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It is demonstrated earlier that the exact Smith-Waterman algorithm yields more accurate results than the members of the heuristic BLAST family of algorithms. Unfortunately, the Smith-Waterman algorithm is much slower than the BLAST and its…
Genome sequences contain hundreds of millions of DNA base pairs. Finding the degree of similarity between two genomes requires executing a compute-intensive dynamic programming algorithm, such as Smith-Waterman. Traditional von Neumann…
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…
Summary: Longer sequencing reads, with at least 200 bases per template are now common. While traditional aligners have adopted new strategies to improve the mapping of longer reads, aligners specific to bisulfite-sequencing were optimized…
Summary: BWA-MEM is a new alignment algorithm for aligning sequence reads or long query sequences against a large reference genome such as human. It automatically chooses between local and end-to-end alignments, supports paired-end reads…
Protein retrieval, which targets the deconstruction of the relationship between sequences, structures and functions, empowers the advancing of biology. Basic Local Alignment Search Tool (BLAST), a sequence-similarity-based algorithm, has…
The prompt online detection of abrupt changes in image data is essential for timely decision-making in broad applications, from video surveillance to manufacturing quality control. Existing methods, however, face three key challenges.…
Given a collection of objects and an associated similarity measure, the all-pairs similarity search problem asks us to find all pairs of objects with similarity greater than a certain user-specified threshold. Locality-sensitive hashing…
A local Bundle Adjustment (BA) on a sliding window of keyframes has been widely used in visual SLAM and proved to be very effective in lowering the drift. But in lidar SLAM, BA method is hardly used because the sparse feature points (e.g.,…
Large Language Models have revolutionized recommender systems (LLM4Rec) by leveraging their generative capabilities to model complex user preferences. However, existing LLM4Rec methods primarily rely on token-level objectives, making it…
Approximate matching (AM) is a concept in digital forensics to determine the similarity between digital artifacts. An important use case of AM is the reliable and efficient detection of case-relevant data structures on a blacklist, if only…
Least-absolute-deviations (LAD) line fitting is robust to outliers but computationally more involved than least squares regression. Although the literature includes linear and near-linear time algorithms for the LAD line fitting problem,…
In genomics, pattern matching against a sequence of nucleotides plays a pivotal role for DNA sequence alignment and comparing genomes. This helps tackling some diseases, such as cancer in humans. The complexity of searching biological…
Mutual correlation between segments of DNA or protein sequences can be detected by Smith-Waterman local alignments. We present a statistical analysis of alignment of such sequences, based on a recent scaling theory. A new fidelity measure…
Computing the similarity between two protein structures is a crucial task in molecular biology, and has been extensively investigated. Many protein structure comparison methods can be modeled as maximum clique problems in specific k-partite…
The exponential growth of DNA sequencing data has outpaced traditional heuristic-based methods, which struggle to scale effectively. Efficient computational approaches are urgently needed to support large-scale similarity search, a…
Large Language Models (LLMs) have demonstrated remarkable performance across a broad spectrum of tasks, including natural language understanding, dialogue systems, and code generation. Despite evident progress, less attention has been paid…
This report presents the implementation of a protein sequence comparison algorithm specifically designed for speeding up time consuming part on parallel hardware such as SSE instructions, multicore architectures or graphic boards. Three…
Dense vector retrieval is the practical backbone of Retrieval- Augmented Generation (RAG), but similarity search can suffer from precision limitations. Conversely, utility-based approaches leveraging LLM re-ranking often achieve superior…
The stable marriage problem with incomplete lists and ties (SMTI) and the hospitals/residents problem with ties (HRT) are important in matching theory with broad practical applications. In this paper, we introduce a tie-breaking based local…