Subspace estimation and prediction methods for hidden Markov models

Computational cancer phylogenetics can play an important role in delineating possible tumor progression pathways and identifying molecular subtypes and mechanisms of action. We previously developed a pipeline for constructing tumor phylogenies from recurring cell types computationally inferred from whole genome copy number data. The accuracy and detail of these tumor phylogenies, however, depends on the identification of accurate and high-resolution molecular markers of progression, i.e., reproducible regions of copy number variation that can be used to robustly differentiate different subtypes and stages of progression. Here we present a new method for the problem using hidden Markov models (HMMs) to derive robust, high resolution progression markers from sets of tumor samples. We demonstrate our method on a publicly available array comparative genome hybridization (aCGH) dataset (NCBI GEO GSE16672, Navin et al., 2010) from sectioned primary ductal breast tumors. Our method uses an HMM, a class of probabilistic models, to classify sets of aCGH data into a partitioning of samples into normal (diploid) or amplified at each copy number probe. It differs from other similar HMM methods primarily in seeking a parsimonious set of combinations of amplification states able to explain all aCGH profiles simultaneously in order to identify robust markers of progression across samples. The model learns frequencies with which different combinations of amplifications are observed across the samples by modeling individual probes as Gaussian random variables with either normal or tetraploid means, with data more consistent with tetraploid being classified as amplified and those more consistent with diploid classified as normal. To handle a combinatorial explosion in combinations of amplification states with increasing numbers of samples, the method introduces a Gibbs sampling algorithm to learn a parsimonious model of the most frequently occurring combinations of amplification states. We applied our methods to a previously constructed set of inferred cell types derived from the Navin et al. data (Tolliver et al., 2010) and to a comparison set of 9 random samples from the raw aCGH data. We validated our model relative to manual labeling of amplicons on the same data. In both experiments, the HMM method was able to pick up significantly larger numbers of robustly amplified segments per chromosome than did prior methods or manual analysis. The resulting segments can be directly fed into downstream analysis routines for phylogeny inference or other predictions. In future work, the HMM method may be improved by fine-tuning the underlying model for copy number variation. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3964. doi:1538-7445.AM2012-3964

Speech to Text was one of speech recognition applications which speech signal was processed, recognized and converted into a textual representation. Hidden Markov Model (HMM) was the widely used method in speech recognition. However, the level of accuracy using HMM was strongly influenced by the optimalization of extraction process and modellling methods. Hence in this research, the use of genetic algorithm (GA) method to optimize the Ergodic HMM was tested. In Hybrid HMM-GA, GA was used to optimize the Baum-welch method in the training process. It was useful to improve the accuracy of the recognition result which is produced by the HMM parameters that generate the low accuracy when the HMM are tested. Based on the research, the percentage increases the level of accuracy of 20% to 41%. Proved that the combination of GA in HMM method can gives more optimal results when compared with the HMM system that not combine with any method.

This paper introduces a non-temporal multiple silhouettes in Hidden Markov Model (HMM) for offering view independent human posture recognition. The multiple silhouettes are used to reduce the ambiguity problem of posture recognition. A simple feature extraction of the 2D shape contour based histogram is used for image encoding and K-Means algorithm is applied for clustering and code-wording of eight simple postures from multiple views. Therefore, 3D volume reconstruction is not required, in return helps to reduce the complexity of modeling and computational power of feature extraction. HMM is trained to obtain view independent recognition model using multiple silhouettes. A combination of non-temporal multiple silhouettes, code-wording and HMM methods in this proposed approach make it possible to recognize human posture in view independent. The experimental results demonstrate the effectiveness of non-temporal multiple silhouettes in HMM for recognizing posture.

A codebook design method for Hidden Markov Model (HMM) by using a Centroid Neural Network (CNN) is applied to a Korean monophone recognition problem in this paper. In order to alleviate the accuracy degradation problem in tied mixture HMM (TMHMM), this paper utilizes a clustering algorithm, called Centroid Neural Network with State Dependence measure (CNN(SD)), for TMHMMs. The CNN(SD) uses a novel distance measure that discriminates between two observation densities in the HMM from the same state and those from different states. When compared with other conventional unsupervised neural networks, the CNN(SD) successfully allocates more code vectors to the regions where Gaussian Probability Density Function (GPDF) data of different states overlap each other while it allocates fewer code vectors to the regions where GPDF data are from the same states. Experiments and results on a Korean monophone data, the CNN(SD) shows improvements on the recognition accuracy over CNN and the traditional k-means algorithm.

