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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,25 @@ | ||
| { | ||
| "py/object": "dfpl.options.Options", | ||
| "inputFile": "/home/shanavas/PycharmProjects/deepFPlearn/example/data/Clearance_Microsome_AZ_nn_clean.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 | ||
| } | ||
|
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,25 @@ | ||
| { | ||
| "py/object": "dfpl.options.Options", | ||
| "inputFile": "/home/shanavas/PycharmProjects/deepFPlearn/example/data//Lipophilicity_AstraZeneca_nn.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 | ||
| } | ||
|
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,25 @@ | ||
| { | ||
| "py/object": "dfpl.options.Options", | ||
| "inputFile": "/home/shanavas/PycharmProjects/deepFPlearn/example/data/Solubility_AqSolDB_nn.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 | ||
| } | ||
|
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,25 @@ | ||
| { | ||
| "py/object": "dfpl.options.Options", | ||
| "inputFile": "/home/shanavas/PycharmProjects/deepFPlearn/example/data/Zhu_LD50_rat.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 | ||
| } | ||
|
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,25 @@ | ||
| { | ||
| "py/object": "dfpl.options.Options", | ||
| "inputFile": "/home/shanavas/PycharmProjects/deepFPlearn/example/data/caco2_wang_nn_clean.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 | ||
| } | ||
|
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,23 @@ | ||
| { | ||
| "py/object": "dfpl.options.Options", | ||
| "inputFile": "/home/shanavas/PycharmProjects/deepFPlearn/example/data/cytoxicity_zscore.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": 5, | ||
| "testSize": 0.2, | ||
| "optimizer": "Adam", | ||
| "lossFunction": "mse", | ||
| "epochs": 5000, | ||
| "fnnType": "REG", | ||
| "wabTracking": true | ||
| } | ||
|
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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": 5, | ||
| "testSize": 0.2, | ||
| "optimizer": "Adam", | ||
| "batchSize": 128, | ||
| "lossFunction": "mse", | ||
| "epochs": 5000, | ||
| "activationFunction": "tanh", | ||
| "fnnType": "REG", | ||
| "wabTracking": true | ||
| } | ||
|
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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/Clearance.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 | ||
|
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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/Lipophilicity.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 | ||
|
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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/Solubility.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 | ||
|
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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/Zhu.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 | ||
|
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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/caco.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 | ||
|
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,37 @@ | ||
| program: dfpl | ||
| command: | ||
| - ${env} | ||
| - "/home/shanavas/miniforge3/envs/dfpl_env/bin/python" | ||
| - "-m" | ||
| - ${program} | ||
| - "train" | ||
| - "-f" | ||
| - "/home/shanavas/PycharmProjects/deepFPlearn/example/dilshana-sweep-trial/cytotoxicity.json" | ||
| - ${args} | ||
| method: random | ||
| metric: | ||
| name: val_loss | ||
| goal: minimize | ||
| parameters: | ||
| dropout: | ||
| distribution: uniform | ||
| min: 0.001 | ||
| max: 0.5 | ||
| l2reg: | ||
| distribution: uniform | ||
| min: 0.000001 | ||
| max: 0.0001 | ||
| activationFunction: | ||
| values: | ||
| - "relu" | ||
| - "selu" | ||
| - "tanh" | ||
| batchSize: | ||
| values: [64, 128, 256] | ||
| learningRate: | ||
| distribution: uniform | ||
| min: 0.000001 | ||
| max: 0.001 | ||
| wabTarget: | ||
| value: AR | ||
|
|
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