mlsanityData to 7 Oct 2026

ET-Flow: Equivariant Flow-Matching for Molecular Conformer Generation

arXiv 2410.22388 ↗First posted 29 Oct 2024q-bio.QM cs.LGcited by 41

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Cited by 20 in Diffusion models, but placed by its own abstract, which didn’t fit.

Abstract (arXiv)

Predicting low-energy molecular conformations given a molecular graph is an important but challenging task in computational drug discovery. Existing state-of-the-art approaches either resort to large scale transformer-based models that diffuse over conformer fields, or use computationally expensive methods to generate initial structures and diffuse over torsion angles. In this work, we introduce Equivariant Transformer Flow (ET-Flow). We showcase that a well-designed flow matching approach with equivariance and harmonic prior alleviates the need for complex internal geometry calculations and large architectures, contrary to the prevailing methods in the field. Our approach results in a straightforward and scalable method that directly operates on all-atom coordinates with minimal assumptions. With the advantages of equivariance and flow matching, ET-Flow significantly increases the precision and physical validity of the generated conformers, while being a lighter model and faster at inference. Code is available https://github.com/shenoynikhil/ETFlow.

Key facts. Cited by 41 papers in the map (data through 7 Oct 2026). Builds on 45 of its 74 references that are in the map. First posted on arXiv 29 Oct 2024.

Builds on

45 of 74 references.

References · 45

  1. 2017Attention Is All You Needcited by 59,932
  2. 2020Denoising Diffusion Probabilistic Modelscited by 20,851
  3. 2020Denoising Diffusion Implicit Modelscited by 9,655
  4. 2016Layer Normalizationcited by 5,579
  5. 2022Flow Matching for Generative Modelingcited by 5,426
  6. 2024Scaling Rectified Flow Transformers for High-Resolution Image Synthesiscited by 4,094
  7. 2019Generative Modeling by Estimating Gradients of the Data Distributioncited by 4,067
  8. 2022Flow Straight and Fast: Learning to Generate and Transfer Data with Rectified Flowcited by 3,550
  9. 2022Elucidating the Design Space of Diffusion-Based Generative Modelscited by 2,994
  10. 2016Density estimation using Real NVPcited by 2,029
  11. 2022Building Normalizing Flows with Stochastic Interpolantscited by 964
  12. 2021E(n) Equivariant Graph Neural Networkscited by 951
33 more
  1. 2023Stochastic Interpolants: A Unifying Framework for Flows and Diffusionscited by 897
  2. 2018Tensor field networks: Rotation- and translation-equivariant neural networks for 3D point cloudscited by 735
  3. 2023Scaling Vision Transformers to 22 Billion Parameterscited by 690
  4. 2020SE(3)-Transformers: 3D Roto-Translation Equivariant Attention Networkscited by 602
  5. 2020Directional Message Passing for Molecular Graphscited by 556
  6. 2022Fast Sampling of Diffusion Models with Exponential Integratorcited by 526
  7. 2022GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generationcited by 511
  8. 2022MACE: Higher Order Equivariant Message Passing Neural Networks for Fast and Accurate Force Fieldscited by 467
  9. 2021Equivariant message passing for the prediction of tensorial properties and molecular spectracited by 438
  10. 2023Multisample Flow Matching: Straightening Flows with Minibatch Couplingscited by 267
  11. 2019Cormorant: Covariant Molecular Neural Networkscited by 262
  12. 2022Torsional Diffusion for Molecular Conformer Generationcited by 262
  13. 2022Learning Local Equivariant Representations for Large-Scale Atomistic Dynamicscited by 254
  14. 2020GEOM: Energy-annotated molecular conformations for property prediction and molecular generationcited by 238
  15. 2023EquiformerV2: Improved Equivariant Transformer for Scaling to Higher-Degree Representationscited by 201
  16. 2022TorchMD-NET: Equivariant Transformers for Neural Network based Molecular Potentialscited by 179
  17. 2021Learning Gradient Fields for Molecular Conformation Generationcited by 162
  18. 2023Equivariant flow matchingcited by 131
  19. 2023Reducing SO(3) Convolutions to SO(2) for Efficient Equivariant GNNscited by 113
  20. 2021GeoMol: Torsional Geometric Generation of Molecular 3D Conformer Ensemblescited by 106
  21. 2024AlphaFold Meets Flow Matching for Generating Protein Ensemblescited by 105
  22. 2021Learning Neural Generative Dynamics for Molecular Conformation Generationcited by 87
  23. 2021SE(3) Equivariant Graph Neural Networks with Complete Local Framescited by 75
  24. 2019A Generative Model for Molecular Distance Geometrycited by 73
  25. 2023A Hitchhiker's Guide to Geometric GNNs for 3D Atomic Systemscited by 65
  26. 2023EigenFold: Generative Protein Structure Prediction with Diffusion Modelscited by 63
  27. 2023Equivariant Flow Matching with Hybrid Probability Transportcited by 59
  28. 2023Swallowing the Bitter Pill: Simplified Scalable Conformer Generationcited by 55
  29. 2023TensorNet: Cartesian Tensor Representations for Efficient Learning of Molecular Potentialscited by 53
  30. 2022So3krates: Equivariant attention for interactions on arbitrary length-scales in molecular systemscited by 39
  31. 2023Diffusion Probabilistic Fieldscited by 28
  32. 2020Molecular machine learning with conformer ensemblescited by 27
  33. 2024Deconstructing equivariant representations in molecular systemscited by 2

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Cited by year (2026 to 7 Oct)

Citing papers per year: 2024: 1; 2025: 27; 2026: 13.

