7c
		run-20241120_154315-7i2068pl