Add new SentenceTransformer model

1_Pooling/config.json

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+{
+    "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
+}

README.md

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+---
+tags:
+- sentence-transformers
+- sentence-similarity
+- feature-extraction
+- dense
+- generated_from_trainer
+- dataset_size:13270
+- loss:ContrastiveLoss
+base_model: cambridgeltl/SapBERT-from-PubMedBERT-fulltext
+widget:
+- source_sentence: PGE2
+  sentences:
+  - Dinoprostone
+  - Cardiovascular Diseases
+  - Seizures
+- source_sentence: heparin
+  sentences:
+  - Heart Failure
+  - Hyperalgesia
+  - Heparin
+- source_sentence: bipolar mania
+  sentences:
+  - Mood Disorders
+  - Serotonin
+  - Bipolar Disorder
+- source_sentence: cardiac arrhythmia
+  sentences:
+  - Acquired Immunodeficiency Syndrome
+  - Arrhythmias, Cardiac
+  - Hyperemia
+- source_sentence: pulmonary hypertension
+  sentences:
+  - Hypertension, Pulmonary
+  - cabergoline
+  - Neuroleptic Malignant Syndrome
+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-SapBERT4")
+# Run inference
+sentences = [
+    'pulmonary hypertension',
+    'Hypertension, Pulmonary',
+    'Neuroleptic Malignant Syndrome',
+]
+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, 0.9967, 0.4133],
+#         [0.9967, 1.0000, 0.4165],
+#         [0.4133, 0.4165, 1.0000]])
+```
+
+<!--
+### Direct Usage (Transformers)
+
+<details><summary>Click to see the direct usage in Transformers</summary>
+
+</details>
+-->
+
+<!--
+### Downstream Usage (Sentence Transformers)
+
+You can finetune this model on your own dataset.
+
+<details><summary>Click to expand</summary>
+
+</details>
+-->
+
+<!--
+### Out-of-Scope Use
+
+*List how the model may foreseeably be misused and address what users ought not to do with the model.*
+-->
+
+<!--
+## Bias, Risks and Limitations
+
+*What are the known or foreseeable issues stemming from this model? You could also flag here known failure cases or weaknesses of the model.*
+-->
+
+<!--
+### Recommendations
+
+*What are recommendations with respect to the foreseeable issues? For example, filtering explicit content.*
+-->
+
+## 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>1: 100.00%</li></ul> |
+* Samples:
+  | mention                                   | entity                             | label          |
+  |:------------------------------------------|:-----------------------------------|:---------------|
+  | <code>human immunodeficiency virus</code> | <code>HIV Infections</code>        | <code>1</code> |
+  | <code>non-Hodgkin's lymphoma</code>       | <code>Lymphoma, Non-Hodgkin</code> | <code>1</code> |
+  | <code>renal cell carsinom</code>          | <code>Carcinoma, Renal Cell</code> | <code>1</code> |
+* Loss: [<code>ContrastiveLoss</code>](https://sbert.net/docs/package_reference/sentence_transformer/losses.html#contrastiveloss) with these parameters:
+  ```json
+  {
+      "distance_metric": "SiameseDistanceMetric.COSINE_DISTANCE",
+      "margin": 0.5,
+      "size_average": true
+  }
+  ```
+
+### 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>1: 100.00%</li></ul> |
+* Samples:
+  | mention                            | entity                             | label          |
+  |:-----------------------------------|:-----------------------------------|:---------------|
+  | <code>Postoperative myalgia</code> | <code>Pain, Postoperative</code>   | <code>1</code> |
+  | <code>blood loss</code>            | <code>Postpartum Hemorrhage</code> | <code>1</code> |
+  | <code>urethane</code>              | <code>Urethane</code>              | <code>1</code> |
+* Loss: [<code>ContrastiveLoss</code>](https://sbert.net/docs/package_reference/sentence_transformer/losses.html#contrastiveloss) with these parameters:
+  ```json
+  {
+      "distance_metric": "SiameseDistanceMetric.COSINE_DISTANCE",
+      "margin": 0.5,
+      "size_average": true
+  }
+  ```
+
+### 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  | 0.0042        |
+| 0.6028 | 1000 | 0.0034        |
+| 0.9042 | 1500 | 0.0032        |
+| 1.2055 | 2000 | 0.0022        |
+| 1.5069 | 2500 | 0.002         |
+| 1.8083 | 3000 | 0.0023        |
+| 2.1097 | 3500 | 0.0019        |
+| 2.4111 | 4000 | 0.0017        |
+| 2.7125 | 4500 | 0.0018        |
+
+
+### 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",
+}
+```
+
+#### ContrastiveLoss
+```bibtex
+@inproceedings{hadsell2006dimensionality,
+    author={Hadsell, R. and Chopra, S. and LeCun, Y.},
+    booktitle={2006 IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR'06)},
+    title={Dimensionality Reduction by Learning an Invariant Mapping},
+    year={2006},
+    volume={2},
+    number={},
+    pages={1735-1742},
+    doi={10.1109/CVPR.2006.100}
+}
+```
+
+<!--
+## Glossary
+
+*Clearly define terms in order to be accessible across audiences.*
+-->
+
+<!--
+## Model Card Authors
+
+*Lists the people who create the model card, providing recognition and accountability for the detailed work that goes into its construction.*
+-->
+
+<!--
+## Model Card Contact
+
+*Provides a way for people who have updates to the Model Card, suggestions, or questions, to contact the Model Card authors.*
+-->

