--- license: llama3.1 base_model: - meta-llama/Llama-3.1-8B-Instruct language: - fr tags: - biomedical-entity-linking - entity-linking - entity-disambiguation - named-entity-linking - biomedical - healthcare - umls - quaero - emea - text-generation - constrained-decoding - causal-lm - llm library_name: transformers pipeline_tag: text-generation datasets: - AnonymousARR42/EMEA finetuning_task: - entity-linking metrics: - recall model-index: - name: LongBEL-8B-QUAERO-EMEA results: - task: type: entity-linking name: Biomedical Entity Linking dataset: type: AnonymousARR42/EMEA name: QUAERO-EMEA metrics: - type: recall name: Recall@1 value: 0.754 --- # LongBEL: Long-Context and Document-Consistent Biomedical Entity Linking ## LongBEL **LongBEL** is a novel document-level framework for biomedical entity linking (BEL). Instead of normalizing each mention independently, LongBEL conditions each prediction on the document context and on previous normalizations produced in the same document. This design enforces document-level consistency and is enhanced by our **robust memory** mechanism. The method is introduced in our paper, currently under review. ## LongBEL (QUAERO-EMEA Edition) This is a **finetuned version of LLaMA-3-8B** trained on **QUAERO-EMEA**, applying the LongBEL framework to enable long context and robust memory predictions. | Field | Value | |---|---| | Base model | `meta-llama/Llama-3.1-8B-Instruct` | | Task | Biomedical Entity Linking | | Dataset | QUAERO-EMEA | | Knowledge base | UMLS 2014AA | | Input | BigBio-like documents with mention spans and semantic groups | | Output | Ranked UMLS concept predictions | | Decoding | Semantic-guided constrained decoding | | Main metric | Recall@1 | ## Intended Use This model is intended for research on biomedical entity linking and document-level consistency. It assumes that mention spans and semantic groups are already provided. It does **not** perform named entity recognition. In a full pipeline, a NER model should first detect mentions and assign semantic groups, then LongBEL can normalize these mentions to UMLS concepts. ## Usage ### Loading the model ```python import torch from transformers import AutoModelForCausalLM model = AutoModelForCausalLM.from_pretrained( "AnonymousARR42/LongBEL_8B_QUAERO_EMEA", trust_remote_code=True, torch_dtype=torch.bfloat16, device_map="auto", ) ```` ### Inference example The model expects BigBio-like documents. Each entity should include a mention text, character offsets, and a semantic group in the `type` field. ```python num_beams = 5 bigbio_pages = [ { "id": "001", "document_id": "doc_001", "passages": [ { "id": "0", "type": "paragraph", "text": [ "Une femme enceinte de 29 ans s'est présentée avec une hypertension sévère, " "des céphalées et une douleur épigastrique. Les analyses biologiques ont montré " "une protéinurie et une légère élévation des enzymes hépatiques. Elle a été " "hospitalisée pendant la nuit avec une suspicion de PET et un traitement urgent " "a été débuté." ], "offsets": [[0, 321]], } ], "entities": [ { "id": "T1", "type": "Living Beings", "text": ["femme enceinte"], "offsets": [[4, 18]], }, { "id": "T2", "type": "Disorders", "text": ["hypertension sévère"], "offsets": [[54, 73]], }, { "id": "T3", "type": "Disorders", "text": ["protéinurie"], "offsets": [[158, 169]], }, { "id": "T4", "type": "Disorders", "text": ["PET"], "offsets": [[280, 283]], }, ], "events": [], "coreferences": [], "relations": [], } ] predictions = model.sample( bigbio_pages=bigbio_pages, num_beams=num_beams, ) for i in range(0, len(predictions), num_beams): mention = predictions[i]["mention"] print(f"## Mention {(i // num_beams) + 1}: {mention}") for j in range(num_beams): pred = predictions[i + j] print( f" - Beam {j + 1}:\n" f" Predicted concept name: {pred['pred_concept_name']}\n" f" Predicted code: {pred['pred_concept_code']}\n" f" Beam score: {pred['beam_score']:.3f}\n" ) ``` **Example Output:** ```text ## Mention 1: femme enceinte - Beam 1: Predicted concept name: Femmes enceintes Predicted code: C0033011 Beam score: 1.000 - Beam 2: Predicted concept name: Femmes (mariage) Predicted code: C0242665 Beam score: 0.000 - Beam 3: Predicted concept name: Femmes en postpartum Predicted code: C0032804 Beam score: 0.000 - Beam 4: Predicted concept name: Femmes en post-partum Predicted code: C0032804 Beam score: 0.000 - Beam 5: Predicted concept name: Females Predicted code: C0086287 Beam score: 0.000 ## Mention 2: hypertension sévère - Beam 1: Predicted concept name: Hypotension, non précisée Predicted code: C0020649 Beam score: 0.029 - Beam 2: Predicted concept name: Pression sanguine augmentée Predicted code: C0497247 Beam score: 0.007 - Beam 3: Predicted concept name: Hypertension; encephalopathy Predicted code: C1396475 Beam score: 