Generative Models for Automatic Chemical Design
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Abstract (arXiv)
Materials discovery is decisive for tackling urgent challenges related to energy, the environment, health care and many others. In chemistry, conventional methodologies for innovation usually rely on expensive and incremental strategies to optimize properties from molecular structures. On the other hand, inverse approaches map properties to structures, thus expediting the design of novel useful compounds. In this chapter, we examine the way in which current deep generative models are addressing the inverse chemical discovery paradigm. We begin by revisiting early inverse design algorithms. Then, we introduce generative models for molecular systems and categorize them according to their architecture and molecular representation. Using this classification, we review the evolution and performance of important molecular generation schemes reported in the literature. Finally, we conclude highlighting the prospects and challenges of generative models as cutting edge tools in materials discovery.
Key facts. Cited by 23 papers in the map (data through 7 Oct 2026). First posted on arXiv 2 Jul 2019.
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Citing papers per year: 2021: 5; 2022: 6; 2023: 5; 2024: 3; 2025: 2; 2026: 2.
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- 2021MARS: Markov Molecular Sampling for Multi-objective Drug Discoverycited by 125
- 2022Exploring Chemical Space with Score-based Out-of-distribution Generationcited by 95
- 2021Combining Latent Space and Structured Kernels for Bayesian Optimization over Combinatorial Spacescited by 45
- 2021Amortized Tree Generation for Bottom-up Synthesis Planning and Synthesizable Molecular Designcited by 44
- 2022Physics Guided Deep Learning for Generative Design of Crystal Materials with Symmetry Constraintscited by 30
- 2023Single-model uncertainty quantification in neural network potentials does not consistently outperform model ensemblescited by 30
- 2021How Much Space Has Been Explored? Measuring the Chemical Space Covered by Databases and Machine-Generated Moleculescited by 27
- 2021Differentiable sampling of molecular geometries with uncertainty-based adversarial attackscited by 25
- 2023Deep Learning Methods for Small Molecule Drug Discovery: A Surveycited by 10
- 2022Mario Plays on a Manifold: Generating Functional Content in Latent Space through Differential Geometrycited by 5
- 2025A Generative Diffusion Model for Amorphous Materialscited by 5
- 2023Automated patent extraction powers generative modeling in focused chemical spacescited by 4
11 more
- 2024Diffusion Twigs with Loop Guidance for Conditional Graph Generationcited by 4
- 2024Enhanced sampling of robust molecular datasets with uncertainty-based collective variablescited by 2
- 2024Instruction Multi-Constraint Molecular Generation Using a Teacher-Student Large Language Modelcited by 2
- 2022Molecular Dipole Moment Learning via Rotationally Equivariant Gaussian Process Regression with Derivatives in Molecular-orbital-based Machine Learningcited by 1
- 2022Accelerating Antimicrobial Peptide Discovery with Latent Structurecited by 1
- 2025Designing ReLU Generative Networks to Enumerate Trees with a Given Tree Edit Distancecited by 1
- 2022Topology-Driven Generative Completion of Lacunae in Molecular Datacited by 0
- 2023Human-AI Co-Creation Approach to Find Forever Chemicals Replacementscited by 0
- 2023Molecular design method based on novel molecular representation and variational auto-encodercited by 0
- 2026ReLU Networks for Exact Generation of Similar Graphscited by 0
- 2026AtomComposer: Discovering Chemical Space from First Principles with Reinforcement Learningcited by 0
- 2026AtomComposer: Discovering Chemical Space from First Principles with Reinforcement Learning27 May 2026
- 2026ReLU Networks for Exact Generation of Similar Graphs7 Apr 2026
- 2025Designing ReLU Generative Networks to Enumerate Trees with a Given Tree Edit Distance12 Oct 2025
- 2025A Generative Diffusion Model for Amorphous Materials7 Jul 2025
- 2024Diffusion Twigs with Loop Guidance for Conditional Graph Generation31 Oct 2024
- 2024Instruction Multi-Constraint Molecular Generation Using a Teacher-Student Large Language Model20 Mar 2024
- 2024Enhanced sampling of robust molecular datasets with uncertainty-based collective variables6 Feb 2024
