Published on Wed Dec 16 2015

Learning a Hybrid Architecture for Sequence Regression and Annotation

Yizhe Zhang, Ricardo Henao, Lawrence Carin, Jianling Zhong, Alexander J. Hartemink

When learning a hidden Markov model (HMM), sequen- tial observations can often be complemented by real-valued summary response variables. Such settings arise in numerous domains, includ-ing many applications in biology.

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Abstract

When learning a hidden Markov model (HMM), sequen- tial observations can often be complemented by real-valued summary response variables generated from the path of hid- den states. Such settings arise in numerous domains, includ- ing many applications in biology, like motif discovery and genome annotation. In this paper, we present a flexible frame- work for jointly modeling both latent sequence features and the functional mapping that relates the summary response variables to the hidden state sequence. The algorithm is com- patible with a rich set of mapping functions. Results show that the availability of additional continuous response vari- ables can simultaneously improve the annotation of the se- quential observations and yield good prediction performance in both synthetic data and real-world datasets.