Add new SentenceTransformer model

552ae17 verified 11 months ago

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tags:
  - sentence-transformers
  - sentence-similarity
  - feature-extraction
  - generated_from_trainer
  - dataset_size:16890
  - loss:CosineSimilarityLoss
base_model: sentence-transformers/all-MiniLM-L6-v2
widget:
  - source_sentence: >-
      What effect does Concanavalin-A have on the generation of cytotoxic
      lymphocytes in alloimmunized mice when administered before or during
      immunization?
    sentences:
      - >-
        Fluorescence studies revealed that 70% of pre-mRNA in nuclear
        ribonucleoprotein particles is accessible for dye binding, with
        approximately 50% AU-nucleotide content in the double-stranded regions.
      - >-
        Concanavalin-A enhances the generation of cytotoxic lymphocytes in
        alloimmunized mice when administered before or during immunization.
      - >-
        Between 1966 and 1973, of 600 mediastinoscopies for pulmonary carcinoma,
        43% were positive, leading to varied surgical outcomes, with a 63%
        survival rate after 2 to 3.5 years for the first 100 operated patients.
  - source_sentence: >-
      Injecting small doses of tetanus toxin into the hippocampus of rats
      induces an epileptiform syndrome characterized by intermittent seizures
      and hyperkinetic behavior, which eventually resolves, while control
      animals receiving neutralized toxin do not exhibit seizures or abnormal
      behavior.
    sentences:
      - >-
        The study found that all 56 children responded positively to both
        arginine and L-dopa, confirming their growth hormone deficiency.
      - >-
        Injecting small doses of tetanus toxin into the hippocampus causes
        immediate paralysis and death in rats, while control animals show no
        effects.
      - >-
        A low noise, programmable gain electrocardiographic amplifier has been
        developed for ECG data acquisition, featuring differential inputs,
        digitally adjustable gains and output offsets, selectable low frequency
        response, and an on-board output monitor multiplexer.
  - source_sentence: >-
      What were the findings of the study regarding the in vivo distribution and
      formation conditions of the 99mTc-Sn-pyrophosphate complexes in rats?
    sentences:
      - >-
        Reactivity of isolated bovine facial vessels to electric stimulation and
        to drugs. The effects of electric stimulation on isometric force
        generation of isolated helical strips of bovine facial arteries (BFA)
        and veins (BFV) were investigated. Whereas BFA always contracted,
        electrically stimulated BFV showed a biphasic response, i.e. a small,
        transient contraction followed by an intense relaxation. The findings
        presented suggest a neurogenic response for the vasodilator component of
        BFV response to electric stimulation. Exogenous catecholamines and
        serotonin dilated the veins; the effects were antagonized by propranolol
        and dihydroergotamine, respectively. Dopamine-induced relaxations were
        only partially inhibited by propranolol; the residual relaxations were
        antagonized by chlorpormazine and haloperidol. Relaxations of the veins
        after electric stimulation or after administration of noradrenaline were
        accompanied by an increase of the cAMP content. In the BFA
        catecholamines, serotonin and histamine increased the tension, whereas
        isoprenaline was ineffective. Acetylcholine contracted the veins and
        relaxed the arteries; both effects were antagonized by atropine.
      - >-
        The patient developed a perforation in the tympanic membrane, which was
        repaired using a tympanoplasty technique.
      - >-
        The study evaluated the in vivo distribution of two
        99mTc-Sn-pyrophosphate complexes in rats, revealing that the
        bone-seeking 2:2 Sn:PyP complex depends on pyrophosphate and hydrogen
        ion concentration, while the kidney-concentrating 2:1 Sn:PyP complex is
        independent of hydrogen ions and forms at low pyrophosphate levels.
  - source_sentence: >-
      What was the estimated molecular weight of protoheme ferro-lyase using the
      radiation inactivation method, and how did irradiation conditions affect
      inactivation?
    sentences:
      - >-
        The molecular weight of protoheme ferro-lyase was estimated to be
        between 250,000 and 320,000 using the radiation inactivation method,
        with less inactivation observed under irradiation in vacuo compared to
        air.
      - >-
        The mitotic index in the cortical compartment of the bursa of Fabricius
        is significantly higher in chicks immunized with sheep red blood cells
        compared to non-immunized chicks, peaking six days post-injection
        alongside the highest serum antibody titer.
      - >-
        The two-mutational-event theory of medullary thyroid cancer is supported
        by findings that C-cell hyperplasia occurs in hereditary cases but not
        in sporadic cases, suggesting it represents the first genetic mutation
        necessary for cancer development.
  - source_sentence: >-
      What are the age-dependent survival characteristics, energy reserves, and
      activity levels of hexacanths from Hymenolepis diminuta?
    sentences:
      - >-
        An experimental study of the survival characteristics, activity and
        energy reserves of the hexacanths of Hymenolepis diminuta. Similar
        survival characteristics were demonstrated for hexacanths of Hymenolepis
        diminuta incubated in Tyrode's solution with or without a glucose
        supplement (0-50 mg/ml). The survival rate of hexacanths in all media
        tested was shown to be age-dependent and led to a maximum life-span of
        approximately 11 h. The amount of energy reserves, as measured by
        microdensitometric determination of PAS+ material, declined rapidly in
        time to a plateau at approximately 8 h. Residual PAS+ matter present
        beyond that period was interpreted as structural and thus non-utilizable
        material. The rate of activity as measured by hook movements declined
        more rapidly, and continuous hook cycles were rarely observed after 2 h
        and ceased after 4 h. A close correlation was demonstrated between the
        decline in PAS+ material and the total number of hook cycles completed
        per unit of time. The quantitative results on survival, energy reserves
        and activity are discussed in relation to the penetration of hexacanths
        into the haemocoele of the intermediate host.
      - >-
        A review of 1500 consecutive coronary angiograms at Harefield Hospital
        since 1970 indicates a significant reduction in mortality, with only 2
        deaths in the last 1000 cases attributed to improved operator training
        and attention to detail, highlighting the necessity of experienced
        oversight for new units.
      - >-
        Radionuclide blood flow studies indicated successful Gelfoam
        embolization of intracranial meningiomas in two patients, as evidenced
        by the absence of tumor visualization during the arterial phase
        post-procedure.
pipeline_tag: sentence-similarity
library_name: sentence-transformers

