Hidden Markov Models

Hidden Markov Models (HMMs), although known for decades, have made a big career nowadays and are still in state of development. This book presents theoretical issues and a variety of HMMs applications in speech recognition and synthesis, medicine, neurosciences, computational biology, bioinformatics, seismology, environment protection and engineering. I hope that the reader will find this book useful and helpful for their own research

Soft computing and non-parametric techniques for effective video surveillance systems

Esta tesis propone varios objetivos interconectados para el diseño de un sistema de vídeovigilancia cuyo funcionamiento es pensado para un amplio rango de condiciones. Primeramente se propone una métrica de evaluación del detector y sistema de seguimiento basada en una mínima referencia. Dicha técnica es una respuesta a la demanda de ajuste de forma rápida y fácil del sistema adecuándose a distintos entornos. También se propone una técnica de optimización basada en Estrategias Evolutivas y la combinación de funciones de idoneidad en varios pasos. El objetivo es obtener los parámetros de ajuste del detector y el sistema de seguimiento adecuados para el mejor funcionamiento en una amplia gama de situaciones posibles Finalmente, se propone la construcción de un clasificador basado en técnicas no paramétricas que pudieran modelar la distribución de datos de entrada independientemente de la fuente de generación de dichos datos. Se escogen actividades detectables a corto plazo que siguen un patrón de tiempo que puede ser fácilmente modelado mediante HMMs. La propuesta consiste en una modificación del algoritmo de Baum-Welch con el fin de modelar las probabilidades de emisión del HMM mediante una técnica no paramétrica basada en estimación de densidad con kernels (KDE). _____________________________________This thesis proposes several interconnected objectives for the design of a video-monitoring system whose operation is thought for a wide rank of conditions. Firstly an evaluation technique of the detector and tracking system is proposed and it is based on a minimum reference or ground-truth. This technique is an answer to the demand of fast and easy adjustment of the system adapting itself to different contexts. Also, this thesis proposes a technique of optimization based on Evolutionary Strategies and the combination of fitness functions. The objective is to obtain the parameters of adjustment of the detector and tracking system for the best operation in an ample range of possible situations. Finally, it is proposed the generation of a classifier in which a non-parametric statistic technique models the distribution of data regardless the source generation of such data. Short term detectable activities are chosen that follow a time pattern that can easily be modeled by Hidden Markov Models (HMMs). The proposal consists in a modification of the Baum-Welch algorithm with the purpose of modeling the emission probabilities of the HMM by means of a nonparametric technique based on the density estimation with kernels (KDE)

Recognizing Teamwork Activity In Observations Of Embodied Agents

This thesis presents contributions to the theory and practice of team activity recognition. A particular focus of our work was to improve our ability to collect and label representative samples, thus making the team activity recognition more efficient. A second focus of our work is improving the robustness of the recognition process in the presence of noisy and distorted data. The main contributions of this thesis are as follows: We developed a software tool, the Teamwork Scenario Editor (TSE), for the acquisition, segmentation and labeling of teamwork data. Using the TSE we acquired a corpus of labeled team actions both from synthetic and real world sources. We developed an approach through which representations of idealized team actions can be acquired in form of Hidden Markov Models which are trained using a small set of representative examples segmented and labeled with the TSE. We developed set of team-oriented feature functions, which extract discrete features from the high-dimensional continuous data. The features were chosen such that they mimic the features used by humans when recognizing teamwork actions. We developed a technique to recognize the likely roles played by agents in teams even before the team action was recognized. Through experimental studies we show that the feature functions and role recognition module significantly increase the recognition accuracy, while allowing arbitrary shuffled inputs and noisy data

