Related papers: Reply to "Issues arising from benchmarking single-…

We consider the classical 1D phase retrieval problem. In order to overcome the difficulties associated with phase retrieval from measurements of the Fourier magnitude, we treat recovery from the magnitude of the short-time Fourier transform…

Single-Cell RNA sequencing (scRNA-seq) measurements have facilitated genome-scale transcriptomic profiling of individual cells, with the hope of deconvolving cellular dynamic changes in corresponding cell sub-populations to better…

Small-angle X-ray scattering (SAXS) experiments are increasingly used to probe RNA structure. A number of \emph{forward models} that relate measured SAXS intensities and structural features, and that are suitable to model either…

We formulate a unified framework for the separation of signals that are sparse in "morphologically" different redundant dictionaries. This formulation incorporates the so-called "analysis" and "synthesis" approaches as special cases and…

A new algorithm is developed to jointly recover a temporal sequence of images from noisy and under-sampled Fourier data. Specifically, we consider the case where each data set is missing vital information that prevents its (individual)…

Detecting differences in gene expression is an important part of single-cell RNA sequencing experiments, and many statistical methods have been developed for this aim. Most differential expression analyses focus on comparing expression…

Self-supervised learning (SSL) has proven to be a powerful approach for extracting biologically meaningful representations from single-cell data. To advance our understanding of SSL methods applied to single-cell data, we present…

Compressed sensing allows perfect recovery of sparse signals (or signals sparse in some basis) using only a small number of random measurements. Existing results in compressed sensing literature have focused on characterizing the achievable…

The increasing concern with misinformation has stimulated research efforts on automatic fact checking. The recently-released FEVER dataset introduced a benchmark fact-verification task in which a system is asked to verify a claim using…

Subsampling is an effective approach to alleviate the computational burden associated with large-scale datasets. Nevertheless, existing subsampling estimators incur a substantial loss in estimation efficiency compared to estimators based on…

Timestamp automatic annotation (TAA) is a crucial procedure for analyzing time-series ScRNA-seq data, as they unveil dynamic biological developments and cell regeneration process. However, current TAA methods heavily rely on manual…

In the first part of the series papers, we set out to answer the following question: given specific restrictions on a set of samplers, what kind of signal can be uniquely represented by the corresponding samples attained, as the foundation…

Recent advancements in single-cell RNA-sequencing (scRNA-seq) have enhanced our understanding of cell heterogeneity at a high resolution. With the ability to sequence over 10,000 cells per hour, researchers can collect large scRNA-seq…

In genomics, differential abundance and expression analyses are complicated by the compositional nature of sequence count data, which reflect only relative-not absolute-abundances or expression levels. Many existing methods attempt to…

Many machine learning tasks -- particularly those in affective computing -- are inherently subjective. When asked to classify facial expressions or to rate an individual's attractiveness, humans may disagree with one another, and no single…

Precision is of utmost importance in the realm of clinical entity extraction from clinical notes and reports. Encoder Models fine-tuned for Named Entity Recognition (NER) are an efficient choice for this purpose, as they don't hallucinate.…

Audio processing methods based on deep neural networks are typically trained at a single sampling frequency (SF). To handle untrained SFs, signal resampling is commonly employed, but it can degrade performance, particularly when the input…

This paper presents the system description of our entry for the COLING 2025 RegNLP RIRAG (Regulatory Information Retrieval and Answer Generation) challenge, focusing on leveraging advanced information retrieval and answer generation…

Sequencing technologies have revolutionised the field of molecular biology. We now have the ability to routinely capture the complete RNA profile in tissue samples. This wealth of data allows for comparative analyses of RNA levels at…

Speech separation has been successfully applied as a frontend processing module of conversation transcription systems thanks to its ability to handle overlapped speech and its flexibility to combine with downstream tasks such as automatic…