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Algorithms in Bioinformatics : Theory and Implementation
Explores a comprehensive and insightful treatment of the practical application of bioinformatic algorithms in a variety of fields. Delivers a fulsome treatment of some of the main algorithms used to explain biological functions and relationships. It introduces readers to the art of algorithms in a practical manner which is linked with biological theory and interpretation. The book covers many key areas of bioinformatics, including global and local sequence alignment, forced alignment, detection of motifs, Sequence logos, Markov chains or information entropy. Other novel approaches are also described, such as Self-Sequence alignment, Objective Digital Stains (ODSs) or Spectral Forecast and the Discrete Probability Detector (DPD) algorithm. Readers will also benefit from the inclusion of: A detailed presentation of new methods, such as Self-sequence alignment, Objective Digital Stains and Spectral Forecast ; A treatment of sequence alignment, including local sequence alignment, global sequence alignment and forced sequence alignment with full implementations ; Discussions of position-specific weight matrices, including the count, weight, relative frequencies, and log-likelihoods matrices ; A detailed presentation of the methods related to Markov Chains as well as a description of their implementation in Bioinformatics and adjacent fields ; An examination of information and entropy, including sequence logos and explanations related to their meaning ; A chapter on philosophical transactions that allows the reader a broader view of the prediction process ; Extensive worked examples with detailed case studies that point out the meaning of different results
Markov Chains : Models, Algorithms and Applications
Markov chains are a particularly powerful and widely used tool for analyzing a variety of stochastic (probabilistic) systems over time. This monograph will present a series of Markov models, starting from the basic models and then building up to higher-order models. Included in the higher-order discussions are multivariate models, higher-order multivariate models, and higher-order hidden models. In each case, the focus is on the important kinds of applications that can be made with the class of models being considered in the current chapter. Special attention is given to numerical algorithms that can efficiently solve the models. Therefore, Markov Chains: Models, Algorithms and Applications outlines recent developments of Markov chain models for modeling queueing sequences, Internet, re-manufacturing systems, reverse logistics, inventory systems, bio-informatics, DNA sequences, genetic networks, data mining, and many other practical systems.
Lectures on Probability Theory and Statistics : Ecole d'Eté de Probabilités de Saint-Flour XXXIII - 2003
Contains two of the three lectures that were given at the 33rd Probability Summer School in Saint-Flour (July 6-23, 2003). Amir Dembo’s course is devoted to recent studies of the fractal nature of random sets, focusing on some fine properties of the sample path of random walk and Brownian motion. In particular, the cover time for Markov chains, the dimension of discrete limsup random fractals, the multi-scale truncated second moment and the Ciesielski-Taylor identities are explored. Tadahisa Funaki’s course reviews recent developments of the mathematical theory on stochastic interface models, mostly on the so-called nabla varphi interface model. The results are formulated as classical limit theorems in probability theory, and the text serves with good applications of basic probability techniques.
Le raisonnement bayésien : Modélisation et inférence = Bayesian reasoning : Modeling and inference
Describes in detail the practice of the Bayesian statistical approach using many examples chosen for their educational interest. The first part gives the general principles of statistical modeling making it possible to supervise but also to come to the aid of the imagination of the apprentice modeler. By examining examples of increasing difficulty, the reader forges the keys to building their own model. The second part presents the most useful calculation algorithms for estimating the unknowns of the model. Each inference method is presented and illustrated by numerous application cases.
Arithmetical investigations : Representation theory, orthogonal polynomials, and quantum interpolations
In this volume the author further develops his philosophy of quantum interpolation between the real numbers and the p-adic numbers. The p-adic numbers contain the p-adic integers Zp which are the inverse limit of the finite rings Z/pn. This gives rise to a tree, and probability measures w on Zp correspond to Markov chains on this tree. From the tree structure one obtains special basis for the Hilbert space L2(Zp,w). The real analogue of the p-adic integers is the interval [-1,1], and a probability measure w on it gives rise to a special basis for L2([-1,1],w) - the orthogonal polynomials, and to a Markov chain on "finite approximations" of [-1,1]. For special (gamma and beta) measures there is a "quantum" or "q-analogue" Markov chain, and a special basis, that within certain limits yield the real and the p-adic theories. This idea can be generalized variously. In representation theory, it is the quantum general linear group GLn(q)that interpolates between the p-adic group GLn(Zp), and between its real (and complex) analogue -the orthogonal On (and unitary Un )groups. There is a similar quantum interpolation between the real and p-adic Fourier transform and between the real and p-adic (local unramified part of) Tate thesis, and Weil explicit sums.
An Introduction to Markov Processes
Provides a more accessible introduction than other books on Markov processes by emphasizing the structure of the subject and avoiding sophisticated measure theoryLeads the reader to a rigorous understanding of basic theory
