SynFlowNet: Design of Diverse and Novel Molecules with Synthesis Constraints
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| Main Authors: | , , , , , , , , |
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| Format: | Preprint |
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2024
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| _version_ | 1866917981277126656 |
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| author | Cretu, Miruna Harris, Charles Igashov, Ilia Schneuing, Arne Segler, Marwin Correia, Bruno Roy, Julien Bengio, Emmanuel Liò, Pietro |
| author_facet | Cretu, Miruna Harris, Charles Igashov, Ilia Schneuing, Arne Segler, Marwin Correia, Bruno Roy, Julien Bengio, Emmanuel Liò, Pietro |
| contents | Generative models see increasing use in computer-aided drug design. However, while performing well at capturing distributions of molecular motifs, they often produce synthetically inaccessible molecules. To address this, we introduce SynFlowNet, a GFlowNet model whose action space uses chemical reactions and purchasable reactants to sequentially build new molecules. By incorporating forward synthesis as an explicit constraint of the generative mechanism, we aim at bridging the gap between in silico molecular generation and real world synthesis capabilities. We evaluate our approach using synthetic accessibility scores and an independent retrosynthesis tool to assess the synthesizability of our compounds, and motivate the choice of GFlowNets through considerable improvement in sample diversity compared to baselines. Additionally, we identify challenges with reaction encodings that can complicate traversal of the MDP in the backward direction. To address this, we introduce various strategies for learning the GFlowNet backward policy and thus demonstrate how additional constraints can be integrated into the GFlowNet MDP framework. This approach enables our model to successfully identify synthesis pathways for previously unseen molecules. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2405_01155 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | SynFlowNet: Design of Diverse and Novel Molecules with Synthesis Constraints Cretu, Miruna Harris, Charles Igashov, Ilia Schneuing, Arne Segler, Marwin Correia, Bruno Roy, Julien Bengio, Emmanuel Liò, Pietro Machine Learning Biomolecules Generative models see increasing use in computer-aided drug design. However, while performing well at capturing distributions of molecular motifs, they often produce synthetically inaccessible molecules. To address this, we introduce SynFlowNet, a GFlowNet model whose action space uses chemical reactions and purchasable reactants to sequentially build new molecules. By incorporating forward synthesis as an explicit constraint of the generative mechanism, we aim at bridging the gap between in silico molecular generation and real world synthesis capabilities. We evaluate our approach using synthetic accessibility scores and an independent retrosynthesis tool to assess the synthesizability of our compounds, and motivate the choice of GFlowNets through considerable improvement in sample diversity compared to baselines. Additionally, we identify challenges with reaction encodings that can complicate traversal of the MDP in the backward direction. To address this, we introduce various strategies for learning the GFlowNet backward policy and thus demonstrate how additional constraints can be integrated into the GFlowNet MDP framework. This approach enables our model to successfully identify synthesis pathways for previously unseen molecules. |
| title | SynFlowNet: Design of Diverse and Novel Molecules with Synthesis Constraints |
| topic | Machine Learning Biomolecules |
| url | https://arxiv.org/abs/2405.01155 |