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-rw-r--r--app/prod/checkpoints/LSTM_Chem-01-0.58.hdf5bin0 -> 3440640 bytes
-rw-r--r--app/prod/checkpoints/LSTM_Chem-02-0.43.hdf5bin0 -> 3440640 bytes
-rw-r--r--app/prod/checkpoints/LSTM_Chem-03-0.38.hdf5bin0 -> 3440640 bytes
-rw-r--r--app/prod/checkpoints/LSTM_Chem-04-0.35.hdf5bin0 -> 3440640 bytes
-rw-r--r--app/prod/checkpoints/LSTM_Chem-05-0.33.hdf5bin0 -> 3440640 bytes
-rw-r--r--app/prod/checkpoints/LSTM_Chem-06-0.32.hdf5bin0 -> 3440640 bytes
-rw-r--r--app/prod/checkpoints/LSTM_Chem-07-0.31.hdf5bin0 -> 3440640 bytes
-rw-r--r--app/prod/checkpoints/LSTM_Chem-08-0.30.hdf5bin0 -> 3440640 bytes
-rw-r--r--app/prod/checkpoints/LSTM_Chem-09-0.29.hdf5bin0 -> 3440640 bytes
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-rw-r--r--app/prod/checkpoints/LSTM_Chem-18-0.26.hdf5bin0 -> 3440640 bytes
-rw-r--r--app/prod/checkpoints/LSTM_Chem-19-0.26.hdf5bin0 -> 3440640 bytes
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-rw-r--r--app/prod/checkpoints/LSTM_Chem-23-0.25.hdf5bin0 -> 3440640 bytes
-rw-r--r--app/prod/checkpoints/LSTM_Chem-24-0.25.hdf5bin0 -> 3440640 bytes
-rw-r--r--app/prod/checkpoints/LSTM_Chem-25-0.25.hdf5bin0 -> 3440640 bytes
-rw-r--r--app/prod/checkpoints/LSTM_Chem-26-0.25.hdf5bin0 -> 3440640 bytes
-rw-r--r--app/prod/checkpoints/LSTM_Chem-27-0.24.hdf5bin0 -> 3440640 bytes
-rw-r--r--app/prod/checkpoints/LSTM_Chem-28-0.24.hdf5bin0 -> 3440640 bytes
-rw-r--r--app/prod/checkpoints/LSTM_Chem-29-0.24.hdf5bin0 -> 3440640 bytes
-rw-r--r--app/prod/checkpoints/LSTM_Chem-30-0.24.hdf5bin0 -> 3440640 bytes
-rw-r--r--app/prod/checkpoints/LSTM_Chem-31-0.24.hdf5bin0 -> 3440640 bytes
-rw-r--r--app/prod/checkpoints/LSTM_Chem-32-0.24.hdf5bin0 -> 3440640 bytes
-rw-r--r--app/prod/checkpoints/LSTM_Chem-33-0.24.hdf5bin0 -> 3440640 bytes
-rw-r--r--app/prod/checkpoints/LSTM_Chem-34-0.24.hdf5bin0 -> 3440640 bytes
-rw-r--r--app/prod/checkpoints/LSTM_Chem-35-0.24.hdf5bin0 -> 3440640 bytes
-rw-r--r--app/prod/checkpoints/LSTM_Chem-36-0.24.hdf5bin0 -> 3440640 bytes
-rw-r--r--app/prod/checkpoints/LSTM_Chem-37-0.24.hdf5bin0 -> 3440640 bytes
-rw-r--r--app/prod/checkpoints/LSTM_Chem-38-0.24.hdf5bin0 -> 3440640 bytes
-rw-r--r--app/prod/checkpoints/LSTM_Chem-39-0.23.hdf5bin0 -> 3440640 bytes
-rw-r--r--app/prod/checkpoints/LSTM_Chem-40-0.23.hdf5bin0 -> 3440640 bytes
-rw-r--r--app/prod/checkpoints/LSTM_Chem-41-0.23.hdf5bin0 -> 3440640 bytes
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-rw-r--r--app/prod/config.json30
-rw-r--r--app/prod/logs/train/events.out.tfevents.1594644989.Jiamin.local.31642.1238.v2bin0 -> 175733 bytes
-rw-r--r--app/prod/logs/train/events.out.tfevents.1594645021.Jiamin.local.profile-emptybin0 -> 40 bytes
