Related papers: Distance Measures for Sequences
Recent works in the information science literature have presented cases of using patent databases and patent classification information to construct network maps of technology fields, which aim to aid in competitive intelligence analysis…
Rotation distance between rooted binary trees measures the number of simple operations it takes to transform one tree into another. There are no known polynomial-time algorithms for computing rotation distance. We give an efficient,…
We introduce the diffusion and superposition distances as two metrics to compare signals supported in the nodes of a network. Both metrics consider the given vectors as initial temperature distributions and diffuse heat trough the edges of…
Thinning is the removal of contour pixels/points of connected components in an image to produce their skeleton with retained connectivity and structural properties. The output requirements of a thinning procedure often vary with…
The goal of metagenomics is to study the composition of microbial communities, typically using high-throughput shotgun sequencing. In the metagenomic binning problem, we observe random substrings (called contigs) from a mixture of genomes…
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…
Testing the equality of two conditional distributions is crucial in various modern applications, including transfer learning and causal inference. Despite its importance, this fundamental problem has received surprisingly little attention…
All poetic forms come from somewhere. Prosodic templates can be copied for generations, altered by individuals, imported from foreign traditions, or fundamentally changed under the pressures of language evolution. Yet these relationships…
Given a complex system with a given interface to the rest of the world, what does it mean for a the system to behave close to a simpler specification describing the behavior at the interface? We give several definitions for useful notions…
Inversions, also sometimes called reversals, are a major contributor to variation among bacterial genomes, with studies suggesting that those involving small numbers of regions are more likely than larger inversions. Deletions may arise in…
This paper considers three kinds of length sequences of the complete genome. Detrended fluctuation analysis, spectral analysis, and the mean distance spanned within time $L$ are used to discuss the correlation property of these sequences.…
We study the problem of aligning multiple sequences with the goal of finding an alignment that either maximizes the number of aligned symbols (the longest common subsequence (LCS)), or minimizes the number of unaligned symbols (the…
In this paper we present a simple framework to study various distance problems of permutations, including the transposition and block-interchange distance of permutations as well as the reversal distance of signed permutations. These…
To quantify the fundamental evolution of time-varying networks, and detect abnormal behavior, one needs a notion of temporal difference that captures significant organizational changes between two successive instants. In this work, we…
Tree structures appear in many fields of the life sciences, including phylogenetics, developmental biology and nucleic acid structures. Trees can be used to represent RNA secondary structures, which directly relate to the function of…
Ancestral mixture model, proposed by Chen and Lindsay (2006), is an important model to build a hierarchical tree from high dimensional binary sequences. Mixture trees created from ancestral mixture models involve in the inferred…
Twisted permutation codes, introduced recently by the second and third authors, are frequency permutation arrays. They are similar to repetition permutation codes, in that they are obtained by a repetition construction applied to a smaller…
In this paper we describe a new technique for the comparison of populations of DNA strands. Comparison is vital to the study of ecological systems, at both the micro and macro scales. Existing methods make use of DNA sequencing and cloning,…
Genomic distance between two genomes, i.e., the smallest number of genome rearrangements required to transform one genome into the other, is often used as a measure of evolutionary closeness of the genomes in comparative genomics studies.…
Distances are fundamental primitives whose choice significantly impacts the performances of algorithms in machine learning and signal processing. However selecting the most appropriate distance for a given task is an endeavor. Instead of…