Related papers: Reoptimization of the Closest Substring Problem un…
Sequence discriminative training is a great tool to improve the performance of an automatic speech recognition system. It does, however, necessitate a sum over all possible word sequences, which is intractable to compute in practice.…
In the Shortest Common Superstring (SCS) problem, one is given a collection of strings, and needs to find a shortest string containing each of them as a substring. SCS admits $2\frac{11}{23}$-approximation in polynomial time (Mucha,…
Partitioning a sequence of length $n$ into $k$ coherent segments (Seg) is one of the classic optimization problems. As long as the optimization criterion is additive, Seg can be solved exactly in $O(n^2k)$ time using a classic dynamic…
String matching is the problem of deciding whether a given $n$-bit string contains a given $k$-bit pattern. We study the complexity of this problem in three settings. Communication complexity. For small $k$, we provide near-optimal upper…
Motivated by computing duplication patterns in sequences, a new fundamental problem called the longest subsequence-repeated subsequence (LSRS) is proposed. Given a sequence $S$ of length $n$, a letter-repeated subsequence is a subsequence…
The primary focus of this paper is on designing an inexact first-order algorithm for solving constrained nonlinear optimization problems. By controlling the inexactness of the subproblem solution, we can significantly reduce the…
Recurrent neural network (RNN)'s architecture is a key factor influencing its performance. We propose algorithms to optimize hidden sizes under running time constraint. We convert the discrete optimization into a subset selection problem.…
A critical problem in the emerging high-throughput genotyping protocols is to minimize the number of polymerase chain reaction (PCR) primers required to amplify the single nucleotide polymorphism loci of interest. In this paper we study PCR…
Sequence-to-Sequence models were introduced to tackle many real-life problems like machine translation, summarization, image captioning, etc. The standard optimization algorithms are mainly based on example-to-example matching like maximum…
In this work we investigate the min-max-min robust optimization problem and the k-adaptability robust optimization problem for binary problems with uncertain costs. The idea of the first approach is to calculate a set of k feasible…
Repeat finding in strings has important applications in subfields such as computational biology. Surprisingly, all prior work on repeat finding did not consider the constraint on the locality of repeats. In this paper, we propose and study…
The problem of reconstructing strings from substring information has found many applications due to its importance in genomic data sequencing and DNA- and polymer-based data storage. One practically important and challenging paradigm…
In this paper we address the constrained longest common subsequence problem. Given two sequences $X$, $Y$ and a constrained sequence $P$, a sequence $Z$ is a constrained longest common subsequence for $X$ and $Y$ with respect to $P$ if $Z$…
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…
Polytrees are a subclass of Bayesian networks that seek to capture the conditional dependencies between a set of $n$ variables as a directed forest and are motivated by their more efficient inference and improved interpretability. Since the…
The problem of string reconstruction based on its substrings spectrum has received significant attention recently due to its applicability to DNA data storage and sequencing. In contrast to previous works, we consider in this paper a setup…
In the classic longest common substring (LCS) problem, we are given two strings $S$ and $T$, each of length at most $n$, over an alphabet of size $\sigma$, and we are asked to find a longest string occurring as a fragment of both $S$ and…
We revisit the exact shortest unique substring (SUS) finding problem, and propose its approximate version where mismatches are allowed, due to its applications in subfields such as computational biology. We design a generic in-place…
Maximizing a monotone submodular function under cardinality constraint $k$ is a core problem in machine learning and database with many basic applications, including video and data summarization, recommendation systems, feature extraction,…
The well-known trace reconstruction problem is the problem of inferring an unknown source string $x \in \{0,1\}^n$ from independent "traces", i.e. copies of $x$ that have been corrupted by a $\delta$-deletion channel which independently…