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tags:
  - sentence-transformers
  - sentence-similarity
  - feature-extraction
  - generated_from_trainer
  - dataset_size:1260000
  - loss:MultipleNegativesRankingLoss
base_model: Qwen/Qwen3-0.6B
widget:
  - source_sentence: >-
      Given a web search query, retrieve relevant passages that answer the
      query: how many days am i supposed to have my period
    sentences:
      - >-
        You answered: Correct Answer: While 3-5 days is most common, anywhere
        between 2 and 7 days is considered normal. See your doctor if your
        period lasts longer than a week or suddenly changes from what's regular
        for you. Next. Question 1/14.
      - msmarco
      - >-
        These flow out as blood. It lasts from 3-7 days in general. The woman
        goes through this cycle until menopause stage, that is typically around
        50-60 years of age. Until this time, she is capable of getting pregnant
        and bearing a child. It is generally said that sex during periods does
        not cause pregnancy. The first menstrual period is called  menarche ..
        The menstrual cycle is about four weeks long, starting on the first day
        of bleeding and ending when the next period begins. However, it can vary
        greatly when a girl first starts her period. It may skip months or come
        several times per month in the beginning.
  - source_sentence: >-
      Given a premise, retrieve hypotheses that are entailed by the premise: All
      such Robin Hood allusions have long since been extinguished.
    sentences:
      - All Robin Hood allusions have stopped.
      - Robin Hood's allusions still remain.
      - nli
  - source_sentence: >-
      Given a question, retrieve relevant Pubmed passages that answer the
      question: Does inhibition of NF-κB and AP-1 by dimethylfumarate correlate
      with down-regulated IL-6 secretion and proliferation in human lung
      fibroblasts?
    sentences:
      - >-
        QUESTION UNDER STUDY/PRINCIPLES: Dimethylfumarate (DMF) had been
        reported to reduce asthma symptoms and to improve the quality of life of
        asthma patients. Therefore, we assessed the anti-inflammatory and
        anti-remodeling effect of DMF on isolated lung fibroblasts, which are
        relevant to inflammatory lung diseases. We determined the effect of DMF
        on platelet derived growth factor (PDGF)-BB induced proliferation, as
        well as on PDGF-BB and tumor necrosis factor (TNF)-α induced interleukin
        (IL)-6 secretion and on activation of activated protein (AP)-1 and
        nuclear factor kappaB (NF-ĸB). Confluent lung fibroblasts were incubated
        with DMF (0.1-100 μM) 1 hour before stimulation with PDGF-BB or TNF-α
        (both 10 ng/ml). IL-6 secretion was measured by ELISA. NF-ĸB and AP-1
        activation was determined by immuno-blotting and EMSA. Cell
        proliferation was assessed by [3H]-thymidine incorporation in
        subconfluent fibroblasts. PDGF-BB but not TNF-α induced fibroblast
        proliferation. This was dose dependently reduced by DMF in a
        concentration range of 10-100 μM. PDGF-BB and TNF-α induced IL-6
        secretion by lung fibroblasts and this was inhibited by DMF in a
        dose-dependent manner. However, PDGF-BB induced IL-6 secretion did not
        correlate with NF-ĸB activity, while TNF-α did. DMF inhibited the TNF-α
        induced NF-ĸB-DNA binding, but had neither an inhibitory effect on NF-ĸB
        nuclear entry nor on the degradation of IκB-α. PDGF-BB and TNF-α
        activated AP-1, which was also inhibited by DMF
      - qa_pairs
      - >-
        Increasing evidence shows that NLRP3 inflammasome is closely associated
        with the progression of atherosclerosis. The purpose of the present
        study was to evaluate the effects of atorvastatin on NLRP3 inflammasome
        in PMA-stimulated THP-1 cells and explore its underlying mechanism.
        Human monocytic THP-1 cells were pretreated with atorvastatin for 1h and
        then induced by PMA for 48h. Total protein was collected for real-time
        PCR and Western blot analysis. Cytokine IL-1β release was detected by
        ELISA assay. And the NF-κB p65 translocation was detected by cellular
        NF-κB translocation kit. It was shown that atorvastatin significantly
        reduced the expression of NLRP3, the cleavage of caspase-1 and IL-1β in
        PMA-induced THP-1 cells. Moreover, Bay (a NF-κB inhibitor) treatment
        greatly suppressed the expression of NLRP3, the cleavage of caspase-1
        and IL-1β in PMA-induced THP-1 cells, suggesting that the activation of
        NF-κB pathway takes part in regulating the expression of NLRP3
        inflammasome. In addition, atorvastatin markedly inhibited the
        up-regulation of toll-like receptor 4 (TLR4), myeloid differentiation
        factor 88 (MyD88) and the activation of nuclear factor kappa b (NF-κB)
        in PMA-stimulated THP-1 cells Glioblastomas are characterized by rapid
        cell growth, aggressive CNS infiltration, and are resistant to all known
        anticancer regimens. Recent studies indicate that fibrates and statins
