NothingMuch/GO-Term-Embeddings

SentenceTransformer

This is a sentence-transformers model trained on the parquet dataset. It maps sentences & paragraphs to a 128-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: 128 dimensions
• Similarity Function: Cosine Similarity
• Training Dataset:
  • parquet

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("NothingMuch/GO-Term-Embeddings")
# Run inference
sentences = [
    'The sex chromosome present in both sexes of species in which the male is the heterogametic sex. Two copies of the X chromosome are present in each somatic cell of females and one copy is present in males.',
    'X chromosome',
    'somatic diversification of immune receptors by N region addition',
]
embeddings = model.encode(sentences)
print(embeddings.shape)
# [3, 128]

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

Evaluation

Metrics

Translation

• Evaluated with TranslationEvaluator

Metric	Value
src2trg_accuracy	0.7841
trg2src_accuracy	0.7757
mean_accuracy	0.7799

Training Details

Training Dataset

parquet

• Dataset: parquet
• Size: 40,906 training samples
• Columns: anchor and positive
• Approximate statistics based on the first 1000 samples:

  	anchor	positive
  type	string	string
  details	min: 8 tokens mean: 42.05 tokens max: 192 tokens	min: 3 tokens mean: 10.48 tokens max: 40 tokens

• Samples:

  anchor	positive
  Catalysis of the transfer of a mannose residue to an oligosaccharide, forming an alpha-(1->6) linkage.	1,6-alpha-mannosyltransferase activity
  Catalysis of the hydrolysis of ester linkages within a single-stranded deoxyribonucleic acid molecule by creating internal breaks.	single-stranded DNA specific endodeoxyribonuclease activity
  Catalysis of the hydrolysis of ester linkages within a single-stranded deoxyribonucleic acid molecule by creating internal breaks.	ssDNA-specific endodeoxyribonuclease activity

• Loss: MatryoshkaLoss with these parameters:

  {
      "loss": "MegaBatchMarginLoss",
      "matryoshka_dims": [
          64,
          32
      ],
      "matryoshka_weights": [
          1,
          1
      ],
      "n_dims_per_step": -1
  }
  

Evaluation Dataset

parquet

• Dataset: parquet
• Size: 6,585 evaluation samples
• Columns: anchor and positive
• Approximate statistics based on the first 1000 samples:

  	anchor	positive
  type	string	string
  details	min: 8 tokens mean: 41.29 tokens max: 253 tokens	min: 3 tokens mean: 9.23 tokens max: 44 tokens

• Samples:

  anchor	positive
  The maintenance of the structure and integrity of the mitochondrial genome; includes replication and segregation of the mitochondrial chromosome.	mitochondrial genome maintenance
  The repair of single strand breaks in DNA. Repair of such breaks is mediated by the same enzyme systems as are used in base excision repair.	single strand break repair
  Any process that modulates the frequency, rate or extent of DNA recombination, a DNA metabolic process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents.	regulation of DNA recombination

• Loss: MatryoshkaLoss with these parameters:

  {
      "loss": "MegaBatchMarginLoss",
      "matryoshka_dims": [
          64,
          32
      ],
      "matryoshka_weights": [
          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
• torch_empty_cache_steps: 250
• learning_rate: 0.00025
• lr_scheduler_type: cosine_with_restarts
• warmup_steps: 25
• seed: 25
• load_best_model_at_end: True
• 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: 1
• eval_accumulation_steps: None
• torch_empty_cache_steps: 250
• learning_rate: 0.00025
• weight_decay: 0.0
• adam_beta1: 0.9
• adam_beta2: 0.999
• adam_epsilon: 1e-08
• max_grad_norm: 1.0
• num_train_epochs: 3
• max_steps: -1
• lr_scheduler_type: cosine_with_restarts
• lr_scheduler_kwargs: {}
• warmup_ratio: 0.0
• warmup_steps: 25
• 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: 25
• data_seed: None
• jit_mode_eval: False
• use_ipex: False
• bf16: False
• 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: 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
• 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	Validation Loss	mean_accuracy
1.0016	641	0.2501	0.6276	0.7343
2.0016	1282	0.3146	0.5520	0.7651
2.9969	1920	0.1976	0.5097	0.7799

• The bold row denotes the saved checkpoint.

Framework Versions

• Python: 3.10.14
• Sentence Transformers: 3.3.1
• Transformers: 4.47.0
• PyTorch: 2.4.0
• Accelerate: 1.2.0
• Datasets: 3.2.0
• 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",
}

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}
}

MegaBatchMarginLoss

@inproceedings{wieting-gimpel-2018-paranmt,
    title = "{P}ara{NMT}-50{M}: Pushing the Limits of Paraphrastic Sentence Embeddings with Millions of Machine Translations",
    author = "Wieting, John and Gimpel, Kevin",
    editor = "Gurevych, Iryna and Miyao, Yusuke",
    booktitle = "Proceedings of the 56th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers)",
    month = jul,
    year = "2018",
    address = "Melbourne, Australia",
    publisher = "Association for Computational Linguistics",
    url = "https://aclanthology.org/P18-1042",
    doi = "10.18653/v1/P18-1042",
    pages = "451--462",
}