lsy9874205/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]

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Downstream Usage (Sentence Transformers)

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Training Details

Training Dataset

Unnamed Dataset

• —Size: 247,936 training samples
• —Columns: <code>sentence0</code>, <code>sentence1</code>, and <code>label</code>
• —Approximate statistics based on the first 1000 samples: | | sentence0 | sentence1 | 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: | sentence0 | sentence1 | 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: {'minnumparams': 0, 'xla': False, 'xlafsdpv2': False, 'xlafsdpgrad_ckpt': False}
• —fsdp_transformer_layer_cls_to_wrap: None
• —accelerator_config: {'splitbatches': False, 'dispatchbatches': None, 'evenbatches': True, 'useseedablesampler': True, 'nonblocking': False, 'gradientaccumulationkwargs': 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. 1.Retrieval Strategy
2. 2.Implement hybrid search combining semantic and keyword matching
3. 3.Add re-ranking for better result ordering

1. 1.Model Architecture
2. 2.Experiment with larger base models
3. 3.Fine-tune with domain-specific loss functions

1. 1.Data Processing
2. 2.Optimize chunking strategy
3. 3.Increase training data diversity <!--

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