相关论文: Orthologs from maxmer sequence context
We consider the problem of sorting $n$ elements in the case of \emph{persistent} comparison errors. In this model (Braverman and Mossel, SODA'08), each comparison between two elements can be wrong with some fixed (small) probability $p$,…
Enumerating matchings is a classical problem in the field of enumeration algorithms. There are polynomial-delay enumeration algorithms for several settings, such as enumerating perfect matchings, maximal matchings, and (weighted) matchings…
This paper presents OG-RAG, an Ontology-Grounded Retrieval Augmented Generation method designed to enhance LLM-generated responses by anchoring retrieval processes in domain-specific ontologies. While LLMs are widely used for tasks like…
The proliferation of ontologies and taxonomies in many domains increasingly demands the integration of multiple such ontologies. The goal of ontology integration is to merge two or more given ontologies in order to provide a unified view on…
We investigate the behavior of optimal alignment paths for homologous (related) and independent random sequences. An alignment between two finite sequences is optimal if it corresponds to the longest common subsequence (LCS). We prove the…
Ontology matching is defined as finding a relationship or correspondence between two or more entities in two or more ontologies. To solve the interoperability problem of the domain ontologies, semantically similar entities in these…
Euclidean embedding from noisy observations containing outlier errors is an important and challenging problem in statistics and machine learning. Many existing methods would struggle with outliers due to a lack of detection ability. In this…
Network alignment task, which aims to identify corresponding nodes in different networks, is of great significance for many subsequent applications. Without the need for labeled anchor links, unsupervised alignment methods have been…
We describe several algorithms for matrix completion and matrix approximation when only some of its entries are known. The approximation constraint can be any whose approximated solution is known for the full matrix. For low rank…
DNA sequence alignment involves assigning short DNA reads to the most probable locations on an extensive reference genome. This process is crucial for various genomic analyses, including variant calling, transcriptomics, and epigenomics.…
Large language models (LLMs) are pretrained by minimizing the cross-entropy loss for next-token prediction. In this paper, we study whether this optimization strategy can induce geometric structure in the learned model weights and context…
Background: Significance analysis plays a major role in identifying and ranking genes, transcription factor binding sites, DNA methylation regions, and other high-throughput features for association with disease. We propose a new approach,…
Many important geometric estimation problems take the form of synchronization over the special Euclidean group: estimate the values of a set of poses given a set of relative measurements between them. This problem is typically formulated as…
In this paper, we study a number of well-known combinatorial optimization problems that fit in the following paradigm: the input is a collection of (potentially inconsistent) local relationships between the elements of a ground set (e.g.,…
Best match graphs (BMGs) are a class of colored digraphs that naturally appear in mathematical phylogenetics and can be approximated with the help of similarity measures between gene sequences, albeit not without errors. The corresponding…
Modern information systems are changing the idea of "data processing" to the idea of "concept processing", meaning that instead of processing words, such systems process semantic concepts which carry meaning and share contexts with other…
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…
Identifying palindromes in sequences has been an interesting line of research in combinatorics on words and also in computational biology, after the discovery of the relation of palindromes in the DNA sequence with the HIV virus. Efficient…
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…
This paper presents an $O(\log\log \bar{d})$ round massively parallel algorithm for $1+\epsilon$ approximation of maximum weighted $b$-matchings, using near-linear memory per machine. Here $\bar{d}$ denotes the average degree in the graph…