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Generalist pathology foundation models (PFMs), pretrained on large-scale multi-organ datasets, have demonstrated remarkable predictive capabilities across diverse clinical applications. However, their proficiency on the full spectrum of…
Background: Significance analysis plays a major role in identifying and ranking genes, transcription factor binding sites, DNA methylation regions, and other high-throughput features for association with disease. We propose a new approach,…
Meta-analysis of multiple genome-wide association studies (GWAS) is effective for detecting single or multi marker associations with complex traits. We develop a flexible procedure ("STAMP") based on mixture models to perform region based…
Generating executable CAD programs from images requires alignment between visual geometry and symbolic program representations, a capability that current methods fail to learn reliably as design complexity increases. Existing fine-tuning…
Background: Recent assays for individual-specific genome-wide DNA methylation profiles have enabled epigenome-wide association studies to identify specific CpG sites associated with a phenotype. Computational prediction of CpG site-specific…
Metamorphic testing is a testing method for problems without test oracles. Integration testing allows for detecting errors in complex systems that may not be found during the testing of their components. In this paper, we propose a novel…
Finding local correspondences between images with different viewpoints requires local descriptors that are robust against geometric transformations. An approach for transformation invariance is to integrate out the transformations by…
Motivated by gene set enrichment analysis, we investigate the problem of combined hypothesis testing on a graph. We introduce a general framework to effectively use the structural information of the underlying graph when testing…
Gene expression and DNA methylation are two interconnected biological processes and understanding their relationship is important in advancing understanding in diverse areas, including disease pathogenesis, environmental adaptation,…
High-throughput genetic and epigenetic data are often screened for associations with an observed phenotype. For example, one may wish to test hundreds of thousands of genetic variants, or DNA methylation sites, for an association with…
Genetic programming is an evolutionary approach known for its performance in program synthesis. However, it is not yet mature enough for a practical use in real-world software development, since usually many training cases are required to…
Increasingly used high throughput experimental techniques, like DNA or protein microarrays give as a result groups of interesting, e.g. differentially regulated genes which require further biological interpretation. With the systematic…
\textbf{Background}: Identifying differentially methylated regions (DMRs) is a basic task in DNA methylation analysis. However, due to the different strategies adopted, different DMR sets will be predicted on the same dataset, which poses a…
With the advance of high-throughput sequencing technologies, it has become feasible to investigate the influence of the entire spectrum of sequencing variations on complex human diseases. Although association studies utilizing the new…
Research on the localization of the genetic basis associated with diseases or traits has been widely conducted in the last a few decades. Scan methods have been developed for region-based analysis in whole-genome association studies,…
Reshef & Reshef recently published a paper in which they present a method called the Maximal Information Coefficient (MIC) that can detect all forms of statistical dependence between pairs of variables as sample size goes to infinity. While…
DNA methylation is an important epigenetic mark that has been studied extensively for its regulatory role in biological processes and diseases. WGBS allows for genome-wide measurements of DNA methylation up to single-base resolutions, yet…
Given multi-platform genome data with prior knowledge of functional gene sets, how can we extract interpretable latent relationships between patients and genes? More specifically, how can we devise a tensor factorization method which…
Genetic association studies, in particular the genome-wide association study design, have provided a wealth of novel insights into the aetiology of a wide range of human diseases and traits. The next challenge consists of understanding the…
Medical imaging is an essential tool for diagnosing and treating diseases. However, lacking medical images can lead to inaccurate diagnoses and ineffective treatments. Generative models offer a promising solution for addressing medical…