        possess anticancer potential. Fenofibrate is a potent agonist of
        peroxisome proliferator activated receptor alpha (PPARalpha) that can
        switch energy metabolism from glycolysis to fatty acid beta-oxidation,
        and has low systemic toxicity. Fenofibrate also attenuates
        IGF-I-mediated cellular responses, which could be relevant in the
        process of glioblastoma cell dispersal. The effects of fenofibrate on
        Glioma cell motility, IGF-I receptor (IGF-IR) signaling, PPARalpha
        activity, reactive oxygen species (ROS) metabolism, mitochondrial
        potential, and ATP production were analyzed in human glioma cell lines.
        Fenofibrate treatment attenuated IGF-I signaling responses and repressed
        cell motility of LN-229 and T98G Glioma cell lines. In the absence of
        fenofibrate, specific inhibition of the IGF-IR had only modest effects
        on Glioma cell motility. Further experiments revealed that
        PPARalpha-dependent accumulation of ROS is a strong contributing factor
        in Glioma cell lines responses to fenofibrate. The ROS scavenger,
        N-acetyl-cysteine (NAC), restored cell motility, improved mitochondrial
        potential, and increased ATP levels in fenofibrate treated Glioma cell
        lines
  - source_sentence: >-
      Given a question, retrieve Pubmed passages that answer the question: what
      is a val mapping
    sentences:
      - synthetic
      - >-
        BACKGROUND/OBJECTIVE: Virtual assisted lung mapping (VAL-MAP) is a
        bronchoscopic lung marking technique developed to assist in navigational
        lung resection. It can be used for nodule localization and segmental
        identification. This article presents our initial experience of
        thoracoscopic pulmonary segmentectomy using combined VAL-MAP and
        computed tomography (CT)-guided localization.MATERIAL AND METHODS:
        Markings with India Ink were made bronchoscopically, before surgery,
        using a virtual bronchoscopy system (LungPoint Planner) without
        fluoroscopy guidance. Post VAL-MAP CT scans localized the actual
        markings. All data on patients, markings, and outcomes were
        retrospectively collected, and the contribution of VAL-MAP to the
        operation was graded by the surgeon.RESULTS: From March 2017 to
        September 2017, 24 consecutive patients received the VAL-MAP marking
        procedure before thoracoscopic segmentectomy. Nineteen patients also
        received pre-operative CT-guided percutaneous localization after
        VAL-MAP; fifteen patients received CT-guided localization with dye
        (patent blue V) and microcoil, and four patients received with dye only.
        Of the 101 marking attempts made in all the patients, 71 (70.3%) were
        identified as contributing to the surgery. No clinically evident
        complications were associated with the procedure. A total of 24
        segmentectomies were thoracoscopically conducted for 18 cases of lung
        cancer and six cases of benign diseases.CONCLUSION: The combination of
        VAL-MAP and CT-guided percutaneous localization contribute to precise
        thoracoscopic pulmonary segmentectomy.
      - >-
        BACKGROUND: Despite advancements, the goal of durable pulmonary vein
        isolation (PVI) in all patients undergoing ablation for atrial
        fibrillation (AF) remains elusive. New high-density mapping (HDM) allows
        detection of concealed low-voltage signals (CLVSs) that persist after
        PVI and may represent vulnerabilities in the lesion set.OBJECTIVE: The
        purpose of this study was to determine the incidence of CLVSs after PVI
        and the effect of CLVS ablation on outcomes.METHODS: We conducted a case
        control study comparing 150 patients undergoing HDM-guided PVI and
        subsequent CLVS mapping and ablation (39 redo, 111 de novo) against 452
        historical controls undergoing traditional PVI alone. PVI was similarly
        performed and confirmed in both groups.RESULTS: Baseline characteristics
        were similar, except left atrial size was larger in the HDM-guided
        group. Acute PVI was achieved in nearly all patients in both groups. In
        the HDM group, 31 of 150 patients exhibited CLVS after luminal PVI, and
        all were subsequently eliminated. During mean follow-up of 320 days,
        after controlling for baseline characteristics, the HDM-guided group
        exhibited a hazard ratio of 0.19 in freedom from AF (P <.001). De novo
        patients exhibited a hazard ratio of 0.44 relative to redo patients in
        the HDM-guided group. Both subgroups exhibited significantly lower event
        rates compared to controls in log-rank analysis (P <.001).CONCLUSION:
        CLVSs are commonly identified with HDM after PVI, likely representing
        vulnerabilities in antral lesion sets. Ablation of these targets seems
        to significantly improve freedom from AF compared to PVI alone.
        Endocardial mapping is typically considered as the first step of VT
        ablation procedures. Nevertheless, when the electrocardiogram is highly
