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README.md

@@ -16,6 +16,7 @@ tags:
   - healthcare
   - umls
   - quaero
+  - emea
   - text-generation
   - constrained-decoding
   - causal-lm
@@ -172,114 +173,134 @@ for i in range(0, len(predictions), num_beams):
 **Example Output:**
 
 ```text
-## Mention 1: pregnant woman
+## Mention 1: femme enceinte
    - Beam 1:
-   - Predicted concept name:Pregnant Woman
-   - Predicted code: C0033011
-   - Beam score: 1.000
+     Predicted concept name: Femmes enceintes
+     Predicted code: C0033011
+     Beam score: 1.000
 
    - Beam 2:
-   - Predicted concept name:Pregnant woman
-   - Predicted code: C0033011
-   - Beam score: 0.003
+     Predicted concept name: Femmes (mariage)
+     Predicted code: C0242665
+     Beam score: 0.000
 
    - Beam 3:
-   - Predicted concept name:Pregnant woman (person)
-   - Predicted code: C0033011
-   - Beam score: 0.001
+     Predicted concept name: Femmes en postpartum
+     Predicted code: C0032804
+     Beam score: 0.000
 
    - Beam 4:
-   - Predicted concept name:Pregnancy Partner
-   - Predicted code: C3538996
-   - Beam score: 0.000
+     Predicted concept name: Femmes en post-partum
+     Predicted code: C0032804
+     Beam score: 0.000
 
    - Beam 5:
-   - Predicted concept name:Pregnant woman (person)
-   - Predicted code: C0033011
-   - Beam score: 0.000
+     Predicted concept name: Females
+     Predicted code: C0086287
+     Beam score: 0.000
 
-## Mention 2: severe-range hypertension
+## Mention 2: hypertension sévère
    - Beam 1:
-   - Predicted concept name:Hypertensive disease
-   - Predicted code: C0020538
-   - Beam score: 0.078
+     Predicted concept name: Hypotension, non précisée
+     Predicted code: C0020649
+     Beam score: 0.029
 
    - Beam 2:
-   - Predicted concept name:Hypertension (in some patients)
-   - Predicted code: C3280936
-   - Beam score: 0.022
+     Predicted concept name: Pression sanguine augmentée
+     Predicted code: C0497247
+     Beam score: 0.007
 
    - Beam 3:
-   - Predicted concept name:Hypertensive disease (disorder)
-   - Predicted code: C0020538
-   - Beam score: 0.010
+     Predicted concept name: Hypertension; encephalopathy
+     Predicted code: C1396475
+     Beam score: 0.001
 
    - Beam 4:
-   - Predicted concept name:Hypertension, severe
-   - Predicted code: C4013784
-   - Beam score: 0.010
+     Predicted concept name: Hypertension;in pregnancy
+     Predicted code: C0565599
+     Beam score: 0.001
 
    - Beam 5:
-   - Predicted concept name:Hypertension (patient A)
-   - Predicted code: C4313262
-   - Beam score: 0.004
+     Predicted concept name: Pression sanguine non mesurable
+     Predicted code: C0858911
+     Beam score: 0.000
 
-## Mention 3: proteinuria
+## Mention 3: protéinurie
    - Beam 1:
-   - Predicted concept name:Proteinurias
-   - Predicted code: C0033687
-   - Beam score: 1.000
+     Predicted concept name: Protéinurie
+     Predicted code: C0033687
+     Beam score: 1.000
 
    - Beam 2:
-   - Predicted concept name:Proteinuric diabetic nephropathy (disorder)
-   - Predicted code: C0403519
-   - Beam score: 0.003
+     Predicted concept name: Protéinurie - aggravée
+     Predicted code: C0856146
+     Beam score: 0.002
 
    - Beam 3:
-   - Predicted concept name:Proteinuria
-   - Predicted code: C0033687
-   - Beam score: 0.003
