相关论文: Average-Case to (shifted) Worst-Case Reduction for…

We find that current text embedding models produce outputs with a consistent bias, i.e., each embedding vector $e$ can be decomposed as $\tilde{e} + \mu$, where $\mu$ is almost identical across all sentences. We propose a plug-and-play,…

We study approximation algorithms for variants of the \emph{median string} problem, which asks for a string that minimizes the sum of edit distances from a given set of $m$ strings of length $n$. Only the straightforward $2$-approximation…

The Shortest Common Superstring (SCS) problem is a fundamental task in sequence analysis. In genome assembly, however, the double-stranded nature of DNA implies that each fragment may occur either in its original orientation or as its…

There are efficient dynamic programming solutions to the computation of the Edit Distance from $S\in[1..\sigma]^n$ to $T\in[1..\sigma]^m$, for many natural subsets of edit operations, typically in time within $O(nm)$ in the worst-case over…

The {\em binary deletion channel} with deletion probability $d$ ($\text{BDC}_d$) is a random channel that deletes each bit of the input message i.i.d with probability $d$. It has been studied extensively as a canonical example of a channel…

We study the query complexity of exactly reconstructing a string from adaptive queries, such as substring, subsequence, and jumbled-index queries. Such problems have applications, e.g., in computational biology. We provide a number of new…

We study semidefinite programs with diagonal constraints. This problem class appears in combinatorial optimization and has a wide range of engineering applications such as in circuit design, channel assignment in wireless networks, phase…

This paper studies the problem of recovering a non-negative sparse signal $\x \in \Re^n$ from highly corrupted linear measurements $\y = A\x + \e \in \Re^m$, where $\e$ is an unknown error vector whose nonzero entries may be unbounded.…

We develop a new technique for constructing sparse graphs that allow us to prove near-linear lower bounds on the round complexity of computing distances in the CONGEST model. Specifically, we show an $\widetilde{\Omega}(n)$ lower bound for…

We consider error-correcting coding for deoxyribonucleic acid (DNA)-based storage using nanopore sequencing. We model the DNA storage channel as a sampling noise channel where the input data is chunked into $M$ short DNA strands, which are…

The classic string indexing problem is to preprocess a string $S$ into a compact data structure that supports efficient subsequent pattern matching queries, that is, given a pattern string $P$, report all occurrences of $P$ within $S$. In…

In the Network Inference problem, one seeks to recover the edges of an unknown graph from the observations of cascades propagating over this graph. In this paper, we approach this problem from the sparse recovery perspective. We introduce a…

We study regular expression membership testing: Given a regular expression of size $m$ and a string of size $n$, decide whether the string is in the language described by the regular expression. Its classic $O(nm)$ algorithm is one of 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 improve the lower bound on worst case trace reconstruction from $\Omega\left(\frac{n^{5/4}}{\sqrt{\log n}}\right)$ to $\Omega\left(\frac{n^{3/2}}{\log^{7} n}\right)$. As a consequence, we improve the lower bound on average case trace…

We investigate the sparse recovery problem of reconstructing a high-dimensional non-negative sparse vector from lower dimensional linear measurements. While much work has focused on dense measurement matrices, sparse measurement schemes are…

In the longest common substring (LCS) problem, we are given two strings $S$ and $T$, each of length at most $n$, and we are asked to find a longest string occurring as a fragment of both $S$ and $T$. This is a classical and well-studied…

This paper investigates the number of quantum queries made to solve the problem of reconstructing an unknown string from its substrings in a certain query model. More concretely, the goal of the problem is to identify an unknown string $S$…

We consider the problem of coding for the substring channel, in which information strings are observed only through their (multisets of) substrings. Due to existing DNA sequencing techniques and applications in DNA-based storage systems,…

One of the difficulties of neural machine translation (NMT) is the recall and appropriate translation of low-frequency words or phrases. In this paper, we propose a simple, fast, and effective method for recalling previously seen…