Related papers: iTreePack: Protein Complex Side-Chain Packing by D…

Distributed algorithms for solving coupled semidefinite programs (SDPs) commonly require many iterations to converge. They also put high computational demand on the computational agents. In this paper we show that in case the coupled…

Clustering is a well-known and studied problem, one of its variants, called contiguity-constrained clustering, accepts as a second input a graph used to encode prior information about cluster structure by means of contiguity constraints…

This paper tackles the problem of finding optimal variable-height transport packaging. The goal is to reduce the empty space left in a box when shipping goods to customers, thereby saving on filler and reducing waste. We cast this problem…

Coarse-grained (CG) molecular dynamics simulations enable efficient exploration of protein conformational ensembles. However, reconstructing atomic details from CG structures (backmapping) remains a challenging problem. Current approaches…

Compression aims to reduce the size of an input, while maintaining its relevant properties. For multi-parameter persistent homology, compression is a necessary step in any computational pipeline, since standard constructions lead to large…

Sidechain rotamer libraries of the common amino acids of a protein are useful for folded protein structure determination and for generating ensembles of intrinsically disordered proteins (IDPs). However much of protein function is modulated…

Constrained image splicing detection and localization (CISDL) is a fundamental task of multimedia forensics, which detects splicing operation between two suspected images and localizes the spliced region on both images. Recent works regard…

Searching in P2P networks is fundamental to all overlay networks. P2P networks based on Distributed Hash Tables (DHT) are optimized for single key lookups, whereas unstructured networks offer more complex queries at the cost of increased…

Motivation Protein fold recognition is an important problem in structural bioinformatics. Almost all traditional fold recognition methods use sequence (homology) comparison to indirectly predict the fold of a tar get protein based on the…

An important application of distance geometry to biochemistry studies the embeddings of the vertices of a weighted graph in the three-dimensional Euclidean space such that the edge weights are equal to the Euclidean distances between…

The paper investigates a novel approach, based on Constraint Logic Programming (CLP), to predict the 3D conformation of a protein via fragments assembly. The fragments are extracted by a preprocessor-also developed for this work- from a…

We present a tree-based construction of LDPC codes that have minimum pseudocodeword weight equal to or almost equal to the minimum distance, and perform well with iterative decoding. The construction involves enumerating a $d$-regular tree…

Steiner Tree Packing (STP) is a notoriously hard problem in classical complexity theory, which is of practical relevance to VLSI circuit design. Previous research has approached this problem by providing heuristic or approximate algorithms.…

Predicting which proteins interact together from amino-acid sequences is an important task. We develop a method to pair interacting protein sequences which leverages the power of protein language models trained on multiple sequence…

How can we design protein sequences folding into the desired structures effectively and efficiently? AI methods for structure-based protein design have attracted increasing attention in recent years; however, few methods can simultaneously…

Scientific paper retrieval, particularly framed as document-to-document retrieval, aims to identify relevant papers in response to a long-form query paper, rather than a short query string. Previous approaches to this task have focused…

Deep learning approaches exhibit promising performances on various text tasks. However, they are still struggling on medical text classification since samples are often extremely imbalanced and scarce. Different from existing mainstream…

Structure-based drug discovery, encompassing the tasks of protein-ligand docking and pocket-aware 3D drug design, represents a core challenge in drug discovery. However, no existing work can deal with both tasks to effectively leverage the…

The notion of treewidth plays an important role in theoretical and practical studies of graph problems. It has been recognized that, especially in practical environments, when computing the treewidth of a graph it is invaluable to first…

Contour trees offer an abstract representation of the level set topology in scalar fields and are widely used in topological data analysis and visualization. However, applying contour trees to large-scale scientific datasets remains…