Add new SentenceTransformer model

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tags:
  - sentence-transformers
  - sentence-similarity
  - feature-extraction
  - dense
  - generated_from_trainer
  - dataset_size:5424
  - loss:MultipleNegativesRankingLoss
base_model: cambridgeltl/SapBERT-from-PubMedBERT-fulltext
widget:
  - source_sentence: >-
      liver injury [SEP] d up all transplant-free survivors of
      paracetamol-induced acute liver injury, hospitalized in a Danish national
      referral centre during 1984-
    sentences:
      - >-
        Drug-Induced Liver Injury [SEP] A spectrum of clinical liver diseases
        ranging from mild biochemical abnormalities to ACUTE LIVER FAILURE,
        caused by drugs, drug 
      - >-
        Venous Thrombosis [SEP] The formation or presence of a blood clot
        (THROMBUS) within a vein.
            
      - >-
        Isoflurophate [SEP] A di-isopropyl-fluorophosphate which is an
        irreversible cholinesterase inhibitor used to investigate the NERVOUS
        SYSTEM.
            
  - source_sentence: >-
      renal impairment [SEP] 6, 95% CI 1.57-2.44) in patients with diabetes. A
      lower risk of renal impairment was seen in both groups with beta-blocker
      therapy (RR 0.70, 95%
    sentences:
      - >-
        Acetylcholine [SEP] A neurotransmitter found at neuromuscular junctions,
        autonomic ganglia, parasympathetic effector junctions, a subset of
        sympathe
      - >-
        Pilocarpine [SEP] A slowly hydrolyzed muscarinic agonist with no
        nicotinic effects. Pilocarpine is used as a miotic and in the treatment
        of glauco
      - >-
        Renal Insufficiency [SEP] Conditions in which the KIDNEYS perform below
        the normal level in the ability to remove wastes, concentrate URINE, and
        maintain 
  - source_sentence: >-
      grand mal seizures [SEP] MMARY: A 46-year-old African-American man
      experienced recurrent grand mal seizures during intravenous infusion of
      amphotericin B, then petit mal s
    sentences:
      - >-
        Lithium Carbonate [SEP] A lithium salt, classified as a mood-stabilizing
        agent. Lithium ion alters the metabolism of BIOGENIC MONOAMINES in the
        CENTRAL 
      - >-
        Epilepsy, Tonic-Clonic [SEP] A generalized seizure disorder
        characterized by recurrent major motor seizures. The initial brief tonic
        phase is marked by trunk
      - >-
        Neurotoxicity Syndromes [SEP] Neurologic disorders caused by exposure to
        toxic substances through ingestion, injection, cutaneous application, or
        other method
  - source_sentence: >-
      seizure [SEP] OBJECTIVE: To report a case of multiple episodes of seizure
      activity in an AIDS patent following amphotericin B infusion. C
    sentences:
      - >-
        Catalepsy [SEP] A condition characterized by inactivity, decreased
        responsiveness to stimuli, and a tendency to maintain an immobile
        posture. Th
      - >-
        Seizures [SEP] Clinical or subclinical disturbances of cortical function
        due to a sudden, abnormal, excessive, and disorganized discharge of br
      - 'ammonium acetate [SEP] '
  - source_sentence: >-
      insomnia [SEP] pressive symptoms was admitted to a psychiatric hospital
      due to insomnia, loss of appetite, exhaustion, and agitation. Medical
      treatment
    sentences:
      - >-
        Atrioventricular Block [SEP] Impaired impulse conduction from HEART
        ATRIA to HEART VENTRICLES. AV block can mean delayed or completely
        blocked impulse conduc
      - >-
        Sodium [SEP] A member of the alkali group of metals. It has the atomic
        symbol Na, atomic number 11, and atomic weight 23.
            
      - >-
        Sleep Initiation and Maintenance Disorders [SEP] Disorders characterized
        by impairment of the ability to initiate or maintain sleep. This may
        occur as a primary disorder or in a
datasets:
  - Stevenf232/BC5CDR_MeSH2015_complete
pipeline_tag: sentence-similarity
library_name: sentence-transformers

SentenceTransformer based on cambridgeltl/SapBERT-from-PubMedBERT-fulltext

This is a sentence-transformers model finetuned from cambridgeltl/SapBERT-from-PubMedBERT-fulltext on the bc5_cdr_me_sh2015_complete dataset. 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: cambridgeltl/SapBERT-from-PubMedBERT-fulltext
Maximum Sequence Length: 512 tokens
Output Dimensionality: 768 dimensions
Similarity Function: Cosine Similarity
Training Dataset:
- bc5_cdr_me_sh2015_complete

