相关论文: AnySeq: A High Performance Sequence Alignment Libr…

We are in the era where the Big Data analytics has changed the way of interpreting the various biomedical phenomena, and as the generated data increase, the need for new machine learning methods to handle this evolution grows. An indicative…

Despite the impressive performance of large language models (LLMs) in general domains, they often underperform in specialized domains. Existing approaches typically rely on data synthesis methods and yield promising results by using…

Cell and nucleus segmentation are fundamental tasks for quantitative bioimage analysis. Despite progress in recent years, biologists and other domain experts still require novel algorithms to handle increasingly large and complex real-world…

Generative retrieval, a promising new paradigm in information retrieval, employs a seq2seq model to encode document features into parameters and decode relevant document identifiers (IDs) based on search queries. Existing generative…

Multi-sequence MRIs can be necessary for reliable diagnosis in clinical practice due to the complimentary information within sequences. However, redundant information exists across sequences, which interferes with mining efficient…

This paper presents a novel DNA sequences alignment method based on inverted index. Now most large scale information retrieval system are all use inverted index as the basic data structure. But its application in DNA sequence alignment is…

Signature-based methods have recently gained significant traction in machine learning for sequential data. In particular, signature kernels have emerged as powerful discriminators and training losses for generative models on time-series,…

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…

ABCpy is a highly modular scientific library for Approximate Bayesian Computation (ABC) written in Python. The main contribution of this paper is to document a software engineering effort that enables domain scientists to easily apply ABC…

While sequence-to-sequence (seq2seq) models achieve state-of-the-art performance in many natural language processing tasks, they can be too slow for real-time applications. One performance bottleneck is predicting the most likely next token…

Background: With the rapid growth of massively parallel sequencing technologies, still more laboratories are utilizing sequenced DNA fragments for genomic analyses. Interpretation of sequencing data is, however, strongly dependent on…

Large Language Models (LLMs) are increasingly deployed in critical applications requiring reliable reasoning, yet their internal reasoning processes remain difficult to evaluate systematically. Existing methods focus on final-answer…

The regulation of various cellular processes heavily relies on the protein complexes within a living cell, necessitating a comprehensive understanding of their three-dimensional structures to elucidate the underlying mechanisms. While…

Transcriptome assembly from RNA-Seq reads is an active area of bioinformatics research. The ever-declining cost and the increasing depth of RNA-Seq have provided unprecedented opportunities to better identify expressed transcripts. However,…

AlphaFold2 (AF2) has transformed protein structure prediction by harnessing co-evolutionary constraints embedded in multiple sequence alignments (MSAs). MSAs not only encode static structural information, but also hold critical details…

Sleep is essential for good health throughout our lives, yet studying its dynamics requires manual sleep staging, a labor-intensive step in sleep research and clinical care. Across centers, polysomnography (PSG) recordings are traditionally…

The alignment of biological networks has the potential to teach us as much about biology and disease as has sequence alignment. Sequence alignment can be optimally solved in polynomial time. In contrast, network alignment is $NP$-hard,…

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…

Sequence alignment algorithms are a basic and critical component of many bioinformatics fields. With rapid development of sequencing technology, the fast growing reference database volumes and longer length of query sequence become new…

Motivation: Assigning RNA-seq reads to their transcript of origin is a fundamental task in transcript expression estimation. Where ambiguities in assignments exist due to transcripts sharing sequence, e.g. alternative isoforms or alleles,…