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Genome sequencing is the basis for many modern biological and medicinal studies. With recent technological advances, metagenomics has become a problem of interest. This problem entails the analysis and reconstruction of multiple DNA…
We review connections between coding-theoretic objects and sparse learning problems. In particular, we show how seemingly different combinatorial objects such as error-correcting codes, combinatorial designs, spherical codes, compressed…
Low-Dose computer tomography (LDCT) is an ideal alternative to reduce radiation risk in clinical applications. Although supervised-deep-learning-based reconstruction methods have demonstrated superior performance compared to conventional…
Computed tomography (CT) has become an essential part of modern science and medicine. A CT scanner consists of an X-ray source that is spun around an object of interest. On the opposite end of the X-ray source, a detector captures X-rays…
Recently, network error correction coding (NEC) has been studied extensively. Several bounds in classical coding theory have been extended to network error correction coding, especially the Singleton bound. In this paper, following the…
We establish convergence of the training dynamics of residual neural networks (ResNets) to their joint infinite depth L, hidden width M, and embedding dimension D limit. Specifically, we consider ResNets with two-layer perceptron blocks in…
We study codes that can correct backtracking errors during nanopore sequencing. In this channel, a sequence of length $n$ over an alphabet of size $q$ is being read by a sliding window of length $\ell$, where from each window we obtain only…
Because of its high data density and longevity, DNA is emerging as a promising candidate for satisfying increasing data storage needs. Compared to conventional storage media, however, data stored in DNA is subject to a wider range of errors…
Recurrent neural networks (RNNs) have drawn interest from machine learning researchers because of their effectiveness at preserving past inputs for time-varying data processing tasks. To understand the success and limitations of RNNs, it is…
We describe a family of recursive methods for the synthesis of qubit permutations on quantum computers with limited qubit connectivity. Two objectives are of importance: circuit size and depth. In each case we combine a scalable heuristic…
The explosion in the volumes of data being stored online has resulted in distributed storage systems transitioning to erasure coding based schemes. Yet, the codes being deployed in practice are fairly short. In this work, we address what we…
Limited-angle tomography is a highly ill-posed linear inverse problem. It arises in many applications, such as digital breast tomosynthesis. Reconstructions from limited-angle data typically suffer from severe stretching of features along…
Motivated by mass-spectrometry protein sequencing, we consider a simply-stated problem of reconstructing a string from the multiset of its substring compositions. We show that all strings of length 7, one less than a prime, or one less than…
In distributed storage systems that employ erasure coding, the issue of minimizing the total {\it repair bandwidth} required to exactly regenerate a storage node after a failure arises. This repair bandwidth depends on the structure of the…
We study permutations over the set of $\ell$-grams, that are feasible in the sense that there is a sequence whose $\ell$-gram frequency has the same ranking as the permutation. Codes, which are sets of feasible permutations, protect…
The ability to store data in the DNA of a living organism has applications in a variety of areas including synthetic biology and watermarking of patented genetically-modified organisms. Data stored in this medium is subject to errors…
Most DNA sequencing technologies are based on the shotgun paradigm: many short reads are obtained from random unknown locations in the DNA sequence. A fundamental question, studied in arXiv:1203.6233, is what read length and coverage depth…
Deep metric learning (DML) aims to minimize empirical expected loss of the pairwise intra-/inter- class proximity violations in the embedding space. We relate DML to feasibility problem of finite chance constraints. We show that minimizer…
We prove a list recovery guarantee for random low-rate linear codes over sufficiently large prime fields. For fixed dimension $d$, error fraction $\alpha$, and accuracy parameter $\varepsilon$, a random $d$-dimensional linear code $C…
In this paper, we prove that with high probability, random Reed-Solomon codes approach the half-Singleton bound - the optimal rate versus error tradeoff for linear insdel codes - with linear-sized alphabets. More precisely, we prove that,…