mlsanityData to 7 Oct 2026

Equivariant Energy-Guided SDE for Inverse Molecular Design

arXiv 2209.15408 ↗First posted 30 Sep 2022physics.chem-ph cs.LG q-bio.BMcited by 72

Not on the map. Why?

Cited by 44 in Diffusion models, but placed by its own abstract, which didn’t fit.

Abstract (arXiv)

Inverse molecular design is critical in material science and drug discovery, where the generated molecules should satisfy certain desirable properties. In this paper, we propose equivariant energy-guided stochastic differential equations (EEGSDE), a flexible framework for controllable 3D molecule generation under the guidance of an energy function in diffusion models. Formally, we show that EEGSDE naturally exploits the geometric symmetry in 3D molecular conformation, as long as the energy function is invariant to orthogonal transformations. Empirically, under the guidance of designed energy functions, EEGSDE significantly improves the baseline on QM9, in inverse molecular design targeted to quantum properties and molecular structures. Furthermore, EEGSDE is able to generate molecules with multiple target properties by combining the corresponding energy functions linearly.

Key facts. Cited by 72 papers in the map (data through 7 Oct 2026). Builds on 42 of its 55 references that are in the map. First posted on arXiv 30 Sep 2022.

Builds on

42 of 55 references.

References · 42

  1. 2021Learning Transferable Visual Models From Natural Language Supervisioncited by 33,456
  2. 2020Denoising Diffusion Probabilistic Modelscited by 20,851
  3. 2020Score-Based Generative Modeling through Stochastic Differential Equationscited by 8,964
  4. 2021Diffusion Models Beat GANs on Image Synthesiscited by 8,185
  5. 2015Deep Unsupervised Learning using Nonequilibrium Thermodynamicscited by 7,005
  6. 2022Hierarchical Text-Conditional Image Generation with CLIP Latentscited by 6,539
  7. 2021Improved Denoising Diffusion Probabilistic Modelscited by 3,736
  8. 2022DPM-Solver: A Fast ODE Solver for Diffusion Probabilistic Model Sampling in Around 10 Stepscited by 1,961
  9. 2020DiffWave: A Versatile Diffusion Model for Audio Synthesiscited by 1,339
  10. 2021E(n) Equivariant Graph Neural Networkscited by 951
  11. 2022Equivariant Diffusion for Molecule Generation in 3Dcited by 666
  12. 2018Junction Tree Variational Autoencoder for Molecular Graph Generationcited by 647
30 more
  1. 2021Score-based Generative Modeling in Latent Spacecited by 634
  2. 2020WaveGrad: Estimating Gradients for Waveform Generationcited by 620
  3. 2020SE(3)-Transformers: 3D Roto-Translation Equivariant Attention Networkscited by 602
  4. 2022GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generationcited by 511
  5. 2018GraphVAE: Towards Generation of Small Graphs Using Variational Autoencoderscited by 375
  6. 2018Graph Convolutional Policy Network for Goal-Directed Molecular Graph Generationcited by 363
  7. 2022Analytic-DPM: an Analytic Estimate of the Optimal Reverse Variance in Diffusion Probabilistic Modelscited by 331
  8. 2017Grammar Variational Autoencodercited by 283
  9. 2022Torsional Diffusion for Molecular Conformer Generationcited by 262
  10. 2020Fast and Uncertainty-Aware Directional Message Passing for Non-Equilibrium Moleculescited by 254
  11. 2020Equivariant Flows: Exact Likelihood Generative Learning for Symmetric Densitiescited by 248
  12. 2020GEOM: Energy-annotated molecular conformations for property prediction and molecular generationcited by 238
  13. 2021Score-Based Generative Modeling with Critically-Damped Langevin Diffusioncited by 230
  14. 2018Optimization of Molecules via Deep Reinforcement Learningcited by 199
  15. 2020MoFlow: An Invertible Flow Model for Generating Molecular Graphscited by 183
  16. 2018Constrained Graph Variational Autoencoders for Molecule Designcited by 182
  17. 2021GraphDF: A Discrete Flow Model for Molecular Graph Generationcited by 177
  18. 2022EGSDE: Unpaired Image-to-Image Translation via Energy-Guided Stochastic Differential Equationscited by 172
  19. 2019Symmetry-adapted generation of 3d point sets for the targeted discovery of moleculescited by 171
  20. 2021E(n) Equivariant Normalizing Flowscited by 165
  21. 2019GraphNVP: An Invertible Flow Model for Generating Molecular Graphscited by 115
  22. 2018Syntax-Directed Variational Autoencoder for Structured Datacited by 103
  23. 2021Inverse design of 3d molecular structures with conditional generative neural networkscited by 93
  24. 2022Estimating the Optimal Covariance with Imperfect Mean in Diffusion Probabilistic Modelscited by 83
  25. 2019MolecularRNN: Generating realistic molecular graphs with optimized propertiescited by 80
  26. 2021Keeping it Simple: Language Models can learn Complex Molecular Distributionscited by 68
  27. 2019Augmenting Genetic Algorithms with Deep Neural Networks for Exploring the Chemical Spacecited by 66
  28. 2018DEFactor: Differentiable Edge Factorization-based Probabilistic Graph Generationcited by 24
  29. 2019Generating valid Euclidean distance matricescited by 19
  30. 20203DMolNet: A Generative Network for Molecular Structurescited by 19