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

This is a sentence-transformers model finetuned from sentence-transformers/all-MiniLM-L6-v2. 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

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("jaimevera1107/all-MiniLM-pubmed")
# Run inference
sentences = [
    'What are the age-dependent survival characteristics, energy reserves, and activity levels of hexacanths from Hymenolepis diminuta?',
    "An experimental study of the survival characteristics, activity and energy reserves of the hexacanths of Hymenolepis diminuta. Similar survival characteristics were demonstrated for hexacanths of Hymenolepis diminuta incubated in Tyrode's solution with or without a glucose supplement (0-50 mg/ml). The survival rate of hexacanths in all media tested was shown to be age-dependent and led to a maximum life-span of approximately 11 h. The amount of energy reserves, as measured by microdensitometric determination of PAS+ material, declined rapidly in time to a plateau at approximately 8 h. Residual PAS+ matter present beyond that period was interpreted as structural and thus non-utilizable material. The rate of activity as measured by hook movements declined more rapidly, and continuous hook cycles were rarely observed after 2 h and ceased after 4 h. A close correlation was demonstrated between the decline in PAS+ material and the total number of hook cycles completed per unit of time. The quantitative results on survival, energy reserves and activity are discussed in relation to the penetration of hexacanths into the haemocoele of the intermediate host.",
    'A review of 1500 consecutive coronary angiograms at Harefield Hospital since 1970 indicates a significant reduction in mortality, with only 2 deaths in the last 1000 cases attributed to improved operator training and attention to detail, highlighting the necessity of experienced oversight for new units.',
]
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]

Training Details

Training Dataset

Unnamed Dataset

Size: 16,890 training samples
Columns: sentence_0, sentence_1, and label
Approximate statistics based on the first 1000 samples:
sentence_0 sentence_1 label
type string string float
details
min: 10 tokens
mean: 72.87 tokens
max: 256 tokens

min: 4 tokens
mean: 60.5 tokens
max: 256 tokens

min: 0.0
mean: 0.62
max: 1.0

	sentence_0	sentence_1	label
type	string	string	float
details	min: 10 tokens mean: 72.87 tokens max: 256 tokens	min: 4 tokens mean: 60.5 tokens max: 256 tokens	min: 0.0 mean: 0.62 max: 1.0

Samples:

sentence_0	sentence_1	label
`Injecting small doses of tetanus toxin into the hippocampus of rats induces an epileptiform syndrome characterized by intermittent seizures and hyperkinetic behavior, which eventually resolves, while control animals receiving neutralized toxin do not exhibit seizures or abnormal behavior.`	`Injecting small doses of tetanus toxin into the hippocampus causes immediate paralysis and death in rats, while control animals show no effects.`	`0.2`
`Phosphorylation of rat kidney pyruvate kinase type L by cyclic AMP-dependent protein kinase regulates its activity, suggesting hormonal control of gluconeogenesis in the renal cortex.`	`Phosphorylation of rat kidney pyruvate kinase type L by cyclic AMP-dependent protein kinase has no effect on its activity or gluconeogenesis in the renal cortex.`	`0.2`
`What challenges do facially disfigured individuals face in their rehabilitation and social integration, and what measures are needed to address these issues?`	`Public and professional attitudes towards facially disfigured individuals often hinder their rehabilitation and social integration, necessitating improved education and care strategies for healthcare providers.`	`0.75`

Loss: CosineSimilarityLoss with these parameters:

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

Training Hyperparameters

Non-Default Hyperparameters

per_device_train_batch_size: 32
per_device_eval_batch_size: 32
num_train_epochs: 4
fp16: True
multi_dataset_batch_sampler: round_robin

All Hyperparameters

Click to expand

overwrite_output_dir: False
do_predict: False
eval_strategy: no
prediction_loss_only: True
per_device_train_batch_size: 32
per_device_eval_batch_size: 32
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
num_train_epochs: 4
max_steps: -1
lr_scheduler_type: linear
lr_scheduler_kwargs: {}
warmup_ratio: 0.0
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: True
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
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: round_robin

Training Logs

Epoch	Step	Training Loss
0.9470	500	0.0306
1.8939	1000	0.0197
2.8409	1500	0.0165
3.7879	2000	0.0149

Framework Versions

Python: 3.11.9
Sentence Transformers: 4.1.0
Transformers: 4.52.3
PyTorch: 2.7.0+cu118
Accelerate: 1.7.0
Datasets: 3.6.0
Tokenizers: 0.21.1

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",
}