10 accepted papers
Learning discrete neural samplers is challenging due to the lack of gradients and combinatorial complexity. While stochastic optimal control (SOC) and Schrödinger bridge (SB) provide principled solutions, efficient SOC solvers like adjoint matching (AM), which excel in continuous domains, remain une…
Diffusion-based samplers learn to sample complex, high-dimensional distributions using energies or log densities alone, without training data. Yet, they remain impractical for molecular sampling because they are often slower than molecular dynamics and miss thermodynamically relevant modes. Inspired…
Molecular dynamics is crucial for understanding molecular systems but its applicability is often limited by the vast timescales of rare events like protein folding. Enhanced sampling techniques overcome this by accelerating the simulation along key reaction pathways, which are defined by collective…
Sampling from discrete distributions with multiple modes and energy barriers is fundamental to machine learning and computational physics. Recent discrete neural samplers like MDNS suffer from mode collapse and fail to sample high-energy barrier regions between modes, which is critical for free ener…
Deep generative models have recently been applied to physical systems governed by partial differential equations (PDEs), offering scalable simulation and uncertainty-aware inference. However, enforcing physical constraints, such as conservation laws (linear and nonlinear) and physical consistencies,…
Discrete diffusion has achieved state-of-the-art performance, outperforming or approaching autoregressive models on standard benchmarks. In this work, we introduce *Discrete Diffusion with Planned Denoising* (DDPD), a novel framework that separates the generation process into two models: a planner a…
Coarse-graining (CG) accelerates molecular simulations of protein dynamics by simulating sets of atoms as singular beads. Backmapping is the opposite operation of bringing lost atomistic details back from the CG representation. While machine learning (ML) has produced accurate and efficient CG simul…
Simulating rare events, such as the transformation of a reactant into a product in a chemical reaction typically requires enhanced sampling techniques that rely on heuristically chosen collective variables (CVs). We propose using differentiable simulations (DiffSim) for the discovery and enhanced sa…
Coarse-graining (CG) of molecular simulations simplifies the particle representation by grouping selected atoms into pseudo-beads and therefore drastically accelerates simulation. However, such CG procedure induces information losses, which makes accurate backmapping, i.e., restoring fine-grained (F…
Predicting molecular conformations (or 3D structures) from molecular graphs is a fundamental problem in many applications. Most existing approaches are usually divided into two steps by first predicting the distances between atoms and then generating a 3D structure through optimizing a distance geom…