Related papers: iTreePack: Protein Complex Side-Chain Packing by D…
We present approximation algorithms for the following NP-hard optimization problems related to bottleneck spanning trees in metric spaces. 1. The disjoint bottleneck spanning tree problem: Given $n$ pairs of points in a metric space, find…
With the development of IPv6 and edge computing, the edge network should support IPv6 lookup (the longest prefix matching, LPM) with high lookup speed, high update speed, and low memory cost. However, the trie-based algorithms, e.g., SAIL…
Determining the interaction partners among protein/domain families poses hard computational problems, in particular in the presence of paralogous proteins. Available approaches aim to identify interaction partners among protein/domain…
We continue the study of graph classes in which the treewidth can only be large due to the presence of a large clique, and, more specifically, of graph classes with bounded tree-independence number. In [Dallard, Milani\v{c}, and…
Recent advances in protein large language models, such as ProtTeX, represent both side-chain amino acids and backbone structure as discrete token sequences of residue length. While this design enables unified modeling of multimodal protein…
This paper introduces Tree-NET, a novel framework for medical image segmentation that leverages bottleneck feature supervision to enhance both segmentation accuracy and computational efficiency. While previous studies have employed…
Despite the significant increase in computational power, molecular modeling of protein structure using classical all-atom approaches remains inefficient, at least for most of the protein targets in the focus of biomedical research. Perhaps…
Proteins are macromolecules that perform essential functions in all living organisms. Designing novel proteins with specific structures and desired functions has been a long-standing challenge in the field of bioengineering. Existing…
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…
Treewidth and hypertree width have proven to be highly successful structural parameters in the context of the Constraint Satisfaction Problem (CSP). When either of these parameters is bounded by a constant, then CSP becomes solvable in…
As the performance and popularity of deep neural networks has increased, so too has their computational cost. There are many effective techniques for reducing a network's computational footprint (quantisation, pruning, knowledge…
Transformation of protein 3D structures from their all-atom representation (AAR) to the double-centroid reduced representation (DCRR) is a prerequisite to the implementation of both the tetrahedral three-dimensional search motif (3D SM)…
A widely used method for determining the similarity of two labeled trees is to compute a maximum agreement subtree of the two trees. Previous work on this similarity measure is only concerned with the comparison of labeled trees of two…
Inverse Protein Folding (IPF) is a critical subtask in the field of protein design, aiming to engineer amino acid sequences capable of folding correctly into a specified three-dimensional (3D) conformation. Although substantial progress has…
The inapplicability of amino acid covariation methods to small protein families has limited their use for structural annotation of whole genomes. Recently, deep learning has shown promise in allowing accurate residue-residue contact…
This paper offers a new authentication algorithm based on image matching of nano-resolution visual identifiers with tree-shaped patterns. The algorithm includes image-to-tree conversion by greedy extraction of the fractal pattern skeleton…
Coarse-graining is a powerful tool for extending the reach of dynamic models of proteins and other biological macromolecules. Topological coarse-graining, in which biomolecules or sets thereof are represented via graph structures, is a…
Intrathoracic airway segmentation in computed tomography (CT) is a prerequisite for various respiratory disease analyses such as chronic obstructive pulmonary disease (COPD), asthma and lung cancer. Unlike other organs with simpler shapes…
Packet classification is a fundamental problem in computer networking. This problem exposes a hard tradeoff between the computation and state complexity, which makes it particularly challenging. To navigate this tradeoff, existing solutions…
While accurate protein structure predictions are now available for nearly every observed protein sequence, predicted structures lack much of the functional context offered by experimental structure determination. We address this gap with…