---
base_model: sentence-transformers/all-mpnet-base-v2
datasets: []
language:
- en
library_name: sentence-transformers
license: apache-2.0
metrics:
- cosine_accuracy@1
- cosine_accuracy@3
- cosine_accuracy@5
- cosine_accuracy@10
- cosine_precision@1
- cosine_precision@3
- cosine_precision@5
- cosine_precision@10
- cosine_recall@1
- cosine_recall@3
- cosine_recall@5
- cosine_recall@10
- cosine_ndcg@10
- cosine_mrr@10
- cosine_map@100
pipeline_tag: sentence-similarity
tags:
- sentence-transformers
- sentence-similarity
- feature-extraction
- generated_from_trainer
- dataset_size:4012
- loss:MatryoshkaLoss
- loss:MultipleNegativesRankingLoss
widget:
- source_sentence: 'Extensive messenger RNA editing generates transcript and protein
diversity in genes involved in neural excitability, as previously described, as
well as in genes participating in a broad range of other cellular functions. '
sentences:
- Do cephalopods use RNA editing less frequently than other species?
- GV1001 vaccine targets which enzyme?
- Which event results in the acetylation of S6K1?
- source_sentence: Yes, exposure to household furry pets influences the gut microbiota
of infants.
sentences:
- Can pets affect infant microbiomed?
- What is the mode of action of Thiazovivin?
- What are the effects of CAMK4 inhibition?
- source_sentence: "In children with heart failure evidence of the effect of enalapril\
\ is empirical. Enalapril was clinically safe and effective in 50% to 80% of for\
\ children with cardiac failure secondary to congenital heart malformations before\
\ and after cardiac surgery, impaired ventricular function , valvar regurgitation,\
\ congestive cardiomyopathy, , arterial hypertension, life-threatening arrhythmias\
\ coexisting with circulatory insufficiency. \nACE inhibitors have shown a transient\
\ beneficial effect on heart failure due to anticancer drugs and possibly a beneficial\
\ effect in muscular dystrophy-associated cardiomyopathy, which deserves further\
\ studies."
sentences:
- Which receptors can be evaluated with the [18F]altanserin?
- In what proportion of children with heart failure has Enalapril been shown to
be safe and effective?
- Which major signaling pathways are regulated by RIP1?
- source_sentence: Cellular senescence-associated heterochromatic foci (SAHFS) are
a novel type of chromatin condensation involving alterations of linker histone
H1 and linker DNA-binding proteins. SAHFS can be formed by a variety of cell types,
but their mechanism of action remains unclear.
sentences:
- What is the relationship between the X chromosome and a neutrophil drumstick?
- Which microRNAs are involved in exercise adaptation?
- How are SAHFS created?
- source_sentence: 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.
sentences:
- What are the effects of the deletion of all three Pcdh clusters (tricluster deletion)
in mice?
- what is the role of MEF-2 in cardiomyocyte differentiation?
- How many periods of regulatory innovation led to the evolution of vertebrates?
model-index:
- name: BGE base Financial Matryoshka
results:
- task:
type: information-retrieval
name: Information Retrieval
dataset:
name: dim 768
type: dim_768
metrics:
- type: cosine_accuracy@1
value: 0.8373408769448374
name: Cosine Accuracy@1
- type: cosine_accuracy@3
value: 0.9306930693069307
name: Cosine Accuracy@3
- type: cosine_accuracy@5
value: 0.9448373408769448
name: Cosine Accuracy@5
- type: cosine_accuracy@10
value: 0.958981612446959
name: Cosine Accuracy@10
- type: cosine_precision@1
value: 0.8373408769448374
name: Cosine Precision@1
- type: cosine_precision@3
value: 0.31023102310231027
name: Cosine Precision@3
- type: cosine_precision@5
value: 0.18896746817538893
name: Cosine Precision@5
- type: cosine_precision@10
value: 0.09589816124469587
