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README.md
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- Embedding similarity (SimE): cosine similarity between document embeddings
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- Label similarity (SimL): cosine similarity over weighted MeSH multi-label vectors
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### Training Objective
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- Mean Squared Error (MSE): aligns SimE with SimL
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- Hierarchical contrastive loss: separates unrelated documents while preserving ontology structure
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---
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## 📖 Citation
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If you use this model, please cite:
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```bibtex
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@article{lan2026biohicl,
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title={BioHiCL: Hierarchical Multi-Label Contrastive Learning for Biomedical Retrieval with MeSH Labels},
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author={Lan, Mengfei and Zheng, Lecheng and Kilicoglu, Halil},
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booktitle={ACL 2026},
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year={2026}
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}
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---
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## 🚀 Usage (BEIR Evaluation)
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# Evaluation
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ndcg, _map, recall, precision = EvaluateRetrieval.evaluate(
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qrels, results, k_values=[1, 3, 5, 10]
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- Embedding similarity (SimE): cosine similarity between document embeddings
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- Label similarity (SimL): cosine similarity over weighted MeSH multi-label vectors
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---
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---
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## 🚀 Usage (BEIR Evaluation)
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# Evaluation
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ndcg, _map, recall, precision = EvaluateRetrieval.evaluate(
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qrels, results, k_values=[1, 3, 5, 10]
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```
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## 📖 Citation
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If you use this model, please cite:
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```bibtex
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@article{lan2026biohicl,
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title={BioHiCL: Hierarchical Multi-Label Contrastive Learning for Biomedical Retrieval with MeSH Labels},
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author={Lan, Mengfei and Zheng, Lecheng and Kilicoglu, Halil},
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booktitle={ACL 2026},
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year={2026}
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}
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```
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