---
language:
- en
license: apache-2.0
tags:
- sentence-transformers
- sentence-similarity
- feature-extraction
- generated_from_trainer
- dataset_size:1567
- loss:MatryoshkaLoss
- loss:MultipleNegativesRankingLoss
base_model: nomic-ai/modernbert-embed-base
widget:
- source_sentence: How many authors are listed for the trial?
sentences:
- 'chemotherapy and bone marrow transplantation for certain malignancies and has
a long track
record of safe use in adults and children. The incidence of adverse events such
as fever, chills,
bone pain, dyspnea, tachycardia, and hemodynamic instability was no different
between GM-
CSF and placebo-treated groups in controlled adult BMT studies. Rapid IV administration
of'
- 'clinical ICU staff in accordance with institutional practice and judgment.
Child Assent Subjects who are eligible for this study will be critically ill,
and child assent is
typically not possible at the time of study enrollment. However, during follow
up after discharge
from the ICU, issues about assent become applicable. Children who are capable
of giving assent'
- 'Controlled Phase 2 Trial. Stroke, 49(5):1210–1216, 2018.
[76] M. K. R. Somagutta, M. K. Lourdes Pormento, P. Hamid, A. Hamdan, M. A. Khan,
R. Desir, R. Vijayan, S. Shirke, R. Jeyakumar, Z. Dogar, S. S. Makkar, P. Guntipalli,
N. N. Ngardig, M. S. Nagineni, T. Paul, E. Luvsannyam, C. Riddick, and M. A. Sanchez-'
- source_sentence: What type of event can lead to the suspension of enrollment in
the study?
sentences:
- 'and data generated by this study must be available for inspection upon request
by representatives
(when applicable) of the Food and Drug Administration (FDA), NIH, other Federal
funders or
study sponsors, and the Institutional Review Board (IRB) for each study site.
9 Protection of Human Subjects
9.1 Risks to Human Subjects
9.1.1 Human Subjects Involvement and Characteristics'
- 'two consecutive days while receiving study drug, the drug will be discontinued.
Adverse events will be monitored as described in Section 10.2.6 on page 61. The
medical
monitor has the authority to suspend enrollment in the event of an unexpected,
study-related
serious adverse event that is judged to change the risk/benefit of subject participation.'
- 'innate immune system is common and measurable in pediatric sepsis. Innate immune
cells such
as monocytes and neutrophils serve critical functions including migration to sites
of infection,
phagocytosis of pathogens, promotion of microbial killing, antigen presentation,
and production
of immunomodulatory cytokines. We have repeatedly shown that severe reduction
in the ability'
- source_sentence: When will the reviews start?
sentences:
- 'mg/kg/day given for three days by continuous infusion was used.23, 63 Despite
its apparent safety
in adults, this dose is substantially higher than what has been used in children
with HLH/MAS
or adults with COVID-19.
In the largest (to date) published study of anakinra in hospitalized, hyper-inflamed
adults
with COVID-19 (N=392), a dose of 10 mg/kg/day IV divided every 12 hours (infused
over 1'
- 'data are required for Federal reporting purposes to delineate subject accrual
by race, ethnicity,
and gender.
For purposes of the DCC handling potential protected health information (PHI)
and pro-
ducing the de–identified research data sets that will be used for analyses, all
study sites have
been offered a Business Associate Agreement with the University of Utah. Copies
of executed'
- 'empirically whether these patients differ from those remaining in the study for
the scheduled
treatment and follow-up time. Missingness for primary, secondary, exploratory,
and safety
outcomes will be reviewed in aggregate and by site. Reviews will start as soon
as enrollment
opens and will be regulatory monitored so missing data problems can be addressed
early in the
study.'
- source_sentence: What type of results will be communicated to the Data Coordinating
Center and clinical site investigator?
sentences:
- 'ing of a medical condition that was present at the time of randomization will
be considered a
new adverse event and reported.
After patient randomization all adverse events (including serious adverse events)
will be
recorded according to relatedness, severity, and expectedness, as well as their
duration and'
- '12.2 Health Insurance Portability and Accountability Act
Data elements collected include the date of birth and date of admission. Prior
to statistical
analyses, dates will be used to calculate patient age at the time of the study
events.
Data elements for race, ethnicity, and gender are also being collected. These
demographic'
- 'The Collaborative Pediatric Critical Care Research NetworkPage 34 of 76 Protocol
90 (Hall, Zuppa and Mourani)
4.5 Randomization
Upon determination of a subject’s immunophenotype, Dr. Hall or his designee will
notify the
Data Coordinating Center and the clinical site investigator of the laboratory
results. Subjects'
- source_sentence: What age groups will be enrolled in the study?
sentences:
- 'have mild to moderate inflammation (i.e. a serum ferritin level <2,000 ng/ml)
from the TRIPS
trial. Those subjects will be instead entered into a completely distinct clinical
trial of immune
stimulation with GM-CSF (GRACE-2) that is covered by a separate IND (#112277).
