MOTIVATION: Structural variants (SVs) play a causal role in numerous diseases but can be difficult to detect and accurately genotype (determine zygosity) with short-read genome sequencing data (SRS). Improving SV genotyping accuracy in SRS data, part...
MOTIVATION: Emergent biological dynamics derive from the evolution of lower-level spatial and temporal processes. A long-standing challenge for scientists and engineers is identifying simple low-level rules that give rise to complex higher-level dyna...
MOTIVATION: Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the structures of large protein complexes. Picking single protein particles from cryo-EM micrographs (images) is a crucial step in reconstructing protein structure...
MOTIVATION: Liquid chromatography retention times prediction can assist in metabolite identification, which is a critical task and challenge in nontargeted metabolomics. However, different chromatographic conditions may result in different retention ...
MOTIVATION: Creating knowledge bases and ontologies is a time consuming task that relies on manual curation. AI/NLP approaches can assist expert curators in populating these knowledge bases, but current approaches rely on extensive training data, and...
SUMMARY: Deep neural networks (DNNs) have been widely applied to predict the molecular functions of the non-coding genome. DNNs are data hungry and thus require many training examples to fit data well. However, functional genomics experiments typical...
MOTIVATION: We explored how explainable artificial intelligence (XAI) can help to shed light into the inner workings of neural networks for protein function prediction, by extending the widely used XAI method of integrated gradients such that latent ...
MOTIVATION: The field of geometric deep learning has recently had a profound impact on several scientific domains such as protein structure prediction and design, leading to methodological advancements within and outside of the realm of traditional m...
MOTIVATION: Cell-type annotation is fundamental in revealing cell heterogeneity for single-cell data analysis. Although a host of works have been developed, the low signal-to-noise-ratio single-cell RNA-sequencing data that suffers from batch effects...
MOTIVATION: Accurate prediction of RNA subcellular localization plays an important role in understanding cellular processes and functions. Although post-transcriptional processes are governed by trans-acting RNA binding proteins (RBPs) through intera...