Related papers: Solving Maximum Clique Problem for Protein Structu…
Virtual screening (VS) is an essential task in drug discovery, focusing on the identification of small-molecule ligands that bind to specific protein pockets. Existing deep learning methods, from early regression models to recent…
We apply the concept of subset seeds proposed in [1] to similarity search in protein sequences. The main question studied is the design of efficient seed alphabets to construct seeds with optimal sensitivity/selectivity trade-offs. We…
We describe Ccluster, a software for computing natural $\epsilon$-clusters of complex roots in a given box of the complex plane. This algorithm from Becker et al.~(2016) is near-optimal when applied to the benchmark problem of isolating all…
The profile-based matching problem is the problem of finding a matching that optimizes profile from an instance $(G, r, \langle u_1, \dots, u_r \rangle)$, where $G$ is a bipartite graph $(A \cup B, E)$, $r$ is the number of utility…
With the aggressive scaling of VLSI technology, the explosion of layout patterns creates a critical bottleneck for DFM applications like OPC. Pattern clustering is essential to reduce data complexity, yet existing methods struggle with…
In this study, we propose an analytic statistical mechanics approach to solve a fundamental problem in biological physics called protein design. Protein design is an inverse problem of protein structure prediction, and its solution is the…
Given a structure made up of n sites connected by b bars, the problem of recognizing which subsets of sites form rigid units is not a trivial one, because of the non-local character of rigidity in central-force systems. Even though this is…
The structure of an RNA molecule plays a significant role in its biological function. Predicting structure given a one dimensional sequence of RNA nucleotide bases is a difficult and important problem. Many computer programs (known as in…
Binding affinity prediction of three-dimensional (3D) protein ligand complexes is critical for drug repositioning and virtual drug screening. Existing approaches transform a 3D protein-ligand complex to a two-dimensional (2D) graph, and…
Robust model fitting plays a vital role in computer vision, and research into algorithms for robust fitting continues to be active. Arguably the most popular paradigm for robust fitting in computer vision is consensus maximisation, which…
The problem of {\em efficiently} finding the best match for a query in a given set with respect to the Euclidean distance or the cosine similarity has been extensively studied in literature. However, a closely related problem of efficiently…
The Cell Formation Problem has been studied as an optimization problem in manufacturing for more than 90 years. It consists of grouping machines and parts into manufacturing cells in order to maximize loading of cells and minimize movement…
When studying multi-body protein complexes, biochemists use computational tools that can suggest hundreds or thousands of their possible spatial configurations. However, it is not feasible to experimentally verify more than only a very…
The Gene or DNA sequence in every cell does not control genetic properties on its own; Rather, this is done through translation of DNA into protein and subsequent formation of a certain 3D structure. The biological function of a protein is…
This paper explores the problem of clustering ensemble, which aims to combine multiple base clusterings to produce better performance than that of the individual one. The existing clustering ensemble methods generally construct a…
We propose an algorithm for generating explicit solutions of multiparametric mixed-integer convex programs to within a given suboptimality tolerance. The algorithm is applicable to a very general class of optimization problems, but is most…
We study the problem of instance segmentation in biological images with crowded and compact cells. We formulate this task as an integer program where variables correspond to cells and constraints enforce that cells do not overlap. To solve…
Order picking and order packing entail retrieving items from storage and packaging them according to customer requests. These activities have always been the main concerns of the companies in reducing warehouse management costs. This paper…
Drug discovery represents a time-consuming and financially intensive process, and virtual screening can accelerate it. Scoring functions, as one of the tools guiding virtual screening, have their precision closely tied to screening…
We study the problem of approximating the number of $k$-cliques in a graph when given query access to the graph. We consider the standard query model for general graphs via (1) degree queries, (2) neighbor queries and (3) pair queries. Let…