Related papers: Trace Reconstruction Problems in Computational Bio…
Reproducibility is a cornerstone of science, as the replication of findings is the process through which they become knowledge. It is widely considered that many fields of science are undergoing a reproducibility crisis. This has led to the…
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…
Worm origin identification and propagation path reconstruction are essential problems in digital forensics. However, a small number of studies have specifically investigated these problems so far. In this paper, we extend a distributed…
This tutorial covers biomedical image reconstruction, from the foundational concepts of system modeling and direct reconstruction to modern sparsity and learning-based approaches. Imaging is a critical tool in biological research and…
Clusters of genes that have evolved by repeated segmental duplication present difficult challenges throughout genomic analysis, from sequence assembly to functional analysis. Improved understanding of these clusters is of utmost importance,…
The reconstruction of shredded documents consists of coherently arranging fragments of paper (shreds) to recover the original document(s). A great challenge in computational reconstruction is to properly evaluate the compatibility between…
Performing machine learning on structured data is complicated by the fact that such data does not have vectorial form. Therefore, multiple approaches have emerged to construct vectorial representations of structured data, from kernel and…
In the trace reconstruction problem an unknown string ${\bf x}=(x_0,\dots,x_{n-1})\in\{0,1,...,m-1\}^n$ is observed through the deletion channel, which deletes each $x_k$ with a certain probability, yielding a contracted string…
Photoelastic techniques have a long tradition in both qualitative and quantitative analysis of the stresses in granular materials. Over the last two decades, computational methods for reconstructing forces between particles from their…
\emph{Population recovery} is the problem of learning an unknown distribution over an unknown set of $n$-bit strings, given access to independent draws from the distribution that have been independently corrupted according to some noise…
Ptychography has rapidly grown in the fields of X-ray and electron imaging for its unprecedented ability to achieve nano or atomic scale resolution while simultaneously retrieving chemical or magnetic information from a sample. A…
The field of deep learning has witnessed significant breakthroughs, spanning various applications, and fundamentally transforming current software capabilities. However, alongside these advancements, there have been increasing concerns…
Learning-based methods for inverse problems, adapting to the data's inherent structure, have become ubiquitous in the last decade. Besides empirical investigations of their often remarkable performance, an increasing number of works…
Rapid advances in computing technology over the past few decades have spurred two extraordinary phenomena in science: large-scale and high-throughput data collection coupled with the creation and implementation of complex statistical…
In the paper, the Levenshtein's sequence reconstruction problem is considered in the case where at most $t$ substitution errors occur in each of the $N$ channels and the decoder outputs a list of length $\mathcal{L}$. Moreover, it is…
In models to generate program source code from natural language, representing this code in a tree structure has been a common approach. However, existing methods often fail to generate complex code correctly due to a lack of ability to…
We introduce the problem of reconstructing a sequence of multidimensional real vectors where some of the data are missing. This problem contains regression and mapping inversion as particular cases where the pattern of missing data is…
Consider two or more strings $\mathbf{x}^1,\mathbf{x}^2,\ldots,$ that are concatenated to form $\mathbf{x}=\langle \mathbf{x}^1,\mathbf{x}^2,\ldots \rangle$. Suppose that up to $\delta$ deletions occur in each of the concatenated strings.…
Modern neural sequence generation models are built to either generate tokens step-by-step from scratch or (iteratively) modify a sequence of tokens bounded by a fixed length. In this work, we develop Levenshtein Transformer, a new partially…
Successful development of software systems involves efficient navigation among software artifacts. One state-of-practice approach to structure information is to establish trace links between artifacts, a practice that is also enforced by…