Hierarchical Multi-Label Contrastive Learning for Protein-Protein Interaction Prediction Across Organisms
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arXiv
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| Main Authors: | Liu, Shiyi, Liang, Buwen, Fang, Yuetong, Jiang, Zixuan, Xu, Renjing |
|---|---|
| Format: | Preprint |
| Published: |
2025
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| Subjects: | |
| Online Access: | |
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