相关论文: Fundamental Bounds and Approaches to Sequence Reco…

Locally Decodable Codes (LDCs) are error-correcting codes for which individual message symbols can be quickly recovered despite errors in the codeword. LDCs for Hamming errors have been studied extensively in the past few decades, where a…

Deep learning-based models have demonstrated remarkable success in solving illposed inverse problems; however, many fail to strictly adhere to the physical constraints imposed by the measurement process. In this work, we introduce a…

Fault tolerance in Deep Neural Networks (DNNs) deployed on resource-constrained systems presents unique challenges for high-accuracy applications with strict timing requirements. Memory bit-flips can severely degrade DNN accuracy, while…

Encoding data as a set of unordered strings is receiving great attention as it captures one of the basic features of DNA storage systems. However, the challenge of constructing optimal redundancy codes for this channel remained elusive. In…

DNA sequences encode critical genetic information, yet their variable length and discrete nature impede direct utilization in deep learning models. Existing DNA representation schemes convert sequences into numerical vectors but fail to…

We consider the problem of coding for the substring channel, in which information strings are observed only through their (multisets of) substrings. Due to existing DNA sequencing techniques and applications in DNA-based storage systems,…

Robustness to bit errors is a key requirement for the reliable use of neural networks (NNs) on emerging approximate computing platforms and error-prone memory technologies. A common approach to achieve bit error tolerance in NNs is…

With continuous progression of Moore's Law, integrated circuit (IC) device complexity is also increasing. Scanning Electron Microscope (SEM) image based extensive defect inspection and accurate metrology extraction are two main challenges…

Due to its high data density and longevity, DNA is considered a promising medium for satisfying ever-increasing data storage needs. However, the diversity of errors that occur in DNA sequences makes efficient error-correction a challenging…

The problem of reconstructing a sequence of independent and identically distributed symbols from a set of equal size, consecutive, fragments, as well as a dependent reference sequence, is considered. First, in the regime in which the…

Genome rearrangement distances are an established method in genome comparison. Works in this area may include various rearrangement operations representing large-scale mutations, gene orientation information, the number of nucleotides in…

The high-throughput short-reads RNA-seq protocols often produce paired-end reads, with the middle portion of the fragments being unsequenced. We explore if the full-length fragments can be computationally reconstructed from the sequenced…

In evolutionary biology, the speciation history of living organisms is represented graphically by a phylogeny, that is, a rooted tree whose leaves correspond to current species and branchings indicate past speciation events. Phylogenies are…

In the (deletion-channel) trace reconstruction problem, there is an unknown $n$-bit source string $x$. An algorithm is given access to independent traces of $x$, where a trace is formed by deleting each bit of~$x$ independently with…

In the usual trace reconstruction problem, the goal is to exactly reconstruct an unknown string of length $n$ after it passes through a deletion channel many times independently, producing a set of traces (i.e., random subsequences of the…

This paper studies sequential methods for recovery of sparse signals in high dimensions. When compared to fixed sample size procedures, in the sparse setting, sequential methods can result in a large reduction in the number of samples…

Inversion by Direct Iteration (InDI) is a new formulation for supervised image restoration that avoids the so-called "regression to the mean" effect and produces more realistic and detailed images than existing regression-based methods. It…

Ancestral sequence reconstruction is a key task in computational biology. It consists in inferring a molecular sequence at an ancestral species of a known phylogeny, given descendant sequences at the tip of the tree. In addition to its many…

In this paper, fundamental limits in sequencing of a set of closely related DNA molecules are addressed. This problem is called pooled-DNA sequencing which encompasses many interesting problems such as haplotype phasing, metageomics, and…

The central problem in sequence reconstruction is to find the minimum number of distinct channel outputs required to uniquely reconstruct the transmitted sequence. According to Levenshtein's work in 2001, this number is determined by the…