Robust Molecular Property Prediction via Densifying Scarce Labeled Data
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arXiv
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| Hauptverfasser: | , , , |
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| Format: | Preprint |
| Veröffentlicht: |
2025
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| _version_ | 1866908742537183232 |
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| author | Kim, Jina Willette, Jeffrey Andreis, Bruno Hwang, Sung Ju |
| author_facet | Kim, Jina Willette, Jeffrey Andreis, Bruno Hwang, Sung Ju |
| contents | A widely recognized limitation of molecular prediction models is their reliance on structures observed in the training data, resulting in poor generalization to out-of-distribution compounds. Yet in drug discovery, the compounds most critical for advancing research often lie beyond the training set, making the bias toward the training data particularly problematic. This mismatch introduces substantial covariate shift, under which standard deep learning models produce unstable and inaccurate predictions. Furthermore, the scarcity of labeled data-stemming from the onerous and costly nature of experimental validation-further exacerbates the difficulty of achieving reliable generalization. To address these limitations, we propose a novel bilevel optimization approach that leverages unlabeled data to interpolate between in-distribution (ID) and out-of-distribution (OOD) data, enabling the model to learn how to generalize beyond the training distribution. We demonstrate significant performance gains on challenging real-world datasets with substantial covariate shift, supported by t-SNE visualizations highlighting our interpolation method. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2506_11877 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Robust Molecular Property Prediction via Densifying Scarce Labeled Data Kim, Jina Willette, Jeffrey Andreis, Bruno Hwang, Sung Ju Machine Learning Artificial Intelligence A widely recognized limitation of molecular prediction models is their reliance on structures observed in the training data, resulting in poor generalization to out-of-distribution compounds. Yet in drug discovery, the compounds most critical for advancing research often lie beyond the training set, making the bias toward the training data particularly problematic. This mismatch introduces substantial covariate shift, under which standard deep learning models produce unstable and inaccurate predictions. Furthermore, the scarcity of labeled data-stemming from the onerous and costly nature of experimental validation-further exacerbates the difficulty of achieving reliable generalization. To address these limitations, we propose a novel bilevel optimization approach that leverages unlabeled data to interpolate between in-distribution (ID) and out-of-distribution (OOD) data, enabling the model to learn how to generalize beyond the training distribution. We demonstrate significant performance gains on challenging real-world datasets with substantial covariate shift, supported by t-SNE visualizations highlighting our interpolation method. |
| title | Robust Molecular Property Prediction via Densifying Scarce Labeled Data |
| topic | Machine Learning Artificial Intelligence |
| url | https://arxiv.org/abs/2506.11877 |