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harshitsoni1903
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sapbert-finetuned-semra

Sentence Similarity
sentence-transformers
Safetensors
bert
feature-extraction
dense
Generated from Trainer
dataset_size:181760
loss:MultipleNegativesRankingLoss
text-embeddings-inference
Model card Files
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SentenceTransformer based on cambridgeltl/SapBERT-from-PubMedBERT-fulltext

This is a sentence-transformers model finetuned from 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 Sources

Full Model Architecture 

SentenceTransformer(
  (0): Transformer({'max_seq_length': 32, 'do_lower_case': False, 'architecture': 'BertModel'})
  (1): Pooling({'word_embedding_dimension': 768, '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("sentence_transformers_model_id")
# Run inference
sentences = [
    'GM10834',
    'GM10834 cell',
    'Malignant neoplasm of uvula',
]
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, 0.9904, 0.0661],
#         [0.9904, 1.0000, 0.0802],
#         [0.0661, 0.0802, 1.0000]])

Training Details

Training Dataset

Unnamed Dataset

  • Size: 181,760 training samples
  • Columns: sentence_0 and sentence_1
  • Approximate statistics based on the first 1000 samples:
    sentence_0 sentence_1
    type string string
    details
    • min: 3 tokens
    • mean: 6.76 tokens
    • max: 25 tokens
    • min: 3 tokens
    • mean: 6.78 tokens
    • max: 24 tokens
  • Samples:
    sentence_0 sentence_1
    GM14492 GM17243 cell
    DA06122 cell DA06122
    GM05380 GM17257 cell
  • Loss: MultipleNegativesRankingLoss with these parameters:
    {
    "scale": 20.0,
    "similarity_fct": "cos_sim",
    "gather_across_devices": false
}

Training Hyperparameters

Non-Default Hyperparameters

  • per_device_train_batch_size: 512
  • per_device_eval_batch_size: 512
  • num_train_epochs: 2
  • fp16: True
  • disable_tqdm: True
  • multi_dataset_batch_sampler: round_robin

All Hyperparameters

Click to expand
  • overwrite_output_dir: False
  • do_predict: False
  • eval_strategy: no
  • prediction_loss_only: True
  • per_device_train_batch_size: 512
  • per_device_eval_batch_size: 512
  • 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: 2
  • 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: 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: True
  • 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_fused
  • 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: round_robin
  • router_mapping: {}
  • learning_rate_mapping: {}

Training Logs

Epoch Step Training Loss
1.4085 500 1.7207

Framework Versions

  • Python: 3.9.23
  • Sentence Transformers: 5.1.2
  • Transformers: 4.57.3
  • PyTorch: 2.8.0+cu128
  • Accelerate: 1.10.1
  • Datasets: 2.14.6
  • Tokenizers: 0.22.1

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{henderson2017efficient,
    title={Efficient Natural Language Response Suggestion for Smart Reply},
    author={Matthew Henderson and Rami Al-Rfou and Brian Strope and Yun-hsuan Sung and Laszlo Lukacs and Ruiqi Guo and Sanjiv Kumar and Balint Miklos and Ray Kurzweil},
    year={2017},
    eprint={1705.00652},
    archivePrefix={arXiv},
    primaryClass={cs.CL}
}
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