Escaping the Phylogenetic Trap: Persistent Homology Enables Cross-Species Ion Channel Classification via Multimodal Graph Neural Networks

Overview

arXiv:2610.30394v1 Announce Type: new Abstract: Protein classifiers are highly sensitive to evaluation protocol: random train/test splits induce phylogenetic leakage, allowing models to exploit taxon-specific correlations and substantially overestimate out-of-distribution performance. This issue is particularly acute for venom compound classification by ion-channel target (Ca2+, K+, Na+), where reported accuracies of 80-90% do not reflect generalization to unseen taxa. We formulate cross-species

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