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Microarrays are research tools used in gene discovery as well as disease and cancer diagnostics. Two prominent but challenging problems related to microarrays are the Border Minimization Problem (BMP) and the Border Minimization Problem…
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…
Oligonucleotide arrays are used in a wide range of genomic analyses, such as gene expression profiling, comparative genomic hybridization, chromatin immunoprecipitation, SNP detection, etc. During fabrication, the sites of an…
This paper introduces weighted-BMP, a variant of the Bandwidth Minimization Problem (BMP), with a significant application in optimizing quantum emulation. Weighted-BMP optimizes particles ordering to reduce the emulation costs, by designing…
The problem of sparse approximation and the closely related compressed sensing have received tremendous attention in the past decade. Primarily studied from the viewpoint of applied harmonic analysis and signal processing, there have been…
The Matrix Bandwidth Minimization Problem (MBMP) seeks for a simultaneous reordering of the rows and the columns of a square matrix such that the nonzero entries are collected within a band of small width close to the main diagonal. The…
Crossing minimization is one of the central problems in graph drawing. Recently, there has been an increased interest in the problem of minimizing crossings between paths in drawings of graphs. This is the metro-line crossing minimization…
In this paper we investigate the colorful components framework, motivated by applications emerging from comparative genomics. The general goal is to remove a collection of edges from an undirected vertex-colored graph $G$ such that in the…
The study of genetic map linearization leads to a combinatorial hard problem, called the {\em minimum breakpoint linearization} (MBL) problem. It is aimed at finding a linearization of a partial order which attains the minimum breakpoint…
Genome rearrangements are events in which large blocks of DNA exchange pieces during evolution. The analysis of such events is a tool for understanding evolutionary genomics, based on finding the minimum number of rearrangements to…
Given a redundant dictionary $\Phi$, represented by an $M \times N$ matrix ($\Phi \in \mathbb{R}^{M \times N}$) and a target signal $y \in \mathbb{R}^M$, the \emph{sparse approximation problem} asks to find an approximate representation of…
A novel multi-resolution technique called border mapping multi-resolution (BMMR) is proposed for projection-based particle methods. The BMMR aims to obtain background equivalent particle distributions in the two sides of a border between…
In order to formulate mathematical conjectures likely to be true, a number of base cases must be determined. However, many combinatorial problems are NP-hard and the computational complexity makes this research approach difficult using a…
Formulations of the Image Decomposition Problem as a Multicut Problem (MP) w.r.t. a superpixel graph have received considerable attention. In contrast, instances of the MP w.r.t. a pixel grid graph have received little attention, firstly,…
The submodular partitioning problem asks to minimize, over all partitions $P$ of a ground set $V$, the sum of a given submodular function $f$ over the parts of $P$. The problem has seen considerable work in approximability, as it…
The Partitioning Min-Max Weighted Matching (PMMWM) problem is an NP-hard problem that combines the problem of partitioning a group of vertices of a bipartite graph into disjoint subsets with limited size and the classical Min-Max Weighted…
MAP is the problem of finding a most probable instantiation of a set of nvariables in a Bayesian network, given some evidence. MAP appears to be a significantly harder problem than the related problems of computing the probability of…
The current paper investigates the bounded distance decoding (BDD) problem for ensembles of lattices whose generator matrices have sub-Gaussian entries. We first prove that, for these ensembles the BDD problem is NP-hard in the worst case.…
Since the Bin Packing Problem (BPP) is one of the main NP-hard problems, a lot of approximation algorithms have been suggested for it. It has been proven that the best algorithm for BPP has the approximation ratio of 3/2 and the time order…
The Minimum Cost Multicut Problem (MP) is a popular way for obtaining a graph decomposition by optimizing binary edge labels over edge costs. While the formulation of a MP from independently estimated costs per edge is highly flexible and…