Model: mariakrissmer/pubmedbert_jonatan_100k_50s_20250711
Author: mariakrissmer
Pipeline: sentence-similarity
Library: sentence-transformers
Tags: sentence-transformers, safetensors, bert, sentence-similarity, feature-extraction, generated_from_trainer, dataset_size:303605, loss:MultipleNegativesRankingLoss, arxiv:1908.10084, arxiv:1705.00652, base_model:NeuML/pubmedbert-base-embeddings, base_model:finetune:NeuML/pubmedbert-base-embeddings, model-index, text-embeddings-inference, endpoints_compatible, region:us
Base models (finetune): id: NeuML/pubmedbert-base-embeddings
Card metadata: tags: sentence-transformers, sentence-similarity, feature-extraction, generated_from_trainer, dataset_size:303605, loss:MultipleNegativesRankingLoss
base_model: NeuML/pubmedbert-base-embeddings
widget: source_sentence: This cell likely originates from the CD8-positive, alpha-beta T cell family, based on expression of MALAT1, RPS27, RPL34, RPL10, TMSB4X, RPS27A, RPL13, RPLP2, RPS15A, RPL13A, RPS12, RPL11, RPS8, RPS14, RPL32, RPS28, RPS15, RPLP1, RPS3, RPL26, RPL23A, RPS16, RPS13, RPL36, RPS6, RPL30, TMSB10, RPL28, RPL14, RPL12, RPS20, IL7R, RPS4X, RPL18, RPL3, RPL37, FAU, PTMA, MT-CO1, RPL5, TPT1, BTG1, RPS23, RPL37A, MT-ND3, MT-ATP6, GIMAP4, RPS24, RPS7, PABPC1.
sentences: Presence of TMSB4X, CD74, MALAT1, CST3, ACTB, TMSB10, RPL10, FTH1, RPLP1, RPL13A, RPS14, RPL13, RPS19, RPS23, RPS27, RPL32, RPL34, RPS6, RPS27A, RPL26, PTMA, RPS12, RPL11, RPS15, RPS8, RPL8, VIM, RPL3, RPL28, RPL19, RPLP2, RPS16, SNX3, RPS24, RPL23A, FTL, LYZ, RPS15A, RPS4X, RPS3, RPS13, HLA-DRB5, RPS28, MYL6, S100B, RPL12, PFN1, RPL35, CPVL, RPS20 supports classification as conventional dendritic cell., Highly expressed genes: MALAT1, TMSB4X, RPS27, RPL13A, RPL10, RPL13, RPS12, RPL34, RPS15A, RPS27A, RPLP2, MT-CO1, RPLP1, RPS19, RPL28, RPL32, RPL23A, RPS14, TMSB10, RPS4X, RPS6, RPL11, RPS3, RPL30, RPL26, RPL19, RPS15, RPS23, MT-ND2, RPS28, RPS20, ACTB, RPL3, RPL37, RPS16, RPL36, TPT1, RPS8, RPL14, RPL12, RPS24, MT-CYB, MT-ND3, RPS13, RPL35, FAU, RPS7, RPL37A, RPL8, PTMA., Observed genes (MALAT1, NEAT1, SPP1, FTL, MT-CO1, CTSD, PSAP, ZEB2, MSR1, FNDC3B, ACTB, FN1, APOE, SAT1, CD36, BMP2K, RBM47, ABCA1, ATG7, HIF1A, FRMD4B, ASAP1, RUNX1, ALCAM, MT-ATP6, CD44, ARHGAP10, NRP1, LGMN, TRPS1, NAMPT, CCDC88A, RNASE1, TNS3, ETV6, LPP, IQGAP2, MERTK, PSD3, COLEC12, FTH1, AKAP13, MITF, FMN1, CD74, GAB2, FNIP2, KMT2C, VMP1, KLF6) are indicative of macrophage cell function., source_sentence: oligodendrocyte cells are known to express: MALAT1, PDE4B, MBP, PRUNE2, LINC01608, FRMD4B, DOCK5, GAB1, ENPP2, AK5, C10orf90, ZEB2, ARAP2, CCDC88A, KIRREL3, KCNH8, ZNF536, PLEKHH1, HIPK2, NFASC, CLMN, ALCAM, TCF4, MAP4K5, SLC12A2, BCAS1, TF, COBL, TMEM165, MBNL2, APP, CREB5, CNDP1, QDPR, HHIP, PXK, SLCO3A1, DSCAML1, GLDN, LPAR1, NEAT1, ZFYVE16, SCD, POLR2F, RNF130, ENOX1, SORT1, RAPGEF5, DOCK1, PIEZO2.
