UMLS-ED-Bioformer-8L-V-1

SentenceTransformer

This is a sentence-transformers model trained. It maps sentences & paragraphs to a 512-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:** [Unknown](https://huggingface.co/unknown) -->

• Maximum Sequence Length: 512 tokens
• Output Dimensionality: 512 tokens
• 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': 512, 'do_lower_case': False}) with Transformer model: BertModel 
  (1): Pooling({'word_embedding_dimension': 512, '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})
)

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("pankajrajdeo/328500_bioformer_8L")
# Run inference
sentences = [
    'vägtrafikolyckor',
    'accidente vial',
    'trimeresurus andersoni',
]
embeddings = model.encode(sentences)
print(embeddings.shape)
# [3, 512]

# 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: 9,358,675 training samples
• Columns: <code>anchor</code>, <code>positive</code>, and <code>negative</code>
• Approximate statistics based on the first 1000 samples:

  	anchor	positive	negative
  type	string	string	string
  details	<ul><li>min: 6 tokens</li><li>mean: 12.84 tokens</li><li>max: 23 tokens</li></ul>	<ul><li>min: 3 tokens</li><li>mean: 15.45 tokens</li><li>max: 187 tokens</li></ul>	<ul><li>min: 3 tokens</li><li>mean: 14.75 tokens</li><li>max: 91 tokens</li></ul>

• Samples:

  anchor	positive	negative
  <code>(131)i-makroaggregerat albumin</code>	<code>macroagrégats d'albumine humaine marquée à l'iode 131</code>	<code>1-acylglycerophosphorylinositol</code>
  <code>(131)i-makroaggregerat albumin</code>	<code>albumin, radio-iodinated serum</code>	<code>allo-aromadendrane-10alpha,14-diol</code>
  <code>(131)i-makroaggregerat albumin</code>	<code>serum albumin, radio iodinated</code>	<code>acquired zygomatic hyperplasia</code>

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

  {
      "distance_metric": "TripletDistanceMetric.EUCLIDEAN",
      "triplet_margin": 5
  }
  

Evaluation Dataset

Unnamed Dataset

• Size: 820,102 evaluation samples
• Columns: <code>anchor</code>, <code>positive</code>, and <code>negative</code>
• Approximate statistics based on the first 1000 samples:

  	anchor	positive	negative
  type	string	string	string
  details	<ul><li>min: 3 tokens</li><li>mean: 10.54 tokens</li><li>max: 20 tokens</li></ul>	<ul><li>min: 3 tokens</li><li>mean: 13.21 tokens</li><li>max: 183 tokens</li></ul>	<ul><li>min: 3 tokens</li><li>mean: 14.98 tokens</li><li>max: 322 tokens</li></ul>

• Samples:

  anchor	positive	negative
  <code>15-ketosteryloleathydrolase</code>	<code>steroid esterase, lipoidal</code>	<code>glutamic acid-lysine-tyrosine terpolymer</code>
  <code>15-ketosteryloleathydrolase</code>	<code>hydrolase, cholesterol ester</code>	<code>unionicola parvipora</code>
  <code>15-ketosteryloleathydrolase</code>	<code>acylhydrolase, sterol ester</code>	<code>mayamaea fossalis var. fossalis</code>

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

  {
      "distance_metric": "TripletDistanceMetric.EUCLIDEAN",
      "triplet_margin": 5
  }
  

Training Hyperparameters

Non-Default Hyperparameters

• eval_strategy: steps
• per_device_train_batch_size: 128
• learning_rate: 2e-05
• num_train_epochs: 10
• warmup_ratio: 0.1
• fp16: True
• load_best_model_at_end: True

All Hyperparameters

<details><summary>Click to expand</summary>

• overwrite_output_dir: False
• do_predict: False
• eval_strategy: steps
• prediction_loss_only: True
• per_device_train_batch_size: 128
• 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: 2e-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: 10
• max_steps: -1
• lr_scheduler_type: linear
• lr_scheduler_kwargs: {}
• warmup_ratio: 0.1
• 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: True
• 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: True
• 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: False
• hub_always_push: False
• gradient_checkpointing: False
• gradient_checkpointing_kwargs: None
• include_inputs_for_metrics: False
• 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
• batch_sampler: batch_sampler
• multi_dataset_batch_sampler: proportional

</details>

Training Logs

<details><summary>Click to expand</summary> </details>

Framework Versions

• Python: 3.9.16
• Sentence Transformers: 3.1.1
• Transformers: 4.45.2
• PyTorch: 2.4.1+cu121
• Accelerate: 1.0.0
• Datasets: 3.0.1
• Tokenizers: 0.20.0

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",
}

TripletLoss

@misc{hermans2017defense,
    title={In Defense of the Triplet Loss for Person Re-Identification},
    author={Alexander Hermans and Lucas Beyer and Bastian Leibe},
    year={2017},
    eprint={1703.07737},
    archivePrefix={arXiv},
    primaryClass={cs.CV}
}

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