Reconstruction of ionic single-channel currents based on hidden Markov model

BackgroundA nanopore detector has a nanometer-scale trans-membrane channel across which a potential difference is established, resulting in an ionic current through the channel in the pA-nA range. A distinctive channel current blockade signal is created as individually "captured" DNA molecules interact with the channel and modulate the channel's ionic current. The nanopore detector is sensitive enough that nearly identical DNA molecules can be classified with very high accuracy using machine learning techniques such as Hidden Markov Models (HMMs) and Support Vector Machines (SVMs).ResultsA non-standard implementation of an HMM, emission inversion, is used for improved classification. Additional features are considered for the feature vector employed by the SVM for classification as well: The addition of a single feature representing spike density is shown to notably improve classification results. Another, much larger, feature set expansion was studied (2500 additional features instead of 1), deriving from including all the HMM's transition probabilities. The expanded features can introduce redundant, noisy information (as well as diagnostic information) into the current feature set, and thus degrade classification performance. A hybrid Adaptive Boosting approach was used for feature selection to alleviate this problem.ConclusionThe methods shown here, for more informed feature extraction, improve both classification and provide biologists and chemists with tools for obtaining a better understanding of the kinetic properties of molecules of interest.

This paper describes an automatic text‐ and speaker‐independent language identification method based on hidden Markov models (HMMs) for acoustic features. The hidden Markov modeling is used to represent the phonotactics for each language. Each language has its proper phonotactics.The HMM topology here is a fully structured (ergodic) model wherein any state could transit to all states. Two kinds of HMMs are used: the discrete HMM (DHMM) with the codebook and the continuous density HMM (CHMM). The HMM was trained using both the Baum‐Welch (forward‐backward) algorithm and the Viterbi algorithm. The latter was used for emphasizing the state transition probability.For comparison, experiments also were conducted on the identification using a mixtured Gaussian distribution model with one state. This single‐state Gaussian distribution model gave the same performance as the HMM trained with the Baum‐Welch algorithm. This is because the transition between states which reflects the characteristics of each language does not affect the likelihood scores very much. This problem was addressed by emphasizing the transition probabilities and using the Viterbi algorithm, which resulted in an improvement in the recognition rates. The trigram for optimal state sequence is introduced. Combining it with the HMM produced the best results.

A new model has been constructed to generalise the force and torque information during a manual peg-in-a-hole (PiH) assembly process. The paper uses Hidden Markov Model analysis to interpret the state topology (transition probability) and observations (force/torque signal) in the manipulation task. The task can be recognised as several discrete states that reflect the intrinsic nature of the process. Since the whole manipulation process happens so fast, even the operator themselves cannot articulate the exact states. Those are tacit skills which are difficult to extract using human factors methodologies. In order to programme a robot to complete tasks at skill level, numerical representation of the sub-goals are necessary. Therefore, those recognised ‘hidden’ states become valuable when a detail explanation of the task is needed and when a robot controller needs to change its behaviour in different states. The Gaussian Mixture model (GMM) is used as the initial guess of observations distribution. Then a Hidden Markov Model is used to encode the state (sub-goal) topology and observation density associated with those sub-goals. The Viterbi algorithm is then applied for the model-based analysis of the force and torque signal and the classification into sub-goals. The Baum-Welch algorithm is used for training and to estimate the most likely model parameters. In addition to generic states recognition, the proposed method also enhances our understanding of the skill based performances in manual tasks.

Bayesian Restoration of Ion Channel Records using Hidden Markov Models

State-of-the-art speaker diarization systems for meetings are now at a point where overlapped speech contributes significantly to the errors made by the system. However, little if no work has yet been done on detecting overlapped speech. We present our initial work toward developing an overlap detection system for improved meeting diarization. We investigate various features, with a focus on high-precision performance for use in the detector, and examine performance results on a subset of the AMI Meeting Corpus. For the high-quality signal case of a single mixed-headset channel signal, we demonstrate a relative improvement of about 7.4% DER over the baseline diarization system, while for the more challenging case of the single far-field channel signal relative improvement is 3.6%. We also outline steps towards improvement and moving beyond this initial phase.

