Generating Physically Consistent Molecules with Energy-Based Models

• URL: http://arxiv.org/abs/2605.18381v1
• Date: Mon, 18 May 2026 13:26:52 GMT
• Title: Generating Physically Consistent Molecules with Energy-Based Models
• Abstract summary: We introduce EBMol, an energy-based model that restores inductive bias by learning an atom-additive scalar potential without explicit simulation.<n>EBMol is the first EBM for 3D molecular generation to achieve state-of-the-art performance on QM9 and GEOM-Drugs.
• Score: 6.4105959373235875
• License: http://creativecommons.org/licenses/by/4.0/
• Abstract: Molecules in equilibrium follow a Boltzmann distribution, making the underlying energy landscape a physically grounded modeling objective. However, such landscapes are difficult to learn from data and, once learned, hard to sample from. Diffusion and flow-matching models sidestep these difficulties by learning a time-conditional score or transport field between noise and data, losing the energy inductive bias in exchange for a more tractable training objective. We introduce EBMol, an energy-based model (EBM) that restores this inductive bias by learning an atom-additive scalar potential without explicit simulation during training. Our method employs a flow-inspired Restoring Field Matching objective to approximate the energy landscape. We adopt the Mirror-Langevin algorithm for sampling, enabling unified updates of atomic positions and types, and incorporate parallel tempering for inference-time compute scaling. EBMol is the first EBM for 3D molecular generation to achieve state-of-the-art performance on QM9 and GEOM-Drugs. Moreover, we show that the learned energy landscape serves as a principled quality metric for ranking and filtering configurations, and demonstrate controllable generation without retraining through shape-steered sampling via potential composition and zero-shot linker design.

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