arctic-pubmed-v0.2 / README.md
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metadata
tags:
  - sentence-transformers
  - sentence-similarity
  - feature-extraction
  - generated_from_trainer
  - dataset_size:10053
  - loss:MultipleNegativesRankingLoss
base_model: Snowflake/snowflake-arctic-embed-l-v2.0
widget:
  - source_sentence: Nursing Reform
    sentences:
      - 'Staff nurses speak out on reform. '
      - >-
        Synthesis of graphene with different layers on paper-like sintered
        stainless steel fibers and its application as a metal-free catalyst for
        catalytic wet peroxide oxidation of phenol. 
      - 'Nursing reformation. '
  - source_sentence: NiTiO3 composite
    sentences:
      - 'Fabrication and electromagnetic performance of talc/NiTiO 3 composite. '
      - 'Nickel-titanium usage and breakage: an update. '
      - 'Innervational plasticity of the oculomotor system. '
  - source_sentence: Single-Session Competency Framework
    sentences:
      - 'Competency assessment: one step at the time. '
      - >-
        Optothermal molecule trapping by opposing fluid flow with thermophoretic
        drift. 
      - >-
        Describing a Clinical Group Coding Method for Identifying Competencies
        in an Allied Health Single Session. 
  - source_sentence: Streptococcal myositis treatment outcomes
    sentences:
      - >-
        Evaluation of penicillin and hyperbaric oxygen in the treatment of
        streptococcal myositis. 
      - 'Polymicrobial myositis. '
      - >-
        Parse's criteria for evaluation of theory with a comparison of Fawcett's
        and Parse's approaches. 
  - source_sentence: Risk-based water quality monitoring framework
    sentences:
      - >-
        Development of a new risk-based framework to guide investment in water
        quality monitoring. 
      - >-
        NADPH oxidase 1 supports proliferation of colon cancer cells by
        modulating reactive oxygen species-dependent signal transduction. 
      - 'Water quality monitoring strategies - A review and future perspectives. '
pipeline_tag: sentence-similarity
library_name: sentence-transformers
metrics:
  - cosine_accuracy
model-index:
  - name: SentenceTransformer based on Snowflake/snowflake-arctic-embed-l-v2.0
    results:
      - task:
          type: triplet
          name: Triplet
        dataset:
          name: triplet dev
          type: triplet-dev
        metrics:
          - type: cosine_accuracy
            value: 0.72
            name: Cosine Accuracy

SentenceTransformer based on Snowflake/snowflake-arctic-embed-l-v2.0

This is a sentence-transformers model finetuned from Snowflake/snowflake-arctic-embed-l-v2.0 on the json dataset. It maps sentences & paragraphs to a 1024-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: Snowflake/snowflake-arctic-embed-l-v2.0
  • Maximum Sequence Length: 8192 tokens
  • Output Dimensionality: 1024 dimensions
  • Similarity Function: Cosine Similarity
  • Training Dataset:
    • json

Model Sources

Full Model Architecture

SentenceTransformer(
  (0): Transformer({'max_seq_length': 8192, 'do_lower_case': False}) with Transformer model: PeftModelForFeatureExtraction 
  (1): Pooling({'word_embedding_dimension': 1024, '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("sentence_transformers_model_id")
# Run inference
sentences = [
    'Risk-based water quality monitoring framework',
    'Development of a new risk-based framework to guide investment in water quality monitoring. ',
    'Water quality monitoring strategies - A review and future perspectives. ',
]
embeddings = model.encode(sentences)
print(embeddings.shape)
# [3, 1024]

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

Evaluation

Metrics

Triplet

Metric Value
cosine_accuracy 0.72

Training Details

Training Dataset

json

  • Dataset: json
  • Size: 10,053 training samples
  • Columns: anchor, positive, and negative
  • Approximate statistics based on the first 1000 samples:
    anchor positive negative
    type string string string
    details
    • min: 4 tokens
    • mean: 10.58 tokens
    • max: 33 tokens
    • min: 5 tokens
    • mean: 26.91 tokens
    • max: 79 tokens
    • min: 4 tokens
    • mean: 15.99 tokens
    • max: 61 tokens
  • Samples:
    anchor positive negative
    Pediatric Infectious Disease Control [Urgent tasks in scientific studies concerning the control of infectious diseases in children]. Pediatric workforce: a look at pediatric infectious diseases data from the American Board of Pediatrics.
    Thermal coefficient of phase shift Thermal characteristics of phase shift in jacketed optical fibers. Thermal effects.
    Renal biomarkers in heart failure Current and novel renal biomarkers in heart failure. Cardiac biomarkers of heart failure in chronic kidney disease.
  • Loss: MultipleNegativesRankingLoss with these parameters:
    {
        "scale": 20.0,
        "similarity_fct": "cos_sim"
    }
    

Training Hyperparameters

Non-Default Hyperparameters

  • eval_strategy: steps
  • per_device_train_batch_size: 256
  • per_device_eval_batch_size: 256
  • num_train_epochs: 1
  • lr_scheduler_type: cosine_with_restarts
  • warmup_ratio: 0.1
  • bf16: True
  • batch_sampler: no_duplicates

All Hyperparameters

Click to expand
  • overwrite_output_dir: False
  • do_predict: False
  • eval_strategy: steps
  • prediction_loss_only: True
  • per_device_train_batch_size: 256
  • per_device_eval_batch_size: 256
  • per_gpu_train_batch_size: None
  • per_gpu_eval_batch_size: None
  • gradient_accumulation_steps: 1
  • eval_accumulation_steps: None
  • torch_empty_cache_steps: None
  • learning_rate: 5e-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: 1
  • max_steps: -1
  • lr_scheduler_type: cosine_with_restarts
  • 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: 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: False
  • 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
  • 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
  • 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
  • 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 triplet-dev_cosine_accuracy
0 0 - 0.58
0.025 1 1.922 -
0.05 2 1.7637 -
0.075 3 1.8049 -
0.1 4 1.4954 -
0.125 5 1.7383 -
0.15 6 1.4773 -
0.175 7 1.3947 -
0.2 8 1.5337 -
0.225 9 1.2705 -
0.25 10 1.167 -
0.275 11 1.3125 -
0.3 12 1.4049 -
0.325 13 1.3382 -
0.35 14 1.1542 -
0.375 15 1.2514 -
0.4 16 1.1141 -
0.425 17 1.2267 -
0.45 18 1.1781 -
0.475 19 1.269 -
0.5 20 1.0684 -
0.525 21 1.2045 -
0.55 22 0.9869 -
0.575 23 1.2933 -
0.6 24 1.0751 -
0.625 25 1.2671 -
0.65 26 1.1874 -
0.675 27 1.241 -
0.7 28 1.1735 -
0.725 29 1.247 -
0.75 30 1.1166 -
0.775 31 1.1484 -
0.8 32 1.2556 -
0.825 33 1.1028 -
0.85 34 1.215 -
0.875 35 1.3421 -
0.9 36 1.1762 -
0.925 37 1.2029 -
0.95 38 1.1283 -
0.975 39 1.0871 -
1.0 40 0.7317 0.72

Framework Versions

  • Python: 3.12.3
  • Sentence Transformers: 3.3.1
  • Transformers: 4.48.0.dev0
  • PyTorch: 2.5.1
  • Accelerate: 1.2.1
  • Datasets: 2.19.0
  • Tokenizers: 0.21.0

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",
}

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}
}