PART I: FOUNDATIONS 1. Introduction to Fixed-Parameter Algorithms 2. Preliminaries and Agreements 3. Parameterized Complexity Theory - A Primer 4. Vertex Cover - An Illustrative Example 5. The Art of Problem Parameterization 6. Summary and Concluding Remarks PART II: ALGORITHMIC METHODS 7. Data Reduction and Problem Kernels 8. Depth-Bounded Search Trees 9. Dynamic Programming 10. Tree Decompositions of Graphs 11. Further Advanced Techniques 12. Summary and Concluding Remarks PART III: SOME THEORY, SOME CASE STUDIES 13. Parameterized Complexity Theory 14. Connections to Approximation Algorithms 15. Selected Case Studies 16. Zukunftsmusik References Index

Invitation to fixed-parameter algorithms

Constraint programming is a powerful paradigm for solving combinatorial search problems that draws on a wide range of techniques from artificial intelligence, computer science, databases, programming languages, and operations research. Constraint programming is currently applied with success to many domains, such as scheduling, planning, vehicle routing, configuration, networks, and bioinformatics.

The aim of this handbook is to capture the full breadth and depth of the constraint programming field and to be encyclopedic in its scope and coverage. While there are several excellent books on constraint programming, such books necessarily focus on the main notions and techniques and cannot cover also extensions, applications, and languages. The handbook gives a reasonably complete coverage of all these lines of work, based on constraint programming, so that a reader can have a rather precise idea of the whole field and its potential. Of course each line of work is dealt with in a survey-like style, where some details may be neglected in favor of coverage. However, the extensive bibliography of each chapter will help the interested readers to find suitable sources for the missing details. Each chapter of the handbook is intended to be a self-contained survey of a topic, and is written by one or more authors who are leading researchers in the area.

The intended audience of the handbook is researchers, graduate students, higher-year undergraduates and practitioners who wish to learn about the state-of-the-art in constraint programming. No prior knowledge about the field is necessary to be able to read the chapters and gather useful knowledge. Researchers from other fields should find in this handbook an effective way to learn about constraint programming and to possibly use some of the constraint programming concepts and techniques in their work, thus providing a means for a fruitful cross-fertilization among different research areas.

The handbook is organized in two parts. The first part covers the basic foundations of constraint programming, including the history, the notion of constraint propagation, basic search methods, global constraints, tractability and computational complexity, and important issues in modeling a problem as a constraint problem. The second part covers constraint languages and solver, several useful extensions to the basic framework (such as interval constraints, structured domains, and distributed CSPs), and successful application areas for constraint programming.

- Covers the whole field of constraint programming
- Survey-style chapters
- Five chapters on applications

Table of Contents

Foreword (Ugo Montanari) 
Part I : Foundations
Chapter 1. Introduction (Francesca Rossi, Peter van Beek, Toby Walsh) 
Chapter 2. Constraint Satisfaction: An Emerging Paradigm (Eugene C. Freuder, Alan K. Mackworth) 
Chapter 3. Constraint Propagation (Christian Bessiere) 
Chapter 4. Backtracking Search Algorithms (Peter van Beek) 
Chapter 5. Local Search Methods (Holger H. Hoos, Edward Tsang) 
Chapter 6. Global Constraints (Willem-Jan van Hoeve, Irit Katriel)
Chapter 7. Tractable Structures for CSPs (Rina Dechter)
Chapter 8. The Complexity of Constraint Languages
(David Cohen, Peter Jeavons) 
Chapter 9. Soft Constraints (Pedro Meseguer, Francesca Rossi, Thomas Schiex) 
Chapter 10. Symmetry in Constraint Programming
(Ian P. Gent, Karen E. Petrie, Jean-Francois Puget)
Chapter 11. Modelling (Barbara M. Smith) 
Part II : Extensions, Languages, and Applications

Chapter 12. Constraint Logic Programming (Kim Marriott, Peter J. Stuckey, Mark Wallace) 
Chapter 13. Constraints in Procedural and Concurrent Languages (Thom Fruehwirth, Laurent Michel, Christian Schulte)
Chapter 14. Finite Domain Constraint Programming Systems (Christian Schulte, Mats Carlsson) 
Chapter 15. Operations Research Methods in Constraint Programming (John Hooker) 
Chapter 16. Continuous and Interval Constraints(Frederic Benhamou, Laurent Granvilliers) 
Chapter 17. Constraints over Structured Domains
(Carmen Gervet) 
Chapter 18. Randomness and Structure (Carla Gomes, Toby Walsh)
Chapter 19. Temporal CSPs (Manolis Koubarakis)
Chapter 20. Distributed Constraint Programming
(Boi Faltings) 
Chapter 21. Uncertainty and Change (Kenneth N. Brown, Ian Miguel)
Chapter 22. Constraint-Based Scheduling and Planning
(Philippe Baptiste, Philippe Laborie, Claude Le Pape, Wim Nuijten)
Chapter 23. Vehicle Routing (Philip Kilby, Paul Shaw) 
Chapter 24. Configuration (Ulrich Junker)
Chapter 25. Constraint Applications in Networks
(Helmut Simonis)
Chapter 26. Bioinformatics and Constraints (Rolf Backofen, David Gilbert)

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Handbook of Constraint Programming

