Get Biomathematics: Modelling and Simulation PDF

By J. C. Misra

ISBN-10: 9812381104

ISBN-13: 9789812381101

Presents details on modelling and simulation in biomathematics. This ebook is of curiosity to researchers who're drawn to a few of the parts of the sphere, and to graduate scholars in similar parts, in addition to academics. a number of the chapters were written via amazing specialists within the box.

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Additional resources for Biomathematics: Modelling and Simulation

Example text

The Markov process is homogeneous: P(yi(s + t)\yi(s))=P(yi(t)\yi{0)). ,N}. • Substitutions at different positions are independent of each other: N P(yi(t),.. ,yN(0)) = »=i Y[P(yi(t)\yi(0)). y(t) P(y(t) P(y(t) P(«) lP(y(t) A) A) A) A) P(y(t) P(y(t) P(y{t) P(y(t) A\y(0) T) G\y(Q) T) C\y(0) -T) T\y(0) T) (1) Because of the site independence, the site label (that is, the subscript) has been dropped to simplify the notation. Equation (1) obviously implies that P(0) = I, (2) where I is the unit matrix.

13 The factorization (17) allows us to compute the probability of a complete configuration of nucleotides. However, while we obtain the nucleotides of the extant species, yi, from the DNA sequence alignment, the nucleotides at the inner nodes, z$, are never observed. This requires us to marginalize over them, as illustrated in Fig. 6: P(yi, 2/2,2/3,2/4 |w, S) = Y^ X I p ( y i - 2/2,2/3,2/4,21, Z2|w, 5). (21) There are efficient message-passing algorithms to carry out this marginalization and decrease the computational complexity of the summation; see [6].

G. McGuire, F. Wright and M. J. Prentice, A Bayesian method for detecting recombination in DNA multiple alignments, J. Computational Biology 7(1/2) (2000) 159-170. M. Moniz de Sa and G. Drouin, Phytogeny and substitution rates of angiosperm actin genes, Molecular Biology Evolution 13 (1996) 1198-1212. R. M. Neal and G. E. Hinton, A view of the EM algorithm that justifies incremental, sparse, and other variants, in Learning in Graphical Models, ed. M. I. Jordan (MIT Press, Cambridge, MA, 1999), pp.

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Biomathematics: Modelling and Simulation by J. C. Misra


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