-rw-r--r--app/prod/logs/train/plugins/profile/2020_07_13_20_57_01/Jiamin.local.input_pipeline.pbbin0 -> 2499 bytes
-rw-r--r--app/prod/logs/train/plugins/profile/2020_07_13_20_57_01/Jiamin.local.kernel_stats.pb0
-rw-r--r--app/prod/logs/train/plugins/profile/2020_07_13_20_57_01/Jiamin.local.overview_page.pbbin0 -> 3383 bytes
-rw-r--r--app/prod/logs/train/plugins/profile/2020_07_13_20_57_01/Jiamin.local.tensorflow_stats.pbbin0 -> 56401 bytes
-rw-r--r--app/prod/logs/train/plugins/profile/2020_07_13_20_57_01/Jiamin.local.trace.json.gzbin0 -> 244284 bytes
-rw-r--r--app/prod/logs/validation/events.out.tfevents.1594646871.Jiamin.local.31642.8717.v2bin0 -> 2054 bytes
-rw-r--r--app/prod/model_arch.json149
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diff --git a/app/prod/config.json b/app/prod/config.json
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@@ -0,0 +1,30 @@
+{
+ "exp_name": "LSTM_Chem",
+ "data_filename": "./datasets/all_smiles_clean.txt",
+ "data_length": 0,
+ "units": 256,
+ "num_epochs": 42,
+ "optimizer": "adam",
+ "seed": 71,
+ "batch_size": 512,
+ "validation_split": 0.1,
+ "verbose_training": true,
+ "checkpoint_monitor": "val_loss",
+ "checkpoint_mode": "min",
+ "checkpoint_save_best_only": false,
+ "checkpoint_save_weights_only": true,
+ "checkpoint_verbose": 1,
+ "tensorboard_write_graph": true,
+ "sampling_temp": 0.75,
+ "smiles_max_length": 128,
+ "finetune_epochs": 12,
+ "finetune_batch_size": 1,
+ "finetune_data_filename": "./datasets/protease_inhibitors_for_fine-tune.txt",
+ "config_file": "experiments/base_experiment/LSTM_Chem/config.json",
+ "exp_dir": "experiments/2020-07-13/LSTM_Chem",
+ "tensorboard_log_dir": "experiments/2020-07-13/LSTM_Chem/logs/",
+ "checkpoint_dir": "experiments/2020-07-13/LSTM_Chem/checkpoints/",
+ "train_smi_max_len": 128,
+ "model_arch_filename": "experiments/2020-07-13/LSTM_Chem/model_arch.json",
+ "model_weight_filename": "experiments/2020-07-13/LSTM_Chem/checkpoints/LSTM_Chem-42-0.23.hdf5"
+} \ No newline at end of file
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+++ b/app/prod/logs/train/plugins/profile/2020_07_13_20_57_01/Jiamin.local.trace.json.gz
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diff --git a/app/prod/logs/validation/events.out.tfevents.1594646871.Jiamin.local.31642.8717.v2 b/app/prod/logs/validation/events.out.tfevents.1594646871.Jiamin.local.31642.8717.v2
new file mode 100644
index 0000000..47519ee
--- /dev/null
+++ b/app/prod/logs/validation/events.out.tfevents.1594646871.Jiamin.local.31642.8717.v2
Binary files differ
diff --git a/app/prod/model_arch.json b/app/prod/model_arch.json
new file mode 100644
index 0000000..e41f8b2
--- /dev/null
+++ b/app/prod/model_arch.json
@@ -0,0 +1,149 @@
+{
+ "class_name": "Sequential",
+ "config": {
