相关论文: Orthologs from maxmer sequence context
Orthology and paralogy relations are often inferred by methods based on gene similarity, which usually yield a graph depicting the relationships between gene pairs. Such relation graphs are known to frequently contain errors, as they cannot…
A frame is a generalization of a basis of a vector space to a redundant overspanning set whose vectors are linearly dependent. Frames find applications in signal processing and quantum information theory. We present a genetic algorithm that…
Unbalanced translocations are among the most frequent chromosomal alterations, accounted for 30\% of all losses of heterozygosity, a major genetic event causing inactivation of tumor suppressor genes. Despite of their central role in…
In this paper, we describe a new type of match between a pattern and a text that aren't necessarily maximal in the query, but still contain useful matching information: locally maximal exact matches (LEMs). There are usually a large amount…
Ontology matching (OM) plays an essential role in enabling semantic interoperability and integration across heterogeneous knowledge sources, particularly in the biomedical domain which contains numerous complex concepts related to diseases…
We study the problem of efficiently recovering the matching between an unlabelled collection of $n$ points in $\mathbb{R}^d$ and a small random perturbation of those points. We consider a model where the initial points are i.i.d. standard…
Ontologies usually suffer from the semantic heterogeneity when simultaneously used in information sharing, merging, integrating and querying processes. Therefore, the similarity identification between ontologies being used becomes a…
In this paper, we study the problem of recovering the latent vertex correspondence between two correlated random graphs with vastly inhomogeneous and unknown edge probabilities between different pairs of vertices. Inspired by and extending…
Random graph matching refers to recovering the underlying vertex correspondence between two random graphs with correlated edges; a prominent example is when the two random graphs are given by Erd\H{o}s-R\'{e}nyi graphs $G(n,\frac{d}{n})$.…
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…
In the absence of horizontal gene transfer it is possible to reconstruct the history of gene families from empirically determined orthology relations, which are equivalent to event-labeled gene trees. Knowledge of the event labels…
The statistical properties of local alignment algorithms with gaps are analyzed theoretically for uncorrelated and correlated DNA sequences. In the vicinity of the log-linear phase transition, the statistics of alignment with gaps is shown…
Ontologies are widely used for representing domain knowledge and meta data, playing an increasingly important role in Information Systems, the Semantic Web, Bioinformatics and many other domains. However, logical reasoning that ontologies…
Considering the high heterogeneity of the ontologies pub-lished on the web, ontology matching is a crucial issue whose aim is to establish links between an entity of a source ontology and one or several entities from a target ontology.…
Modern ontology debugging methods allow efficient identification and localization of faulty axioms defined by a user while developing an ontology. The ontology development process in this case is characterized by rather frequent and regular…
In-context learning (ICL) allows Transformers to adapt to novel tasks without weight updates, yet the underlying algorithms remain poorly understood. We adopt a statistical decision-theoretic perspective by investigating simple binary…
The study of approximate matching in the Massively Parallel Computations (MPC) model has recently seen a burst of breakthroughs. Despite this progress, however, we still have a far more limited understanding of maximal matching which is one…
This article proposes a novel approach to statistical alignment of nucleotide sequences by introducing a context dependent structure on the substitution process in the underlying evolutionary model. We propose to estimate alignments and…
Sequence comparison and alignment has had an enormous impact on our understanding of evolution, biology, and disease. Comparison and alignment of biological networks will likely have a similar impact. Existing network alignments use…
Typically an ontology matching technique is a combination of much different type of matchers operating at various abstraction levels such as structure, semantic, syntax, instance etc. An ontology matching technique which employs matchers at…