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This article provides recommendations for implementing quantitative susceptibility mapping (QSM) for clinical brain research. It is a consensus of the ISMRM Electro-Magnetic Tissue Properties Study Group. While QSM technical development…
Motivation: Computational methods are essential to extract actionable information from raw sequencing data, and to thus fulfill the promise of next-generation sequencing technology. Unfortunately, computational tools developed to call…
In the early stages of semiconductor equipment development, obtaining large quantities of raw optical images poses a significant challenge. This data scarcity hinder the advancement of AI-powered solutions in semiconductor manufacturing. To…
Molecule optimization is a fundamental task for accelerating drug discovery, with the goal of generating new valid molecules that maximize multiple drug properties while maintaining similarity to the input molecule. Existing generative…
Advancements in clinical treatment are increasingly constrained by the limitations of supervised learning techniques, which depend heavily on large volumes of annotated data. The annotation process is not only costly but also demands…
The challenge of estimating similarity between sets has been a significant concern in data science, finding diverse applications across various domains. However, previous approaches, such as MinHash, have predominantly centered around…
Beyond their primary diagnostic purpose, radiology reports have been an invaluable source of information in medical research. Given a corpus of radiology reports, researchers are often interested in identifying a subset of reports…
Spatial transcriptomics (ST) technologies enable gene expression profiling with spatial resolution, offering unprecedented insights into tissue organization and disease heterogeneity. However, current analysis methods often struggle with…
Quantitative susceptibility mapping (QSM) utilizes MRI signal phase to infer estimates of local tissue magnetism (magnetic susceptibility), which has been shown useful to provide novel image contrast and as biomarkers of abnormal tissue.…
Semiconductor imaging and analysis are critical yet understudied in deep learning, limiting our ability for precise control and optimization in semiconductor manufacturing. We introduce a small-scale multimodal framework for analyzing…
We present an application, Superplot, for calculating and plotting statistical quantities relevant to parameter inference from a "chain" of samples drawn from a parameter space, produced by e.g. MultiNest. A simple graphical interface…
There are currently plenty of programs available for mapping short sequences (reads) to a genome. Most of them, however, including such popular and actively developed programs as Bowtie, BWA, TopHat and many others, are based on…
Small-angle X-ray and neutron scattering experiments are used in many fields of the life sciences and condensed matter research to obtain answers to questions about the shape and size of nano-sized structures, typically in the range of 1 to…
Deep neural networks are increasingly applied in automated histopathology. Yet, whole-slide images (WSIs) are often acquired at gigapixel sizes, rendering them computationally infeasible to analyze entirely at high resolution. Diagnostic…
Motivation: Recent advances in sequencing technologies promise ultra-long reads of $\sim$100 kilo bases (kb) in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 mega bases (Mb) in length. Existing…
We propose SemCSE-Multi, a novel unsupervised framework for generating multifaceted embeddings of scientific abstracts, evaluated in the domains of invasion biology and medicine. These embeddings capture distinct, individually specifiable…
SimOmics is an R package designed to generate realistic, multivariate, and multi-omics synthetic datasets. It is intended for use in benchmarking, method development, and reproducibility in bioinformatics, particularly in the context of…
Motivation: Seed location filtering is critical in DNA read mapping, a process where billions of DNA fragments (reads) sampled from a donor are mapped onto a reference genome to identify genomic variants of the donor. State-of-the-art read…
MA plots are used to analyze the genome-wide differences in gene expression between two distinct biological conditions. An MA plot is usually rendered as a static scatter plot. Our interview with 3 experts in genomics showed that we could…
SAXSFit is a computer analysis program that has been developed to assist in the fitting of small-angle x-ray and neutron scattering spectra primarily from nanoparticles (nanopores). The fitting procedure yields the pore or particle size…