1. Use MultiLayerConfiguration to construct the autoencoder network:

NeuralNetConfiguration.Builder configBuilder = new NeuralNetConfiguration.Builder();
 configBuilder.seed(12345);
 configBuilder.weightInit(WeightInit.XAVIER);
 configBuilder.updater(new AdaGrad(0.05));
 configBuilder.activation(Activation.RELU);
 configBuilder.l2(l2RegCoefficient);
 NeuralNetConfiguration.ListBuilder builder = configBuilder.list();

2. Create input layers using DenseLayer:

builder.layer(new DenseLayer.Builder().nIn(784).nOut(250).build());
 builder.layer(new DenseLayer.Builder().nIn(250).nOut(10).build());