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Skin cancer is one of the most prevalent and potentially life-threatening diseases worldwide, necessitating early and accurate diagnosis to improve patient outcomes. Conventional diagnostic methods, reliant on clinical expertise and…
Phylogenetic profiles - presence-absence patterns of genes across taxa - are rich information sources for inferring the evolutionary history of genes and gene families. When aggregated across many genes, these profiles can reveal…
Proteins are essential for almost all biological processes and derive their diverse functions from complex 3D structures, which are in turn determined by their amino acid sequences. In this paper, we exploit the rich biological inductive…
Refactoring is a common software engineering practice that improves code quality without altering program behavior. Although tools like ReExtractor+, RefactoringMiner, and RefDiff have been developed to detect refactorings automatically,…
One critical challenge in 6D object pose estimation from a single RGBD image is efficient integration of two different modalities, i.e., color and depth. In this work, we tackle this problem by a novel Deep Fusion Transformer~(DFTr) block…
The growth of global consumption has motivated important applications of deep learning to smart manufacturing and machine health monitoring. In particular, analyzing vibration data offers great potential to extract meaningful insights into…
Recent advances in protein function prediction exploit graph-based deep learning approaches to correlate the structural and topological features of proteins with their molecular functions. However, proteins in vivo are not static but…
The transcription of DNA into mRNA is initiated and aided by a number of transcription factors (TFs), proteins with DNA-binding regions that attach themselves to binding sites in the DNA (transcription factor binding sites, TFBSs). As it…
The activation/repression of a given gene is typically regulated by multiple transcription factors (TFs) that bind at the gene regulatory region and recruit RNA polymerase (RNAP). The interactions between the promoter region and TFs and…
Fast and Relaxed Vector Fitting (FRVF) is a frequency-domain system identification approach that has been widely adopted in electrical system modelling, while its application to mechanical systems has remained relatively unexplored. In this…
Modal identification is crucial for structural health monitoring and structural control, providing critical insights into structural dynamics and performance. This study presents a novel deep learning framework that integrates graph neural…
Phylogenetics is a fundamental component of evolutionary analysis frameworks in biology and linguistics. Recently, the advent of large-scale genomics and the SARS-CoV-2 pandemic has highlighted the necessity for phylogenetic software to…
Protein-ligand interactions are one of the fundamental types of molecular interactions in living systems. Ligands are small molecules that interact with protein molecules at specific regions on their surfaces called binding sites. Tasks…
Human genetics offers a promising route to therapeutic discovery, yet practical frameworks translating genotype-derived signal into ranked target and drug hypotheses remain limited, particularly when matched disease transcriptomics are…
The identification and property prediction of chemical molecules is of central importance in the advancement of drug discovery and material science, where the tandem mass spectrometry technology gives valuable fragmentation cues in the form…
Variant calling refinement is crucial for distinguishing true genetic variants from technical artifacts in high-throughput sequencing data. Manual review is time-consuming while heuristic filtering often lacks optimal solutions. Traditional…
Cross-slide image analysis provides additional information by analysing the expression of different biomarkers as compared to a single slide analysis. These biomarker stained slides are analysed side by side, revealing unknown relations…
Survival analysis plays a vital role in making clinical decisions. However, the models currently in use are often difficult to interpret, which reduces their usefulness in clinical settings. Prototype learning presents a potential solution,…
Fragment-based drug design is a promising strategy leveraging the binding of small chemical moieties that can efficiently guide drug discovery. The initial step of fragment identification remains challenging, as fragments often bind weakly…
Identifying transcription factor binding sites (TFBS) is crucial for understanding gene regulation, as these sites enable transcription factors (TFs) to bind to DNA and modulate gene expression. Despite advances in high-throughput…