---
tags:
- sentence-transformers
- sentence-similarity
- feature-extraction
- dense
- generated_from_trainer
- dataset_size:13270
- loss:OnlineContrastiveLoss
base_model: cambridgeltl/SapBERT-from-PubMedBERT-fulltext
widget:
- source_sentence: prostaglandin E
  sentences:
  - Prostaglandins E
  - profenamine
  - Serotonin
- source_sentence: PGE2
  sentences:
  - Dizocilpine Maleate
  - azelastine
  - Dinoprostone
- source_sentence: Dexamethasone
  sentences:
  - Liver Neoplasms
  - Neuroleptic Malignant Syndrome
  - Dexamethasone
- source_sentence: testosterone
  sentences:
  - Contracture
  - Testosterone
  - Retinal Diseases
- source_sentence: IBS
  sentences:
  - Irritable Bowel Syndrome
  - Propranolol
  - Flushing
pipeline_tag: sentence-similarity
library_name: sentence-transformers
---

# SentenceTransformer based on cambridgeltl/SapBERT-from-PubMedBERT-fulltext

This is a [sentence-transformers](https://www.SBERT.net) model finetuned from [cambridgeltl/SapBERT-from-PubMedBERT-fulltext](https://huggingface.co/cambridgeltl/SapBERT-from-PubMedBERT-fulltext). It maps sentences & paragraphs to a 768-dimensional dense vector space and can be used for semantic textual similarity, semantic search, paraphrase mining, text classification, clustering, and more.

## Model Details

### Model Description
- **Model Type:** Sentence Transformer
- **Base model:** [cambridgeltl/SapBERT-from-PubMedBERT-fulltext](https://huggingface.co/cambridgeltl/SapBERT-from-PubMedBERT-fulltext) <!-- at revision 090663c3ae57bf35ffe4d0d468a2a88d03051a4d -->
- **Maximum Sequence Length:** 512 tokens
- **Output Dimensionality:** 768 dimensions
- **Similarity Function:** Cosine Similarity
<!-- - **Training Dataset:** Unknown -->
<!-- - **Language:** Unknown -->
<!-- - **License:** Unknown -->

### Model Sources

- **Documentation:** [Sentence Transformers Documentation](https://sbert.net)
- **Repository:** [Sentence Transformers on GitHub](https://github.com/huggingface/sentence-transformers)
- **Hugging Face:** [Sentence Transformers on Hugging Face](https://huggingface.co/models?library=sentence-transformers)

### Full Model Architecture

```
SentenceTransformer(
  (0): Transformer({'max_seq_length': 512, 'do_lower_case': False, 'architecture': 'BertModel'})
  (1): Pooling({'word_embedding_dimension': 768, 'pooling_mode_cls_token': True, 'pooling_mode_mean_tokens': False, 'pooling_mode_max_tokens': False, 'pooling_mode_mean_sqrt_len_tokens': False, 'pooling_mode_weightedmean_tokens': False, 'pooling_mode_lasttoken': False, 'include_prompt': True})
)
```

## Usage

### Direct Usage (Sentence Transformers)

First install the Sentence Transformers library:

```bash
pip install -U sentence-transformers
```

Then you can load this model and run inference.
```python
from sentence_transformers import SentenceTransformer

# Download from the 🤗 Hub
model = SentenceTransformer("Stevenf232/fine-tuned-SapBERT3")
# Run inference
sentences = [
    'IBS',
    'Irritable Bowel Syndrome',
    'Flushing',
]
embeddings = model.encode(sentences)
print(embeddings.shape)
# [3, 768]

# Get the similarity scores for the embeddings
similarities = model.similarity(embeddings, embeddings)
print(similarities)
# tensor([[1.0000, 0.7023, 0.4470],
#         [0.7023, 1.0000, 0.4476],
#         [0.4470, 0.4476, 1.0000]])
```