Built on by

Cited by year (2026 to 7 Oct)

Citing papers per year: 2022: 1; 2023: 17; 2024: 25; 2025: 20; 2026: 9.

72 papers.

Sort:

By area:

  1. 2023Reduce, Reuse, Recycle: Compositional Generation with Energy-Based Diffusion Models and MCMCcited by 216
  2. 2023One Transformer Fits All Distributions in Multi-Modal Diffusion at Scalecited by 185
  3. 2023Contrastive Energy Prediction for Exact Energy-Guided Diffusion Sampling in Offline Reinforcement Learningcited by 145
  4. 2023Crystal Structure Prediction by Joint Equivariant Diffusioncited by 142
  5. 2024TFG: Unified Training-Free Guidance for Diffusion Modelscited by 103
  6. 2023MiDi: Mixed Graph and 3D Denoising Diffusion for Molecule Generationcited by 96
  7. 2022Physics-Informed Machine Learning: A Survey on Problems, Methods and Applicationscited by 88
  8. 2023Generative Diffusion Models on Graphs: Methods and Applicationscited by 79
  9. 2024Discrete-state Continuous-time Diffusion for Graph Generationcited by 73
  10. 2023The Blessing of Randomness: SDE Beats ODE in General Diffusion-based Image Editingcited by 61
  11. 2023On the Design Fundamentals of Diffusion Models: A Surveycited by 59
  12. 2024Graph Diffusion Transformers for Multi-Conditional Molecular Generationcited by 44
38 more
  1. 2023Diffusion Models and Semi-Supervised Learners Benefit Mutually with Few Labelscited by 37
  2. 2023A Survey on Graph Diffusion Models: Generative AI in Science for Molecule, Protein and Materialcited by 34
  3. 2024A Survey of Geometric Graph Neural Networks: Data Structures, Models and Applicationscited by 28
  4. 2023Learning Joint 2D & 3D Diffusion Models for Complete Molecule Generationcited by 27
  5. 2024Diffusion Models in textitDe Novo Drug Designcited by 26
  6. 2024UniGEM: A Unified Approach to Generation and Property Prediction for Moleculescited by 20
  7. 2023Spiking Denoising Diffusion Probabilistic Modelscited by 18
  8. 2024DiffPhyCon: A Generative Approach to Control Complex Physical Systemscited by 17
  9. 2025NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule Generationcited by 17
  10. 2023A Closer Look at Parameter-Efficient Tuning in Diffusion Modelscited by 15
  11. 2025A Periodic Bayesian Flow for Material Generationcited by 15
  12. 2023SDDM: Score-Decomposed Diffusion Models on Manifolds for Unpaired Image-to-Image Translationcited by 13
  13. 2025Equivariant Neural Diffusion for Molecule Generationcited by 13
  14. 2024TAGMol: Target-Aware Gradient-guided Molecule Generationcited by 12
  15. 2023Efficient Planning with Latent Diffusioncited by 11
  16. 2024Extended Flow Matching: a Method of Conditional Generation with Generalized Continuity Equationcited by 11
  17. 2024Geometry Informed Tokenization of Molecules for Language Model Generationcited by 10
