Best model for K562 data downsampled to 1M
Browse filesDownsampling was unbiased, loss function was MSE.
K562/Unbiased_downsampling/1M/K562-10.h5
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version https://git-lfs.github.com/spec/v1
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oid sha256:8ade915db058f2a614fea8576612eae8cdcae5f53fd3b94bbd39dfc62cb6bbe7
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size 63138304
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K562/Unbiased_downsampling/1M/K562-10.json
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{"class_name": "Functional", "config": {"name": "model", "trainable": true, "layers": [{"module": "keras.layers", "class_name": "InputLayer", "config": {"batch_input_shape": [null, 300, 4], "dtype": "float32", "sparse": false, "ragged": false, "name": "input_1"}, "registered_name": null, "name": "input_1", "inbound_nodes": []}, {"module": "keras.layers", "class_name": "Conv1D", "config": {"name": "conv1d", "trainable": true, "dtype": "float32", "filters": 1024, "kernel_size": [8], "strides": [1], "padding": "same", "data_format": "channels_last", "dilation_rate": [1], "groups": 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, 300, 4]}, "name": "conv1d", "inbound_nodes": [[["input_1", 0, 0, {}]]]}, {"module": "keras.layers", "class_name": "BatchNormalization", "config": {"name": "batch_normalization", "trainable": true, "dtype": "float32", "axis": [2], "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, 300, 1024]}, "name": "batch_normalization", "inbound_nodes": [[["conv1d", 0, 0, {}]]]}, {"module": "keras.layers", "class_name": "Activation", "config": {"name": "activation", "trainable": true, "dtype": "float32", "activation": "relu"}, "registered_name": null, "build_config": {"input_shape": [null, 300, 1024]}, "name": "activation", "inbound_nodes": [[["batch_normalization", 0, 0, {}]]]}, {"module": "keras.layers", "class_name": "Dropout", "config": {"name": "dropout", "trainable": true, "dtype": "float32", "rate": 0.5, "noise_shape": null, "seed": null}, "registered_name": null, "build_config": {"input_shape": [null, 300, 1024]}, "name": "dropout", "inbound_nodes": [[["activation", 0, 0, {}]]]}, {"module": "keras.layers", "class_name": "Conv1D", "config": {"name": "conv1d_1", "trainable": true, "dtype": "float32", "filters": 512, "kernel_size": [16], "strides": [1], "padding": "same", "data_format": "channels_last", "dilation_rate": [1], "groups": 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, 300, 1024]}, "name": "conv1d_1", "inbound_nodes": [[["dropout", 0, 0, {}]]]}, {"module": "keras.layers", "class_name": "BatchNormalization", "config": {"name": "batch_normalization_1", "trainable": true, "dtype": "float32", "axis": [2], "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, 300, 512]}, "name": "batch_normalization_1", "inbound_nodes": [[["conv1d_1", 0, 0, {}]]]}, {"module": "keras.layers", "class_name": "Activation", "config": {"name": "activation_1", "trainable": true, "dtype": "float32", "activation": "relu"}, "registered_name": null, "build_config": {"input_shape": [null, 300, 512]}, "name": "activation_1", "inbound_nodes": [[["batch_normalization_1", 0, 0, {}]]]}, {"module": "keras.layers", "class_name": "Dropout", "config": {"name": "dropout_1", "trainable": true, "dtype": "float32", "rate": 0.5, "noise_shape": null, "seed": null}, "registered_name": null, "build_config": {"input_shape": [null, 300, 512]}, "name": "dropout_1", "inbound_nodes": [[["activation_1", 0, 0, {}]]]}, {"module": "keras.layers", "class_name": "Conv1D", "config": {"name": "conv1d_2", "trainable": true, "dtype": "float32", "filters": 256, "kernel_size": [32], "strides": [1], "padding": "same", "data_format": "channels_last", "dilation_rate": [1], "groups": 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, 300, 512]}, "name": "conv1d_2", "inbound_nodes": [[["dropout_1", 0, 0, {}]]]}, {"module": "keras.layers", "class_name": "BatchNormalization", "config": {"name": "batch_normalization_2", "trainable": true, "dtype": "float32", "axis": [2], "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, 300, 256]}, "name": "batch_normalization_2", "inbound_nodes": [[["conv1d_2", 0, 0, {}]]]}, {"module": "keras.layers", "class_name": "Activation", "config": {"name": "activation_2", "trainable": true, "dtype": "float32", "activation": "relu"}, "registered_name": null, "build_config": {"input_shape": [null, 300, 256]}, "name": "activation_2", "inbound_nodes": [[["batch_normalization_2", 0, 0, {}]]]}, {"module": "keras.layers", "class_name": "Dropout", "config": {"name": "dropout_2", "trainable": true, "dtype": "float32", "rate": 0.5, "noise_shape": null, "seed": null}, "registered_name": null, "build_config": {"input_shape": [null, 300, 