相关论文: Orthologs from maxmer sequence context

Protein sequences are abundant in repeating segments, both as exact copies and as approximate segments with mutations. These repeats are important for protein structure and function, motivating decades of algorithmic work on repeat…

Dendrograms are a way to represent evolutionary relationships between organisms. Nowadays, these are inferred based on the comparison of genes or protein sequences by taking into account their differences and similarities. The genetic…

Genome-to-genome comparisons require designating anchor points, which are given by Maximum Exact Matches (MEMs) between their sequences. For large genomes this is a challenging problem and the performance of existing solutions, even in…

This paper considers the matrix completion problem. We show that it is not necessary to assume joint incoherence, which is a standard but unintuitive and restrictive condition that is imposed by previous studies. This leads to a sample…

The detection of similarities between long DNA and protein sequences is studied using concepts of statistical physics. It is shown that mutual similarities can be detected by sequence alignment methods only if their amount exceeds a…

We use machine learning algorithms to detect the crystalline phase in undercooled melts in molecular dynamics simulations. Our classification method is based on local conformation and environmental fingerprints of individual monomers. In…

Ontology matching (OM) entails the identification of semantic relationships between concepts within two or more knowledge graphs (KGs) and serves as a critical step in integrating KGs from various sources. Recent advancements in deep OM…

Comparative and evolutive ecologists are interested in the distribution of quantitative traits among related species. The classical framework for these distributions consists of a random process running along the branches of a phylogenetic…

The algorithm for finding the optimal consistent approximation of an inconsistent pairwise comparisons matrix is based on a logarithmic transformation of a pairwise comparisons matrix into a vector space with the Euclidean metric.…

Large language models (LLMs) have exhibited remarkable capabilities in learning from explanations in prompts, but there has been limited understanding of exactly how these explanations function or why they are effective. This work aims to…

Despite their widespread adoption in various domains, especially due to their powerful reasoning capabilities, Large Language Models (LLMs) are not the off-the-shelf choice to drive multi-objective optimization yet. Conventional strategies…

Ocular biometric systems working in unconstrained environments usually face the problem of small within-class compactness caused by the multiple factors that jointly degrade the quality of the obtained data. In this work, we propose an…

We study fully dynamic algorithms for maximum matching. This is a well-studied problem, known to admit several update-time/approximation trade-offs. For instance, it is known how to maintain a 1/2-approximate matching in $\log^{O(1)} n$…

Sequence comparison is a prerequisite to virtually all comparative genomic analyses. It is often realised by sequence alignment techniques, which are computationally expensive. This has led to increased research into alignment-free…

We present SOS-Match, a novel framework for detecting and matching objects in unstructured environments. Our system consists of 1) a front-end mapping pipeline using a zero-shot segmentation model to extract object masks from images and…

Although the applications of Non-Homogeneous Poisson Processes to model and study the threshold overshoots of interest in different time series of measurements have proven to provide good results, they needed to be complemented with an…

Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can…

Building machine learning prediction models for a specific NLP task requires sufficient training data, which can be difficult to obtain for less-resourced languages. Cross-lingual embeddings map word embeddings from a less-resourced…

Real world data often have a long-tailed and open-ended distribution. A practical recognition system must classify among majority and minority classes, generalize from a few known instances, and acknowledge novelty upon a never seen…

The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…