Related papers: On the Approximability of Comparing Genomes with D…
Subgraph matching is the problem of determining the presence and location(s) of a given query graph in a large target graph. Despite being an NP-complete problem, the subgraph matching problem is crucial in domains ranging from network…
Extracting associations that recur across multiple studies while controlling the false discovery rate is a fundamental challenge. Here, we consider an extension of Efron's single-study two-groups model to allow joint analysis of multiple…
This paper rigorously solves the challenging problem of recognizing periodic patterns under rigid motion in Euclidean geometry. The 3-dimensional case is practically important for justifying the novelty of solid crystalline materials…
The Maximum Betweenness Centrality problem (MBC) can be defined as follows. Given a graph find a $k$-element node set $C$ that maximizes the probability of detecting communication between a pair of nodes $s$ and $t$ chosen uniformly at…
Model misspecification can create significant challenges for the implementation of probabilistic models, and this has led to development of a range of robust methods which directly account for this issue. However, whether these more…
Similarity search is one of the most fundamental computations that are regularly performed on ever-increasing protein datasets. Scalability is of paramount importance for uncovering novel phenomena that occur at very large scales. We…
2D display is a fast and economical way of visualizing polymorphism and comparing genomes, which is based on the separation of DNA fragments in two steps, according first to their size and then to their sequence composition. In this paper,…
Inside individual cells, expression of genes is inherently stochastic and manifests as cell-to-cell variability or noise in protein copy numbers. Since proteins half-lives can be comparable to the cell-cycle length, randomness in…
Let $P$ be a set of at most $n$ points and let $R$ be a set of at most $n$ geometric ranges, such as for example disks or rectangles, where each $p \in P$ has an associated supply $s_{p} > 0$, and each $r \in R$ has an associated demand…
Many major works in social science employ matching to make causal conclusions, but different matches on the same data may produce different treatment effect estimates, even when they achieve similar balance or minimize the same loss…
Hypergraph matching has recently become a popular approach for solving correspondence problems in computer vision as it allows to integrate higher-order geometric information. Hypergraph matching can be formulated as a third-order…
In this work we explore the dissimilarity between symmetric word pairs, by comparing the inter-word distance distribution of a word to that of its reversed complement. We propose a new measure of dissimilarity between such distributions.…
Genetic information is encoded in a linear sequence of nucleotides, represented by letters ranging from thousands to billions. Mutations refer to changes in the DNA or RNA nucleotide sequence. Thus, mutation detection is vital in all areas…
Sequence classification algorithms, such as SVM, require a definition of distance (similarity) measure between two sequences. A commonly used notion of similarity is the number of matches between $k$-mers ($k$-length subsequences) in the…
Gene regulatory networks (GRNs) are increasingly used for explaining biological processes with complex transcriptional regulation. A GRN links the expression levels of a set of genes via regulatory controls that gene products exert on one…
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 $X$…
Determining whether two STRIPS planning instances are isomorphic is the simplest form of comparison between planning instances. It is also a particular case of the problem concerned with finding an isomorphism between a planning instance…
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…
We consider the problem of detecting multiple changepoints in large data sets. Our focus is on applications where the number of changepoints will increase as we collect more data: for example in genetics as we analyse larger regions of the…
DNA sequencing is the physical/biochemical process of identifying the location of the four bases (Adenine, Guanine, Cytosine, Thymine) in a DNA strand. As semiconductor technology revolutionized computing, modern DNA sequencing technology…