+     Predicted concept name: Protéine urinaire positive
+     Predicted code: C0033687
+     Beam score: 0.000
 
    - Beam 4:
-   - Predicted concept name:Proteinuric diabetic nephropathy
-   - Predicted code: C0403519
-   - Beam score: 0.002
+     Predicted concept name: Protéine urinaire de Bence Jones présente
+     Predicted code: C0854075
+     Beam score: 0.000
 
    - Beam 5:
-   - Predicted concept name:Proteinuric hypertension of pregnancy (disorder)
-   - Predicted code: C0032914
-   - Beam score: 0.001
+     Predicted concept name: Protéine urinaire de Bence Jones absente
+     Predicted code: C0855589
+     Beam score: 0.000
 
 ## Mention 4: PET
    - Beam 1:
-   - Predicted concept name:PET - Pre-eclamptic toxemia
-   - Predicted code: C0032914
-   - Beam score: 0.075
+     Predicted concept name: Petechial hemorrhage
+     Predicted code: C0031256
+     Beam score: 0.073
 
    - Beam 2:
-   - Predicted concept name:PET - Pre-eclamptic toxaemia
-   - Predicted code: C0032914
-   - Beam score: 0.039
+     Predicted concept name: Petechial; hemorrhage
+     Predicted code: C0031256
+     Beam score: 0.022
 
    - Beam 3:
-   - Predicted concept name:Preeclamptic toxemia
-   - Predicted code: C2931877
-   - Beam score: 0.027
+     Predicted concept name: Petechia
+     Predicted code: C0031256
+     Beam score: 0.008
 
    - Beam 4:
-   - Predicted concept name:Preeclampsia
-   - Predicted code: C0032914
-   - Beam score: 0.023
+     Predicted concept name: PET - Pre-eclamptic toxaemia
+     Predicted code: C0032914
+     Beam score: 0.001
 
    - Beam 5:
-   - Predicted concept name:Preeclampsia with Severe Features
-   - Predicted code: C0341950
-   - Beam score: 0.019
+     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`:
+
+<p align="center">
+  <img src="saliency_map.png" alt="Saliency map for PET prediction" width="900">
+</p>
+
 ## 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 <u>underlined</u>.
+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 <u>underlined</u> and ⭐ marks the main LongBEL-8B model.
 
 | Model | MM-ST21PV<br>(English) | QUAERO-EMEA<br>(French) | SympTEMIST<br>(Spanish) | DisTEMIST<br>(Spanish) | MedProcNER<br>(Spanish) |
 | :--- | :---: | :---: | :---: | :---: | :---: |
@@ -297,7 +318,7 @@ Entity linking performance is reported using Recall@1 with bootstrap confidence
 | **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 | <u>77.2 ± 3.0</u> | 61.8 ± 2.5 | <u>64.3 ± 2.2</u> | <u>69.0 ± 2.0</u> |
-| **LongBEL-8B** | <u>79.3 ± 0.8</u> | 75.4 ± 3.4 | <u>62.0 ± 2.6</u> | 63.6 ± 2.1 | <u>69.0 ± 2.1</u> |
+| **⭐ LongBEL-8B** | <u>79.3 ± 0.8</u> | 75.4 ± 3.4 | <u>62.0 ± 2.6</u> | 63.6 ± 2.1 | <u>69.0 ± 2.1</u> |
 | 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.
@@ -327,17 +348,4 @@ This model is intended for research use. It should not be used for clinical deci
 
 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.
-
-<!-- ## Citation
-
-If you use this model, please cite the LongBEL paper.
-
-```bibtex
-@inproceedings{longbel2026,
-  title = {LongBEL: Long-Context and Document-Consistent Biomedical Entity Linking},
-  author = {Anonymous},
-  booktitle = {Anonymous submission},
-  year = {2026}
-}
-``` -->
+Trained model checkpoints and processed datasets are available in the anonymous Hugging Face collection associated with LongBEL.