Automatic genome segmentation with HMM-ANN hybrid models

We consider the problem of automatic genome segmentation (AGS) that aims to assign discrete labels to all genomic regions based on multiple ChIP-seq samples. We propose to use a hybrid model that combines a hidden Markov model (HMM) with an artificial neural network (ANN) to overcome the weaknesses of a standard HMM. Our contributions are threefold: first, we benchmark two approaches to generate targets for ANN training on an example dataset; second, we investigate many different ANN models to identify the ones with best predictions on chromatin states; third, we test different hyperparameters and discuss how they affect the machine learning algorithms’ performance. We find our best performing models to beat two pervious state-of-the-art methods for AGS by large margins.