Expression.- Spectral Clustering Gene Ontology Terms to Group Genes by Function.- Dynamic De-Novo Prediction of microRNAs Associated with Cell Conditions: A Search Pruned by Expression.- Clustering Gene Expression Series with Prior Knowledge.- A Linear Time Biclustering Algorithm for Time Series Gene Expression Data.- Time-Window Analysis of Developmental Gene Expression Data with Multiple Genetic Backgrounds.- Phylogeny.- A Lookahead Branch-and-Bound Algorithm for the Maximum Quartet Consistency Problem.- Computing the Quartet Distance Between Trees of Arbitrary Degree.- Using Semi-definite Programming to Enhance Supertree Resolvability.- An Efficient Reduction from Constrained to Unconstrained Maximum Agreement Subtree.- Pattern Identification in Biogeography.- On the Complexity of Several Haplotyping Problems.- A Hidden Markov Technique for Haplotype Reconstruction.- Algorithms for Imperfect Phylogeny Haplotyping (IPPH) with a Single Homoplasy or Recombination Event.- Networks.- A Faster Algorithm for Detecting Network Motifs.- Reaction Motifs in Metabolic Networks.- Reconstructing Metabolic Networks Using Interval Analysis.- Genome Rearrangements.- A 1.375-Approximation Algorithm for Sorting by Transpositions.- A New Tight Upper Bound on the Transposition Distance.- Perfect Sorting by Reversals Is Not Always Difficult.- Minimum Recombination Histories by Branch and Bound.- Sequences.- A Unifying Framework for Seed Sensitivity and Its Application to Subset Seeds.- Generalized Planted (l,d)-Motif Problem with Negative Set.- Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI).- The Peres-Shields Order Estimator for Fixed and Variable Length Markov Models with Applications to DNA Sequence Similarity.- Multiple Structural RNA Alignment with Lagrangian Relaxation.- Faster Algorithms for Optimal Multiple Sequence Alignment Based on Pairwise Comparisons.- Ortholog Clustering on a Multipartite Graph.- Linear Time Algorithm for Parsing RNA Secondary Structure.- A Compressed Format for Collections of Phylogenetic Trees and Improved Consensus Performance.- Structure.- Optimal Protein Threading by Cost-Splitting.- Efficient Parameterized Algorithm for Biopolymer Structure-Sequence Alignment.- Rotamer-Pair Energy Calculations Using a Trie Data Structure.- Improved Maintenance of Molecular Surfaces Using Dynamic Graph Connectivity.- The Main Structural Regularities of the Sandwich Proteins.- Discovery of Protein Substructures in EM Maps.

Algorithms in Bioinformatics: 5th International Workshop, WABI 2005, Mallorca, Spain, October 3-6, 2005, Proceedings (Lecture Notes in Computer Science / Lecture Notes in Bioinformatics)

Computational statistics & data analysis

The rapidly growing field of computational social choice, at the intersection of computer science and economics, deals with the computational aspects of collective decision making. This handbook, written by thirty-six prominent members of the computational social choice community, covers the field comprehensively. Chapters devoted to each of the field's major themes offer detailed introductions. Topics include voting theory (such as the computational complexity of winner determination and manipulation in elections), fair allocation (such as algorithms for dividing divisible and indivisible goods), coalition formation (such as matching and hedonic games), and many more. Graduate students, researchers, and professionals in computer science, economics, mathematics, political science, and philosophy will benefit from this accessible and self-contained book.

/pdf/handbook-of-computational-social-choice-12i1xbv1b8.pdf

Handbook of Computational Social Choice

This paper reports on the fifth version of theMixed Integer Programming Library. The miplib 2010 is the first miplib release that has been assembled by a large group from academia and from industry, all of whom work in integer programming. There was mutual consent that the concept of the library had to be expanded in order to fulfill the needs of the community. The new version comprises 361 instances sorted into several groups. This includes the main benchmark test set of 87 instances, which are all solvable by today’s codes, and also the challenge test set with 164 instances, many of which are currently unsolved. For the first time, we include scripts to run automated tests in a predefined way. Further, there is a solution checker to test the accuracy of provided solutions using exact arithmetic.

MIPLIB 2010 - Mixed Integer Programming Library version 5

Control and bribery are settings in which an external agent seeks to influence the outcome of an election. Constructive control of elections refers to attempts by an agent to, via such actions as addition/deletion/partition of candidates or voters, ensure that a given candidate wins. Destructive control refers to attempts by an agent to, via the same actions, preclude a given candidate's victory. An election system in which an agent can sometimes affect the result and it can be determined in polynomial time on which inputs the agent can succeed is said to be vulnerable to the given type of control. An election system in which an agent can sometimes affect the result, yet in which it is NP-hard to recognize the inputs on which the agent can succeed, is said to be resistant to the given type of control.

