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Sickle cell disease (SCD) is a severe genetic hemoglobin disorder that results in premature destruction of red blood cells. Assessment of the severity of the disease is a challenging task in clinical routine since the causes of broad…
The classification of DNA sequences is a key research area in bioinformatics as it enables researchers to conduct genomic analysis and detect possible diseases. In this paper, three state-of-the-art algorithms, namely Convolutional Neural…
Graph clustering discovers groups or communities within networks. Deep learning methods such as autoencoders (AE) extract effective clustering and downstream representations but cannot incorporate rich structural information. While Graph…
Motivation: Most existing methods for DNA sequence analysis rely on accurate sequences or genotypes. However, in applications of the next-generation sequencing (NGS), accurate genotypes may not be easily obtained (e.g. multi-sample…
With recent advances in sequencing technology it has become affordable and practical to sequence genomes to very high depth-of-coverage, allowing researchers to discover low-frequency variants in the genome. However, due to the errors in…
Structure-based drug design (SBDD) is crucial for developing specific and effective therapeutics against protein targets but remains challenging due to complex protein-ligand interactions and vast chemical space. Although language models…
The spectral energy distribution (SED) of observed stars in wide-field images is crucial for chromatic point spread function (PSF) modelling methods, which use unresolved stars as integrated spectral samples of the PSF across the field of…
The variation in DNA copy number carries information on the modalities of genome evolution and misregulation of DNA replication in cancer cells; its study can be helpful to localize tumor suppressor genes, distinguish different populations…
Biological cells replicate their genomes in a well-planned manner. The DNA replication program of an organism determines the timing at which different genomic regions are replicated, with fundamental consequences for cell homeostasis and…
Motivated by empirical observations of algebraic duplicated sequence length distributions in a broad range of natural genomes, we analytically formulate and solve a class of simple discrete duplication/substitution models that generate…
Sparse reduced-rank regression is an important tool to uncover meaningful dependence structure between large numbers of predictors and responses in many big data applications such as genome-wide association studies and social media…
Single source domain generalization (SDG) holds promise for more reliable and consistent image segmentation across real-world clinical settings particularly in the medical domain, where data privacy and acquisition cost constraints often…
Pedigrees, or family trees, are graphs of family relationships that are used to study inheritance. A fundamental problem in computational biology is to find, for a pedigree with $n$ individuals genotyped at every site, a set of…
Whole slide images (WSIs) are massive digital pathology files illustrating intricate tissue structures. Selecting a small, representative subset of patches from each WSI is essential yet challenging. Therefore, following the "Divide &…
Genome sequence analysis, which examines the DNA sequences of organisms, drives advances in many critical medical and biotechnological fields. Given its importance and the exponentially growing volumes of genomic sequence data, there are…
Low-density parity-check (LDPC) codes together with belief propagation (BP) decoding yield exceptional error correction capabilities in the large block length regime. Yet, there remains a gap between BP decoding and maximum likelihood…
With the rapid advancement of image generation techniques, robust forgery detection has become increasingly imperative to ensure the trustworthiness of digital media. Recent research indicates that the learned semantic concepts of…
The detection of genomic structural variations (SV) remains a difficult challenge in analyzing sequencing data, and the growing size and number of sequenced genomes have rendered SV detection a bona fide big data problem. MapReduce is a…
Centromeres are essential for chromosome segregation, yet their DNA sequences evolve rapidly. In most animals and plants that have been studied, centromeres contain megabase-scale arrays of tandem repeats. Despite their importance, very…
Image-based crack detection algorithms are increasingly in demand in infrastructure monitoring, as early detection of cracks is of paramount importance for timely maintenance planning. While deep learning has significantly advanced crack…