Re-evaluating sample efficiency in de novo molecule generation
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arXiv
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| Auteurs principaux: | , , , |
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| Format: | Preprint |
| Publié: |
2022
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| _version_ | 1866912674305015808 |
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| author | Thomas, Morgan O'Boyle, Noel M. Bender, Andreas De Graaf, Chris |
| author_facet | Thomas, Morgan O'Boyle, Noel M. Bender, Andreas De Graaf, Chris |
| contents | De novo molecule generation can suffer from data inefficiency; requiring large amounts of training data or many sampled data points to conduct objective optimization. The latter is a particular disadvantage when combining deep generative models with computationally expensive molecule scoring functions (a.k.a. oracles) commonly used in computer-aided drug design. Recent works have therefore focused on methods to improve sample efficiency in the context of de novo molecule drug design, or to benchmark it. In this work, we discuss and adapt a recent sample efficiency benchmark to better reflect realistic goals also with respect to the quality of chemistry generated, which must always be considered in the context of small-molecule drug design; we then re-evaluate all benchmarked generative models. We find that accounting for molecular weight and LogP with respect to the training data, and the diversity of chemistry proposed, re-orders the ranking of generative models. In addition, we benchmark a recently proposed method to improve sample efficiency (Augmented Hill-Climb) and found it ranked top when considering both the sample efficiency and chemistry of molecules generated. Continual improvements in sample efficiency and chemical desirability enable more routine integration of computationally expensive scoring functions on a more realistic timescale. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2212_01385 |
| institution | arXiv |
| publishDate | 2022 |
| record_format | arxiv |
| spellingShingle | Re-evaluating sample efficiency in de novo molecule generation Thomas, Morgan O'Boyle, Noel M. Bender, Andreas De Graaf, Chris Computational Engineering, Finance, and Science Machine Learning Biomolecules De novo molecule generation can suffer from data inefficiency; requiring large amounts of training data or many sampled data points to conduct objective optimization. The latter is a particular disadvantage when combining deep generative models with computationally expensive molecule scoring functions (a.k.a. oracles) commonly used in computer-aided drug design. Recent works have therefore focused on methods to improve sample efficiency in the context of de novo molecule drug design, or to benchmark it. In this work, we discuss and adapt a recent sample efficiency benchmark to better reflect realistic goals also with respect to the quality of chemistry generated, which must always be considered in the context of small-molecule drug design; we then re-evaluate all benchmarked generative models. We find that accounting for molecular weight and LogP with respect to the training data, and the diversity of chemistry proposed, re-orders the ranking of generative models. In addition, we benchmark a recently proposed method to improve sample efficiency (Augmented Hill-Climb) and found it ranked top when considering both the sample efficiency and chemistry of molecules generated. Continual improvements in sample efficiency and chemical desirability enable more routine integration of computationally expensive scoring functions on a more realistic timescale. |
| title | Re-evaluating sample efficiency in de novo molecule generation |
| topic | Computational Engineering, Finance, and Science Machine Learning Biomolecules |
| url | https://arxiv.org/abs/2212.01385 |