Search · four archives
Search · four archives
15 papers · ranked by Valyu relevance
Mikhail A. Bragin, Emily L. Tucker
Mixed-Integer Linear Programming (MILP) plays an important role across a range of scientific disciplines and within areas of strategic importance to society. The MILP problems, however, suffer from combinatorial complexity. Because of integer decision variables, as the problem size increases, the number of possible…
Lara Scavuzzo, Karen Aardal, Andrea Lodi, Neil Yorke-Smith
Mixed Integer Linear Programming (MILP) is a pillar of mathematical optimization that offers a powerful modeling language for a wide range of applications. The main engine for solving MILPs is the branch-and-bound algorithm. Adding to the enormous algorithmic progress in MILP solving of the past decades, in more recent…
Albert No
The size of the largest binary single deletion code has been unknown for more than 50 years. It is known that Varshamov-Tenengolts (VT) code is an optimum single deletion code for block length $n\leq10$; however, only a few upper bounds of the size of single deletion code are proposed for larger n. We provide improved…
Ritchie Lee, Susmit Jha, Anastasia Mavridou, Dimitra Giannakopoulou + 4 more
'Ralph Bottesch' 'Max W. Haslbeck' 'Alban Reynaud' 'René Thiemann'] We implement a decision procedure for linear mixed integer arithmetic and formally verify its soundness in Isabelle/HOL. We further integrate this procedure into one application, namely into CeTA, a formally verified certifier to check untrusted…
Konstantinos Gkiotsalitis, Tao Liu
Considering the COVID-19 Capacity Limits: A Dutch Case Study Authors: Konstantinos Gkiotsalitis, Tao Liu The COVID-19 pandemic has had serious adverse impacts on public transport service providers. Most public transport lines exhibit reduced ridership levels while, at the same time, some of them may exhibit passenger…
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…
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…
Pierre Salvy, Vassily Hatzimanikatis
Since the introduction of metabolic models and flux balance analysis (FBA) in systems biology, several attempts have been made to supplement these formulations with expression information to form metabolic and expression models (ME-models). However, directly accounting for enzyme and mRNA production in the mathematical…
Zixiang Xu
Gene knockout has been used to improve the conversion ratio of strains for some chemical products. Based on mixed integer bi-level linear programming (MIBLP) and cell network models, there have been several algorithms to predict the target for deletion to improve the productivity of chemicals. At present, the cell…
Daniel Molina-Pérez, Edgar Alfredo Portilla-Flores, Efrén Mezura-Montes, Eduardo Vega-Alvarado + 2 more
'Efrén Mezura-Montes' 'Eduardo Vega-Alvarado' 'María Bárbara Calva-Yañez' 'Thomas Stützle'] Mixed integer nonlinear programming (MINLP) addresses optimization problems that involve continuous and discrete/integer decision variables, as well as nonlinear functions. These problems often exhibit multiple discontinuous…
Xinyu Liu, Qun Chen, Yong Deng
This paper proposes an optimization algorithm, the dimension-down iterative algorithm (DDIA), for solving a mixed transportation network design problem (MNDP), which is generally expressed as a mathematical programming with equilibrium constraint (MPEC). The upper level of the MNDP aims to optimize the network…
Josh A. Taylor, Alain Rapaport, Denis Dochain
Polyhedral models of metabolic networks are computationally tractable and can predict some cellular functions. A longstanding challenge is incorporating metabolites without losing tractability. In this paper, we do so using a new second-order cone representation of the Michaelis-Menten kinetics. The resulting model…
Elisabeth Gaar, Jon Lee, Ivana Ljubić, Markus Sinnl + 1 more
We study a class of integer bilevel programs with second-order cone constraints at the upper-level and a convex-quadratic objective function and linear constraints at the lower-level. We develop disjunctive cuts (DCs) to separate bilevel-infeasible solutions using a second-order-cone-based cut-generating procedure. We…
Deniz Akdemir
Optimal subset selection is an important task that has numerous algorithms designed for it and has many application areas. STPGA contains a special genetic algorithm supplemented with a tabu memory property (that keeps track of previously tried solutions and their fitness for a number of iterations), and with a…
Giovanny Covarrubias-Pazaran
In the last decade the use of mixed models has become a pivotal part in the implementation of genome-assisted prediction in plant and animal breeding programs. Exploiting the use genetic correlation among traits through multivariate predictions has been proposed in recent years as a way to boost prediction accuracy and…