PRECISE Protocol Version 1.07
Protocol Version Date: June 16, 2023'
- 'Subject Population to be Studied Participating sites will enroll infants, children
and adoles-
cent patients who are admitted to a Pediatric or Cardiac Intensive Care Unit with
sepsis-induced
multiple organ dysfunction syndrome (MODS). The goal is to determine if personalized
im-
munomodulation is an effective strategy to reduce mortality and morbidity from
sepsis-induced'
- 'Loosdregt, N. M. Wulffraat, S. de Roock, and S. J. Vastert. Treatment to target
using
recombinant interleukin-1 receptor antagonist as first-line monotherapy in new-onset
systemic juvenile idiopathic arthritis: Results from a five-year follow-up study.
Arthritis
Rheumatol, 71(7):1163–1173, 2019.
[78] R. K. Thakkar, R. Devine, J. Popelka, J. Hensley, R. Fabia, J. A. Muszynski,
and M. W.'
pipeline_tag: sentence-similarity
library_name: sentence-transformers
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
model-index:
- name: Fine-tuned with [QuicKB](https://github.com/ALucek/QuicKB)
results:
- task:
type: information-retrieval
name: Information Retrieval
dataset:
name: dim 768
type: dim_768
metrics:
- type: cosine_accuracy@1
value: 0.5714285714285714
name: Cosine Accuracy@1
- type: cosine_accuracy@3
value: 0.7828571428571428
name: Cosine Accuracy@3
- type: cosine_accuracy@5
value: 0.8114285714285714
name: Cosine Accuracy@5
- type: cosine_accuracy@10
value: 0.8742857142857143
name: Cosine Accuracy@10
- type: cosine_precision@1
value: 0.5714285714285714
name: Cosine Precision@1
- type: cosine_precision@3
value: 0.2609523809523809
name: Cosine Precision@3
- type: cosine_precision@5
value: 0.16228571428571423
name: Cosine Precision@5
- type: cosine_precision@10
value: 0.08742857142857141
name: Cosine Precision@10
- type: cosine_recall@1
value: 0.5714285714285714
name: Cosine Recall@1
- type: cosine_recall@3
value: 0.7828571428571428
name: Cosine Recall@3
- type: cosine_recall@5
value: 0.8114285714285714
name: Cosine Recall@5
- type: cosine_recall@10
value: 0.8742857142857143
name: Cosine Recall@10
- type: cosine_ndcg@10
value: 0.7304617900805063
name: Cosine Ndcg@10
- type: cosine_mrr@10
value: 0.6836485260770975
name: Cosine Mrr@10
- type: cosine_map@100
value: 0.6898282619821292
name: Cosine Map@100
- task:
type: information-retrieval
name: Information Retrieval
dataset:
name: dim 512
type: dim_512
metrics:
- type: cosine_accuracy@1
value: 0.5485714285714286
name: Cosine Accuracy@1
- type: cosine_accuracy@3
value: 0.7885714285714286
name: Cosine Accuracy@3
- type: cosine_accuracy@5
value: 0.8285714285714286
name: Cosine Accuracy@5
- type: cosine_accuracy@10
value: 0.8685714285714285
name: Cosine Accuracy@10
- type: cosine_precision@1
value: 0.5485714285714286
name: Cosine Precision@1
- type: cosine_precision@3
value: 0.2628571428571428
name: Cosine Precision@3
- type: cosine_precision@5
value: 0.16571428571428568
name: Cosine Precision@5
- type: cosine_precision@10
value: 0.08685714285714283
name: Cosine Precision@10
- type: cosine_recall@1
value: 0.5485714285714286
name: Cosine Recall@1
- type: cosine_recall@3
value: 0.7885714285714286
name: Cosine Recall@3
- type: cosine_recall@5
value: 0.8285714285714286
name: Cosine Recall@5
- type: cosine_recall@10
value: 0.8685714285714285
name: Cosine Recall@10
- type: cosine_ndcg@10
value: 0.7172419802927883
name: Cosine Ndcg@10
- type: cosine_mrr@10
value: 0.6675759637188208
name: Cosine Mrr@10
- type: cosine_map@100
value: 0.6741729815259775
name: Cosine Map@100
- task:
type: information-retrieval
name: Information Retrieval
dataset:
name: dim 256
type: dim_256
metrics:
- type: cosine_accuracy@1
value: 0.5485714285714286
name: Cosine Accuracy@1
- type: cosine_accuracy@3
value: 0.76
name: Cosine Accuracy@3
- type: cosine_accuracy@5
value: 0.84
name: Cosine Accuracy@5
- type: cosine_accuracy@10
value: 0.9085714285714286
name: Cosine Accuracy@10
- type: cosine_precision@1
value: 0.5485714285714286
name: Cosine Precision@1
- type: cosine_precision@3
value: 0.2533333333333333
name: Cosine Precision@3
