metadata

tags:
  - sentence-transformers
  - sentence-similarity
  - feature-extraction
  - generated_from_trainer
  - dataset_size:8994
  - loss:MultipleNegativesRankingLoss
base_model: pankajrajdeo/UMLS-Pubmed-ST-TCE-Epoch-2
widget:
  - source_sentence: >-
      Real estate data to analyse the relationship between property prices,
      sustainability levels and socio-economic indicators. Recent studies have
      sought to explore the relationship between environmental and financial
      performance, in particular the relationship between the energy efficiency
      level of a building and its financial value. The present real estate
      dataset contains 43 variables of repeat sales transactions, energy
      performance certificate (EPC) rating, index of multiple deprivation (IMD),
      and geographical location of properties in England and Wales involved in a
      total of 4,201 transactions from 1995 to 2012. This dataset enables
      researchers and practitioners to further explore important questions
      regarding the nexus between the real estate industry, sustainability
      levels, and socio-economic aspects. Due to the scarcity of publicly
      available quality real estate data, the dataset detailed in this article
      may play a relevant role by becoming easily discoverable, clearly
      explained, and structured to be ready to be used by researchers, analysts,
      and policymakers. The empirical analysis of the economic case for
      energy-efficient dwellings in the UK private rental market performed in
      Fuerst, et al. is based on this dataset.
    sentences:
      - >-
        How do congenital glycosylation disorders impact the development and
        function of various bodily systems, and what are the implications for
        patient care and management?
      - >-
        How do environmental and socio-economic factors influence property
        prices and what are the implications for sustainable development
        policies?
      - >-
        How do anisotropic properties of organic semiconductors influence their
        kinetic behavior and potential applications?
  - source_sentence: >-
      Mitochondrial DNA sequence and gene organization in the [corrected]
      Australian blacklip [corrected] abalone Haliotis rubra (leach). The
      complete mitochondrial DNA of the blacklip abalone Haliotis rubra
      (Gastropoda: Mollusca) was cloned and 16,907 base pairs were sequenced.
      The sequence represents an estimated 99.85% of the mitochondrial genome,
      and contains 2 ribosomal RNA, 22 transfer RNA, and 13 protein-coding genes
      found in other metazoan mtDNA. An AT tandem repeat and a possible C-rich
      domain within the putative control region could not be fully sequenced.
      The H. rubra mtDNA gene order is novel for mollusks, separated from the
      black chiton Katharina tunicata by the individual translocations of 3
      tRNAs. Compared with other mtDNA regions, sequences from the ATP8, NAD2,
      NAD4L, NAD6, and 12S rRNA genes, as well as the control region, are the
      most variable among representatives from Mollusca, Arthropoda, and
      Rhynchonelliformea, with similar mtDNA arrangements to H. rubra. These
      sequences are being evaluated as genetic markers within commercially
      important Haliotis species, and some applications and considerations for
      their use are discussed.
    sentences:
      - >-
        What are the potential mechanisms underlying the high variability of
        certain mitochondrial DNA sequences, such as those found in the ATP8,
        NAD2, NAD4L, NAD6, and 12S rRNA genes, and how might this impact their
        use as genetic markers?
      - >-
        How do interactions between an individual's genetic makeup and their
        diet influence the development of their gut microbiome?
      - >-
        How do animal models contribute to our understanding of human metabolic
        disorders and what are the implications for developing therapeutic
        interventions?
  - source_sentence: >-
      Maxillary lateral incisor with two roots: a case report. Although the
      dental literature has indicated that 100% of maxillary lateral incisors
      have a single canal anatomy, it is possible for these teeth to have extra
      canals. These extra canals must be identified and debrided to prevent
      endodontic failure. This report presents an uncommon case involving a
      maxillary lateral incisor with two roots. Even when the frequency of
      radicular anatomy abnormality is extremely low, dentists must consider the
      possibility that a tooth has extra root canals or even extra roots.
    sentences:
      - >-
        What are the underlying neural mechanisms by which early life
        experiences, such as malnutrition or enriched environments, shape
        synaptic plasticity and memory formation in adulthood?
      - >-
        How do the complexities of identifying and managing multiple root canals
        or roots in a single tooth impact endodontic procedures and success
        rates?
      - >-
        What are the molecular mechanisms underlying the aberrant processing and
        signaling of truncated receptor polypeptides, and how can these be
        targeted therapeutically?
  - source_sentence: >-
      Novel methodology for the evaluation of symptoms reported by patients with
      newly diagnosed atrial fibrillation: Application of natural language
      processing to electronic medical records data. INTRODUCTION: Understanding
      symptom patterns in atrial fibrillation patients. The incidence rate of
      symptom reports was highest at 0-3 months post-diagnosis and lower at >3-6
      and >6-12 months (pre-defined timepoints). Across all time periods, the
      most common symptoms were dyspnea or shortness of breath, followed by
      syncope, presyncope, lightheadedness, or dizziness. Similar temporal
      patterns of symptom reports were observed among patients with
      prescriptions for dronedarone or sotalol as first-line treatment.
      CONCLUSION: This study illustrates that NLP can be applied to EMR data to
      characterize symptom reports in patients with incident AF, and the
      potential for these methods to inform comparative effectiveness.
    sentences:
      - >-
        How do electronic medical records and natural language processing
        contribute to understanding patient-reported symptoms across various
        chronic conditions?
      - >-
        How do advances in endoscopic technologies impact the diagnosis and
        treatment of gastrointestinal diseases?
      - >-
        What are the fundamental limitations and challenges associated with
        generating high-quality 3D phase-only holograms using deep
        learning-based methods, and how might these be addressed through
        innovative dataset creation or training protocols?
  - source_sentence: >-
      Integrating virtual reality video games into practice: clinicians'
      experiences. The Nintendo Wii is a popular virtual reality (VR) video
      gaming system in rehabilitation practice and research. As evidence emerges
      related to its effectiveness as a physical therapy training method,
      clinicians require information about the pragmatics of its use in
      practice. The purpose of this descriptive qualitative study is to explore
      observations and insights from a sample of physical therapists (PTs)
      working with children with acquired brain injury regarding practical
      implications of using the Wii as a physical therapy intervention. Six PTs
      employed at a children's rehabilitation center participated in
      semi-structured interviews, which were transcribed and analyzed using
      content analysis. Two themes summarize the practical implications of Wii
      use: 1) technology meets clinical practice; and 2) onus is on the
      therapist. Therapists described both beneficial and challenging
      implications arising from the intersection of technology and practice, and
      reported the personal commitment required to orient oneself to the gaming
      system and capably implement this intervention. Findings include issues
      that may be relevant to professional development in a broader
      rehabilitation context, including suggestions for the content of
      educational initiatives and the need for institutional support from
      managers in the form of physical resources for VR implementation.
    sentences:
      - >-
        What are the broader implications of using viral vectors like rVSV for
        vaccine development against emerging and re-emerging pathogens,
        particularly those with high mortality rates?
      - >-
        How do variations in surface preparation and condensation techniques
        affect the bonding and mechanical integrity of amalgam repairs?
      - >-
        How do clinicians balance the integration of emerging technologies with
        established clinical practices?
pipeline_tag: sentence-similarity
library_name: sentence-transformers

