Related papers: Trace Reconstruction Problems in Computational Bio…
V. Levenshtein first proposed the sequence reconstruction problem in 2001. This problem studies the model where the same sequence from some set is transmitted over multiple channels, and the decoder receives the different outputs. Assume…
Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…
This paper studies reconstruction of strings based upon their substrings spectrum. Under this paradigm, it is assumed that all substrings of some fixed length are received and the goal is to reconstruct the string. While many existing works…
Recently, DNA storage has surfaced as a promising alternative for data storage, presenting notable benefits in terms of storage capacity, cost-effectiveness in maintenance, and the capability for parallel replication. Mathematically, the…
Being able to reconstruct training data from the parameters of a neural network is a major privacy concern. Previous works have shown that reconstructing training data, under certain circumstances, is possible. In this work, we analyse such…
A challenging problem in complex networks is the network reconstruction problem from data. This work deals with a class of networks denoted as conserved networks, in which a flow associated with every edge and the flows are conserved at all…
DNA sequencing is the basic workhorse of modern day biology and medicine. Shotgun sequencing is the dominant technique used: many randomly located short fragments called reads are extracted from the DNA sequence, and these reads are…
Historical linguistics aims at inferring the most likely language phylogenetic tree starting from information concerning the evolutionary relatedness of languages. The available information are typically lists of homologous (lexical,…
Transforming error-prone immunosequencing datasets into antibody repertoires is a fundamental problem in immunogenomics, and a prerequisite for studies of immune responses. Although various repertoire reconstruction algorithms were released…
Neuron reconstruction is essential to generate exquisite neuron connectivity map for understanding brain function. Despite the significant amount of effect that has been made on automatic reconstruction methods, manual tracing by…
The prevalent technique for DNA sequencing consists of two main steps: shotgun sequencing, where many randomly located fragments, called reads, are extracted from the overall sequence, followed by an assembly algorithm that aims to…
We study inverse problems of reconstructing static and dynamic discrete structures from tomographic data (with a special focus on the `classical' task of reconstructing finite point sets in $\mathbb{R}^d$). The main emphasis is on recent…
Reproducibility is one of the core dimensions that concur to deliver Trustworthy Artificial Intelligence. Broadly speaking, reproducibility can be defined as the possibility to reproduce the same or a similar experiment or method, thereby…
DNA as a data storage medium has several advantages, including far greater data density compared to electronic media. We propose that schemes for data storage in the DNA of living organisms may benefit from studying the reconstruction…
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…
Reconstruction tasks in computer vision aim fundamentally to recover an undetermined signal from a set of noisy measurements. Examples include super-resolution, image denoising, and non-rigid structure from motion, all of which have seen…
The reduction of the fragment assembly problem to (variations of) the classical Eulerian trail problem [Pevzner et al., PNAS 2001] has led to remarkable progress in genome assembly. This reduction employs the notion of de Bruijn graph…
With distributed computing and mobile applications becoming ever more prevalent, synchronizing diverging replicas of the same data is a common problem. Reconciliation -- bringing two replicas of the same data structure as close as possible…
Traces and their extension called combined traces (comtraces) are two formal models used in the analysis and verification of concurrent systems. Both models are based on concepts originating in the theory of formal languages, and they are…
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…