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| Main Authors: | , , , , |
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| Format: | Preprint |
| Published: |
2026
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| Subjects: | |
| Online Access: | https://arxiv.org/abs/2602.07002 |
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| _version_ | 1866911428582047744 |
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| author | Okada, Masahi Sakai, Kazuki Yoshida, Hiroaki Okoshi, Masaki Taniguchi, Tadahiro |
| author_facet | Okada, Masahi Sakai, Kazuki Yoshida, Hiroaki Okoshi, Masaki Taniguchi, Tadahiro |
| contents | We study sample-efficient molecular optimization under a limited budget of oracle evaluations. We propose MolLIBRA (MultimOdaLity and Language Integrated Bayesian and evolutionaRy optimizAtion), a genetic algorithm based framework that pre-ranks candidate molecules using multiple critics before oracle calls: (i) an ensemble of Gaussian process (GP) surrogates defined over multiple molecular fingerprints and (ii) a pretrained text-molecule aligned encoder CLAMP. The GP ensemble enables adaptive selection of task-appropriate fingerprints, while CLAMP provides a zero-shot scoring signal from task descriptions by measuring the similarity between molecular and text embeddings. On the Practical Molecular Optimization (PMO) benchmark with a budget of 1,000 evaluations (PMO-1K), MolLIBRA-L, our variant with a language-model-based candidate generator, attains the best Top-10 AUC on 14/22 tasks and the highest overall sum of Top-10 AUC across tasks among prior methods. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2602_07002 |
| institution | arXiv |
| publishDate | 2026 |
| record_format | arxiv |
| spellingShingle | MolLIBRA: Genetic Molecular Optimization with Multi-Fingerprint Surrogates and Text-Molecule Aligned Critic Okada, Masahi Sakai, Kazuki Yoshida, Hiroaki Okoshi, Masaki Taniguchi, Tadahiro Neural and Evolutionary Computing Materials Science Machine Learning We study sample-efficient molecular optimization under a limited budget of oracle evaluations. We propose MolLIBRA (MultimOdaLity and Language Integrated Bayesian and evolutionaRy optimizAtion), a genetic algorithm based framework that pre-ranks candidate molecules using multiple critics before oracle calls: (i) an ensemble of Gaussian process (GP) surrogates defined over multiple molecular fingerprints and (ii) a pretrained text-molecule aligned encoder CLAMP. The GP ensemble enables adaptive selection of task-appropriate fingerprints, while CLAMP provides a zero-shot scoring signal from task descriptions by measuring the similarity between molecular and text embeddings. On the Practical Molecular Optimization (PMO) benchmark with a budget of 1,000 evaluations (PMO-1K), MolLIBRA-L, our variant with a language-model-based candidate generator, attains the best Top-10 AUC on 14/22 tasks and the highest overall sum of Top-10 AUC across tasks among prior methods. |
| title | MolLIBRA: Genetic Molecular Optimization with Multi-Fingerprint Surrogates and Text-Molecule Aligned Critic |
| topic | Neural and Evolutionary Computing Materials Science Machine Learning |
| url | https://arxiv.org/abs/2602.07002 |