BGE small finetuned BIOASQ
This is a sentence-transformers model finetuned from sentence-transformers/sentence-t5-base. It maps sentences & paragraphs to a 768-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/sentence-t5-base
- Maximum Sequence Length: 256 tokens
- Output Dimensionality: 768 tokens
- Similarity Function: Cosine Similarity
- 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': 256, 'do_lower_case': False}) with Transformer model: T5EncoderModel
(1): Pooling({'word_embedding_dimension': 768, '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): Dense({'in_features': 768, 'out_features': 768, 'bias': False, 'activation_function': 'torch.nn.modules.linear.Identity'})
(3): 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("juanpablomesa/sentence-t5-base-bioasq-1epoch-batch32-100steps")
# Run inference
sentences = [
'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.',
'What are the effects of the deletion of all three Pcdh clusters (tricluster deletion) in mice?',
'How many periods of regulatory innovation led to the evolution of vertebrates?',
]
embeddings = model.encode(sentences)
print(embeddings.shape)
# [3, 768]
# Get the similarity scores for the embeddings
similarities = model.similarity(embeddings, embeddings)
print(similarities.shape)
# [3, 3]
Evaluation
Metrics
Information Retrieval
- Dataset:
sentence-transformers/sentence-t5-base
- Evaluated with
InformationRetrievalEvaluator
Metric | Value |
---|---|
cosine_accuracy@1 | 0.0 |
cosine_accuracy@3 | 0.0 |
cosine_accuracy@5 | 0.0 |
cosine_accuracy@10 | 0.0 |
cosine_precision@1 | 0.0 |
cosine_precision@3 | 0.0 |
cosine_precision@5 | 0.0 |
cosine_precision@10 | 0.0 |
cosine_recall@1 | 0.0 |
cosine_recall@3 | 0.0 |
cosine_recall@5 | 0.0 |
cosine_recall@10 | 0.0 |
cosine_ndcg@10 | 0.0 |
cosine_mrr@10 | 0.0 |
cosine_map@100 | 0.0 |
Training Details
Training Dataset
Unnamed Dataset
- Size: 4,012 training samples
- Columns:
positive
andanchor
- Approximate statistics based on the first 1000 samples:
positive anchor type string string details - min: 2 tokens
- mean: 66.95 tokens
- max: 256 tokens
- min: 6 tokens
- mean: 16.85 tokens
- max: 53 tokens
- Samples:
positive anchor 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 implication of histone lysine methylation in medulloblastoma?
STAG1/STAG2 proteins are tumour suppressor proteins that suppress cell proliferation and are essential for differentiation.
What is the role of STAG1/STAG2 proteins in differentiation?
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.
What is the association between cell phone use and glioblastoma?
- Loss:
MultipleNegativesRankingLoss
with these parameters:{ "scale": 20.0, "similarity_fct": "cos_sim" }
Training Hyperparameters
Non-Default Hyperparameters
eval_strategy
: stepsper_device_train_batch_size
: 32per_device_eval_batch_size
: 16learning_rate
: 2e-05num_train_epochs
: 1warmup_ratio
: 0.1fp16
: Truebatch_sampler
: no_duplicates
All Hyperparameters
Click to expand
overwrite_output_dir
: Falsedo_predict
: Falseeval_strategy
: stepsprediction_loss_only
: Trueper_device_train_batch_size
: 32per_device_eval_batch_size
: 16per_gpu_train_batch_size
: Noneper_gpu_eval_batch_size
: Nonegradient_accumulation_steps
: 1eval_accumulation_steps
: Nonelearning_rate
: 2e-05weight_decay
: 0.0adam_beta1
: 0.9adam_beta2
: 0.999adam_epsilon
: 1e-08max_grad_norm
: 1.0num_train_epochs
: 1max_steps
: -1lr_scheduler_type
: linearlr_scheduler_kwargs
: {}warmup_ratio
: 0.1warmup_steps
: 0log_level
: passivelog_level_replica
: warninglog_on_each_node
: Truelogging_nan_inf_filter
: Truesave_safetensors
