Related papers: CLePAPS: Fast Pair Alignment of Protein Structures…

Shape complementarity of molecular surfaces at the interfaces is a well-known characteristic of protein-protein binding regions, and it is critical in influencing the stability of the complex. Measuring such complementarity is at the basis…

Many tools exist for extracting structural and physiochemical descriptors from linear peptides to predict their properties, but similar tools for hydrocarbon-stapled peptides are lacking.Here, we present StaPep, a Python-based toolkit…

This paper considers the problems of detecting a change point and estimating the location in the correlation matrices of a sequence of high-dimensional vectors, where the dimension is large enough to be comparable to the sample size or even…

The recent breakthrough of AlphaFold3 in modeling complex biomolecular interactions, including those between proteins and ligands, nucleotides, or metal ions, creates new opportunities for protein design. In so-called inverse protein…

We propose Fast Language-Audio Pre-training (FLAP), a self-supervised approach that efficiently and effectively learns aligned audio and language representations through masking, contrastive learning and reconstruction. For efficiency, FLAP…

Set similarity search is a problem of central interest to a wide variety of applications such as data cleaning and web search. Past approaches on set similarity search utilize either heavy indexing structures, incurring large search costs…

The Automated Protein Structure Analysis (APSA) method, which describes the protein backbone as a smooth line in 3-dimensional space and characterizes it by curvature kappa and torsion tau as a function of arc length s, was applied on 77…

High-throughput spectrometers are capable of producing data sets containing thousands of spectra for a single biological sample. These data sets contain a substantial amount of redundancy from peptides that may get selected multiple times…

A popular paradigm for 3D point cloud registration is by extracting 3D keypoint correspondences, then estimating the registration function from the correspondences using a robust algorithm. However, many existing 3D keypoint techniques tend…

Frameshift translation is an important phenomenon that contributes to the appearance of novel Coding DNA Sequences (CDS) and functions in gene evolution, by allowing alternative amino acid translations of genes coding regions. Frameshift…

Establishing dense correspondence between two images is a fundamental computer vision problem, which is typically tackled by matching local feature descriptors. However, without global awareness, such local features are often insufficient…

Large language models (LLMs) often exhibit performance disparities across languages, with naive multilingual fine-tuning frequently degrading performance due to negative cross-lingual interference. To address this, we introduce COMPASS…

The protein backbone is described as a smooth curved and twisted line in three-dimensional (3D) space and characterized by its curvature $\kappa(s)$ and torsion $\tau(s)$ both expressed as a function of arc length s. It is shown that the…

Computation of bounding boxes is a fundamental problem in high performance rendering, as it is an input to visibility culling and binning operations. In a scene description structured as a tree, clip nodes and blend nodes entail…

The Basic Local Alignment Search Tool (BLAST) is currently the most popular method for searching databases of biological sequences. BLAST compares sequences via similarity defined by a weighted edit distance, which results in it being…

The proliferation of high-throughput sequencing machines ensures rapid generation of up to billions of short nucleotide fragments in a short period of time. This massive amount of sequence data can quickly overwhelm today's storage and…

This paper studies density-based clustering of point sets. These methods use dense regions of points to detect clusters of arbitrary shapes. In particular, we study variants of density peaks clustering, a popular type of algorithm that has…

Machine learning models depend critically on feature quality, yet useful features are often scattered across multiple relational tables. Feature augmentation enriches a base table by discovering and integrating features from related tables…

Developing a reliable and practical face recognition system is a long-standing goal in computer vision research. Existing literature suggests that pixel-wise face alignment is the key to achieve high-accuracy face recognition. By assuming a…

Motivation: High throughput DNA sequencing (HTS) technologies generate an excessive number of small DNA segments -- called short reads -- that cause significant computational burden. To analyze the entire genome, each of the billions of…