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Most existing algorithms for dictionary learning assume that all entries of the (high-dimensional) input data are fully observed. However, in several practical applications (such as hyper-spectral imaging or blood glucose monitoring), only…
Evaluating treatment effects is critical in clinical trials but sometimes involves lengthy, invasive, or costly follow-up procedures. In these cases, surrogate markers, which provide intermediate measures of the long-term treatment effect,…
Synthetic data has been proposed as a solution to address the issue of high-quality data scarcity in the training of large language models (LLMs). Studies have shown that synthetic data can effectively improve the performance of LLMs on…
In healthcare applications, predictive uncertainty has been used to assess predictive accuracy. In this paper, we demonstrate that predictive uncertainty estimated by the current methods does not highly correlate with prediction error by…
Detecting variation in the evolutionary process along chromosomes is increasingly important as whole-genome data becomes more widely available. For example, factors such as incomplete lineage sorting, horizontal gene transfer, and…
This paper studies two potential modifications of XTrace (Epperly et al., SIMAX 45(1):1-23, 2024), a randomized algorithm for estimating the trace of a matrix. The first is a variance reduction step that averages the output of XTrace over…
Transcription of genes is the focus of most forms of regulation of gene expression. Even though careful biochemical experimentation has revealed the molecular mechanisms of transcription initiation for a number of different promoters in…
Transcriptomic foundation models pretrained with masked language modeling can achieve low pretraining loss yet produce poor cell representations for downstream tasks. We introduce whole-cell expression decoding (WCED), where models…
Imperfect molecular detection in single-cell experiments introduces technical noise that obscures the true stochastic dynamics of gene regulatory networks. While binomial models of molecular capture provide a principled description of…
Genome-wide gene expression profiles, as measured with microarrays or RNA-Seq experiments, have revolutionized biological and biomedical research by providing a quantitative measure of the entire mRNA transcriptome. Typically, researchers…
Test-time scaling aims to improve language model performance by leveraging additional compute during inference. Many works have empirically studied techniques such as Best-of-N (BoN) and Rejection Sampling (RS) that make use of a verifier…
In this paper, the problem of training a classifier on a dataset with incomplete features is addressed. We assume that different subsets of features (random or structured) are available at each data instance. This situation typically occurs…
Eliciting preferences from human judgements is inherently imprecise, yet most decision analysis methods force a single priority vector from pairwise comparisons, discarding the information embedded in inconsistencies. We instead leverage…
We present an error-diagnostic validation method for posterior distributions in Bayesian signal inference, an advancement of a previous work. It transfers deviations from the correct posterior into characteristic deviations from a uniform…
Short-read DNA sequencing instruments can yield over 1e+12 bases per run, typically composed of reads 150 bases long. Despite this high throughput, de novo assembly algorithms have difficulty reconstructing contiguous genome sequences using…
Next-generation sequencing technologies now constitute a method of choice to measure gene expression. Data to analyze are read counts, commonly modeled using Negative Binomial distributions. A relevant issue associated with this…
We propose a new compression scheme for genomic data given as sequence fragments called reads. The scheme uses a reference genome at the decoder side only, freeing the encoder from the burdens of storing references and performing…
Motivated by mutation processes occurring in in-vivo DNA-storage applications, a channel that mutates stored strings by duplicating substrings as well as substituting symbols is studied. Two models of such a channel are considered: one in…
Whole exome sequencing was performed on HLA-matched stem cell donors and transplant recipients to measure sequence variation contributing to minor histocompatibility antigen differences between the two. A large number of nonsynonymous…
The ability to store data in the DNA of a living organism has applications in a variety of areas including synthetic biology and watermarking of patented genetically-modified organisms. Data stored in this medium is subject to errors…