: Truesave_on_each_node
: Falsesave_only_model
: Falserestore_callback_states_from_checkpoint
: Falseno_cuda
: Falseuse_cpu
: Falseuse_mps_device
: Falseseed
: 42data_seed
: Nonejit_mode_eval
: Falseuse_ipex
: Falsebf16
: Falsefp16
: Truefp16_opt_level
: O1half_precision_backend
: autobf16_full_eval
: Falsefp16_full_eval
: Falsetf32
: Nonelocal_rank
: 0ddp_backend
: Nonetpu_num_cores
: Nonetpu_metrics_debug
: Falsedebug
: []dataloader_drop_last
: Falsedataloader_num_workers
: 0dataloader_prefetch_factor
: Nonepast_index
: -1disable_tqdm
: Falseremove_unused_columns
: Truelabel_names
: Noneload_best_model_at_end
: Falseignore_data_skip
: Falsefsdp
: []fsdp_min_num_params
: 0fsdp_config
: {'min_num_params': 0, 'xla': False, 'xla_fsdp_v2': False, 'xla_fsdp_grad_ckpt': False}fsdp_transformer_layer_cls_to_wrap
: Noneaccelerator_config
: {'split_batches': False, 'dispatch_batches': None, 'even_batches': True, 'use_seedable_sampler': True, 'non_blocking': False, 'gradient_accumulation_kwargs': None}deepspeed
: Nonelabel_smoothing_factor
: 0.0optim
: adamw_torchoptim_args
: Noneadafactor
: Falsegroup_by_length
: Falselength_column_name
: lengthddp_find_unused_parameters
: Noneddp_bucket_cap_mb
: Noneddp_broadcast_buffers
: Falsedataloader_pin_memory
: Truedataloader_persistent_workers
: Falseskip_memory_metrics
: Trueuse_legacy_prediction_loop
: Falsepush_to_hub
: Falseresume_from_checkpoint
: Nonehub_model_id
: Nonehub_strategy
: every_savehub_private_repo
: Falsehub_always_push
: Falsegradient_checkpointing
: Falsegradient_checkpointing_kwargs
: Noneinclude_inputs_for_metrics
: Falseeval_do_concat_batches
: Truefp16_backend
: autopush_to_hub_model_id
: Nonepush_to_hub_organization
: Nonemp_parameters
:auto_find_batch_size
: Falsefull_determinism
: Falsetorchdynamo
: Noneray_scope
: lastddp_timeout
: 1800torch_compile
: Falsetorch_compile_backend
: Nonetorch_compile_mode
: Nonedispatch_batches
: Nonesplit_batches
: Noneinclude_tokens_per_second
: Falseinclude_num_input_tokens_seen
: Falseneftune_noise_alpha
: Noneoptim_target_modules
: Nonebatch_eval_metrics
: Falsebatch_sampler
: no_duplicatesmulti_dataset_batch_sampler
: proportional
Training Logs
Epoch | Step | Training Loss | sentence-transformers/sentence-t5-base_cosine_map@100 |
---|---|---|---|
0.7937 | 100 | 0.0 | 0.0 |
Framework Versions
- Python: 3.11.5
- Sentence Transformers: 3.0.1
- Transformers: 4.41.2
- PyTorch: 2.1.2+cu121
- Accelerate: 0.31.0
- Datasets: 2.19.1
- Tokenizers: 0.19.1
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",
}
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}
}
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Model tree for juanpablomesa/sentence-t5-base-bioasq-1epoch-batch32-100steps
Base model
sentence-transformers/sentence-t5-base
Finetuned
this model
Evaluation results
- Cosine Accuracy@1 on sentence transformers/sentence t5 baseself-reported0.000
- Cosine Accuracy@3 on sentence transformers/sentence t5 baseself-reported0.000
- Cosine Accuracy@5 on sentence transformers/sentence t5 baseself-reported0.000
- Cosine Accuracy@10 on sentence transformers/sentence t5 baseself-reported0.000
- Cosine Precision@1 on sentence transformers/sentence t5 baseself-reported0.000
- Cosine Precision@3 on sentence transformers/sentence t5 baseself-reported0.000
- Cosine Precision@5 on sentence transformers/sentence t5 baseself-reported0.000
- Cosine Precision@10 on sentence transformers/sentence t5 baseself-reported0.000
- Cosine Recall@1 on sentence transformers/sentence t5 baseself-reported0.000
- Cosine Recall@3 on sentence transformers/sentence t5 baseself-reported0.000