K562 Best Models

K562/1Kbp/K562-MSELoss-1000bp.config

@@ -0,0 +1,34 @@
+UseCustomLoss = 0
+Tasks = K562
+TaskWeights = 1
+Verbose = 2
+NumConvLayers = 5
+KernelSizes = 8,16,32,64,128
+NumKernels = 1024,512,256,128,64
+MaxTrain=3000000 
+MaxTest=999999999
+ShouldTest=1
+Epochs = 200
+
+RevComp = 0
+BatchSize = 16
+EarlyStop = 5
+DropoutRate = 0.5
+LearningRate = 0.002
+ConvResidualSkip = 0
+ConvDropout = 1
+ConvPad = same
+DilationFactor = 1
+ConvPoolSize = 1
+GlobalMaxPool = 0
+GlobalAvePool = 1
+NumDense = 0
+DenseSizes = 0
+NumAttentionLayers = 0
+AttentionHeads = 0
+AttentionKeyDim = 0
+AttentionResidualSkip = 0
+
+
+
+

K562/1Kbp/K562_1000bp-3.h5

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+size 63138304

K562/1Kbp/K562_1000bp-3.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, 1000, 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, 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K562/Biased_downsampling/K562-1.h5

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K562/Biased_downsampling/K562-1.json

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K562/Biased_downsampling/K562-MSELoss.config

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+NumKernels = 1024,512,256,128,64
+MaxTrain=3000000 
+MaxTest=999999999
+ShouldTest=1
+Epochs = 200
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+EarlyStop = 10
+DropoutRate = 0.5
+LearningRate = 0.002
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+ConvDropout = 1
+ConvPad = same
+DilationFactor = 1
+ConvPoolSize = 1
+GlobalMaxPool = 0
+GlobalAvePool = 1
+NumDense = 0
+DenseSizes = 0
+NumAttentionLayers = 0
+AttentionHeads = 0
+AttentionKeyDim = 0
+AttentionResidualSkip = 0
+
+
+
+

K562/CustomLoss/K562-CustomLoss.config

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+UseCustomLoss = 1
+Tasks = K562
+TaskWeights = 1
+Verbose = 2
+NumConvLayers = 5
+KernelSizes = 8,16,32,64,128
+NumKernels = 1024,512,256,128,64
+MaxTrain=3000000 
+MaxTest=999999999
+ShouldTest=1
+Epochs = 200
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+RevComp = 0
+BatchSize = 128
+EarlyStop = 10
+DropoutRate = 0.5
+LearningRate = 0.002
+ConvResidualSkip = 0
+ConvDropout = 1
+ConvPad = same
+DilationFactor = 1
+ConvPoolSize = 1
+GlobalMaxPool = 0
+GlobalAvePool = 1
+NumDense = 0
+DenseSizes = 0
+NumAttentionLayers = 0
+AttentionHeads = 0
+AttentionKeyDim = 0
+AttentionResidualSkip = 0
+
+
+
+

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K562/CustomLoss/K562_Custom-7.json

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K562/DeepSTARR-BlueSTARR/K562_DeepSTARR.config

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+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

K562/MSELoss/K562-2.h5

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+size 63138304

K562/MSELoss/K562-2.json

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K562/MSELoss/K562-MSELoss.config

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+UseCustomLoss = 0
+Tasks = K562
+TaskWeights = 1
+Verbose = 2
+NumConvLayers = 5
+KernelSizes = 8,16,32,64,128
+NumKernels = 1024,512,256,128,64
+MaxTrain=3000000 
+MaxTest=999999999
+ShouldTest=1
+Epochs = 200
+
+RevComp = 0
+BatchSize = 128
+EarlyStop = 10
+DropoutRate = 0.5
+LearningRate = 0.002
+ConvResidualSkip = 0
+ConvDropout = 1
+ConvPad = same
+DilationFactor = 1
+ConvPoolSize = 1
+GlobalMaxPool = 0
+GlobalAvePool = 1
+NumDense = 0
+DenseSizes = 0
+NumAttentionLayers = 0
+AttentionHeads = 0
+AttentionKeyDim = 0
+AttentionResidualSkip = 0
+
+
+
+

K562/TE/K562-TE.config

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+UseCustomLoss = 0
+Tasks = K562
+TaskWeights = 1
+Verbose = 2
+NumConvLayers = 4
+KernelSizes = 8,16,32,64
+NumKernels = 1024,512,256,128
+MaxTrain = 3000000
+MaxTest = 999999999
+ShouldTest=1
+Epochs = 200
+
+RevComp = 0
+BatchSize = 128
+EarlyStop = 10
+DropoutRate = 0.5
+LearningRate = 0.002
+ConvResidualSkip = 0
+ConvDropout = 1
+ConvPad = same
+DilationFactor = 1
+ConvPoolSize = 1
+GlobalAvePool = 1
+GlobalMaxPool = 0
+NumDense = 0
+DenseSizes = 0
+NumAttentionLayers = 1
+AttentionHeads = 8
+AttentionKeyDim = 64
+AttentionResidualSkip = 0

K562/TE/K562_TE-6.h5

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K562/TE/K562_TE-6.json

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K562/Unbiased_downsampling/0.8M/K562-10.h5

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K562/Unbiased_downsampling/0.8M/K562-MSELoss-downsampled0.8M.config

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K562/Unbiased_downsampling/1.3M/K562-MSELoss-downsampled1.3M.config

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+DenseSizes = 0
+NumAttentionLayers = 0
+AttentionHeads = 0
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+AttentionResidualSkip = 0
+
+
+
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K562/Unbiased_downsampling/1.5M/K562-9.json

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K562/Unbiased_downsampling/1.5M/K562-MSELoss-downsampled1.5M.config

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+
+
+
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K562/Unbiased_downsampling/1M/K562-10.json

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"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, 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{"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": 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K562/Unbiased_downsampling/1M/K562-MSELoss-downsampled1M.config

@@ -0,0 +1,34 @@
+UseCustomLoss = 0
+Tasks = K562
+TaskWeights = 1
+Verbose = 2
+NumConvLayers = 5
+KernelSizes = 8,16,32,64,128
+NumKernels = 1024,512,256,128,64
+MaxTrain=1000000
+MaxTest=999999999
+ShouldTest=1
+Epochs = 200
+
+RevComp = 0
+BatchSize = 128
+EarlyStop = 10
+DropoutRate = 0.5
+LearningRate = 0.002
+ConvResidualSkip = 0
+ConvDropout = 1
+ConvPad = same
+DilationFactor = 1
+ConvPoolSize = 1
+GlobalMaxPool = 0
+GlobalAvePool = 1
+NumDense = 0
+DenseSizes = 0
+NumAttentionLayers = 0
+AttentionHeads = 0
+AttentionKeyDim = 0
+AttentionResidualSkip = 0
+
+
+
+