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Over the past two decades, a series of works have aimed at studying the problem of genome assembly: the process of reconstructing a genome from sequence reads. An early formulation of the genome assembly problem showed that genome…
We establish a broad methodological foundation for mixed-integer optimization with learned constraints. We propose an end-to-end pipeline for data-driven decision making in which constraints and objectives are directly learned from data…
In the Levenshtein's sequence reconstruction problem a codeword is transmitted through $N$ channels and in each channel a set of errors is introduced to the transmitted word. In previous works, the restriction that each channel provides a…
The paper explores the problem of \emph{spectral compressed sensing}, which aims to recover a spectrally sparse signal from a small random subset of its $n$ time domain samples. The signal of interest is assumed to be a superposition of $r$…
The synthesis of DNA strands remains the most costly part of the DNA storage system. Thus, to make DNA storage system more practical, the time and materials used in the synthesis process have to be optimized. We consider the most common…
In this letter, we consider a problem of reconstructing an unknown discrete signal taking values in a finite alphabet from incomplete linear measurements. The difficulty of this problem is that the computational complexity of the…
In the standard trace reconstruction problem, the goal is to \emph{exactly} reconstruct an unknown source string $\mathsf{x} \in \{0,1\}^n$ from independent "traces", which are copies of $\mathsf{x}$ that have been corrupted by a…
Distributed storage systems provide reliable access to data through redundancy spread over individually unreliable nodes. Application scenarios include data centers, peer-to-peer storage systems, and storage in wireless networks. Storing…
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…
Regenerating codes allow distributed storage systems to recover from the loss of a storage node while transmitting the minimum possible amount of data across the network. We present a systematic computer search for optimal systematic…
Parameterized mathematical models play a central role in understanding and design of complex information systems. However, they often cannot take into account the intricate interactions innate to such systems. On the contrary, purely…
Peer-to-peer distributed storage systems provide reliable access to data through redundancy spread over nodes across the Internet. A key goal is to minimize the amount of bandwidth used to maintain that redundancy. Storing a file using an…
Finding desired information from large data set is a difficult problem. Information retrieval is concerned with the structure, analysis, organization, storage, searching, and retrieval of information. Index is the main constituent of an IR…
We examine the problem of allocating a given total storage budget in a distributed storage system for maximum reliability. A source has a single data object that is to be coded and stored over a set of storage nodes; it is allowed to store…
We consider tensor data completion of an incomplete observation of multidimensional harmonic (MH) signals. Unlike existing tensor-based techniques for MH retrieval (MHR), which mostly adopt the canonical polyadic decomposition (CPD) to…
To increase the information capacity of DNA storage, composite DNA letters were introduced. We propose a novel channel model for composite DNA in which composite sequences are decomposed into ordered standard non-composite sequences. The…
A new class of exact-repair regenerating codes is constructed by combining two layers of erasure correction codes together with combinatorial block designs, e.g., Steiner systems, balanced incomplete block designs and t-designs. The…
Error-correcting codes over sets, with applications to DNA storage, are studied. The DNA-storage channel receives a set of sequences, and produces a corrupted version of the set, including sequence loss, symbol substitution, symbol…
In this paper, we propose two new constructions of exact-repair minimum storage regenerating (exact-MSR) codes. For both constructions, the encoded symbols are obtained by treating the message vector over GF(q) as a linearized polynomial…
In audio processing applications, the generation of expressive sounds based on high-level representations demonstrates a high demand. These representations can be used to manipulate the timbre and influence the synthesis of creative…