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 .
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Notes
- 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.
The identification of a tree composed of a single element is a case that is strongly influenced by noise.
References
Bar-Yam, Y.: Dynamics of Complex Systems. Studies in Nonlinearity. Perseus Publishing, Reading (1997)
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)
Beerenwinkel, N., Schwarz, R.F., Gerstung, M., Markowetz, F.: Cancer evolution: mathematical models and computational inference. Syst. Biol. 64(1), e1–e25 (2014)
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)
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)
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)
Cover, T., Thomas, A.: Elements of Information Theory, 2nd edn. Wiley-Interscience, New York (2006)
Davis, A., Gao, R., Navin, N.: Tumor evolution: linear, branching, neutral or punctuated? Biochim. Biophys. Acta (BBA) Rev. Cancer 1867(2), 151–161 (2017)
Gao, Y., Church, G.: Improving molecular cancer class discovery through sparse non-negative matrix factorization. Bioinformatics 21(21), 3970–3975 (2005)
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)
Hofree, M., Shen, J.P., Carter, H., Gross, A., Ideker, T.: Network-based stratification of tumor mutations. Nat. Methods 10(11), 1108 (2013)
Holme, P., Saramäki, J.: Temporal networks. Phys. Rep. 519(3), 97–125 (2012)
Hordijk, W., Steel, M.: Detecting autocatalytic, self-sustaining sets in chemical reaction systems. J. Theor. Biol. 227(4), 451–461 (2004)
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)
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)
Lu, J., et al.: Microrna expression profiles classify human cancers. Nature 435(7043), 834 (2005)
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)
Network, C.G.A., et al.: Comprehensive molecular characterization of human colon and rectal cancer. Nature 487(7407), 330 (2012)
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)
Nowell, P.C.: The clonal evolution of tumor cell populations. Science 194(4260), 23–28 (1976)
Papoulis, A., Pillai, S.U.: Probability, Random Variables, and Stochastic Processes. McGraw-Hill, Boston (2015)
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)
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)
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
Roli, A., Villani, M., Caprari, R., Serra, R.: Identifying critical states through the relevance index. Entropy 19(2), 73 (2017)
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
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
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
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
Suppes, P.: A probabilistic theory of causality (1973)
Tononi, G., McIntosh, A., Russel, D., Edelman, G.: Functional clustering: identifying strongly interactive brain regions in neuroimaging data. Neuroimage 7, 133–149 (1998)
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)
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
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
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)
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
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
Vogelstein, B., Papadopoulos, N., Velculescu, V.E., Zhou, S., Diaz, L.A., Kinzler, K.W.: Cancer genome landscapes. Science 339(6127), 1546–1558 (2013)
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.
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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
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