Automatic Analysis of Large-scale Nanopore Data Using Hidden Markov Models

This work presents a detailed framework to detect the location of heart sound within the respiratory sound based on temporal fuzzy c-means (TFCM) algorithm. In the proposed method, respiratory sound is first divided into frames and for each frame, the logarithmic energy features are calculated. Then, these features are used to classify the respiratory sound as heart sound (HS containing lung sound) and non-HS (only lung sound) by the TFCM algorithm. The TFCM is the modified version fuzzy c-means (FCM) algorithm. While the FCM algorithm uses only the local information about the current frame, the TFCM algorithm uses the temporal information from both the current and the neighboring frames in decision making. To measure the detection performance of the proposed method, several experiments have been conducted on a database of 24 healthy subjects. The experimental results show that the average false-negative rate values are 0.8 ± 1.1 and 1.5 ± 1.4 %, and the normalized area under detection error curves are 0.0145 and 0.0269 for the TFCM method in the low and medium respiratory flow rates, respectively. These average values are significantly lower than those obtained by FCM algorithm and by the other compared methods in the literature, which demonstrates the efficiency of the proposed TFCM algorithm. On the other hand, the average elapsed time of the TFCM for a data with length of 0.2 ± 0.05 s is 0.2 ± 0.05 s, which is slightly higher than that of the FCM and lower than those of the other compared methods.

Sleep quantity affects an individual's personal health. The gold standard of measuring sleep and diagnosing sleep disorders is Polysomnography (PSG). Although PSG is accurate, it is expensive and it lacks portability. A number of wearable devices with embedded sensors have emerged in the recent past as an alternative to PSG for regular sleep monitoring directly by the user. These devices are intrusive and cause discomfort besides being expensive. In this work, we present an algorithm to detect sleep using a smartphone with the help of its inbuilt accelerometer sensor. We present three different approaches to classify raw acceleration data into two states - Sleep and Wake. In the first approach, we take an equation from Kushida's algorithm to process accelerometer data. Henceforth, we call it Kushida's equation. While the second is based on statistical functions, the third is based on Hidden Markov Model (HMM) training. Although all the three approaches are suitable for a phone's resources, each approach demands different amount of resources. While Kushida's equation-based approach demands the least, the HMM training-based approach demands the maximum. We collected data from mobile phone's accelerometer for four subjects for twelve days each. We compare accuracy of sleep detection using each of the three approaches with that of Zeo sensor, which is based on Electroencephalogram (EEG) sensor to detect sleep. EEG is an important modality in PSG. We find that HMM training-based approach is as much as 84% accurate. It is 15% more accurate as compared to Kushida's equation-based approach and 10% more accurate as compared to statistical method-based approach. In order to concisely represent the sleep quality of people, we model their sleep data using HMM. We present an analysis to find out a tradeoff between the amount of training data and the accuracy provided in the modeling of sleep. We find that six days of sleep data is sufficient for accurate modeling. We compare accuracy of our HMM training-based algorithm with a representative third party app SleepTime available from Google Play Store for Android. We find that the detection done using HMM approach is closer to that done by Zeo by 13% as compared to the third party Android application SleepTime. We show that our HMM training-based approach is efficient as it takes less than ten seconds to get executed on Moto G Android phone.

Most of the systems for recognition of activities aim to identify a set of normal human activities. Data is either recorded by computer vision or sensor based networks. These systems may not work properly if an unusual event or abnormal activity occurs, especially ones that have not been encountered in the past. By definition, unusual events are mostly rare and unexpected, and therefore very little or no data may be available for training. In this paper, we focus on the challenging problem of detecting unusual temporal events in a sensor network and present three Hidden Markov Models (HMM) based approaches to tackle this problem. The first approach models each normal activity separately as an HMM and the second approach models all the normal activities together as one common HMM. If the likelihood is lower than a threshold, an unusual event is identified. The third approach models all normal activities together in one HMM and approximates an HMM for the the unusual events. All the methods train HMM models on data of the usual events and do not require training data from the unusual events. We perform our experiments on a Locomotion Analysis dataset that contains gyroscope, force sensor, and accelerometer readings. To test the performance of our approaches, we generate five types of unusual events that represent random activity, extremely unusual events, unusual events similar to specific normal activities, no or little motion and normal activity followed by no or little motion. Our experiments suggest that for a moderately sized time frame window, these approaches can identify all the five types of unusual events with high confidence.

