Volume 45 Issue 2
Apr.  2025
Turn off MathJax
Article Contents
ZHU Xuesong, QU Enrui, ZHU Yufeng, QUAN Yuan. Construction and Application of a Ternary Relationship Prediction Model for Microgravity Biological Knowledge Graph (in Chinese). Chinese Journal of Space Science, 2025, 45(2): 493-505 doi: 10.11728/cjss2025.02.2024-0167
Citation: ZHU Xuesong, QU Enrui, ZHU Yufeng, QUAN Yuan. Construction and Application of a Ternary Relationship Prediction Model for Microgravity Biological Knowledge Graph (in Chinese). Chinese Journal of Space Science, 2025, 45(2): 493-505 doi: 10.11728/cjss2025.02.2024-0167

Construction and Application of a Ternary Relationship Prediction Model for Microgravity Biological Knowledge Graph

doi: 10.11728/cjss2025.02.2024-0167 cstr: 32142.14.cjss.2024-0167
  • Received Date: 2024-11-19
  • Rev Recd Date: 2025-01-17
  • Available Online: 2025-03-25
  • With the advancement of science and technology, the demand for space exploration has become particularly urgent. However, the microgravity environment in space has negative impacts on the physiological and psychological health of astronauts, including decreased bone density, muscle atrophy, and changes in cardiovascular function. These challenges pose significant barriers to the realization of long-term space habitation and deep space exploration. To address these challenges, this study integrates Microgravity Biomedical Knowledge Graphs (MBKG) and Drug Repurposing Knowledge Graphs (DRKG) to construct a comprehensive knowledge graph that covers a wide range of diseases, drugs, and genes, as well as the complex relationships between entities. Based on this, the study trains and uses a new ternary relationship prediction model, Heterogeneous Causal Meta path Graph Neural Network (HCMGNN), to obtain prediction results. The results show that compared with traditional binary link prediction in knowledge graphs, the ternary prediction method proposed in this study has a significant advantage in improving the accuracy of gene and drug predictions. The study concludes that the ternary relationship model is effective and has the potential to explore the prediction of gene-drug-disease ternary relationships, provide new methods and research ideas for the physiological and psychological health of astronauts in future space exploration and drug repurposing research, and opening up new perspectives in the field of drug repurposing.

     

