相关论文: Orthologs from maxmer sequence context

As a new method for detecting change-points in high-resolution time series, we apply Maximum Mean Discrepancy to the distributions of ordinal patterns in different parts of a time series. The main advantage of this approach is its…

Comparative genetic studies of non-model organisms are transforming rapidly due to major advances in sequencing technology. A limiting factor in these studies has been the identification and screening of orthologous loci across an…

Building effective human-robot interaction requires robots to derive conclusions from their experiences that are both logically sound and communicated in ways aligned with human expectations. This paper presents a hybrid framework that…

Two strings of the same length are said to Cartesian-tree match (CT-match) if their Cartesian-trees are isomorphic [Park et al., TCS 2020]. Cartesian-tree matching is a natural model that allows for capturing similarities of numerical…

In this paper, we study the maximum matching problem in RDV graphs, i.e., graphs that are vertex-intersection graphs of downward paths in a rooted tree. We show that this problem can be reduced to a problem of testing (repeatedly) whether a…

We consider the problem of detecting the overlap between a pair of short fragments sampled in random locations from an exponentially longer sequence, via their possibly noisy reads. We consider a noiseless setting, in which the reads are…

Directed cographs (di-cographs) play a crucial role in the reconstruction of evolutionary histories of genes based on homology relations which are binary relations between genes. A variety of methods based on pairwise sequence comparisons…

Meaningful comparison between sets of observations often necessitates alignment or registration between them, and the resulting optimization problems range in complexity from those admitting simple closed-form solutions to those requiring…

Protein sequence alignment is a cornerstone of bioinformatics, traditionally approached using dynamic programming (DP) algorithms that find an optimal sequential path. This paper introduces UniOTalign, a novel framework that recasts…

Stratifying cancer patients based on their gene expression levels allows improving diagnosis, survival analysis and treatment planning. However, such data is extremely highly dimensional as it contains expression values for over 20000 genes…

In this paper, we focus on methods to reduce the size and improve the quality of the prompt context required for question-answering systems. Attempts to increase the number of retrieved chunked documents and thereby enlarge the context…

Recent years have witnessed the successful application of low-dimensional vector space representations of knowledge graphs to predict missing facts or find erroneous ones. However, it is not yet well-understood to what extent ontological…

Metric embeddings into structured spaces, particularly hierarchically well-separated trees (HSTs), are a fundamental tool in the design of online algorithms. In the classical online embedding setting, points arrive sequentially and must be…

This work studies fundamental limits for recovering the underlying correspondence among multiple correlated graphs. In the setting of inhomogeneous random graphs, we present and analyze a matching algorithm: first partially match the graphs…

We experiment with new methods for learning how related words are positioned relative to each other in word embedding spaces. Previous approaches learned constant vector offsets: vectors that point from source tokens to target tokens with…

In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$…

Baswana, Gupta and Sen [FOCS'11] showed that fully dynamic maximal matching can be maintained in general graphs with logarithmic amortized update time. More specifically, starting from an empty graph on $n$ fixed vertices, they devised a…

Pattern matching can be used to calculate the support of patterns, and is a key issue in sequential pattern mining (or sequence pattern mining). Nonoverlapping pattern matching means that two occurrences cannot use the same character in the…

2-colored best match graphs (2-BMGs) form a subclass of sink-free bi-transitive graphs that appears in phylogenetic combinatorics. There, 2-BMGs describe evolutionarily most closely related genes between a pair of species. They are…

Ontologies provide a formal description of concepts and their relationships in a knowledge domain. The goal of ontology alignment is to identify semantically matching concepts and relationships across independently developed ontologies that…