name: Cosine Precision@10
- type: cosine_recall@1
value: 0.8373408769448374
name: Cosine Recall@1
- type: cosine_recall@3
value: 0.9306930693069307
name: Cosine Recall@3
- type: cosine_recall@5
value: 0.9448373408769448
name: Cosine Recall@5
- type: cosine_recall@10
value: 0.958981612446959
name: Cosine Recall@10
- type: cosine_ndcg@10
value: 0.9038566618329213
name: Cosine Ndcg@10
- type: cosine_mrr@10
value: 0.8855380436002787
name: Cosine Mrr@10
- type: cosine_map@100
value: 0.8867903631779396
name: Cosine Map@100
- task:
type: information-retrieval
name: Information Retrieval
dataset:
name: dim 512
type: dim_512
metrics:
- type: cosine_accuracy@1
value: 0.8373408769448374
name: Cosine Accuracy@1
- type: cosine_accuracy@3
value: 0.9335219236209336
name: Cosine Accuracy@3
- type: cosine_accuracy@5
value: 0.9462517680339463
name: Cosine Accuracy@5
- type: cosine_accuracy@10
value: 0.9603960396039604
name: Cosine Accuracy@10
- type: cosine_precision@1
value: 0.8373408769448374
name: Cosine Precision@1
- type: cosine_precision@3
value: 0.31117397454031115
name: Cosine Precision@3
- type: cosine_precision@5
value: 0.18925035360678924
name: Cosine Precision@5
- type: cosine_precision@10
value: 0.09603960396039603
name: Cosine Precision@10
- type: cosine_recall@1
value: 0.8373408769448374
name: Cosine Recall@1
- type: cosine_recall@3
value: 0.9335219236209336
name: Cosine Recall@3
- type: cosine_recall@5
value: 0.9462517680339463
name: Cosine Recall@5
- type: cosine_recall@10
value: 0.9603960396039604
name: Cosine Recall@10
- type: cosine_ndcg@10
value: 0.9045496377971035
name: Cosine Ndcg@10
- type: cosine_mrr@10
value: 0.8860549830493253
name: Cosine Mrr@10
- type: cosine_map@100
value: 0.8870969130410834
name: Cosine Map@100
- task:
type: information-retrieval
name: Information Retrieval
dataset:
name: dim 256
type: dim_256
metrics:
- type: cosine_accuracy@1
value: 0.8288543140028288
name: Cosine Accuracy@1
- type: cosine_accuracy@3
value: 0.9222065063649222
name: Cosine Accuracy@3
- type: cosine_accuracy@5
value: 0.942008486562942
name: Cosine Accuracy@5
- type: cosine_accuracy@10
value: 0.9533239038189534
name: Cosine Accuracy@10
- type: cosine_precision@1
value: 0.8288543140028288
name: Cosine Precision@1
- type: cosine_precision@3
value: 0.3074021687883074
name: Cosine Precision@3
- type: cosine_precision@5
value: 0.18840169731258838
name: Cosine Precision@5
- type: cosine_precision@10
value: 0.09533239038189532
name: Cosine Precision@10
- type: cosine_recall@1
value: 0.8288543140028288
name: Cosine Recall@1
- type: cosine_recall@3
value: 0.9222065063649222
name: Cosine Recall@3
- type: cosine_recall@5
value: 0.942008486562942
name: Cosine Recall@5
- type: cosine_recall@10
value: 0.9533239038189534
name: Cosine Recall@10
- type: cosine_ndcg@10
value: 0.8963408137245359
name: Cosine Ndcg@10
- type: cosine_mrr@10
value: 0.8774370804427385
name: Cosine Mrr@10
- type: cosine_map@100
value: 0.8786914503856871
name: Cosine Map@100
- task:
type: information-retrieval
name: Information Retrieval
dataset:
name: dim 128
type: dim_128
metrics:
- type: cosine_accuracy@1
value: 0.809052333804809
name: Cosine Accuracy@1
- type: cosine_accuracy@3
value: 0.8995756718528995
name: Cosine Accuracy@3
- type: cosine_accuracy@5
value: 0.9207920792079208
name: Cosine Accuracy@5
- type: cosine_accuracy@10
value: 0.9405940594059405
name: Cosine Accuracy@10
- type: cosine_precision@1
value: 0.809052333804809
name: Cosine Precision@1
- type: cosine_precision@3
value: 0.29985855728429983
name: Cosine Precision@3
- type: cosine_precision@5
value: 0.18415841584158416
name: Cosine Precision@5
- type: cosine_precision@10
value: 0.09405940594059406
name: Cosine Precision@10
- type: cosine_recall@1
value: 0.809052333804809
