---
base_model: allenai/specter2_base
library_name: sentence-transformers
pipeline_tag: sentence-similarity
tags:
- sentence-transformers
- sentence-similarity
- feature-extraction
- generated_from_trainer
- dataset_size:6574
- loss:MultipleNegativesRankingLoss
widget:
- source_sentence: sigma N protein interactions
sentences:
- 'Smoking Relapse After Lung Transplantation: Is a Second Transplant Justified? '
- 'Core RNA polymerase and promoter DNA interactions of purified domains of sigma
N: bipartite functions. '
- 'Protein-protein interactions mapped by artificial proteases: where sigma factors
bind to RNA polymerase. '
- source_sentence: Frailty pathway co-design
sentences:
- 'High-Sensitivity Cardiac Troponin I Levels in Normal and Hypertensive Pregnancy. '
- 'The systematic approach to improving care for Frail Older Patients (SAFE) study:
A protocol for co-designing a frail older person''s pathway. '
- 'Frailty: successful clinical practice implementation. '
- source_sentence: Diurnal lipid metabolism in lactating sheep
sentences:
- 'Interpreting and applying the EUFEST results using number needed to treat: antipsychotic
effectiveness in first-episode schizophrenia. '
- 'Diurnal variations in the concentration, arteriovenous difference, extraction
ratio, and uptake of 3-hydroxybutyrate and plasma free fatty acids in the hind
limb of lactating sheep. '
- 'Diurnal regulation of milk lipid production and milk secretion in the rat: effect
of dietary protein and energy restriction. '
- source_sentence: Ectopic gastric mucosa
sentences:
- '[Ectopic cardia and gastroesophageal reflux]. '
- 'A bacterial toxicity assay performed with microplates, microluminometry and Microtox
reagent. '
- 'Gastric polyp. '
- source_sentence: monograph editing
sentences:
- 'Monographs editor. '
- 'Maternal stress and high-fat diet effect on maternal behavior, milk composition,
and pup ingestive behavior. '
- 'The editing life. '
---
# SentenceTransformer based on allenai/specter2_base
This is a [sentence-transformers](https://www.SBERT.net) model finetuned from [allenai/specter2_base](https://huggingface.co/allenai/specter2_base) on the json 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:** [allenai/specter2_base](https://huggingface.co/allenai/specter2_base)
- **Maximum Sequence Length:** 512 tokens
- **Output Dimensionality:** 768 tokens
- **Similarity Function:** Cosine Similarity
- **Training Dataset:**
- json
### Model Sources
- **Documentation:** [Sentence Transformers Documentation](https://sbert.net)
- **Repository:** [Sentence Transformers on GitHub](https://github.com/UKPLab/sentence-transformers)
- **Hugging Face:** [Sentence Transformers on Hugging Face](https://huggingface.co/models?library=sentence-transformers)
### 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': 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})
)
```
## Usage
### Direct Usage (Sentence Transformers)
First install the Sentence Transformers library:
```bash
pip install -U sentence-transformers
```
Then you can load this model and run inference.
```python
from sentence_transformers import SentenceTransformer
# Download from the 🤗 Hub
model = SentenceTransformer("sentence_transformers_model_id")
# Run inference
sentences = [
'monograph editing',
'Monographs editor. ',
'The editing life. ',
]
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]
```
## Training Details
### Training Dataset
#### json
* Dataset: json
* Size: 6,574 training samples
* Columns: anchor, positive, and negative
* Approximate statistics based on the first 1000 samples:
| | anchor | positive | negative |
|:--------|:---------------------------------------------------------------------------------|:----------------------------------------------------------------------------------|:----------------------------------------------------------------------------------|
| type | string | string | string |
| details | - min: 3 tokens
- mean: 7.59 tokens
- max: 33 tokens
| - min: 4 tokens
- mean: 19.89 tokens
- max: 70 tokens
| - min: 3 tokens
- mean: 11.97 tokens
- max: 50 tokens
|
* Samples:
| anchor | positive | negative |
|:-------------------------------------------------|:--------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------|
| α-Alumina Nanoparticle Grafting | Grafting PMMA Brushes from α-Alumina Nanoparticles via SI-ATRP. | Mesoporous alumina from colloidal biotemplating of Al clusters. |
| Congenital candidiasis septic shock | Congenital candidiasis presenting as septic shock without rash. | Congenital cutaneous candidiasis: clinical presentation, pathogenesis, and management guidelines. |
| Chronic Venous Occlusion | Anatomic response of canine hindlimb vasculature to chronic venous occlusion. | Chronic venous insufficiency. |
* Loss: [MultipleNegativesRankingLoss](https://sbert.net/docs/package_reference/sentence_transformer/losses.html#multiplenegativesrankingloss) with these parameters:
```json
{
"scale": 20.0,
"similarity_fct": "cos_sim"
}
```
### Training Hyperparameters
#### Non-Default Hyperparameters
- `per_device_train_batch_size`: 32
- `per_device_eval_batch_size`: 32
- `learning_rate`: 2e-05
- `num_train_epochs`: 1
- `lr_scheduler_type`: cosine_with_restarts
- `warmup_ratio`: 0.1
- `bf16`: True
- `batch_sampler`: no_duplicates
#### 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`: 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`: 1
- `max_steps`: -1
- `lr_scheduler_type`: cosine_with_restarts
- `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`: True
- `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`: 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`: False
- `hub_always_push`: False
- `gradient_checkpointing`: False
- `gradient_checkpointing_kwargs`: None
- `include_inputs_for_metrics`: False
- `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
- `batch_sampler`: no_duplicates
- `multi_dataset_batch_sampler`: proportional