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Viral infections are causing significant morbidity and mortality worldwide. Understanding the interaction patterns between a particular virus and human proteins plays a crucial role in unveiling the underlying mechanism of viral infection…

In the fight against the COVID-19 pandemic, leveraging artificial intelligence to predict disease outcomes from chest radiographic images represents a significant scientific aim. The challenge, however, lies in the scarcity of large,…

A novel group of small non-coding RNA, known as microRNA (miRNA) is predicted to regulate as high as 90% of the coding genes in human. The diversity and abundance of miRNA targets offer an enormous level of combinatorial possibilities and…

In the context of personalized medicine, text mining methods pose an interesting option for identifying disease-gene associations, as they can be used to generate novel links between diseases and genes which may complement knowledge from…

This paper introduces a novel Functional Graph Convolutional Network (funGCN) framework that combines Functional Data Analysis and Graph Convolutional Networks to address the complexities of multi-task and multi-modal learning in digital…

Biological function emerges from coupled constraints across sequence, structure, regulation, evolution, and cellular context, yet most foundation models in biology are trained within one modality or for a fixed forward task. We present…

Accumulated clinical studies show that microbes living in humans interact closely with human hosts, and get involved in modulating drug efficacy and drug toxicity. Microbes have become novel targets for the development of antibacterial…

ChronoMID builds on the success of cross-modal convolutional neural networks (X-CNNs), making the novel application of the technique to medical imaging data. Specifically, this paper presents and compares alternative approaches - timestamps…

Background: Pharmacokinetic evaluation is one of the key processes in drug discovery and development. However, current absorption, distribution, metabolism, excretion prediction models still have limited accuracy. Aim: This study aims to…

Deep Learning (DL) can predict biomarkers directly from digitized cancer histology in a weakly-supervised setting. Recently, the prediction of continuous biomarkers through regression-based DL has seen an increasing interest. Nonetheless,…

Discovery of microRNAs (miRNAs) relies on predictive models for characteristic features from miRNA precursors (pre-miRNAs). The short length of miRNA genes and the lack of pronounced sequence features complicate this task. To accommodate…

Microbiome data analysis is essential for understanding host health and disease, yet its inherent sparsity and noise pose major challenges for accurate imputation, hindering downstream tasks such as biomarker discovery. Existing imputation…

With the spread of COVID-19 over the world, the need arose for fast and precise automatic triage mechanisms to decelerate the spread of the disease by reducing human efforts e.g. for image-based diagnosis. Although the literature has shown…

Magnetic Resonance Imaging (MRI) is instrumental in clinical diagnosis, offering diverse contrasts that provide comprehensive diagnostic information. However, acquiring multiple MRI contrasts is often constrained by high costs, long…

Since microRNAs (miRNAs) play a crucial role in post-transcriptional gene regulation, miRNA identification is one of the most essential problems in computational biology. miRNAs are usually short in length ranging between 20 and 23 base…

Multi-modal data comprising imaging (MRI, fMRI, PET, etc.) and non-imaging (clinical test, demographics, etc.) data can be collected together and used for disease prediction. Such diverse data gives complementary information about the…

Collaborative filtering often suffers from sparsity and cold start problems in real recommendation scenarios, therefore, researchers and engineers usually use side information to address the issues and improve the performance of recommender…

With the rising global burden of chronic diseases and the multimodal and heterogeneous clinical data (medical imaging, free-text recordings, wearable sensor streams, etc.), there is an urgent need for a unified multimodal AI framework that…

Integrating multi-omics data, such as DNA methylation, mRNA expression, and microRNA (miRNA) expression, offers a comprehensive view of the biological mechanisms underlying disease. However, the high dimensionality of multi-omics data, the…

Major depressive disorder (MDD) requires study of brain functional connectivity alterations for patients, which can be uncovered by resting-state functional magnetic resonance imaging (rs-fMRI) data. We consider the problem of identifying…