Aside from election systems with an NP-hard winner problem, the only systems previously known to be resistant to all the standard control types were highly artificial election systems created by hybridization. This paper studies a parameterized version of Copeland voting, denoted by Copelandα, where the parameter α is a rational number between 0 and 1 that specifies how ties are valued in the pairwise comparisons of candidates. In every previously studied constructive or destructive control scenario, we determine which of resistance or vulnerability holds for Copelandα for each rational α, 0 ≤ α ≤ 1. In particular, we prove that Copeland0.5, the system commonly referred to as "Copeland voting," provides full resistance to constructive control, and we prove the same for Copelandα, for all rational α, 0 < α < 1. Among systems with a polynomial-time winner problem, Copeland voting is the first natural election system proven to have full resistance to constructive control. In addition, we prove that both Copeland0 and Copeland1 (interestingly, Copeland1 is an election system developed by the thirteenth-century mystic Llull) are resistant to all standard types of constructive control other than one variant of addition of candidates. Moreover,we show that for each rational α, 0 ≤ α ≤ 1, Copelandα voting is fully resistant to bribery attacks, and we establish fixed-parameter tractability of bounded-case control for Copelandα.

We also study Copelandα elections under more flexible models such as microbribery and extended control, we integrate the potential irrationality of voter preferences into many of our results, and we prove our results in both the unique-winner model and the nonunique-winner model. Our vulnerability results for microbribery are proven via a novel technique involving min-cost network flow.

/pdf/llull-and-copeland-voting-computationally-resist-bribery-and-422xhdsh6i.pdf

Llull and Copeland voting computationally resist bribery and constructive control

We investigate two systems of fully proportional representation suggested by Chamberlin & Courant and Monroe. Both systems assign a representative to each voter so that the "sum of misrepresentations" is minimized. The winner determination problem for both systems is known to be NP-hard, hence this work aims at investigating whether there are variants of the proposed rules and/or specific electorates for which these problems can be solved efficiently. As a variation of these rules, instead of minimizing the sum of misrepresentations, we considered minimizing the maximal misrepresentation introducing effectively two new rules. In the general case these "minimax" versions of classical rules appeared to be still NP-hard.

We investigated the parameterized complexity of winner determination of the two classical and two new rules with respect to several parameters. Here we have a mixture of positive and negative results: e.g., we proved fixed-parameter tractability for the parameter the number of candidates but fixed-parameter intractability for the number of winners.

For single-peaked electorates our results are overwhelmingly positive: we provide polynomial-time algorithms for most of the considered problems. The only rule that remains NP-hard for single-peaked electorates is the classical Monroe rule.

/pdf/on-the-computation-of-fully-proportional-representation-2h0v9dvvf5.pdf

On the computation of fully proportional representation

The Borda voting rule is a positional scoring rule where, for m candidates, for every vote the first candidate receives m- 1 points, the second m- 2 points and so on. A Borda winner is a candidate with highest total score. It has been a prominent open problem to determine the computational complexity of UNWEIGHTED COALITIONAL MANIPULATION UNDER BORDA: Can one add a certain number of additional votes (called manipulators) to an election such that a distinguished candidate becomes a winner? We settle this open problem by showing NP-hardness even for two manipulators and three input votes. Moreover, we discuss extensions and limitations of this hardness result.

/pdf/unweighted-coalitional-manipulation-under-the-borda-rule-is-2rcu61tc6e.pdf

Unweighted coalitional manipulation under the Borda rule Is NP-hard

http://www.akt.tu-berlin.de/fileadmin/fg34/publications-akt/dichlong.pdf

Towards a dichotomy for the Possible Winner problem in elections based on scoring rules

The POSSIBLE WINNER problem asks whether some distinguished candidate may become the winner of an election when the given incomplete votes are extended into complete ones in a favorable way. POSSIBLE WINNER is NP-complete for common voting rules such as Borda, many other positional scoring rules, Bucklin, Copeland etc. We investigate how three different parameterizations influence the computational complexity of POSSIBLE WINNER for a number of voting rules. We show fixed-parameter tractability results with respect to the parameter "number of candidates" but intractability results with respect to the parameter "number of votes". Finally, we derive fixed-parameter tractability results with respect to the parameter "total number of undetermined candidate pairs" and identify an interesting polynomial-time solvable special case for Borda.

/pdf/a-multivariate-complexity-analysis-of-determining-possible-4fw797185q.pdf

A multivariate complexity analysis of determining possible winners given incomplete votes

http://www.akt.tu-berlin.de/fileadmin/fg34/publications-akt/cocoa08-stamped.pdf

Nadja Betzler

Papers

On the computation of fully proportional representation

Unweighted coalitional manipulation under the Borda rule Is NP-hard

Towards a dichotomy for the Possible Winner problem in elections based on scoring rules

A multivariate complexity analysis of determining possible winners given incomplete votes

Parameterized complexity of candidate control in elections and related digraph problems