heal-protocol-embeddings

SentenceTransformer based on sentence-transformers/all-MiniLM-L6-v2

This is a sentence-transformers model finetuned from sentence-transformers/all-MiniLM-L6-v2. It maps sentences & paragraphs to a 384-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: sentence-transformers/all-MiniLM-L6-v2 <!-- at revision fa97f6e7cb1a59073dff9e6b13e2715cf7475ac9 -->
• Maximum Sequence Length: 256 tokens
• Output Dimensionality: 384 dimensions
• Similarity Function: Cosine Similarity

<!-- - **Training Dataset:** Unknown --> <!-- - **Language:** Unknown --> <!-- - **License:** Unknown -->

Model Sources

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

Full Model Architecture

SentenceTransformer(
  (0): Transformer({'max_seq_length': 256, 'do_lower_case': False}) with Transformer model: BertModel 
  (1): Pooling({'word_embedding_dimension': 384, 'pooling_mode_cls_token': False, 'pooling_mode_mean_tokens': True, 'pooling_mode_max_tokens': False, 'pooling_mode_mean_sqrt_len_tokens': False, 'pooling_mode_weightedmean_tokens': False, 'pooling_mode_lasttoken': False, 'include_prompt': True})
  (2): Normalize()
)

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 = [
    'To evaluate the cost-effectiveness of ED-initiated buprenorphine with peer navigator support compared to enhanced referral to treatment.',
    'Concerns about withdrawal precipitation',
    '11.1.2 Steering Committee\n\nComposition:\n- Executive Committee members\n- Site investigators\n- Patient/community representatives\n- Key co-investigators\n\nResponsibilities:\n- Protocol revisions\n- Implementation monitoring\n- Recruitment oversight\n- Review of study progress\n- Addressing operational challenges',
]
embeddings = model.encode(sentences)
print(embeddings.shape)
# [3, 384]

# Get the similarity scores for the embeddings
similarities = model.similarity(embeddings, embeddings)
print(similarities.shape)
# [3, 3]

<!-- ### 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: 247,936 training samples
• Columns: <code>sentence_0</code>, <code>sentence_1</code>, and <code>label</code>
• Approximate statistics based on the first 1000 samples:

  	sentence_0	sentence_1	label
  type	string	string	float
  details	<ul><li>min: 3 tokens</li><li>mean: 48.16 tokens</li><li>max: 256 tokens</li></ul>	<ul><li>min: 3 tokens</li><li>mean: 44.76 tokens</li><li>max: 256 tokens</li></ul>	<ul><li>min: 0.5</li><li>mean: 0.5</li><li>max: 1.0</li></ul>

• Samples:

  sentence_0	sentence_1	label
  <code>10.4 Participant Confidentiality</code>	<code>9.1.1 Data and Safety Monitoring Board (DSMB)<br><br>An independent DSMB will be established, consisting of experts in emergency medicine, addiction medicine, biostatistics, and ethics. The DSMB will:<br>- Review and approve the monitoring plan<br>- Meet at least annually to review study progress and safety<br>- Review any serious adverse events<br>- Make recommendations regarding study continuation or modification</code>	<code>0.5</code>
  <code>7.1 Randomization<br><br>Participants will be randomly assigned in a 1:1 ratio to receive either BUP-NX or XR-NTX using a computer-generated randomization sequence with permuted blocks of varying sizes. Randomization will be stratified by site and by opioid type (short-acting prescription opioids, heroin, or fentanyl as primary opioid of use).</code>	<code>10.3 Risk Mitigation</code>	<code>0.5</code>
  <code>11.1 Study Leadership and Governance</code>	<code>To examine patient perspectives on intervention acceptability and barriers/facilitators to engagement through qualitative interviews with a subset of participants.</code>	<code>0.5</code>

• Loss: <code>CosineSimilarityLoss</code> with these parameters:

  {
      "loss_fct": "torch.nn.modules.loss.MSELoss"
  }
  

Training Hyperparameters

Non-Default Hyperparameters

• per_device_train_batch_size: 16
• per_device_eval_batch_size: 16
• multi_dataset_batch_sampler: round_robin

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: 16
• per_device_eval_batch_size: 16
• 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: 5e-05
• weight_decay: 0.0
• adam_beta1: 0.9
• adam_beta2: 0.999
• adam_epsilon: 1e-08
• max_grad_norm: 1
• 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
• use_ipex: 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}
• deepspeed: None
• label_smoothing_factor: 0.0
• optim: adamw_torch
• optim_args: None
• adafactor: False
• group_by_length: False
• length_column_name: length
• 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
• 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
• dispatch_batches: None
• split_batches: None
• include_tokens_per_second: False
• include_num_input_tokens_seen: False
• neftune_noise_alpha: None
• optim_target_modules: None
• batch_eval_metrics: False
• eval_on_start: False
• use_liger_kernel: False
• eval_use_gather_object: False
• average_tokens_across_devices: False
• prompts: None
• batch_sampler: batch_sampler
• multi_dataset_batch_sampler: round_robin

</details>

Training Logs

Framework Versions

• Python: 3.13.2
• Sentence Transformers: 3.4.1
• Transformers: 4.49.0
• PyTorch: 2.6.0
• Accelerate: 1.4.0
• Datasets: 3.3.2
• Tokenizers: 0.21.0

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",
}

HEAL Protocol Embeddings

This model is fine-tuned from all-MiniLM-L6-v2 on HEAL Initiative clinical protocols.

Performance Evaluation

Comparison with OpenAI embeddings:

Key Findings

• Improved faithfulness to source material
• Maintained high answer relevancy
• Trade-off in context recall

Future Improvements

1. Retrieval Strategy

   • Implement hybrid search combining semantic and keyword matching
   • Add re-ranking for better result ordering

2. Model Architecture

   • Experiment with larger base models
   • Fine-tune with domain-specific loss functions

3. Data Processing

   • Optimize chunking strategy
   • Increase training data diversity

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