potsu-potsu/medembed-small-biomedical-matryoshka-v2

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 <!-- - Base model: Unknown -->
• —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-small-biomedical-matryoshka-v2")
# 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]

<!--

Direct Usage (Transformers)

<details><summary>Click to see the direct usage in Transformers</summary>

</details> -->

<!--

Downstream Usage (Sentence Transformers)

You can finetune this model on your own dataset.

<details><summary>Click to expand</summary>

</details> -->

<!--

Out-of-Scope Use

List how the model may foreseeably be misused and address what users ought not to do with the model. -->

Evaluation

Metrics

Information Retrieval

• —Dataset: dim_384
• —Evaluated with <code>InformationRetrievalEvaluator</code> with these parameters:

  {
      "truncate_dim": 384
  }

Information Retrieval

• —Dataset: dim_256
• —Evaluated with <code>InformationRetrievalEvaluator</code> with these parameters:

  {
      "truncate_dim": 256
  }

Information Retrieval

• —Dataset: dim_128
• —Evaluated with <code>InformationRetrievalEvaluator</code> with these parameters:

  {
      "truncate_dim": 128
  }

Information Retrieval

• —Dataset: dim_64
• —Evaluated with <code>InformationRetrievalEvaluator</code> with these parameters:

  {
      "truncate_dim": 64
  }

<!--

Bias, Risks and Limitations

What are the known or foreseeable issues stemming from this model? You could also flag here known failure cases or weaknesses of the model. -->

<!--

Recommendations

What are recommendations with respect to the foreseeable issues? For example, filtering explicit content. -->

Training Details

Training Dataset

json

• —Dataset: json
• —Size: 4,012 training samples
• —Columns: <code>anchor</code> and <code>positive</code>
• —Approximate statistics based on the first 1000 samples: | | anchor | positive | |:--------|:----------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------| | type | string | string | | details | <ul><li>min: 5 tokens</li><li>mean: 16.13 tokens</li><li>max: 49 tokens</li></ul> | <ul><li>min: 3 tokens</li><li>mean: 63.38 tokens</li><li>max: 485 tokens</li></ul> |
• —Samples: | anchor | positive | |:---------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| | <code>What is the implication of histone lysine methylation in medulloblastoma?</code> | <code>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.</code> | | <code>What is the role of STAG1/STAG2 proteins in differentiation?</code> | <code>STAG1/STAG2 proteins are tumour suppressor proteins that suppress cell proliferation and are essential for differentiation.</code> | | <code>What is the association between cell phone use and glioblastoma?</code> | <code>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.</code> |
• —Loss: <code>MatryoshkaLoss</code> 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: 8
• —lr_scheduler_type: cosine
• —warmup_ratio: 0.1
• —bf16: True
• —tf32: True
• —load_best_model_at_end: True
• —optim: adamwtorchfused
• —batch_sampler: no_duplicates

All Hyperparameters

<details><summary>Click to expand</summary>

• —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: 8
• —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: {'minnumparams': 0, 'xla': False, 'xlafsdpv2': False, 'xlafsdpgrad_ckpt': False}
• —fsdp_transformer_layer_cls_to_wrap: None
• —accelerator_config: {'splitbatches': False, 'dispatchbatches': None, 'evenbatches': True, 'useseedablesampler': True, 'nonblocking': False, 'gradientaccumulationkwargs': None}
• —deepspeed: None
• —label_smoothing_factor: 0.0
• —optim: adamwtorchfused
• —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

</details>

Training Logs

• —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}
}

<!--

Glossary

Clearly define terms in order to be accessible across audiences. -->

<!--

Model Card Authors

Lists the people who create the model card, providing recognition and accountability for the detailed work that goes into its construction. -->

<!--

Model Card Contact

Provides a way for people who have updates to the Model Card, suggestions, or questions, to contact the Model Card authors. -->