Heuristic search heuristic search attempts to find the best tree, without looking at all possible trees.

Slides:

Advertisements

Similar presentations

Review: Search problem formulation

Advertisements

Parsimony Small Parsimony and Search Algorithms Genome 559: Introduction to Statistical and Computational Genomics Elhanan Borenstein.

Traveling Salesperson Problem

Lecture 12: Revision Lecture Dr John Levine Algorithms and Complexity March 27th 2006.

Artificial Intelligence Adversarial search Fall 2008 professor: Luigi Ceccaroni.

Cladogram Building - 1 ß How complex is this problem anyway ? ß NP-complete:  Time needed to find solution in- creases exponentially with size of problem.

Parsimony based phylogenetic trees Sushmita Roy BMI/CS 576 Sep 30 th, 2014.

Algorithm Strategies Nelson Padua-Perez Chau-Wen Tseng Department of Computer Science University of Maryland, College Park.

“Inferring Phylogenies” Joseph Felsenstein Excellent reference

1. 2 Rooting the tree and giving length to branches.

Shirokuro : A Backtracking Approach Benjamin Bush Faculty Advisors: Dr. Russ Abbott, Dr. Gary Brookfield Department of Computer Science, Department of.

Building phylogenetic trees Jurgen Mourik & Richard Vogelaars Utrecht University.

5 - 1 Chap 5 The Evolution Trees Evolutionary Tree.

. Phylogenetic Trees Lecture 3 Based on: Durbin et al 7.4; Gusfield 17.

SubSea: An Efficient Heuristic Algorithm for Subgraph Isomorphism Vladimir Lipets Ben-Gurion University of the Negev Joint work with Prof. Ehud Gudes.

NJ was originally described as a method for approximating a tree that minimizes the sum of least- squares branch lengths – the minimum – evolution criterion.

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Phylogenetic Reconstruction: Parsimony Anders Gorm Pedersen

A forest of trees even with modest numbers of tip species, the number of possible trees is frightening. Fitch W.M Syst. Zool. 20:

Chapter 5 The Evolution Trees.

Given Connections Solution

MAE 552 – Heuristic Optimization Lecture 5 February 1, 2002.

Probabilistic methods for phylogenetic trees (Part 2)

Building Phylogenies Parsimony 2.

Parsimony methods the evolutionary tree to be preferred involves ‘the minimum amount of evolution’ Edwards & Cavalli-Sforza Reconstruct all evolutionary.

Degree A F H G B E D C. Adjacent A F H G B E D C.

Lecture 8 – Searching Tree Space. The Search Tree.

Angles Opposite Corresponding Alternate Supplementary.

Maximum parsimony Kai Müller.

Escaping local optimas Accept nonimproving neighbors – Tabu search and simulated annealing Iterating with different initial solutions – Multistart local.

Minimum Spanning Trees

PARSIMONY ANALYSIS and Characters. Genetic Relationships Genetic relationships exist between individuals within populations These include ancestor-descendent.

Molecular phylogenetics 1 Level 3 Molecular Evolution and Bioinformatics Jim Provan Page and Holmes: Sections

Parsimony-Based Approaches to Inferring Phylogenetic Trees BMI/CS 576 Colin Dewey Fall 2010.

Problem Solving by Searching Search Methods : informed (Heuristic) search.

Games. Adversaries Consider the process of reasoning when an adversary is trying to defeat our efforts In game playing situations one searches down the.

Cladogram construction Thanks to Leandro Gaetano.

 One of the tree applications in Chapter 10 is binary search trees.  In Chapter 10, binary search trees are used to implement bags and sets.  This presentation.

Evolutionary tree reconstruction

GAME PLAYING 1. There were two reasons that games appeared to be a good domain in which to explore machine intelligence: 1.They provide a structured task.

Divide and Conquer Optimization problem: z = max{cx : x  S}

Parsimony-Based Approaches to Inferring Phylogenetic Trees BMI/CS 576 Colin Dewey Fall 2015.

Maximum Likelihood Given competing explanations for a particular observation, which explanation should we choose? Maximum likelihood methodologies suggest.

Tree Searching Methods Exhaustive search (exact) Branch-and-bound search (exact) Heuristic search methods (approximate) –Stepwise addition –Branch swapping.

1 Alignment Matrix vs. Distance Matrix Sequence a gene of length m nucleotides in n species to generate an… n x m alignment matrix n x n distance matrix.

Parsimony and searching tree-space. The basic idea To infer trees we want to find clades (groups) that are supported by synapomorpies (shared derived.

The n queens problem Many solutions to a classic problem: On an n x n chess board, place n queens so no queen threatens another.

Best-first search is a search algorithm which explores a graph by expanding the most promising node chosen according to a specified rule.

Spanning Trees Dijkstra (Unit 10) SOL: DM.2 Classwork worksheet Homework (day 70) Worksheet Quiz next block.

南亚和印度.

Dept. Computer Science, Korea Univ. Intelligent Information System Lab A I (Artificial Intelligence) Professor I. J. Chung.

Molecular phylogenetics continued…

Adversarial Search and Game-Playing

School of Computer Science & Engineering

Traveling Salesperson Problem

CS 460 Spring 2011 Lecture 4.

#31 - Phylogenetics Character-Based Methods

General Purpose Procedures Applied to Scheduling

BNFO 602 Phylogenetics Usman Roshan.

