potsu-potsu/bge-base-mrl

Biomedical MRL

This is a sentence-transformers model trained 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
• 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("potsu-potsu/bge-base-mrl")
# Run inference
sentences = [
    'What are the effects of the deletion of all three Pcdh clusters (tricluster deletion) in mice?',
    'Multicluster Pcdh diversity is required for mouse olfactory neural circuit assembly. The vertebrate clustered protocadherin (Pcdh) cell surface proteins are encoded by three closely linked gene clusters (Pcdhα, Pcdhβ, and Pcdhγ). Although deletion of individual Pcdh clusters had subtle phenotypic consequences, the loss of all three clusters (tricluster deletion) led to a severe axonal arborization defect and loss of self-avoidance.',
    'Investigators proposed that there have been three extended periods in the evolution of gene regulatory elements. Early vertebrate evolution was characterized by regulatory gains near transcription factors and developmental genes, but this trend was replaced by innovations near extracellular signaling genes, and then innovations near posttranslational protein modifiers.',
]
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

• Dataset: dim_768
• Evaluated with InformationRetrievalEvaluator with these parameters:

  {
      "truncate_dim": 768
  }
  

Metric	Value
cosine_accuracy@1	0.8614
cosine_accuracy@3	0.9335
cosine_accuracy@5	0.9477
cosine_accuracy@10	0.9646
cosine_precision@1	0.8614
cosine_precision@3	0.3112
cosine_precision@5	0.1895
cosine_precision@10	0.0965
cosine_recall@1	0.8614
cosine_recall@3	0.9335
cosine_recall@5	0.9477
cosine_recall@10	0.9646
cosine_ndcg@10	0.9156
cosine_mrr@10	0.8995
cosine_map@100	0.9007

Information Retrieval

• Dataset: dim_512
• Evaluated with InformationRetrievalEvaluator with these parameters:

  {
      "truncate_dim": 512
  }
  

Metric	Value
cosine_accuracy@1	0.86
cosine_accuracy@3	0.9321
cosine_accuracy@5	0.9505
cosine_accuracy@10	0.9646
cosine_precision@1	0.86
cosine_precision@3	0.3107
cosine_precision@5	0.1901
cosine_precision@10	0.0965
cosine_recall@1	0.86
cosine_recall@3	0.9321
cosine_recall@5	0.9505
cosine_recall@10	0.9646
cosine_ndcg@10	0.9156
cosine_mrr@10	0.8995
cosine_map@100	0.9006

Information Retrieval

• Dataset: dim_256
• Evaluated with InformationRetrievalEvaluator with these parameters:

  {
      "truncate_dim": 256
  }
  

Metric	Value
cosine_accuracy@1	0.8402
cosine_accuracy@3	0.9293
cosine_accuracy@5	0.9406
cosine_accuracy@10	0.9547
cosine_precision@1	0.8402
cosine_precision@3	0.3098
cosine_precision@5	0.1881
cosine_precision@10	0.0955
cosine_recall@1	0.8402
cosine_recall@3	0.9293
cosine_recall@5	0.9406
cosine_recall@10	0.9547
cosine_ndcg@10	0.9032
cosine_mrr@10	0.8861
cosine_map@100	0.8874

Information Retrieval

• Dataset: dim_128
• Evaluated with InformationRetrievalEvaluator with these parameters:

  {
      "truncate_dim": 128
  }
  

Metric	Value
cosine_accuracy@1	0.8175
cosine_accuracy@3	0.9165
cosine_accuracy@5	0.9335
cosine_accuracy@10	0.9434
cosine_precision@1	0.8175
cosine_precision@3	0.3055
cosine_precision@5	0.1867
cosine_precision@10	0.0943
cosine_recall@1	0.8175
cosine_recall@3	0.9165
cosine_recall@5	0.9335
cosine_recall@10	0.9434
cosine_ndcg@10	0.8878
cosine_mrr@10	0.8692
cosine_map@100	0.8708

Information Retrieval

• Dataset: dim_64
• Evaluated with InformationRetrievalEvaluator with these parameters:

  {
      "truncate_dim": 64
  }
  

Metric	Value
cosine_accuracy@1	0.7893
cosine_accuracy@3	0.8953
cosine_accuracy@5	0.9137
cosine_accuracy@10	0.9307
cosine_precision@1	0.7893
cosine_precision@3	0.2984
cosine_precision@5	0.1827
cosine_precision@10	0.0931
cosine_recall@1	0.7893
cosine_recall@3	0.8953
cosine_recall@5	0.9137
cosine_recall@10	0.9307
cosine_ndcg@10	0.8666
cosine_mrr@10	0.8454
cosine_map@100	0.8466

Training Details

Training Dataset

json

• Dataset: json
• Size: 4,012 training samples
• Columns: anchor and positive
• Approximate statistics based on the first 1000 samples:

  	anchor	positive
  type	string	string
  details	min: 5 tokens mean: 16.13 tokens max: 49 tokens	min: 3 tokens mean: 63.38 tokens max: 485 tokens

• Samples:

  anchor	positive
  What is the implication of histone lysine methylation in medulloblastoma?	Aberrant patterns of H3K4, H3K9, and H3K27 histone lysine methylation were shown to result in histone code alterations, which induce changes in gene expression, and affect the proliferation rate of cells in medulloblastoma.
  What is the role of STAG1/STAG2 proteins in differentiation?	STAG1/STAG2 proteins are tumour suppressor proteins that suppress cell proliferation and are essential for differentiation.
  What is the association between cell phone use and glioblastoma?	The association between cell phone use and incident glioblastoma remains unclear. Some studies have reported that cell phone use was associated with incident glioblastoma, and with reduced survival of patients diagnosed with glioblastoma. However, other studies have repeatedly replicated to find an association between cell phone use and glioblastoma.

• 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
• bf16: True
• tf32: True
• 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
• 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: 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: True
• fp16: False
• fp16_opt_level: O1
• half_precision_backend: auto
• bf16_full_eval: False
• fp16_full_eval: False
• tf32: True
• 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: 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
• 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: 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
1.0	8	-	0.9163	0.9157	0.9074	0.8853	0.8466
1.2540	10	24.9925	-	-	-	-	-
2.0	16	-	0.9154	0.9149	0.9031	0.8901	0.8608
2.5079	20	11.2826	-	-	-	-	-
3.0	24	-	0.9144	0.9158	0.9034	0.8895	0.8654
3.7619	30	8.9263	-	-	-	-	-
4.0	32	-	0.9156	0.9156	0.9032	0.8878	0.8666

• The bold row denotes the saved checkpoint.

Framework Versions

• Python: 3.12.6
• Sentence Transformers: 4.1.0
• Transformers: 4.52.4
• PyTorch: 2.6.0+cu124
• Accelerate: 1.7.0
• Datasets: 3.6.0
• Tokenizers: 0.21.1

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}
}