bge_based_arg_minibio_matryoshka

This is a sentence-transformers model finetuned from BAAI/bge-base-en-v1.5 on the json dataset. 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 Type: Sentence Transformer
• Base model: BAAI/bge-base-en-v1.5
• Maximum Sequence Length: 512 tokens
• Output Dimensionality: 768 dimensions
• Similarity Function: Cosine Similarity
• Training Dataset:
  • json
• Language: en
• License: apache-2.0

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': True}) with Transformer model: BertModel 
  (1): Pooling({'word_embedding_dimension': 768, 'pooling_mode_cls_token': True, 'pooling_mode_mean_tokens': False, '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("Thyme233/bge_based_arg_minibio_matryoshka")
# Run inference
sentences = [
    'Which proteins are regulated by Nrf2?',
    'Keap1-Nrf2 system is known as a sensor of electrophilic compounds, and protects cells from oxidative stress through induction of various antioxidant enzymes.',
    'Muenke syndrome is an autosomal dominant disorder characterized by coronal suture craniosynostosis, hearing loss, developmental delay, carpal and tarsal fusions, and the presence of the Pro250Arg mutation in the FGFR3 gene.   Muenke syndrome is characterized by coronal craniosynostosis (bilateral more often than unilateral), hearing loss, developmental delay, and carpal and/or tarsal bone coalition. Tarsal coalition is a distinct feature of Muenke syndrome and has been reported since the initial description of the disorder in the 1990s.   ',
]
embeddings = model.encode(sentences)
print(embeddings.shape)
# [3, 768]

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

Evaluation

Metrics

Information Retrieval

• Datasets: dim_768, dim_512, dim_256, dim_128 and dim_64
• Evaluated with InformationRetrievalEvaluator

Metric	dim_768	dim_512	dim_256	dim_128	dim_64
cosine_accuracy@1	0.8559	0.8496	0.8432	0.8263	0.7881
cosine_accuracy@3	0.9386	0.9343	0.9301	0.9131	0.8919
cosine_accuracy@5	0.9534	0.9534	0.9513	0.9386	0.911
cosine_accuracy@10	0.9725	0.9746	0.9661	0.9555	0.9301
cosine_precision@1	0.8559	0.8496	0.8432	0.8263	0.7881
cosine_precision@3	0.3129	0.3114	0.31	0.3044	0.2973
cosine_precision@5	0.1907	0.1907	0.1903	0.1877	0.1822
cosine_precision@10	0.0972	0.0975	0.0966	0.0956	0.093
cosine_recall@1	0.8559	0.8496	0.8432	0.8263	0.7881
cosine_recall@3	0.9386	0.9343	0.9301	0.9131	0.8919
cosine_recall@5	0.9534	0.9534	0.9513	0.9386	0.911
cosine_recall@10	0.9725	0.9746	0.9661	0.9555	0.9301
cosine_ndcg@10	0.9176	0.916	0.9096	0.8962	0.8642
cosine_mrr@10	0.8996	0.8969	0.891	0.8767	0.8426
cosine_map@100	0.9002	0.8973	0.8918	0.878	0.8445

Training Details

Training Dataset

json

• Dataset: json
• Size: 4,247 training samples
• Columns: question and answer
• Approximate statistics based on the first 1000 samples:

  	question	answer
  type	string	string
  details	min: 6 tokens mean: 15.83 tokens max: 49 tokens	min: 3 tokens mean: 59.36 tokens max: 512 tokens

• Samples:

  question	answer
  Is TNNI3K a cardiac-specific protein?	Yes, TNNI3K is highly expressed in heart but is undetectable in other tissues.
  Which are the effects of ALDH2 deficiency?	In alcohol drinkers, ALDH2-deficiency is a well-known risk factor for upper aerodigestive tract cancers, i.e., head and neck cancer and esophageal cancer. Diabetic patients with ALDH2 mutations are predisposed to worse diastolic dysfunction. These data demonstrate that ALDH2 deficiency enhances EtOH-induced disruption of intestinal epithelial tight junctions, barrier dysfunction, and liver damage.
  Has intepirdine been evaluated in clinical trials? (November 2017)	Yes, intepirdine was in Phase III clinical trials in November 2017.

• Loss: MatryoshkaLoss with these parameters:

  {
      "loss": "MultipleNegativesRankingLoss",
      "matryoshka_dims": [
          768,
          512,
          256,
          128,
          64
      ],
      "matryoshka_weights": [
          1,
          1,
          1,
          1,
          1
      ],
      "n_dims_per_step": -1
  }
  

Training Hyperparameters

Non-Default Hyperparameters

• eval_strategy: epoch
• per_device_train_batch_size: 32
• per_device_eval_batch_size: 16
• gradient_accumulation_steps: 16
• learning_rate: 2e-05
• num_train_epochs: 4
• lr_scheduler_type: cosine
• warmup_ratio: 0.1
• load_best_model_at_end: True
• optim: adamw_torch_fused
• batch_sampler: no_duplicates

All Hyperparameters

Click to expand

• overwrite_output_dir: False
• do_predict: False
• eval_strategy: epoch
• prediction_loss_only: True
• per_device_train_batch_size: 32
• per_device_eval_batch_size: 16
• per_gpu_train_batch_size: None
• per_gpu_eval_batch_size: None
• gradient_accumulation_steps: 16
• eval_accumulation_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: 4
• max_steps: -1
• lr_scheduler_type: cosine
• 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: 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: 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_fused
• 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
• prompts: None
• batch_sampler: no_duplicates
• multi_dataset_batch_sampler: proportional

Training Logs

Epoch	Step	Training Loss	dim_768_cosine_ndcg@10	dim_512_cosine_ndcg@10	dim_256_cosine_ndcg@10	dim_128_cosine_ndcg@10	dim_64_cosine_ndcg@10
0.9624	8	-	0.9242	0.9186	0.9157	0.8907	0.8504
1.2030	10	1.6488	-	-	-	-	-
1.9248	16	-	0.9166	0.9169	0.9099	0.8949	0.8623
2.4060	20	0.6601	-	-	-	-	-
2.8872	24	-	0.9173	0.916	0.9096	0.8966	0.8645
3.6090	30	0.5199	-	-	-	-	-
3.8496	32	-	0.9176	0.9160	0.9096	0.8962	0.8642

• The bold row denotes the saved checkpoint.

Framework Versions

• Python: 3.10.8
• Sentence Transformers: 3.3.1
• Transformers: 4.41.2
• PyTorch: 2.5.1+cu124
• Accelerate: 1.1.1
• Datasets: 2.19.1
• Tokenizers: 0.19.1

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",
}

MatryoshkaLoss

@misc{kusupati2024matryoshka,
    title={Matryoshka Representation Learning},
    author={Aditya Kusupati and Gantavya Bhatt and Aniket Rege and Matthew Wallingford and Aditya Sinha and Vivek Ramanujan and William Howard-Snyder and Kaifeng Chen and Sham Kakade and Prateek Jain and Ali Farhadi},
    year={2024},
    eprint={2205.13147},
    archivePrefix={arXiv},
    primaryClass={cs.LG}
}

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}
}