26 - Patch-Clamp Techniques and Analysis

This paper introduces two unsupervised learning methods for analyzing functional magnetic resonance imaging (fMRI) data based on hidden Markov model (HMM). HMM approach is focused on capturing the first-order statistical evolution among the samples of a voxel time series, and it can provide a complimentary perspective of the BOLD signals. Two-state HMM is created for each voxel, and the model parameters are estimated from the voxel time series and the stimulus paradigm. Two different activation detection methods are presented in this paper. The first method is based on the likelihood and likelihood-ratio test, in which an additional Gaussian model is used to enhance the contrast of the HMM likelihood map. The second method is based on certain distance measures between the two state distributions, in which the most likely HMM state sequence is estimated through the Viterbi algorithm. The distance between the on-state and off-state distributions is measured either through a t-test, or using the Kullback-Leibler distance (KLD). Experimental results on both normal subject and brain tumor subject are presented. HMM approach appears to be more robust in detecting the supplemental active voxels comparing with SPM, especially for brain tumor subject.

BACKGROUND A hidden Markov model (HMM) is used for exon prediction on DNA of genes Plasmodium falciparum that has a model structure based on exon region structure in coding sequence (CDS). The objective research was to develop a new structure model to predict exon on DNA-genes of Plasmodium falciparum based on CDS structure using the HMM system. METHODS Model design in CDS, between two exon regions can be found one intron region and the model state number is used for its region. Its state number is used by separating start codon from first exon region and stop codon from the last exon region up to 9. The Viterbi algorithm and the backward-forward method for transition as well as emission states are used for training process. Furthermore, Viterbi and Baum-Welch algorithms are used for the testing process. The correlation coefficient (CC) was used as performance indicator, as the ratio of the estimated state in the output and the original state in the input of the model. RESULTS The simulation results has shown that the CC values depend on the given of the backward-forward transition state values randomly. The model with state number 9 showed the highest average of CC values of 0.7289 for Viterbi algorithm, and is 0.7166 for Baum-Welch algorithm. However, the lowest average of CC values has been found for the model with state number five. Its values are 0.6735 by using Viterbi algorithm and 0.6661 by using Baum-Welch algorithm. CONCLUSION The new structure model based on HMM system was valid to predict exon on DNA-genes of Plasmodium falciparum.

Currently, the most popular algorithm for hidden Markov model (HMM) decoding is the Viterbi algorithm with beam search to reduce search space. However, it is a difficult problem in determining a beam width beforehand. To address this problem, we propose a novel approach on search space reduction. Following the definition of HMM, we first detect the possible change points between HMM states sequentially, then use the change points to locate a subspace for searching. Using a combined forward and backward scheme, we can detect two boundaries consisting of change points to enclose the subspace. The Viterbi algorithm or any other search algorithms can then be applied in the subspace. The experiments on a speaker verification task show that the proposed algorithm is about 4 times faster than a full search algorithm while the accuracy is almost the same. On the same decoding speed, the proposed algorithm provides a better accuracy than a beam-search approach. For an HMM with S states, the upper bound of speedup comparing to the full search approach is approximately S/3.

In order to further enhance the performance of syntax parsing, for the shortcomings of hidden Markov model (HMM) in the parameter optimization, an improved syntax parsing method based on adaptive genetic annealing and HMM was presented. First, an adaptive hybrid genetic annealing algorithm was adopted to optimize HMM initial parameters. Second, the improved HMM was trained by Baum Welch algorithm, and then a modified Viterbi algorithm was used to recognize various types of phrases at the same layer, finally a hierarchical analysis algorithm and Viterbi algorithm were combined together to solve hierarchy and recursion in the sentence. In the adaptive genetic annealing HMM algorithm, genetic operators and parameters of simulated annealing (SA) were first respectively improved, subpopulations were classified according to the adaptive crossover and mutation probability of GA in order to realize the multi-group parallel search and information exchange, which could avoid premature and accelerate convergence, then SA was taken as a GA operator to strengthen the local search capability. Compared with several new approaches, Fβ = 1 value is averagely increased by 3%. The experiment results prove that this method is very effective for syntactic parsing.