SentenceTransformer based on pankajrajdeo/UMLS-Pubmed-ST-TCE-Epoch-2

This is a sentence-transformers model finetuned from pankajrajdeo/UMLS-Pubmed-ST-TCE-Epoch-2. 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: pankajrajdeo/UMLS-Pubmed-ST-TCE-Epoch-2
Maximum Sequence Length: 1024 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': 1024, '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})
)

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("pankajrajdeo/UMLS-Pubmed-ST-TCE-Epoch-2-QA_10K")
# Run inference
sentences = [
    "Integrating virtual reality video games into practice: clinicians' experiences. The Nintendo Wii is a popular virtual reality (VR) video gaming system in rehabilitation practice and research. As evidence emerges related to its effectiveness as a physical therapy training method, clinicians require information about the pragmatics of its use in practice. The purpose of this descriptive qualitative study is to explore observations and insights from a sample of physical therapists (PTs) working with children with acquired brain injury regarding practical implications of using the Wii as a physical therapy intervention. Six PTs employed at a children's rehabilitation center participated in semi-structured interviews, which were transcribed and analyzed using content analysis. Two themes summarize the practical implications of Wii use: 1) technology meets clinical practice; and 2) onus is on the therapist. Therapists described both beneficial and challenging implications arising from the intersection of technology and practice, and reported the personal commitment required to orient oneself to the gaming system and capably implement this intervention. Findings include issues that may be relevant to professional development in a broader rehabilitation context, including suggestions for the content of educational initiatives and the need for institutional support from managers in the form of physical resources for VR implementation.",
    'How do clinicians balance the integration of emerging technologies with established clinical practices?',
    'How do variations in surface preparation and condensation techniques affect the bonding and mechanical integrity of amalgam repairs?',
]
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: 8,994 training samples
Columns: anchor and positive
Approximate statistics based on the first 1000 samples:
anchor positive
type string string
details
min: 19 tokens
mean: 268.28 tokens
max: 808 tokens