        suggestive of an epicardial VT, a minimally invasive procedure performed
        exclusively via the coronary sinus might be considered. This
        straightforward approach avoids all potential complications associated
        with access to the left ventricular endocardium, the aortic root, and
        the pericardial space.
  - source_sentence: >-
      Given a question, retrieve relevant Pubmed passages that answer the
      question: Do experimental pain models reveal no sex differences in
      pentazocine analgesia in humans?
    sentences:
      - >-
        The purpose of this study was to elucidate the relationship between
        thermal and mechanical sensation, as well as pain thresholds degrees and
        the dynamics of the TRPV1 level in almost healthy young males and
        females in the follicular and luteal phases of the OMC. We found gender
        differences for some pain sensation indices, taking into account OMC
        phases of females. Mechanical pain tolerance and heat pain thresholds
        were significantly higher in males compared with females in both phases
        of the OMC, also, mechanical pain, mechanical pressure, cold pain and
        heat sensation thresholds were insignificantly higher in males compared
        with females in follicular phase of the OMC and significantly higher -
        in luteal phase of the OMC. We haven't found any differences in cold
        sensation threshold between males and females in both phases of OMC.
        Moreover, we found significant gender and interphase differences in
        receptor protein TRPV1 level - the maximal level in females in luteal
        phase of the OMC, lower in males and minimal in females in follicular
        phase of the OMC. Worldwide, women account for approximately 51% of
        human immunodeficiency virus-1 (HIV) seropositive individuals. The
        prevalence of neuropathic pain among individuals with HIV and a lack of
        preclinical data characterizing sex differences prompted us to address
        this knowledge gap. C57BL/6 male and female mice received multiple
        intrathecal injections of HIV-glycoprotein 120 (gp120), followed by
        determination of mechanical allodynia and thermal hypersensitivity for
        four weeks. The influence of ovarian hormones in the gp120 pain model
        was evaluated by comparison of ovariectomized (OVX) mice versus sham
        control. We found that gp120-induced neuropathic pain-like behaviors are
        sex-dependent. Female mice showed both increased mechanical allodynia
        and increased cold sensitivity relative to their male counterparts. The
        OVX mice showed reduced pain sensitivity compared to sham, suggesting a
        role of the ovarian hormones in sex differences in pain sensitivity to
        gp120. Gp120-induced neuropathic pain caused a shift in estrous cycle
        toward the estrus phase. However, there is a lack of clear correlation
        between the estrous cycle and the development of neuropathic pain-like
        behaviors during the four week recording period. This data provided the
        first evidence for sex differences in a rodent model of HIV-related
        neuropathic pain, along with a potential role of ovarian hormones.
      - qa_pairs
      - >-
        Accumulating evidence suggests that there are sex differences in
        analgesic responses to opioid agonists. Several studies using an oral
        surgery pain model have reported more robust analgesia to
        kappa-agonist-antagonists (e.g., pentazocine, nalbuphine, butorphanol)
        among women than among men. However, evidence of sex differences in
        kappa-agonist-antagonist effects from studies of experimentally induced
        pain in humans is lacking. Therefore, the analgesic effects of
        intravenous pentazocine (0.5 mg/kg) were determined in healthy women (n
        = 41) and men (n = 38) using three experimental pain models: heat pain,
        pressure pain, and ischemic pain. Each pain procedure was conducted
        before and after double-blind administration of both pentazocine and
        saline, which occurred on separate days in counterbalanced order.
        Compared with saline, pentazocine produced significant analgesic
        responses for all pain stimuli. However, no sex differences in
        pentazocine analgesia emerged. Effect sizes for the sex differences were
        computed; the magnitude of effects was small, and an equal number of
        measures showed greater analgesia in men than in women. Also, analgesic
        responses were not highly correlated across pain modalities, suggesting
        that different mechanisms may underlie analgesia for disparate types of
        pain
datasets:
  - BMRetriever/biomed_retrieval_dataset
pipeline_tag: sentence-similarity
library_name: sentence-transformers
metrics:
  - cosine_accuracy
model-index:
  - name: SentenceTransformer based on Qwen/Qwen3-0.6B
    results:
      - task:
          type: triplet
          name: Triplet
        dataset:
          name: bmretriever
          type: bmretriever
        metrics:
          - type: cosine_accuracy
            value: 0.9783856868743896
            name: Cosine Accuracy

