Skip to main content

The Detection of Dynamical Organization in Cancer Evolution Models

  • Conference paper
  • First Online:
Artificial Life and Evolutionary Computation (WIVACE 2019)

Part of the book series: Communications in Computer and Information Science ((CCIS,volume 1200))

Included in the following conference series:

Abstract

Many systems in nature, society and technology are composed of numerous interacting parts. Very often these dynamics lead to the formation of medium-level structures, whose detection could allow a high-level description of the dynamical organization of the system itself, and thus to its understanding. In this work we apply this idea to the “cancer evolution” models, of which each individual patient represents a particular instance. This approach - in this paper based on the RI methodology, which is based on entropic measures - allows us to identify distinct independent cancer progression patterns in simulated patients, planning a road towards applications to real cases .

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

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 49.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 64.99
Price excludes VAT (USA)
  • 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

Notes

  1. 1.

    Note that this observation is related to the number of observations that is possible to have in currently available clinical studies, rather than to the method we are applying.

  2. 2.

    The identification of a tree composed of a single element is a case that is strongly influenced by noise.

References

  1. Bar-Yam, Y.: Dynamics of Complex Systems. Studies in Nonlinearity. Perseus Publishing, Reading (1997)

    Google Scholar 

  2. Bazzi, M., Porter, M.A., Williams, S., McDonald, M., Fenn, D.J., Howison, S.D.: Community detection in temporal multilayer networks, with an application to correlation networks. Multiscale Model. Simul. 14(1), 1–41 (2016)

    Article  MathSciNet  MATH  Google Scholar 

  3. Beerenwinkel, N., Schwarz, R.F., Gerstung, M., Markowetz, F.: Cancer evolution: mathematical models and computational inference. Syst. Biol. 64(1), e1–e25 (2014)

    Article  Google Scholar 

  4. Bennett, J.M., Catovsky, D., Daniel, M.T., Flandrin, G., Galton, D.A., Gralnick, H.R., Sultan, C.: Proposals for the classification of the acute leukaemias french-american-british (fab) co-operative group. Br. J. Haematol. 33(4), 451–458 (1976)

    Article  Google Scholar 

  5. Burrell, R.A., McGranahan, N., Bartek, J., Swanton, C.: The causes and consequences of genetic heterogeneity in cancer evolution. Nature 501(7467), 338–345 (2013)

    Article  Google Scholar 

  6. Caravagna, G., Graudenzi, A., Ramazzotti, D., Sanz-Pamplona, R., De Sano, L., Mauri, G., Moreno, V., Antoniotti, M., Mishra, B.: Algorithmic methods to infer the evolutionary trajectories in cancer progression. Proc. Natl. Acad. Sci. 113(28), E4025–E4034 (2016)

    Article  Google Scholar 

  7. Cover, T., Thomas, A.: Elements of Information Theory, 2nd edn. Wiley-Interscience, New York (2006)

    MATH  Google Scholar 

  8. Davis, A., Gao, R., Navin, N.: Tumor evolution: linear, branching, neutral or punctuated? Biochim. Biophys. Acta (BBA) Rev. Cancer 1867(2), 151–161 (2017)

    Google Scholar 

  9. Gao, Y., Church, G.: Improving molecular cancer class discovery through sparse non-negative matrix factorization. Bioinformatics 21(21), 3970–3975 (2005)

    Article  Google Scholar 

  10. Gillies, R.J., Verduzco, D., Gatenby, R.A.: Evolutionary dynamics of carcinogenesis and why targeted therapy does not work. Nat. Rev. Cancer 12(7), 487 (2012)

    Article  Google Scholar 

  11. Hofree, M., Shen, J.P., Carter, H., Gross, A., Ideker, T.: Network-based stratification of tumor mutations. Nat. Methods 10(11), 1108 (2013)

    Article  Google Scholar 

  12. Holme, P., Saramäki, J.: Temporal networks. Phys. Rep. 519(3), 97–125 (2012)

    Article  Google Scholar 

  13. Hordijk, W., Steel, M.: Detecting autocatalytic, self-sustaining sets in chemical reaction systems. J. Theor. Biol. 227(4), 451–461 (2004)

    Article  MathSciNet  MATH  Google Scholar 

  14. Lane, D., Pumain, D., van der Leeuw, S.E., West, G.: Complexity Perspectives in Innovation and Social Change, vol. 7. Springer Science & Business Media, Dordrecht (2009)

