A Set-Covering Approach with Column Generation for Parsimony Haplotyping

被引：4

作者：

Lancia, Giuseppe ^{[1
]}

Serafini, Paolo ^{[1
]}

机构：

[1] Univ Udine, Dipartimento Matemat & Informat, I-33100 Udine, Italy

来源：

INFORMS JOURNAL ON COMPUTING | 2009年 / 21卷 / 01期

关键词：

integer programming; computational biology; haplotyping; branch and price; branch and cut; set covering; INFERENCE; SAMPLES;

D O I：

10.1287/ijoc.1080.0285

中图分类号：

TP39 [计算机的应用];

学科分类号：

081203 ; 0835 ;

摘要：

W e introduce an exact algorithm, based on integer linear programming (ILP), for the parsimony haplotyping problem (PHP). The PHP uses molecular data and is aimed at the determination of a smallest set of haplotypes that explain a given set of genotypes. Our approach is based on a set-covering formulation of the problem, solved by branch and bound with both column and row generation. Existing ILP methods for the PHP suffer from the large size of the solution space, when the genotypes are long and with many heterozygous sites. Our approach, on the other hand, is based on an effective implicit representation of the solution space, and allows the solution of both real data and simulated instances, which are very hard to solve for other ILPs.

引用

页码：151 / 166

页数：16

共 50 条

[41] THE WORST AND THE MOST PROBABLE PERFORMANCE OF A CLASS OF SET-COVERING ALGORITHMS
LIFSCHITZ, V
PITTEL, B
SIAM JOURNAL ON COMPUTING, 1983, 12 (02) : 329 - 346
[42] CUTTING-PLANE ALGORITHM FOR QUADRATIC SET-COVERING PROBLEM
BAZARAA, MS
GOODE, JJ
OPERATIONS RESEARCH, 1975, 23 (01) : 150 - 158
[43] SCE: A Manifold Regularized Set-Covering Method for Data Partitioning
Li, Xuelong
Lu, Quanmao
Dong, Yongsheng
Tao, Dacheng
IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS, 2018, 29 (05) : 1760 - 1773
[44] Survey of 8 UAV Set-Covering Algorithms for Terrain Photogrammetry
Hammond, Joshua E.
Vernon, Cory A.
Okeson, Trent J.
Barrett, Benjamin J.
Arce, Samuel
Newell, Valerie
Janson, Joseph
Franke, Kevin W.
Hedengren, John D.
REMOTE SENSING, 2020, 12 (14)
[45] A Cost-Based Set-Covering Location-Allocation Problem with Unknown Covering Radius
Bashiri, Mahdi
Fotuhi, Fateme
2009 IEEE INTERNATIONAL CONFERENCE ON INDUSTRIAL ENGINEERING AND ENGINEERING MANAGEMENT, VOLS 1-4, 2009, : 1979 - 1983
[46] USING SET-COVERING PROBLEM TO ASSIGN FIRE COMPANIES TO FIRE HOUSES
WALKER, W
OPERATIONS RESEARCH, 1974, 22 (02) : 275 - 277
[47] A stochastic set-covering location model for both ameliorating and deteriorating items
Hwang, HS
COMPUTERS & INDUSTRIAL ENGINEERING, 2004, 46 (02) : 313 - 319
[48] A formal model of enterprise diagnostic expert systembased on fuzzy set-covering
Yu, W
Shen, H
Liu, JP
Chen, YL
Li, Q
Proceedings of the Second International Conference on Information and Management Sciences, 2002, 2 : 306 - 310
[49] POLYNOMIAL-TIME ALGORITHMS FOR REGULAR SET-COVERING AND THRESHOLD SYNTHESIS
PELED, UN
SIMEONE, B
DISCRETE APPLIED MATHEMATICS, 1985, 12 (01) : 57 - 69
[50] A set-covering based heuristic algorithm for the periodic vehicle routing problem
Cacchiani, V.
Hemmelmayr, V. C.
Tricoire, F.
DISCRETE APPLIED MATHEMATICS, 2014, 163 : 53 - 64

← 1 2 3 4 5 →