SentenceTransformer based on Qwen/Qwen3-0.6B

This is a sentence-transformers model finetuned from Qwen/Qwen3-0.6B on the biomed_retrieval_dataset dataset. It maps sentences & paragraphs to a 1024-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: Qwen/Qwen3-0.6B
Maximum Sequence Length: 512 tokens
Output Dimensionality: 1024 dimensions
Similarity Function: Cosine Similarity
Training Dataset:
- biomed_retrieval_dataset

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': 512, 'do_lower_case': False}) with Transformer model: Qwen3Model 
  (1): Pooling({'word_embedding_dimension': 1024, 'pooling_mode_cls_token': False, 'pooling_mode_mean_tokens': False, 'pooling_mode_max_tokens': False, 'pooling_mode_mean_sqrt_len_tokens': False, 'pooling_mode_weightedmean_tokens': False, 'pooling_mode_lasttoken': True, '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("sentence_transformers_model_id")
# Run inference
sentences = [
    'Given a question, retrieve relevant Pubmed passages that answer the question: Do experimental pain models reveal no sex differences in pentazocine analgesia in humans?',
    'Accumulating evidence suggests that there are sex differences in analgesic responses to opioid agonists. Several studies using an oral surgery pain model have reported more robust analgesia to kappa-agonist-antagonists (e.g., pentazocine, nalbuphine, butorphanol) among women than among men. However, evidence of sex differences in kappa-agonist-antagonist effects from studies of experimentally induced pain in humans is lacking. Therefore, the analgesic effects of intravenous pentazocine (0.5 mg/kg) were determined in healthy women (n = 41) and men (n = 38) using three experimental pain models: heat pain, pressure pain, and ischemic pain. Each pain procedure was conducted before and after double-blind administration of both pentazocine and saline, which occurred on separate days in counterbalanced order. Compared with saline, pentazocine produced significant analgesic responses for all pain stimuli. However, no sex differences in pentazocine analgesia emerged. Effect sizes for the sex differences were computed; the magnitude of effects was small, and an equal number of measures showed greater analgesia in men than in women. Also, analgesic responses were not highly correlated across pain modalities, suggesting that different mechanisms may underlie analgesia for disparate types of pain',
    "The purpose of this study was to elucidate the relationship between thermal and mechanical sensation, as well as pain thresholds degrees and the dynamics of the TRPV1 level in almost healthy young males and females in the follicular and luteal phases of the OMC. We found gender differences for some pain sensation indices, taking into account OMC phases of females. Mechanical pain tolerance and heat pain thresholds were significantly higher in males compared with females in both phases of the OMC, also, mechanical pain, mechanical pressure, cold pain and heat sensation thresholds were insignificantly higher in males compared with females in follicular phase of the OMC and significantly higher - in luteal phase of the OMC. We haven't found any differences in cold sensation threshold between males and females in both phases of OMC. Moreover, we found significant gender and interphase differences in receptor protein TRPV1 level - the maximal level in females in luteal phase of the OMC, lower in males and minimal in females in follicular phase of the OMC. Worldwide, women account for approximately 51% of human immunodeficiency virus-1 (HIV) seropositive individuals. The prevalence of neuropathic pain among individuals with HIV and a lack of preclinical data characterizing sex differences prompted us to address this knowledge gap. C57BL/6 male and female mice received multiple intrathecal injections of HIV-glycoprotein 120 (gp120), followed by determination of mechanical allodynia and thermal hypersensitivity for four weeks. The influence of ovarian hormones in the gp120 pain model was evaluated by comparison of ovariectomized (OVX) mice versus sham control. We found that gp120-induced neuropathic pain-like behaviors are sex-dependent. Female mice showed both increased mechanical allodynia and increased cold sensitivity relative to their male counterparts. The OVX mice showed reduced pain sensitivity compared to sham, suggesting a role of the ovarian hormones in sex differences in pain sensitivity to gp120. Gp120-induced neuropathic pain caused a shift in estrous cycle toward the estrus phase. However, there is a lack of clear correlation between the estrous cycle and the development of neuropathic pain-like behaviors during the four week recording period. This data provided the first evidence for sex differences in a rodent model of HIV-related neuropathic pain, along with a potential role of ovarian hormones.",
]
embeddings = model.encode(sentences)
print(embeddings.shape)
# [3, 1024]

