potsu-potsu/medembed-sm-mrl

MedEmbed Biomedical MRL

This is a sentence-transformers model trained on the json dataset. It maps sentences & paragraphs to a 384-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: 384 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': 384, '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-sm-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, 384]

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

Evaluation

Metrics

Information Retrieval

• Dataset: dim_384
• Evaluated with InformationRetrievalEvaluator with these parameters:

  {
      "truncate_dim": 384
  }
  

Metric	Value
cosine_accuracy@1	0.8331
cosine_accuracy@3	0.9165
cosine_accuracy@5	0.9378
cosine_accuracy@10	0.9505
cosine_precision@1	0.8331
cosine_precision@3	0.3055
cosine_precision@5	0.1876
cosine_precision@10	0.095
cosine_recall@1	0.8331
cosine_recall@3	0.9165
cosine_recall@5	0.9378
cosine_recall@10	0.9505
cosine_ndcg@10	0.8978
cosine_mrr@10	0.8803
cosine_map@100	0.8817

Information Retrieval

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

  {
      "truncate_dim": 256
  }
  

Metric	Value
cosine_accuracy@1	0.8289
cosine_accuracy@3	0.9151
cosine_accuracy@5	0.9307
cosine_accuracy@10	0.9448
cosine_precision@1	0.8289
cosine_precision@3	0.305
cosine_precision@5	0.1861
cosine_precision@10	0.0945
cosine_recall@1	0.8289
cosine_recall@3	0.9151
cosine_recall@5	0.9307
cosine_recall@10	0.9448
cosine_ndcg@10	0.8923
cosine_mrr@10	0.8749
cosine_map@100	0.8765

Information Retrieval

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

  {
      "truncate_dim": 128
  }
  

Metric	Value
cosine_accuracy@1	0.8076
cosine_accuracy@3	0.9151
cosine_accuracy@5	0.9264
cosine_accuracy@10	0.9378
cosine_precision@1	0.8076
cosine_precision@3	0.305
cosine_precision@5	0.1853
cosine_precision@10	0.0938
cosine_recall@1	0.8076
cosine_recall@3	0.9151
cosine_recall@5	0.9264
cosine_recall@10	0.9378
cosine_ndcg@10	0.8821
cosine_mrr@10	0.8633
cosine_map@100	0.8644

Information Retrieval

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

  {
      "truncate_dim": 64
  }
  

Metric	Value
cosine_accuracy@1	0.7751
cosine_accuracy@3	0.884
cosine_accuracy@5	0.9024
cosine_accuracy@10	0.9165
cosine_precision@1	0.7751
cosine_precision@3	0.2947
cosine_precision@5	0.1805
cosine_precision@10	0.0917
cosine_recall@1	0.7751
cosine_recall@3	0.884
cosine_recall@5	0.9024
cosine_recall@10	0.9165
cosine_ndcg@10	0.8514
cosine_mrr@10	0.8298
cosine_map@100	0.8308

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": [
          384,
          256,
          128,
          64
      ],
      "matryoshka_weights": [
          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_384_cosine_ndcg@10	dim_256_cosine_ndcg@10	dim_128_cosine_ndcg@10	dim_64_cosine_ndcg@10
1.0	8	-	0.9037	0.899	0.8822	0.8482
1.2540	10	30.6759	-	-	-	-
2.0	16	-	0.9006	0.8930	0.8809	0.8498
2.5079	20	14.701	-	-	-	-
3.0	24	-	0.8986	0.8923	0.8820	0.8504
3.7619	30	12.3176	-	-	-	-
4.0	32	-	0.8978	0.8923	0.8821	0.8514

• 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}
}