added AI model

52 files changed, 179 insertions, 0 deletions

diff --git a/app/prod/checkpoints/LSTM_Chem-01-0.58.hdf5 b/app/prod/checkpoints/LSTM_Chem-01-0.58.hdf5
new file mode 100644
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--- /dev/null
+++ b/app/prod/checkpoints/LSTM_Chem-01-0.58.hdf5
diff --git a/app/prod/checkpoints/LSTM_Chem-02-0.43.hdf5 b/app/prod/checkpoints/LSTM_Chem-02-0.43.hdf5
new file mode 100644
index 0000000..9fa1f36
--- /dev/null
+++ b/app/prod/checkpoints/LSTM_Chem-02-0.43.hdf5
diff --git a/app/prod/checkpoints/LSTM_Chem-03-0.38.hdf5 b/app/prod/checkpoints/LSTM_Chem-03-0.38.hdf5
new file mode 100644
index 0000000..0234965
--- /dev/null
+++ b/app/prod/checkpoints/LSTM_Chem-03-0.38.hdf5
diff --git a/app/prod/checkpoints/LSTM_Chem-04-0.35.hdf5 b/app/prod/checkpoints/LSTM_Chem-04-0.35.hdf5
new file mode 100644
index 0000000..0758848
--- /dev/null
+++ b/app/prod/checkpoints/LSTM_Chem-04-0.35.hdf5
diff --git a/app/prod/checkpoints/LSTM_Chem-05-0.33.hdf5 b/app/prod/checkpoints/LSTM_Chem-05-0.33.hdf5
new file mode 100644
index 0000000..f46d338
--- /dev/null
+++ b/app/prod/checkpoints/LSTM_Chem-05-0.33.hdf5
diff --git a/app/prod/checkpoints/LSTM_Chem-06-0.32.hdf5 b/app/prod/checkpoints/LSTM_Chem-06-0.32.hdf5
new file mode 100644
index 0000000..02d3154
--- /dev/null
+++ b/app/prod/checkpoints/LSTM_Chem-06-0.32.hdf5
diff --git a/app/prod/checkpoints/LSTM_Chem-07-0.31.hdf5 b/app/prod/checkpoints/LSTM_Chem-07-0.31.hdf5
new file mode 100644
index 0000000..1c2718a
--- /dev/null
+++ b/app/prod/checkpoints/LSTM_Chem-07-0.31.hdf5
diff --git a/app/prod/checkpoints/LSTM_Chem-08-0.30.hdf5 b/app/prod/checkpoints/LSTM_Chem-08-0.30.hdf5
new file mode 100644
index 0000000..f2985a1
--- /dev/null
+++ b/app/prod/checkpoints/LSTM_Chem-08-0.30.hdf5
diff --git a/app/prod/checkpoints/LSTM_Chem-09-0.29.hdf5 b/app/prod/checkpoints/LSTM_Chem-09-0.29.hdf5
new file mode 100644
index 0000000..3a8efa2
--- /dev/null
+++ b/app/prod/checkpoints/LSTM_Chem-09-0.29.hdf5
diff --git a/app/prod/checkpoints/LSTM_Chem-10-0.29.hdf5 b/app/prod/checkpoints/LSTM_Chem-10-0.29.hdf5
new file mode 100644
index 0000000..38f6136
--- /dev/null
+++ b/app/prod/checkpoints/LSTM_Chem-10-0.29.hdf5
diff --git a/app/prod/checkpoints/LSTM_Chem-11-0.28.hdf5 b/app/prod/checkpoints/LSTM_Chem-11-0.28.hdf5
new file mode 100644
index 0000000..c2d5a03
--- /dev/null
+++ b/app/prod/checkpoints/LSTM_Chem-11-0.28.hdf5
diff --git a/app/prod/checkpoints/LSTM_Chem-12-0.28.hdf5 b/app/prod/checkpoints/LSTM_Chem-12-0.28.hdf5
new file mode 100644
index 0000000..2224b23
--- /dev/null
+++ b/app/prod/checkpoints/LSTM_Chem-12-0.28.hdf5
diff --git a/app/prod/checkpoints/LSTM_Chem-13-0.28.hdf5 b/app/prod/checkpoints/LSTM_Chem-13-0.28.hdf5
new file mode 100644
index 0000000..8e3063e
--- /dev/null
+++ b/app/prod/checkpoints/LSTM_Chem-13-0.28.hdf5
diff --git a/app/prod/checkpoints/LSTM_Chem-14-0.27.hdf5 b/app/prod/checkpoints/LSTM_Chem-14-0.27.hdf5
