Energy-Guided Flow Matching Enables Few-Step Conformer Generation and Ground-State Identification

TL;DR

EnFlow is a unified framework combining flow matching and an energy model with energy-guided sampling to efficiently generate low-energy molecular conformers and identify ground states with minimal steps.

Contribution

It introduces a novel energy-guided flow matching approach that improves conformer generation and ground-state prediction in molecular modeling.

Findings

Achieves high-quality conformer generation with 1-2 ODE steps.

Reduces ground-state prediction errors compared to existing methods.

Enhances conformational fidelity through energy-gradient guidance.

Abstract

Generating low-energy conformer ensembles and identifying ground-state conformations from molecular graphs remain computationally demanding with physics-based pipelines. Current learning-based approaches often suffer from a fragmented paradigm: generative models capture diversity but lack reliable energy calibration, whereas deterministic predictors target a single structure and fail to represent ensemble variability. Here we present EnFlow, a unified framework that couples flow matching (FM) with an explicitly learned energy model through an energy-guided sampling scheme defined along a non-Gaussian FM path. By incorporating energy-gradient guidance during sampling, our method steers trajectories toward lower-energy regions, substantially improving conformational fidelity, particularly in the few-step regime. The learned energy function further enables efficient energy-based ranking of generated ensembles for accurate ground-state identification. Extensive experiments on GEOM-QM9 and GEOM-Drugs demonstrate that EnFlow simultaneously improves generation metrics with 1--2 ODE-steps and reduces ground-state prediction errors compared with state-of-the-art methods.