sentences: This cell likely originates from the endothelial cell family, based on expression of MALAT1, MEIS2, PTPRM, ARL15, LDB2, LDLRAD3, FKBP5, KIAA1217, PRSS23, SPIDR, FTL, FLT1, PHACTR1, EPAS1, ETS1, NHSL1, APP, FER, ASAP1, TANC2, NEAT1, PIK3C2A, PIAS1, SYNE2, TAB2, KMT2C, RPL18, ANKS1A, NHERF2, PLPP1, CADPS2, DOCK9, RPL3, CST3, NCOA7, SASH1, C7, IGFBP5, EHBP1, ADGRL2, RSRP1, SDC4, MT2A, IL6ST, NAV1, ARGLU1, ENTPD1, HSPG2, ATP1B1, GSN., Gene ranking includes: MALAT1, MBP, PDE4B, PTGDS, FTH1, TMEM165, NEAT1, TF, GAB1, FRMD4B, SPP1, ZEB2, ANKIB1, ANLN, ZFYVE16, FAM107B, RNF13, PRUNE2, CRYAB, RAPGEF5, ENPP2, OSBPL1A, APP, PKP4, DOCK5, CNDP1, C10orf90, S100B, ALCAM, KCNH8, ZNF536, TRIM59, LMCD1-AS1, SELENOP, LINC00609, SLC25A13, MAP4K5, AGPAT4, VRK2, GAB2, ARAP2, KIF1B, PLEKHH1, WNK1, SLC12A2, BCAS1, FGFR2, NEO1, PLD1, CTTNBP2., A cell that expresses the following genes: MALAT1, SERPINE1, C3, TSHZ2, NEAT1, EXT1, PCSK6, NAMPT, MT2A, GALNT2, A2M, PSD3, RALGAPA2, CFH, RORA, FKBP5, AOPEP, ABCA1, FOXP1, RRBP1, ALDH1A2, LPP, ACSL1, ETS2, STAT3, TGM2, TFPI, FAM107B, FNDC3B, ITGB5, FTL, TF, ABLIM1, ZBTB16, GMDS, TENT5A, SIPA1L2, ADGRL2, FOXO3, MYO1B, APOC1, SLC38A2, TNS3, MBNL2, GAREM1, PID1, ADK, ANGPTL4, INSR, PCCA is likely a hepatocyte cell., source_sentence: A cell that expresses the following genes: RPS12, RPS27, MALAT1, RPL13, RPL32, RPL10, RPL30, RPS28, RPL28, RPL11, RPL19, TPT1, RPS15A, RPLP1, RPS8, RPS23, RPL3, RPL34, RPS19, ACTB, RPS27A, RPS13, RPL37, RPS3, RPS15, RPL36, RPL26, RPS4X, RPL23A, RPL18, RPS14, RPS6, RPL12, JUNB, RPS7, RPLP2, TMSB4X, RPL5, RPL37A, FAU, MT-CO1, TMSB10, RPS24, RPL8, PFN1, NACA, MT-ATP6, MT-ND3, RPS11, PTMA is likely a memory T cell cell.
