PPT-Network algorithms in biology:

from accurate genome annotations to personalized medicine Jianhua Ruan PhD Computer Science Department University of Texas at San Antonio httpwwwcsutsaedu jruan Molecular biology in a nutshell. for Linear Algebra and Beyond. Jim . Demmel. EECS & Math Departments. UC Berkeley. 2. Why avoid communication? (1/3). Algorithms have two costs (measured in time or energy):. Arithmetic (FLOPS). Communication: moving data between . Some of the fastest known algorithms for certain tasks rely on chance. Stochastic/Randomized Algorithms. Two common variations. Monte Carlo. Las Vegas. We have already encountered some of both in this class. 1. Graph Algorithms. Many problems are naturally represented as graphs. Networks, Maps, Possible paths, Resource Flow, etc.. Ch. 3 focuses on algorithms to find connectivity in graphs. Ch. 4 focuses on algorithms to find paths within graphs. Optimization problems, Greedy Algorithms, Optimal Substructure and Greedy choice. Learning & Development Team. http://academy.telerik.com. . Telerik Software Academy. Table of Contents. Optimization Problems. Lars . Arge. Spring . 2012. February . 27, 2012. Lars Arge. I/O-algorithms. 2. Random Access Machine Model. Standard theoretical model of computation:. Infinite memory. Uniform access cost. R . A. M. BIT 1003- Presentation 4. An algorithm is a method for solving a class of problems. . While computer scientists think a lot about algorithms, the term applies to any method of solving a particular type of problem. . 1. Evolutionary Algorithms. CS 478 - Evolutionary Algorithms. 2. Evolutionary Computation/Algorithms. Genetic Algorithms. Simulate “natural” evolution of structures via selection and reproduction, based on performance (fitness). Algorithm. Input. Output. 1. Analysis of Algorithms. How long does this take to open 1) know 2) don’t know. . Analysis of Algorithms. 2. If know combination O(n) . where n is number of rings. . If the alphabet is size m, O(nm). Instructor: Arun Sen. Office: BYENG . 530. Tel: 480-965-6153. E-mail: asen@asu.edu. Office Hours: . MW 3:30-4:30 or by appointment. TA: . TBA. Office. : TBA. Tel: . TBA. E-mail: . TBA. Office Hours. : . appeared in the 1950s and 1960s. used to find approximations in search problems. use principles of natural selection to find an optimized solution. part of evolutionary algorithms. What is it?. subset of evolutionary computation. 1. Decrease-and-Conquer. Reduce . original problem . instance to . smaller . instance . of the same problem. Solve smaller . instance. Extend solution . of smaller . instance . to obtain solution to original instance. 10 Bat Algorithms Xin-She Yang, Nature-Inspired Optimization Algorithms, Elsevier, 2014 The bat algorithm (BA) is a bio-inspired algorithm developed by Xin-She Yang in 2010. 10.1 Echolocation of Bats . Balantidium. . coli. o. nly Ciliate . known to be pathogenic to humans. . t. he . largest protozoan parasite of humans. . p. rimarily . a parasite of pigs, with strains adapted to various other . ;. . the. . study of . biology. at the . molecular. level.. Molecular biology. ;. . the. . study of . gene . structure and functions at the . molecular level. . to understand the molecular basis of hereditary, genetic variation, and the expression patterns of genes. .