README.md

---
id: sap_umls_MedRoBERTa.nl
name: sap_umls_MedRoBERTa.nl
description: >-
  MedRoBERTa.nl continued pre-training on hard medical terms pairs from the UMLS
  ontology, using the multi-similarity loss function
license: gpl-3.0
language: nl
tags:
- embedding
- bionlp
- biology
- science
- entity linking
- lexical semantic
- biomedical
pipeline_tag: feature-extraction
base_model:
- CLTL/MedRoBERTa.nl
---

# Model Card for Sap Umls Medroberta.Nl

The model was trained on medical entity triplets (anchor, term, synonym)

### Training specifics

```
epochs : 2
batch_size : 64
learning_rate : 5e-6
weight_decay : 1e-4
max_length : 30
loss : ms_loss
pairwise : true
type_of_triplets : all
agg_mode : CLS
```

### Expected input and output
The input should be a string of biomedical entity names, e.g., "covid infection" or "Hydroxychloroquine". The [CLS] embedding of the last layer is regarded as the output.

#### Extracting embeddings from sap_umls_MedRoBERTa.nl

The following script converts a list of strings (entity names) into embeddings.
```python
import numpy as np
import torch
from tqdm.auto import tqdm
from transformers import AutoTokenizer, AutoModel

tokenizer = AutoTokenizer.from_pretrained("UMCU/sap_umls_MedRoBERTa.nl")
model = AutoModel.from_pretrained("UMCU/sap_umls_MedRoBERTa.nl").cuda()

# replace with your own list of entity names
all_names = ["covid-19", "Coronavirus infection", "high fever", "Tumor of posterior wall of oropharynx"]

bs = 128 # batch size during inference
all_embs = []
for i in tqdm(np.arange(0, len(all_names), bs)):
    toks = tokenizer.batch_encode_plus(all_names[i:i+bs],
                                       padding="max_length",
                                       max_length=25,
                                       truncation=True,
                                       return_tensors="pt")
    toks_cuda = {}
    for k,v in toks.items():
        toks_cuda[k] = v.cuda()
    cls_rep = model(**toks_cuda)[0][:,0,:] # use CLS representation as the embedding
    all_embs.append(cls_rep.cpu().detach().numpy())

all_embs = np.concatenate(all_embs, axis=0)
```

# Wrapping it in SBERT
```python
from sentence_transformers import SentenceTransformer, models
```

# 1) Define the transformer module pointing at your checkpoint
```python
word_embedding_model = models.Transformer(
    "UMCU/sap_umls_MedRoBERTa.nl",
    max_seq_length=25
)
```

# 2) Pooling: use the [CLS] token representation
```python
pooling_model = models.Pooling(
    word_embedding_model.get_word_embedding_dimension(),
    pooling_mode_cls_token=True,
    pooling_mode_mean_token=False,
    pooling_mode_max_token=False
)
```

# 3) Build the SentenceTransformer
```python
sbert_model = SentenceTransformer(modules=[word_embedding_model, pooling_model])
sbert_model.cuda()  # move to GPU if available
```

# 4) Save it as an SBERT model

```python
save_path = "./sap_umls_sbert"
sbert_model.save(save_path)
```


# Now you can encode your list of phrases directly:
```python
all_names = [
    "covid-19",
    "Coronavirus infection",
    "high fever",
    "Tumor of posterior wall of oropharynx",
    # …etc.
]
```

# `.encode` handles batching/padding/truncation internally:
```python
all_embs = sbert_model.encode(
    all_names,
    batch_size=128,
    show_progress_bar=True,
    convert_to_numpy=True,
    normalize_embeddings=False   # or True if you want unit-norm embeddings
)
```

# Data description

Hard Dutch UMLS synonym pairs (terms referring to the same CUI). Dutch UMLS extended with matching Dutch SNOMEDCT term, and including English medication names


# Acknowledgement

This is part of the [DT4H project](https://www.datatools4heart.eu/).

# Doi and reference

...


For more details about training and eval, see SapBERT [github repo](https://github.com/cambridgeltl/sapbert).


### Citation
```bibtex
@inproceedings{liu-etal-2021-self,
    title = "Self-Alignment Pretraining for Biomedical Entity Representations",
    author = "Liu, Fangyu  and
      Shareghi, Ehsan  and
      Meng, Zaiqiao  and
      Basaldella, Marco  and
      Collier, Nigel",
    booktitle = "Proceedings of the 2021 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies",
    month = jun,
    year = "2021",
    address = "Online",
    publisher = "Association for Computational Linguistics",
    url = "https://www.aclweb.org/anthology/2021.naacl-main.334",
    pages = "4228--4238",
    abstract = "Despite the widespread success of self-supervised learning via masked language models (MLM), accurately capturing fine-grained semantic relationships in the biomedical domain remains a challenge. This is of paramount importance for entity-level tasks such as entity linking where the ability to model entity relations (especially synonymy) is pivotal. To address this challenge, we propose SapBERT, a pretraining scheme that self-aligns the representation space of biomedical entities. We design a scalable metric learning framework that can leverage UMLS, a massive collection of biomedical ontologies with 4M+ concepts. In contrast with previous pipeline-based hybrid systems, SapBERT offers an elegant one-model-for-all solution to the problem of medical entity linking (MEL), achieving a new state-of-the-art (SOTA) on six MEL benchmarking datasets. In the scientific domain, we achieve SOTA even without task-specific supervision. With substantial improvement over various domain-specific pretrained MLMs such as BioBERT, SciBERTand and PubMedBERT, our pretraining scheme proves to be both effective and robust.",
}
```

For more details about training/eval and other scripts, see CardioNER [github repo](https://github.com/DataTools4Heart/CardioNER).
and for more information on the background, see Datatools4Heart [Huggingface](https://huggingface.co/DT4H)/[Website](https://www.datatools4heart.eu/)