biencoder/README.md

metadata

tags:
  - sentence-transformers
  - sentence-similarity
  - feature-extraction
  - dense
  - generated_from_trainer
  - dataset_size:28932
  - loss:MultipleNegativesRankingLoss
base_model: cambridgeltl/SapBERT-from-PubMedBERT-fulltext
widget:
  - source_sentence: sleep
    sentences:
      - asleep
      - sleep
      - chest pain
  - source_sentence: shower
    sentences:
      - bathing
      - shower
      - pump
  - source_sentence: ulcers
    sentences:
      - ulceration
      - person name
      - ulcer
  - source_sentence: tunneling
    sentences:
      - tunnel
      - gangrene
      - surgery
  - source_sentence: tbd
    sentences:
      - stridor
      - undetermined
      - decibel
pipeline_tag: sentence-similarity
library_name: sentence-transformers

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

This is a sentence-transformers model finetuned from cambridgeltl/SapBERT-from-PubMedBERT-fulltext. It maps inputs to a 768-dimensional dense vector space and can be used for semantic textual similarity, semantic search, paraphrase mining, classification, clustering, and more.

Model Details

Model Description

• Model Type: Sentence Transformer
• Base model: cambridgeltl/SapBERT-from-PubMedBERT-fulltext
• Maximum Sequence Length: 48 tokens
• Output Dimensionality: 768 dimensions
• Similarity Function: Cosine Similarity
• Supported Modality: Text

Model Sources

• Documentation: Sentence Transformers Documentation
• Repository: Sentence Transformers on GitHub
• Hugging Face: Sentence Transformers on Hugging Face

Full Model Architecture

SentenceTransformer(
  (0): Transformer({'transformer_task': 'feature-extraction', 'modality_config': {'text': {'method': 'forward', 'method_output_name': 'last_hidden_state'}}, 'module_output_name': 'token_embeddings', 'architecture': 'BertModel'})
  (1): Pooling({'embedding_dimension': 768, 'pooling_mode': 'cls', 'include_prompt': True})
)

Usage

Direct Usage (Sentence Transformers)

First install the Sentence Transformers library:

pip install -U sentence-transformers

Then you can load this model and run inference.

from sentence_transformers import SentenceTransformer

# Download from the 🤗 Hub
model = SentenceTransformer("sentence_transformers_model_id")
# Run inference
sentences = [
    'tbd',
    'undetermined',
    'decibel',
]
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, 0.4227, 0.4667],
#         [0.4227, 1.0000, 0.3473],
#         [0.4667, 0.3473, 1.0000]])

Training Details

Training Dataset

Unnamed Dataset

• Size: 28,932 training samples
• Columns: anchor, positive, and negative
• Approximate statistics based on the first 100 samples:

  	anchor	positive	negative
  type	string	string	string
  modality	text	text	text
  details	min: 3 tokens mean: 6.06 tokens max: 18 tokens	min: 3 tokens mean: 5.9 tokens max: 17 tokens	min: 3 tokens mean: 6.68 tokens max: 17 tokens

• Samples:

  anchor	positive	negative
  shallow irregular breathing	abnormal breathing	slow shallow breathing
  mindful nutrition management	nutrition management	nutrition care
  rrr s murmur	cardiac bruit nos	functional cardiac murmur

• Loss: MultipleNegativesRankingLoss with these parameters:

  {
      "scale": 20.0,
      "similarity_fct": "cos_sim",
      "gather_across_devices": false,
      "directions": [
          "query_to_doc"
      ],
      "partition_mode": "joint",
      "hardness_mode": null,
      "hardness_strength": 0.0
  }
  

Training Hyperparameters

Non-Default Hyperparameters

• per_device_train_batch_size: 64
• num_train_epochs: 2
• learning_rate: 2e-05
• warmup_steps: 0.1
• fp16: True
• seed: 7
• data_seed: 7
• batch_sampler: no_duplicates