BackgroundProfile Hidden Markov Model (HMM) is a powerful statistical model to represent a family of DNA, RNA, and protein sequences. Profile HMM has been widely used in bioinformatics research such as sequence alignment, gene structure prediction, motif identification, protein structure prediction, and biological database search. However, few comprehensive, visual editing tools for profile HMM are publicly available.ResultsWe develop a visual editor for profile Hidden Markov Models (HMMEditor). HMMEditor can visualize the profile HMM architecture, transition probabilities, and emission probabilities. Moreover, it provides functions to edit and save HMM and parameters. Furthermore, HMMEditor allows users to align a sequence against the profile HMM and to visualize the corresponding Viterbi path.ConclusionHMMEditor provides a set of unique functions to visualize and edit a profile HMM. It is a useful tool for biological sequence analysis and modeling. Both HMMEditor software and web service are freely available.

In this paper, the driver's intention recognition on roads without crossings is investigated. Because of uncertain characters between driver's intention and behaviors, analyzing and modeling methods based on the hidden Markov model (HMM) were proposed and used for setting hidden or observed states, obtaining probabilities of intention transition and observation, and building a graphical network of those definitions. In order to meet the dynamic requirement of the state transition, the structure of the HMM is improved to a sectional form, which is named SHMM, with road subsections. The transition probability of alternative intentions is designed as a time-domain continuous function, and the probabilities of observation are counted and made into statistics with the respective distribution in the subsections. The Viterbi algorithm is used for recognizing intention, with sequences of operation in the whole process of driving. The judging rule is drawn up to decide all operations in the sequence they're driven by, i.e. which type of intention with number comparison. The data used for modeling and verifying in this study is collected by a real vehicle driving experimental platform, and the test is held on urban traffic roads with ten participants involved. The results of intention recognition under the proposed method is quite satisfying and credible.

As one kind of current main power sources, internal combustion engines require high-reliability to ensure mechanical systems working well in normal operation. This paper studies vibration signals in order to detect multiple types of faults by a single channel signal. First, for the decomposition level of variational mode decomposition (VMD) which needs to be chosen non-automatically, this paper analyzes the features of various faults and optimizes the iteration initial values of center frequency so as to reduce the adverse effect of inappropriate decomposition level. Moreover, considering that VMD cannot decompose different signal sources in the same frequency, robust independent component analysis (ICA) is an excellent method to overcome this challenge. Then, the fourth-order cumulant of restructured signals from VMD and robust ICA is taken as fault indexes. Finally, because of the high error rate of original fuzzy C-Mean clustering, Euclidean distance between test points and cluster center of fuel injection failure is taken as a fault detection threshold in order to achieve high-recognition rate. In conclusion, through optimizing several algorithms, the purpose of detecting multiple types of faults by single channel signal is achieved in the current research.

For pt.II. see ibid., vol.46, p.1916-29 (1998). Hidden Markov models (HMMs) have been used to model single channel currents as recorded with the patch clamp technique from living cells. Continuous time patch-clamp recordings are typically passed through an antialiasing filter and sampled before analysis. In this paper, an adaptation of the Baum-Welch weighted least squares (BW-WLS) algorithm called the H-noise algorithm is presented to estimate the HMM and noise model parameters from bandlimited, sampled data. The effects of the antialiasing filter and the correlated background noise are considered in a metastate or vector HMM framework. The "correlated emission probability", which plays a central role in the algorithm, is redefined to consider the noise correlation in successive filtered, sampled data points. The performance of the H-noise algorithm is demonstrated with simulated data.

In this work, we perform a first approach to emotion recognition from EEG single channel signals extracted in four (4) mother-child dyads experiment in developmental psychology. Single channel EEG signals are analyzed and processed using several window sizes by performing a statistical analysis over features in the time and frequency domains. Finally, a neural network obtained an average accuracy rate of 99% of classification in two emotional states such as happiness and sadness.