The central nervous system (CNS) plays an important role in regulation of human gait. Parkinson's disease (PD) is a common neurodegenerative disease that may cause neurophysiologic change in the CNS and as a result change the gait cycle duration (stride interval). This article used the Hidden Markov Model (HMM) with Gaussian Mixtures to separate the patients with PD from healthy subjects. The results showed that the performance of the HMM classifier in classifying the gait data corresponding to 16 healthy and 15 PD subjects is comparable to the results obtained from the least squares support vector machine (LS-SVM) classifier. In this study, the leave-one-out cross-validation method was used to evaluate the performance of each classifier. The HMM method could effectively separate the gait data in terms of stride interval obtained from healthy subjects and PD patients with an accuracy rate of 90.3 % . All in all, the results showed that the proposed method can be used for distinguishing PD patients from healthy subjects based on the gait data classification.

A method is presented for using hidden Markov models (HMMs) for the analysis of force, torque, and position signals from sensors in manufacturing machines. The HMM can detect the transitions between contact states and compute a measure of the task quality using a model of the task developed by the manufacturing engineer and optimized on training data. The HMM method has been evaluated in extensive experimentation with teleoperation and the results suggest even higher effectiveness in automation and manufacturing applications. >

Face recognition based on multi-class mapping of Fisher scores

This paper presents a minimum generation error (MGE) training method for hidden Markov model (HMM) based prediction of articulatory movements when both text and audio inputs are given. In this method, MGE criterion is adopted to replace the maximum likelihood (ML) criterion to estimate model parameters for the unified acoustic-articulatory HMMs. Different from the MGE training for HMM-based acoustic speech synthesis, the generation error used here is defined as the distance between the generated and natural articulatory features. Experimental results show that our proposed method can improve the accuracy of articulatory movement prediction significantly. The average root mean square (RMS) error reduces from 1.002 mm to 0.913 mm on the test set.

This paper highlights the need for intelligent analysis of students’ behavioral states in physical education tasks. The hand-ring inertial data is used to identify students’ motion sequence states. First, statistical feature extraction is performed based on the acceleration and angular velocity data collected from the bracelet. After completing the filtering and noise reduction of the data, we perform feature extraction by Back Propagation Neural Network (BPNN) and use the sliding window method for analysis. Finally, the classification capability of the model sequence is enhanced by the Hidden Markov Model (HMM). The experimental results indicate that the classification accuracy of student action sequences in physical education exceeds 96% after optimization by the HMM method. This provides intelligent means and new ideas for future student state recognition in physical education and teaching reform.

There are strong evidences of that multimodal biometric score fusion can significantly improve human identification performance. Score level fusion usually involves score normalization, score fusion, and fusion decision. There are several types of score fusion methods, direct combination of fusion scores, classifier-based fusion, and density-based fusion. The real applications require achieving greater reliability in determining or verifying person's identity. The goal of this research is to improve the accuracy and robustness of human identification by using multimodal biometrics score fusion. The accuracy means high verification rate if tested on a closed dataset, or a high genuine accept rate under low false accept rate if tested on an open dataset. While the robustness means the fusion performance is stable with variant biometric scores. We propose a hidden Markov model (HMM) for multiple score fusion, where the biometric scores include multimodal scores and multi-matcher scores. The state probability density functions in a HHM model are estimated by Gaussian mixture model. The proposed HMM model for multiple score fusion is accurate for identification, flexible and reliable with biometrics. The proposed HMM method are tested on three NIST-BSSR1 multimodal databases and on three face-score databases. The results show the HMM method is an excellent and reliable score fusion method.

In this paper, we briefly compare the performance of gene finding methods which are based on hidden Markov models (HMMs) and digital signal processing (DSP). We apply the methods to three benchmark datasets consisting of sequences from various species (mammalian, vertebrate and non-vertebrate) to investigate the strength and weakness of these two classes of methods from different aspects. We study the effect of training on the HMM-based methods. In addition, we analyze the effect of the threshold and window length parameters on the performance of the DSP-based methods. In our work, we present the receiver operating characteristic (ROC) plots of the DSP-based methods and the numerical results of applying the HMM and DSP-based methods to the three datasets. In addition, the plots of the prediction accuracy of the DSP-based methods when they are applied to exons of specific lengths and with different values of the window length parameter are presented in this study.