0.001 - Beam 4: Predicted concept name: Hypertension;in pregnancy Predicted code: C0565599 Beam score: 0.001 - Beam 5: Predicted concept name: Pression sanguine non mesurable Predicted code: C0858911 Beam score: 0.000 ## Mention 3: protéinurie - Beam 1: Predicted concept name: Protéinurie Predicted code: C0033687 Beam score: 1.000 - Beam 2: Predicted concept name: Protéinurie - aggravée Predicted code: C0856146 Beam score: 0.002 - Beam 3: Predicted concept name: Protéine urinaire positive Predicted code: C0033687 Beam score: 0.000 - Beam 4: Predicted concept name: Protéine urinaire de Bence Jones présente Predicted code: C0854075 Beam score: 0.000 - Beam 5: Predicted concept name: Protéine urinaire de Bence Jones absente Predicted code: C0855589 Beam score: 0.000 ## Mention 4: PET - Beam 1: Predicted concept name: Petechial hemorrhage Predicted code: C0031256 Beam score: 0.073 - Beam 2: Predicted concept name: Petechial; hemorrhage Predicted code: C0031256 Beam score: 0.022 - Beam 3: Predicted concept name: Petechia Predicted code: C0031256 Beam score: 0.008 - Beam 4: Predicted concept name: PET - Pre-eclamptic toxaemia Predicted code: C0032914 Beam score: 0.001 - Beam 5: Predicted concept name: Petechial hemorrhages Predicted code: C0031256 Beam score: 0.000 ``` ### Saliency map example The model can also return token-level saliency maps during inference. ```python predictions, saliency_maps = model.sample( bigbio_pages=bigbio_pages, num_beams=num_beams, with_saliency_maps=True, ) model.display_saliency_map(saliency_maps[3]) ```` Example saliency map for the mention `PET`:

Saliency map for PET prediction

## Evaluation Entity linking performance is reported using Recall@1 with bootstrap confidence intervals. The best result is shown in **bold**, and the second-best result is underlined and ⭐ marks the main LongBEL-8B model. | Model | MM-ST21PV
(English) | QUAERO-EMEA
(French) | SympTEMIST
(Spanish) | DisTEMIST
(Spanish) | MedProcNER
(Spanish) | | :--- | :---: | :---: | :---: | :---: | :---: | | **Context-Free BEL** ||||| | | SciSpacy | 53.8 ± 1.0 | 37.1 ± 4.3 | 9.8 ± 1.3 | 21.1 ± 1.9 | 10.3 ± 1.2 | | SapBERT | 65.6 ± 1.0 | 59.7 ± 3.8 | 34.2 ± 2.0 | 38.6 ± 2.6 | 30.4 ± 2.1 | | CODER-all | 62.9 ± 1.1 | 66.9 ± 4.0 | 42.2 ± 2.2 | 47.0 ± 2.6 | 42.7 ± 2.1 | | SapBERT-all | 64.6 ± 1.1 | 67.9 ± 3.9 | 49.8 ± 2.4 | 49.6 ± 2.6 | 45.1 ± 2.2 | | BERGAMOT | 60.9 ± 1.1 | 63.8 ± 4.9 | 48.0 ± 2.7 | 48.9 ± 2.4 | 42.3 ± 2.2 | | **Local-Context BEL** ||||| | | ArboEL | 76.9 ± 0.9 | 63.0 ± 3.9 | 55.4 ± 2.5 | 54.7 ± 2.6 | 59.7 ± 2.6 | | GENRE / mBART-large | 69.6 ± 1.0 | 69.3 ± 5.4 | 59.8 ± 2.7 | 58.7 ± 2.7 | 66.0 ± 2.3 | | GENRE / Llama-1B | 73.1 ± 1.0 | 75.1 ± 3.6 | 60.5 ± 2.4 | 62.5 ± 2.3 | 67.4 ± 2.1 | | GENRE / Llama-8B | 75.0 ± 0.9 | 73.8 ± 4.0 | 61.7 ± 2.5 | 63.2 ± 2.5 | 68.3 ± 2.2 | | **Global-Context BEL: LongBEL** ||||| | | LongBEL-1B | 77.6 ± 0.9 | 74.5 ± 3.7 | 59.8 ± 2.5 | 61.9 ± 2.4 | 66.6 ± 2.1 | | LongBEL-1B + Ensemble | 78.6 ± 0.8 | 77.2 ± 3.0 | 61.8 ± 2.5 | 64.3 ± 2.2 | 69.0 ± 2.0 | | **⭐ LongBEL-8B** | 79.3 ± 0.8 | 75.4 ± 3.4 | 62.0 ± 2.6 | 63.6 ± 2.1 | 69.0 ± 2.1 | | LongBEL-8B + Ensemble | **80.0 ± 0.8** | **77.6 ± 3.0** | **63.3 ± 2.5** | **65.8 ± 2.2** | **71.0 ± 2.0** | The score reported for this checkpoint is the **single LongBEL-8B model**. The ensemble result requires fusing several LongBEL input configurations and is not produced by this checkpoint alone. ## Speed and Memory Measured on a single NVIDIA H100 80GB GPU. | Model | Model memory | Candidate memory | Speed | | ----------------------- | -----------: | ---------------: | --------------: | | GENRE-Llama-8B baseline | 28.6 GB | 5.4 GB | 38.2 mentions/s | | LongBEL-8B | 28.6 GB | 5.4 GB | 15.2 mentions/s | LongBEL has the same model memory footprint as the sentence-level Llama-8B baseline, but it is slower because it processes longer contexts and updates document-level memory during inference. ## Limitations This model assumes that mention spans and semantic groups are given. It does not perform mention detection. LongBEL is most useful when concepts recur within a document. When most concepts appear only once, the memory mechanism has less information to exploit. Because LongBEL uses previous predictions as memory, early mistakes can still influence later predictions. Robust memory training reduces this risk but does not remove it completely. This model is intended for research use. It should not be used for clinical decision-making without additional validation and human oversight. ## Reproducibility Code and evaluation scripts are available in this [GitHub repository](https://anonymous.4open.science/r/LongBEL-31AD). Trained model checkpoints and processed datasets are available in the anonymous Hugging Face collection associated with LongBEL.