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## Training Details

### Training Dataset

#### Unnamed Dataset

* Size: 13,270 training samples
* Columns: <code>mention</code>, <code>entity</code>, and <code>label</code>
* Approximate statistics based on the first 1000 samples:
  |         | mention                                                                          | entity                                                                           | label                           |
  |:--------|:---------------------------------------------------------------------------------|:---------------------------------------------------------------------------------|:--------------------------------|
  | type    | string                                                                           | string                                                                           | int                             |
  | details | <ul><li>min: 3 tokens</li><li>mean: 4.88 tokens</li><li>max: 39 tokens</li></ul> | <ul><li>min: 3 tokens</li><li>mean: 4.97 tokens</li><li>max: 36 tokens</li></ul> | <ul><li>True: 100.00%</li></ul> |
* Samples:
  | mention                                   | entity                             | label             |
  |:------------------------------------------|:-----------------------------------|:------------------|
  | <code>human immunodeficiency virus</code> | <code>HIV Infections</code>        | <code>True</code> |
  | <code>non-Hodgkin's lymphoma</code>       | <code>Lymphoma, Non-Hodgkin</code> | <code>True</code> |
  | <code>renal cell carsinom</code>          | <code>Carcinoma, Renal Cell</code> | <code>True</code> |
* Loss: [<code>OnlineContrastiveLoss</code>](https://sbert.net/docs/package_reference/sentence_transformer/losses.html#onlinecontrastiveloss)

### Evaluation Dataset

#### Unnamed Dataset

* Size: 12,795 evaluation samples
* Columns: <code>mention</code>, <code>entity</code>, and <code>label</code>
* Approximate statistics based on the first 1000 samples:
  |         | mention                                                                         | entity                                                                           | label                           |
  |:--------|:--------------------------------------------------------------------------------|:---------------------------------------------------------------------------------|:--------------------------------|
  | type    | string                                                                          | string                                                                           | int                             |
  | details | <ul><li>min: 3 tokens</li><li>mean: 4.7 tokens</li><li>max: 31 tokens</li></ul> | <ul><li>min: 3 tokens</li><li>mean: 4.99 tokens</li><li>max: 41 tokens</li></ul> | <ul><li>True: 100.00%</li></ul> |
* Samples:
  | mention                            | entity                             | label             |
  |:-----------------------------------|:-----------------------------------|:------------------|
  | <code>Postoperative myalgia</code> | <code>Pain, Postoperative</code>   | <code>True</code> |
  | <code>blood loss</code>            | <code>Postpartum Hemorrhage</code> | <code>True</code> |
  | <code>urethane</code>              | <code>Urethane</code>              | <code>True</code> |
* Loss: [<code>OnlineContrastiveLoss</code>](https://sbert.net/docs/package_reference/sentence_transformer/losses.html#onlinecontrastiveloss)

