Applications of the Vendi score in genomic epidemiology

2025/09/26 by Bjarke Frost Nielsen, Amey P. Pasarkar, Nielsen, Bjarke Frost +7 · 1 voice
Biochemistry, Genetics and Molecular Biology · #FOS: Biological sciences #Populations and Evolution (q-bio.PE) #Quantitative Methods (q-bio.QM) #q-bio.PE #q-bio.QM

paper · pdf · doi:10.48550/arxiv.2509.22520

Abstract

The Vendi score (VS), a diversity metric recently conceived in the context of machine learning, with applications in a wide range of fields, has a few distinct advantages over the metrics commonly used in ecology. It is classification-independent, incorporates abundance information, and has a tunable sensitivity to rare/abundant types. Using rich COVID-19 sequence data as a paradigm, we develop methods for applying the VS to time-resolved sequence data. We show how the VS allows for characterization of the overall diversity of circulating viruses and for discernment of emerging variants prior to formal identification. Furthermore, applying the VS to phylogenetic trees provides a convenient overview of within-clade diversity which can aid viral variant detection.

Citations

• A Unified and Predictive Measure of Functional Diversity
• Vendi Information Gain: An Alternative To Mutual Information For Science And Machine Learning
• Vendi-RAG: Adaptively Trading-Off Diversity And Quality Significantly Improves Retrieval Augmented Generation With LLMs
• The Vendiscope: An Algorithmic Microscope For Data Collections
• Quality-Weighted Vendi Scores And Their Application To Diverse Experimental Design
• Cousins Of The Vendi Score: A Family Of Similarity-Based Diversity Metrics For Science And Machine Learning
• The Vendi Score: A Diversity Evaluation Metric for Machine Learning
• Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool
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• WHO Declares COVID-19 a Pandemic.
• IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
• The gut microbiome: Relationships with disease and opportunities for therapy
• Integrating influenza antigenic dynamics with molecular evolution
• MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
• Algorithm Runtime Prediction: Methods & Evaluation
• Measuring diversity: the importance of species similarity
• Canalization of the evolutionary trajectory of the human influenza virus
• The Alpha-Alternator: Dynamic Adaptation To Varying Noise Levels In Sequences Using The Vendi Score For Improved Robustness and Performance

Discussions

• In our #NewPaper, we showcase the Vendi Score in genomic epidemiology, showing how you can use it to detect new COVID-19 variants before formal identification. Check it out! #Ecology #Genomics #Health [bsky, 4 points, 0 comments]

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