41 papers.

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  1. 2025Adjoint Sampling: Highly Scalable Diffusion Samplers via Adjoint Matchingcited by 78
  2. 2025Flow Matching Meets Biology and Life Science: A Surveycited by 14
  3. 2025High-order Equivariant Flow Matching for Density Functional Theory Hamiltonian Predictioncited by 10
  4. 2025Physics-Constrained Fine-Tuning of Flow-Matching Models for Generation and Inverse Problemscited by 8
  5. 2025Efficient Flow Matching using Latent Variablescited by 6
  6. 2025Audio synthesizer inversion in symmetric parameter spaces with approximately equivariant flow matchingcited by 6
  7. 2025Feynman-Kac-Flow: Inference Steering of Conditional Flow Matching to an Energy-Tilted Posteriorcited by 6
  8. 2025Sampling 3D Molecular Conformers with Diffusion Transformerscited by 5
  9. 2025SynCoGen: Synthesizable 3D Molecule Generation via Joint Reaction and Coordinate Modelingcited by 5
  10. 2025Rao-Blackwell Gradient Estimators for Equivariant Denoising Diffusioncited by 4
  11. 2025Efficient Molecular Conformer Generation with SO(3)-Averaged Flow Matching and Reflowcited by 4
  12. 2025Energy-Based Flow Matching for Generating 3D Molecular Structurecited by 4
29 more
  1. 2025MolGuidance: Advanced Guidance Strategies for Conditional Molecular Generation with Flow Matchingcited by 4
  2. 2025Disentangling Total-Variance and Signal-to-Noise-Ratio Improves Diffusion Modelscited by 3
  3. 2025PolyConf: Unlocking Polymer Conformation Generation through Hierarchical Generative Modelscited by 3
  4. 2025Data-driven particle dynamics: Structure-preserving coarse-graining for emergent behavior in non-equilibrium systemscited by 3
  5. 2026Geometric Flow Matching for Molecular Conformation Generation via Manifold Decompositioncited by 3
  6. 2025Template-Guided 3D Molecular Pose Generation via Flow Matching and Differentiable Optimizationcited by 2
  7. 2026AbFlow : End-to-end Paratope-Centric Antibody Design by Interaction Enhanced Flow Matchingcited by 2
  8. 2026A Unified Density Operator View of Flow Control and Mergingcited by 2
  9. 2024Riemannian Denoising Model for Molecular Structure Optimization with Chemical Accuracycited by 1
  10. 2025Self-Refining Training for Amortized Density Functional Theorycited by 1
  11. 2025READ: A Retrieval-Alignment Diffusion Framework for Structure-based Drug Designcited by 1
  12. 2025GAGA: Gaussianity-Aware Gaussian Approximation for Efficient 3D Molecular Generationcited by 1
  13. 2025Flow-Matching Based Refiner for Molecular Conformer Generationcited by 1
  14. 2026Boltzmann Generators for Condensed Matter via Riemannian Flow Matchingcited by 1
  15. 2026FlashMol: High-Quality Molecule Generation in as Few as Four Stepscited by 1
  16. 2026Vilya-1: An all-atom foundation model for macrocycle structure prediction and designcited by 1
  17. 2025Discriminative protein sequence modelling with Latent Space Diffusioncited by 0
  18. 2025polyGen: A Learning Framework for Atomic-level Polymer Structure Generationcited by 0
  19. 2025A standard transformer and attention with linear biases for molecular conformer generationcited by 0
  20. 2025A Conformation-Centric Generative Foundation Model for Linear Polymer Modeling and Designcited by 0
  21. 2025Energy Loss Functions for Physical Systemscited by 0
  22. 2025Energy-Guided Generative Modeling for Low-Energy Molecular Structure Discoverycited by 0
  23. 2026Recurrent Equivariant Constraint Modulation: Learning Per-Layer Symmetry Relaxation from Datacited by 0
  24. 2026Can We Build Scene Graphs, Not Classify Them? FlowSG: Progressive Image-Conditioned Scene Graph Generation with Flow Matchingcited by 0
  25. 2026Quotient-Space Diffusion Modelscited by 0
  26. 2026SymDrift: One-Shot Generative Modeling under Symmetriescited by 0
  27. 2026AquaGen: Scaling generative models to molecular dynamics precision on thousands of atomscited by 0
  28. 2026Lantern: Conflict-Aware Gradient Blending for Physics-Guided Diffusion Models in Calorimeter Simulationcited by 0
  29. 2026Where Should Physics Enter a Molecular Crystal Generator?cited by 0

Similar, not cited

Close in wording, no citation either way

  1. 2024EquiFlow: Equivariant Conditional Flow Matching with Optimal Transport for 3D Molecular Conformation Prediction
  2. 2026Equivariant Efficient Joint Discrete and Continuous MeanFlow for Molecular Graph Generation
  3. 2026Fixed-Dimensional Latent Flow for Generating Variable-Size 3D Molecules
  4. 2025FlexiFlow: decomposable flow matching for generation of flexible molecular ensemble
  5. 2024Equivariant Blurring Diffusion for Hierarchical Molecular Conformer Generation
  6. 2025EquiBoost: An Equivariant Boosting Approach to Molecular Conformation Generation
  7. 2026Generating Cyclic Conformers with Flow Matching in Cremer-Pople Coordinates
  8. 2024Accelerating the Generation of Molecular Conformations with Progressive Distillation of Equivariant Latent Diffusion Models