Application Of Linear And Integer Programming To Three Challenging Problems In Computational Biology
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Application Of Linear And Integer Programming To Three Challenging Problems In Computational Biology
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Author : Hooman Zabeti
language : en
Publisher:
Release Date : 2021
Application Of Linear And Integer Programming To Three Challenging Problems In Computational Biology written by Hooman Zabeti and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021 with categories.
Linear Programming (LP) and Integer Linear Programming (ILP) have increasingly been used in computational and systems biology methods in the past 24 years. From RNA and protein structure prediction to analyzing biological networks, ILP and ILP-based methods provide natural, easy to maintain, and extendable solutions for many NP-hard biological optimization problems. This thesis aims to provide solutions to three challenging problems in system biology, infectious disease, and epidemiology. First, we present a four-step framework to verify and diagnose elemental balance violation in metabolic networks. Identifying such violations can be specifically challenging since chemical formulas of the metabolites in a metabolic network are often partially or entirely left unspecified. However, our framework is able to detect such violations efficiently and makes suggestions for correction without the need for specifying the chemical formula for each metabolite. We have applied our framework to a collection of 94 previously published metabolic network models and successfully detected elemental balance violations in 46 of them. Next, we introduce INGOT-DR, an interpretable classifier for predicting drug resistance. Our classifier utilizes group testing and Boolean compressed sensing to provide highly accurate and interpretable predictions, which could be helpful to investigate the mechanism of drug resistance in pathogenic bacteria such as Mycobacterium tuberculosis. Our method is also flexible enough to be optimized for various evaluation metrics at the same time. INGOT- DR has been tested for predicting drug resistance on five first-line and seven second-line antibiotics used for treating tuberculosis and showed higher or comparable accuracy to commonly used machine learning models for phenotype-genotype prediction. Our method was also able to identify variants located in genes previously reported to be associated with drug resistance. Finally, we present GroupTesing, a modular software platform for a comprehensive evaluation of non-adaptive group testing strategies. This software can perform the evaluation in both a noiseless setting and in the presence of single or multiple realistic noise sources modeled on published experimental observations, which makes them applicable to polymerase chain reaction (PCR) tests, the dominant type of tests for SARS-CoV-2.
Integer Linear Programming In Computational And Systems Biology
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Author : Dan Gusfield
language : en
Publisher: Cambridge University Press
Release Date : 2019-06-13
Integer Linear Programming In Computational And Systems Biology written by Dan Gusfield and has been published by Cambridge University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-06-13 with Computers categories.
This hands-on tutorial text for non-experts demonstrates biological applications of a versatile modeling and optimization technique.
Convexification And Global Optimization In Continuous And Mixed Integer Nonlinear Programming
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Author : Mohit Tawarmalani
language : en
Publisher: Springer Science & Business Media
Release Date : 2013-04-17
Convexification And Global Optimization In Continuous And Mixed Integer Nonlinear Programming written by Mohit Tawarmalani and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013-04-17 with Mathematics categories.
Interest in constrained optimization originated with the simple linear pro gramming model since it was practical and perhaps the only computationally tractable model at the time. Constrained linear optimization models were soon adopted in numerous application areas and are perhaps the most widely used mathematical models in operations research and management science at the time of this writing. Modelers have, however, found the assumption of linearity to be overly restrictive in expressing the real-world phenomena and problems in economics, finance, business, communication, engineering design, computational biology, and other areas that frequently demand the use of nonlinear expressions and discrete variables in optimization models. Both of these extensions of the linear programming model are NP-hard, thus representing very challenging problems. On the brighter side, recent advances in algorithmic and computing technology make it possible to re visit these problems with the hope of solving practically relevant problems in reasonable amounts of computational time. Initial attempts at solving nonlinear programs concentrated on the de velopment of local optimization methods guaranteeing globality under the assumption of convexity. On the other hand, the integer programming liter ature has concentrated on the development of methods that ensure global optima. The aim of this book is to marry the advancements in solving nonlinear and integer programming models and to develop new results in the more general framework of mixed-integer nonlinear programs (MINLPs) with the goal of devising practically efficient global optimization algorithms for MINLPs.
Integer Programming And Combinatorial Optimization
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Author : Michael Jünger
language : en
Publisher: Springer Science & Business Media
Release Date : 2005-06
Integer Programming And Combinatorial Optimization written by Michael Jünger and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2005-06 with Computers categories.
This book constitutes the refereed proceedings of the 11th International Conference on Integer Programming and Combinatorial Optimization, IPCO 2005, held in Berlin, Germany in June 2005. The 34 revised full papers presented were carefully reviewed and selected from 119 submissions. Among the topics addressed are mixed-integer programming, graph theory, graph algorithms, approximation, linear programming, approximability, packing, scheduling, computational geometry, randomization, network algorithms, sequencing, TSP, and travelling salesman problem.
From Computational Logic To Computational Biology
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Author : Domenico Cantone
language : en
Publisher: Springer Nature
Release Date : 2024-03-15
From Computational Logic To Computational Biology written by Domenico Cantone and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2024-03-15 with Mathematics categories.