Comparison of classifiers for human activity recognition

The human activity recognition in video sequences is a field where many types of classifiers have been used as well as a wide range of input features that feed these classifiers. This work has a double goal. First of all, we extracted the most relevant features for the activity recognition by only utilizing motion features provided by a simple tracker based on the 2D centroid coordinates and the height and width of each person's blob. Second, we present a performance comparison among seven different classifiers (two Hidden Markov Models (HMM), a J.48 tree, two Bayesian classifiers, a classifier based on rules and a Neuro-Fuzzy system). The video sequences under study present four human activities (inactive, active, walking and running) that have been manual labeled previously. The results show that the classifiers reveal different performance according to the number of features employed and the set of classes to sort. Moreover, the basic motion features are not enough to have a complete description of the problem and obtain a good classification. © Springer-Verlag Berlin Heidelberg 2007

Reduction of False Positives in Intrusion Detection Based on Extreme Learning Machine with Situation Awareness

Protecting computer networks from intrusions is more important than ever for our privacy, economy, and national security. Seemingly a month does not pass without news of a major data breach involving sensitive personal identity, financial, medical, trade secret, or national security data. Democratic processes can now be potentially compromised through breaches of electronic voting systems. As ever more devices, including medical machines, automobiles, and control systems for critical infrastructure are increasingly networked, human life is also more at risk from cyber-attacks. Research into Intrusion Detection Systems (IDSs) began several decades ago and IDSs are still a mainstay of computer and network protection and continue to evolve. However, detecting previously unseen, or zero-day, threats is still an elusive goal. Many commercial IDS deployments still use misuse detection based on known threat signatures. Systems utilizing anomaly detection have shown great promise to detect previously unseen threats in academic research. But their success has been limited in large part due to the excessive number of false positives that they produce. This research demonstrates that false positives can be better minimized, while maintaining detection accuracy, by combining Extreme Learning Machine (ELM) and Hidden Markov Models (HMM) as classifiers within the context of a situation awareness framework. This research was performed using the University of New South Wales - Network Based 2015 (UNSW-NB15) data set which is more representative of contemporary cyber-attack and normal network traffic than older data sets typically used in IDS research. It is shown that this approach provides better results than either HMM or ELM alone and with a lower False Positive Rate (FPR) than other comparable approaches that also used the UNSW-NB15 data set

A MACHINE LEARNING APPROACH TO QUERY TIME-SERIES MICROARRAY DATA SETS FOR FUNCTIONALLY RELATED GENES USING HIDDEN MARKOV MODELS

Microarray technology captures the rate of expression of genes under varying experimental conditions. Genes encode the information necessary to build proteins; proteins used by cellular functions exhibit higher rates of expression for the associated genes. If multiple proteins are required for a particular function then their genes show a pattern of coexpression during time periods when the function is active within a cell. Cellular functions are generally complex and require groups of genes to cooperate; these groups of genes are called functional modules. Modular organization of genetic functions has been evident since 1999. Detecting functionally related genes in a genome and detecting all genes belonging to particular functional modules are current research topics in this field. The number of microarray gene expression datasets available in public repositories increases rapidly, and advances in technology have now made it feasible to routinely perform whole-genome studies where the behavior of every gene in a genome is captured. This promises a wealth of biological and medical information, but making the amount of data accessible to researchers requires intelligent and efficient computational algorithms. Researchers working on specific cellular functions would benefit from this data if it was possible to quickly extract information useful to their area of research. This dissertation develops a machine learning algorithm that allows one or multiple microarray data sets to be queried with a set of known and functionally related input genes in order to detect additional genes participating in the same or closely related functions. The focus is on time-series microarray datasets where gene expression values are obtained from the same experiment over a period of time from a series of sequential measurements. A feature selection algorithm selects relevant time steps where the provided input genes exhibit correlated expression behavior. Time steps are the columns in microarray data sets, rows list individual genes. A specific linear Hidden Markov Model (HMM) is then constructed to contain one hidden state for each of the selected experiments and is trained using the expression values of the input genes from the microarray. Given the trained HMM the probability that a sequence of gene expression values was generated by that particular HMM can be calculated. This allows for the assignment of a probability score for each gene in the microarray. High-scoring genes are included in the result set (of genes with functional similarities to the input genes.) P-values can be calculated by repeating this algorithm to train multiple individual HMMs using randomly selected genes as input genes and calculating a Parzen Density Function (PDF) from the probability scores of all HMMs for each gene. A feedback loop uses the result generated from one algorithm run as input set for another iteration of the algorithm. This iterated HMM algorithm allows for the characterization of functional modules from very small input sets and for weak similarity signals. This algorithm also allows for the integration of multiple microarray data sets; two approaches are studied: Meta-Analysis (combination of the results from individual data set runs) and the extension of the linear HMM across multiple individual data sets. Results indicate that Meta-Analysis works best for integration of closely related microarrays and a spanning HMM works best for the integration of multiple heterogeneous datasets. The performance of this approach is demonstrated relative to the published literature on a number of widely used synthetic data sets. Biological application is verified by analyzing biological data sets of the Fruit Fly D. Melanogaster and Baker‟s Yeast S. Cerevisiae. The algorithm developed in this dissertation is better able to detect functionally related genes in common data sets than currently available algorithms in the published literature