min: 14 tokens
mean: 27.58 tokens
max: 51 tokens

	anchor	positive
type	string	string
details	min: 19 tokens mean: 268.28 tokens max: 808 tokens	min: 14 tokens mean: 27.58 tokens max: 51 tokens

Samples:

anchor	positive
Biallelic variants in DNA2 cause microcephalic primordial dwarfism. Microcephalic primordial dwarfism and c.74+4A>C) found in these individuals substantially impair DNA2 transcript splicing. Additionally, we identify a missense variant, affecting a residue of the ATP-dependent helicase domain that is highly conserved between humans and yeast, with the resulting substitution (p.Thr655Ala) predicted to directly impact ATP/ADP (adenosine diphosphate) binding by DNA2. Our findings support the pathogenicity of these variants as biallelic hypomorphic mutations, establishing DNA2 as an MPD disease gene.	`How do genetic variations in genes involved in DNA replication and repair contribute to human developmental disorders?`
Psychological Distress as a Primer for Sexual Risk Taking Among Emerging Adults. Emerging adults experience increased morbidity as a result of psychological distress and risky sexual behavior. This study examines how sexual behaviors (for example, condom use inconsistency and past year STI history) differ among emerging adults with low, moderate, and high psychological distress. Participants are 251,254 emerging adults attending colleges and universities in the United States who participated in the National College Health Assessment (NCHA). Findings suggest a dose-response relationship between psychological distress, condom use inconsistency, and past STI history, such that an association between greater psychological distress and condom use inconsistency and/or past year history of sexually transmitted infections (STIs).	`How do mental health factors influence the likelihood of engaging in high-risk behaviors among young adults?`
Long-Term Safety of Teriflunomide in Multiple Sclerosis Patients: Results of Prospective Comparative Studies in Three European Countries. BACKGROUND AND OBJECTIVES: Teriflunomide is a disease-modifying therapy (DMT) for multiple sclerosis (MS). This post authorisation safety study assessed risks of adverse events of special interest (AESI) associated with teriflunomide use. METHODS: Secondary use of individual data from the Danish MS Registry (DMSR), the French National Health Data System (SNDS), the Belgian national database of health care claims (AIM-IMA) and the Belgian Treatments in MS Registry (Beltrims). We included patients treated with a DMT at the date of teriflunomide reimbursement or initiating another DMT. Adjusted hazard rates (aHR) and 95% confidence intervals were derived from Cox models with time-dependent exposure comparing teriflunomide treatment with another DMT. RESULTS: Of 81 620 patients (72% women) included in the cohort, 22 324 (27%) were treated with teriflunom...	`What are the potential mechanisms underlying the observed differences in risk profiles between teriflunomide and other disease-modifying therapies, particularly with regards to opportunistic infections and renal failure?`

Loss: MultipleNegativesRankingLoss with these parameters:

{
    "scale": 20.0,
    "similarity_fct": "cos_sim"
}

Evaluation Dataset

Unnamed Dataset

Size: 1,000 evaluation samples
Columns: anchor and positive
Approximate statistics based on the first 1000 samples:
anchor positive
type string string
details
min: 20 tokens
mean: 272.12 tokens
max: 935 tokens

min: 14 tokens
mean: 27.77 tokens
max: 56 tokens

	anchor	positive
type	string	string
details	min: 20 tokens mean: 272.12 tokens max: 935 tokens	min: 14 tokens mean: 27.77 tokens max: 56 tokens

