Michal Pavelka

Sanjeev Raja, Martin Šípka, Michael Psenka et al.

Transition path sampling (TPS), which involves finding probable paths connecting two points on an energy landscape, remains a challenge due to the complexity of real-world atomistic systems. Current machine learning approaches use expensive, task-specific, and data-free training procedures, limiting their ability to benefit from high-quality datasets and large-scale pre-trained models. In this work, we address TPS by interpreting candidate paths as trajectories sampled from stochastic dynamics induced by the learned score function of pre-trained generative models, specifically denoising diffusion and flow matching. Under these dynamics, finding high-likelihood transition paths becomes equivalent to minimizing the Onsager-Machlup (OM) action functional. This enables us to repurpose pre-trained generative models for TPS in a zero-shot manner, in contrast with bespoke, task-specific approaches in previous work. We demonstrate our approach on varied molecular systems, obtaining diverse, physically realistic transition pathways and generalizing beyond the pre-trained model's original training dataset. Our method can be easily incorporated into new generative models, making it practically relevant as models continue to scale and improve with increased data availability. Code is available at github.com/ASK-Berkeley/OM-TPS.

Vojtěch Votruba, Zequn He, Weilun Qiu et al.

We introduce Nonlinear GENERIC Informed Neural Networks (N-GINNs), a deep learning framework for discovering evolution equations of systems governed by the nonlinear GENERIC formalism (General Equation for Non-Equilibrium Reversible-Irreversible Coupling). Such systems exhibit coupled conservative and dissipative dynamics, and can be described via the superposition of a Hamiltonian flow and a generalized gradient flow. In contrast to existing approaches, our formulation incorporates generalized gradient flows via convex dissipation potentials, enabling the identification of a broader class of thermodynamically consistent dynamics, including systems with non-quadratic dissipation potentials. Thermodynamic structure is strongly enforced by construction through suitable reparameterizations of both the bivector operator and the dissipation potential, ensuring exact compliance with the first and second laws of thermodynamics. We validate the proposed approach on three representative examples: a harmonic oscillator coupled to a heat bath, an idealized chemical motor, and a one-dimensional viscoplastic model of Perzyna type. These results demonstrate the method's ability to accurately infer thermodynamically consistent models from data for systems incorporating both conservative and nonlinear dissipative dynamics.

Yuan Qilong, Michal Pavelka

We study the Joint Routing-Assignment (JRA) problem in which items must be assigned one-to-one to placeholders while simultaneously determining a Hamiltonian cycle visiting all nodes exactly once. Extending previous exact MIP solvers with Gurobi and cutting-plane subtour elimination, we develop a solver tailored for practical packaging-planning scenarios with richer constraints.These include multiple placeholder options, time-frame restrictions, and multi-class item packaging. Experiments on 46 mobile manipulation datasets demonstrate that the proposed MIP approach achieves global optima with stable and low computation times, significantly outperforming the shaking-based exact solver by up to an orders of magnitude. Compared to greedy baselines, the MIP solutions achieve consistent optimal distances with an average deviation of 14% for simple heuristics, confirming both efficiency and solution quality. The results highlight the practical applicability of MIP-based JRA optimization for robotic packaging, motion planning, and complex logistics .