Combinatorial search on graphs motivated by bioinformatics applications: a brief survey

Authors:
Mathilde Bouvel;Vladimir Grebinski;Gregory Kucherov
Affiliations:
Département d'Informatique, Ecole normale Supérieure de Cachan, France;CompuGene Inc., Jamesburg, nJ;InRIA/LORIA, Villers-lès-nancy, France
Venue:
WG'05 Proceedings of the 31st international conference on Graph-Theoretic Concepts in Computer Science
Year:
2005

Citing 8
Cited 13

Combinatorial search

Combinatorial search
Kolmogorov complexity arguments in combinatorics

Journal of Combinatorial Theory Series A
Reconstructing a Hamiltonian cycle by querying the graph: application to DNA physical mapping

Discrete Applied Mathematics - Special volume on computational molecular biology DAM-CMB series volume 2
Reconstructing set partitions

Proceedings of the tenth annual ACM-SIAM symposium on Discrete algorithms
Learning a Hidden Matching

FOCS '02 Proceedings of the 43rd Symposium on Foundations of Computer Science
On the Power of Additive Combinatorial Search Model

COCOON '98 Proceedings of the 4th Annual International Conference on Computing and Combinatorics
Optimal robust non-unique probe selection using Integer Linear Programming

Bioinformatics
Optimal group testing strktegies with interval queries and their application to splice site detection

ICCS'05 Proceedings of the 5th international conference on Computational Science - Volume Part II

Optimal query complexity bounds for finding graphs

STOC '08 Proceedings of the fortieth annual ACM symposium on Theory of computing
Learning and Verifying Graphs Using Queries with a Focus on Edge Counting

ALT '07 Proceedings of the 18th international conference on Algorithmic Learning Theory
Nonadaptive algorithms for threshold group testing

Discrete Applied Mathematics
Efficient measurement of complex networks using link queries

INFOCOM'09 Proceedings of the 28th IEEE international conference on Computer Communications Workshops
Optimal query complexity bounds for finding graphs

Artificial Intelligence
Competitive group testing and learning hidden vertex covers with minimum adaptivity

FCT'09 Proceedings of the 17th international conference on Fundamentals of computation theory
Reconstructing weighted graphs with minimal query complexity

ALT'09 Proceedings of the 20th international conference on Algorithmic learning theory
Optimally reconstructing weighted graphs using queries

SODA '10 Proceedings of the twenty-first annual ACM-SIAM symposium on Discrete Algorithms
Toward a deterministic polynomial time algorithm with optimal additive query complexity

MFCS'10 Proceedings of the 35th international conference on Mathematical foundations of computer science
Reconstructing weighted graphs with minimal query complexity

Theoretical Computer Science
Almost tight upper bound for finding Fourier coefficients of bounded pseudo-Boolean functions

Journal of Computer and System Sciences
Reconstruction of hidden graphs and threshold group testing

Journal of Combinatorial Optimization
Graph reconstruction via distance oracles

ICALP'13 Proceedings of the 40th international conference on Automata, Languages, and Programming - Volume Part I

Quantified Score

Hi-index	0.00

Visualization

Abstract

The goal of this paper is to present a brief survey of a collection of methods and results from the area of combinatorial search [1,8] focusing on graph reconstruction using queries of different type. The study is motivated by applications to genome sequencing.