Related papers: SCOPE: Siamese Contrastive Operon Pair Embeddings …

The Spliced Alignment Problem (SAP) that consists in finding an optimal semi-global alignment of a spliced RNA sequence on an unspliced genomic sequence has been largely considered for the prediction and the annotation of gene structures in…

We theorize that phylogenetic profiles provide a quantitative method that can relate the structural and functional properties of proteins, as well as their evolutionary relationships. A key feature of phylogenetic profiles is the…

Improving the ability to predict protein function can potentially facilitate research in the fields of drug discovery and precision medicine. Technically, the properties of proteins are directly or indirectly reflected in their sequence and…

A comparative classification scheme provides a good basis for several approaches to understand proteins, including prediction of relations between their structure and biological function. But it remains a challenge to combine a…

Motivation: Network-based analyses of omics data are widely used, and while many of these methods have been adapted to single-cell scenarios, they often remain memory- and space-intensive. As a result, they are better suited to batch data…

Evolutionary modeling applications are the best way to provide full information to support in-depth understanding of evaluation of organisms. These applications mainly depend on identifying the evolutionary history of existing organisms and…

A novel approach for structure alignment is presented, where the key ingredients are: (1) An error function formulation of the problem simultaneously in terms of binary (Potts) assignment variables and real-valued atomic coordinates. (2)…

The translation of comparative genomics into clinical decision support tools often depends on the quality of sequence alignments. However, currently used methods of multiple sequence alignments suffer from significant biases and problems…

A coreset is a subset of the training set, using which a machine learning algorithm obtains performances similar to what it would deliver if trained over the whole original data. Coreset discovery is an active and open line of research as…

Protein-Protein Interactions (PPIs) are fundamental in various biological processes and play a key role in life activities. The growing demand and cost of experimental PPI assays require computational methods for efficient PPI prediction.…

Predictive coding has emerged as an influential normative model of neural computation, with numerous extensions and applications. As such, much effort has been put into mapping PC faithfully onto the cortex, but there are issues that remain…

String matching algorithm plays the vital role in the Computational Biology. The functional and structural relationship of the biological sequence is determined by similarities on that sequence. For that, the researcher is supposed to aware…

Acoustic word embeddings --- fixed-dimensional vector representations of variable-length spoken word segments --- have begun to be considered for tasks such as speech recognition and query-by-example search. Such embeddings can be learned…

Protein structure prediction often hinges on multiple sequence alignments (MSAs), which underperform on low-homology and orphan proteins. We introduce PLAME, a lightweight MSA design framework that leverages evolutionary embeddings from…

Depth pruning improves the deployment efficiency of large language models (LLMs) by identifying and removing redundant layers. A widely accepted standard for this identification process is to measure the similarity between layers using…

Accurately assigning folds for divergent protein sequences is a major obstacle to structural studies and underlies the inverse protein folding problem. Herein, we outline our theories for fold-recognition in the "twilight-zone" of sequence…

Proteins adopt multiple structural conformations to perform their diverse biological functions, and understanding these conformations is crucial for advancing drug discovery. Traditional physics-based simulation methods often struggle with…

Protein is linked to almost every life process. Therefore, analyzing the biological structure and property of protein sequences is critical to the exploration of life, as well as disease detection and drug discovery. Traditional protein…

Developing artificial intelligence (AI) and machine learning (ML) models for medical imaging typically involves extensive training and testing on large datasets, consuming significant computational time, energy, and resources. There is a…

Text embeddings are useful features for several NLP applications, such as sentence similarity, text clustering, and semantic search. In this paper, we present a Low-rank Adaptation with a Contrastive objective on top of 8-bit Siamese-BLOOM,…