相关论文: Fundamental Bounds and Approaches to Sequence Reco…
Most recent state of the art architectures rely on combinations and variations of three approaches: convolutional, recurrent and self-attentive methods. Our work attempts in laying the basis for a new research direction for sequence…
Finite-difference time-domain method is employed to investigate the optical properties of semiconductor thin films patterned with circular holes. The presence of holes enhances the coupling of the incident plane wave with the thin film and…
Error-correcting codes resilient to synchronization errors such as insertions and deletions are known as insdel codes. Due to their important applications in DNA storage and computational biology, insdel codes have recently become a focal…
Reconstructive spectrometers are a promising emerging class of devices that combine complex light scattering with inference to enable compact, high-resolution spectrometry. Thus far, the physical determinants of these devices' performance…
Many machine learning models use the manipulation of dimensions as a driving force to enable models to identify and learn important features in data. In the case of sequential data this manipulation usually happens on the token dimension…
Deep learning research over the past years has shown that by increasing the scope or difficulty of the learning problem over time, increasingly complex learning problems can be addressed. We study incremental learning in the context of…
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…
DNA emerges as a promising medium for the exponential growth of digital data due to its density and durability. This study extends recent research by addressing the \emph{coverage depth problem} in practical scenarios, exploring optimal…
Several studies suggest strong correlation between different types of cancer and the relative concentration of short circulating RNA sequences (miRNA). Because of short length and low concentration, miRNA detection is not easy. Standard…
Motivation: Next-generation sequencing tools have enabled producing of huge amount of genomic information at low cost. Unfortunately, presence of sequencing errors in such data affects quality of downstream analyzes. Accuracy of them can be…
Precision and Recall are two prominent metrics of generative performance, which were proposed to separately measure the fidelity and diversity of generative models. Given their central role in comparing and improving generative models,…
DNA synthesis is considered as one of the most expensive components in current DNA storage systems. In this paper, focusing on a common synthesis machine, which generates multiple DNA strands in parallel following a fixed supersequence,we…
Integer factorization is a famous computational problem unknown whether being solvable in the polynomial time. With the rise of deep neural networks, it is interesting whether they can facilitate faster factorization. We present an approach…
DNA Data storage has recently attracted much attention due to its durable preservation and extremely high information density (bits per gram) properties. In this work, we propose a hybrid coding strategy comprising of generalized…
RNA design shows growing applications in synthetic biology and therapeutics, driven by the crucial role of RNA in various biological processes. A fundamental challenge is to find functional RNA sequences that satisfy given structural…
The problem of string reconstruction based on its substrings spectrum has received significant attention recently due to its applicability to DNA data storage and sequencing. In contrast to previous works, we consider in this paper a setup…
The goal of Specular Neutron and X-ray Reflectometry is to infer materials Scattering Length Density (SLD) profiles from experimental reflectivity curves. This paper focuses on investigating an original approach to the ill-posed…
The inverse design of metasurfaces faces inherent challenges due to the nonlinear and highly complex relationship between geometric configurations and their electromagnetic behavior. Traditional optimization approaches often suffer from…
Nanopore sequencing is a widely-used high-throughput genome sequencing technology that can sequence long fragments of a genome into raw electrical signals at low cost. Nanopore sequencing requires two computationally-costly processing steps…
In this paper, we consider a tree inference problem motivated by the critical problem in single-cell genomics of reconstructing dynamic cellular processes from sequencing data. In particular, given a population of cells sampled from such a…