Comparative Analysis of Radiomic Features and Gene Expression Profiles in Histopathology Data using Graph Neural Networks | SpringerLink
Skip to main content

Comparative Analysis of Radiomic Features and Gene Expression Profiles in Histopathology Data using Graph Neural Networks

  • Conference paper
  • First Online:
Bildverarbeitung für die Medizin 2024 (BVM 2024)

Part of the book series: Informatik aktuell ((INFORMAT))

Included in the following conference series:

  • 1024 Accesses

Abstract

This study leverages graph neural networks to integrate MELC data with Radiomic-extracted features for melanoma classification, focusing on cellwise analysis. It assesses the effectiveness of gene expression profiles and Radiomic features, revealing that Radiomic features, particularly when combined with UMAP for dimensionality reduction, significantly enhance classification performance. Notably, using Radiomics contributes to increased diagnostic accuracy and computational efficiency, as it allows for the extraction of critical data from fewer stains, thereby reducing operational costs. This methodology marks an advancement in computational dermatology for melanoma cell classification, setting the stage for future research and potential developments.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Subscribe and save

Springer+ Basic
¥17,985 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Chapter
JPY 3498
Price includes VAT (Japan)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
JPY 10690
Price includes VAT (Japan)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
JPY 13363
Price includes VAT (Japan)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Similar content being viewed by others

References

  1. Schubert W. Topological proteomics, toponomics, MELK-technology. Proteomics of Microorganisms: Fundamental Aspects and Application. Berlin, Heidelberg: Springer Berlin Heidelberg, 2003:189–209.

    Google Scholar 

  2. Gao L, Lin F, Han D, Jiang J, Yang C, Zhuang Z et al. Quantitative fluorescence resonance energy transfer analysis on the direct interaction of activation-2b with histone H3/Switch-3B protein in arabidopsis mesophyll protoplasts. J Fluoresc. 2021:981–8.

    Google Scholar 

  3. Ruetze M, Gallinat S, Wenck H, Deppert W, Knott A. In situ localization of epidermal stem cells using a novel multi epitope ligand cartography approach. Integr Biol. 2010;2(5-6):241– 9.

    Google Scholar 

  4. Bonnekoh B, Böckelmann R, Pommer A, Malykh Y, Philipsen L, Gollnick H. The CD11a binding site of Efalizumab in psoriatic skin tissue as analyzed by multi-epitope ligand cartography robot technology: introduction of a novel biological drug-binding biochip assay. Skin Pharmacol Physiol. 2006;20(2):96–111.

    Google Scholar 

  5. Rivera Monroy LC, Rist L, Eberhardt M, Ostalecki C, Baur A, Vera J et al. Employing graph representations for cell-level characterization of melanoma MELC samples. 2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI). 2023:1–5.

    Google Scholar 

  6. Lazic D, Kromp F, Kirr M, Mivalt F, Rifatbegovic F, Halbritter F et al. Single-cell landscape of bone marrow metastases in human neuroblastoma unraveled by deep multiplex imaging. bioRxiv. 2020:2020–9.

    Google Scholar 

  7. Liang W,Wang B, Tao J, Peng M, Tu X, Qiu X et al. A machine learning–based multidimensional model integrating clinical, radiomics, and cell-free DNA methylation biomarkers for the classification of pulmonary nodules. J Clin Oncol. 2023;41(16_suppl):3070–0.

    Google Scholar 

  8. Pattarone G, Acion L, Simian M, Mertelsmann R, Follo M, Iarussi E. Learning deep features for dead and living breast cancer cell classification without staining. Sci Rep. 2021;11(1):10304.

    Google Scholar 

  9. Gómez OV, Herraiz JL, Udías JM, Haug A, Papp L, Cioni D et al. Analysis of crosscombinations of feature selection and machine-learning classification methods based on [18F] F-FDG PET/CT radiomic features for metabolic response prediction of metastatic breast cancer lesions. Cancers (Basel). 2022;14(12):2922.

    Google Scholar 

  10. Mercaldo F, Brunese MC, Merolla F, Rocca A, Zappia M, Santone A. Prostate gleason score detection by calibrated machine learning classification through radiomic features. Appl Sci. 2022;12(23):11900.

    Google Scholar 

  11. Chopra A, Sharma R, Rao UN. Pathology of melanoma. Surg Clin. 2020;100(1):43–59.

    Google Scholar 

  12. Albrecht M, Lucarelli P, Kulms D, Sauter T. Computational models of melanoma. Theor Biol Med Model. 2020;17(1):1–16.

    Google Scholar 

  13. Pachitariu M, Stringer C. Cellpose 2.0: how to train your own model. Nat Methods. 2022;19(12):1634–41.

    Google Scholar 

  14. Wolf FA, Angerer P, Theis FJ. SCANPY: large-scale single-cell gene expression data analysis. Genome Biol. 2018;19:1–5.

    Google Scholar 

  15. Palla G, Spitzer H, Klein M, Fischer D, Schaar AC, Kuemmerle LB et al. Squidpy: a scalable framework for spatial omics analysis. Nat Methods. 2022;19(2):171–8.

    Google Scholar 

  16. Griethuysen JJ van, Fedorov A, Parmar C, Hosny A, Aucoin N, Narayan V et al. Computational radiomics system to decode the radiographic phenotype. Cancer Res. 2017;77(21):e104–e107.

    Google Scholar 

  17. Ardizzoni S, Saccani I, Consolini L, Locatelli M. Local optimization of MAPF solutions on directed graphs. 2023.

    Google Scholar 

  18. Wang HY, Zhao Jp, Zheng CH. SUSCC: secondary construction of feature space based on UMAP for rapid and accurate clustering large-scale single cell RNA-seq data. Interdiscip Sci. 2021;13:83–90.

    Google Scholar 

  19. Do VH, Canzar S. A generalization of t-SNE and UMAP to single-cell multimodal omics. Genome Biol. 2021;22(1):1–9.

    Google Scholar 

  20. Pati P, Jaume G, Fernandes LA, Foncubierta-Rodríguez A, Feroce F, Anniciello AM et al. Hact-net: A hierarchical cell-to-tissue graph neural network for histopathological image classification. Uncertainty for Safe Utilization of Machine Learning in Medical Imaging, and Graphs in Biomedical Image Analysis. Springer. 2020:208–19.

    Google Scholar 

  21. Feng W, Zhang J, Dong Y, Han Y, Luan H, Xu Q et al. Graph random neural networks for semi-supervised learning on graphs. Adv Neural Inf Process Syst. 2020;33:22092–103.

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Luis C. Rivera Monroy .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2024 Der/die Autor(en), exklusiv lizenziert an Springer Fachmedien Wiesbaden GmbH, ein Teil von Springer Nature

About this paper

Check for updates. Verify currency and authenticity via CrossMark

Cite this paper

Monroy, L.C.R. et al. (2024). Comparative Analysis of Radiomic Features and Gene Expression Profiles in Histopathology Data using Graph Neural Networks. In: Maier, A., Deserno, T.M., Handels, H., Maier-Hein, K., Palm, C., Tolxdorff, T. (eds) Bildverarbeitung für die Medizin 2024. BVM 2024. Informatik aktuell. Springer Vieweg, Wiesbaden. https://doi.org/10.1007/978-3-658-44037-4_49

Download citation

Publish with us

Policies and ethics