Skip to content

Commit

Permalink
Merge pull request #17 from yuenler/master
Browse files Browse the repository at this point in the history
LSA pearson correlation results
  • Loading branch information
yuenler authored Jan 19, 2022
2 parents ad3a7fa + 4390268 commit 7c1762b
Show file tree
Hide file tree
Showing 105 changed files with 11,150 additions and 4,926 deletions.
5 changes: 5 additions & 0 deletions L1000/2.train/L1000_reconstruction_metrics.csv
Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
Dataset,VAE,MSE,MSE (Shuffled),Earthmoving,Earthmoving (Shuffled),Earthmoving 5%,Earthmoving 95%,Earthmoving (Shuffled) 5%,Earthmoving (Shuffled) 95%
L1000,Vanilla,0.8452037119390484,1.8494362563126334,0.24882394445956826,0.6103021723670797,0.13763955289541702,0.36123248685914006,0.2790123081418029,1.9438669504238144
L1000,Beta,1.227905820132029,2.1046103081084775,0.4453626099456877,0.6702414785941746,0.2263430389957201,0.7269319835774611,0.2926499691366904,2.2536070693381958
L1000,MMD,1.2725735604257578,2.049749648975954,0.4754432099300577,0.641324975648471,0.24814199525352032,0.7859128293564865,0.2870699983553745,2.0271593721014685
L1000,PCA,0.9176796412742804,3.1799392613294652,0.26463339115417855,0.5748642519295448,0.1791305240932723,0.3850971279437799,0.23937094375381135,2.022195479900004
200 changes: 180 additions & 20 deletions L1000/2.train/generate reconstruction figure L1000.ipynb

Large diffs are not rendered by default.

2,059 changes: 1,159 additions & 900 deletions L1000/2.train/generate training curve.ipynb

Large diffs are not rendered by default.

Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@

�root"_tf_keras_network*�{"name": "model_1", "trainable": true, "expects_training_arg": true, "dtype": "float32", "batch_input_shape": null, "must_restore_from_config": false, "class_name": "Functional", "config": {"name": "model_1", "layers": [{"class_name": "InputLayer", "config": {"batch_input_shape": {"class_name": "__tuple__", "items": [null, 65]}, "dtype": "float32", "sparse": false, "ragged": false, "name": "input_2"}, "name": "input_2", "inbound_nodes": []}, {"class_name": "Dense", "config": {"name": "dense_3", "trainable": true, "dtype": "float32", "units": 500, "activation": "lrelu", "use_bias": true, "kernel_initializer": {"class_name": "GlorotUniform", "config": {"seed": null}}, "bias_initializer": {"class_name": "Zeros", "config": {}}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "name": "dense_3", "inbound_nodes": [[["input_2", 0, 0, {}]]]}, {"class_name": "Dense", "config": {"name": "dense_4", "trainable": true, "dtype": "float32", "units": 978, "activation": "linear", "use_bias": true, "kernel_initializer": {"class_name": "GlorotUniform", "config": {"seed": null}}, "bias_initializer": {"class_name": "Zeros", "config": {}}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "name": "dense_4", "inbound_nodes": [[["dense_3", 0, 0, {}]]]}], "input_layers": [["input_2", 0, 0]], "output_layers": [["dense_4", 0, 0]]}, "shared_object_id": 7, "input_spec": [{"class_name": "InputSpec", "config": {"dtype": null, "shape": {"class_name": "__tuple__", "items": [null, 65]}, "ndim": 2, "max_ndim": null, "min_ndim": null, "axes": {}}}], "build_input_shape": {"class_name": "TensorShape", "items": [null, 65]}, "is_graph_network": true, "full_save_spec": {"class_name": "__tuple__", "items": [[{"class_name": "TypeSpec", "type_spec": "tf.TensorSpec", "serialized": [{"class_name": "TensorShape", "items": [null, 65]}, "float32", "input_2"]}], {}]}, "save_spec": {"class_name": "TypeSpec", "type_spec": "tf.TensorSpec", "serialized": [{"class_name": "TensorShape", "items": [null, 65]}, "float32", "input_2"]}, "keras_version": "2.6.0", "backend": "tensorflow", "model_config": {"class_name": "Functional", "config": {"name": "model_1", "layers": [{"class_name": "InputLayer", "config": {"batch_input_shape": {"class_name": "__tuple__", "items": [null, 65]}, "dtype": "float32", "sparse": false, "ragged": false, "name": "input_2"}, "name": "input_2", "inbound_nodes": [], "shared_object_id": 0}, {"class_name": "Dense", "config": {"name": "dense_3", "trainable": true, "dtype": "float32", "units": 500, "activation": "lrelu", "use_bias": true, "kernel_initializer": {"class_name": "GlorotUniform", "config": {"seed": null}, "shared_object_id": 1}, "bias_initializer": {"class_name": "Zeros", "config": {}, "shared_object_id": 2}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "name": "dense_3", "inbound_nodes": [[["input_2", 0, 0, {}]]], "shared_object_id": 3}, {"class_name": "Dense", "config": {"name": "dense_4", "trainable": true, "dtype": "float32", "units": 978, "activation": "linear", "use_bias": true, "kernel_initializer": {"class_name": "GlorotUniform", "config": {"seed": null}, "shared_object_id": 4}, "bias_initializer": {"class_name": "Zeros", "config": {}, "shared_object_id": 5}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "name": "dense_4", "inbound_nodes": [[["dense_3", 0, 0, {}]]], "shared_object_id": 6}], "input_layers": [["input_2", 0, 0]], "output_layers": [["dense_4", 0, 0]]}}}2
� root.layer-0"_tf_keras_input_layer*�{"class_name": "InputLayer", "name": "input_2", "dtype": "float32", "sparse": false, "ragged": false, "batch_input_shape": {"class_name": "__tuple__", "items": [null, 65]}, "config": {"batch_input_shape": {"class_name": "__tuple__", "items": [null, 65]}, "dtype": "float32", "sparse": false, "ragged": false, "name": "input_2"}}2
�root.layer_with_weights-0"_tf_keras_layer*�{"name": "dense_3", "trainable": true, "expects_training_arg": false, "dtype": "float32", "batch_input_shape": null, "stateful": false, "must_restore_from_config": false, "class_name": "Dense", "config": {"name": "dense_3", "trainable": true, "dtype": "float32", "units": 500, "activation": "lrelu", "use_bias": true, "kernel_initializer": {"class_name": "GlorotUniform", "config": {"seed": null}, "shared_object_id": 1}, "bias_initializer": {"class_name": "Zeros", "config": {}, "shared_object_id": 2}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "inbound_nodes": [[["input_2", 0, 0, {}]]], "shared_object_id": 3, "input_spec": {"class_name": "InputSpec", "config": {"dtype": null, "shape": null, "ndim": null, "max_ndim": null, "min_ndim": 2, "axes": {"-1": 65}}, "shared_object_id": 9}, "build_input_shape": {"class_name": "TensorShape", "items": [null, 65]}}2
�root.layer_with_weights-1"_tf_keras_layer*�{"name": "dense_4", "trainable": true, "expects_training_arg": false, "dtype": "float32", "batch_input_shape": null, "stateful": false, "must_restore_from_config": false, "class_name": "Dense", "config": {"name": "dense_4", "trainable": true, "dtype": "float32", "units": 978, "activation": "linear", "use_bias": true, "kernel_initializer": {"class_name": "GlorotUniform", "config": {"seed": null}, "shared_object_id": 4}, "bias_initializer": {"class_name": "Zeros", "config": {}, "shared_object_id": 5}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "inbound_nodes": [[["dense_3", 0, 0, {}]]], "shared_object_id": 6, "input_spec": {"class_name": "InputSpec", "config": {"dtype": null, "shape": null, "ndim": null, "max_ndim": null, "min_ndim": 2, "axes": {"-1": 500}}, "shared_object_id": 10}, "build_input_shape": {"class_name": "TensorShape", "items": [null, 500]}}2
Binary file not shown.
Binary file not shown.
Binary file not shown.
Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@