The combination of evolutionary algorithms with local search was named "memetic algorithms" (MAs) (Moscato, 1989). These methods are inspired by models of natural systems that combine the evolutionary adaptation of a population with individual learning within the lifetimes of its members. Additionally, MAs are inspired by Richard Dawkin's concept of a meme, which represents a unit of cultural evolution that can exhibit local refinement (Dawkins, 1976). In the case of MA's, "memes" refer to the strategies (e.g., local refinement, perturbation, or constructive methods, etc.) that are employed to improve individuals. In this paper, we review some works on the application of MAs to well-known combinatorial optimization problems, and place them in a framework defined by a general syntactic model. This model provides us with a classification scheme based on a computable index D, which facilitates algorithmic comparisons and suggests areas for future research. Also, by having an abstract model for this class of metaheuristics, it is possible to explore their design space and better understand their behavior from a theoretical standpoint. We illustrate the theoretical and practical relevance of this model and taxonomy for MAs in the context of a discussion of important design issues that must be addressed to produce effective and efficient MAs.

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A tutorial for competent memetic algorithms: model, taxonomy, and design issues

Multiple structural alignment is a fundamental problem in structural genomics. In this article, we define a reliable and robust algorithm, MUSTANG (MUltiple STructural AligNment AlGorithm), for the alignment of multiple protein structures. Given a set of protein structures, the program constructs a multiple alignment using the spatial information of the C(alpha) atoms in the set. Broadly based on the progressive pairwise heuristic, this algorithm gains accuracy through novel and effective refinement phases. MUSTANG reports the multiple sequence alignment and the corresponding superposition of structures. Alignments generated by MUSTANG are compared with several handcurated alignments in the literature as well as with the benchmark alignments of 1033 alignment families from the HOMSTRAD database. The performance of MUSTANG was compared with DALI at a pairwise level, and with other multiple structural alignment tools such as POSA, CE-MC, MALECON, and MultiProt. MUSTANG performs comparably to popular pairwise and multiple structural alignment tools for closely related proteins, and performs more reliably than other multiple structural alignment methods on hard data sets containing distantly related proteins or proteins that show conformational changes.

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MUSTANG: a multiple structural alignment algorithm.

We present Searn, an algorithm for integrating search and learning to solve complex structured prediction problems such as those that occur in natural language, speech, computational biology, and vision. Searn is a meta-algorithm that transforms these complex problems into simple classification problems to which any binary classifier may be applied. Unlike current algorithms for structured learning that require decomposition of both the loss function and the feature functions over the predicted structure, Searn is able to learn prediction functions for any loss function and any class of features. Moreover, Searn comes with a strong, natural theoretical guarantee: good performance on the derived classification problems implies good performance on the structured prediction problem.

Search-based Structured Prediction

We show that the protein folding problem in the two-dimensional H-P model is NP-complete.

On the complexity of protein folding

We show that calculating contact map overlap (a measure of similarity of protein structures) is NP-hard, but can be solved in polynomial time for several interesting and relevant special cases. We identify an important special case of this problem corresponding to self-avoiding walks, and prove a decomposition theorem and a corollary approximation result for this special case. These are the first approximation algorithms with guaranteed error bounds, and NP-completeness results in the literature in the area of protein structure alignment/fold recognition for measures of structure similarity of practical interest.

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Algorithmic aspects of protein structure similarity

forefront of today’s science (often referred to dramatically as “breaking the genetic code” or “the last phase of the We ahow that the protein folding problem in the two-dimensional Mendelian revolution”) This mapping cm be rou&ly &H-P model io NP-complete

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On the complexity of protein folding (extended abstract)

. Proceedings of the 29th Annual ACM Sym- posium on the Theory of Computing, 1997, pp.21-29. [13] R Unger, J. Moult. Finding the lowest free energy con- formation of a protein is an NP-hard problem: proof and implications. Bulletin of Mathematical Biology 55 (1993), pp. 1163-119s.

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On the complexity of protein folding (abstract)

Combinatorial Chemistry is a powerful new technology in drug design and molecular recognition. It is a wet-laboratory methodology aimed at ``massively parallel'' screening of chemical compounds for the discovery of compounds that have a certain biological activity. The power of the method comes from the interaction between experimental design and computational modeling. Principles of ``rational'' drug design are used in the construction of combinatorial libraries to speed up the discovery of lead compounds with the desired biological activity. This paper presents algorithms, software development and computational complexity analysis for problems arising in the design of combinatorial libraries for drug discovery. The authors provide exact polynomial time algorithms and intractability results for several Inverse Problems-formulated as (chemical) graph reconstruction problems-related to the design of combinatorial libraries. These are the first rigorous algorithmic results in the literature. The authors also present results provided by the combinatorial chemistry software package OCOTILLO for combinatorial peptide design using real data libraries. The package provides exact solutions for general inverse problems based on shortest-path topological indices. The results are superior both in accuracy and computing time to the best software reports published in the literature. For 5-peptoid design, the computation is rigorously reduced to an exhaustive search of about 2% of the search space; the exact solutions are found in a few minutes.

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Deborah Goldman

Papers

On the complexity of protein folding

Algorithmic aspects of protein structure similarity

On the complexity of protein folding (extended abstract)

On the complexity of protein folding (abstract)

Algorithmic strategies in combinatorial chemistry