Automatic segmentation of lymph vessel wall using optimal surface graph cut and hidden Markov Models.

The exponential growth and proliferation of wireless devices for different wireless applications have led to the emergence of cognitive radio network (CRN) for optimal utilization of scarce spectrum resources. However, these resources have grossly been under-utilized due to the inaccurate spectrum predictions. Existing spectrum occupancy and prediction techniques which rely on 2-state hidden Markov model (HMM) results in false alarm or missed detection caused by noisy or incomplete observable effects. In this paper, a 3-state HMM spectrum occupancy and prediction technique in CRNs is proposed. The transmission, emission and initial state probabilities of the proposed 3-state HMM parameters were derived based on the three canonical problems associated with HMM. The evaluation, decoding and learning problems were solved using Forward algorithm, Viterbi algorithm and the Baum-Welch algorithm, respectively. The performance of the proposed 3-state HMM spectrum prediction technique was evaluated using prediction accuracy, probability of detection and spectrum utilization efficiency. The simulation results obtained revealed that the 3-state HMM outperformed the 2-state HMM spectrum prediction technique by 24.1% in prediction accuracy.

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.

4 - Optimal surface segmentation with subvoxel accuracy in spectral domain optical coherence tomography images

We present a novel HMM based approach to simultaneous segmentation of vessel walls in Lymphatic confocal images. The vessel borders are parameterized using RBFs to minimize the number of tracking points. The proposed method tracks the hidden states that indicate border locations for both the inner and outer walls. The observation for both borders is obtained using edge-based features from steerable filters. Two separate Gaussian probability distributions for the vessel borders and background are used to infer the emission probability, and the transmission probability is learned using a Baum-Welch algorithm. We transform the segmentation problem into a minimization of an s-excess graph cost, with each node in the graph corresponding to a hidden state and the weight for each node being defined by its emission probability. We define the inter-relations between neighboring nodes based on the transmission probability. We present both qualitative and quantitative analysis in comparison to the popular Viterbi algorithm.

In this paper, a novel bilateral shared control approach is proposed to address the issue of strong dependence on the human, and the resulting burden of manipulation, in classical haptic teleoperation systems for vehicle navigation. A Hidden Markov Model (HMM) is utilized to handle the Human Intention Recognition (HIR), according to the force input by the human—including the HMM solution, i.e., Baum–Welch algorithm, and HMM decoding, i.e., Viterbi algorithm—and the communication delay in teleoperation systems is added to generate a temporary goal. Afterwards, a heuristic and sampling method for online generation of splicing trajectory based on the goal is proposed innovatively, ensuring the vehicle can move feasibly after the change in human intention is detected. Once the trajectory is available, the vehicle velocity is then converted to joystick position information as the haptic cue of the human, which enhances the telepresence. The shared teleoperation control framework is verified in the simulation environment, where its excellent performance in the complex environment is evaluated, and its feasibility is confirmed. The experimental results show that the proposed method can achieve simple and efficient navigation in a complex environment, and can also give a certain situational awareness to the human.

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.

This paper describes a method to recognize the alphabets from a single hand motion using Hidden Markov Models (HMM). In our method, gesture recognition for alphabets is based on three main stages; preprocessing, feature extraction and classification. In preprocessing stage, color and depth information are used to detect both hands and face in connection with morphological operation. After the detection of the hand, the tracking will take place in further step in order to determine the motion trajectory so-called gesture path. The second stage, feature extraction enhances the gesture path which gives us a pure path and also determines the orientation between the center of gravity and each point in a pure path. Thereby, the orientation is quantized to give a discrete vector that used as input to HMM. In the final stage, the gesture of alphabets is recognized by using Left-Right Banded model (LRB) in conjunction with Baum-Welch algorithm (BW) for training the parameters of HMM. Therefore, the best path is obtained by Viterbi algorithm using a gesture database. In our experiment, 520 trained gestures are used for training and also 260 tested gestures for testing. Our method recognizes the alphabets from A to Z and achieves an average recognition rate of 92.3%.

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.