�root"_tf_keras_network*�{"name": "model_1", "trainable": true, "expects_training_arg": true, "dtype": "float32", "batch_input_shape": null, "must_restore_from_config": false, "class_name": "Functional", "config": {"name": "model_1", "layers": [{"class_name": "InputLayer", "config": {"batch_input_shape": {"class_name": "__tuple__", "items": [null, 65]}, "dtype": "float32", "sparse": false, "ragged": false, "name": "input_2"}, "name": "input_2", "inbound_nodes": []}, {"class_name": "Dense", "config": {"name": "dense_3", "trainable": true, "dtype": "float32", "units": 500, "activation": "lrelu", "use_bias": true, "kernel_initializer": {"class_name": "GlorotUniform", "config": {"seed": null}}, "bias_initializer": {"class_name": "Zeros", "config": {}}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "name": "dense_3", "inbound_nodes": [[["input_2", 0, 0, {}]]]}, {"class_name": "Dense", "config": {"name": "dense_4", "trainable": true, "dtype": "float32", "units": 978, "activation": "linear", "use_bias": true, "kernel_initializer": {"class_name": "GlorotUniform", "config": {"seed": null}}, "bias_initializer": {"class_name": "Zeros", "config": {}}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "name": "dense_4", "inbound_nodes": [[["dense_3", 0, 0, {}]]]}], "input_layers": [["input_2", 0, 0]], "output_layers": [["dense_4", 0, 0]]}, "shared_object_id": 7, "input_spec": [{"class_name": "InputSpec", "config": {"dtype": null, "shape": {"class_name": "__tuple__", "items": [null, 65]}, "ndim": 2, "max_ndim": null, "min_ndim": null, "axes": {}}}], "build_input_shape": {"class_name": "TensorShape", "items": [null, 65]}, "is_graph_network": true, "full_save_spec": {"class_name": "__tuple__", "items": [[{"class_name": "TypeSpec", "type_spec": "tf.TensorSpec", "serialized": [{"class_name": "TensorShape", "items": [null, 65]}, "float32", "input_2"]}], {}]}, "save_spec": {"class_name": "TypeSpec", "type_spec": "tf.TensorSpec", "serialized": [{"class_name": "TensorShape", "items": [null, 65]}, "float32", "input_2"]}, "keras_version": "2.6.0", "backend": "tensorflow", "model_config": {"class_name": "Functional", "config": {"name": "model_1", "layers": [{"class_name": "InputLayer", "config": {"batch_input_shape": {"class_name": "__tuple__", "items": [null, 65]}, "dtype": "float32", "sparse": false, "ragged": false, "name": "input_2"}, "name": "input_2", "inbound_nodes": [], "shared_object_id": 0}, {"class_name": "Dense", "config": {"name": "dense_3", "trainable": true, "dtype": "float32", "units": 500, "activation": "lrelu", "use_bias": true, "kernel_initializer": {"class_name": "GlorotUniform", "config": {"seed": null}, "shared_object_id": 1}, "bias_initializer": {"class_name": "Zeros", "config": {}, "shared_object_id": 2}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "name": "dense_3", "inbound_nodes": [[["input_2", 0, 0, {}]]], "shared_object_id": 3}, {"class_name": "Dense", "config": {"name": "dense_4", "trainable": true, "dtype": "float32", "units": 978, "activation": "linear", "use_bias": true, "kernel_initializer": {"class_name": "GlorotUniform", "config": {"seed": null}, "shared_object_id": 4}, "bias_initializer": {"class_name": "Zeros", "config": {}, "shared_object_id": 5}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "name": "dense_4", "inbound_nodes": [[["dense_3", 0, 0, {}]]], "shared_object_id": 6}], "input_layers": [["input_2", 0, 0]], "output_layers": [["dense_4", 0, 0]]}}}2
� root.layer-0"_tf_keras_input_layer*�{"class_name": "InputLayer", "name": "input_2", "dtype": "float32", "sparse": false, "ragged": false, "batch_input_shape": {"class_name": "__tuple__", "items": [null, 65]}, "config": {"batch_input_shape": {"class_name": "__tuple__", "items": [null, 65]}, "dtype": "float32", "sparse": false, "ragged": false, "name": "input_2"}}2
�root.layer_with_weights-0"_tf_keras_layer*�{"name": "dense_3", "trainable": true, "expects_training_arg": false, "dtype": "float32", "batch_input_shape": null, "stateful": false, "must_restore_from_config": false, "class_name": "Dense", "config": {"name": "dense_3", "trainable": true, "dtype": "float32", "units": 500, "activation": "lrelu", "use_bias": true, "kernel_initializer": {"class_name": "GlorotUniform", "config": {"seed": null}, "shared_object_id": 1}, "bias_initializer": {"class_name": "Zeros", "config": {}, "shared_object_id": 2}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "inbound_nodes": [[["input_2", 0, 0, {}]]], "shared_object_id": 3, "input_spec": {"class_name": "InputSpec", "config": {"dtype": null, "shape": null, "ndim": null, "max_ndim": null, "min_ndim": 2, "axes": {"-1": 65}}, "shared_object_id": 9}, "build_input_shape": {"class_name": "TensorShape", "items": [null, 65]}}2
�root.layer_with_weights-1"_tf_keras_layer*�{"name": "dense_4", "trainable": true, "expects_training_arg": false, "dtype": "float32", "batch_input_shape": null, "stateful": false, "must_restore_from_config": false, "class_name": "Dense", "config": {"name": "dense_4", "trainable": true, "dtype": "float32", "units": 978, "activation": "linear", "use_bias": true, "kernel_initializer": {"class_name": "GlorotUniform", "config": {"seed": null}, "shared_object_id": 4}, "bias_initializer": {"class_name": "Zeros", "config": {}, "shared_object_id": 5}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "inbound_nodes": [[["dense_3", 0, 0, {}]]], "shared_object_id": 6, "input_spec": {"class_name": "InputSpec", "config": {"dtype": null, "shape": null, "ndim": null, "max_ndim": null, "min_ndim": 2, "axes": {"-1": 500}}, "shared_object_id": 10}, "build_input_shape": {"class_name": "TensorShape", "items": [null, 500]}}2
Binary file not shown.
Binary file not shown.
Binary file not shown.
Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@

�root"_tf_keras_network*�{"name": "model_3", "trainable": true, "expects_training_arg": true, "dtype": "float32", "batch_input_shape": null, "must_restore_from_config": false, "class_name": "Functional", "config": {"name": "model_3", "layers": [{"class_name": "InputLayer", "config": {"batch_input_shape": {"class_name": "__tuple__", "items": [null, 65]}, "dtype": "float32", "sparse": false, "ragged": false, "name": "input_4"}, "name": "input_4", "inbound_nodes": []}, {"class_name": "Dense", "config": {"name": "dense_8", "trainable": true, "dtype": "float32", "units": 500, "activation": "lrelu", "use_bias": true, "kernel_initializer": {"class_name": "GlorotUniform", "config": {"seed": null}}, "bias_initializer": {"class_name": "Zeros", "config": {}}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "name": "dense_8", "inbound_nodes": [[["input_4", 0, 0, {}]]]}, {"class_name": "Dense", "config": {"name": "dense_9", "trainable": true, "dtype": "float32", "units": 978, "activation": "linear", "use_bias": true, "kernel_initializer": {"class_name": "GlorotUniform", "config": {"seed": null}}, "bias_initializer": {"class_name": "Zeros", "config": {}}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "name": "dense_9", "inbound_nodes": [[["dense_8", 0, 0, {}]]]}], "input_layers": [["input_4", 0, 0]], "output_layers": [["dense_9", 0, 0]]}, "shared_object_id": 7, "input_spec": [{"class_name": "InputSpec", "config": {"dtype": null, "shape": {"class_name": "__tuple__", "items": [null, 65]}, "ndim": 2, "max_ndim": null, "min_ndim": null, "axes": {}}}], "build_input_shape": {"class_name": "TensorShape", "items": [null, 65]}, "is_graph_network": true, "full_save_spec": {"class_name": "__tuple__", "items": [[{"class_name": "TypeSpec", "type_spec": "tf.TensorSpec", "serialized": [{"class_name": "TensorShape", "items": [null, 65]}, "float32", "input_4"]}], {}]}, "save_spec": {"class_name": "TypeSpec", "type_spec": "tf.TensorSpec", "serialized": [{"class_name": "TensorShape", "items": [null, 65]}, "float32", "input_4"]}, "keras_version": "2.6.0", "backend": "tensorflow", "model_config": {"class_name": "Functional", "config": {"name": "model_3", "layers": [{"class_name": "InputLayer", "config": {"batch_input_shape": {"class_name": "__tuple__", "items": [null, 65]}, "dtype": "float32", "sparse": false, "ragged": false, "name": "input_4"}, "name": "input_4", "inbound_nodes": [], "shared_object_id": 0}, {"class_name": "Dense", "config": {"name": "dense_8", "trainable": true, "dtype": "float32", "units": 500, "activation": "lrelu", "use_bias": true, "kernel_initializer": {"class_name": "GlorotUniform", "config": {"seed": null}, "shared_object_id": 1}, "bias_initializer": {"class_name": "Zeros", "config": {}, "shared_object_id": 2}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "name": "dense_8", "inbound_nodes": [[["input_4", 0, 0, {}]]], "shared_object_id": 3}, {"class_name": "Dense", "config": {"name": "dense_9", "trainable": true, "dtype": "float32", "units": 978, "activation": "linear", "use_bias": true, "kernel_initializer": {"class_name": "GlorotUniform", "config": {"seed": null}, "shared_object_id": 4}, "bias_initializer": {"class_name": "Zeros", "config": {}, "shared_object_id": 5}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "name": "dense_9", "inbound_nodes": [[["dense_8", 0, 0, {}]]], "shared_object_id": 6}], "input_layers": [["input_4", 0, 0]], "output_layers": [["dense_9", 0, 0]]}}}2
� root.layer-0"_tf_keras_input_layer*�{"class_name": "InputLayer", "name": "input_4", "dtype": "float32", "sparse": false, "ragged": false, "batch_input_shape": {"class_name": "__tuple__", "items": [null, 65]}, "config": {"batch_input_shape": {"class_name": "__tuple__", "items": [null, 65]}, "dtype": "float32", "sparse": false, "ragged": false, "name": "input_4"}}2
�root.layer_with_weights-0"_tf_keras_layer*�{"name": "dense_8", "trainable": true, "expects_training_arg": false, "dtype": "float32", "batch_input_shape": null, "stateful": false, "must_restore_from_config": false, "class_name": "Dense", "config": {"name": "dense_8", "trainable": true, "dtype": "float32", "units": 500, "activation": "lrelu", "use_bias": true, "kernel_initializer": {"class_name": "GlorotUniform", "config": {"seed": null}, "shared_object_id": 1}, "bias_initializer": {"class_name": "Zeros", "config": {}, "shared_object_id": 2}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "inbound_nodes": [[["input_4", 0, 0, {}]]], "shared_object_id": 3, "input_spec": {"class_name": "InputSpec", "config": {"dtype": null, "shape": null, "ndim": null, "max_ndim": null, "min_ndim": 2, "axes": {"-1": 65}}, "shared_object_id": 9}, "build_input_shape": {"class_name": "TensorShape", "items": [null, 65]}}2
�root.layer_with_weights-1"_tf_keras_layer*�{"name": "dense_9", "trainable": true, "expects_training_arg": false, "dtype": "float32", "batch_input_shape": null, "stateful": false, "must_restore_from_config": false, "class_name": "Dense", "config": {"name": "dense_9", "trainable": true, "dtype": "float32", "units": 978, "activation": "linear", "use_bias": true, "kernel_initializer": {"class_name": "GlorotUniform", "config": {"seed": null}, "shared_object_id": 4}, "bias_initializer": {"class_name": "Zeros", "config": {}, "shared_object_id": 5}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "inbound_nodes": [[["dense_8", 0, 0, {}]]], "shared_object_id": 6, "input_spec": {"class_name": "InputSpec", "config": {"dtype": null, "shape": null, "ndim": null, "max_ndim": null, "min_ndim": 2, "axes": {"-1": 500}}, "shared_object_id": 10}, "build_input_shape": {"class_name": "TensorShape", "items": [null, 500]}}2
Binary file not shown.
Binary file not shown.
Binary file not shown.
Loading

0 comments on commit 7c1762b

Please sign in to comment.