Motivation: One of the most successful methods to date for recognizing protein sequences that are evolutionarily related has been profile hidden Markov models (HMMs). However, these models do not capture pairwise statistical preferences of residues that are hydrogen bonded in beta sheets. These dependencies have been partially captured in the HMM setting by simulated evolution in the training phase and can be fully captured by Markov random fields (MRFs). However, the MRFs can be computationally prohibitive when beta strands are interleaved in complex topologies. We introduce SMURFLite, a method that combines both simplified MRFs and simulated evolution to substantially improve remote homology detection for beta structures. Unlike previous MRF-based methods, SMURFLite is computationally feasible on any beta-structural motif.Results: We test SMURFLite on all propeller and barrel folds in the mainly-beta class of the SCOP hierarchy in stringent cross-validation experiments. We show a mean 26% (median 16%) improvement in area under curve (AUC) for beta-structural motif recognition as compared with HMMER (a well-known HMM method) and a mean 33% (median 19%) improvement as compared with RAPTOR (a well-known threading method) and even a mean 18% (median 10%) improvement in AUC over HHPred (a profile–profile HMM method), despite HHpred's use of extensive additional training data. We demonstrate SMURFLite's ability to scale to whole genomes by running a SMURFLite library of 207 beta-structural SCOP superfamilies against the entire genome of Thermotoga maritima, and make over a 100 new fold predictions.Availability and implementaion: A webserver that runs SMURFLite is available at: http://smurf.cs.tufts.edu/smurflite/Contact: lenore.cowen@tufts.edu; bab@mit.edu

Ion channel data recorded using the patch clamp technique are low-pass filtered to remove high-frequency noise. Almanjahie et al. (Eur Biophys J 44:545-556, 2015) based statistical analysis of such data on a hidden Markov model (HMM) with a moving average adjustment for the filter but without correlated noise, and used the EM algorithm for parameter estimation. In this paper, we extend their model to include correlated noise, using signal processing methods and deconvolution to pre-whiten the noise. The resulting data can be modelled as a standard HMM and parameter estimates are again obtained using the EM algorithm. We evaluate this approach using simulated data and also apply it to real data obtained from the mechanosensitive channel of large conductance (MscL) in Escherichia coli. Estimates of mean conductances are comparable to literature values. The key advantages of this method are that it is much simpler and computationally considerably more efficient than currently used HMM methods that include filtering and correlated noise.

A Combined Method of Hidden Markov Model and <I>K</I>-Means Clustering to Temporary Datasets Grouping

Hidden Markov models (HMM) are used in applications when the data structure contains a latent Markov chain. However, the Fisher information matrix (FIM) of an HMM does not have a closed form. Estimating the parameters of HMM with the commonly used Fisher scoring algorithm is difficult if the FIM cannot be expressed in a closed form. An approximate Fisher scoring algorithm is proposed, which uses an approximation of the exact FIM. This approximate FIM is based on the joint distribution of both observed and latent variables. The difference between the exact FIM and its approximation is investigated under various parameter value assumptions through simulations. We show that the approximate Fisher scoring algorithm has a strong algebraic connection with the EM algorithm, and this connection is further discussed using simulations. To demonstrate HMMs, we propose a stock portfolio creation method that depends on HMMs. By utilizing historical stock closing values over a fixed training period, stock performances are evaluated in terms of capital gain using HMMs. Stocks are selected into a yearly portfolio based on the performances. Under out-of-sample testing, the annual capital gains of yearly portfolios from 2010 to 2018 are calculated, and their performances are compared to the S&P 500 index. Stock prices are highly correlated, but a basic HMM does not allow a covariance structure between multiple sequences. We also consider a copula to generate multivariate Markov chains, which are incorporated into HMM in order to create covariance structure, and this method is demonstrated using this stock market data. The second application is the detection of lameness among dairy cows. The data set involved in this application contains the functional measurement of forces. Due to the dissatisfactory result using the traditional functional regression, we present an alternative that incorporates functional data with HMM assuming multivariate normal sub-distributions. This method is further discussed using simulated data.