Clustering approach is widely used in biomedical applications particularly for brain tumor detection in abnormal magnetic resonance (MR) images. Fuzzy clustering using fuzzy C-means (FCM) algorithm proved to be superior over the other clustering approaches in terms of segmentation efficiency. But the major drawback of the FCM algorithm is the huge computational time required for convergence. The effectiveness of the FCM algorithm in terms of computational rate is improved by modifying the cluster center and membership value updation criterion. In this paper, the application of modified FCM algorithm for MR brain tumor detection is explored. Abnormal brain images from four tumor classes namely metastase, meningioma, glioma and astrocytoma are used in this work. A comprehensive feature vector space is used for the segmentation technique. Comparative analysis in terms of segmentation efficiency and convergence rate is performed between the conventional FCM and the modified FCM. Experimental results show superior results for the modified FCM algorithm in terms of the performance measures.

For soccer video, the algorithm that using semantic shots as observation, the events as the states to construct the Hidden Markov Model (HMM) for event detection was proposed. The nine types of semantic shots such as front region, midfield, penalty area, the medium shot, the players close-up, outside audience, referee shot, slow motion playback shot and other types are used as observation. The four kinds of events to be detected, namely, the normal playing event, play suspension event, shooting event and foul event are defined as the states. According to the decoding principle of HMM, the states sequence with the maximum possibility for the input observation sequence was calculated and thus the event detection was completed. Compared with other event detection algorithms based on HMM assessment principle, the method adopted in this paper only has to construct one HMM and need less computation time. The experiment results show that our algorithm is effective.

With the growing use of crowdsourced location data from smartphones for transportation applications, the task of map-matching raw location sequence data to travel paths in the road network becomes more important. High-frequency sampling of smartphone locations using accurate but power-hungry positioning technologies is not practically feasible as it consumes an undue amount of the smartphone’s bandwidth and battery power. Hence, there exists a need to develop robust algorithms for map-matching inaccurate and sparse location data in an accurate and timely manner. This paper addresses the above-mentioned need by presenting a novel map-matching solution that combines the widely used approach based on a hidden Markov model (HMM) with the concept of drivers’ route choice. Our algorithm uses an HMM tailored for noisy and sparse data to generate partial map-matched paths in an online manner. We use a route choice model, estimated from real drive data, to reassess each HMM-generated partial path along with a set of feasible alternative paths. We evaluated the proposed algorithm with real world as well as synthetic location data under varying levels of measurement noise and temporal sparsity. The results show that the map-matching accuracy of our algorithm is significantly higher than that of the state of the art, especially at high levels of noise.

Fuzzy clustering has been playing an important role in solving many problems. Fuzzy c-means (FCM) algorithm is most frequently used for fuzzy clustering. But some fixed points of FCM algorithm, known as Tucker's counter example, is not a reasonable solution. Moreover, the FCM algorithm is impossible to perform online learning since it is basically a batch learning scheme. This paper presents an unsupervised learning network as an attempt to improve the shortcomings of conventional clustering algorithms. This model integrates the optimization function of FCM algorithm into an unsupervised learning network. The learning rule of the proposed scheme is a result of formal derivation based on the gradient descent procedure of fuzzy objective function. Using the result of formal derivation, two implementations of the proposed scheme, the batch learning version and online learning version, are devised. They are tested on Chiou's data and Iris data and compared with FCM. Experimental results show that the proposed scheme derived the reasonable solution on Tucker's counter example.

Fuzzy C-Means (FCM) algorithm has good clustering efficiency, for which it is widely used in the field of image segmentation. However, problems such as weak robustness of distance measure, the number of initial clustering to be given in advance and not considering local image feature still exist. In essence, FCM is a local search algorithm. Improper selection of initial value will lead to the need for more iterations and convergence to local optimal solution. By combining evolving clustering (ECM) with FCM algorithm, a new method of remote sensing image segmentation is put forward. By using FCM algorithm to solve the choice of ECM's initialization clustering centers and using FCM to optimize the obtained centers, fuzzy clustering is completed. And by converting fuzzy into a certainty classification, clustering segmentation is realized. The algorithm is typical of relatively less iterations of convergence to global optimum, good stability and robustness. Experiment results show that it helps to produce better segmentation effect and improve the efficiency of remote sensing image segmentation.

