A Systematic Survey and Benchmark of Deep Learning for Molecular Property Prediction in the Foundation Model Era
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arXiv
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| Main Authors: | Li, Zongru, Chen, Xingsheng, Wen, Honggang, Zhang, Regina Qianru, Li, Ming, Zhang, Xiaojin, Yin, Hongzhi, Yang, Qiang, Lam, Kwok-Yan, Lio, Pietro, Yiu, Siu-Ming |
|---|---|
| Format: | Preprint |
| Published: |
2026
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| Subjects: | |
| Online Access: | |
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