Related papers: Aligning sequence reads, clone sequences and assem…

Pyro-Align is a multiple alignment program specifically designed for pyrosequencing reads of huge number. Multiple sequence alignment is shown to be NP-hard and heuristics are designed for approximate solutions. Multiple sequence alignment…

Summary: Accurate phenotype prediction from genomic sequences is a highly coveted task in biological and medical research. While machine-learning holds the key to accurate prediction in a variety of fields, the complexity of biological data…

Sequences of nucleotides (for DNA and RNA) or amino acids (for proteins) are central objects in biology. Among the most important computational problems is that of sequence alignment, i.e. arranging sequences from different organisms in…

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…

As Multimodal Large Language Models (MLLMs) grow in size, adapting them to specialized tasks becomes increasingly challenging due to high computational and memory demands. Indeed, traditional fine-tuning methods are costly, due to the need…

New long read sequencing technologies, like PacBio SMRT and Oxford NanoPore, can produce sequencing reads up to 50,000 bp long but with an error rate of at least 15%. Reducing the error rate is necessary for subsequent utilisation of the…

Aligning large language models (LLMs) with human values is a vital task for LLM practitioners. Current alignment techniques have several limitations: (1) requiring a large amount of annotated data; (2) demanding heavy human involvement; (3)…

High throughput sequencing of RNA (RNA-Seq) can provide us with millions of short fragments of RNA transcripts from a sample. How to better recover the original RNA transcripts from those fragments (RNA-Seq assembly) is still a difficult…

Large language models (LLMs) are increasingly being used as decision aids. However, users have diverse values and preferences that can affect their decision-making, which requires novel methods for LLM alignment and personalization.…

BarraCUDA is a C program which uses the BWA algorithm in parallel with nVidia CUDA to align short next generation DNA sequences against a reference genome. The genetically improved (GI) code is up to three times faster on short paired end…

Multiple sequence alignment is a basic procedure in molecular biology, and it is often treated as being essentially a solved computational problem. However, this is not so, and here I review the evidence for this claim, and outline the…

This article investigates beam alignment for multi-user millimeter wave (mmWave) massive multi-input multi-output system. Unlike the existing works using machine learning (ML), an alignment method with partial beams using ML (AMPBML) is…

While short read aligners, which predominantly use the FM-index, are able to easily index one or a few human genomes, they do not scale well to indexing databases containing thousands of genomes. To understand why, it helps to examine the…

Advances in DNA sequencing technology have stimulated the development of algorithms and tools for processing very large collections of short strings (reads). Short-read alignment and assembly are among the most well-studied problems. Many…

Understanding the alignment between large language models (LLMs) and human brain activity can reveal computational principles underlying language processing. We introduce a fine-grained input attribution method to identify the specific…

Biological network alignment aims to identify similar regions between networks of different species. Existing methods compute node "similarities" to rapidly identify from possible alignments the "high-scoring" alignments with respect to the…

Modern neural networks have greatly improved performance across speech recognition benchmarks. However, gains are often driven by frequent words with limited semantic weight, which can obscure meaningful differences in word error rate, the…

Sequence alignments are fundamental to bioinformatics which has resulted in a variety of optimized implementations. Unfortunately, the vast majority of them are hand-tuned and specific to certain architectures and execution models. This not…

Genome sequence alignment is the core of many biological applications. The advancement of sequencing technologies produces a tremendous amount of data, making sequence alignment a critical bottleneck in bioinformatics analysis. The existing…

Beam alignment (BA) is to ensure the transmitter and receiver beams are accurately aligned to establish a reliable communication link in millimeter-wave (mmwave) systems. Existing BA methods search the entire beam space to identify the…