Related papers: The Hybrid k-Deck Problem: Reconstructing Sequence…
We propose a novel approach to solve K-adaptability problems with convex objective and constraints and integer first-stage decisions. A logic-based Benders decomposition is applied to handle the first-stage decisions in a master problem,…
Background: Haplotypes, the ordered lists of single nucleotide variations that distinguish chromosomal sequences from their homologous pairs, may reveal an individual's susceptibility to hereditary and complex diseases and affect how our…
Let $K_k$, $C_k$, $T_k$, and $P_{k}$ denote a complete graph on $k$ vertices, a cycle on $k$ vertices, a tree on $k+1$ vertices, and a path on $k+1$ vertices, respectively. Let $K_{m}-H$ be the graph obtained from $K_{m}$ by removing the…
Tensors, especially higher-order tensors, are typically represented in low-rank formats to preserve the main information of the high-dimensional data while saving memory space. In practice, only a small fraction elements in high-dimensional…
We present a method for reducing the treewidth of a graph while preserving all of its minimal $s-t$ separators up to a certain fixed size $k$. This technique allows us to solve $s-t$ Cut and Multicut problems with various additional…
In the trace reconstruction problem an unknown string ${\bf x}=(x_0,\dots,x_{n-1})\in\{0,1,...,m-1\}^n$ is observed through the deletion channel, which deletes each $x_k$ with a certain probability, yielding a contracted string…
In a classical covering problem, we are given a set of requests that we need to satisfy (fully or partially), by buying a subset of items at minimum cost. For example, in the k-MST problem we want to find the cheapest tree spanning at least…
In this thesis, we address the problem of identifying and quantifying variants (alternative splicing and genomic polymorphism) in RNA-seq data when no reference genome is available, without assembling the full transcripts. Based on the…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
We consider the problem of identifying, from its first $m$ noisy moments, a probability distribution on $[0,1]$ of support $k<\infty$. This is equivalent to the problem of learning a distribution on $m$ observable binary random variables…
In this paper, we study the Random Access Problem in DNA storage, which addresses the challenge of retrieving a specific information strand from a DNA-based storage system. In this framework, the data is represented by $k$ information…
Let $k$ and $n$ be positive integers. Define $R(n,k)$ to be the minimum positive value of $$ | e_i \sqrt{s_1} + e_2 \sqrt{s_2} + ... + e_k \sqrt{s_k} -t | $$ where $ s_1, s_2, ..., s_k$ are positive integers no larger than $n$, $t$ is an…
Given two strings $S$ and $P$, the Episode Matching problem is to find the shortest substring of $S$ that contains $P$ as a subsequence. The best known upper bound for this problem is $\tilde O(nm)$ by Das et al. (1997) , where $n,m$ are…
The NP-complete $k$-Path problem asks whether a given undirected graph has a (simple) path of length at least $k$. We prove that $k$-Path has polynomial-size Turing kernels when restricted to planar graphs, graphs of bounded degree,…
We consider two problems for a directed graph $G$, which we show to be closely related. The first one is to find $k$ edge-disjoint forests in $G$ of maximal size such that the indegree of each vertex in these forests is at most $k$. We…
Motivated by the mode estimation problem of an unknown multivariate probability density function, we study the problem of identifying the point with the minimum k-th nearest neighbor distance for a given dataset of n points. We study the…
Computing cohesive subgraphs is a central problem in graph theory. While many formulations of cohesive subgraphs lead to NP-hard problems, finding a densest subgraph can be done in polynomial time. As such, the densest subgraph model has…
We propose a novel clustering model encompassing two well-known clustering models: k-center clustering and k-median clustering. In the Hybrid k-Clusetring problem, given a set P of points in R^d, an integer k, and a non-negative real r, our…
We illustrate how to invite and excite students about research by exploring higher-dimensional generalizations of the classical egg drop problem, in which the goal is to locate a critical breaking point using the fewest number of trials.…
The $k$-SUM problem is given $n$ input real numbers to determine whether any $k$ of them sum to zero. The problem is of tremendous importance in the emerging field of complexity theory within $P$, and it is in particular open whether it…