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, 'architecture': '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})
)

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("Stevenf232/SapBERT_MultipleNegativesRankingLoss_BC5CDR_Context")
# Run inference
sentences = [
    'insomnia [SEP] pressive symptoms was admitted to a psychiatric hospital due to insomnia, loss of appetite, exhaustion, and agitation. Medical treatment',
    'Sleep Initiation and Maintenance Disorders [SEP] Disorders characterized by impairment of the ability to initiate or maintain sleep. This may occur as a primary disorder or in a',
    'Atrioventricular Block [SEP] Impaired impulse conduction from HEART ATRIA to HEART VENTRICLES. AV block can mean delayed or completely blocked impulse conduc',
]
embeddings = model.encode(sentences)
print(embeddings.shape)
# [3, 768]

# Get the similarity scores for the embeddings
similarities = model.similarity(embeddings, embeddings)
print(similarities)
# tensor([[1.0000, 0.8093, 0.1453],
#         [0.8093, 1.0000, 0.1948],
#         [0.1453, 0.1948, 1.0000]])

Training Details

Training Dataset

bc5_cdr_me_sh2015_complete

Dataset: bc5_cdr_me_sh2015_complete at f40f655
Size: 5,424 training samples
Columns: sentence1, sentence2, and label
Approximate statistics based on the first 1000 samples:
sentence1 sentence2 label
type string string int
details
min: 9 tokens
mean: 29.07 tokens
max: 79 tokens

min: 4 tokens
mean: 25.04 tokens
max: 43 tokens

1: 100.00%

	sentence1	sentence2	label
type	string	string	int
details	min: 9 tokens mean: 29.07 tokens max: 79 tokens	min: 4 tokens mean: 25.04 tokens max: 43 tokens	1: 100.00%

Samples:

sentence1	sentence2	label
`Naloxone [SEP] Naloxone reverses the antihypertensive effect of clonidine.`	`Naloxone [SEP] A specific opiate antagonist that has no agonist activity. It is a competitive antagonist at mu, delta, and kappa opioid recepto`	`1`
`clonidine [SEP] Naloxone reverses the antihypertensive effect of clonidine.`	`Clonidine [SEP] An imidazoline sympatholytic agent that stimulates ALPHA-2 ADRENERGIC RECEPTORS and central IMIDAZOLINE RECEPTORS. It is commonl`	`1`
`hypertensive [SEP] In unanesthetized, spontaneously hypertensive rats the decrease in blood pressure and heart rate produced by`	`Hypertension [SEP] Persistently high systemic arterial BLOOD PRESSURE. Based on multiple readings (BLOOD PRESSURE DETERMINATION), hypertension is c`	`1`

Loss: MultipleNegativesRankingLoss with these parameters:

{
    "scale": 20.0,
    "similarity_fct": "cos_sim",
    "gather_across_devices": false
}

Evaluation Dataset

bc5_cdr_me_sh2015_complete

Dataset: bc5_cdr_me_sh2015_complete at f40f655
Size: 5,445 evaluation samples
Columns: sentence1, sentence2, and label
Approximate statistics based on the first 1000 samples:
sentence1 sentence2 label
type string string int
details
min: 11 tokens
mean: 30.69 tokens
max: 166 tokens

min: 4 tokens
mean: 24.66 tokens
max: 62 tokens

1: 100.00%

	sentence1	sentence2	label
type	string	string	int
details	min: 11 tokens mean: 30.69 tokens max: 166 tokens	min: 4 tokens mean: 24.66 tokens max: 62 tokens	1: 100.00%

Samples:

sentence1	sentence2	label
`Tricuspid valve regurgitation [SEP] Tricuspid valve regurgitation and lithium carbonate toxicity in a newborn infant.`	`Tricuspid Valve Insufficiency [SEP] Backflow of blood from the RIGHT VENTRICLE into the RIGHT ATRIUM due to imperfect closure of the TRICUSPID VALVE.`	`1`
`lithium carbonate [SEP] Tricuspid valve regurgitation and lithium carbonate toxicity in a newborn infant.`	`Lithium Carbonate [SEP] A lithium salt, classified as a mood-stabilizing agent. Lithium ion alters the metabolism of BIOGENIC MONOAMINES in the CENTRAL`	`1`
`toxicity [SEP] Tricuspid valve regurgitation and lithium carbonate toxicity in a newborn infant.`	`Drug-Related Side Effects and Adverse Reactions [SEP] Disorders that result from the intended use of PHARMACEUTICAL PREPARATIONS. Included in this heading are a broad variety of chem`	`1`

