An optimal transport-based low-dimensional visualization framework for high-parameter flow cytometry

Shemonti, A. S.; Gmyrek, G. B.; Quintelier, K. L. A.; Van Gassen, S.; Saeys, Y.; Willemsen, M.; Aerts, J. G. J. V.; Madsen, E. V. E.; Robinson, J. P.; Pothen, A.; Rajwa, B.

doi:10.1101/2025.08.19.670604

bioRxiv · 10.1101/2025.08.19.670604

An optimal transport-based low-dimensional visualization framework for high-parameter flow cytometry

Shemonti, A. S.·Gmyrek, G. B.·Quintelier, K. L. A.·Van Gassen, S.·Saeys, Y.·Willemsen, M.·Aerts, J. G. J. V.·Madsen, E. V. E.·Robinson, J. P.·Pothen, A.·Rajwa, B.

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Abstract

Conventional data visualization techniques in single-cell analysis (such as two-dimensional dot plots, SPADE, PCA, t-SNE, or UMAP) often fall short in providing an intuitive understanding of high-parameter flow cytometry data. These methods tend to oversimplify complex biological relationships, lack biologically meaningful interpretations, and offer no principled framework for downstream quantitative analysis. To address these limitations, we present a graph-based visualization framework grounded in optimal transport theory. In this framework, cell populations are defined by their marker-expression profiles, and inter-population similarity is quantified using an efficiently computable optimal transport formulation known as the Sinkhorn distance. Our approach produces biologically consistent two-dimensional graph layouts using a phenotypeaware Hamming distance. Structural differences between sample graphs are characterized through a customized graph-edit distance that captures changes in population size, marker expression, and relationships between populations. We demonstrate our methods on two flow cytometry datasets: one from a clinical trial of dendritic cell-based immunotherapy in malignant peritoneal mesothelioma, involving 14 patients sampled at three time points with 14-color panels, and another from FlowCAP-II, which involved 43 acute myeloid leukemia patient samples analyzed with 7-color panels. Our framework produces robust, quantitative visual summaries of cell populations and supports statistical analysis based on graph edit distances, thereby offering new insights into disease progression and treatment response. Ultimately, our method bridges the gap between flow cytometry data visualization and biological interpretation.

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Shemonti, A. S., Gmyrek, G. B., Quintelier, K. L. A., Van Gassen, S., Saeys, Y., Willemsen, M., Aerts, J. G. J. V., Madsen, E. V. E., Robinson, J. P., Pothen, A., Rajwa, B.. 2025-08-24. An optimal transport-based low-dimensional visualization framework for high-parameter flow cytometry. https://doi.org/10.1101/2025.08.19.670604

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