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Our work is motivated by Bourque and Pevzner's (2002) simulation study of the effectiveness of the parsimony method in studying genome rearrangement, and leads to a surprising result about the random transposition walk on the group of…
We introduce Permutation and Structured Perturbation Inference (PSPI), a new problem formulation that abstracts many graph matching tasks that arise in systems biology. PSPI can be viewed as a robust formulation of the permutation inference…
Persistence diagrams (PD)s play a central role in topological data analysis, and are used in an ever increasing variety of applications. The comparison of PD data requires computing comparison metrics among large sets of PDs, with metrics…
In the snippets problem, the goal is to preprocess text $T$ so that given two patterns $P_1$ and $P_2$, one can locate the occurrences of the two patterns in $T$ that are closest to each other, or report their distance. Kopelowitz and…
The Damerau-Levenshtein distance between two sequences is the minimum number of operations (deletions, insertions, substitutions, and adjacent transpositions) required to convert one sequence into another. Notwithstanding a long history of…
We develop a new approach to derive single state tight binding (SSTB) model for electron transport in the vicinity of valence-conduction bands of poly(G)-poly(C) and poly(A)-poly(T) DNA. The SSTB parameters are derived from {\it first…
A well-studied continuous model of graphs considers each edge as a continuous unit-length interval of points. In the problem $\delta$-Tour defined within this model, the objective to find a shortest tour that comes within a distance of…
We study the natural problem of Triplet Reconstruction (also Rooted Triplets Consistency or Triplet Clustering), originally motivated in computational biology and relational databases (Aho, Sagiv, Szymanski, and Ullman, 1981): given $n$…
Thompson sampling (TS) is a class of algorithms for sequential decision-making, which requires maintaining a posterior distribution over a model. However, calculating exact posterior distributions is intractable for all but the simplest…
This article studies the poset of simple permutations with respect to the pattern involvement. We specify results on critically indecomposable posets obtained by Schmerl and Trotter to simple permutations and prove that if $\sigma, \pi$ are…
We solve the recognition problem (RP) for the class of Demidenko matrices. Our result closes a remarkable gap in the recognition of specially structured matrices. Indeed, the recognition of permuted Demidenko matrices is a longstanding open…
We consider the cycle structure of a random permutation $\sigma$ chosen uniformly from the symmetric group, subject to the constraint that $\sigma$ does not contain cycles of length exceeding $r.$ We prove that under suitable conditions the…
Let $H$ be a fixed graph. The $H$-Transversal problem, given a graph $G$, asks to remove the smallest number of vertices from $G$ so that $G$ does not contain $H$ as a subgraph. While a simple $|V(H)|$-approximation algorithm exists and is…
High-dimensional planted problems, such as finding a hidden dense subgraph within a random graph, often exhibit a gap between statistical and computational feasibility. While recovering the hidden structure may be statistically possible, it…
Computing accurate splines of degree greater than three is still a challenging task in today's applications. In this type of interpolation, high-order derivatives are needed on the given mesh. As these derivatives are rarely known and are…
While semidefinite programming (SDP) problems are polynomially solvable in theory, it is often difficult to solve large SDP instances in practice. One technique to address this issue is to relax the global positive-semidefiniteness (PSD)…
A finite set of the Euclidean space is called an $s$-distance set provided the number of Euclidean distances in the set is $s$. Determining the largest possible $s$-distance set for the Euclidean space of a given dimension is challenging.…
The discrete prolate spheroidal sequences (DPSS's) provide an efficient representation for discrete signals that are perfectly timelimited and nearly bandlimited. Due to the high computational complexity of projecting onto the DPSS basis -…
Low-rank approximation using time-dependent bases (TDBs) has proven effective for reduced-order modeling of stochastic partial differential equations (SPDEs). In these techniques, the random field is decomposed to a set of deterministic…
The Self-Optimal-Transport (SOT) feature transform is designed to upgrade the set of features of a data instance to facilitate downstream matching or grouping related tasks. The transformed set encodes a rich representation of high order…