Takahiro Mimori

Takahiro Mimori, Michiaki Hamada

Phylogenetic inference, grounded in molecular evolution models, is essential for understanding the evolutionary relationships in biological data. Accounting for the uncertainty of phylogenetic tree variables, which include tree topologies and evolutionary distances on branches, is crucial for accurately inferring species relationships from molecular data and tasks requiring variable marginalization. Variational Bayesian methods are key to developing scalable, practical models; however, it remains challenging to conduct phylogenetic inference without restricting the combinatorially vast number of possible tree topologies. In this work, we introduce a novel, fully differentiable formulation of phylogenetic inference that leverages a unique representation of topological distributions in continuous geometric spaces. Through practical considerations on design spaces and control variates for gradient estimations, our approach, GeoPhy, enables variational inference without limiting the topological candidates. In experiments using real benchmark datasets, GeoPhy significantly outperformed other approximate Bayesian methods that considered whole topologies.

Takahiro Mimori, Keiko Sasada, Hirotaka Matsui et al.

We propose an evaluation framework for class probability estimates (CPEs) in the presence of label uncertainty, which is commonly observed as diagnosis disagreement between experts in the medical domain. We also formalize evaluation metrics for higher-order statistics, including inter-rater disagreement, to assess predictions on label uncertainty. Moreover, we propose a novel post-hoc method called $alpha$-calibration, that equips neural network classifiers with calibrated distributions over CPEs. Using synthetic experiments and a large-scale medical imaging application, we show that our approach significantly enhances the reliability of uncertainty estimates: disagreement probabilities and posterior CPEs.