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Understanding the evolution of brain functional networks over time is of great significance for the analysis of cognitive mechanisms and the diagnosis of neurological diseases. Existing methods often have difficulty in capturing the…
Clinical time series data from electronic health records and medical registries offer unprecedented opportunities to understand patient trajectories and inform medical decision-making. However, leveraging such data presents significant…
Routinely collected clinical blood tests are an emerging molecular data source for large-scale biomedical research but inherently feature irregular sampling and informative observation. Traditional approaches rely on imputation, which can…
Identifying objective neuroimaging biomarkers to forecast Alzheimer's disease (AD) progression is crucial for timely intervention. However, this task remains challenging due to the complex dysfunctions in the spatio-temporal characteristics…
It was recently shown how graphs can be used to provide descriptions of psychopathologies, where symptoms of, say, depression, affect each other and certain configurations determine whether someone could fall into a sudden depression. To…
In this paper we use a time-evolving graph which consists of a sequence of graph snapshots over time to model many real-world networks. We study the path classification problem in a time-evolving graph, which has many applications in…
Disease-gene prediction (DGP) refers to the computational challenge of predicting associations between genes and diseases. Effective solutions to the DGP problem have the potential to accelerate the therapeutic development pipeline at early…
Biological foundation models have shown strong performance in single-cell representation learning by applying transformer architectures directly to gene-expression matrices. However, these approaches predominantly operate in static settings…
Medical researchers are coming to appreciate that many diseases are in fact complex, heterogeneous syndromes composed of subpopulations that express different variants of a related complication. Time series data extracted from individual…
The pathway is a biological term that refers to a series of interactions between molecules in a cell that causes a certain product or a change in the cell. Pathway analysis is a powerful method for gene expression analysis. Through pathway…
Accurate prediction of cancer progression remains a challenge due to the high heterogeneity of molecular omics data across patients. While biologically informed models have improved the interpretability of these predictions, a persistent…
Large observational clinical datasets become increasingly available for mining associations between various disease traits and administered therapy. These datasets can be considered as representations of the landscape of all possible…
Disease progression modeling aims to characterize and predict how a patient's disease complications worsen over time based on longitudinal electronic health records (EHRs). For diseases such as type 2 diabetes, accurate progression modeling…
A central challenge in modeling neurodegenerative diseases is connecting cellular-level mechanisms to tissue-level pathology, in particular to determine whether pathology is driven primarily by cell-autonomous triggers or by propagation…
Integrating heterogeneous biomedical data including imaging, omics, and clinical records supports accurate diagnosis and personalised care. Graph-based models fuse such non-Euclidean data by capturing spatial and relational structure, yet…
This study addresses the challenges of symptom evolution complexity and insufficient temporal dependency modeling in Parkinson's disease progression prediction. It proposes a unified prediction framework that integrates structural…
Self-supervised learning in healthcare has largely relied on invariance-based objectives, which maximize similarity between different views of the same patient. While effective for static anatomy, this paradigm is fundamentally misaligned…
Spatial transcriptomics technologies enable the measurement of gene expression with spatial context, providing opportunities to understand how gene regulatory networks vary across tissue regions. However, existing graphical models focus…
Travel time estimation is one of the core tasks for the development of intelligent transportation systems. Most previous works model the road segments or intersections separately by learning their spatio-temporal characteristics to estimate…
The explosion of data throughout the biomedical sciences provides unprecedented opportunities to learn about the dynamics of evolution and disease progression, but harnessing these large and diverse datasets remains challenging. Here, we…