  • loading
  • [1]
    KIM D H, LIN S C. Human capital and natural resource dependence[J]. Structural Change and Economic Dynamics, 2017, 40: 92-102 doi: 10.1016/j.strueco.2017.01.002
    [2]
    DREES J M, HEUGENS P P M A R. Synthesizing and extending resource dependence theory: a meta-analysis[J]. Journal of Management, 2013, 39(6): 1666-1698 doi: 10.1177/0149206312471391
    [3]
    FANKHAUSER T, WANG Q, GERLICHER A, et al. Resource dependency processing in web scaling frameworks[J]. IEEE Transactions on Services Computing, 2018, 11(1): 155-168 doi: 10.1109/TSC.2016.2561934
    [4]
    DICKERSON B L, SOWINSKI R, KREIDER R B, et al. Impacts of microgravity on amino acid metabolism during spaceflight[J]. Experimental Biology and Medicine, 2023, 248(5): 380-393 doi: 10.1177/15353702221139189
    [5]
    OLUWAFEMI F A, ABDELBAKI R, LAI J C Y, et al. A review of astronaut mental health in manned missions: Potential interventions for cognitive and mental health challenges[J]. Life Sciences in Space Research, 2021, 28: 26-31 doi: 10.1016/j.lssr.2020.12.002
    [6]
    SPRUGNOLI G, CAGLE Y D, SANTARNECCHI E. Microgravity and cosmic radiations during space exploration as a window into neurodegeneration on earth[J]. JAMA Neurology, 2020, 77(2): 157-158 doi: 10.1001/jamaneurol.2019.4003
    [7]
    VAN OMBERGEN A, DEMERTZI A, TOMILOVSKAYA E, et al. The effect of spaceflight and microgravity on the human brain[J]. Journal of Neurology, 2017, 264(1): 18-22
    [8]
    ZHENG D, SONG X, MA C, et al. DGL-KE: training knowledge graph embeddings at scale[C]//Proceedings of the 43rd International ACM SIGIR Conference on Research and Development in Information Retrieval. New York: ACM, 2020
    [9]
    SANG S T, YANG Z H, LIU X X, et al. GrEDeL: a knowledge graph embedding based method for drug discovery from biomedical literatures[J]. IEEE Access, 2018, 7: 8404-8415
    [10]
    FARRUGIA L, AZZOPARDI L M, DEBATTISTA J, et al. Predicting drug-drug interactions using knowledge graphs[OL]. arXiv preprint arXiv: 2308.04172, 2023
    [11]
    ZHENG Y H, PAN G J, QUAN Y, et al. Construction of microgravity biological knowledge graph and its applications in anti-osteoporosis drug prediction, Life Sciences in Space Research, Volume 41, 2024, Pages 64-73, ISSN 2214-5524.
    [12]
    Ioannidis, V. N. et al. Drkg-drug repurposing knowledge graph for covid-19. GitHub https://github.com/gnn4dr /DRKG (2020). Accessed 01 Jan 2022.
    [13]
    ZHU G H, ZHU Z N, CHEN H Y, et al. HAGNN: hybrid aggregation for heterogeneous graph neural networks[OL]. arXiv preprint arXiv: 2307.01636, 2023
    [14]
    LIANG T, LIU J. Meta-path generation online for heterogeneous network embedding[C]//Proceedings of the 2020 International Joint Conference on Neural Networks (IJCNN). Glasgow, UK: IEEE, 2020
    [15]
    RODRIGUEZ J D, PEREZ A, LOZANO J A. Sensitivity analysis of k-fold cross validation in prediction error estimation[J]. IEEE Transactions on Pattern Analysis and Machine Intelligence, 2010, 32(3): 569-575 doi: 10.1109/TPAMI.2009.187
    [16]
    POHJANKUKKA J, PAHIKKALA T, NEVALAINEN P, et al. Estimating the prediction performance of spatial models via spatial k-fold cross validation[J]. International Journal of Geographical Information Science, 2017, 31(10): 2001-2019 doi: 10.1080/13658816.2017.1346255
    [17]
    BERGMEIR C, HYNDMAN R J, KOO B. A note on the validity of cross-validation for evaluating autoregressive time series prediction[J]. Computational Statistics :Times New Roman;">& Data Analysis, 2018, 120: 70-83
    [18]
    SAHA S, ROY D, MITRA M. On modifying evaluation measures to deal with ties in ranked lists[C]//Proceedings of the 22nd ACM/IEEE Joint Conference on Digital Libraries. Cologne, Germany: IEEE, 2022
    [19]
    GOEL S, KUMAR R, KUMAR M, et al. An efficient page ranking approach based on vector norms using sNorm(p) algorithm[J]. Information Processing :Times New Roman;">& Management, 2019, 56(3): 1053-1066
    [20]
    SADEGHI A, GRAUX D, YAZDI H S, et al. MDE: multiple distance embeddings for link prediction in knowledge graphs[OL]. arXiv preprint arXiv: 1905.10702, 2019
    [21]
    TURAL S, KARA N, ALAYLI G, et al. Association between osteoporosis and polymorphisms of the bone Gla protein, estrogen receptor 1, collagen 1-A1 and calcitonin receptor genes in Turkish postmenopausal women[J]. Gene, 2013, 515(1): 167-172 doi: 10.1016/j.gene.2012.10.041
    [22]