Alfredo Ferro’s impact on information technology has traversed diverse domains, encompassing Computational Logic, Data Mining, Bioinformatics, and Complex Systems. After first studying Mathematics at the University of Catania, he received a Ph.D. in Computer Science from NYU in 1981, working under the supervision of Jacob Theodor (Jack) Schwartz. He returned to the University of Catania where he established the Computer Science undergraduate program, served as the coordinator of the Ph.D. program in Computer Science, cofounded the Ph.D. program in Biology, Human Genetics, and Bioinformatics, and retired as a full professor in 2021. Alfredo’s academic career as a computer scientist is characterized by two distinct research phases: Computational Logic until approximately 1995, followed by a notable focus on Data Mining and Bioinformatics. The contributions in this volume reflect the quality and the scope of his personal and collaborative successes. He also taught andinspired many excellent scientists. A pioneering initiative was to establish summer schools for Ph.D. students in 1989, leading to the so-called Lipari School, now the J.T. Schwartz International School for Scientific Research, where Alfredo continues to serve as director. This prestigious series includes schools focused on Computer Science, Complex Systems, and Computational Biology, featuring world-class scientists as lecturers and mentors.
Bioinformatics And Phylogenetics
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Author : Tandy Warnow
language : en
Publisher: Springer
Release Date : 2019-04-08
Bioinformatics And Phylogenetics written by Tandy Warnow and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-04-08 with Science categories.
This volume presents a compelling collection of state-of-the-art work in algorithmic computational biology, honoring the legacy of Professor Bernard M.E. Moret in this field. Reflecting the wide-ranging influences of Prof. Moret’s research, the coverage encompasses such areas as phylogenetic tree and network estimation, genome rearrangements, cancer phylogeny, species trees, divide-and-conquer strategies, and integer linear programming. Each self-contained chapter provides an introduction to a cutting-edge problem of particular computational and mathematical interest. Topics and features: addresses the challenges in developing accurate and efficient software for the NP-hard maximum likelihood phylogeny estimation problem; describes the inference of species trees, covering strategies to scale phylogeny estimation methods to large datasets, and the construction of taxonomic supertrees; discusses the inference of ultrametric distances from additive distance matrices, and the inference of ancestral genomes under genome rearrangement events; reviews different techniques for inferring evolutionary histories in cancer, from the use of chromosomal rearrangements to tumor phylogenetics approaches; examines problems in phylogenetic networks, including questions relating to discrete mathematics, and issues of statistical estimation; highlights how evolution can provide a framework within which to understand comparative and functional genomics; provides an introduction to Integer Linear Programming and its use in computational biology, including its use for solving the Traveling Salesman Problem. Offering an invaluable source of insights for computer scientists, applied mathematicians, and statisticians, this illuminating volume will also prove useful for graduate courses on computational biology and bioinformatics.
Algebraic Statistics For Computational Biology
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Author : L. Pachter
language : en
Publisher: Cambridge University Press
Release Date : 2005-08-22
Algebraic Statistics For Computational Biology written by L. Pachter and has been published by Cambridge University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2005-08-22 with Mathematics categories.
This book, first published in 2005, offers an introduction to the application of algebraic statistics to computational biology.
Discrete And Topological Models In Molecular Biology
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Author : Nataša Jonoska
language : en
Publisher: Springer Science & Business Media
Release Date : 2013-12-23
Discrete And Topological Models In Molecular Biology written by Nataša Jonoska and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013-12-23 with Computers categories.
Theoretical tools and insights from discrete mathematics, theoretical computer science, and topology now play essential roles in our understanding of vital biomolecular processes. The related methods are now employed in various fields of mathematical biology as instruments to "zoom in" on processes at a molecular level. This book contains expository chapters on how contemporary models from discrete mathematics – in domains such as algebra, combinatorics, and graph and knot theories – can provide perspective on biomolecular problems ranging from data analysis, molecular and gene arrangements and structures, and knotted DNA embeddings via spatial graph models to the dynamics and kinetics of molecular interactions. The contributing authors are among the leading scientists in this field and the book is a reference for researchers in mathematics and theoretical computer science who are engaged with modeling molecular and biological phenomena using discrete methods. It may also serve as a guide and supplement for graduate courses in mathematical biology or bioinformatics, introducing nontraditional aspects of mathematical biology.
Computational Advances In Bio And Medical Sciences
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Author : Mukul S. Bansal
language : en
Publisher: Springer Nature
Release Date : 2022-10-18
Computational Advances In Bio And Medical Sciences written by Mukul S. Bansal and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-10-18 with Computers categories.
This book constitutes revised selected papers from the refereed proceedings of the 11th International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2021, held as a virtual event during December 16–18, 2021. The 13 full papers included in this book were carefully reviewed and selected from 17 submissions. They were organized in topical sections as follows: Computational advances in bio and medical sciences; and computational advances in molecular epidemiology.
Theory And Applications Of Satisfiability Testing Sat 2006
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Author : Armin Biere
language : en
Publisher: Springer Science & Business Media
Release Date : 2006-07-26
Theory And Applications Of Satisfiability Testing Sat 2006 written by Armin Biere and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2006-07-26 with Computers categories.
This book constitutes the refereed proceedings of the 9th International Conference on Theory and Applications of Satisfiability Testing, SAT 2006, held in Seattle, WA, USA in August 2006 as part of the 4th Federated Logic Conference, FLoC 2006.The 26 revised full papers presented together with 11 revised short papers presented together with 2 invited talks were carefully selected from 95 submissions. All current research issues in propositional and quantified Boolean formula satisfiability testing are covered; the papers are organized in topical sections on proofs and cores, heuristics and algorithms, applications, SMT, structure, MAX-SAT, local search and survey propagation, QBF, as well as counting and concurrency.