Related papers: Genomic Problems Involving Copy Number Profiles: C…
We devise a novel inference algorithm to effectively solve the cancer progression model reconstruction problem. Our empirical analysis of the accuracy and convergence rate of our algorithm, CAncer PRogression Inference (CAPRI), shows that…
One of the most fundamental problems in machine learning is to compare examples: Given a pair of objects we want to return a value which indicates degree of (dis)similarity. Similarity is often task specific, and pre-defined distances can…
A fundamental graph problem is to recognize whether the vertex set of a graph $G$ can be bipartitioned into sets $A$ and $B$ such that $G[A]$ and $G[B]$ satisfy properties $\Pi_A$ and $\Pi_B$, respectively. This so-called…
NP complete problem is one of the most challenging issues. The question of whether all problems in NP are also in P is generally considered one of the most important open questions in mathematics and theoretical computer science as it has…
The Burning Number Problem (BNP) models the spread of information or contagion in a network through a discrete-time process on a graph. At each step, one new vertex is selected as a burning source, while fire simultaneously spreads from…
This article presents a general solution to the problem of computational complexity. First, it gives a historical introduction to the problem since the revival of the foundational problems of mathematics at the end of the 19th century.…
Kernelization---a mathematical key concept for provably effective polynomial-time preprocessing of NP-hard problems---plays a central role in parameterized complexity and has triggered an extensive line of research. This is in part due to a…
The input of the Test Cover problem consists of a set $V$ of vertices, and a collection ${\cal E}=\{E_1,..., E_m\}$ of distinct subsets of $V$, called tests. A test $E_q$ separates a pair $v_i,v_j$ of vertices if $|\{v_i,v_j\}\cap E_q|=1.$…
We prove that the Minimum Distance Problem (MDP) on linear codes over any fixed finite field and parameterized by the input distance bound is W[1]-hard to approximate within any constant factor. We also prove analogous results for the…
Contemporary genetic programming (GP) systems for general program synthesis have been primarily concerned with evolving programs that can manipulate values from a standard set of primitive data types and simple indexed data structures. In…
Number partitioning is one of the classical NP-hard problems of combinatorial optimization. It has applications in areas like public key encryption and task scheduling. The random version of number partitioning has an "easy-hard" phase…
The Constrained Minimal Supersymmetric Standard Model (CMSSM) is one of the simplest and most widely-studied supersymmetric extensions to the standard model of particle physics. Nevertheless, current data do not sufficiently constrain the…
We study the Parallel Task Scheduling problem $Pm|size_j|C_{\max}$ with a constant number of machines. This problem is known to be strongly NP-complete for each $m \geq 5$, while it is solvable in pseudo-polynomial time for each $m \leq 3$.…
Consensus problems for strings and sequences appear in numerous application contexts, ranging from bioinformatics over data mining to machine learning. Closing some gaps in the literature, we show that several fundamental problems in this…
Discrete Morse theory has emerged as a powerful tool for a wide range of problems, including the computation of (persistent) homology. In this context, discrete Morse theory is used to reduce the problem of computing a topological invariant…
P vs NP problem is the most important unresolved problem in the field of computational complexity. Its impact has penetrated into all aspects of algorithm design, especially in the field of cryptography. The security of cryptographic…
We study pattern matching problems on two major representations of uncertain sequences used in molecular biology: weighted sequences (also known as position weight matrices, PWM) and profiles (i.e., scoring matrices). In the simple version,…
A matching cut is a partition of the vertex set of a graph into two sets $A$ and $B$ such that each vertex has at most one neighbor in the other side of the cut. The MATCHING CUT problem asks whether a graph has a matching cut, and has been…
Targeted amplicon panels are widely used in oncology diagnostics, but providing per-gene performance guarantees for copy number variant (CNV) detection remains challenging due to amplification artifacts, process-mismatch heterogeneity, and…
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…