Search · four archives
Search · four archives
22 papers · ranked by Valyu relevance
Libor Barto, Silvia Butti
In a recent line of work, Butti and Dalmau have shown that a fixed-template Constraint Satisfaction Problem is solvable by a certain natural linear programming relaxation (equivalent to the basic linear programming relaxation) if and only if it is solvable on a certain distributed network, and this happens if and only…
Arvind U. Raghunathan, Carlos Cardonha, David J. Bergman, Carlos Nohra
'Carlos Nohra'] Linear programming (LP) relaxations are widely employed in exact solution methods for multilinear programs (MLP). One example is the family of Recursive McCormick Linearization (RML) strategies, where bilinear products are substituted for artificial variables, which deliver a relaxation of the original…
Abraham P. Punnen, Navpreet Kaur
optimization problem Authors: ['Abraham P. Punnen' 'Navpreet Kaur'] In this paper, we present several new linearizations of a quadratic binary optimization problem (QBOP), primarily using the method of aggregations. Although aggregations were studied in the past in the context of solving system of Diophantine equations…
Esma Yildirim
We consider linear and semidefinite programming relaxations of nonconvex quadratic programs given by the reformulation-linearization technique (RLT relaxation), and the Shor relaxation combined with the RLT relaxation (SDP-RLT relaxation). By incorporating the firstorder optimality conditions, a quadratic program can…
Aida Khajavirad, Yakun Wang
polynomial optimization Authors: ['Aida Khajavirad' 'Yakun Wang'] We consider the problem of inference in higher-order undirected graphical models with binary labels. We formulate this problem as a binary polynomial optimization problem and propose several linear programming relaxations for it. We compare the strength…
Jorge Carrasco Muriel, Christopher Long, Nikolaus Sonnenschein
GEnome-scale Metabolic (GEM) models are knowledge bases of the reactions and metabolites of a particular organism. These GEM models allow for the simulation of the metabolism - e.g. calculating growth and production yields - based on the stoichiometry, reaction directionality and uptake rates of the metabolic network.…
Immanuel Bomze, Bo Peng, Yuzhou Qiu, E. Alper Yıldırım
Standard quadratic optimization problems (StQPs) provide a versatile modelling tool in various applications. In this paper, we consider StQPs with a hard sparsity constraint, referred to as sparse StQPs. We focus on various tractable convex relaxations of sparse StQPs arising from a mixed-binary quadratic formulation…
Elisabeth Gaar, Markus Sinnl
The discrete -neighbor -center problem (d--CP) is an emerging variant of the classical -center problem which recently got attention in literature. In this problem, we are given a discrete set of points and we need to locate facilities on these points in such a way that the maximum distance between each point where no…
Yuzhou Qiu, E. Alper Yıldırım
We study linear programming relaxations of nonconvex quadratic programs given by the reformulation-linearization technique (RLT), referred to as RLT relaxations. We investigate the relations between the polyhedral properties of the feasible regions of a quadratic program and its RLT relaxation. We establish various…
Renichiro Haba, Masayuki Ohzeki, Kazuyuki Tanaka, Dennis Salahub
Quantum annealing has garnered significant attention as meta-heuristics inspired by quantum physics for combinatorial optimization problems. Among its many applications, nonnegative/binary matrix factorization stands out for its complexity and relevance in unsupervised machine learning. The use of reverse annealing, a…
Ahmad Abdi, Gérard Cornuéjols, Bertrand Guenin, Levent Tunçel
A rational number is dyadic if it has a finite binary representation $p/2^k$, where p is an integer and k is a nonnegative integer. Dyadic rationals are important for numerical computations because they have an exact representation in floating-point arithmetic on a computer. A vector is dyadic if all its entries are…
Mengzhen Guo, Stefan Grünewald
We present Lpnet, a variant of the widely used Neighbor-net method that approximates pairwise distances between taxa by a circular phylogenetic network. We first apply standard methods to construct a binary phylogenetic tree and then use integer linear programming to compute an optimal circular orderings that agrees…
Hao Hu, Boshi Yang
Relaxations of Combinatorial Problems Authors: ['Hao Hu' 'Boshi Yang'] We develop a new method called affine FR for recovering Slater's condition for semidefinite programming (SDP) relaxations of combinatorial optimization (CO) problems. Affine FR is a user-friendly method, as it is fully automatic and only requires a…
Henri Schmidt, Benjamin J. Raphael
Reconstructing unobserved ancestral states of a phylogenetic tree provides insight into the history of evolving systems and is one of the fundamental problems in phylogenetics. For a fixed phylogenetic tree, the most parsimonious ancestral reconstruction – a solution to the small parsimony problem – can be efficiently…
Alejandro Arenas-Vasco, Juan Carlos Rivera, Maria Gulnara Baldoquín, Yangming Zhou
This paper presents a new formulation and valid constraints for a periodic capacitated vehicle routing problem with multiple depots, heterogeneous fleet, and hard time-windows (MDHFPCVRP-TW). The problem raises from a real-world application in the vending machine industry in Medellín, Colombia. Our main contribution is…
Qianxiang Ai, Joshua Schrier
In a recent paper in this journal (Chem. Mater. 2022, 34, 2545-2552), Twyman et al. studied the environmental stability of crystals by introducing a greedy heuristic algorithm for determining possible oxidation reactions. We show how the problem can be solved exactly, with less code and comparable computational time by…
Hao Hu, Renata Sotirov, Henry Wolkowicz
We consider both facial reduction, FR, and symmetry reduction, SR, techniques for semidefinite programming, SDP. We show that the two together fit surprisingly well in an alternating direction method of multipliers, ADMM, approach. In fact, this approach allows for simply adding on nonnegativity constraints, and…
Olesya Melnichenko, Venkat S. Malladi
In the field of genomics, bioinformatics pipelines play a crucial role in processing and analyzing vast biological datasets. These pipelines, consisting of interconnected tasks, can be optimized for efficiency and scalability by leveraging cloud platforms such as Microsoft Azure. The choice of compute resources…
Or Zuk
We define and study the problem of genomic block selection for multiple complex traits. In this problem, one constructs a genome by selecting different genomic parts (e.g. chromosomes) from different source genomes. The constructed genome is associated with a vector of polygenic scores, obtained by summing the…
Fernando H. C. Dias, Alexandru I. Tomescu
Minimum flow decomposition (MFD) is a common problem across various fields of Computer Science, where a flow is decomposed into a minimum set of weighted paths. However, in Bioinformatics applications, such as RNA transcript or quasi-species assembly, the flow is erroneous, since is obtained from noisy read coverages.…
Authors not listed
Automated chemistry platforms hold the potential to enable large-scale organic synthesis campaigns, such as producing a library of compounds for biological evaluation. The efficiency of such platforms will depend on the schedule according to which the synthesis operations are executed. In this work, we study the…
Daniel Machado
Genome-scale metabolic modeling is a powerful framework for predicting metabolic phenotypes of any organism with an annotated genome. For two decades, this framework has been used for rational design of microbial cell factories. In the last decade, the range of applications has exploded, and new frontiers have emerged…