A Dataset for Distilling Knowledge Priors from Literature for Therapeutic Design
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| Main Authors: | , , , , , , , , , , , |
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| Format: | Preprint |
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2025
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| _version_ | 1866915491101016064 |
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| author | Jones, Haydn Thomas Maus, Natalie Ludan, Josh Magnus Huan, Maggie Ziyu Liang, Jiaming Torres, Marcelo Der Torossian Liang, Jiatao Ives, Zachary Barash, Yoseph de la Fuente-Nunez, Cesar Gardner, Jacob R. Yatskar, Mark |
| author_facet | Jones, Haydn Thomas Maus, Natalie Ludan, Josh Magnus Huan, Maggie Ziyu Liang, Jiaming Torres, Marcelo Der Torossian Liang, Jiatao Ives, Zachary Barash, Yoseph de la Fuente-Nunez, Cesar Gardner, Jacob R. Yatskar, Mark |
| contents | AI-driven discovery can greatly reduce design time and enhance new therapeutics' effectiveness. Models using simulators explore broad design spaces but risk violating implicit constraints due to a lack of experimental priors. For example, in a new analysis we performed on a diverse set of models on the GuacaMol benchmark using supervised classifiers, over 60\% of molecules proposed had high probability of being mutagenic. In this work, we introduce Medex, a dataset of priors for design problems extracted from literature describing compounds used in lab settings. It is constructed with LLM pipelines for discovering therapeutic entities in relevant paragraphs and summarizing information in concise fair-use facts. Medex consists of 32.3 million pairs of natural language facts, and appropriate entity representations (i.e. SMILES or refseq IDs). To demonstrate the potential of the data, we train LLM, CLIP, and LLava architectures to reason jointly about text and design targets and evaluate on tasks from the Therapeutic Data Commons (TDC). Medex is highly effective for creating models with strong priors: in supervised prediction problems that use our data as pretraining, our best models with 15M learnable parameters outperform larger 2B TxGemma on both regression and classification TDC tasks, and perform comparably to 9B models on average. Models built with Medex can be used as constraints while optimizing for novel molecules in GuacaMol, resulting in proposals that are safer and nearly as effective. We release our dataset at https://huggingface.co/datasets/medexanon/Medex, and will provide expanded versions as available literature grows. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2508_10899 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | A Dataset for Distilling Knowledge Priors from Literature for Therapeutic Design Jones, Haydn Thomas Maus, Natalie Ludan, Josh Magnus Huan, Maggie Ziyu Liang, Jiaming Torres, Marcelo Der Torossian Liang, Jiatao Ives, Zachary Barash, Yoseph de la Fuente-Nunez, Cesar Gardner, Jacob R. Yatskar, Mark Machine Learning AI-driven discovery can greatly reduce design time and enhance new therapeutics' effectiveness. Models using simulators explore broad design spaces but risk violating implicit constraints due to a lack of experimental priors. For example, in a new analysis we performed on a diverse set of models on the GuacaMol benchmark using supervised classifiers, over 60\% of molecules proposed had high probability of being mutagenic. In this work, we introduce Medex, a dataset of priors for design problems extracted from literature describing compounds used in lab settings. It is constructed with LLM pipelines for discovering therapeutic entities in relevant paragraphs and summarizing information in concise fair-use facts. Medex consists of 32.3 million pairs of natural language facts, and appropriate entity representations (i.e. SMILES or refseq IDs). To demonstrate the potential of the data, we train LLM, CLIP, and LLava architectures to reason jointly about text and design targets and evaluate on tasks from the Therapeutic Data Commons (TDC). Medex is highly effective for creating models with strong priors: in supervised prediction problems that use our data as pretraining, our best models with 15M learnable parameters outperform larger 2B TxGemma on both regression and classification TDC tasks, and perform comparably to 9B models on average. Models built with Medex can be used as constraints while optimizing for novel molecules in GuacaMol, resulting in proposals that are safer and nearly as effective. We release our dataset at https://huggingface.co/datasets/medexanon/Medex, and will provide expanded versions as available literature grows. |
| title | A Dataset for Distilling Knowledge Priors from Literature for Therapeutic Design |
| topic | Machine Learning |
| url | https://arxiv.org/abs/2508.10899 |