相关论文: Geometric Aspects of Biological Sequence Compariso…
In this paper we deal with a best approximation of a vector with respect to a closed semi-algebraic set $C$ in the space $\mathbb{R}^n$ endowed with a semi-algebraic norm $\nu$. Under additional assumptions on $\nu$ we prove…
The distance from the origin in the word metric for generalizations F(p) of Thompson's group F is quasi-isometric to the number of carets in the reduced rooted tree diagrams representing the elements of F(p). This interpretation of the…
Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed…
In recent years there have been a lot of interest to test for similarity between biological drug products, commonly known as biologics. Biologics are large and complex molecule drugs that are produced by living cells and hence these are…
Similarity search is an important problem in information retrieval. This similarity is based on a distance. Symbolic representation of time series has attracted many researchers recently, since it reduces the dimensionality of these high…
Comparative analysis of scalar fields is an important problem with various applications including feature-directed visualization and feature tracking in time-varying data. Comparing topological structures that are abstract and succinct…
Edit distance, also known as Levenshtein distance, is an essential way to compare two strings that proved to be particularly useful in the analysis of genetic sequences and natural language processing. However, edit distance is a discrete…
The similarity between objects is significant in a broad range of areas. While similarity can be measured using off-the-shelf distance functions, they may fail to capture the inherent meaning of similarity, which tends to depend on the…
In this paper we consider the concept of `closeness' between nodes in a weighted network that can be defined topologically even in the absence of a metric. The Generalized Erd\H{o}s Numbers (GENs) satisfy a number of desirable properties as…
Positive semi-definite kernels are used to induce pseudo-metrics, or ``distances'', between measures. We write these as an expected quadratic variation of, or expected inner product between, a random field and the difference of measures.…
Compositional generalization is one of the main properties which differentiates lexical learning in humans from state-of-art neural networks. We propose a general framework for building models that can generalize compositionally using the…
We propose a new similarity measure between texts which, contrary to the current state-of-the-art approaches, takes a global view of the texts to be compared. We have implemented a tool to compute our textual distance and conducted…
We present an algorithm for approximating the edit distance $\operatorname{ed}(x, y)$ between two strings $x$ and $y$ in time parameterized by the degree to which one of the strings $x$ satisfies a natural pseudorandomness property. The…
In this paper we present $LCSk$++: a new metric for measuring the similarity of long strings, and provide an algorithm for its efficient computation. With ever increasing size of strings occuring in practice, e.g. large genomes of plants…
We explore the notion of degree of asymmetry for integer sequences and related combinatorial objects. The degree of asymmetry is a new combinatorial statistic that measures how far an object is from being symmetric. We define this notion…
Are two sets of observations drawn from the same distribution? This problem is a two-sample test. Kernel methods lead to many appealing properties. Indeed state-of-the-art approaches use the $L^2$ distance between kernel-based distribution…
We propose a new method for local distance metric learning based on sample similarity as side information. These local metrics, which utilize conical combinations of metric weight matrices, are learned from the pooled spatial…
Of the many modern approaches to calculating evolutionary distance via models of genome rearrangement, most are tied to a particular set of genomic modelling assumptions and to a restricted class of allowed rearrangements. The "position…
Alignments, i.e., position-wise comparisons of two or more strings or ordered lists are of utmost practical importance in computational biology and a host of other fields, including historical linguistics and emerging areas of research in…
The aim of the present article is to give an introduction to the concept of quasi-unitary equivalence and to define several (pseudo-)metrics on the space of self-adjoint operators acting possibly in different Hilbert spaces. As some of the…