    Book  Google Scholar 

  15. Loohuis, L.O., Caravagna, G., Graudenzi, A., Ramazzotti, D., Mauri, G., Antoniotti, M., Mishra, B.: Inferring tree causal models of cancer progression with probability raising. PLoS ONE 9(10), e108358 (2014)

    Article  Google Scholar 

  16. Lu, J., et al.: Microrna expression profiles classify human cancers. Nature 435(7043), 834 (2005)

    Article  Google Scholar 

  17. Merlo, L.M., Pepper, J.W., Reid, B.J., Maley, C.C.: Cancer as an evolutionary and ecological process. Nat. Rev. Cancer 6(12), 924 (2006)

    Article  Google Scholar 

  18. Network, C.G.A., et al.: Comprehensive molecular characterization of human colon and rectal cancer. Nature 487(7407), 330 (2012)

    Article  Google Scholar 

  19. Nik-Zainal, S., Van Loo, P., Wedge, D.C., Alexandrov, L.B., Greenman, C.D., Lau, K.W., Raine, K., Jones, D., Marshall, J., Ramakrishna, M., et al.: The life history of 21 breast cancers. Cell 149(5), 994–1007 (2012)

    Article  Google Scholar 

  20. Nowell, P.C.: The clonal evolution of tumor cell populations. Science 194(4260), 23–28 (1976)

    Article  Google Scholar 

  21. Papoulis, A., Pillai, S.U.: Probability, Random Variables, and Stochastic Processes. McGraw-Hill, Boston (2015)

    Google Scholar 

  22. Ramazzotti, D., Caravagna, G., Olde Loohuis, L., Graudenzi, A., Korsunsky, I., Mauri, G., Antoniotti, M., Mishra, B.: Capri: efficient inference of cancer progression models from cross-sectional data. Bioinformatics 31(18), 3016–3026 (2015)

    Article  Google Scholar 

  23. Ramazzotti, D., Graudenzi, A., De Sano, L., Antoniotti, M., Caravagna, G.: Learning mutational graphs of individual tumour evolution from single-cell and multi-region sequencing data. BMC Bioinform. 20(1), 210 (2019)

    Article  Google Scholar 

  24. Righi, R., Roli, A., Russo, M., Serra, R., Villani, M.: New paths for the application of DCI in social sciences: theoretical issues regarding an empirical analysis. In: Rossi, F., Piotto, S., Concilio, S. (eds.) WIVACE 2016. CCIS, vol. 708, pp. 42–52. Springer, Cham (2017). https://doi.org/10.1007/978-3-319-57711-1_4

    Chapter  Google Scholar 

  25. Roli, A., Villani, M., Caprari, R., Serra, R.: Identifying critical states through the relevance index. Entropy 19(2), 73 (2017)

    Article  Google Scholar 

  26. Sani, L., Amoretti, M., Vicari, E., Mordonini, M., Pecori, R., Roli, A., Villani, M., Cagnoni, S., Serra, R.: Efficient search of relevant structures in complex systems. In: Adorni, G., Cagnoni, S., Gori, M., Maratea, M. (eds.) AI*IA 2016. LNCS (LNAI), vol. 10037, pp. 35–48. Springer, Cham (2016). https://doi.org/10.1007/978-3-319-49130-1_4

    Chapter  Google Scholar 

  27. Sani, L., D’Addese, G., Pecori, R., Mordonini, M., Villani, M., Cagnoni, S.: An integration-based approach to pattern clustering and classification. In: Ghidini, C., Magnini, B., Passerini, A., Traverso, P. (eds.) AI*IA 2018. LNCS (LNAI), vol. 11298, pp. 362–374. Springer, Cham (2018). https://doi.org/10.1007/978-3-030-03840-3_27

    Chapter  Google Scholar 

  28. Sani, L., Lombardo, G., Pecori, R., Fornacciari, P., Mordonini, M., Cagnoni, S.: Social relevance index for studying communities in a Facebook group of patients. In: Sim, K., Kaufmann, P. (eds.) EvoApplications 2018. LNCS, vol. 10784, pp. 125–140. Springer, Cham (2018). https://doi.org/10.1007/978-3-319-77538-8_10

    Chapter  Google Scholar 

  29. Silvestri, G., Sani, L., Amoretti, M., Pecori, R., Vicari, E., Mordonini, M., Cagnoni, S.: Searching relevant variable subsets in complex systems using K-Means PSO. In: Pelillo, M., Poli, I., Roli, A., Serra, R., Slanzi, D., Villani, M. (eds.) WIVACE 2017. CCIS, vol. 830, pp. 308–321. Springer, Cham (2018). https://doi.org/10.1007/978-3-319-78658-2_23

