potsu-potsu/medembed-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': False}) 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/medembed-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	0.8501
cosine_accuracy@3	0.9378
cosine_accuracy@5	0.9505
cosine_accuracy@10	0.9675
cosine_precision@1	0.8501
cosine_precision@3	0.3126
cosine_precision@5	0.1901
cosine_precision@10	0.0967
cosine_recall@1	0.8501
cosine_recall@3	0.9378
cosine_recall@5	0.9505
cosine_recall@10	0.9675
cosine_ndcg@10	0.9123
cosine_mrr@10	0.8942
cosine_map@100	0.8952

Information Retrieval

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

  {
      "truncate_dim": 512
  }
  

Metric	Value
cosine_accuracy@1	0.8487
cosine_accuracy@3	0.9349
cosine_accuracy@5	0.9519
cosine_accuracy@10	0.9675
cosine_precision@1	0.8487
cosine_precision@3	0.3116
cosine_precision@5	0.1904
cosine_precision@10	0.0967
cosine_recall@1	0.8487
cosine_recall@3	0.9349
cosine_recall@5	0.9519
cosine_recall@10	0.9675
cosine_ndcg@10	0.9119
cosine_mrr@10	0.8937
cosine_map@100	0.8948

Information Retrieval

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

  {
      "truncate_dim": 256
  }
  

Metric	Value
cosine_accuracy@1	0.8373
cosine_accuracy@3	0.9279
cosine_accuracy@5	0.9434
cosine_accuracy@10	0.9547
cosine_precision@1	0.8373
cosine_precision@3	0.3093
cosine_precision@5	0.1887
cosine_precision@10	0.0955
cosine_recall@1	0.8373
cosine_recall@3	0.9279
cosine_recall@5	0.9434
cosine_recall@10	0.9547
cosine_ndcg@10	0.9018
cosine_mrr@10	0.8842
cosine_map@100	0.8857

Information Retrieval

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

  {
      "truncate_dim": 128
  }
  

Metric	Value
cosine_accuracy@1	0.819
cosine_accuracy@3	0.9109
cosine_accuracy@5	0.9279
cosine_accuracy@10	0.9406
cosine_precision@1	0.819
cosine_precision@3	0.3036
cosine_precision@5	0.1856
cosine_precision@10	0.0941
cosine_recall@1	0.819
cosine_recall@3	0.9109
cosine_recall@5	0.9279
cosine_recall@10	0.9406
cosine_ndcg@10	0.8856
cosine_mrr@10	0.8674
cosine_map@100	0.8693

Information Retrieval

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

  {
      "truncate_dim": 64
  }
  

Metric	Value
cosine_accuracy@1	0.7737
cosine_accuracy@3	0.8883
cosine_accuracy@5	0.9109
cosine_accuracy@10	0.925
cosine_precision@1	0.7737
cosine_precision@3	0.2961
cosine_precision@5	0.1822
cosine_precision@10	0.0925
cosine_recall@1	0.7737
cosine_recall@3	0.8883
cosine_recall@5	0.9109
cosine_recall@10	0.925
cosine_ndcg@10	0.8574
cosine_mrr@10	0.8349
cosine_map@100	0.8366

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	-	0.9142	0.9151	0.905	0.8892	0.8474
1.2540	10	26.698	-	-	-	-	-
2.0	16	-	0.9120	0.9093	0.8999	0.8869	0.8568
2.5079	20	11.062	-	-	-	-	-
3.0	24	-	0.9116	0.9113	0.9009	0.8849	0.8572
3.7619	30	9.198	-	-	-	-	-
4.0	32	-	0.9123	0.9119	0.9018	0.8856	0.8574

• 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}
}