Model: potsu-potsu/medembed-biomedical-matryoshka
Author: potsu-potsu
Pipeline: sentence-similarity
Library: sentence-transformers
Tags: sentence-transformers, safetensors, bert, sentence-similarity, feature-extraction, generated_from_trainer, dataset_size:4012, loss:MatryoshkaLoss, loss:MultipleNegativesRankingLoss, en, arxiv:1908.10084, arxiv:2205.13147, arxiv:1705.00652, base_model:abhinand/MedEmbed-small-v0.1, base_model:finetune:abhinand/MedEmbed-small-v0.1, license:apache-2.0, model-index, text-embeddings-inference, endpoints_compatible, region:us
Base models (finetune): id: abhinand/MedEmbed-small-v0.1
Card metadata: language: en
license: apache-2.0
tags: sentence-transformers, sentence-similarity, feature-extraction, generated_from_trainer, dataset_size:4012, loss:MatryoshkaLoss, loss:MultipleNegativesRankingLoss
base_model: abhinand/MedEmbed-small-v0.1
widget: source_sentence: Do cephalopods use RNA editing less frequently than other species?
sentences: 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. , GV1001 is a 16-amino-acid vaccine peptide derived from the human telomerase reverse transcriptase sequence. It has been developed as a vaccine against various cancers., Using acetyl-specific K516 antibodies, we show that acetylation of endogenous S6K1 at this site is potently induced upon growth factor stimulation. We propose that K516 acetylation may serve to modulate important kinase-independent functions of S6K1 in response to growth factor signalling. Following mitogen stimulation, S6Ks interact with the p300 and p300/CBP-associated factor (PCAF) acetyltransferases. S6Ks can be acetylated by p300 and PCAF in vitro and S6K acetylation is detected in cells expressing p300, source_sentence: Can pets affect infant microbiomed?
sentences: Yes, exposure to household furry pets influences the gut microbiota of infants., Thiazovivin is a selective small molecule that directly targets Rho-associated kinase (ROCK) and increases expression of pluripotency factors.,  Here, we present evidence that the calcium/calmodulin-dependent protein kinase IV (CaMK4) is increased and required during Th17 cell differentiation. Inhibition of CaMK4 reduced Il17 transcription through decreased activation of the cAMP response element modulator a (CREM-a) and reduced activation of the AKT/mTOR pathway, which is known to enhance Th17 differentiation. CAMK4 knockdown and kinase-dead mutant inhibited crocin-mediated HO-1 expression, Nrf2 activation, and phosphorylation of Akt, indicating that HO-1 expression is mediated by CAMK4 and that Akt is a downstream mediator of CAMK4 in crocin signaling, source_sentence: In what proportion of children with heart failure has Enalapril been shown to be safe and effective?
sentences: 5-HT2A (5-hydroxytryptamine type 2a) receptor can be evaluated with the [18F]altanserin., 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., necroptosis
apoptosis  
pro-survival/inflammation NF-κB activation, source_sentence: How are SAHFS created?
sentences: In particular, up to 17% of neutrophil nuclei of healthy women exhibit a drumstick-shaped appendage that contains the inactive X chromosome., miR-1, miR-133, miR-208a, miR-206, miR-494, miR-146a, miR-222, miR-21, miR-221, miR-20a, miR-133a, miR-133b, miR-23, miR-107 and miR-181 are involved in exercise adaptation, 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., source_sentence: What are the effects of the deletion of all three Pcdh clusters (tricluster deletion) in mice?
