metadata
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.
ACE 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 model finetuned from 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
- Maximum Sequence Length: 384 tokens
- Output Dimensionality: 768 tokens
- Similarity Function: Cosine Similarity
- Language: en
- License: apache-2.0
Model Sources
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:
pip install -U sentence-transformers
Then you can load this model and run inference.
from sentence_transformers import SentenceTransformer
model = SentenceTransformer("juanpablomesa/all-mpnet-base-v2-bioasq-matryoshka")
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)
similarities = model.similarity(embeddings, embeddings)
print(similarities.shape)
Evaluation
Metrics
Information Retrieval
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
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
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
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
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 |
- min: 3 tokens
- mean: 63.14 tokens
- max: 384 tokens
|
- min: 5 tokens
- mean: 16.13 tokens
- max: 49 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:
MatryoshkaLoss
with these parameters:{
"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
Click to expand
overwrite_output_dir
: False
do_predict
: False
eval_strategy
: epoch
prediction_loss_only
: True
per_device_train_batch_size
: 32
per_device_eval_batch_size
: 16
per_gpu_train_batch_size
: None
per_gpu_eval_batch_size
: None
gradient_accumulation_steps
: 16
eval_accumulation_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
: 4
max_steps
: -1
lr_scheduler_type
: cosine
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
: True
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
: True
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_fused
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
batch_sampler
: no_duplicates
multi_dataset_batch_sampler
: proportional
Training Logs
Epoch |
Step |
Training Loss |
dim_128_cosine_map@100 |
dim_256_cosine_map@100 |
dim_512_cosine_map@100 |
dim_64_cosine_map@100 |
dim_768_cosine_map@100 |
0.8889 |
7 |
- |
0.8540 |
0.8752 |
0.8825 |
0.8050 |
0.8864 |
1.2698 |
10 |
1.2032 |
- |
- |
- |
- |
- |
1.9048 |
15 |
- |
0.8569 |
0.8775 |
0.8850 |
0.8169 |
0.8840 |
2.5397 |
20 |
0.5051 |
- |
- |
- |
- |
- |
2.9206 |
23 |
- |
0.861 |
0.8794 |
0.8866 |
0.8242 |
0.8858 |
3.5556 |
28 |
- |
0.8609 |
0.8787 |
0.8871 |
0.8224 |
0.8868 |
- The bold row denotes the saved checkpoint.
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",
}
MatryoshkaLoss
@misc{kusupati2024matryoshka,
title={Matryoshka Representation Learning},
author={Aditya Kusupati and Gantavya Bhatt and Aniket Rege and Matthew Wallingford and Aditya Sinha and Vivek Ramanujan and William Howard-Snyder and Kaifeng Chen and Sham Kakade and Prateek Jain and Ali Farhadi},
year={2024},
eprint={2205.13147},
archivePrefix={arXiv},
primaryClass={cs.LG}
}
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}
}