Loss: MultipleNegativesRankingLoss with these parameters:

{
    "scale": 20.0,
    "similarity_fct": "cos_sim",
    "gather_across_devices": false
}

Training Hyperparameters

Non-Default Hyperparameters

eval_strategy: steps
per_device_train_batch_size: 64
per_device_eval_batch_size: 64
learning_rate: 2e-05
max_steps: 200
warmup_ratio: 0.1
warmup_steps: 0.1
fp16: True

All Hyperparameters

Click to expand

do_predict: False
eval_strategy: steps
prediction_loss_only: True
per_device_train_batch_size: 64
per_device_eval_batch_size: 64
gradient_accumulation_steps: 1
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: 3
max_steps: 200
lr_scheduler_type: linear
lr_scheduler_kwargs: None
warmup_ratio: 0.1
warmup_steps: 0.1
log_level: passive
log_level_replica: warning
log_on_each_node: True
logging_nan_inf_filter: True
enable_jit_checkpoint: False
save_on_each_node: False
save_only_model: False
restore_callback_states_from_checkpoint: False
use_cpu: False
seed: 42
data_seed: None
bf16: False
fp16: True
bf16_full_eval: False
fp16_full_eval: False
tf32: None
local_rank: -1
ddp_backend: None
debug: []
dataloader_drop_last: False
dataloader_num_workers: 0
dataloader_prefetch_factor: None
disable_tqdm: False
remove_unused_columns: True
label_names: None
load_best_model_at_end: False
ignore_data_skip: False
fsdp: []
fsdp_config: {'min_num_params': 0, 'xla': False, 'xla_fsdp_v2': False, 'xla_fsdp_grad_ckpt': False}
accelerator_config: {'split_batches': False, 'dispatch_batches': None, 'even_batches': True, 'use_seedable_sampler': True, 'non_blocking': False, 'gradient_accumulation_kwargs': None}
parallelism_config: None
deepspeed: None
label_smoothing_factor: 0.0
optim: adamw_torch_fused
optim_args: None
group_by_length: False
length_column_name: length
project: huggingface
trackio_space_id: trackio
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
push_to_hub: False
resume_from_checkpoint: None
hub_model_id: None
hub_strategy: every_save
hub_private_repo: None
hub_always_push: False
hub_revision: None
gradient_checkpointing: False
gradient_checkpointing_kwargs: None
include_for_metrics: []
eval_do_concat_batches: True
auto_find_batch_size: False
full_determinism: False
ddp_timeout: 1800
torch_compile: False
torch_compile_backend: None
torch_compile_mode: None
include_num_input_tokens_seen: no
neftune_noise_alpha: None
optim_target_modules: None
batch_eval_metrics: False
eval_on_start: False
use_liger_kernel: False
liger_kernel_config: None
eval_use_gather_object: False
average_tokens_across_devices: True
use_cache: False
prompts: None
batch_sampler: batch_sampler
multi_dataset_batch_sampler: proportional
router_mapping: {}
learning_rate_mapping: {}

Training Logs

Epoch	Step	Training Loss	Validation Loss
0.1176	10	2.6695	2.4324
0.2353	20	2.2030	1.8628
0.3529	30	1.6394	1.5455
0.4706	40	1.5937	1.3570
0.5882	50	1.3294	1.2489
0.7059	60	1.2576	1.1594
0.8235	70	1.0213	1.1042
0.9412	80	1.0295	1.0672
1.0588	90	0.8890	1.0293
1.1765	100	0.9259	1.0030
1.2941	110	0.8096	0.9743
1.4118	120	0.7438	0.9587
1.5294	130	0.7797	0.9442
1.6471	140	0.7999	0.9265
1.7647	150	0.7323	0.9142
1.8824	160	0.7510	0.9070
2.0	170	0.7297	0.9032
2.1176	180	0.6434	0.8985
2.2353	190	0.5984	0.8967
2.3529	200	0.6603	0.8959

Framework Versions

Python: 3.12.12
Sentence Transformers: 5.2.3
Transformers: 5.0.0
PyTorch: 2.10.0+cu128
Accelerate: 1.12.0
Datasets: 4.0.0
Tokenizers: 0.22.2

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}
}