Pretraining Generative Flow Networks with Inexpensive Rewards for Molecular Graph Generation
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arXiv
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| Autores principales: | , , , , |
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| Formato: | Preprint |
| Publicado: |
2025
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| _version_ | 1866916791568039936 |
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| author | Pandey, Mohit Subbaraj, Gopeshh Cherkasov, Artem Ester, Martin Bengio, Emmanuel |
| author_facet | Pandey, Mohit Subbaraj, Gopeshh Cherkasov, Artem Ester, Martin Bengio, Emmanuel |
| contents | Generative Flow Networks (GFlowNets) have recently emerged as a suitable framework for generating diverse and high-quality molecular structures by learning from rewards treated as unnormalized distributions. Previous works in this framework often restrict exploration by using predefined molecular fragments as building blocks, limiting the chemical space that can be accessed. In this work, we introduce Atomic GFlowNets (A-GFNs), a foundational generative model leveraging individual atoms as building blocks to explore drug-like chemical space more comprehensively. We propose an unsupervised pre-training approach using drug-like molecule datasets, which teaches A-GFNs about inexpensive yet informative molecular descriptors such as drug-likeliness, topological polar surface area, and synthetic accessibility scores. These properties serve as proxy rewards, guiding A-GFNs towards regions of chemical space that exhibit desirable pharmacological properties. We further implement a goal-conditioned finetuning process, which adapts A-GFNs to optimize for specific target properties. In this work, we pretrain A-GFN on a subset of ZINC dataset, and by employing robust evaluation metrics we show the effectiveness of our approach when compared to other relevant baseline methods for a wide range of drug design tasks. The code is accessible at https://github.com/diamondspark/AGFN. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2503_06337 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Pretraining Generative Flow Networks with Inexpensive Rewards for Molecular Graph Generation Pandey, Mohit Subbaraj, Gopeshh Cherkasov, Artem Ester, Martin Bengio, Emmanuel Machine Learning Generative Flow Networks (GFlowNets) have recently emerged as a suitable framework for generating diverse and high-quality molecular structures by learning from rewards treated as unnormalized distributions. Previous works in this framework often restrict exploration by using predefined molecular fragments as building blocks, limiting the chemical space that can be accessed. In this work, we introduce Atomic GFlowNets (A-GFNs), a foundational generative model leveraging individual atoms as building blocks to explore drug-like chemical space more comprehensively. We propose an unsupervised pre-training approach using drug-like molecule datasets, which teaches A-GFNs about inexpensive yet informative molecular descriptors such as drug-likeliness, topological polar surface area, and synthetic accessibility scores. These properties serve as proxy rewards, guiding A-GFNs towards regions of chemical space that exhibit desirable pharmacological properties. We further implement a goal-conditioned finetuning process, which adapts A-GFNs to optimize for specific target properties. In this work, we pretrain A-GFN on a subset of ZINC dataset, and by employing robust evaluation metrics we show the effectiveness of our approach when compared to other relevant baseline methods for a wide range of drug design tasks. The code is accessible at https://github.com/diamondspark/AGFN. |
| title | Pretraining Generative Flow Networks with Inexpensive Rewards for Molecular Graph Generation |
| topic | Machine Learning |
| url | https://arxiv.org/abs/2503.06337 |