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We present an approach to denoising spatial transcriptomics images that is particularly effective for uncovering cell identities in the regime of ultra-low sequencing depths, and also allows for interpolation of gene expression. The method…
Genome sequence analysis, which examines the DNA sequences of organisms, drives advances in many critical medical and biotechnological fields. Given its importance and the exponentially growing volumes of genomic sequence data, there are…
We propose a new paradigm for universal information extraction (IE) that is compatible with any schema format and applicable to a list of IE tasks, such as named entity recognition, relation extraction, event extraction and sentiment…
Sequential dynamics are a key feature of many modern recommender systems, which seek to capture the `context' of users' activities on the basis of actions they have performed recently. To capture such patterns, two approaches have…
We consider the correction of errors from nucleotide sequences produced by next-generation targeted amplicon sequencing. The next-generation sequencing (NGS) platforms can provide a great deal of sequencing data thanks to their high…
DNA methylation (DNAme) is a critical component of the epigenetic regulatory machinery and aberrations in DNAme patterns occur in many diseases, such as cancer. Mapping and understanding DNAme profiles offers considerable promise for…
Single-cell RNA-Sequencing (scRNA-Seq) is a revolutionary technique for discovering and describing cell types in heterogeneous tissues, yet its measurement of expression often suffers from large systematic bias. A major source of this bias…
Test-Time Adaptation (TTA) adjusts models using unlabeled test data to handle dynamic distribution shifts. However, existing methods rely on frequent adaptation and high computational cost, making them unsuitable for resource-constrained…
We propose to reduce the original well-posed problem of compressive sensing to weighted-MAX-SAT. Compressive sensing is a novel randomized data acquisition approach that linearly samples sparse or compressible signals at a rate much below…
Extracting the speech of a target speaker from mixed audios, based on a reference speech from the target speaker, is a challenging yet powerful technology in speech processing. Recent studies of speaker-independent speech separation, such…
Single-cell transcriptomic data approximates the abundance of proteins at a high resolution, but its noisiness necessitates transformation by a pipeline of methods before analysis and inference. In the absence of robust validation of these…
Recent advances in DNA sequencing and fluorescence imaging have made it possible to monitor the dynamics of ribosomes actively engaged in messenger RNA (mRNA) translation. Here, we model these experiments within the inhomogeneous totally…
Single-cell RNA-sequencing technologies may provide valuable insights to the understanding of the composition of different cell types and their functions within a tissue. Recent technologies such as spatial transcriptomics, enable the…
Functional or non-coding RNAs are attracting more attention as they are now potentially considered valuable resources in the development of new drugs intended to cure several human diseases. The identification of drugs targeting the…
Background. Dramatic increases in RNA structural data have made it possible to recognize its conformational preferences much better than a decade ago. This has created an opportunity to use discrete restraint-based conformational sampling…
This paper introduces a simple principle for robust high-dimensional statistical inference via an appropriate shrinkage on the data. This widens the scope of high-dimensional techniques, reducing the moment conditions from sub-exponential…
Channel state information (CSI) acquisition and feedback overhead grows with the number of antennas, users, and reported subbands. This growth becomes a bottleneck for many antenna and reconfigurable intelligent surface (RIS) systems as…
Sampling rate offsets (SROs) between devices in a heterogeneous wireless acoustic sensor network (WASN) can hinder the ability of distributed adaptive algorithms to perform as intended when they rely on coherent signal processing. In this…
SELEX (Systematic Evolution of Ligands by Exponential Enrichment) is an experimental procedure that allows extracting, from an initially random pool of DNA, those oligomers with high affinity for a given DNA-binding protein. We address what…
The mismatch between the numerical and actual nonlinear models is a challenge to nonlinear acoustic echo cancellation (NAEC) when the nonlinear adaptive filter is utilized. To alleviate this problem, we combine a basis-generic expansion of…