# Get the similarity scores for the embeddings
similarities = model.similarity(embeddings, embeddings)
print(similarities.shape)
# [3, 3]

Evaluation

Metrics

Triplet

Dataset: bmretriever
Evaluated with TripletEvaluator

Metric	Value
cosine_accuracy	0.9784

Training Details

Training Dataset

biomed_retrieval_dataset

Dataset: biomed_retrieval_dataset at dff25ba
Size: 1,260,000 training samples
Columns: anchor, positive, negative, and source

Approximate statistics based on the first 1000 samples:

	anchor	positive	negative	source
type	string	string	string	string
details	min: 16 tokens mean: 30.12 tokens max: 512 tokens	min: 3 tokens mean: 207.95 tokens max: 512 tokens	min: 2 tokens mean: 323.72 tokens max: 512 tokens	min: 1 tokens mean: 2.3 tokens max: 4 tokens

Samples:

anchor	positive	negative	source
`Given a question, retrieve relevant passages that answer the question: when does the new season of real housewives of beverly hills air?`	`The Real Housewives of Beverly Hills (season 10) This is the latest accepted revision, reviewed on 27 July 2020. The tenth season of The Real Housewives of Beverly Hills, an American reality television series, is broadcast on Bravo. It premiered on April 15 2020, and is primarily filmed in Beverly Hills, California.`	Seasons 1–4. The Real Housewives of Beverly Hills was announced in March 2010 as the sixth installment of The Real Housewives franchise. The first season premiered on October 14, 2010, and starred Kyle Richards, Adrienne Maloof, Kim Richards, Lisa Vanderpump, Camille Grammer and Taylor Armstrong. This is the latest accepted revision, reviewed on 27 July 2020. The tenth season of The Real Housewives of Beverly Hills, an American reality television series, is broadcast on Bravo. It premiered on April 15 2020, and is primarily filmed in Beverly Hills, California.	`gooaq`
`Given a question, retrieve Pubmed passages that answer the question: determinants of the pathway to emergency obstetric care in south africa`	BACKGROUND: Maternity referral systems have been under-documented, under-researched, and under-theorised. Responsive emergency referral systems and appropriate transportation are cornerstones in the continuum of care and central to the complex health system. The pathways that women follow to reach Emergency Obstetric and Neonatal Care (EmONC) once a decision has been made to seek care have received relatively little attention. The aim of this research was to identify patterns and determinants of the pathways pregnant women follow from the onset of labour or complications until they reach an appropriate health facility.METHODS: This study was conducted in Renk County in South Sudan between 2010 and 2012. Data was collected using Critical Incident Technique (CIT) and stakeholder interviews. CIT systematically identified pathways to healthcare during labour, and factors associated with an event of maternal mortality or near miss through a series of in-depth interviews with witnesses or th...	OBJECTIVES: In a rural district hospital in Burundi offering Emergency Obstetric care-(EmOC), we assessed the a) characteristics of women at risk of, or with an obstetric complication and their types b) the number and type of obstetric surgical procedures and anaesthesia performed c) human resource cadres who performed surgery and anaesthesia and d) hospital exit outcomes.METHODS: A retrospective analysis of EmOC data (2011 and 2012).RESULTS: A total of 6084 women were referred for EmOC of whom 2534(42%) underwent a major surgical procedure while 1345(22%) required a minor procedure (36% women did not require any surgical procedure). All cases with uterine rupture(73) and extra-uterine pregnancy(10) and the majority with pre-uterine rupture and foetal distress required major surgery. The two most prevalent conditions requiring a minor surgical procedure were abortions (61%) and normal delivery (34%). A total of 2544 major procedures were performed on 2534 admitted individuals. Of these...	`synthetic`
`Given a question, retrieve Wikipedia passages that answer the question: hindi festival where sisters give bracelets to brothers`	Raksha Bandhan Raksha Bandhan, also Rakshabandhan, or Rakhi, is a popular, traditionally Hindu, annual rite, or ceremony, which is central to a festival of the same name, originating from the Indian subcontinent, celebrated in parts of Indian subcontinent, and among people influenced by Hindu and Indian culture around the world. On this day, sisters of all ages tie a talisman, or amulet, called the ""rakhi"", around the wrists of their brothers, symbolically protecting them, receiving a gift in return, and traditionally investing the brothers with a share of the responsibility of their potential care. Raksha Bandhan is observed on the	Bonalu Bonalu or Goddess Mahankali bonalu (Telugu: బోనాలు ) is a Hindu Festival, Goddess Mahakali is worshiped. Bonalu is an annual festival of Telangana celebrated in Twin Cities Hyderabad, Secunderabad and other parts of Telangana. It is celebrated in the month of Ashada Masam, in July/August. Special poojas are performed for Yellamma on the first and last day of the festival. The festival is also considered a thanksgiving to the Goddess for fulfillment of vows. The word ""Bonam"" is a contraction of the word ""Bhojanam"", a Sanskrit loanword which means a meal or a feast in Telugu, is an ""Offering related to the sixth Guru, Guru Hargobind. According to Sikh history, on this day, Guru Hargobind was released from prison by the Mughal Emperor Jahangir who freed 52 other Hindu kings with him. The Bandi Chhor Divas is celebrated in a manner similar to Diwali, with the lighting of homes and Gurdwaras, feasts, gift giving and family time. It is an important Sikh celebration along with Vai...	`nq`