new file mode 100644
index 0000000..39b1722
--- /dev/null
+++ b/app/prod/checkpoints/LSTM_Chem-14-0.27.hdf5
diff --git a/app/prod/checkpoints/LSTM_Chem-15-0.27.hdf5 b/app/prod/checkpoints/LSTM_Chem-15-0.27.hdf5
new file mode 100644
index 0000000..57f2a61
--- /dev/null
+++ b/app/prod/checkpoints/LSTM_Chem-15-0.27.hdf5
diff --git a/app/prod/checkpoints/LSTM_Chem-16-0.26.hdf5 b/app/prod/checkpoints/LSTM_Chem-16-0.26.hdf5
new file mode 100644
index 0000000..d60637a
--- /dev/null
+++ b/app/prod/checkpoints/LSTM_Chem-16-0.26.hdf5
diff --git a/app/prod/checkpoints/LSTM_Chem-17-0.26.hdf5 b/app/prod/checkpoints/LSTM_Chem-17-0.26.hdf5
new file mode 100644
index 0000000..7bdaa43
--- /dev/null
+++ b/app/prod/checkpoints/LSTM_Chem-17-0.26.hdf5
diff --git a/app/prod/checkpoints/LSTM_Chem-18-0.26.hdf5 b/app/prod/checkpoints/LSTM_Chem-18-0.26.hdf5
new file mode 100644
index 0000000..e8d04cd
--- /dev/null
+++ b/app/prod/checkpoints/LSTM_Chem-18-0.26.hdf5
diff --git a/app/prod/checkpoints/LSTM_Chem-19-0.26.hdf5 b/app/prod/checkpoints/LSTM_Chem-19-0.26.hdf5
new file mode 100644
index 0000000..a61d1d4
--- /dev/null
+++ b/app/prod/checkpoints/LSTM_Chem-19-0.26.hdf5
diff --git a/app/prod/checkpoints/LSTM_Chem-20-0.26.hdf5 b/app/prod/checkpoints/LSTM_Chem-20-0.26.hdf5
new file mode 100644
index 0000000..3c50da0
--- /dev/null
+++ b/app/prod/checkpoints/LSTM_Chem-20-0.26.hdf5
diff --git a/app/prod/checkpoints/LSTM_Chem-21-0.25.hdf5 b/app/prod/checkpoints/LSTM_Chem-21-0.25.hdf5
new file mode 100644
index 0000000..f5eed7f
--- /dev/null
+++ b/app/prod/checkpoints/LSTM_Chem-21-0.25.hdf5
diff --git a/app/prod/checkpoints/LSTM_Chem-22-0.25.hdf5 b/app/prod/checkpoints/LSTM_Chem-22-0.25.hdf5
new file mode 100644
index 0000000..21a1c98
--- /dev/null
+++ b/app/prod/checkpoints/LSTM_Chem-22-0.25.hdf5
diff --git a/app/prod/checkpoints/LSTM_Chem-23-0.25.hdf5 b/app/prod/checkpoints/LSTM_Chem-23-0.25.hdf5
new file mode 100644
index 0000000..21c6a8f
--- /dev/null
+++ b/app/prod/checkpoints/LSTM_Chem-23-0.25.hdf5
diff --git a/app/prod/checkpoints/LSTM_Chem-24-0.25.hdf5 b/app/prod/checkpoints/LSTM_Chem-24-0.25.hdf5
new file mode 100644
index 0000000..4a83e46
--- /dev/null
+++ b/app/prod/checkpoints/LSTM_Chem-24-0.25.hdf5
diff --git a/app/prod/checkpoints/LSTM_Chem-25-0.25.hdf5 b/app/prod/checkpoints/LSTM_Chem-25-0.25.hdf5
new file mode 100644
index 0000000..e3c2126
--- /dev/null
+++ b/app/prod/checkpoints/LSTM_Chem-25-0.25.hdf5
diff --git a/app/prod/checkpoints/LSTM_Chem-26-0.25.hdf5 b/app/prod/checkpoints/LSTM_Chem-26-0.25.hdf5
new file mode 100644
index 0000000..f36f1b6
--- /dev/null
+++ b/app/prod/checkpoints/LSTM_Chem-26-0.25.hdf5
diff --git a/app/prod/checkpoints/LSTM_Chem-27-0.24.hdf5 b/app/prod/checkpoints/LSTM_Chem-27-0.24.hdf5
new file mode 100644
index 0000000..e9b5134
--- /dev/null
+++ b/app/prod/checkpoints/LSTM_Chem-27-0.24.hdf5