- type: cosine_precision@5
value: 0.16799999999999995
name: Cosine Precision@5
- type: cosine_precision@10
value: 0.09085714285714283
name: Cosine Precision@10
- type: cosine_recall@1
value: 0.5485714285714286
name: Cosine Recall@1
- type: cosine_recall@3
value: 0.76
name: Cosine Recall@3
- type: cosine_recall@5
value: 0.84
name: Cosine Recall@5
- type: cosine_recall@10
value: 0.9085714285714286
name: Cosine Recall@10
- type: cosine_ndcg@10
value: 0.7268936400245406
name: Cosine Ndcg@10
- type: cosine_mrr@10
value: 0.6687596371882085
name: Cosine Mrr@10
- type: cosine_map@100
value: 0.6719911574054431
name: Cosine Map@100
- task:
type: information-retrieval
name: Information Retrieval
dataset:
name: dim 128
type: dim_128
metrics:
- type: cosine_accuracy@1
value: 0.49142857142857144
name: Cosine Accuracy@1
- type: cosine_accuracy@3
value: 0.7028571428571428
name: Cosine Accuracy@3
- type: cosine_accuracy@5
value: 0.7885714285714286
name: Cosine Accuracy@5
- type: cosine_accuracy@10
value: 0.8685714285714285
name: Cosine Accuracy@10
- type: cosine_precision@1
value: 0.49142857142857144
name: Cosine Precision@1
- type: cosine_precision@3
value: 0.23428571428571424
name: Cosine Precision@3
- type: cosine_precision@5
value: 0.15771428571428567
name: Cosine Precision@5
- type: cosine_precision@10
value: 0.08685714285714284
name: Cosine Precision@10
- type: cosine_recall@1
value: 0.49142857142857144
name: Cosine Recall@1
- type: cosine_recall@3
value: 0.7028571428571428
name: Cosine Recall@3
- type: cosine_recall@5
value: 0.7885714285714286
name: Cosine Recall@5
- type: cosine_recall@10
value: 0.8685714285714285
name: Cosine Recall@10
- type: cosine_ndcg@10
value: 0.6778419592624233
name: Cosine Ndcg@10
- type: cosine_mrr@10
value: 0.6168730158730158
name: Cosine Mrr@10
- type: cosine_map@100
value: 0.6219971103464577
name: Cosine Map@100
- task:
type: information-retrieval
name: Information Retrieval
dataset:
name: dim 64
type: dim_64
metrics:
- type: cosine_accuracy@1
value: 0.38285714285714284
name: Cosine Accuracy@1
- type: cosine_accuracy@3
value: 0.5714285714285714
name: Cosine Accuracy@3
- type: cosine_accuracy@5
value: 0.6571428571428571
name: Cosine Accuracy@5
- type: cosine_accuracy@10
value: 0.7885714285714286
name: Cosine Accuracy@10
- type: cosine_precision@1
value: 0.38285714285714284
name: Cosine Precision@1
- type: cosine_precision@3
value: 0.19047619047619044
name: Cosine Precision@3
- type: cosine_precision@5
value: 0.1314285714285714
name: Cosine Precision@5
- type: cosine_precision@10
value: 0.07885714285714283
name: Cosine Precision@10
- type: cosine_recall@1
value: 0.38285714285714284
name: Cosine Recall@1
- type: cosine_recall@3
value: 0.5714285714285714
name: Cosine Recall@3
- type: cosine_recall@5
value: 0.6571428571428571
name: Cosine Recall@5
- type: cosine_recall@10
value: 0.7885714285714286
name: Cosine Recall@10
- type: cosine_ndcg@10
value: 0.5697625172066919
name: Cosine Ndcg@10
- type: cosine_mrr@10
value: 0.5015079365079367
name: Cosine Mrr@10
- type: cosine_map@100
value: 0.5090522718083348
name: Cosine Map@100
---
# Fine-tuned with [QuicKB](https://github.com/ALucek/QuicKB)
This is a [sentence-transformers](https://www.SBERT.net) model finetuned from [nomic-ai/modernbert-embed-base](https://huggingface.co/nomic-ai/modernbert-embed-base). 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:** [nomic-ai/modernbert-embed-base](https://huggingface.co/nomic-ai/modernbert-embed-base)
- **Maximum Sequence Length:** 1024 tokens
- **Output Dimensionality:** 768 dimensions
- **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': 1024, 'do_lower_case': False}) with Transformer model: ModernBertModel
(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("Mdean77/modernbert-embed-quickb")
# Run inference
sentences = [
'What age groups will be enrolled in the study?',
'Subject Population to be Studied Participating sites will enroll infants, children and adoles-\ncent patients who are admitted to a Pediatric or Cardiac Intensive Care Unit with sepsis-induced\nmultiple organ dysfunction syndrome (MODS). The goal is to determine if personalized im-\nmunomodulation is an effective strategy to reduce mortality and morbidity from sepsis-induced',