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., The myocyte enhancer factor-2 (MEF2) proteins are MADS-box transcription factors that are essential for differentiation of all muscle lineages but their mechanisms of action remain largely undefined. MEF2C expression initiates cardiomyogenesis, resulting in the up-regulation of Brachyury T, bone morphogenetic protein-4, Nkx2-5, GATA-4, cardiac alpha-actin, and myosin heavy chain expression. Inactivation of the MEF2C gene causes cardiac developmental arrest and severe downregulation of a number of cardiac markers including atrial natriuretic factor (ANF). BMP-2, a regulator of cardiac development during embryogenesis, was shown to increase PI 3-kinase activity in cardiac precursor cells, resulting in increased expression of sarcomeric myosin heavy chain (MHC) and MEF-2A. Furthermore, expression of MEF-2A increased MHC expression in a PI 3-kinase-dependent manner. Other studies showed that Gli2 and MEF2C proteins form a complex, capable of synergizing on cardiomyogenesis-related promoters. Dominant interference of calcineurin/mAKAP binding blunts the increase in MEF2 transcriptional activity seen during myoblast differentiation, as well as the expression of endogenous MEF2-target genes. These findings show that MEF-2 can direct early stages of cell differentiation into a cardiomyogenic pathway., Investigators proposed that there have been three extended periods in the evolution of gene regulatory elements. Early vertebrate evolution was characterized by regulatory gains near transcription factors and developmental genes, but this trend was replaced by innovations near extracellular signaling genes, and then innovations near posttranslational protein modifiers.
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: MedEmbed Biomedical MRL
results: task: type: information-retrieval
name: Information Retrieval
dataset: name: dim 384
type: dim_384
metrics: type: cosine_accuracy@1
value: 0.743988684582744
name: Cosine Accuracy@1
verified: no, type: cosine_accuracy@3
value: 0.8528995756718529
name: Cosine Accuracy@3
verified: no, type: cosine_accuracy@5
value: 0.8811881188118812
name: Cosine Accuracy@5
verified: no, type: cosine_accuracy@10
value: 0.9165487977369166
name: Cosine Accuracy@10
verified: no, type: cosine_precision@1
value: 0.743988684582744
name: Cosine Precision@1
verified: no, type: cosine_precision@3
value: 0.5879302215935879
name: Cosine Precision@3
verified: no, type: cosine_precision@5
value: 0.5083451202263083
name: Cosine Precision@5
verified: no, type: cosine_precision@10
value: 0.39264497878359267
name: Cosine Precision@10
verified: no, type: cosine_recall@1
value: 0.22864925036303255
name: Cosine Recall@1
verified: no, type: cosine_recall@3
value: 0.38726014665705066
name: Cosine Recall@3
verified: no, type: cosine_recall@5
value: 0.47265511620109374
name: Cosine Recall@5
verified: no, type: cosine_recall@10
value: 0.5956514777654228
name: Cosine Recall@10
verified: no, type: cosine_ndcg@10
value: 0.682960418351343
name: Cosine Ndcg@10
verified: no, type: cosine_mrr@10
value: 0.8061196425765028
name: Cosine Mrr@10
verified: no, type: cosine_map@100
value: 0.605512208394002
name: Cosine Map@100
verified: no, task: type: information-retrieval
name: Information Retrieval
dataset: name: dim 256
type: dim_256
metrics: type: cosine_accuracy@1
value: 0.7383309759547383
name: Cosine Accuracy@1
verified: no, type: cosine_accuracy@3
value: 0.8486562942008486
name: Cosine Accuracy@3
verified: no, type: cosine_accuracy@5
value: 0.8698727015558698
name: Cosine Accuracy@5
verified: no, type: cosine_accuracy@10
value: 0.9066478076379066
name: Cosine Accuracy@10
verified: no, type: cosine_precision@1
value: 0.7383309759547383
name: Cosine Precision@1