The discrete channel hidden Markov models indicate the temporal statistical characteristics of the generated error sequences by fading channels with memory precisely. In this paper first the optimal order of the hidden Markov models is estimated using Baum Welch algorithm (BWA) with comparing statistics such as average loglikelihood and autocorrelation function for error modelling of IEEE 802.16/WiMAX standard. As a perfect alternative to HMM error models, a new efficient stochastic swarm intelligent-based particle swarm optimization (PSO)-HMM is suggested for this standard to find the global and optimal solution. Comparing the proposed method with the conventional (BWA) by performing numerical simulations using error sequences of various lengths, the results indicate the superiority of the PSO approach even when the target sequences are as short as 2000 in length; moreover, the appropriateness of the PSO-HMM is investigated for different sampling periods. It can be concluded that the PSO with two states arrives at high level of accuracy in contrast to HMM with much higher number of states. For validating the proposed method, the burst error statistics of the PSO-HMM with respect to the autocorrelation function and error free interval distribution of the original error sequence are presented. The simulation results indicate that the PSO-HMM has better performance to find the optimal model parameters more stable than (BWA).

This book explores important aspects of Markov and hidden Markov processes and the applications of these ideas to various problems in computational biology. It starts from first principles, so that no previous knowledge of probability is necessary. However, the work is rigorous and mathematical, making it useful to engineers and mathematicians, even those not interested in biological applications. A range of exercises is provided, including drills to familiarize the reader with concepts and more advanced problems that require deep thinking about the theory. Biological applications are taken from post-genomic biology, especially genomics and proteomics. The topics examined include standard material such as the Perron–Frobenius theorem, transient and recurrent states, hitting probabilities and hitting times, maximum likelihood estimation, the Viterbi algorithm, and the Baum–Welch algorithm. The book contains discussions of extremely useful topics not usually seen at the basic level, such as ergodicity of Markov processes, Markov Chain Monte Carlo (MCMC), information theory, and large deviation theory for both i.i.d and Markov processes. It also presents state-of-the-art realization theory for hidden Markov models. Among biological applications, it offers an in-depth look at the BLAST (Basic Local Alignment Search Technique) algorithm, including a comprehensive explanation of the underlying theory. Other applications such as profile hidden Markov models are also explored.

Accurate and computationally efficient means of recognizing continuous speech has been a subject of research in recent years. This paper reports the development of a small vocabulary, speaker independent continuous Malayalam speech recognition system based on Hidden Markov Models (HMMs). Continuous density HMM, which is used in this work to model phonemes, represents the general case where the observation probability density functions (pdfs) are continuous. The observation pdf is approximated using a Gaussian mixture density. Mel-frequency Cepstral Coefficients (MFCC) method is used to extract acoustic features from the input signal. To represent temporal variations in the speech signal, the first and second order derivatives of MFCC are added to the set of static parameters. The training and decoding are performed by the Baum-Welch and Viterbi algorithms respectively. The corpus contains naturally and continuously spoken sentences with multiple pronunciations and speaker variations. On evaluation the proposed system has produced promising results with 94.67% word accuracy and 93.33% sentence correct.

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.

The ability to detect malicious domain names is critical for protection against internet security, data theft, and other dangers. Current methods for recognising malicious domain names have demonstrated poor detection accuracy in dealing with massive data. This paper proposes a novel malicious domain name detection method based on an improved Hidden Markov Model (HMM). Firstly, by analysing various characteristics of good and evil domain names in DNS communication, we can use Spark fast extraction to distinguish their attributes; then, we can quickly classify unknown domain names accurately by using Baum-Welch algorithm and Viterbi algorithm in Hidden Markov Model (BVHMM) to achieve the effective detection of malicious domain names; finally, to test our approach, we conducted a series of experiments, and the experimental results demonstrate that our model achieves good accuracy and recall rate as compared with other detection models.

With the constant development of smart devices, Gesture recognition is applied on more and more fields. Gesture recognition devices currently on the market are inconvenient and expensive. A gesture recognition method based on Kinect is proposed in this paper. The camera of Kinect is used to get gesture images and then a hidden Markov model is established to recognize dynamic gesture so that the operation is simple. The assessment, decoding algorithms and training issues of hidden Markov model in gesture recognition is focused in this paper. Viterbi algorithm and Baum-Welch algorithm are used to solve the problems above. After simulation experiments, it is discovered that the gesture recognition algorithm based on Kinect proposed in this paper has a high accuracy rate for a variety of gestures, simultaneously the naturalness of human-computer interaction has been greatly improved.

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.