256]}, "name": "dropout_2", "inbound_nodes": [[["activation_2", 0, 0, {}]]]}, {"module": "keras.layers", "class_name": "Conv1D", "config": {"name": "conv1d_3", "trainable": true, "dtype": "float32", "filters": 128, "kernel_size": [64], "strides": [1], "padding": "same", "data_format": "channels_last", "dilation_rate": [1], "groups": 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, 300, 256]}, "name": "conv1d_3", "inbound_nodes": [[["dropout_2", 0, 0, {}]]]}, {"module": "keras.layers", "class_name": "BatchNormalization", "config": {"name": "batch_normalization_3", "trainable": true, "dtype": "float32", "axis": [2], "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, 300, 128]}, "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, 300, 128]}, "name": "activation_3", "inbound_nodes": [[["batch_normalization_3", 0, 0, {}]]]}, {"module": "keras.layers", "class_name": "Dropout", "config": {"name": "dropout_3", "trainable": true, "dtype": "float32", "rate": 0.5, "noise_shape": null, "seed": null}, "registered_name": null, "build_config": {"input_shape": [null, 300, 128]}, "name": "dropout_3", "inbound_nodes": [[["activation_3", 0, 0, {}]]]}, {"module": "keras.layers", "class_name": "Conv1D", "config": {"name": "conv1d_4", "trainable": true, "dtype": "float32", "filters": 64, "kernel_size": [128], "strides": [1], "padding": "same", "data_format": "channels_last", "dilation_rate": [1], "groups": 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, 300, 128]}, "name": "conv1d_4", "inbound_nodes": [[["dropout_3", 0, 0, {}]]]}, {"module": "keras.layers", "class_name": "BatchNormalization", "config": {"name": "batch_normalization_4", "trainable": true, "dtype": "float32", "axis": [2], "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, 300, 64]}, "name": "batch_normalization_4", "inbound_nodes": [[["conv1d_4", 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, 300, 64]}, "name": "activation_4", "inbound_nodes": [[["batch_normalization_4", 0, 0, {}]]]}, {"module": "keras.layers", "class_name": "AveragePooling1D", "config": {"name": "average_pooling1d", "trainable": true, "dtype": "float32", "strides": [300], "pool_size": [300], "padding": "valid", "data_format": "channels_last"}, "registered_name": null, "build_config": {"input_shape": [null, 300, 64]}, "name": "average_pooling1d", "inbound_nodes": [[["activation_4", 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, 1, 64]}, "name": "K562", "inbound_nodes": [[["average_pooling1d", 0, 0, {}]]]}], "input_layers": [["input_1", 0, 0]], "output_layers": [["K562", 0, 0]]}, "keras_version": "2.15.0", "backend": "tensorflow"}
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K562/Unbiased_downsampling/1M/K562-MSELoss-downsampled1M.config
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UseCustomLoss = 0
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Tasks = K562
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TaskWeights = 1
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Verbose = 2
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NumConvLayers = 5
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KernelSizes = 8,16,32,64,128
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NumKernels = 1024,512,256,128,64
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MaxTrain=1000000
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MaxTest=999999999
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ShouldTest=1
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Epochs = 200
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RevComp = 0
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BatchSize = 128
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EarlyStop = 10
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DropoutRate = 0.5
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LearningRate = 0.002
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ConvResidualSkip = 0
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ConvDropout = 1
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ConvPad = same
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DilationFactor = 1
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ConvPoolSize = 1
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GlobalMaxPool = 0
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GlobalAvePool = 1
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NumDense = 0
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DenseSizes = 0
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NumAttentionLayers = 0
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AttentionHeads = 0
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AttentionKeyDim = 0
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AttentionResidualSkip = 0
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