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Enhancer-promoter interactions (EPIs) regulate the expression of specific genes in cells, and EPIs are important for understanding gene regulation, cell differentiation and disease mechanisms. EPI identification through the wet experiments…

Motivation: Histone modification constitutes a basic mechanism for the genetic regulation of gene expression. In early 2000s, a powerful technique has emerged that couples chromatin immunoprecipitation with high-throughput sequencing…

Chromosome recognition is an essential task in karyotyping, which plays a vital role in birth defect diagnosis and biomedical research. However, existing classification methods face significant challenges due to the inter-class similarity…

Gene expression datasets offer insights into gene regulation mechanisms, biochemical pathways, and cellular functions. Additionally, comparing gene expression profiles between disease and control patients can deepen the understanding of…

The deep Convolutional Neural Network (CNN) is the state-of-the-art solution for large-scale visual recognition. Following basic principles such as increasing the depth and constructing highway connections, researchers have manually…

In cell differentiation, a cell of a less specialized type becomes one of a more specialized type, even though all cells have the same genome. Transcription factors and epigenetic marks like histone modifications can play a significant role…

Gene expression data is essential for understanding how genes are regulated and interact within biological systems, providing insights into disease pathways and potential therapeutic targets. Gene knockout has proven to be a fundamental…

Leveraging the vast genetic diversity within microbiomes offers unparalleled insights into complex phenotypes, yet the task of accurately predicting and understanding such traits from genomic data remains challenging. We propose a framework…

Diabetes is a worldwide health issue affecting millions of people. Machine learning methods have shown promising results in improving diabetes prediction, particularly through the analysis of diverse data types, namely gene expression data.…

Computational pathology models that use digitized histopathology whole-slide images have the potential to become a cost-effective and scalable alternative to molecular assays for the prediction of genomic biomarkers, a key task in precision…

Deep convolutional neural networks have proven their effectiveness, and have been acknowledged as the most dominant method for image classification. However, a severe drawback of deep convolutional neural networks is poor explainability.…

Combination therapy has shown to improve therapeutic efficacy while reducing side effects. Importantly, it has become an indispensable strategy to overcome resistance in antibiotics, anti-microbials, and anti-cancer drugs. Facing enormous…

Histo-genomic multi-modal methods have recently emerged as a powerful paradigm, demonstrating significant potential for improving cancer prognosis. However, genome sequencing, unlike histopathology imaging, is still not widely accessible in…

The value of luxury goods, particularly investment-grade gemstones, is greatly influenced by their origin and authenticity, sometimes resulting in differences worth millions of dollars. Traditionally, human experts have determined the…

Recent advances in high-throughput sequencing technologies have enabled the extraction of multiple features that depict patient samples at diverse and complementary molecular levels. The generation of such data has led to new challenges in…

There exists unexplained diverse variation within the predefined colon cancer stages using only features either from genomics or histopathological whole slide images as prognostic factors. Unraveling this variation will bring about improved…

Motivation: Identifying interaction clusters of large gene regulatory networks (GRNs) is critical for its further investigation, while this task is very challenging, attributed to data noise in experiment data, large scale of GRNs, and…

Many machine learning models have been proposed to classify phenotypes from gene expression data. In addition to their good performance, these models can potentially provide some understanding of phenotypes by extracting explanations for…

In clinical treatment, identifying potential adverse reactions of drugs can help assist doctors in making medication decisions. In response to the problems in previous studies that features are high-dimensional and sparse, independent…

Deep neural networks excel in mapping genomic DNA sequences to associated readouts (e.g., protein-DNA binding). Beyond prediction, the goal of these networks is to reveal to scientists the underlying motifs (and their syntax) which drive…