config.json

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+{
+  "architectures": [
+    "BertModel"
+  ],
+  "attention_probs_dropout_prob": 0.1,
+  "classifier_dropout": null,
+  "dtype": "float32",
+  "gradient_checkpointing": false,
+  "hidden_act": "gelu",
+  "hidden_dropout_prob": 0.1,
+  "hidden_size": 768,
+  "initializer_range": 0.02,
+  "intermediate_size": 3072,
+  "layer_norm_eps": 1e-12,
+  "max_position_embeddings": 512,
+  "model_type": "bert",
+  "num_attention_heads": 12,
+  "num_hidden_layers": 12,
+  "pad_token_id": 0,
+  "position_embedding_type": "absolute",
+  "transformers_version": "4.57.1",
+  "type_vocab_size": 2,
+  "use_cache": true,
+  "vocab_size": 30522
+}

config_sentence_transformers.json

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+{
+  "model_type": "SentenceTransformer",
+  "__version__": {
+    "sentence_transformers": "5.1.2",
+    "transformers": "4.57.1",
+    "pytorch": "2.8.0+cu126"
+  },
+  "prompts": {
+    "query": "",
+    "document": ""
+  },
+  "default_prompt_name": null,
+  "similarity_fn_name": "cosine"
+}

model.safetensors

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+oid sha256:75273e0bcecc6995e33b6f3bbe2962f8acaa9e93c3641413f008f21a6e73a4aa
+size 437951328

modules.json

@@ -0,0 +1,14 @@
+[
+  {
+    "idx": 0,
+    "name": "0",
+    "path": "",
+    "type": "sentence_transformers.models.Transformer"
+  },
+  {
+    "idx": 1,
+    "name": "1",
+    "path": "1_Pooling",
+    "type": "sentence_transformers.models.Pooling"
+  }
+]

sentence_bert_config.json

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+{
+    "max_seq_length": 512,
+    "do_lower_case": false
+}

special_tokens_map.json

@@ -0,0 +1,7 @@
+{
+  "cls_token": "[CLS]",
+  "mask_token": "[MASK]",
+  "pad_token": "[PAD]",
+  "sep_token": "[SEP]",
+  "unk_token": "[UNK]"
+}

tokenizer_config.json

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+{
+  "added_tokens_decoder": {
+    "0": {
+      "content": "[PAD]",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "1": {
+      "content": "[UNK]",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "2": {
+      "content": "[CLS]",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "3": {
+      "content": "[SEP]",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "4": {
+      "content": "[MASK]",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    }
+  },
+  "clean_up_tokenization_spaces": true,
+  "cls_token": "[CLS]",
+  "do_basic_tokenize": true,
+  "do_lower_case": true,
+  "extra_special_tokens": {},
+  "full_tokenizer_file": null,
+  "mask_token": "[MASK]",
+  "model_max_length": 1000000000000000019884624838656,
+  "never_split": null,
+  "pad_token": "[PAD]",
+  "sep_token": "[SEP]",
+  "strip_accents": null,
+  "tokenize_chinese_chars": true,
+  "tokenizer_class": "BertTokenizer",
+  "unk_token": "[UNK]"
+}