Sparse Category Routing and Fairness-Aware Optimization for Medical Decision Extraction

Ahmed Elshehaby, Mohamed Abdalla, Youssef Mohamed


Abstract
Extracting structured medical decisions fromICU discharge summaries is hard because oflong documents, severe category imbalanceacross nine DICTUM decision types, and afairness-aware evaluation that penalizes incon-sistent performance across demographic sub-groups. We present our system for the MedEx-ACT 2026 shared task (Elgaar et al., 2026),which fine-tunes BiomedBERT with a com-posite loss combining label-smoothed cross-entropy, a soft token-F1 auxiliary term, andR-Drop regularization. At inference time weapply a deterministic ensemble: half-offsetsliding-window augmentation across four win-dow configurations, dual-branch logit aggrega-tion from the same checkpoint, per-categorylength calibration on the Anchor Branch, andsparse routing of categories 4 and 7 to a context-weighted specialist branch motivated by theirunusual span-length distributions. Adding R-Drop improved validation Overall_F1 by 1.24points over the CE + soft-F1 baseline, with alarger 1.70-point gain on Worst-Group F1. Ourbest submission achieves Span F1 of 0.4900,Token F1 of 0.6796, and an official Overall_F1of 0.5724, with the African American subgroupas the Worst-Group bottleneck at Base_Score0.5601
Anthology ID:
2026.bionlp-2.27
Volume:
Proceedings of the BioNLP 2026 (Shared Tasks)
Month:
July
Year:
2026
Address:
San Diego, California, USA
Editors:
Deepak Gupta, Dina Demner-Fushman
Venues:
BioNLP | WS
SIG:
Publisher:
Association for Computational Linguistics
Note:
Pages:
201–212
Language:
URL:
https://preview.aclanthology.org/ingest-acl-workshops/2026.bionlp-2.27/
DOI:
Bibkey:
Cite (ACL):
Ahmed Elshehaby, Mohamed Abdalla, and Youssef Mohamed. 2026. Sparse Category Routing and Fairness-Aware Optimization for Medical Decision Extraction. In Proceedings of the BioNLP 2026 (Shared Tasks), pages 201–212, San Diego, California, USA. Association for Computational Linguistics.
Cite (Informal):
Sparse Category Routing and Fairness-Aware Optimization for Medical Decision Extraction (Elshehaby et al., BioNLP 2026)
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https://preview.aclanthology.org/ingest-acl-workshops/2026.bionlp-2.27.pdf
Supplementarymaterial:
 2026.bionlp-2.27.SupplementaryMaterial.txt