### Training Hyperparameters
#### Non-Default Hyperparameters

- `learning_rate`: 1e-05
- `optim`: adamw_torch

#### All Hyperparameters
<details><summary>Click to expand</summary>

- `overwrite_output_dir`: False
- `do_predict`: False
- `eval_strategy`: no
- `prediction_loss_only`: True
- `per_device_train_batch_size`: 8
- `per_device_eval_batch_size`: 8
- `per_gpu_train_batch_size`: None
- `per_gpu_eval_batch_size`: None
- `gradient_accumulation_steps`: 1
- `eval_accumulation_steps`: None
- `torch_empty_cache_steps`: None
- `learning_rate`: 1e-05
- `weight_decay`: 0.0
- `adam_beta1`: 0.9
- `adam_beta2`: 0.999
- `adam_epsilon`: 1e-08
- `max_grad_norm`: 1.0
- `num_train_epochs`: 3
- `max_steps`: -1
- `lr_scheduler_type`: linear
- `lr_scheduler_kwargs`: {}
- `warmup_ratio`: 0.0
- `warmup_steps`: 0
- `log_level`: passive
- `log_level_replica`: warning
- `log_on_each_node`: True
- `logging_nan_inf_filter`: True
- `save_safetensors`: True
- `save_on_each_node`: False
- `save_only_model`: False
- `restore_callback_states_from_checkpoint`: False
- `no_cuda`: False
- `use_cpu`: False
- `use_mps_device`: False
- `seed`: 42
- `data_seed`: None
- `jit_mode_eval`: False
- `bf16`: False
- `fp16`: False
- `fp16_opt_level`: O1
- `half_precision_backend`: auto
- `bf16_full_eval`: False
- `fp16_full_eval`: False
- `tf32`: None
- `local_rank`: 0
- `ddp_backend`: None
- `tpu_num_cores`: None
- `tpu_metrics_debug`: False
- `debug`: []
- `dataloader_drop_last`: False
- `dataloader_num_workers`: 0
- `dataloader_prefetch_factor`: None
- `past_index`: -1
- `disable_tqdm`: False
- `remove_unused_columns`: True
- `label_names`: None
- `load_best_model_at_end`: False
- `ignore_data_skip`: False
- `fsdp`: []
- `fsdp_min_num_params`: 0
- `fsdp_config`: {'min_num_params': 0, 'xla': False, 'xla_fsdp_v2': False, 'xla_fsdp_grad_ckpt': False}
- `fsdp_transformer_layer_cls_to_wrap`: None
- `accelerator_config`: {'split_batches': False, 'dispatch_batches': None, 'even_batches': True, 'use_seedable_sampler': True, 'non_blocking': False, 'gradient_accumulation_kwargs': None}
- `parallelism_config`: None
- `deepspeed`: None
- `label_smoothing_factor`: 0.0
- `optim`: adamw_torch
- `optim_args`: None
- `adafactor`: False
- `group_by_length`: False
- `length_column_name`: length
- `project`: huggingface
- `trackio_space_id`: trackio
- `ddp_find_unused_parameters`: None
- `ddp_bucket_cap_mb`: None
- `ddp_broadcast_buffers`: False
- `dataloader_pin_memory`: True
- `dataloader_persistent_workers`: False
- `skip_memory_metrics`: True
- `use_legacy_prediction_loop`: False
- `push_to_hub`: False
- `resume_from_checkpoint`: None
- `hub_model_id`: None
- `hub_strategy`: every_save
- `hub_private_repo`: None
- `hub_always_push`: False
- `hub_revision`: None
- `gradient_checkpointing`: False
- `gradient_checkpointing_kwargs`: None
- `include_inputs_for_metrics`: False
- `include_for_metrics`: []
- `eval_do_concat_batches`: True
- `fp16_backend`: auto
- `push_to_hub_model_id`: None
- `push_to_hub_organization`: None
- `mp_parameters`: 
- `auto_find_batch_size`: False
- `full_determinism`: False
- `torchdynamo`: None
- `ray_scope`: last
- `ddp_timeout`: 1800
- `torch_compile`: False
- `torch_compile_backend`: None
- `torch_compile_mode`: None
- `include_tokens_per_second`: False
- `include_num_input_tokens_seen`: no
- `neftune_noise_alpha`: None
- `optim_target_modules`: None
- `batch_eval_metrics`: False
- `eval_on_start`: False
- `use_liger_kernel`: False
- `liger_kernel_config`: None
- `eval_use_gather_object`: False
- `average_tokens_across_devices`: True
- `prompts`: None
- `batch_sampler`: batch_sampler
- `multi_dataset_batch_sampler`: proportional
- `router_mapping`: {}
- `learning_rate_mapping`: {}

</details>

### Training Logs
| Epoch  | Step | Training Loss |
|:------:|:----:|:-------------:|
| 0.3014 | 500  | 0.0153        |
| 0.6028 | 1000 | 0.0146        |
| 0.9042 | 1500 | 0.0123        |
| 1.2055 | 2000 | 0.0053        |
| 1.5069 | 2500 | 0.0022        |
| 1.8083 | 3000 | 0.0063        |
| 2.1097 | 3500 | 0.0039        |
| 2.4111 | 4000 | 0.0031        |
| 2.7125 | 4500 | 0.0017        |


### Framework Versions
- Python: 3.12.12
- Sentence Transformers: 5.1.2
- Transformers: 4.57.1
- PyTorch: 2.8.0+cu126
- Accelerate: 1.11.0
- Datasets: 4.0.0
- Tokenizers: 0.22.1

## Citation

### BibTeX

#### Sentence Transformers
```bibtex
@inproceedings{reimers-2019-sentence-bert,
    title = "Sentence-BERT: Sentence Embeddings using Siamese BERT-Networks",
    author = "Reimers, Nils and Gurevych, Iryna",
    booktitle = "Proceedings of the 2019 Conference on Empirical Methods in Natural Language Processing",
    month = "11",
    year = "2019",
    publisher = "Association for Computational Linguistics",
    url = "https://arxiv.org/abs/1908.10084",
}
```

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