Search and Game Playing

CSCI2950-C Lecture 8 Molecular Phylogeny: Parsimony and Likelihood

The n queens problem Many solutions to a classic problem:

Lecture 8 – Searching Tree Space

Approaches to search Simple search Heuristic search Genetic search

PARSIMONY ANALYSIS.

Md. Tanveer Anwar University of Arkansas

Spanning Trees Lecture 20 CS2110 – Spring 2015.

Stephen Chen York University

More Graphs Lecture 19 CS2110 – Fall 2009.

Presentation transcript:

Heuristic search heuristic search attempts to find the best tree, without looking at all possible trees

heuristic search methods tend to be greedy

local optimum global optimum heuristic search methods may fail to find the best solution

Moving through the trees 1.Nearest-neighbour interchanges b a c e d nearest neighbour interchanges ‘swap’ adjacent branches to find alternative trees

Moving through the trees 1.Nearest-neighbour interchanges b a c e d nearest neighbour interchanges starts by erasing an internal branch

Moving through the forest 1.Nearest-neighbour interchanges b a c e d and then erases the two braches connected to it at each end

Moving through the forest 1.Nearest-neighbour interchanges b a c e d b e a c d the four subtrees are now hooked together in all possible ways ((a+c) + e) + (b+d)

Moving through the forest 1.Nearest-neighbour interchanges b a c e d b e a c d b c a e d ((a+e) + c) + (b+d)

Moving through the forest 1.Nearest-neighbour interchanges b a c e d b e a c d b c a e d b a c e d now a second internal branch is erased and the procedure is repeated

Moving through the forest 1.Nearest-neighbour interchanges b a c e d b e a c d b c a e d b a c e d a b c e d b d c e a

Moving through the forest 1.Nearest-neighbour interchanges b a c e d b e a c d b c a e d b a c e d a b c e d b d c e a

b d c e a a b c e d b c e a d a d b c e b a c e d a e b d c a b d e c a d b e c a c b e d a e b c d a e c d b c a b e d a b c d e d a b c e a c d e b

Characters Species Alpha (a) Beta (b) Gamma (c) Delta (d) Epsilon (e)001110

b d c e a a b c e d b c e a d a d b c e b a c e d a e b d c a b d e c a d b e c a c b e d a e b c d a e c d b c a b e d a b c d e d a b c e a c d e b [11] [9] [10] [9] [8] [9]

b d c e a a b c e d b c e a d a d b c e b a c e d a e b d c a b d e c a d b e c a c b e d a e b c d a e c d b c a b e d a b c d e d a b c e a c d e b [11] [9] [10] [9] [8] [11] [9]

b d c e a a b c e d b c e a d a d b c e b a c e d a e b d c a b d e c a d b e c a c b e d a e b c d a e c d b c a b e d a b c d e d a b c e a c d e b [11] [9] [10] [9] [8] [11] [9]

b d c e a a b c e d b c e a d a d b c e b a c e d a e b d c a b d e c a d b e c a c b e d a e b c d a e c d b c a b e d a b c d e d a b c e a c d e b [11] [9] [10] [9] [8] [11] [9]

b d c e a a b c e d b c e a d a d b c e b a c e d a e b d c a b d e c a d b e c a c b e d a e b c d a e c d b c a b e d a b c d e d a b c e a c d e b [11] [9] [10] [9] [8] [11] [9]

Moving through the forest 1.Nearest-neighbour interchanges 2.Subtree pruning and regrafting (SPR) g c a d f b i h j k e in SPR, a branch with a subtree is removed…

Moving through the forest 1.Nearest-neighbour interchanges 2.Subtree pruning and regrafting g c a d f b i h j k e … and reinserted in all possible places.

Moving through the forest 1.Nearest-neighbour interchanges 2.Subtree pruning and regrafting g c a d f b i h j k e

Moving through the forest 1.Nearest-neighbour interchanges 2.Subtree pruning and regrafting g c a d f b i h j k e

Moving through the forest 1.Nearest-neighbour interchanges 2.Subtree pruning and regrafting (SPR) 3.Tree bisection and reconnection (TBR) g c a d f b i h j k e in TBR, the tree is first bisected …

Moving through the forest 1.Nearest-neighbour interchanges 2.Subtree pruning and regrafting 3.Tree bisection and reconnection g c a d f b i h j k e and then all possible connections are made between a branch of one subtree and a branch of the other

Moving through the forest 1.Nearest-neighbour interchanges 2.Subtree pruning and regrafting 3.Tree bisection and reconnection g c a d k e f b i h j

Moving through the forest 1.Nearest-neighbour interchanges 2.Subtree pruning and regrafting 3.Tree bisection and reconnection 4.… many more rearrangement methods exist and new ones are being developed

Sequential addition a b c the sequential addition strategy starts with a simple tree and adds species one by one

Sequential addition a b c a b c d a d b c a c b d [9] [7] [8] every new tree is evaluated on the way,...

Sequential addition a b c a b c d a d b c a c b d a d b c a d b e a d c e a e b c e d b c a d e c b [9] [11] [9] [7] [8] … and the most promising path is taken

Star decomposition a bc d e f a bc d e f a bc d e f a b c d e f star decomposition starts out with an unresolved tree and sequentially pairs species: e.g. UPGMA and neighbour-joining techniques