Related papers: Solving Maximum Clique Problem for Protein Structu…
Summary: Most cellular tasks are performed not by individual proteins, but by groups of functionally associated proteins, often referred to as modules. In a protein assocation network modules appear as groups of densely interconnected…
Point matching refers to the process of finding spatial transformation and correspondences between two sets of points. In this paper, we focus on the case that there is only partial overlap between two point sets. Following the approach of…
This paper proposes an algorithm to search a family of multiple sets of minimum correlated one dimensional uni-polar (optical) orthogonal codes (1-DUOC) or optical orthogonal codes (OOC) with fixed as well as variable code parameters. The…
Evolution in its course found a variety of solutions to the same optimisation problem. The advent of high-throughput genomic sequencing has made available extensive data from which, in principle, one can infer the underlying structure on…
Clustering is a difficult and widely-studied data mining task, with many varieties of clustering algorithms proposed in the literature. Nearly all algorithms use a similarity measure such as a distance metric (e.g. Euclidean distance) to…
The graph matching optimization problem is an essential component for many tasks in computer vision, such as bringing two deformable objects in correspondence. Naturally, a wide range of applicable algorithms have been proposed in the last…
We propose improved exact and heuristic algorithms for solving the maximum weight clique problem, a well-known problem in graph theory with many applications. Our algorithms interleave successful techniques from related work with novel data…
The binding complexes formed by proteins and small molecule ligands are ubiquitous and critical to life. Despite recent advancements in protein structure prediction, existing algorithms are so far unable to systematically predict the…
The maximum clique problem, a well-known graph-based combinatorial optimization problem, has been addressed through various algorithmic approaches, though systematic analyses of the problem instances remain sparse. This study employs the…
The Maximum Balanced Biclique Problem (MBBP) is a prominent model with numerous applications. Yet, the problem is NP-hard and thus computationally challenging. We propose novel ideas for designing effective exact algorithms for MBBP.…
In this paper, we provide polynomial-time algorithms for different extensions of the matching counting problem, namely maximal matchings, path matchings (linear forest) and paths, on graph classes of bounded clique-width. For maximal…
We take an existing implementation of an algorithm for the maximum clique problem and modify it so that we can distribute it over an ad-hoc cluster of machines. Our goal was to achieve a significant speedup in performance with minimal…
Proteins are the basic building blocks of life. They usually perform functions by folding to a particular structure. Understanding the folding process could help the researchers to understand the functions of proteins and could also help to…
Given a set $P$ of $n$ points in the plane, the unit-disk graph $G(P)$ is a graph with $P$ as its vertex set such that two points of $P$ have an edge if their Euclidean distance is at most $1$. We consider the problem of computing a maximum…
In this paper, we study a number of well-known combinatorial optimization problems that fit in the following paradigm: the input is a collection of (potentially inconsistent) local relationships between the elements of a ground set (e.g.,…
The fold recognition methods are promissing tools for capturing the structure of a protein by its amino acid residues sequence but their use is still restricted by the needs of huge computational resources and suitable efficient algorithms…
We present an efficient algorithm for the min-max correlation clustering problem. The input is a complete graph where edges are labeled as either positive $(+)$ or negative $(-)$, and the objective is to find a clustering that minimizes the…
In this paper we study the fine-grained complexity of finding exact and approximate solutions to problems in P. Our main contribution is showing reductions from exact to approximate solution for a host of such problems. As one (notable)…
We have developed an analytical, ligand-specific and scalable algorithm that detects a "signature" of the 3D binding site of a given ligand in a protein 3D structure. The said signature is a 3D motif in the form of an irregular tetrahedron…
We consider the maximum vertex-weighted matching problem (MVM), in which non-negative weights are assigned to the vertices of a graph, the weight of a matching is the sum of the weights of the matched vertices, and we are required to…