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The study of genetic map linearization leads to a combinatorial hard problem, called the {\em minimum breakpoint linearization} (MBL) problem. It is aimed at finding a linearization of a partial order which attains the minimum breakpoint…
We consider the problem of data storage in a geographically distributed (or geo-distributed) network of servers (or nodes) where inter-node communication incurs certain round-trip delays. Every node serves a set of users who can request any…
Large-scale distributed storage systems typically use erasure codes to provide durability of data in the face of failures. A set of $k$ blocks to be stored is encoded using an $[n, k]$ code to generate $n$ blocks that are then stored on…
All inverse problems rely on data to recover unknown parameters, yet not all data are equally informative. This raises the central question of data selection. A distinctive challenge in PDE-based inverse problems is their inherently…
We propose a randomized method for solving linear programs with a large number of columns but a relatively small number of constraints. Since enumerating all the columns is usually unrealistic, such linear programs are commonly solved by…
Compressed indexing is a powerful technique that enables efficient querying over data stored in compressed form, significantly reducing memory usage and often accelerating computation. While extensive progress has been made for…
This paper focuses on pattern matching in the DNA sequence. It was inspired by a previously reported method that proposes encoding both pattern and sequence using prime numbers. Although fast, the method is limited to rather small pattern…
Modern biological science produces vast amounts of genomic sequence data. This is fuelling the need for efficient algorithms for sequence compression and analysis. Data compression and the associated techniques coming from information…
Data storage is one of the main computing issues of this century. Not only storage devices are converging to strict physical limits, but also the amount of data generated by users is growing at an unbelievable rate. To face these…
We consider the setting of data storage across n nodes in a distributed manner. A data collector (DC) should be able to reconstruct the entire data by connecting to any k out of the n nodes and downloading all the data stored in them. When…
Motivated by DNA-based data storage, we investigate a system where digital information is stored in an unordered set of several vectors over a finite alphabet. Each vector begins with a unique index that represents its position in the whole…
The genetic code has been shown to be very error robust compared to randomly selected codes, but to be significantly less error robust than a certain code found by a heuristic algorithm. We formulate this optimisation problem as a Quadratic…
Given a sequence composed of a limit number of characters, we try to "read" it as a "text". This involves to segment the sequence into "words". The difficulty is to distinguish good segmentation from enormous number of random ones.Aiming at…
This work introduces a multi-antenna coded caching problem in a two-dimensional multi-access network, where a server with $L$ transmit antennas and $N$ files communicates to $K_1K_2$ users, each with a single receive antenna, through a…
This chapter deals with the topic of designing reliable and efficient codes for the storage and retrieval of large quantities of data over storage devices that are prone to failure. For long, the traditional objective has been one of…
We consider the canonical {\em shared link network} formed by a source node, hosting a library of $m$ information messages (files), connected via a noiseless common link to $n$ destination nodes (users), each with a cache of size M files.…
Hyperdimensional Computing (HDC) is an emerging computational paradigm for representing compositional information as high-dimensional vectors, and has a promising potential in applications ranging from machine learning to neuromorphic…
The string indexing problem is a fundamental computational problem with numerous applications, including information retrieval and bioinformatics. It aims to efficiently solve the pattern matching problem: given a text T of length n for…
In order to survive, reproduce and (in multicellular organisms) differentiate, cells must control the concentrations of the myriad different proteins that are encoded in the genome. The precision of this control is limited by the inevitable…
Random linear network coding is a particularly decentralized approach to the multicast problem. Use of random network codes introduces a non-zero probability however that some sinks will not be able to successfully decode the required…