name: Cosine Recall@1
- type: cosine_recall@3
value: 0.8995756718528995
name: Cosine Recall@3
- type: cosine_recall@5
value: 0.9207920792079208
name: Cosine Recall@5
- type: cosine_recall@10
value: 0.9405940594059405
name: Cosine Recall@10
- type: cosine_ndcg@10
value: 0.8794609712523561
name: Cosine Ndcg@10
- type: cosine_mrr@10
value: 0.8593930311398488
name: Cosine Mrr@10
- type: cosine_map@100
value: 0.8608652296821839
name: Cosine Map@100
- task:
type: information-retrieval
name: Information Retrieval
dataset:
name: dim 64
type: dim_64
metrics:
- type: cosine_accuracy@1
value: 0.7694483734087695
name: Cosine Accuracy@1
- type: cosine_accuracy@3
value: 0.8613861386138614
name: Cosine Accuracy@3
- type: cosine_accuracy@5
value: 0.8868458274398868
name: Cosine Accuracy@5
- type: cosine_accuracy@10
value: 0.9080622347949081
name: Cosine Accuracy@10
- type: cosine_precision@1
value: 0.7694483734087695
name: Cosine Precision@1
- type: cosine_precision@3
value: 0.2871287128712871
name: Cosine Precision@3
- type: cosine_precision@5
value: 0.17736916548797735
name: Cosine Precision@5
- type: cosine_precision@10
value: 0.09080622347949079
name: Cosine Precision@10
- type: cosine_recall@1
value: 0.7694483734087695
name: Cosine Recall@1
- type: cosine_recall@3
value: 0.8613861386138614
name: Cosine Recall@3
- type: cosine_recall@5
value: 0.8868458274398868
name: Cosine Recall@5
- type: cosine_recall@10
value: 0.9080622347949081
name: Cosine Recall@10
- type: cosine_ndcg@10
value: 0.841605620432732
name: Cosine Ndcg@10
- type: cosine_mrr@10
value: 0.8200012348173592
name: Cosine Mrr@10
- type: cosine_map@100
value: 0.8223782042287946
name: Cosine Map@100
---
# BGE base Financial Matryoshka
This is a [sentence-transformers](https://www.SBERT.net) model finetuned from [sentence-transformers/all-mpnet-base-v2](https://huggingface.co./sentence-transformers/all-mpnet-base-v2). 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/all-mpnet-base-v2](https://huggingface.co./sentence-transformers/all-mpnet-base-v2)
- **Maximum Sequence Length:** 384 tokens
- **Output Dimensionality:** 768 tokens
- **Similarity Function:** Cosine Similarity
- **Language:** en
- **License:** apache-2.0
### 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': 384, 'do_lower_case': False}) with Transformer model: MPNetModel
(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): Normalize()
)
```
## 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("juanpablomesa/all-mpnet-base-v2-bioasq-matryoshka")
# 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: `dim_768`
* Evaluated with [InformationRetrievalEvaluator
](https://sbert.net/docs/package_reference/sentence_transformer/evaluation.html#sentence_transformers.evaluation.InformationRetrievalEvaluator)
| Metric | Value |
|:--------------------|:-----------|
| cosine_accuracy@1 | 0.8373 |
| cosine_accuracy@3 | 0.9307 |
| cosine_accuracy@5 | 0.9448 |
| cosine_accuracy@10 | 0.959 |
| cosine_precision@1 | 0.8373 |
| cosine_precision@3 | 0.3102 |
| cosine_precision@5 | 0.189 |
| cosine_precision@10 | 0.0959 |
| cosine_recall@1 | 0.8373 |
| cosine_recall@3 | 0.9307 |
| cosine_recall@5 | 0.9448 |
| cosine_recall@10 | 0.959 |
| cosine_ndcg@10 | 0.9039 |
| cosine_mrr@10 | 0.8855 |
| **cosine_map@100** | **0.8868** |
#### Information Retrieval
* Dataset: `dim_512`
* Evaluated with [InformationRetrievalEvaluator
](https://sbert.net/docs/package_reference/sentence_transformer/evaluation.html#sentence_transformers.evaluation.InformationRetrievalEvaluator)
| Metric | Value |
|:--------------------|:-----------|
| cosine_accuracy@1 | 0.8373 |
| cosine_accuracy@3 | 0.9335 |
| cosine_accuracy@5 | 0.9463 |
| cosine_accuracy@10 | 0.9604 |
| cosine_precision@1 | 0.8373 |
| cosine_precision@3 | 0.3112 |
