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Motivated by applications in cancer genomics and following the work of Hajirasouliha and Raphael (WABI 2014), Hujdurovi\'c et al. (IEEE TCBB, to appear) introduced the minimum conflict-free row split (MCRS) problem: split each row of a…
Kloks, Kratsch, and Spinrad showed how treewidth and minimum-fill, NP-hard combinatorial optimization problems related to minimal triangulations, are broken into subproblems by block subgraphs defined by minimal separators. These ideas were…
Recently, Hajirasouliha and Raphael (WABI 2014) proposed a model for deconvoluting mixed tumor samples measured from a collection of high-throughput sequencing reads. This is related to understanding tumor evolution and critical cancer…
Optimization problems consist of either maximizing or minimizing an objective function. Instead of looking for a maximum solution (resp. minimum solution), one can find a minimum maximal solution (resp. maximum minimal solution). Such…
The transversal hypergraph problem is the task of enumerating the minimal hitting sets of a hypergraph. It is a long-standing open question whether this can be done in output-polynomial time. For hypergraphs whose solutions have bounded…
We consider the Minimum Coverage Kernel problem: given a set $B$ of $d$-dimensional boxes, find a subset of $B$ of minimum size covering the same region as $B$. This problem is $\mathsf{NP}$-hard, but as for many $\mathsf{NP}$-hard problems…
The min-rank of a digraph was shown by Bar-Yossef et al. (2006) to represent the length of an optimal scalar linear solution of the corresponding instance of the Index Coding with Side Information (ICSI) problem. In this work, the graphs…
We consider the problems of finding a maximum clique in a graph and finding a maximum-edge biclique in a bipartite graph. Both problems are NP-hard. We write both problems as matrix-rank minimization and then relax them using the nuclear…
One powerful technique to solve NP-hard optimization problems in practice is branch-and-reduce search---which is branch-and-bound that intermixes branching with reductions to decrease the input size. While this technique is known to be very…
Biclustering, also called co-clustering, block clustering, or two-way clustering, involves the simultaneous clustering of both the rows and columns of a data matrix into distinct groups, such that the rows and columns within a group display…
We consider problems that can be formulated as a task of finding an optimal triangulation of a graph w.r.t. some notion of optimality. We present algorithms parameterized by the size of a minimum edge clique cover ($cc$) to such problems.…
First, we study geometric variants of the standard set cover motivated by assignment of directional antenna and shipping with deadlines, providing the first known polynomial-time exact solutions. Next, we consider the following general…
Geometric hitting set problems, in which we seek a smallest set of points that collectively hit a given set of ranges, are ubiquitous in computational geometry. Most often, the set is discrete and is given explicitly. We propose new…
We consider the densest submatrix problem, which seeks the submatrix of fixed size of a given binary matrix that contains the most nonzero entries. This problem is a natural generalization of fundamental problems in combinatorial…
Low-rank matrix completion consists of computing a matrix of minimal complexity that recovers a given set of observations as accurately as possible. Unfortunately, existing methods for matrix completion are heuristics that, while highly…
In the numerical linear algebra community, it was suggested that to obtain nearly optimal bounds for various problems such as rank computation, finding a maximal linearly independent subset of columns (a basis), regression, or low-rank…
Inferring probabilistic networks from data is a notoriously difficult task. Under various goodness-of-fit measures, finding an optimal network is NP-hard, even if restricted to polytrees of bounded in-degree. Polynomial-time algorithms are…
This paper introduces the Simultaneous assignment problem. Let us given a graph with a weight and a capacity function on its edges, and a set of its subgraphs along with a degree upper bound function for each of them. We are also given a…
Two kinds of approximation algorithms exist for the k-BALANCED PARTITIONING problem: those that are fast but compute unsatisfying approximation ratios, and those that guarantee high quality ratios but are slow. In this paper we prove that…
Protein/Peptide microarrays are rapidly gaining momentum in the diagnosis of cancer. High-density and highthroughput peptide arrays are being extensively used to detect tumor biomarkers, examine kinase activity, identify antibodies having…