Related papers: Reconstructing Mixtures of Coded Strings from Pref…
We consider the problem of correcting mass readout errors in information encoded in binary polymer strings. Our work builds on results for string reconstruction problems using composition multisets [Acharya et al., 2015] and the unique…
Relative compression, where a set of similar strings are compressed with respect to a reference string, is a very effective method of compressing DNA datasets containing multiple similar sequences. Relative compression is fast to perform…
Encoding data as a set of unordered strings is receiving great attention as it captures one of the basic features of DNA storage systems. However, the challenge of constructing optimal redundancy codes for this channel remained elusive. In…
In this paper, we propose a new indexing structure for parameterized strings which we call PLSTs, by generalizing linear-size suffix tries for ordinary strings. Two parameterized strings are said to match if there is a bijection on the…
Reconstruction codes are generalizations of error-correcting codes that can correct errors by a given number of noisy reads. The study of such codes was initiated by Levenshtein in 2001 and developed recently due to applications in modern…
Subgraph reconfiguration is a family of problems focusing on the reachability of the solution space in which feasible solutions are subgraphs, represented either as sets of vertices or sets of edges, satisfying a prescribed graph structure…
Motivated by DNA-based storage applications, we study the problem of reconstructing a coded sequence from multiple traces. We consider the model where the traces are outputs of independent deletion channels, where each channel deletes each…
The problem of storing permutations in a distributed manner arises in several common scenarios, such as efficient updates of a large, encrypted, or compressed data set. This problem may be addressed in either a combinatorial or a coding…
Several recent works have considered the \emph{trace reconstruction problem}, in which an unknown source string $x\in\{0,1\}^n$ is transmitted through a probabilistic channel which may randomly delete coordinates or insert random bits,…
We investigate the task of retrieving information from compositional distributed representations formed by Hyperdimensional Computing/Vector Symbolic Architectures and present novel techniques which achieve new information rate bounds.…
Music rearrangement involves reshuffling, deleting, and repeating sections of a music piece with the goal of producing a standalone version that has a different duration. It is a creative and time-consuming task commonly performed by an…
We address the problem of super-resolution frequency recovery using prior knowledge of the structure of a spectrally sparse, undersampled signal. In many applications of interest, some structure information about the signal spectrum is…
The task of calculating similarities between strings held by different organizations without revealing these strings is an increasingly important problem in areas such as health informatics, national censuses, genomics, and fraud detection.…
The suffix tree is arguably the most fundamental data structure on strings: introduced by Weiner (SWAT 1973) and McCreight (JACM 1976), it allows solving a myriad of computational problems on strings in linear time. Motivated by its large…
Reconstructing complex networks from measurable data is a fundamental problem for understanding and controlling collective dynamics of complex networked systems. However, a significant challenge arises when we attempt to decode structural…
We introduce a new string matching problem called order-preserving matching on numeric strings where a pattern matches a text if the text contains a substring whose relative orders coincide with those of the pattern. Order-preserving…
Computing the {\em matching statistics} of a string $P[1..m]$ with respect to a text $T[1..n]$ is a fundamental problem which has application to genome sequence comparison. In this paper, we study the problem of computing the matching…
In models to generate program source code from natural language, representing this code in a tree structure has been a common approach. However, existing methods often fail to generate complex code correctly due to a lack of ability to…
Redescription mining is a data analysis technique that has found applications in diverse fields. The most used redescription mining approaches involve two phases: finding matching pairs among data attributes and extending the pairs. This…
It is known that the majority of the human genome consists of repeated sequences. Furthermore, it is believed that a significant part of the rest of the genome also originated from repeated sequences and has mutated to its current form. In…