kwondw/bert-base-uncased-trec-covid-tsdae-tiny

SentenceTransformer based on google-bert/bert-base-uncased

This is a sentence-transformers model finetuned from google-bert/bert-base-uncased. It maps sentences & paragraphs to a 768-dimensional dense vector space and can be used for retrieval.

Model Details

Model Description

• Model Type: Sentence Transformer
• Base model: google-bert/bert-base-uncased
• Maximum Sequence Length: 75 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("kwondw/bert-base-uncased-trec-covid-tsdae-tiny")
# Run inference
sentences = [
    'processes sales care products in a similar manner such mode on basis.',
    'RODS processes sales of over-the-counter health care products in a similar manner but receives such data in batch mode on a daily basis.',
    'Similar to the wild-type hnRNP A1, the hnRNP A1 mutant complexed with an MHV polymerase gene product, the nucleocapsid protein and the viral RNA.',
]
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, 0.7380, 0.5206],
#         [0.7380, 1.0000, 0.6766],
#         [0.5206, 0.6766, 1.0000]])

Evaluation

Metrics

Information Retrieval

• Dataset: trec-covid
• Evaluated with InformationRetrievalEvaluator

Metric	Value
cosine_accuracy@1	0.06
cosine_accuracy@3	0.18
cosine_accuracy@5	0.22
cosine_accuracy@10	0.34
cosine_precision@1	0.06
cosine_precision@3	0.06
cosine_precision@5	0.044
cosine_precision@10	0.038
cosine_recall@1	0.0002
cosine_recall@3	0.0005
cosine_recall@5	0.0005
cosine_recall@10	0.0009
cosine_ndcg@10	0.0426
cosine_mrr@10	0.1304
cosine_map@100	0.002

Training Details

Training Dataset

Unnamed Dataset

• Size: 100 training samples
• Columns: noisy and text
• Approximate statistics based on the first 100 samples:

  	noisy	text
  type	string	string
  details	min: 4 tokens mean: 22.89 tokens max: 49 tokens	min: 8 tokens mean: 36.97 tokens max: 75 tokens

• Samples:

  noisy	text
  of pneumoniae infections at Abdulaziz University Hospital Jeddah Arabia OBJECTIVE chart review describes the epidemiology of 40 patients culture-proven Mycoplasma pneumoniae at King Abdulaziz University Hospital,, Arabia	Clinical features of culture-proven Mycoplasma pneumoniae infections at King Abdulaziz University Hospital, Jeddah, Saudi Arabia OBJECTIVE: This retrospective chart review describes the epidemiology and clinical features of 40 patients with culture-proven Mycoplasma pneumoniae infections at King Abdulaziz University Hospital, Jeddah, Saudi Arabia.
  : Patients with M. pneumoniae respiratory specimens January through were identified through the.	METHODS: Patients with positive M. pneumoniae cultures from respiratory specimens from January 1997 through December 1998 were identified through the Microbiology records.
  Charts patients were.	Charts of patients were reviewed.

• Loss: DenoisingAutoEncoderLoss with these parameters:

  {
      "decoder_name_or_path": "google-bert/bert-base-uncased",
      "need_retokenization": false
  }
  

Training Hyperparameters

Non-Default Hyperparameters

• learning_rate: 3e-05
• num_train_epochs: 1
• warmup_ratio: 0.1
• fp16: True

All Hyperparameters

Click to expand

• overwrite_output_dir: False
• do_predict: False
• prediction_loss_only: True
• per_device_train_batch_size: 8
• 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: 3e-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: 1
• max_steps: -1
• lr_scheduler_type: linear
• lr_scheduler_kwargs: None
• 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
• 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: 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: proportional
• router_mapping: {}
• learning_rate_mapping: {}

Training Logs

Epoch	Step	trec-covid_cosine_ndcg@10
-1	-1	0.0426

Training Time

• Training: 17.6 minutes

Framework Versions

• Python: 3.12.13
• Sentence Transformers: 5.4.1
• Transformers: 4.57.6
• PyTorch: 2.10.0+cu128
• Accelerate: 1.13.0
• Datasets: 5.0.0
• Tokenizers: 0.22.2

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",
}

DenoisingAutoEncoderLoss

@inproceedings{wang-2021-TSDAE,
    title = "TSDAE: Using Transformer-based Sequential Denoising Auto-Encoderfor Unsupervised Sentence Embedding Learning",
    author = "Wang, Kexin and Reimers, Nils and Gurevych, Iryna",
    booktitle = "Findings of the Association for Computational Linguistics: EMNLP 2021",
    month = nov,
    year = "2021",
    address = "Punta Cana, Dominican Republic",
    publisher = "Association for Computational Linguistics",
    pages = "671--688",
    url = "https://arxiv.org/abs/2104.06979",
}