'have mild to moderate inflammation (i.e. a serum ferritin level <2,000 ng/ml) from the TRIPS\ntrial. Those subjects will be instead entered into a completely distinct clinical trial of immune\nstimulation with GM-CSF (GRACE-2) that is covered by a separate IND (#112277).\nPRECISE Protocol Version 1.07\nProtocol Version Date: June 16, 2023',
]
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
* Datasets: `dim_768`, `dim_512`, `dim_256`, `dim_128` and `dim_64`
* Evaluated with [InformationRetrievalEvaluator
](https://sbert.net/docs/package_reference/sentence_transformer/evaluation.html#sentence_transformers.evaluation.InformationRetrievalEvaluator)
| Metric | dim_768 | dim_512 | dim_256 | dim_128 | dim_64 |
|:--------------------|:-----------|:-----------|:-----------|:-----------|:-----------|
| cosine_accuracy@1 | 0.5714 | 0.5486 | 0.5486 | 0.4914 | 0.3829 |
| cosine_accuracy@3 | 0.7829 | 0.7886 | 0.76 | 0.7029 | 0.5714 |
| cosine_accuracy@5 | 0.8114 | 0.8286 | 0.84 | 0.7886 | 0.6571 |
| cosine_accuracy@10 | 0.8743 | 0.8686 | 0.9086 | 0.8686 | 0.7886 |
| cosine_precision@1 | 0.5714 | 0.5486 | 0.5486 | 0.4914 | 0.3829 |
| cosine_precision@3 | 0.261 | 0.2629 | 0.2533 | 0.2343 | 0.1905 |
| cosine_precision@5 | 0.1623 | 0.1657 | 0.168 | 0.1577 | 0.1314 |
| cosine_precision@10 | 0.0874 | 0.0869 | 0.0909 | 0.0869 | 0.0789 |
| cosine_recall@1 | 0.5714 | 0.5486 | 0.5486 | 0.4914 | 0.3829 |
| cosine_recall@3 | 0.7829 | 0.7886 | 0.76 | 0.7029 | 0.5714 |
| cosine_recall@5 | 0.8114 | 0.8286 | 0.84 | 0.7886 | 0.6571 |
| cosine_recall@10 | 0.8743 | 0.8686 | 0.9086 | 0.8686 | 0.7886 |
| **cosine_ndcg@10** | **0.7305** | **0.7172** | **0.7269** | **0.6778** | **0.5698** |
| cosine_mrr@10 | 0.6836 | 0.6676 | 0.6688 | 0.6169 | 0.5015 |
| cosine_map@100 | 0.6898 | 0.6742 | 0.672 | 0.622 | 0.5091 |
## Training Details
### Training Dataset
#### Unnamed Dataset
* Size: 1,567 training samples
* Columns: anchor
and positive
* Approximate statistics based on the first 1000 samples:
| | anchor | positive |
|:--------|:----------------------------------------------------------------------------------|:------------------------------------------------------------------------------------|
| type | string | string |
| details |
How many terabytes of data are referenced?
| over 125 terabytes of data.
Information systems are available 24/7/365 unless a scheduled maintenance period or
mitigation of an unexpected event is required. Critical systems availability has exceeded 99.9%
for the past 5 years.
7.2.3 Security, Support, Encryption, and Confidentiality
The data center coordinates the network infrastructure and security with University Information
|
| What regulation allows single parent permission for the study?
| for their child in the study. Single parent permission is permitted under 45 CFR §46.405. The
parent or legal guardian will be informed about the objectives of the study and the potential
risks and benefits of their child’s participation. If the parent or legal guardian refuses permission
for their child to participate, then all clinical management will continue to be provided by the
|
| What is included in the follow-up plan for non-compliant sites?
| planned site visits, criteria for focused visits, additional visits or remote monitoring, a plan for
chart review and a follow up plan for non-compliant sites. The monitoring plan also describes
the type of monitoring that will take place (e.g., sample of all subjects within a site; key data or
all data), the schedule of visits, how they are reported and a time frame to resolve any issues
found.
|
* 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`: 16
- `gradient_accumulation_steps`: 16
- `learning_rate`: 2e-05
- `num_train_epochs`: 4
- `lr_scheduler_type`: cosine
- `warmup_ratio`: 0.1
- `tf32`: False
- `load_best_model_at_end`: True
- `batch_sampler`: no_duplicates
#### All Hyperparameters