Loss: MultipleNegativesRankingLoss with these parameters:

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

Evaluation Dataset

biomed_retrieval_dataset

Dataset: biomed_retrieval_dataset at dff25ba
Size: 70,000 evaluation samples
Columns: anchor, positive, negative, and source

Approximate statistics based on the first 1000 samples:

	anchor	positive	negative	source
type	string	string	string	string
details	min: 16 tokens mean: 29.95 tokens max: 305 tokens	min: 3 tokens mean: 196.37 tokens max: 512 tokens	min: 3 tokens mean: 317.98 tokens max: 512 tokens	min: 1 tokens mean: 2.31 tokens max: 4 tokens

Samples:

anchor	positive	negative	source
`Given a question, retrieve Pubmed passages that answer the question: what is considered the reference gene for bone marrow osteoblasts?`	Quantitative real-time polymerase chain reaction (qRT-PCR) is a powerful tool to evaluate gene expression, but its accuracy depends on the choice and stability of the reference genes used for normalization. In this study, we aimed to identify reference genes for studies on osteoblasts derived from rat bone marrow mesenchymal stem cells (bone marrow osteoblasts), osteoblasts derived from newborn rat calvarial (calvarial osteoblasts), and rat osteosarcoma cell line UMR-106. The osteoblast phenotype was characterized by ALP activity and extracellular matrix mineralization. Thirty-one candidates for reference genes from a Taqman array were assessed by qRT-PCR, and their expressions were analyzed by five different approaches. The data showed that several of the most traditional reference genes, such as Actb and Gapdh, were inadequate for normalization and that the experimental conditions may affect gene stability. Eif2b1 was frequently identified among the best reference genes in bone marro...	Fast progress of the next generation sequencing (NGS) technology has allowed global transcriptional profiling and genome-wide mapping of transcription factor binding sites in various cellular contexts. However, limited number of replicates and high amount of data processing may weaken the significance of the findings. Comparative analyses of independent data sets acquired in the different laboratories would greatly increase the validity of the data. Runx2 is the key transcription factor regulating osteoblast differentiation and bone formation. We performed a comparative analysis of three published Runx2 data sets of chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) analysis in osteoblasts from mouse and human origin. Moreover, we assessed the similarity of the corresponding transcription data of these studies available online. The ChIP-seq data analysis confirmed general features of Runx2 binding, including location at genic vs intergenic regions and abundant Runx2 b...	`synthetic`
`Given a question, retrieve Pubmed passages that answer the question: what does gper1 do in the oviduct`	Oviducts play roles in reproductive processes, including gametes transport, fertilization and early embryo development. Oviductal transport is controlled by various factors such as endothelins (EDNs) and nitric oxide (NO), smooth muscle contracting and relaxing factor, respectively. EDNs and NO production depend on an ovarian steroid hormone, oestradiol-17 (E2) and E2 quickly exerts their biological functions through G protein-coupled oestrogen receptor 1 (GPER1), which mediates rapid intracellular signalling. Because follicular fluid which contains a high concentration of E2 enters the oviduct, we hypothesized that E2 in the follicular fluid participates via GPER1 in producing EDNs and NO. To test this hypothesis, we investigated 1) the expression and localization of GPER1 in bovine oviductal tissues and 2) rapid effects of E2 via GPER1 on EDN1, EDN2 and inducible NO synthase (iNOS) expression in cultured bovine oviductal isthmic epithelial cells. GPER1 was observed in the oviductal e...	BACKGROUND: The G protein estrogen receptor GPER/GPR30 mediates estrogen action in breast cancer cells as well as in breast cancer-associated fibroblasts (CAFs), which are key components of microenvironment driving tumor progression. GPER is a transcriptional target of hypoxia inducible factor 1 alpha (HIF-1) and activates VEGF expression and angiogenesis in hypoxic breast tumor microenvironment. Furthermore, IGF1/IGF1R signaling, which has angiogenic effects, has been shown to activate GPER in breast cancer cells.METHODS: We analyzed gene expression data from published studies representing almost 5000 breast cancer patients to investigate whether GPER and IGF1 signaling establish an angiocrine gene signature in breast cancer patients. Next, we used GPER-positive but estrogen receptor (ER)-negative primary CAF cells derived from patient breast tumours and SKBR3 breast cancer cells to investigate the role of GPER in the regulation of VEGF expression and angiogenesis triggered by IGF1. W...	`synthetic`