Differential Evolution to Optimize Hidden Markov Models Training: Application to Facial Expression Recognition

The base system in this paper uses Hidden Markov Models (HMMs) to model dynamic relationships among facial features in facial behavior interpretation and understanding field. The input of HMMs is a new set of derived features from geometrical distances obtained from detected and automatically tracked facial points. Numerical data representation which is in the form of multi-time series is transformed to a symbolic representation in order to reduce dimensionality, extract the most pertinent information and give a meaningful representation to humans. The main problem of the use of HMMs is that the training is generally trapped in local minima, so we used the Differential Evolution (DE) algorithm to offer more diversity and so limit as much as possible the occurrence of stagnation. For this reason, this paper proposes to enhance HMM learning abilities by the use of DE as an optimization tool, instead of the classical Baum and Welch algorithm. Obtained results are compared against the traditional learning approach and significant improvements have been obtained.</p

Hidden Markov Model with Binned Duration and Its Application

Hidden Markov models (HMM) have been widely used in various applications such as speech processing and bioinformatics. However, the standard hidden Markov model requires state occupancy durations to be geometrically distributed, which can be inappropriate in some real-world applications where the distributions on state intervals deviate signi cantly from the geometric distribution, such as multi-modal distributions and heavy-tailed distributions. The hidden Markov model with duration (HMMD) avoids this limitation by explicitly incor- porating the appropriate state duration distribution, at the price of signi cant computational expense. As a result, the applications of HMMD are still quited limited. In this work, we present a new algorithm - Hidden Markov Model with Binned Duration (HMMBD), whose result shows no loss of accuracy compared to the HMMD decoding performance and a com- putational expense that only diers from the much simpler and faster HMM decoding by a constant factor. More precisely, we further improve the computational complexity of HMMD from (TNN +TND) to (TNN +TND ), where TNN stands for the computational com- plexity of the HMM, D is the max duration value allowed and can be very large and D generally could be a small constant value

Adaptive probability scheme for behaviour monitoring of the elderly using a specialised ambient device

A Hidden Markov Model (HMM) modified to work in combination with a Fuzzy System is utilised to determine the current behavioural state of the user from information obtained with specialised hardware. Due to the high dimensionality and not-linearly-separable nature of the Fuzzy System and the sensor data obtained with the hardware which informs the state decision, a new method is devised to update the HMM and replace the initial Fuzzy System such that subsequent state decisions are based on the most recent information. The resultant system first reduces the dimensionality of the original information by using a manifold representation in the high dimension which is unfolded in the lower dimension. The data is then linearly separable in the lower dimension where a simple linear classifier, such as the perceptron used here, is applied to determine the probability of the observations belonging to a state. Experiments using the new system verify its applicability in a real scenario