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

This paper shows that a choice of weights in the fuzzy c-means algorithm affect the performance of a room equalizer. The ordinary fuzzy c-means (FCM) algorithm already proves useful to deriving an equalizing filter for multiple listeners. A room impulse response models the behaviour of the sounds reflection in the room at each listener location. The FCM algorithm finds similar room impulse responses based on Euclidean distances among the impulse responses and groups them together. But the Euclidean distance used in the FCM implies equal weights for all parts of sound reverberation or reflection. The paper proposes an algorithm to obtain a room acoustic equalization filter based on weighted fuzzy c-means (WFCM) algorithm. The use of WFCM can give clustering more flexibility in obtaining a prototype for each cluster. Then combining the prototypes to obtain a representative room response that derives the inverse filter will be more effective. We use spectral deviation to measure how well each equalizing filter works. Experiments show that different weights in the WFCM algorithm can enhance or degrade the performance of the equalizing filter.

Fuzzy C-Means (FCM) algorithm is a fuzzy pattern recognition method. Clustering precision of the algorithm is affected by its equal partition trend for data set of large discrepancy of each class samples number, and the optimal clustering result of the algorithm mightn't be a right partition in this case. In order to overcome this disadvantage, a Gaussian function Weighted Fuzzy C-Means (WFCM) algorithm is proposed, which the weighted function is produced by a Gaussian function calculating dot density of each sample. To certain extent, the WFCM algorithm has not only overcome the limitation of equal partition trend in fuzzy Cmeans algorithm, but also been favorable convergence and stability. The calculation of the weighted function and the choice of sample dot density range restriction value for the algorithm are both objective. When partially supervised information obtained from a few labeled samples is introduced to the WFCM algorithm, the classification performance of the WFCM algorithm is further enhanced and the convergent speed of objective function is further accelerated.

The movements of talkers' face, nose, mouth and throat are known to convey visual cues and represent several different kinds of informationl, and that can improve speech recognition rate, especially for persons with speech-impairments. We proposed a new speech recognition method using these visual features and hidden Markov model (HMM). Based on global optimisation, a new genetic algorithm (GA) for training HMM was proposed. Six chinese vowels were taken as the experimental data, ten handicapped speakers were taken as the testee. Recognition experiments show that the method is effective and high speed and accuracy for speech recognition. At present, the average recognition rate is 91.47% using improved HMM and 88.96% using the classic training HMM algorithm, So the features has very good robustness and the improved HMM is very good.

In order to overcome the poor anti-noise performance of traditional fuzzy C-Means (FCM) algorithm in image segmentation, a novel improved FCM algorithm was proposed in this paper based on Particle Swarm Optimization (PSO) algorithm and Markov Random Field (MRF) model, which can make full use of the global searching ability of PSO and the spatial information integrating ability of MRF for image segmentation. In this algorithm, the image segmentation is converted to a PSO optimization problem, in which the fitness function is set up to containing the spatial information based on the spectral value and the neighboring pixels modeled by MRFs. And segmentation results can be iteratively obtained during the PSO iterations according to the newly designed membership function of FCM in which the spatial information is integrated. The experiments herein reported in this paper illustrate the better performance of this algorithm than the traditional FCM algorithm and the PSO algorithm for image segmentation.

The localization accuracy of a fingerprint-based localization system is dependent on several factors, one of which is the accuracy and efficiency at which the fingerprint database is clustered. Most highly efficient and accurate clustering algorithms have high time-dependent computational complexity (CC), which tends to limit their practical applicability. A technique that has yet to be explored is the sequential hybridization of multiple low-time CC clustering algorithms to produce a single moderate-time CC clustering algorithm with high localization accuracy. As a result, this paper proposes a clustering algorithm with a moderate time CC that is based on the sequential hybridization of the closest access point (CAP) and improved k-means clustering algorithms. The performance of the proposed sequential hybrid clustering algorithm is determined and compared to the modified affinity propagation clustering (m-APC), fuzzy c-mean (FCM), and 2-CAP algorithms presented in earlier research works using four experimentally generated and publicly available fingerprint databases. The performance metrics considered for the comparisons are the position root mean square error (RMSE) and clustering time based on big O notation. The simulation results show that the proposed sequential hybrid clustering algorithm has improved localization accuracy with position RMSEs of about 54%, 77%, and 52%, respectively, higher than those of the m-APC, FCM, and 2-CAP algorithms. In terms of clustering time, it is 99% and 79% faster than the m-APC and FCM algorithms, respectively, but 90% slower than the 2-CAP algorithm. The results have shown that it is possible to develop a clustering algorithm that has a moderate clustering time with very high localization accuracy through sequential hybridization of multiple clustering algorithms that have a low clustering time with poor localization accuracy. Doi: 10.28991/ESJ-2024-08-02-02 Full Text: PDF

Bias-correction fuzzy clustering algorithms