Related papers: Genomic Problems Involving Copy Number Profiles: C…
In this paper we present a collection of results pertaining to haplotyping. The first set of results concerns the combinatorial problem of reconstructing haplotypes from incomplete and/or imperfectly sequenced haplotype data. More…
Motivated by problems of comparative genomics and paleogenomics, in [Chauve et al., 2009], the authors introduced the Gapped Consecutive-Ones Property Problem (k,delta)-C1P: given a binary matrix M and two integers k and delta, can the…
The Consecutive-Ones Property (C1P) is a classical concept in discrete mathematics that has been used in several genomics applications, from physical mapping of contemporary genomes to the assembly of ancient genomes. A common issue in…
The Critical Node Problem (CNP) is concerned with identifying the critical nodes in a complex network. These nodes play a significant role in maintaining the connectivity of the network, and removing them can negatively impact network…
The massive quantities of genomic data being made available through gene sequencing techniques are enabling breakthroughs in genomic science in many areas such as medical advances in the diagnosis and treatment of diseases. Analyzing this…
We tackle a stochastic version of the Critical Node Problem (CNP) where the goal is to minimize the pairwise connectivity of a graph by attacking a subset of its nodes. In the stochastic setting considered, the attacks on nodes can fail…
The closest pair problem (CPP) is one of the well studied and fundamental problems in computing. Given a set of points in a metric space, the problem is to identify the pair of closest points. Another closely related problem is the fixed…
Cancer is a genetic disorder whose clonal evolution can be monitored by tracking noisy genome-wide copy number variants. We introduce the Copy Number Stochastic Block Model (CN-SBM), a probabilistic framework that jointly clusters samples…
A difficult step in the process of karyotyping is segmenting chromosomes that touch or overlap. In an attempt to automate the process, previous studies turned to Deep Learning methods, with some formulating the task as a semantic…
Changes in the number of copies of certain parts of the genome, known as copy number alterations (CNAs), due to somatic mutation processes are a hallmark of many cancers. This genomic complexity is known to be associated with poorer…
As neural networks (NNs) are increasingly introduced into safety-critical domains, there is a growing need to formally verify NNs before deployment. In this work we focus on the formal verification problem of NN equivalence which aims to…
A number of bioinformatic or biostatistical methods are available for analyzing DNA copy number profiles measured from microarray or sequencing technologies. In the absence of rich enough gold standard data sets, the performance of these…
The maximum clique problem (MCP) is a fundamental problem in graph theory and in computational complexity. Given a graph G, the problem is that of finding the largest clique (complete subgraph) in G. The MCP has many important applications…
Two genomes over the same set of gene families form a canonical pair when each of them has exactly one gene from each family. Different distances of canonical genomes can be derived from a structure called breakpoint graph, which represents…
We present several new results pertaining to haplotyping. These results concern the combinatorial problem of reconstructing haplotypes from incomplete and/or imperfectly sequenced haplotype fragments. We consider the complexity of the…
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…
In the number partitioning problem (NPP) one aims to partition a given set of $N$ real numbers into two subsets with approximately equal sum. The NPP is a well-studied optimization problem and is famous for possessing a…
It is widely believed that the practical success of Convolutional Neural Networks (CNNs) and Recurrent Neural Networks (RNNs) owes to the fact that CNNs and RNNs use a more compact parametric representation than their Fully-Connected Neural…
Motivated by comparative genomics, Chen et al. [9] introduced the Maximum Duo-preservation String Mapping (MDSM) problem in which we are given two strings $s_1$ and $s_2$ from the same alphabet and the goal is to find a mapping $\pi$…
Optimization problems involving complex variables, when solved, are typically transformed into real variables, often at the expense of convergence rate and interpretability. This paper introduces a novel formalism for a prominent problem in…