All Hyperparameters

Click to expand

• per_device_train_batch_size: 64
• num_train_epochs: 2
• max_steps: -1
• learning_rate: 2e-05
• lr_scheduler_type: linear
• lr_scheduler_kwargs: None
• warmup_steps: 0.1
• optim: adamw_torch_fused
• optim_args: None
• weight_decay: 0.0
• adam_beta1: 0.9
• adam_beta2: 0.999
• adam_epsilon: 1e-08
• optim_target_modules: None
• gradient_accumulation_steps: 1
• average_tokens_across_devices: True
• max_grad_norm: 1.0
• label_smoothing_factor: 0.0
• bf16: False
• fp16: True
• bf16_full_eval: False
• fp16_full_eval: False
• tf32: None
• gradient_checkpointing: False
• gradient_checkpointing_kwargs: None
• torch_compile: False
• torch_compile_backend: None
• torch_compile_mode: None
• use_liger_kernel: False
• liger_kernel_config: None
• use_cache: False
• neftune_noise_alpha: None
• torch_empty_cache_steps: None
• auto_find_batch_size: False
• log_on_each_node: True
• logging_nan_inf_filter: True
• include_num_input_tokens_seen: no
• log_level: passive
• log_level_replica: warning
• disable_tqdm: False
• project: huggingface
• trackio_space_id: None
• trackio_bucket_id: None
• trackio_static_space_id: None
• per_device_eval_batch_size: 8
• prediction_loss_only: True
• eval_on_start: False
• eval_do_concat_batches: True
• eval_use_gather_object: False
• eval_accumulation_steps: None
• include_for_metrics: []
• batch_eval_metrics: False
• save_only_model: False
• save_on_each_node: False
• enable_jit_checkpoint: False
• push_to_hub: False
• hub_private_repo: None
• hub_model_id: None
• hub_strategy: every_save
• hub_always_push: False
• hub_revision: None
• load_best_model_at_end: False
• ignore_data_skip: False
• restore_callback_states_from_checkpoint: False
• full_determinism: False
• seed: 7
• data_seed: 7
• use_cpu: False
• 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
• dataloader_drop_last: False
• dataloader_num_workers: 0
• dataloader_pin_memory: True
• dataloader_persistent_workers: False
• dataloader_prefetch_factor: None
• dataloader_multiprocessing_context: None
• dataloader_in_order: True
• remove_unused_columns: True
• label_names: None
• train_sampling_strategy: random
• length_column_name: length
• ddp_find_unused_parameters: None
• ddp_bucket_cap_mb: None
• ddp_broadcast_buffers: False
• ddp_static_graph: None
• ddp_backend: None
• ddp_timeout: 1800
• fsdp: None
• fsdp_config: None
• deepspeed: None
• debug: []
• skip_memory_metrics: True
• do_predict: False
• resume_from_checkpoint: None
• local_rank: -1
• prompts: None
• batch_sampler: no_duplicates
• multi_dataset_batch_sampler: proportional
• router_mapping: {}
• learning_rate_mapping: {}
• warmup_ratio: None

Training Logs

Epoch	Step	Training Loss
0.1104	50	1.6316
0.2208	100	1.4744
0.3311	150	1.3472
0.4415	200	1.2047
0.5519	250	1.2150
0.6623	300	1.1534
0.7726	350	1.1347
0.8830	400	1.1183
0.9934	450	1.0440
1.1038	500	0.8791
1.2141	550	0.8986
1.3245	600	0.7986
1.4349	650	0.8086
1.5453	700	0.8054
1.6556	750	0.7862
1.7660	800	0.7940
1.8764	850	0.8011
1.9868	900	0.7768

Training Time

• Training: 11.6 minutes

Framework Versions

• Python: 3.13.7
• Sentence Transformers: 6.1.0
• Transformers: 5.20.1
• PyTorch: 2.11.0+cu128
• Accelerate: 1.15.0
• Datasets: 5.1.0
• Tokenizers: 0.23.3

Additional Resources

• Training and Finetuning Embedding Models with Sentence Transformers: the end-to-end guide for training or finetuning Sentence Transformer models.
• Introduction to Matryoshka Embedding Models: variable-size embeddings that can be truncated with minimal quality loss.
• Binary and Scalar Embedding Quantization for Significantly Faster & Cheaper Retrieval: post-training compression of embedding vectors.
• Multimodal Embedding & Reranker Models with Sentence Transformers: use text, image, audio, and video models through the same API.
• Training and Finetuning Multimodal Embedding & Reranker Models with Sentence Transformers: train multimodal embedding models, with a Visual Document Retrieval walkthrough.

Citation

BibTeX

Sentence Transformers

@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",
}

MultipleNegativesRankingLoss

@misc{oord2019representationlearningcontrastivepredictive,
      title={Representation Learning with Contrastive Predictive Coding},
      author={Aaron van den Oord and Yazhe Li and Oriol Vinyals},
      year={2019},
      eprint={1807.03748},
      archivePrefix={arXiv},
      primaryClass={cs.LG},
      url={https://arxiv.org/abs/1807.03748},
}