- 2023Single-model uncertainty quantification in neural network potentials does not consistently outperform model ensembles2 May 2023
- 2023Human-AI Co-Creation Approach to Find Forever Chemicals Replacements11 Apr 2023
- 2023Automated patent extraction powers generative modeling in focused chemical spaces14 Mar 2023
- 2023Deep Learning Methods for Small Molecule Drug Discovery: A Survey1 Mar 2023
- 2023Molecular design method based on novel molecular representation and variational auto-encoder20 Feb 2023
11 more
- 2022Accelerating Antimicrobial Peptide Discovery with Latent Structure28 Nov 2022
- 2022Topology-Driven Generative Completion of Lacunae in Molecular Data29 Jul 2022
- 2022Exploring Chemical Space with Score-based Out-of-distribution Generation6 Jun 2022
- 2022Mario Plays on a Manifold: Generating Functional Content in Latent Space through Differential Geometry31 May 2022
- 2022Molecular Dipole Moment Learning via Rotationally Equivariant Gaussian Process Regression with Derivatives in Molecular-orbital-based Machine Learning31 May 2022
- 2022Physics Guided Deep Learning for Generative Design of Crystal Materials with Symmetry Constraints27 Mar 2022
- 2021How Much Space Has Been Explored? Measuring the Chemical Space Covered by Databases and Machine-Generated Molecules22 Dec 2021
- 2021Combining Latent Space and Structured Kernels for Bayesian Optimization over Combinatorial Spaces1 Nov 2021
- 2021Amortized Tree Generation for Bottom-up Synthesis Planning and Synthesizable Molecular Design12 Oct 2021
- 2021MARS: Markov Molecular Sampling for Multi-objective Drug Discovery18 Mar 2021
- 2021Differentiable sampling of molecular geometries with uncertainty-based adversarial attacks27 Jan 2021
- 2025A Generative Diffusion Model for Amorphous Materialscited by 5
- 2025A Generative Diffusion Model for Amorphous Materials7 Jul 2025
- 2021MARS: Markov Molecular Sampling for Multi-objective Drug Discoverycited by 125
- 2022Exploring Chemical Space with Score-based Out-of-distribution Generationcited by 95
- 2021Combining Latent Space and Structured Kernels for Bayesian Optimization over Combinatorial Spacescited by 45
- 2021Amortized Tree Generation for Bottom-up Synthesis Planning and Synthesizable Molecular Designcited by 44
- 2022Physics Guided Deep Learning for Generative Design of Crystal Materials with Symmetry Constraintscited by 30
- 2023Single-model uncertainty quantification in neural network potentials does not consistently outperform model ensemblescited by 30
- 2021How Much Space Has Been Explored? Measuring the Chemical Space Covered by Databases and Machine-Generated Moleculescited by 27
- 2021Differentiable sampling of molecular geometries with uncertainty-based adversarial attackscited by 25
- 2023Deep Learning Methods for Small Molecule Drug Discovery: A Surveycited by 10
- 2022Mario Plays on a Manifold: Generating Functional Content in Latent Space through Differential Geometrycited by 5
- 2023Automated patent extraction powers generative modeling in focused chemical spacescited by 4
- 2024Diffusion Twigs with Loop Guidance for Conditional Graph Generationcited by 4
12 most cited of 22 All 22 (JSON)
- 2026AtomComposer: Discovering Chemical Space from First Principles with Reinforcement Learning27 May 2026
- 2026ReLU Networks for Exact Generation of Similar Graphs7 Apr 2026
- 2025Designing ReLU Generative Networks to Enumerate Trees with a Given Tree Edit Distance12 Oct 2025
- 2024Diffusion Twigs with Loop Guidance for Conditional Graph Generation31 Oct 2024
- 2024Instruction Multi-Constraint Molecular Generation Using a Teacher-Student Large Language Model20 Mar 2024
- 2024Enhanced sampling of robust molecular datasets with uncertainty-based collective variables6 Feb 2024
- 2023Single-model uncertainty quantification in neural network potentials does not consistently outperform model ensembles2 May 2023
- 2023Human-AI Co-Creation Approach to Find Forever Chemicals Replacements11 Apr 2023
- 2023Automated patent extraction powers generative modeling in focused chemical spaces14 Mar 2023
- 2023Deep Learning Methods for Small Molecule Drug Discovery: A Survey1 Mar 2023
- 2023Molecular design method based on novel molecular representation and variational auto-encoder20 Feb 2023
- 2022Accelerating Antimicrobial Peptide Discovery with Latent Structure28 Nov 2022
12 newest of 22 All 22 (JSON)