Hidden Markov Models for Gene Sequence Classification: Classifying the VSG genes in the Trypanosoma brucei Genome

The article presents an application of Hidden Markov Models (HMMs) for pattern recognition on genome sequences. We apply HMM for identifying genes encoding the Variant Surface Glycoprotein (VSG) in the genomes of Trypanosoma brucei (T. brucei) and other African trypanosomes. These are parasitic protozoa causative agents of sleeping sickness and several diseases in domestic and wild animals. These parasites have a peculiar strategy to evade the host's immune system that consists in periodically changing their predominant cellular surface protein (VSG). The motivation for using patterns recognition methods to identify these genes, instead of traditional homology based ones, is that the levels of sequence identity (amino acid and DNA sequence) amongst these genes is often below of what is considered reliable in these methods. Among pattern recognition approaches, HMM are particularly suitable to tackle this problem because they can handle more naturally the determination of gene edges. We evaluate the performance of the model using different number of states in the Markov model, as well as several performance metrics. The model is applied using public genomic data. Our empirical results show that the VSG genes on T. brucei can be safely identified (high sensitivity and low rate of false positives) using HMM.Comment: Accepted article in July, 2015 in Pattern Analysis and Applications, Springer. The article contains 23 pages, 4 figures, 8 tables and 51 reference

A statistical multiresolution approach for face recognition using structural hidden Markov models

This paper introduces a novel methodology that combines the multiresolution feature of the discrete wavelet transform (DWT) with the local interactions of the facial structures expressed through the structural hidden Markov model (SHMM). A range of wavelet filters such as Haar, biorthogonal 9/7, and Coiflet, as well as Gabor, have been implemented in order to search for the best performance. SHMMs perform a thorough probabilistic analysis of any sequential pattern by revealing both its inner and outer structures simultaneously. Unlike traditional HMMs, the SHMMs do not perform the state conditional independence of the visible observation sequence assumption. This is achieved via the concept of local structures introduced by the SHMMs. Therefore, the long-range dependency problem inherent to traditional HMMs has been drastically reduced. SHMMs have not previously been applied to the problem of face identification. The results reported in this application have shown that SHMM outperforms the traditional hidden Markov model with a 73% increase in accuracy

Deep Markov Random Field for Image Modeling

Markov Random Fields (MRFs), a formulation widely used in generative image modeling, have long been plagued by the lack of expressive power. This issue is primarily due to the fact that conventional MRFs formulations tend to use simplistic factors to capture local patterns. In this paper, we move beyond such limitations, and propose a novel MRF model that uses fully-connected neurons to express the complex interactions among pixels. Through theoretical analysis, we reveal an inherent connection between this model and recurrent neural networks, and thereon derive an approximated feed-forward network that couples multiple RNNs along opposite directions. This formulation combines the expressive power of deep neural networks and the cyclic dependency structure of MRF in a unified model, bringing the modeling capability to a new level. The feed-forward approximation also allows it to be efficiently learned from data. Experimental results on a variety of low-level vision tasks show notable improvement over state-of-the-arts.Comment: Accepted at ECCV 201

Constrained Circular Hidden Markov Models for Recognizing Deformed Shapes

In this paper, we analyse the properties of the standard circular hidden Markov model (HMM) on 2D shape recognition. We point out the limitations of the circular HMMs and further propose to impose the constraint on the relationship between the initial and final states of circular HMMs to improve the performance. We develop two modified Viterbi algorithms to implement our proposal. The proposed algorithms have been tested on the database of the MPEG-7 Core Experiments Shape-1, Part B. The experiments show that both proposed algorithms can achieve better performance than that of the standard circular HMM in terms of accuracy. In particular, the second proposed algorithm, which is faster than elastic matching algorithms, has much potential due to its accuracy and speed