sentences: This cell shows significant expression of: MALAT1, TMSB4X, RPS27, RPLP1, RPL10, NKG7, MT-CO1, GNLY, RPL13A, RPS27A, RPL13, RPS3, RPS14, TMSB10, RPL34, RPS6, RPLP2, RPS19, RPS12, RPL23A, RPL3, RPS15, RPS23, ACTB, RPL19, RPL11, RPL32, RPL26, RPS4X, PFN1, TPT1, RPS15A, RPL37, RPL30, RPL8, FTH1, RPS7, EIF1, S100A4, MT-ATP6, RPS28, RPS13, DUSP1, BTG1, RPL35, RPS24, RPS11, RPS8, FAU, UBB., These expression features — RPS27, RPL10, RPS12, MALAT1, RPL13, RPLP1, RPL28, RPL32, RPS14, RPS28, RPL34, RPS3, RPS15A, TPT1, RPS8, RPL11, RPL30, RPL37, RPL19, RPS27A, RPS6, JUNB, RPS4X, RPS23, ACTB, RPL3, RPL26, TMSB10, RPLP2, RPL12, MT-ND3, TMSB4X, RPS19, RPS13, MT-CYB, RPS15, RPL36, RPS7, MT-CO1, RPL18, PTMA, FTH1, RPL23A, RPS24, FOS, RPL14, RPL37A, DUSP1, FAU, RPS16 — are typical of a memory T cell identity., ACTB, MALAT1, TMSB4X, RPL13, RPL10, RPL28, RPS12, RPL19, RPLP1, RPL11, RPS19, RPL30, TMSB10, RPL32, RPS15A, RPS27A, RPS7, RPS23, RPL12, RPS4X, MT-CO1, RPL18, PFN1, RPS15, RPS24, RPS3, RPS14, RPS27, RPL34, GAPDH, TPT1, RPS8, FAU, IL32, RPS13, RPL35, RPS6, RPL8, FTH1, RPL14, MT-CYB, RPS28, RPL3, ARHGDIB, SH3BGRL3, S100A4, NACA, MYL6, RPL5, RPL37 expression places this cell in the naive T cell category., source_sentence: According to gene expression (GPC6, NRG1, DGKB, FOXP2, MALAT1, NLGN4Y, ERC1, THSD4, XKR4, CELF2, TTTY14, ZNF804A, PKP4, MEG3, VTI1A, SPIDR, VPS13B, ZCCHC7, LINC01473, TTC28, PBX3, MYCBP2, NTRK3, UTY, ZNF462, OSBPL8, SGCD, SEZ6L, ZEB1, GRID1, USP34, BICD1, CCDC91, FTO, RFX3, PSD3, CPNE8, PLPPR1, UBR5, MGAT5, RUNX1T1, GTDC1, PLEKHA5, JAK2, MDFIC, DPYSL2, PHACTR1, DENND1A, C8orf34, CAMK1D), this is a neuron.
sentences: STK38, CALM1, TUBA1B, FTH1, MAP1B, TTTY14, GAPDH, ACTB, FTL, GNAS, DYNLL1, DPYSL2, CPE, DPYSL3, ATP5F1E, DSTN, PCNX2, FAU, CALM3, CKB, EIF1, BASP1, SOX18, NCK2, GSTP1, APLP2, DNAJA1, GNAO1, NRP1, CIRBP, MYH9, DAAM1, SNRNP70, PCOLCE, SEPTIN4, CCDC88A, OGFRL1, CLU, HNRNPA2B1, HP1BP3, AKAP9, H3-3B, APC, SKIL, UACA, SOD1, APP, ATP1B1, SCD5, FEZ1 expression pattern defines this as a glutamatergic neuron cell., MALAT1, CXCL14, FSTL5, CCK, INPP4B, SORCS1, TCF4, THSD7B, ATP1B1, CDH12, MT-ND3, CCNH, KALRN, MT-CO1, PHACTR1, MT-ATP6, MEF2C, SYNPR, CHSY3, MEG3, TMEM108, ZNF385D, CHL1, SEMA6D, ZNF385B, C8orf34, MT-CYB, ADAMTS9-AS2, PLEKHA5, DGKB, APP, SDK1, ZEB2, TAFA1, PRELID2, IL1RAPL2, SYNE1, PID1, CACNA2D3, ARPP21, PTPRM, EXT1, CALM1, SHISA9, THSD7A, TTC28, NFIB, PLD5, RGS6, DCC expression pattern defines this as a neuron cell., Gene ranking includes: MALAT1, VIP, ATP1B1, SPARCL1, CXCL14, HSP90AA1, SORCS1, CCK, INPP4B, CLU, SGCD, TCF4, CACNA2D3, PBX1, ALCAM, GNAS, PCSK1N, GAPDH, NR3C2, ZNF536, RPL10, TMEM132D, PSAP, MEG3, TTC28, ABI1, SYNPR, C8orf34, SLC6A1-AS1, SYNE1, HECW2, APP, PTPRJ, PID1, CKB, FLRT2, CHSY3, CALM1, TAFA2, RORA, RFX3, HSP90AB1, BICC1, TUBA1B, ITM2B, ATP1A1, DNER, SUPT3H, SEC62, CELF2., source_sentence: The pattern MALAT1, JUN, HSP90AA1, JUND, TMSB4X, MT-CO1, RPLP1, RPS27, HSP90AB1, UBC, TPT1, EIF1, H3-3B, DNAJB1, RPS12, RPL10, ACTB, RPL28, RPS3, HSPA6, RPS14, RPL13, MT-ATP6, RPS15, RPL30, FOS, JUNB, RPS27A, NFKBIA, ZFP36, RPS15A, RPL37, PTMA, RPS19, RPL34, RPL11, RPS8, RPL32, MT-CYB, RPL3, RPL19, YPEL5, DUSP1, FTH1, RPS28, TMSB10, DNAJA1, RPS13, HSPE1, KLF2 is indicative of gamma-delta T cell differentiation.
sentences: Gene expression matches that of endothelial cell of lymphatic vessel cells, including: UBC, DNAJB1, JUNB, MALAT1, PLCG2, NFKBIA, RPS27, KMT2E, GADD45B, INTS6, RPL12, MT-ND3, TMSB4X, RPL36, SLC38A2, MT-CO1, MT-ATP6, SFPQ, SOX4, TPT1, RPS24, PHLDB2, RPL26, ATF3, EIF1, JUN, RPL37A, RPS28, PDK4, CLK1, VIM, AGPAT4, TMSB10, PREX2, KLF6, CXCL2, FTL, HSP90AB1, RPS16, HSPB1, RPL28, PPFIBP1, ELK3, JUND, KLF4, RPL35, RPLP1, BCAR3, RPS11, RPL13A., This profile resembles gamma-delta T cell cells, based on genes like MALAT1, TMSB4X, ACTB, MT-CO1, RPLP1, RPS27, RPS12, RPL10, RPL13, NKG7, RPL28, RPS15A, RPS14, CD74, RPS3, RPL12, MT-CYB, RPS27A, RPS19, RPS8, RPL32, RPL30, RPLP2, RPL19, FOS, JUN, PTMA, RPS28, PFN1, RPL34, GAPDH, FAU, MT-ATP6, TMSB10, RPL18, HSP90AA1, COTL1, RPS15, SH3BGRL3, RPL11, RPS23, RPL23A, DNAJB1, RPS24, RPL13A, RPL26, DUSP1, RPL36, H3-3B, RPS6., The pattern MALAT1, RPL10, RPS27, RPL32, RPL34, RPS15A, RPL30, RPS28, RPS4X, RPS12, RPS19, RPLP1, RPL13, RPL19, RPL11, RPS14, MT-ND3, DNAJB1, RPS13, RPL26, TMSB4X, RPL3, MT-CYB, RPLP2, RPL14, ACTB, RPL8, MT-ND1, RPS15, RPL12, RPL18, RPL28, RPL36, TPT1, RPS6, RPS8, MT-CO1, RPS27A, RPS7, TMSB10, RPL37, PTMA, MT-ND2, RPS24, RPS3, FAU, RPS23, ARHGDIB, HSPE1, ZFP36L2 is indicative of regulatory T cell differentiation.
pipeline_tag: sentence-similarity
library_name: sentence-transformers
metrics: cosine_accuracy
model-index: name: SentenceTransformer based on NeuML/pubmedbert-base-embeddings
results: task: type: triplet
name: Triplet
dataset: name: train celltype scrna MNR
type: train_celltype_scrna_MNR
metrics: type: cosine_accuracy
value: 1
name: Cosine Accuracy
verified: no
Likes: 0 | All-time downloads: 6
Created: 2025-07-11 07:13:16