verified: no, type: cosine_precision@3
value: 0.5851013672795851
name: Cosine Precision@3
verified: no, type: cosine_precision@5
value: 0.49589816124469593
name: Cosine Precision@5
verified: no, type: cosine_precision@10
value: 0.38500707213578506
name: Cosine Precision@10
verified: no, type: cosine_recall@1
value: 0.2258018493225622
name: Cosine Recall@1
verified: no, type: cosine_recall@3
value: 0.3831143517659884
name: Cosine Recall@3
verified: no, type: cosine_recall@5
value: 0.46043165645745454
name: Cosine Recall@5
verified: no, type: cosine_recall@10
value: 0.5802246010255446
name: Cosine Recall@10
verified: no, type: cosine_ndcg@10
value: 0.6702777283455285
name: Cosine Ndcg@10
verified: no, type: cosine_mrr@10
value: 0.7981118520015267
name: Cosine Mrr@10
verified: no, type: cosine_map@100
value: 0.593002873023239
name: Cosine Map@100
verified: no, task: type: information-retrieval
name: Information Retrieval
dataset: name: dim 128
type: dim_128
metrics: type: cosine_accuracy@1
value: 0.7185289957567186
name: Cosine Accuracy@1
verified: no, type: cosine_accuracy@3
value: 0.8302687411598303
name: Cosine Accuracy@3
verified: no, type: cosine_accuracy@5
value: 0.8642149929278642
name: Cosine Accuracy@5
verified: no, type: cosine_accuracy@10
value: 0.8953323903818954
name: Cosine Accuracy@10
verified: no, type: cosine_precision@1
value: 0.7185289957567186
name: Cosine Precision@1
verified: no, type: cosine_precision@3
value: 0.5596416784535597
name: Cosine Precision@3
verified: no, type: cosine_precision@5
value: 0.4746817538896747
name: Cosine Precision@5
verified: no, type: cosine_precision@10
value: 0.36605374823196607
name: Cosine Precision@10
verified: no, type: cosine_recall@1
value: 0.21741492026039794
name: Cosine Recall@1
verified: no, type: cosine_recall@3
value: 0.3643446931786265
name: Cosine Recall@3
verified: no, type: cosine_recall@5
value: 0.4415110089630148
name: Cosine Recall@5
verified: no, type: cosine_recall@10
value: 0.5535910093833504
name: Cosine Recall@10
verified: no, type: cosine_ndcg@10
value: 0.6417304469454738
name: Cosine Ndcg@10
verified: no, type: cosine_mrr@10
value: 0.7807463909656271
name: Cosine Mrr@10
verified: no, type: cosine_map@100
value: 0.5556071606830145
name: Cosine Map@100
verified: no, task: type: information-retrieval
name: Information Retrieval
dataset: name: dim 64
type: dim_64
metrics: type: cosine_accuracy@1
value: 0.6534653465346535
name: Cosine Accuracy@1
verified: no, type: cosine_accuracy@3
value: 0.7765205091937766
name: Cosine Accuracy@3
verified: no, type: cosine_accuracy@5
value: 0.8118811881188119
name: Cosine Accuracy@5
verified: no, type: cosine_accuracy@10
value: 0.842998585572843
name: Cosine Accuracy@10
verified: no, type: cosine_precision@1
value: 0.6534653465346535
name: Cosine Precision@1
verified: no, type: cosine_precision@3
value: 0.49882131070249874
name: Cosine Precision@3
verified: no, type: cosine_precision@5
value: 0.42574257425742584
name: Cosine Precision@5
verified: no, type: cosine_precision@10
value: 0.3258840169731259
name: Cosine Precision@10
verified: no, type: cosine_recall@1
value: 0.19782326300239175
name: Cosine Recall@1
verified: no, type: cosine_recall@3
value: 0.32007460761434003
name: Cosine Recall@3
verified: no, type: cosine_recall@5
value: 0.38490547346807885
name: Cosine Recall@5
verified: no, type: cosine_recall@10
value: 0.4811566314336906
name: Cosine Recall@10
verified: no, type: cosine_ndcg@10
value: 0.5700147989809387
name: Cosine Ndcg@10
verified: no, type: cosine_mrr@10
value: 0.7207000291865919
name: Cosine Mrr@10
verified: no, type: cosine_map@100
value: 0.4772717799101714
name: Cosine Map@100
verified: no
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Created: 2025-06-09 19:23:02