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| Format: | Preprint |
| Published: |
2026
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| Online Access: | https://arxiv.org/abs/2605.28521 |
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| _version_ | 1866911724884459520 |
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| author | Remy, François |
| author_facet | Remy, François |
| contents | ClinicalEncoder26AM is a multilingual Diagnosable ColBERT for clinical and biomedical texts, which aligns at multiple levels its token-level semantic with ClinicalMap25, a clinical latent space inspired by BioLORD-2023 and enriched with synthetic and annotated supervision. The post-training recipe builds upon BGE-M3, and combines synthetic clinical notes, patient--doctor conversations, and annotated resources such as MedMentions, while considering both named-entity-level and sentence-level representations in a multi-adapter distillation, along with a ColBERT-style retrieval objective. In this system demonstration paper, we evaluate the model in the MultiClinNER shared task by finetuning it as a BIO tagger for patient symptoms, disorders, and procedure spans, using a lightweight two-layer CNN head to improve local boundary detection. The resulting system remains simple, processes most documents in a single 8192-token window, and achieves state-of-the-art multilingual entity recall, while achieving Top 5 overall across all entity types and languages in Character-weighted F1 scores. Training curves further show that ClinicalEncoder26AM is markedly more data-efficient than the base M3 model, supporting the usefulness of its clinical post-training for downstream information extraction.
The model can be downloaded on https://huggingface.co/Parallia/ClinicalEncoder26AM-Diagnosable-Colbert-L2-for-multilingual-medical-texts |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2605_28521 |
| institution | arXiv |
| publishDate | 2026 |
| record_format | arxiv |
| spellingShingle | ClinicalEncoder26AM: A Multlilingual Diagnosable ColBERT Model; Evidences from the MultiClinNER Shared Task Remy, François Computation and Language ClinicalEncoder26AM is a multilingual Diagnosable ColBERT for clinical and biomedical texts, which aligns at multiple levels its token-level semantic with ClinicalMap25, a clinical latent space inspired by BioLORD-2023 and enriched with synthetic and annotated supervision. The post-training recipe builds upon BGE-M3, and combines synthetic clinical notes, patient--doctor conversations, and annotated resources such as MedMentions, while considering both named-entity-level and sentence-level representations in a multi-adapter distillation, along with a ColBERT-style retrieval objective. In this system demonstration paper, we evaluate the model in the MultiClinNER shared task by finetuning it as a BIO tagger for patient symptoms, disorders, and procedure spans, using a lightweight two-layer CNN head to improve local boundary detection. The resulting system remains simple, processes most documents in a single 8192-token window, and achieves state-of-the-art multilingual entity recall, while achieving Top 5 overall across all entity types and languages in Character-weighted F1 scores. Training curves further show that ClinicalEncoder26AM is markedly more data-efficient than the base M3 model, supporting the usefulness of its clinical post-training for downstream information extraction. The model can be downloaded on https://huggingface.co/Parallia/ClinicalEncoder26AM-Diagnosable-Colbert-L2-for-multilingual-medical-texts |
| title | ClinicalEncoder26AM: A Multlilingual Diagnosable ColBERT Model; Evidences from the MultiClinNER Shared Task |
| topic | Computation and Language |
| url | https://arxiv.org/abs/2605.28521 |