In this study, we present a novel molecular fingerprint generation method based on multiparameter persistent homology. This approach reveals the latent structures and relationships within molecular geometry, and detects topological features that exhibit persistence across multiple scales along multiple parameters, such as atomic mass, partial charge, and bond type, and can be further enhanced by incorporating additional parameters like ionization energy, electron affinity, chirality and orbital hybridization. The proposed fingerprinting method provides fresh perspectives on molecular structure that are not easily discernible from single-parameter or single-scale analysis. Besides, in comparison with traditional graph neural networks, multiparameter persistent homology has the advantage of providing a more comprehensive and interpretable characterization of the topology of the molecular data. We have established theoretical stability guarantees for multiparameter persistent homology, and have conducted extensive experiments on the Lipophilicity, FreeSolv, and ESOL datasets to demonstrate its effectiveness in predicting molecular properties.
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