Related papers: Solving Maximum Clique Problem for Protein Structu…
Lattice rules are among the most prominently studied quasi-Monte Carlo methods to approximate multivariate integrals. A rank-1 lattice rule to approximate an $s$-dimensional integral is fully specified by its generating vector $\mathbf{z}…
Recent computational advances in the accurate prediction of protein three-dimensional (3D) structures from amino acid sequences now present a unique opportunity to decipher the interrelationships between proteins. This task entails--but is…
Sequence Alignment is the process of aligning biological sequences in order to identify similarities between multiple sequences. In this paper, a Quantum Algorithm for finding the optimal alignment between DNA sequences has been…
In this paper, we consider the computational protein design (CPD) problem, which is usually modeled as a 0/1 programming and is extremely challenging due to its combinatorial properties. We propose an efficient algorithm for solving it.…
In this paper we propose a unified framework to simultaneously discover the number of clusters and group the data points into them using subspace clustering. Real data distributed in a high-dimensional space can be disentangled into a union…
Quantum heuristics have shown promise in solving various optimization problems, including lattice protein folding. Equally relevant is the inverse problem, protein design, where one seeks sequences that fold to a given target structure. The…
We consider a variant of treewidth that we call clique-partitioned treewidth in which each bag is partitioned into cliques. This is motivated by the recent development of FPT-algorithms based on similar parameters for various problems. With…
Finding large "cliquish" subgraphs is a central topic in graph mining and community detection. A popular clique relaxation are 2-clubs: instead of asking for subgraphs of diameter one (these are cliques), one asks for subgraphs of diameter…
Listing dense subgraphs in large graphs plays a key task in varieties of network analysis applications like community detection. Clique, as the densest model, has been widely investigated. However, in practice, communities rarely form as…
The present work proposes a solution to the challenging problem of registering two partial point sets of the same object with very limited overlap. We leverage the fact that most objects found in man-made environments contain a plane of…
We propose an algorithm inspired by optical coherent Ising machines to solve the problem of polynomial unconstrained binary optimization (PUBO). We benchmark the proposed algorithm against existing PUBO algorithms on the extended…
We consider a similarity measure between two sets $A$ and $B$ of vectors, that balances the average and maximum cosine distance between pairs of vectors, one from set $A$ and one from set $B$. As a motivation for this measure, we present…
The advent of highly accurate protein structure prediction methods has fueled an exponential expansion of the protein structure database. Consequently, there is a rising demand for rapid and precise structural homolog search. Traditional…
A disk graph is an intersection graph of disks in the Euclidean plane, where the disks correspond to the vertices of the graph and a pair of vertices are adjacent if and only if their corresponding disks intersect. The problem of…
Understanding the principles of protein folding is a cornerstone of computational biology, with implications for drug design, bioengineering, and the understanding of fundamental biological processes. Lattice protein folding models offer a…
We study algorithms for construction of composable coresets for the task of Determinant Maximization under partition constraint. Given a point set $V\subset \mathbb{R}^d$ that is partitioned into $s$ groups $V_1,\cdots, V_s$, and integers…
We investigate a number of recently reported exact algorithms for the maximum clique problem (MCQ, MCR, MCS, BBMC). The program code used is presented and critiqued showing how small changes in implementation can have a drastic effect on…
Sequence matching algorithms such as BLAST and FASTA have been widely used in searching for evolutionary origin and biological functions of newly discovered nucleic acid and protein sequences. As parts of these search tools, alignment…
Recognition and binding of specific sites on DNA by proteins is central for many cellular functions such as transcription, replication, and recombination. In the process of recognition, a protein rapidly searches for its specific site on a…
The study of approximate matching in the Massively Parallel Computations (MPC) model has recently seen a burst of breakthroughs. Despite this progress, however, we still have a far more limited understanding of maximal matching which is one…