    SEHMISCH S, UFFENORDE J, MAEHLMEYER S, et al. Evaluation of bone quality and quantity in osteoporotic mice–the effects of genistein and equol[J]. Phytomedicine, 2010, 17(6): 424-430 doi: 10.1016/j.phymed.2009.10.004
    [23]
    Da Silva F R P, Vasconcelos A C C G, Casimiro G S, et al. Quantitative assessment of the association between polymorphisms in osteoprotegerin gene and risk of low bone mineral density[J]. International Archives of Medicine, 2015: 8(169)
    [24]
    ŞIRIN Ö K, AYDOĞAN H Y, UYAR M, et al. PPARγ Pro12Ala and C161T polymorphisms, but not PPARα L162V, are associated with osteoporosis risk in Turkish postmenopausal women[J]. İstanbul Journal of Pharmacy, 2019, 49(1): 14-19
    [25]
    SCHOLTYSEK C, KATZENBEISSER J, FU H, et al. PPARβ/δ governs Wnt signaling and bone turnover[J]. Nature Medicine, 2013, 19(5): 608-613 doi: 10.1038/nm.3146
    [26]
    ZAYZAFOON M, GATHINGS W E, MCDONALD J M. Modeled microgravity inhibits osteogenic differentiation of human mesenchymal stem cells and increases Adipogenesis[J]. Endocrinology, 2004, 145(5): 2421-2432 doi: 10.1210/en.2003-1156
    [27]
    MANN V, GRIMM D, CORYDON T J, et al. Changes in human foetal osteoblasts exposed to the random positioning machine and bone construct tissue engineering[J]. International Journal of Molecular Sciences, 2019, 20(6): 1357 doi: 10.3390/ijms20061357
    [28]
    JURZAK M, ADAMCZYK K, ANTOŃCZAK P, et al. Evaluation of genistein ability to modulate CTGF mRNA/protein expression, genes expression of TGFβ isoforms and expression of selected genes regulating cell cycle in keloid fibroblasts in vitro[J]. Acta Poloniae Pharmaceutica, 2014, 71(6): 972-986
    [29]
    Plourde P V, SCHWARTZBERG L S, GREENE G L, et al. An open-label, randomized, multi-center phase 2 study evaluating the activity of lasofoxifene relative to fulvestrant for the treatment of postmenopausal women with locally advanced or Metastatic ER+/HER2- Breast Cancer (MBC) with an ESR1 mutation[C]//Cancer Research, San Antonio: San Antonio Breast Cancer Symposium, 2019
    [30]
    GOETZ M P, GAL-YAM E, STOVER D, et al. Abstract P5-05-04: Estrogen Receptor 1 (ESR1) mutations in circulating tumor DNA (ctDNA) from patients with ER+/HER2-metastatic Breast Cancer (mBC) treated with lasofoxifene or fulvestrant in the ELAINE 1 study[J]. Cancer Research, 2023, 83(S5): P5-05-04
    [31]
    SEFRIOUI D, PERDRIX A, SARAFAN-VASSEUR N, et al. Short report: monitoring ESR1 mutations by circulating tumor DNA in aromatase inhibitor resistant metastatic breast cancer[J]. International Journal of Cancer, 2015, 137(10): 2513-2519 doi: 10.1002/ijc.29612
    [32]
    NOORDIN S, GLOWACKI J. Parathyroid hormone and its receptor gene polymorphisms: implications in osteoporosis and in fracture healing[J]. Rheumatology International, 2016, 36(1): 1-6 doi: 10.1007/s00296-015-3319-9
    [33]
    STYRKARSDOTTIR U, THORLEIFSSON G, GUDJONSSON S A, et al. Sequence variants in the PTCH1 gene associate with spine bone mineral density and osteoporotic fractures[J]. Nature Communications, 2016, 7(1): 10129 doi: 10.1038/ncomms10129
    [34]
    NAKAMURA T, SUGIMOTO T, NAKANO T, et al. Randomized Teriparatide [Human Parathyroid Hormone (PTH) 1–34] Once-Weekly Efficacy Research (TOWER) trial for examining the reduction in new vertebral fractures in subjects with primary osteoporosis and high fracture risk[J]. The Journal of Clinical Endocrinology :Times New Roman;">& Metabolism, 2012, 97(9): 3097-3106
    [35]
    CUMMINGS S R, MCCLUNG M, REGINSTER J Y, et al. Arzoxifene for prevention of fractures and invasive breast cancer in postmenopausal women[J]. Journal of Bone and Mineral Research, 2011, 26(2): 397-404 doi: 10.1002/jbmr.191
    [36]
    VICO L, HARGENS A. Skeletal changes during and after spaceflight[J]. Nature Reviews Rheumatology, 2018, 14(2): 229-245
    [37]
    SMITH S M, HEER M A, SHACKELFORD L C, et al. Benefits for bone from resistance exercise and nutrition in long-duration spaceflight[J]. Journal of Applied Physiology, 2012, 112(1): 105-113
    [38]
    CARTER J A, BUCKEY J C, GREENHALGH L, et al. An interactive media program for managing psychosocial problems on long-duration spaceflights[J]. Aviation, Space, and Environmental Medicine, 2005, 76(S6): B213-B223
  • 加载中

Catalog

    通讯作者: 陈斌, bchen63@163.com
    • 1. 

      沈阳化工大学材料科学与工程学院 沈阳 110142

    1. 本站搜索
    2. 百度学术搜索
    3. 万方数据库搜索
    4. CNKI搜索

    Figures(4)  / Tables(5)

    Article Metrics

    Article Views(272) PDF Downloads(21) Cited by()
    Proportional views
    Related

    /

    DownLoad:  Full-Size Img  PowerPoint
    Return
    Return