`Given a question, retrieve Pubmed passages that answer the question: what are ovine hair follicle stem cells`	Hair follicle stem cells (HFSCs) possess fascinating self-renewal capacity and multipotency, which play important roles in mammalian hair growth and skin wound repair. Although HFSCs from other mammalian species have been obtained, the characteristics of ovine HFSCs, as well as the methods to isolate them have not been well addressed. Here, we report an efficient strategy to obtain multipotent ovine HFSCs. Through microdissection and organ culture, we obtained keratinocytes that grew from the bulge area of vibrissa hair follicles, and even abundant keratinocytes were harvested from a single hair follicle. These bulge-derived keratinocytes are highly positive for Krt15, Krt14, Tp63, Krt19 and Itga6; in addition to their strong proliferation abilities in vitro, these keratinocytes formed new epidermis, hair follicles and sebaceous glands in skin reconstitution experiments, showing that these are HFSCs from the bulge outer root sheath. Taken together, we developed an efficient in vitro sy...	Hair differentiates from follicle stem cells through progenitor cells in the matrix. In contrast to stem cells in the bulge, the identities of the progenitors and the mechanisms by which they regulate hair shaft components are poorly understood. Hair is also pigmented by melanocytes in the follicle. However, the niche that regulates follicular melanocytes is not well characterized. Here, we report the identification of hair shaft progenitors in the matrix that are differentiated from follicular epithelial cells expressing transcription factor KROX20. Depletion of Krox20 lineage cells results in arrest of hair growth, confirming the critical role of KROX20+ cells as antecedents of structural cells found in hair. Expression of stem cell factor (SCF) by these cells is necessary for the maintenance of differentiated melanocytes and for hair pigmentation. Our findings reveal the identities of hair matrix progenitors that regulate hair growth and pigmentation, partly by creating an SCF-depen...	`synthetic`

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: 256
per_device_eval_batch_size: 256
num_train_epochs: 1
warmup_steps: 100
bf16: True
dataloader_drop_last: True
optim: adamw_bnb_8bit
ddp_find_unused_parameters: False
gradient_checkpointing: True
gradient_checkpointing_kwargs: {'use_reentrant': False}
use_liger_kernel: 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: 256
per_device_eval_batch_size: 256
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: 5e-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: linear
lr_scheduler_kwargs: {}
warmup_ratio: 0.0
warmup_steps: 100
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
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: True
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}
parallelism_config: None
deepspeed: None
label_smoothing_factor: 0.0
optim: adamw_bnb_8bit
optim_args: None
adafactor: False
group_by_length: False
length_column_name: length
project: huggingface
trackio_space_id: trackio
ddp_find_unused_parameters: False
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: None
hub_always_push: False
hub_revision: None
gradient_checkpointing: True
gradient_checkpointing_kwargs: {'use_reentrant': False}
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
include_tokens_per_second: False
include_num_input_tokens_seen: no
neftune_noise_alpha: None
optim_target_modules: None
batch_eval_metrics: False
eval_on_start: False
use_liger_kernel: True
liger_kernel_config: None
eval_use_gather_object: False
average_tokens_across_devices: True
prompts: None
batch_sampler: batch_sampler
multi_dataset_batch_sampler: proportional

