Schrödinger Bridges on Lie Group Manifolds for Probabilistic Intrinsic Generation

Generative modeling directly on geometric manifolds can avoid errors introduced by flattening non-Euclidean data, repeated ambient projection, and coordinate inconsistency in Euclidean representations. Schrodinger bridges provide a probabilistic generative framework for entropy-regularized transport between prescribed endpoint distributions. We study Schrodinger bridges for kinetic dynamics on Lie group manifolds with state X_t = (g_t, xi_t) in G x g, allowing endpoint observations to constrain only the variables that are actually measured. In particular, the entropy projection determines the conditional law of the unobserved endpoint velocities. For the same observed endpoint bridge, we develop two computational realizations: Wrapped-Kernel Bridge Calibration (WKBC) uses an explicit periodized kinetic kernel on compact Abelian groups, whereas Reciprocal Conditional-Control Bridge Matching (RCCBM) handles compact non-Abelian groups through two-sided endpoint calibration and mollified conditional-control matching. The canonical teacher-mixture path law is itself a Markov reciprocal law, so forward generation uses a calibrated initial law and one learned Doob controller. Moreover, we establish a modular error bound in the bounded-Lipschitz path metric that provides a clean separation of errors due to endpoints, control regression, initialization, discretization, and related approximations. Experiments on multiple Lie group manifold datasets validate the feasibility and consistency of our proposed method, covering protein and RNA torsions, SO(3), U(n), and the Protein Conformational Transition Pathway Generation task using mdCATH trajectories in a compact reduced representation. The source code is publicly available at https://github.com/cafferyzhang12/Schr-dinger_Bridge_on_LieGroup.

Learning Topological Representations for Molecular Dynamics

Molecular dynamics (MD) simulations generate trajectories in a high-dimensional configuration space whose analysis critically depends on molecular descriptors, typically handcrafted observables or learned kinetic embeddings. Designing descriptors that are both expressive and broadly applicable, however, remains challenging. We study persistent homology (PH) as a general-purpose representation for MD and introduce the masked Flood complex, a protein-tailored modification of a recently introduced simplicial complex construction that emphasizes inter-residue structure at low computational cost. Vectorized persistence diagrams then provide information-rich, geometry-aware summaries of protein conformations, which we evaluate on protein class prediction, frame-level observable regression, and Markov state model (MSM) estimation from learned low-dimensional coordinates in a single shared representation space. Results on the mdCATH dataset show that PH-based descriptors are competitive across tasks, with masked Flood PH yielding the most consistent overall performance. Further, when using topologically-informed MSMs as a drop-in replacement within the recent MarS-FM framework for generative modeling of protein conformations, we obtain consistently better ensemble statistics than MSMs based on physical observables. Finally, we explore the transferability of the generative model to qualitatively different, fast folding, proteins.