Samples:

anchor	positive
Posttraumatic Cognitions and Suicidal Ideation among Veterans receiving PTSD Treatment. With approximately 20 veteran suicide deaths per day, suicidal ideation (SI) among veterans is an important concern. Posttraumatic stress disorder (PTSD) is associated with SI among veterans, yet mechanisms of this relationship remain unclear. Negative posttraumatic cognitions contribute to the development and maintenance of PTSD, yet no studies have prospectively examined the relationship between posttraumatic cognitions and SI. Veterans (N = 177; 66% Male) participating in a 3-week intensive outpatient program for PTSD completed assessments of PTSD severity, depressive symptoms, SI, and posttraumatic cognitions. Negative posttraumatic cognitions about the self significantly predicted SI at posttreatment, controlling for pretreatment levels of SI, depression, and PTSD symptom severity. Self-blame and negative posttraumatic cognitions about others/world did not predict SI prospectively. Negative pos...	`What are the underlying psychological mechanisms by which self-blame and negative cognitions about oneself or others/world influence suicidal ideation in veterans with PTSD?`
Bilirubin increases insulin sensitivity in leptin-receptor deficient and diet-induced obese mice through suppression of ER stress and chronic inflammation. Obesity-induced endoplasmic reticulum (ER) stress causes chronic inflammation in adipose tissue and steatosis in the liver, and eventually leads to insulin resistance and type 2 diabetes (T2D). The goal of this study was to understand the mechanisms by which administration of bilirubin, a powerful antioxidant, reduces hyperglycemia and ameliorates obesity in leptin-receptor-deficient (db/db) and diet-induced obese (DIO) mouse models. db/db or DIO mice were injected with bilirubin or vehicle ip. Blood glucose and body weight were measured. Activation of insulin-signaling pathways, expression of inflammatory cytokines, and ER stress markers were measured in skeletal muscle, adipose tissue, and liver of mice. Bilirubin administration significantly reduced hyperglycemia and increased insulin sensitivity in db/db mice. Bilirubin treatmen...	`What cellular pathways and stress responses contribute to the development of insulin resistance in obesity, and how can they be targeted therapeutically?`
Repair strength of dental amalgams. This study tested the hypothesis that newly triturated amalgam condensed vertically on old amalgam was essential for establishing a bond between the new and old amalgams. Twelve rectangular bars were prepared with Dispersalloy and Tytin to establish their baseline flexure strength values. An additional 12 specimens were made and separated into 24 equal halves. All fracture surfaces were abraded with a flat end fissure bur. Twelve surfaces were paired with the original amalgam, and the remaining 12 surfaces were repaired with a different amalgam. At first, freshly triturated amalgam was condensed vertically on the floor of the specimen mold (Group A). The majority of specimens repaired with Group A failed to establish bond at the repair interface. All repair surfaces were abraded again and prepared by a second method. A metal spacer was used to create a four-wall cavity to facilitate vertical condensation directly on the repair surface (Group B). The ...	`How do variations in surface preparation and condensation techniques affect the bonding and mechanical integrity of amalgam repairs?`

Loss: MultipleNegativesRankingLoss with these parameters:

{
    "scale": 20.0,
    "similarity_fct": "cos_sim"
}

Training Hyperparameters

Non-Default Hyperparameters

eval_strategy: epoch
per_device_train_batch_size: 16
per_device_eval_batch_size: 16
learning_rate: 2e-05
num_train_epochs: 5
fp16: True
load_best_model_at_end: True
resume_from_checkpoint: True

All Hyperparameters

Click to expand

overwrite_output_dir: False
do_predict: False
eval_strategy: epoch
prediction_loss_only: True
per_device_train_batch_size: 16
per_device_eval_batch_size: 16
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: 5
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: 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
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: True
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
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
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
average_tokens_across_devices: False
prompts: None
batch_sampler: batch_sampler
multi_dataset_batch_sampler: proportional

Training Logs

Epoch	Step	Training Loss	Validation Loss
0.1776	100	0.0228	-
0.3552	200	0.0096	-
0.5329	300	0.013	-
0.7105	400	0.0175	-
0.8881	500	0.0154	-
1.0	563	-	0.0096
1.0657	600	0.0132	-
1.2433	700	0.0056	-
1.4210	800	0.0071	-
1.5986	900	0.0081	-
1.7762	1000	0.011	-
1.9538	1100	0.0103	-
2.0	1126	-	0.0074
2.1314	1200	0.0149	-
2.3091	1300	0.01	-
2.4867	1400	0.008	-
2.6643	1500	0.0066	-
2.8419	1600	0.0097	-
3.0	1689	-	0.0058

Framework Versions

Python: 3.10.12
Sentence Transformers: 3.3.1
Transformers: 4.46.2
PyTorch: 2.5.1+cu121
Accelerate: 1.1.1
Datasets: 3.1.0
Tokenizers: 0.20.3

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",
}

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}
}