  18. 2024Rethinking Specificity in SBDD: Leveraging Delta Score and Energy-Guided Diffusioncited by 9
  19. 2025Adaptive Diffusion Guidance via Stochastic Optimal Controlcited by 9
  20. 2024Stabilizing Policy Gradients for Stochastic Differential Equations via Consistency with Perturbation Processcited by 8
  21. 2025Siamese Foundation Models for Crystal Structure Predictioncited by 8
  22. 2024Lift Your Molecules: Molecular Graph Generation in Latent Euclidean Spacecited by 7
  23. 2025Unified Guidance for Geometry-Conditioned Molecular Generationcited by 7
  24. 2024Chemistry-Inspired Diffusion with Non-Differentiable Guidancecited by 6
  25. 2024Empower Structure-Based Molecule Optimization with Gradient Guided Bayesian Flow Networkscited by 6
  26. 2024General Binding Affinity Guidance for Diffusion Models in Structure-Based Drug Designcited by 5
  27. 2024Text-guided Diffusion Model for 3D Molecule Generationcited by 5
  28. 2024Conditional Synthesis of 3D Molecules with Time Correction Samplercited by 5
  29. 2025DiffSpectra: Molecular Structure Elucidation from Spectra using Diffusion Modelscited by 5
  30. 2024Nonlinear Inverse Design of Mechanical Multi-Material Metamaterials Enabled by Video Denoising Diffusion and Structure Identifiercited by 4
  31. 2024Diffusion Twigs with Loop Guidance for Conditional Graph Generationcited by 4
  32. 2024DeepSN: A Sheaf Neural Framework for Influence Maximizationcited by 4
  33. 2025TFG-Flow: Training-free Guidance in Multimodal Generative Flowcited by 4
  34. 2025Zero-Shot Cyclic Peptide Design via Composable Geometric Constraintscited by 4
  35. 2024Spiking Diffusion Modelscited by 3
  36. 20263D Molecule Generation from Rigid Motifs via SE(3) Flowscited by 3
  37. 2026Plug-and-Play Guidance for Discrete Diffusion Models via Gradient-Informed Logit Correctioncited by 3
  38. 2023Inversion-by-Inversion: Exemplar-based Sketch-to-Photo Synthesis via Stochastic Differential Equations without Trainingcited by 2

50 most cited of 72 All 72 (JSON)

Similar, not cited

Close in wording, no citation either way

  1. 2023Navigating the Design Space of Equivariant Diffusion-Based Generative Models for De Novo 3D Molecule Generation
  2. 2025D3MES: Diffusion Transformer with multihead equivariant self-attention for 3D molecule generation
  3. 2026Domain-Gated Latent Diffusion: Generative Inverse Design of HMX-Class Energetic Materials with First-Principles Validation
  4. 2026Equivariant Asynchronous Diffusion: An Adaptive Denoising Schedule for Accelerated Molecular Conformation Generation
  5. 2024Equivariant Blurring Diffusion for Hierarchical Molecular Conformer Generation
  6. 2025EquiBoost: An Equivariant Boosting Approach to Molecular Conformation Generation
  7. 2024ET-Flow: Equivariant Flow-Matching for Molecular Conformer Generation
  8. 20233D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction