databio/sbert-encode-cellines-tuned

SentenceTransformer based on sentence-transformers/all-MiniLM-L6-v2

This is a sentence-transformers model finetuned from sentence-transformers/all-MiniLM-L6-v2 on the mock-stsb 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: sentence-transformers/all-MiniLM-L6-v2
• Maximum Sequence Length: 256 tokens
• Output Dimensionality: 384 dimensions
• Similarity Function: Cosine Similarity
• Training Dataset:
  • mock-stsb

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': 256, 'do_lower_case': False}) with Transformer model: BertModel 
  (1): Pooling({'word_embedding_dimension': 384, 'pooling_mode_cls_token': False, 'pooling_mode_mean_tokens': True, '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 = [
    'GM12873',
    'leukocyte',
    'pancreas',
]
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

Semantic Similarity

• Dataset: sts-dev
• Evaluated with EmbeddingSimilarityEvaluator

Metric	Value
pearson_cosine	0.7059
spearman_cosine	0.6954

Training Details

Training Dataset

mock-stsb

• Dataset: mock-stsb at d5ba748
• Size: 1,128 training samples
• Columns: sentence1, sentence2, and score
• Approximate statistics based on the first 1000 samples:

  	sentence1	sentence2	score
  type	string	string	float
  details	min: 3 tokens mean: 5.46 tokens max: 10 tokens	min: 3 tokens mean: 5.55 tokens max: 10 tokens	min: 0.0 mean: 0.44 max: 0.9

• Samples:

  sentence1	sentence2	score
  OVCAR3	pancreas	0.05
  L1-S8	respiratory system	0.001
  peripheral nervous system	22Rv1	0.001

• Loss: CosineSimilarityLoss with these parameters:

  {
      "loss_fct": "torch.nn.modules.loss.MSELoss"
  }
  

Evaluation Dataset

mock-stsb

• Dataset: mock-stsb at d5ba748
• Size: 284 evaluation samples
• Columns: sentence1, sentence2, and score
• Approximate statistics based on the first 284 samples:

  	sentence1	sentence2	score
  type	string	string	float
  details	min: 3 tokens mean: 5.6 tokens max: 9 tokens	min: 3 tokens mean: 5.71 tokens max: 9 tokens	min: 0.0 mean: 0.45 max: 0.9

• Samples:

  sentence1	sentence2	score
  SJCRH30	cancer cell	0.9
  CWRU1	exocrine gland	0.05
  epithelial cell	Caki2	0.9

• Loss: CosineSimilarityLoss with these parameters:

  {
      "loss_fct": "torch.nn.modules.loss.MSELoss"
  }
  

Training Hyperparameters

Non-Default Hyperparameters

• eval_strategy: epoch
• per_device_train_batch_size: 4
• per_device_eval_batch_size: 4
• learning_rate: 1e-05
• num_train_epochs: 50
• warmup_ratio: 0.1
• load_best_model_at_end: True

All Hyperparameters

Click to expand

• overwrite_output_dir: False
• do_predict: False
• eval_strategy: epoch
• prediction_loss_only: True
• per_device_train_batch_size: 4
• per_device_eval_batch_size: 4
• 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: 1e-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: 50
• max_steps: -1
• lr_scheduler_type: linear
• 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: 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: batch_sampler
• multi_dataset_batch_sampler: proportional

Training Logs

Epoch	Step	Training Loss	Validation Loss	sts-dev_spearman_cosine
1.0	282	0.2157	0.1413	0.4340
2.0	564	0.1402	0.1207	0.6198
3.0	846	0.1239	0.0973	0.6541
4.0	1128	0.1102	0.0858	0.6820
5.0	1410	0.1006	0.0867	0.6664
6.0	1692	0.0882	0.0886	0.6547
7.0	1974	0.076	0.0842	0.6660
8.0	2256	0.0639	0.0883	0.6392
9.0	2538	0.0538	0.0896	0.6300
10.0	2820	0.046	0.0884	0.6424
11.0	3102	0.0427	0.0858	0.6600
12.0	3384	0.0363	0.0878	0.6454
13.0	3666	0.0331	0.0838	0.6710
14.0	3948	0.0309	0.0839	0.6534
15.0	4230	0.0277	0.0841	0.6650
16.0	4512	0.026	0.0843	0.6933
17.0	4794	0.0238	0.0884	0.6557
18.0	5076	0.0229	0.0868	0.6649
19.0	5358	0.022	0.0867	0.6629
20.0	5640	0.021	0.0809	0.6815
21.0	5922	0.0196	0.0827	0.6844
22.0	6204	0.0189	0.0857	0.6770
23.0	6486	0.0186	0.0833	0.6868
24.0	6768	0.0172	0.0889	0.6710
25.0	7050	0.0171	0.0806	0.6954

Framework Versions

• Python: 3.11.5
• Sentence Transformers: 3.3.1
• Transformers: 4.47.0
• PyTorch: 2.5.1+cu124
• Accelerate: 1.2.0
• Datasets: 3.1.0
• 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",
}