    Chapter  Google Scholar 

  30. Suppes, P.: A probabilistic theory of causality (1973)

    Google Scholar 

  31. Tononi, G., McIntosh, A., Russel, D., Edelman, G.: Functional clustering: identifying strongly interactive brain regions in neuroimaging data. Neuroimage 7, 133–149 (1998)

    Article  Google Scholar 

  32. Tononi, G., Sporns, O., Edelman, G.M.: A measure for brain complexity: relating functional segregation and integration in the nervous system. Proc. Natl. Acad. Sci. 91(11), 5033–5037 (1994)

    Article  Google Scholar 

  33. Vicari, E., Amoretti, M., Sani, L., Mordonini, M., Pecori, R., Roli, A., Villani, M., Cagnoni, S., Serra, R.: GPU-based parallel search of relevant variable sets in complex systems. In: Rossi, F., Piotto, S., Concilio, S. (eds.) WIVACE 2016. CCIS, vol. 708, pp. 14–25. Springer, Cham (2017). https://doi.org/10.1007/978-3-319-57711-1_2

    Chapter  Google Scholar 

  34. Villani, M., Filisetti, A., Benedettini, S., Roli, A., Lane, D., Serra, R.: The detection of intermediate-level emergent structures and patterns. In: Miglino, O., et al. (eds.) Advances in Artificial Life, ECAL 2013, pp. 372–378. The MIT Press (2013). http://mitpress.mit.edu/books/advances-artificial-life-ecal-2013

  35. Villani, M., Roli, A., Filisetti, A., Fiorucci, M., Poli, I., Serra, R.: The search for candidate relevant subsets of variables in complex systems. Artif. Life 21(4), 412–431 (2015)

    Article  Google Scholar 

  36. Villani, M., Sani, L., Amoretti, M., Vicari, E., Pecori, R., Mordonini, M., Cagnoni, S., Serra, R.: A relevance index method to infer global properties of biological networks. In: Pelillo, M., Poli, I., Roli, A., Serra, R., Slanzi, D., Villani, M. (eds.) WIVACE 2017. CCIS, vol. 830, pp. 129–141. Springer, Cham (2018). https://doi.org/10.1007/978-3-319-78658-2_10

    Chapter  Google Scholar 

  37. Villani, M., Sani, L., Pecori, R., Amoretti, M., Roli, A., Mordonini, M., Serra, R., Cagnoni, S.: An iterative information-theoretic approach to the detection of structures in complex systems. Complexity 2018, 1–15 (2018). https://doi.org/10.1155/2018/3687839

    Article  Google Scholar 

  38. Vogelstein, B., Papadopoulos, N., Velculescu, V.E., Zhou, S., Diaz, L.A., Kinzler, K.W.: Cancer genome landscapes. Science 339(6127), 1546–1558 (2013)

    Article  Google Scholar 

Download references

Acknowledgments

The work of Laura Sani was supported by a grant from Regione Emilia Romagna (“Creazione di valore per imprese e società con la gestione e l’analisi di BIG DATA”, POR FSE 2014/2020, Obiettivo Tematico 10) within the “Piano triennale alte competenze per la ricerca, il trasferimento tecnologico e l’imprenditorialità” framework, and by Infor srl.

Marco Villani thanks the support provided by the FAR2019 project of the Department of Physics, Informatics and Mathematics of the University of Modena and Reggio Emilia.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Marco Villani .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2020 Springer Nature Switzerland AG

About this paper

Check for updates. Verify currency and authenticity via CrossMark

Cite this paper

Sani, L., D’Addese, G., Graudenzi, A., Villani, M. (2020). The Detection of Dynamical Organization in Cancer Evolution Models. In: Cicirelli, F., Guerrieri, A., Pizzuti, C., Socievole, A., Spezzano, G., Vinci, A. (eds) Artificial Life and Evolutionary Computation. WIVACE 2019. Communications in Computer and Information Science, vol 1200. Springer, Cham. https://doi.org/10.1007/978-3-030-45016-8_6

Download citation

  • DOI: https://doi.org/10.1007/978-3-030-45016-8_6

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-45015-1

  • Online ISBN: 978-3-030-45016-8

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics