Best model using DeepSTARR layout with K562 data

Downsampling was unbiased, loss function was MSE.

K562/DeepSTARR-BlueSTARR/K562-4.h5

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+size 2919176

K562/DeepSTARR-BlueSTARR/K562-4.json

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{"module": "keras.initializers", "class_name": "Ones", "config": {}, "registered_name": null}, "moving_mean_initializer": {"module": "keras.initializers", "class_name": "Zeros", "config": {}, "registered_name": null}, "moving_variance_initializer": {"module": "keras.initializers", "class_name": "Ones", "config": {}, "registered_name": null}, "beta_regularizer": null, "gamma_regularizer": null, "beta_constraint": null, "gamma_constraint": null}, "registered_name": null, "build_config": {"input_shape": [null, 37, 120]}, "name": "batch_normalization_3", "inbound_nodes": [[["conv1d_3", 0, 0, {}]]]}, {"module": "keras.layers", "class_name": "Activation", "config": {"name": "activation_3", "trainable": true, "dtype": "float32", "activation": "relu"}, "registered_name": null, "build_config": {"input_shape": [null, 37, 120]}, "name": "activation_3", "inbound_nodes": [[["batch_normalization_3", 0, 0, {}]]]}, {"module": "keras.layers", "class_name": "MaxPooling1D", "config": {"name": "max_pooling1d_3", "trainable": true, "dtype": "float32", "strides": [2], "pool_size": [2], "padding": "valid", "data_format": "channels_last"}, "registered_name": null, "build_config": {"input_shape": [null, 37, 120]}, "name": "max_pooling1d_3", "inbound_nodes": [[["activation_3", 0, 0, {}]]]}, {"module": "keras.layers", "class_name": "Flatten", "config": {"name": "flatten", "trainable": true, "dtype": "float32", "data_format": "channels_last"}, "registered_name": null, "build_config": {"input_shape": [null, 18, 120]}, "name": "flatten", "inbound_nodes": [[["max_pooling1d_3", 0, 0, {}]]]}, {"module": "keras.layers", "class_name": "Dense", "config": {"name": "dense", "trainable": true, "dtype": "float32", "units": 256, "activation": "linear", "use_bias": true, "kernel_initializer": {"module": "keras.initializers", "class_name": "GlorotUniform", "config": {"seed": null}, "registered_name": null}, "bias_initializer": {"module": "keras.initializers", "class_name": "Zeros", "config": {}, "registered_name": null}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "registered_name": null, "build_config": {"input_shape": [null, 2160]}, "name": "dense", "inbound_nodes": [[["flatten", 0, 0, {}]]]}, {"module": "keras.layers", "class_name": "BatchNormalization", "config": {"name": "batch_normalization_4", "trainable": true, "dtype": "float32", "axis": [1], "momentum": 0.99, "epsilon": 0.001, "center": true, "scale": true, "beta_initializer": {"module": "keras.initializers", "class_name": "Zeros", "config": {}, "registered_name": null}, "gamma_initializer": {"module": "keras.initializers", "class_name": "Ones", "config": {}, "registered_name": null}, "moving_mean_initializer": {"module": "keras.initializers", "class_name": "Zeros", "config": {}, "registered_name": null}, "moving_variance_initializer": {"module": "keras.initializers", "class_name": "Ones", "config": {}, "registered_name": null}, "beta_regularizer": null, "gamma_regularizer": null, "beta_constraint": null, "gamma_constraint": null}, "registered_name": null, "build_config": {"input_shape": [null, 256]}, "name": "batch_normalization_4", "inbound_nodes": [[["dense", 0, 0, {}]]]}, {"module": "keras.layers", "class_name": "Activation", "config": {"name": "activation_4", "trainable": true, "dtype": "float32", "activation": "relu"}, "registered_name": null, "build_config": {"input_shape": [null, 256]}, "name": "activation_4", "inbound_nodes": [[["batch_normalization_4", 0, 0, {}]]]}, {"module": "keras.layers", "class_name": "Dropout", "config": {"name": "dropout", "trainable": true, "dtype": "float32", "rate": 0.4, "noise_shape": null, "seed": null}, "registered_name": null, "build_config": {"input_shape": [null, 256]}, "name": "dropout", "inbound_nodes": [[["activation_4", 0, 0, {}]]]}, {"module": "keras.layers", "class_name": "Dense", "config": {"name": "dense_1", "trainable": true, "dtype": "float32", 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"config": {}, "registered_name": null}, "moving_mean_initializer": {"module": "keras.initializers", "class_name": "Zeros", "config": {}, "registered_name": null}, "moving_variance_initializer": {"module": "keras.initializers", "class_name": "Ones", "config": {}, "registered_name": null}, "beta_regularizer": null, "gamma_regularizer": null, "beta_constraint": null, "gamma_constraint": null}, "registered_name": null, "build_config": {"input_shape": [null, 256]}, "name": "batch_normalization_5", "inbound_nodes": [[["dense_1", 0, 0, {}]]]}, {"module": "keras.layers", "class_name": "Activation", "config": {"name": "activation_5", "trainable": true, "dtype": "float32", "activation": "relu"}, "registered_name": null, "build_config": {"input_shape": [null, 256]}, "name": "activation_5", "inbound_nodes": [[["batch_normalization_5", 0, 0, {}]]]}, {"module": "keras.layers", "class_name": "Dropout", "config": {"name": "dropout_1", "trainable": true, "dtype": "float32", "rate": 0.4, "noise_shape": null, "seed": null}, "registered_name": null, "build_config": {"input_shape": [null, 256]}, "name": "dropout_1", "inbound_nodes": [[["activation_5", 0, 0, {}]]]}, {"module": "keras.layers", "class_name": "Dense", "config": {"name": "K562", "trainable": true, "dtype": "float32", "units": 1, "activation": "linear", "use_bias": true, "kernel_initializer": {"module": "keras.initializers", "class_name": "GlorotUniform", "config": {"seed": null}, "registered_name": null}, "bias_initializer": {"module": "keras.initializers", "class_name": "Zeros", "config": {}, "registered_name": null}, "kernel_regularizer": null, "bias_regularizer": null, "activity_regularizer": null, "kernel_constraint": null, "bias_constraint": null}, "registered_name": null, "build_config": {"input_shape": [null, 256]}, "name": "K562", "inbound_nodes": [[["dropout_1", 0, 0, {}]]]}], "input_layers": [["input_1", 0, 0]], "output_layers": [["K562", 0, 0]]}, "keras_version": "2.15.0", "backend": "tensorflow"}

K562/DeepSTARR-BlueSTARR/K562_DeepSTARR.config

@@ -0,0 +1,31 @@
+UseCustomLoss = 0
+Tasks = K562
+TaskWeights = 1
+Verbose = 2
+NumConvLayers = 4
+KernelSizes = 7,3,5,3
+NumKernels = 246,60,60,120
+MaxTrain=3000000 
+MaxTest=999999999
+ShouldTest=1
+Epochs = 200
+
+RevComp = 0
+BatchSize = 128
+EarlyStop = 10
+DropoutRate = 0.4
+LearningRate = 0.002
+ConvResidualSkip = 0
+ConvDropout = 0
+ConvPad = same
+DilationFactor = 1
+ConvPoolSize = 2
+Flatten = 1
+GlobalMaxPool = 0
+GlobalAvePool = 0
+NumDense = 2
+DenseSizes = 256,256
+NumAttentionLayers = 0
+AttentionHeads = 0
+AttentionKeyDim = 0
+AttentionResidualSkip = 0