Training Logs

Epoch	Step	Training Loss	Validation Loss	bmretriever_cosine_accuracy
0.0102	50	4.6537	-	-
0.0203	100	0.3978	-	-
0.0305	150	0.1825	-	-
0.0406	200	0.1429	-	-
0.0508	250	0.1217	-	-
0.0610	300	0.1185	-	-
0.0711	350	0.1121	-	-
0.0813	400	0.1088	-	-
0.0914	450	0.0943	-	-
0.1016	500	0.0935	-	-
0.1118	550	0.0948	-	-
0.1219	600	0.0911	-	-
0.1321	650	0.0847	-	-
0.1422	700	0.0839	-	-
0.1524	750	0.0809	-	-
0.1626	800	0.083	-	-
0.1727	850	0.0815	-	-
0.1829	900	0.0726	-	-
0.1931	950	0.0748	-	-
0.2032	1000	0.0753	-	-
0.2134	1050	0.0707	-	-
0.2235	1100	0.0672	-	-
0.2337	1150	0.0739	-	-
0.2439	1200	0.0678	-	-
0.2540	1250	0.0685	-	-
0.2642	1300	0.068	-	-
0.2743	1350	0.0658	-	-
0.2845	1400	0.0636	-	-
0.2947	1450	0.0683	-	-
0.3048	1500	0.0641	-	-
0.3150	1550	0.0569	-	-
0.3251	1600	0.064	-	-
0.3353	1650	0.0607	-	-
0.3455	1700	0.0711	-	-
0.3556	1750	0.0612	-	-
0.3658	1800	0.0587	-	-
0.3759	1850	0.0596	-	-
0.3861	1900	0.0613	-	-
0.3963	1950	0.0571	-	-
0.4064	2000	0.0672	-	-
0.4166	2050	0.0587	-	-
0.4267	2100	0.0602	-	-
0.4369	2150	0.0633	-	-
0.4471	2200	0.0601	-	-
0.4572	2250	0.0572	-	-
0.4674	2300	0.0568	-	-
0.4775	2350	0.0604	-	-
0.4877	2400	0.0615	-	-
0.4979	2450	0.0543	-	-
0.5080	2500	0.0529	-	-
0.5182	2550	0.0563	-	-
0.5283	2600	0.0538	-	-
0.5385	2650	0.0559	-	-
0.5487	2700	0.0568	-	-
0.5588	2750	0.0533	-	-
0.5690	2800	0.0543	-	-
0.5792	2850	0.0498	-	-
0.5893	2900	0.0494	-	-
0.5995	2950	0.0536	-	-
0.6096	3000	0.0492	-	-
0.6198	3050	0.053	-	-
0.6300	3100	0.0536	-	-
0.6401	3150	0.05	-	-
0.6503	3200	0.0513	-	-
0.6604	3250	0.0458	-	-
0.6706	3300	0.0509	-	-
0.6808	3350	0.0524	-	-
0.6909	3400	0.0541	-	-
0.7011	3450	0.0518	-	-
0.7112	3500	0.0501	-	-
0.7214	3550	0.0488	-	-
0.7316	3600	0.05	-	-
0.7417	3650	0.0511	-	-
0.7519	3700	0.05	-	-
0.7620	3750	0.0492	-	-
0.7722	3800	0.0511	-	-
0.7824	3850	0.0489	-	-
0.7925	3900	0.0534	-	-
0.8027	3950	0.0431	-	-
0.8128	4000	0.0492	-	-
0.8230	4050	0.0486	-	-
0.8332	4100	0.052	-	-
0.8433	4150	0.0525	-	-
0.8535	4200	0.0454	-	-
0.8636	4250	0.0488	-	-
0.8738	4300	0.0455	-	-
0.8840	4350	0.0494	-	-
0.8941	4400	0.0487	-	-
0.9043	4450	0.0482	-	-
0.9144	4500	0.0486	-	-
0.9246	4550	0.0465	-	-
0.9348	4600	0.0516	-	-
0.9449	4650	0.0481	-	-
0.9551	4700	0.0493	-	-
0.9653	4750	0.0457	-	-
0.9754	4800	0.0479	-	-
0.9856	4850	0.0427	-	-
0.9957	4900	0.0423	-	-
1.0	4921	-	0.0460	0.9784

Framework Versions

Python: 3.11.9
Sentence Transformers: 4.1.0
Transformers: 4.57.1
PyTorch: 2.6.0+cu124
Accelerate: 1.6.0
Datasets: 2.21.0
Tokenizers: 0.22.1

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",
}

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}
}