| cosine_precision@5 | 0.1893 |
| cosine_precision@10 | 0.096 |
| cosine_recall@1 | 0.8373 |
| cosine_recall@3 | 0.9335 |
| cosine_recall@5 | 0.9463 |
| cosine_recall@10 | 0.9604 |
| cosine_ndcg@10 | 0.9045 |
| cosine_mrr@10 | 0.8861 |
| **cosine_map@100** | **0.8871** |
#### Information Retrieval
* Dataset: `dim_256`
* Evaluated with [InformationRetrievalEvaluator
](https://sbert.net/docs/package_reference/sentence_transformer/evaluation.html#sentence_transformers.evaluation.InformationRetrievalEvaluator)
| Metric | Value |
|:--------------------|:-----------|
| cosine_accuracy@1 | 0.8289 |
| cosine_accuracy@3 | 0.9222 |
| cosine_accuracy@5 | 0.942 |
| cosine_accuracy@10 | 0.9533 |
| cosine_precision@1 | 0.8289 |
| cosine_precision@3 | 0.3074 |
| cosine_precision@5 | 0.1884 |
| cosine_precision@10 | 0.0953 |
| cosine_recall@1 | 0.8289 |
| cosine_recall@3 | 0.9222 |
| cosine_recall@5 | 0.942 |
| cosine_recall@10 | 0.9533 |
| cosine_ndcg@10 | 0.8963 |
| cosine_mrr@10 | 0.8774 |
| **cosine_map@100** | **0.8787** |
#### Information Retrieval
* Dataset: `dim_128`
* Evaluated with [InformationRetrievalEvaluator
](https://sbert.net/docs/package_reference/sentence_transformer/evaluation.html#sentence_transformers.evaluation.InformationRetrievalEvaluator)
| Metric | Value |
|:--------------------|:-----------|
| cosine_accuracy@1 | 0.8091 |
| cosine_accuracy@3 | 0.8996 |
| cosine_accuracy@5 | 0.9208 |
| cosine_accuracy@10 | 0.9406 |
| cosine_precision@1 | 0.8091 |
| cosine_precision@3 | 0.2999 |
| cosine_precision@5 | 0.1842 |
| cosine_precision@10 | 0.0941 |
| cosine_recall@1 | 0.8091 |
| cosine_recall@3 | 0.8996 |
| cosine_recall@5 | 0.9208 |
| cosine_recall@10 | 0.9406 |
| cosine_ndcg@10 | 0.8795 |
| cosine_mrr@10 | 0.8594 |
| **cosine_map@100** | **0.8609** |
#### Information Retrieval
* Dataset: `dim_64`
* Evaluated with [InformationRetrievalEvaluator
](https://sbert.net/docs/package_reference/sentence_transformer/evaluation.html#sentence_transformers.evaluation.InformationRetrievalEvaluator)
| Metric | Value |
|:--------------------|:-----------|
| cosine_accuracy@1 | 0.7694 |
| cosine_accuracy@3 | 0.8614 |
| cosine_accuracy@5 | 0.8868 |
| cosine_accuracy@10 | 0.9081 |
| cosine_precision@1 | 0.7694 |
| cosine_precision@3 | 0.2871 |
| cosine_precision@5 | 0.1774 |
| cosine_precision@10 | 0.0908 |
| cosine_recall@1 | 0.7694 |
| cosine_recall@3 | 0.8614 |
| cosine_recall@5 | 0.8868 |
| cosine_recall@10 | 0.9081 |
| cosine_ndcg@10 | 0.8416 |
| cosine_mrr@10 | 0.82 |
| **cosine_map@100** | **0.8224** |
## Training Details
### Training Dataset
#### Unnamed Dataset
* Size: 4,012 training samples
* Columns: positive
and anchor
* Approximate statistics based on the first 1000 samples:
| | positive | anchor |
|:--------|:-----------------------------------------------------------------------------------|:----------------------------------------------------------------------------------|
| type | string | string |
| details |
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: [MatryoshkaLoss
](https://sbert.net/docs/package_reference/sentence_transformer/losses.html#matryoshkaloss) with these parameters:
```json
{
"loss": "MultipleNegativesRankingLoss",
"matryoshka_dims": [
768,
512,
256,
128,
64
],
"matryoshka_weights": [
1,
1,
1,
1,
1
],
"n_dims_per_step": -1
}
```
### Training Hyperparameters
#### Non-Default Hyperparameters
- `eval_strategy`: epoch
- `per_device_train_batch_size`: 32
- `per_device_eval_batch_size`: 16
- `gradient_accumulation_steps`: 16
- `learning_rate`: 2e-05
- `num_train_epochs`: 4
- `lr_scheduler_type`: cosine
- `warmup_ratio`: 0.1
- `bf16`: True
- `tf32`: True
- `load_best_model_at_end`: True
- `optim`: adamw_torch_fused
- `batch_sampler`: no_duplicates
#### All Hyperparameters