相关论文: Multi-strand Reconstruction from Substrings
High-dimensional data often lie in low-dimensional subspaces corresponding to different classes they belong to. Finding sparse representations of data points in a dictionary built using the collection of data helps to uncover…
Lifted Reed-Solomon and multiplicity codes are classes of codes, constructed from specific sets of $m$-variate polynomials. These codes allow for the design of high-rate codes that can recover every codeword or information symbol from many…
In this article we show that the reconstructions of semiconductor surfaces can be determined using a genetic procedure. Coupled with highly optimized interatomic potentials, the present approach represents an efficient tool for finding and…
This paper presents a construction for high-rate MDS codes that enable bandwidth-efficient repair of a single node. Such MDS codes are also referred to as the minimum storage regenerating (MSR) codes in the distributed storage literature.…
In modern practical data centers, storage nodes are usually organized into equally sized groups, which is called racks. The cost of cross-rack communication is much more expensive compared with the intra-rack communication cost. The codes…
The sequence reconstruction problem was proposed by Levenshtein in 2001. In this model, a sequence from a code is transmitted over several channels, and the decoder receives the distinct outputs from each channel. The main problem is to…
In the problem of multiple support recovery, we are given access to linear measurements of multiple sparse samples in $\mathbb{R}^{d}$. These samples can be partitioned into $\ell$ groups, with samples having the same support belonging to…
Nanopore sequencers are emerging as promising new platforms for high-throughput sequencing. As with other technologies, sequencer errors pose a major challenge for their effective use. In this paper, we present a novel information theoretic…
We propose and analyze an online algorithm for reconstructing a sequence of signals from a limited number of linear measurements. The signals are assumed sparse, with unknown support, and evolve over time according to a generic nonlinear…
Recovering a tree that represents the evolutionary history of a group of species is a key task in phylogenetics. Performing this task using sequence data from multiple genetic markers poses two key challenges. The first is the discordance…
Regenerating codes and codes with locality are two schemes that have recently been proposed to ensure data collection and reliability in a distributed storage network. In a situation where one is attempting to repair a failed node,…
We explore whether medium-resolution stellar spectra can be reconstructed from photometric observations, taking advantage of the highly compressible nature of the spectra. We formulate the spectral reconstruction as a least-squares problem…
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…
The sequence reconstruction problem, introduced by Levenshtein in 2001, considers a communication scenario where the sender transmits a codeword from some codebook and the receiver obtains multiple noisy reads of the codeword. Motivated by…
Repeat finding in strings has important applications in subfields such as computational biology. Surprisingly, all prior work on repeat finding did not consider the constraint on the locality of repeats. In this paper, we propose and study…
In a DNA sequence, we have the celebrated Watson-Crick complement $\overline{T}=A$, $\overline{A}=T$, $\overline{C}=G$, and $\overline{G}=C$. Given an integer $m\ge 2$, a secondary structure in a DNA sequence refers to the existence of two…
We investigate the problem of encoding data into an $(n, t)$-break-resilient code ($(n, t)$-BRC), i.e., a collections of sequences of length~$n$ from which the original data can be reconstructed even if they are adversarially broken at up…
We analyze the fixed-angle high-energy ($\alpha' \to \infty$) structure of $n$-point tree-level string amplitudes from complementary perspectives: locally via saddle-point expansions, algebraically via difference equations and their…
We study the problem of coded information retrieval for block-structured data, motivated by DNA-based storage systems where a database is partitioned into multiple files that must each be recoverable as an atomic unit. We initiate and…
String constraint solving refers to solving combinatorial problems involving constraints over string variables. String solving approaches have become popular over the last years given the massive use of strings in different application…