NEBULA: Neural Empirical Bayes Under Latent Representations for Efficient and Controllable Design of Molecular Libraries
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arXiv
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| Auteurs principaux: | , , , , , , |
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| Format: | Preprint |
| Publié: |
2024
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| _version_ | 1866914859277352960 |
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| author | Nowara, Ewa M. Pinheiro, Pedro O. Mahajan, Sai Pooja Mahmood, Omar Watkins, Andrew Martin Saremi, Saeed Maser, Michael |
| author_facet | Nowara, Ewa M. Pinheiro, Pedro O. Mahajan, Sai Pooja Mahmood, Omar Watkins, Andrew Martin Saremi, Saeed Maser, Michael |
| contents | We present NEBULA, the first latent 3D generative model for scalable generation of large molecular libraries around a seed compound of interest. Such libraries are crucial for scientific discovery, but it remains challenging to generate large numbers of high quality samples efficiently. 3D-voxel-based methods have recently shown great promise for generating high quality samples de novo from random noise (Pinheiro et al., 2023). However, sampling in 3D-voxel space is computationally expensive and use in library generation is prohibitively slow. Here, we instead perform neural empirical Bayes sampling (Saremi & Hyvarinen, 2019) in the learned latent space of a vector-quantized variational autoencoder. NEBULA generates large molecular libraries nearly an order of magnitude faster than existing methods without sacrificing sample quality. Moreover, NEBULA generalizes better to unseen drug-like molecules, as demonstrated on two public datasets and multiple recently released drugs. We expect the approach herein to be highly enabling for machine learning-based drug discovery. The code is available at https://github.com/prescient-design/nebula |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2407_03428 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | NEBULA: Neural Empirical Bayes Under Latent Representations for Efficient and Controllable Design of Molecular Libraries Nowara, Ewa M. Pinheiro, Pedro O. Mahajan, Sai Pooja Mahmood, Omar Watkins, Andrew Martin Saremi, Saeed Maser, Michael Machine Learning Biomolecules We present NEBULA, the first latent 3D generative model for scalable generation of large molecular libraries around a seed compound of interest. Such libraries are crucial for scientific discovery, but it remains challenging to generate large numbers of high quality samples efficiently. 3D-voxel-based methods have recently shown great promise for generating high quality samples de novo from random noise (Pinheiro et al., 2023). However, sampling in 3D-voxel space is computationally expensive and use in library generation is prohibitively slow. Here, we instead perform neural empirical Bayes sampling (Saremi & Hyvarinen, 2019) in the learned latent space of a vector-quantized variational autoencoder. NEBULA generates large molecular libraries nearly an order of magnitude faster than existing methods without sacrificing sample quality. Moreover, NEBULA generalizes better to unseen drug-like molecules, as demonstrated on two public datasets and multiple recently released drugs. We expect the approach herein to be highly enabling for machine learning-based drug discovery. The code is available at https://github.com/prescient-design/nebula |
| title | NEBULA: Neural Empirical Bayes Under Latent Representations for Efficient and Controllable Design of Molecular Libraries |
| topic | Machine Learning Biomolecules |
| url | https://arxiv.org/abs/2407.03428 |