diff --git a/app/prod/checkpoints/LSTM_Chem-28-0.24.hdf5 b/app/prod/checkpoints/LSTM_Chem-28-0.24.hdf5
new file mode 100644
index 0000000..2226f68
--- /dev/null
+++ b/app/prod/checkpoints/LSTM_Chem-28-0.24.hdf5
diff --git a/app/prod/checkpoints/LSTM_Chem-29-0.24.hdf5 b/app/prod/checkpoints/LSTM_Chem-29-0.24.hdf5
new file mode 100644
index 0000000..aaee10f
--- /dev/null
+++ b/app/prod/checkpoints/LSTM_Chem-29-0.24.hdf5
diff --git a/app/prod/checkpoints/LSTM_Chem-30-0.24.hdf5 b/app/prod/checkpoints/LSTM_Chem-30-0.24.hdf5
new file mode 100644
index 0000000..1a9bf6a
--- /dev/null
+++ b/app/prod/checkpoints/LSTM_Chem-30-0.24.hdf5
diff --git a/app/prod/checkpoints/LSTM_Chem-31-0.24.hdf5 b/app/prod/checkpoints/LSTM_Chem-31-0.24.hdf5
new file mode 100644
index 0000000..2d3d8ff
--- /dev/null
+++ b/app/prod/checkpoints/LSTM_Chem-31-0.24.hdf5
diff --git a/app/prod/checkpoints/LSTM_Chem-32-0.24.hdf5 b/app/prod/checkpoints/LSTM_Chem-32-0.24.hdf5
new file mode 100644
index 0000000..ec54aa3
--- /dev/null
+++ b/app/prod/checkpoints/LSTM_Chem-32-0.24.hdf5
diff --git a/app/prod/checkpoints/LSTM_Chem-33-0.24.hdf5 b/app/prod/checkpoints/LSTM_Chem-33-0.24.hdf5
new file mode 100644
index 0000000..8adf067
--- /dev/null
+++ b/app/prod/checkpoints/LSTM_Chem-33-0.24.hdf5
diff --git a/app/prod/checkpoints/LSTM_Chem-34-0.24.hdf5 b/app/prod/checkpoints/LSTM_Chem-34-0.24.hdf5
new file mode 100644
index 0000000..76519de
--- /dev/null
+++ b/app/prod/checkpoints/LSTM_Chem-34-0.24.hdf5
diff --git a/app/prod/checkpoints/LSTM_Chem-35-0.24.hdf5 b/app/prod/checkpoints/LSTM_Chem-35-0.24.hdf5
new file mode 100644
index 0000000..d85fde1
--- /dev/null
+++ b/app/prod/checkpoints/LSTM_Chem-35-0.24.hdf5
diff --git a/app/prod/checkpoints/LSTM_Chem-36-0.24.hdf5 b/app/prod/checkpoints/LSTM_Chem-36-0.24.hdf5
new file mode 100644
index 0000000..d30fbe3
--- /dev/null
+++ b/app/prod/checkpoints/LSTM_Chem-36-0.24.hdf5
diff --git a/app/prod/checkpoints/LSTM_Chem-37-0.24.hdf5 b/app/prod/checkpoints/LSTM_Chem-37-0.24.hdf5
new file mode 100644
index 0000000..56c1f4c
--- /dev/null
+++ b/app/prod/checkpoints/LSTM_Chem-37-0.24.hdf5
diff --git a/app/prod/checkpoints/LSTM_Chem-38-0.24.hdf5 b/app/prod/checkpoints/LSTM_Chem-38-0.24.hdf5
new file mode 100644
index 0000000..77f1542
--- /dev/null
+++ b/app/prod/checkpoints/LSTM_Chem-38-0.24.hdf5
diff --git a/app/prod/checkpoints/LSTM_Chem-39-0.23.hdf5 b/app/prod/checkpoints/LSTM_Chem-39-0.23.hdf5
new file mode 100644
index 0000000..f2309e0
--- /dev/null
+++ b/app/prod/checkpoints/LSTM_Chem-39-0.23.hdf5
diff --git a/app/prod/checkpoints/LSTM_Chem-40-0.23.hdf5 b/app/prod/checkpoints/LSTM_Chem-40-0.23.hdf5
new file mode 100644
index 0000000..1938a09
--- /dev/null
+++ b/app/prod/checkpoints/LSTM_Chem-40-0.23.hdf5
diff --git a/app/prod/checkpoints/LSTM_Chem-41-0.23.hdf5 b/app/prod/checkpoints/LSTM_Chem-41-0.23.hdf5
new file mode 100644
index 0000000..b43d8f5
