New AI techniques developed by Cardiff University researchers could help unlock complex biological data, from the behaviour of individual cells to the organisation of whole tissues.
Researchers at Cardiff University have published two studies addressing fundamental challenges in modern AI: understanding the complex geometry and relationships within data, and recognising patterns that occur across very different scales.
Dr You Zhou, Senior Lecturer at Cardiff University's School of Medicine and senior author of the studies, said: "Biological research generates enormous amounts of complex data, but much of today's AI still struggles to understand the way biological systems are naturally organised.
"Cells interact within tissues, and important patterns can appear at many different scales."
Our research addresses these challenges by developing AI methods that can better understand both the geometry of biological data and the relationships between local details and larger-scale structures.
Vector Bundle Attention (VBA) - Teaching AI to Understand the Geometry of Biology
In the first paper, VBA: Vector Bundle Attention for Intrinsically Geometric Representation Learning , the researchers introduce Vector Bundle Attention (VBA), a new AI architecture that rethinks how machines compare and interpret information.
"Most current advanced AI systems are built on transformers, which use a mechanism to determine how different pieces of information relate to one another. While highly effective, conventional attention mechanisms do not naturally account for the geometric structure that underlies many forms of complex data," added Dr Zhou.
The geometric limitations of AI are particularly important in biology, where individual cells are not isolated pieces of data. They exist within intricate molecular and spatial relationships that influence how tissues function and diseases develop.
The VBA model incorporates geometric relationships directly into the AI's attention mechanism, aligning information from cells according to their underlying geometry before making comparisons when modelling biological systems.
To test the VBA model, the researchers used single-cell RNA sequencing and spatial transcriptomics - technologies that enable scientists to examine the molecular characteristics of individual cells and understand how cells are organised within tissues. The VBA model achieved state-of-the-art performance in single-cell RNA sequencing tasks, strong performance in spatial transcriptomics, and competitive results on 3D datasets, highlighting its potential beyond biomedical applications.
Dynamic Fractal Mamba - Helping AI See Both Detail and Context
In a further study, Dynamic Fractal Mamba: A Neural Renormalization Group Flow for Scale-Invariant Sequence Modeling , the second AI model, Dynamic Fractal Mamba (DF-Mamba), tackles another major challenge in AI - understanding information across dramatically different scales.
"Many AI systems struggle to generalise when trained on relatively small data segments and then applied to much larger datasets. In biomedical research, this is a significant issue," said Dr Zhou.
Inspired by concepts from physics used to describe how systems behave across scales, DF-Mamba repeatedly applies the same learned rules as it moves from smaller to increasingly larger patterns. This enables the model to integrate information within broader contexts efficiently.
The DF-Mamba model learns from smaller-scale data and can successfully analyse much larger-scale datasets that it has never previously encountered, without requiring retraining.
The two new approaches tackle current challenges when using AI to understand biological data, including how information is geometrically related, and how patterns are connected across different scales.
Dr You Zhou said: "What is particularly exciting is that challenges arising from biomedical research have inspired new developments in AI itself. Research motivated by biomedical challenges can contribute not only to biomedical science, but also to fundamental advances in AI."
We hope these approaches will ultimately give scientists more powerful tools to understand complex biological systems and help advance precision medicine.
The studies, VBA: Vector Bundle Attention for Intrinsically Geometric Representation Learning and Dynamic Fractal Mamba: A Neural Renormalization Group Flow for Scale-Invariant Sequence Modeling , were presented at the 2026 International Conference on Machine Learning (ICML). The work was carried out by researchers from Cardiff University's School of Medicine and School of Computer Science and Informatics.
