相关论文: Hardness Results on Characteristics for Elastic-De…

Strings form a fundamental data type in computer systems. String searching has been extensively studied since the inception of computer science. Increasingly many applications have to deal with imprecise strings or strings with fuzzy…

We consider the problem of efficiently designing sets (codes) of equal-length DNA strings (words) that satisfy certain combinatorial constraints. This problem has numerous motivations including DNA computing and DNA self-assembly. Previous…

String complexity is defined as the cardinality of a set of all distinct words (factors) of a given string. For two strings, we introduce the joint string complexity as the cardinality of a set of words that are common to both strings.…

Convolution is a broadly useful operation with applications including signal processing, machine learning, probability, optics, polynomial multiplication, and efficient parsing. Usually, however, this operation is understood and implemented…

Genome assembly, the process of reconstructing a long genetic sequence by aligning and merging short fragments, or reads, is known to be NP-hard, either as a version of the shortest common superstring problem or in a Hamiltonian-cycle…

The Longest Common Subsequence (LCS) is the problem of finding a subsequence among a set of strings that has two properties of being common to all and is the longest. The LCS has applications in computational biology and text editing, among…

A degenerate symbol x* over an alphabet A is a non-empty subset of A, and a sequence of such symbols is a degenerate string. A degenerate string is said to be conservative if its number of non-solid symbols is upper-bounded by a fixed…

A key feature of human intelligence is the ability to generalize beyond the training distribution, for instance, parsing longer sentences than seen in the past. Currently, deep neural networks struggle to generalize robustly to such shifts…

DNA storage has emerged as an important area of research. The reliability of DNA storage system depends on designing the DNA strings (called DNA codes) that are sufficiently dissimilar. In this work, we introduce DNA codes that satisfy a…

We study a new generalization of palindromes and gapped palindromes called block palindromes. A block palindrome is a string that becomes a palindrome when identical substrings are replaced with a distinct character. We investigate several…

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…

This paper deals with the complexity of strings, which play an important role in biology (nucleotid sequences), information theory and computer science. The d-complexity of a string is defined as the number of its distinct d-substrings…

Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards…

The problem of detecting and measuring the repetitiveness of one-dimensional strings has been extensively studied in data compression and text indexing. Our understanding of these issues has been significantly improved by the introduction…

Compositional generalization, the ability of an agent to generalize to unseen combinations of latent factors, is easy for humans but hard for deep neural networks. A line of research in cognitive science has hypothesized a process,…

Motivation: The pan-genome can be stored as elastic-degenerate (ED) string, a recently introduced compact representation of multiple overlapping sequences. However, a search over the ED string does not indicate which individuals (if any)…

Exact string matching has been a fundamental problem in computer science for decades because of many practical applications. Some are related to common procedures, such as searching in files and text editors, or, more recently, to more…

We investigate the computational complexity of various problems for simple recurrent neural networks (RNNs) as formal models for recognizing weighted languages. We focus on the single-layer, ReLU-activation, rational-weight RNNs with…

Algorithms to find optimal alignments among strings, or to find a parsimonious summary of a collection of strings, are well studied in a variety of contexts, addressing a wide range of interesting applications. In this paper, we consider…

Obtaining per-beat information is a key task in the analysis of cardiac electrocardiograms (ECG), as many downstream diagnosis tasks are dependent on ECG-based measurements. Those measurements, however, are costly to produce, especially in…