Related papers: Distance Measures for Sequences
In this work we study the interleaving distance between merge trees from a combinatorial point of view. We use a particular type of matching between trees to obtain a novel formulation of the distance. With such formulation, we tackle the…
Phylogenetic trees are a central tool in understanding evolution. They are typically inferred from sequence data, and capture evolutionary relationships through time. It is essential to be able to compare trees from different data sources…
We propose a metric for the space of multiple sequence alignments that can be used to compare two alignments to each other. In the case where one of the alignments is a reference alignment, the resulting accuracy measure improves upon…
Single-cell omics enable the profiles of cells, which contain large numbers of biological features, to be quantified. Cluster analysis, a dimensionality reduction process, is used to reduce the dimensions of the data to make it…
This paper presents methods to compare networks where relationships between pairs of nodes in a given network are defined. We define such network distance by searching for the optimal method to embed one network into another network, prove…
The rapid development of such natural language processing tasks as style transfer, paraphrase, and machine translation often calls for the use of semantic similarity metrics. In recent years a lot of methods to measure the semantic…
Trajectories that capture object movement have numerous applications, in which similarity computation between trajectories often plays a key role. Traditionally, the similarity between two trajectories is quantified by means of heuristic…
The problem of similarity search is one of the main problems in computer science. This problem has many applications in text-retrieval, web search, computational biology, bioinformatics and others. Similarity between two data objects can be…
The purpose of this paper is to give a survey on the notions of distance between subsets either of a metric space or of a measure space, including definitions, a classification, and a discussion of the best-known distance functions, which…
Merge trees, a type of topological descriptor, serve to identify and summarize the topological characteristics associated with scalar fields. They present a great potential for the analysis and visualization of time-varying data. First,…
Mapping between sequence and structure is currently an open problem in structural biology. Despite many experimental and computational efforts it is not clear yet how the structure is encoded in the sequence. Answering this question may…
Background: Alignment of biological sequences such as DNA, RNA or proteins is one of the most widely used tools in computational bioscience. All existing alignment algorithms rely on heuristic scoring schemes based on biological expertise.…
Computing the similarity between two probability distributions is a recurring theme across control. We introduce a unified family of distances between the probability distributions of two random variables that is based on the discrepancy…
DNA sequence alignment is important today as it is usually the first step in finding gene mutation, evolutionary similarities, protein structure, drug development and cancer treatment. Covid-19 is one recent example. There are many…
In systems biology, it is becoming increasingly common to measure biochemical entities at different levels of the same biological system. Hence, data fusion problems are abundant in the life sciences. With the availability of a multitude of…
Motivation: The comparison of diverse genomic datasets is fundamental to understanding genome biology. Researchers must explore many large datasets of genome intervals (e.g., genes, sequence alignments) to place their experimental results…
Formulae for the line-of-sight and transverse comoving distances, proper motion distance, angular diameter distance, luminosity distance, k-correction, distance modulus, comoving volume, lookback time, age, and object intersection…
Learning to hash is an efficient paradigm for exact and approximate nearest neighbor search from massive databases. Binary hash codes are typically extracted from an image by rounding output features from a CNN, which is trained on a…
The existence of trace links between artifacts of the software development life cycle can improve the efficiency of many activities during software development, maintenance and operations. Unfortunately, the creation and maintenance of…
The use of skew polynomial rings allows to endow linear codes with cyclic structures which are not cyclic in the classical (commutative) sense. Whenever these skew cyclic structures are carefully chosen, some control over the Hamming…