+ "name": "sequential",
+ "layers": [
+ {
+ "class_name": "LSTM",
+ "config": {
+ "name": "lstm",
+ "trainable": true,
+ "batch_input_shape": [
+ null,
+ null,
+ 52
+ ],
+ "dtype": "float32",
+ "return_sequences": true,
+ "return_state": false,
+ "go_backwards": false,
+ "stateful": false,
+ "unroll": false,
+ "time_major": false,
+ "units": 256,
+ "activation": "tanh",
+ "recurrent_activation": "sigmoid",
+ "use_bias": true,
+ "kernel_initializer": {
+ "class_name": "RandomNormal",
+ "config": {
+ "mean": 0.0,
+ "stddev": 0.05,
+ "seed": 71
+ }
+ },
+ "recurrent_initializer": {
+ "class_name": "Orthogonal",
+ "config": {
+ "gain": 1.0,
+ "seed": null
+ }
+ },
+ "bias_initializer": {
+ "class_name": "Zeros",
+ "config": {}
+ },
+ "unit_forget_bias": true,
+ "kernel_regularizer": null,
+ "recurrent_regularizer": null,
+ "bias_regularizer": null,
+ "activity_regularizer": null,
+ "kernel_constraint": null,
+ "recurrent_constraint": null,
+ "bias_constraint": null,
+ "dropout": 0.3,
+ "recurrent_dropout": 0.0,
+ "implementation": 2
+ }
+ },
+ {
+ "class_name": "LSTM",
+ "config": {
+ "name": "lstm_1",
+ "trainable": true,
+ "batch_input_shape": [
+ null,
+ null,
+ 52
+ ],
+ "dtype": "float32",
+ "return_sequences": true,
+ "return_state": false,
+ "go_backwards": false,
+ "stateful": false,
+ "unroll": false,
+ "time_major": false,
+ "units": 256,
+ "activation": "tanh",
+ "recurrent_activation": "sigmoid",
+ "use_bias": true,
+ "kernel_initializer": {
+ "class_name": "RandomNormal",
+ "config": {
+ "mean": 0.0,
+ "stddev": 0.05,
+ "seed": 71
+ }
+ },
+ "recurrent_initializer": {
+ "class_name": "Orthogonal",
+ "config": {
+ "gain": 1.0,
+ "seed": null
+ }
+ },
+ "bias_initializer": {
+ "class_name": "Zeros",
+ "config": {}
+ },
+ "unit_forget_bias": true,
+ "kernel_regularizer": null,
+ "recurrent_regularizer": null,
+ "bias_regularizer": null,
+ "activity_regularizer": null,
+ "kernel_constraint": null,
+ "recurrent_constraint": null,
+ "bias_constraint": null,
+ "dropout": 0.5,
+ "recurrent_dropout": 0.0,
+ "implementation": 2
+ }
+ },
+ {
+ "class_name": "Dense",
+ "config": {
+ "name": "dense",
+ "trainable": true,
+ "dtype": "float32",
+ "units": 52,
+ "activation": "softmax",
+ "use_bias": true,
+ "kernel_initializer": {
+ "class_name": "RandomNormal",
+ "config": {
+ "mean": 0.0,
+ "stddev": 0.05,
+ "seed": 71
+ }
+ },
+ "bias_initializer": {
+ "class_name": "Zeros",
+ "config": {}
+ },
+ "kernel_regularizer": null,
+ "bias_regularizer": null,
+ "activity_regularizer": null,
+ "kernel_constraint": null,
+ "bias_constraint": null
+ }
+ }
+ ],
+ "build_input_shape": [
+ null,
+ null,
+ 52
+ ]
+ },
+ "keras_version": "2.3.0-tf",
+ "backend": "tensorflow"
+} \ No newline at end of file