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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.

This is an intellectual biography of Gregory Bateson, one of the most important holistic writers of the twentieth century, whose qualitative approach to information and intelligence in living systems challenges modern science’s exclusive attachment to technical premises of cyber-information and Artificial Intelligence. Hesubstitutes ‘pattern’ and ‘meaning’ for the ‘thinginess’ of data and places his emphasis on ‘mapping’ and gestalt. His approach appears first in his anthropological studies of New Guinea culture and ‘body/mind’ interaction in Balinese which he undertook with his spouse, Margaret Mead. Later, he shows how patterns of relationship and communication exist at a ‘higher,’ or meta-level, to those of biophysical interaction. Perceptions of ‘difference’ and the ‘difference that makes a difference’ create contexts for interpersonal communication; these ‘mind-like’ characteristics are also apparent in the world of living systems, enabling species to co-evolve in a mutually supportive manner—unlike natural selection. One of his legacies is biosemiotics, which focuses on the ability of all organisms and all cells to respond to patterns, even in microorganisms like bacteria and viruses. All are semiotic, that is, they can interpret and develop meaningful preferences in their ordering of events. In ecology, his ‘post-genomic’ stance considers organism-plus-environment as the fundamental unit of life, and not the gene; in so doing he turns many notions of causality ‘upside-down.’ Bateson’s holism yields an ecological aesthetics, never achieved in any of the natural sciences, which underlines the moral divide between sustainable creativity and current biocide in planetary biodiversity.