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Tree search algorithms, such as branch-and-bound, are the most widely used tools for solving combinatorial and nonconvex problems. For example, they are the foremost method for solving (mixed) integer programs and constraint satisfaction…
A phylogeny describes the evolutionary history of an evolving population. Evolutionary search algorithms can perfectly track the ancestry of candidate solutions, illuminating a population's trajectory through the search space. However,…
In recent years, there has been considerable interest in the transformative potential of additive manufacturing (AM) since it allows for producing highly customizable and complex components while reducing lead times and costs. The rise of…
The ancestral maximum-likelihood and phylogeography problems are two fundamental problems involving evolutionary studies. The ancestral maximum-likelihood problem involves identifying a rooted tree alongside internal node sequences that…
Given an undirected graph, the k-vertex cut problem (k-VCP) asks for a minimum-cost set of vertices whose removal yields at least k connected components in the resulting graph. The k-VCP is an important problem in network optimization, with…
Branch-and-cut is the most widely used algorithm for solving integer programs, employed by commercial solvers like CPLEX and Gurobi. Branch-and-cut has a wide variety of tunable parameters that have a huge impact on the size of the search…
We present a novel algorithm for the minimum-depth elimination tree problem, which is equivalent to the optimal treedepth decomposition problem. Our algorithm makes use of two cheaply-computed lower bound functions to prune the search tree,…
We give a 2-approximation algorithm for the Maximum Agreement Forest problem on two rooted binary trees. This NP-hard problem has been studied extensively in the past two decades, since it can be used to compute the Subtree…
This work attempts to combine the strengths of two major technologies that have matured over the last three decades: global mixed-integer nonlinear optimization and branch-and-price. We consider a class of generally nonconvex mixed-integer…
The irregular strip-packing problem consists of the computation of a non-overlapping placement of a set of polygons onto a rectangular strip of fixed width and the minimal length possible. Recent performance gains of the Mixed-Integer…
In this paper we study formulations and algorithms for the cycle clustering problem, a partitioning problem over the vertex set of a directed graph with nonnegative arc weights that is used to identify cyclic behavior in simulation data…
We introduce the fastest known exact algorithm~for~the multiterminal cut problem with k terminals. In particular, we engineer existing as well as new data reduction rules. We use the rules within a branch-and-reduce framework and to boost…
The reconstruction of phylogenetic trees from mixed populations has become important in the study of cancer evolution, as sequencing is often performed on bulk tumor tissue containing mixed populations of cells. Recent work has shown how to…
Lineage tracing, the joint segmentation and tracking of living cells as they move and divide in a sequence of light microscopy images, is a challenging task. Jug et al. have proposed a mathematical abstraction of this task, the moral…
In this paper, we consider the network slicing problem which attempts to map multiple customized virtual network requests (also called services) to a common shared network infrastructure and allocate network resources to meet diverse…
Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…
The Persistent-Phylogeny Model is an extension of the widely studied Perfect-Phylogeny Model, encompassing a broader range of evolutionary phenomena. Biological and algorithmic questions concerning persistent phylogeny have been intensely…
Linear programming (LP) decoding approximates maximum-likelihood (ML) decoding of a linear block code by relaxing the equivalent ML integer programming (IP) problem into a more easily solved LP problem. The LP problem is defined by a set of…
Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…
The reconstruction of phylogenetic networks is an important but challenging problem in phylogenetics and genome evolution, as the space of phylogenetic networks is vast and cannot be sampled well. One approach to the problem is to solve the…