--- /dev/null
+++ b/app/prod/checkpoints/LSTM_Chem-41-0.23.hdf5
diff --git a/app/prod/checkpoints/LSTM_Chem-42-0.23.hdf5 b/app/prod/checkpoints/LSTM_Chem-42-0.23.hdf5
new file mode 100644
index 0000000..717ab2d
--- /dev/null
+++ b/app/prod/checkpoints/LSTM_Chem-42-0.23.hdf5
diff --git a/app/prod/config.json b/app/prod/config.json
new file mode 100644
index 0000000..4b72262
--- /dev/null
+++ b/app/prod/config.json
@@ -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
diff --git a/app/prod/logs/train/events.out.tfevents.1594644989.Jiamin.local.31642.1238.v2 b/app/prod/logs/train/events.out.tfevents.1594644989.Jiamin.local.31642.1238.v2
new file mode 100644
index 0000000..52526ff
--- /dev/null
+++ b/app/prod/logs/train/events.out.tfevents.1594644989.Jiamin.local.31642.1238.v2
diff --git a/app/prod/logs/train/events.out.tfevents.1594645021.Jiamin.local.profile-empty b/app/prod/logs/train/events.out.tfevents.1594645021.Jiamin.local.profile-empty
new file mode 100644
index 0000000..94d6821
--- /dev/null
+++ b/app/prod/logs/train/events.out.tfevents.1594645021.Jiamin.local.profile-empty
diff --git a/app/prod/logs/train/plugins/profile/2020_07_13_20_57_01/Jiamin.local.input_pipeline.pb b/app/prod/logs/train/plugins/profile/2020_07_13_20_57_01/Jiamin.local.input_pipeline.pb
new file mode 100644
index 0000000..2555aa7
--- /dev/null
+++ b/app/prod/logs/train/plugins/profile/2020_07_13_20_57_01/Jiamin.local.input_pipeline.pb
diff --git a/app/prod/logs/train/plugins/profile/2020_07_13_20_57_01/Jiamin.local.kernel_stats.pb b/app/prod/logs/train/plugins/profile/2020_07_13_20_57_01/Jiamin.local.kernel_stats.pb
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/app/prod/logs/train/plugins/profile/2020_07_13_20_57_01/Jiamin.local.kernel_stats.pb
diff --git a/app/prod/logs/train/plugins/profile/2020_07_13_20_57_01/Jiamin.local.overview_page.pb b/app/prod/logs/train/plugins/profile/2020_07_13_20_57_01/Jiamin.local.overview_page.pb
new file mode 100644
index 0000000..18cffd7
--- /dev/null
+++ b/app/prod/logs/train/plugins/profile/2020_07_13_20_57_01/Jiamin.local.overview_page.pb
diff --git a/app/prod/logs/train/plugins/profile/2020_07_13_20_57_01/Jiamin.local.tensorflow_stats.pb b/app/prod/logs/train/plugins/profile/2020_07_13_20_57_01/Jiamin.local.tensorflow_stats.pb
new file mode 100644
index 0000000..8c5eb9e
--- /dev/null
+++ b/app/prod/logs/train/plugins/profile/2020_07_13_20_57_01/Jiamin.local.tensorflow_stats.pb
diff --git a/app/prod/logs/train/plugins/profile/2020_07_13_20_57_01/Jiamin.local.trace.json.gz b/app/prod/logs/train/plugins/profile/2020_07_13_20_57_01/Jiamin.local.trace.json.gz
new file mode 100644
index 0000000..9e4ffce
--- /dev/null
+++ b/app/prod/logs/train/plugins/profile/2020_07_13_20_57_01/Jiamin.local.trace.json.gz
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
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