Dr Matteo Cavaliere
Senior Lecturer
My profile
Biography
My general scientific aim is to understand the role of information-processing and computation in complex systems.
My research is interdisciplinary and collaborative.
I use mathematical, computational and experimental approaches combining biologically-inspired computing, synthetic / systems biology and game theory.
Applications of my research range from the computational study of cooperation and cheating in communities to the spreading of cancer in tissues.
Academic and professional qualifications
PhD in Computer Science and Artificial Intelligence, University of Seville (Spain)
Career History
Research Associate at the University of Edinburgh, UK
Researcher at the Spanish National Biotechnology Centre - Spanish National Research Council, Madrid, Spain
Microsoft Research - University of Trento, Centre for Computational and Systems Biology, Trento, Italy
Languages
english; italian; spanish
Prizes and awards
Member of the Editorial Board of “Mathematics” (MDPI)
Member of the Editorial Board of “SynBio” (MDPI)
Steering Committee Member of the Conference on Membrane Computing
Academy New Appointments Grant (British Computer Society).
Microsoft Artificial Intelligence for Earth Grant
Invited Participant, National Academies Kecks Future Initiatives (NAKFI) Conference on Collective Behavior
National Academies Keck Future Initiatives Grant
Personal website address
Interests and expertise
Study of Complex Systems; Theory of Computing; Synthetic and Systems Biology; Bio-Inspired Computing; Evolutionary Game Theory.
Teaching
Subject areas
Theory and Applications of Computing; Algorithms
Why study…
Research:
I study the role of information-processing in living systems. In particular, I investigate the way in which living systems process and manipulate information and how their ability to do that in an efficient way can affect their possibility to compete and cooperate.
This line of research can increase our understanding of the meaning of “computation” and can allow us to use inspiration from living systems to get more reliable and more efficient computational systems.
Moreover, it allows us to understand Nature in a computational way providing new opportunities to tackle social and biological issues.
Postgraduate teaching
Algorithms and Data Structures
Research outputs
Research expertise
Study of Complex Systems; Theory of Computing; Synthetic and Systems Biology; Bio-Inspired Computing; Evolutionary Game Theory.
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Chapters in books
Csikász-Nagy, A., Cavaliere, M., Sedwards, S. (2012) 'Combining game theory and graph theory to model interactions between cells in the tumor microenvironment.' SEMA SIMAI Springer Series. pp. 3-18.
Cavaliere, M., Mazza, T. (2010) 'A (Natural) Computing Perspective on Cellular Processes.'
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Journal articles
Miles, A.L., Cavaliere, M. (2022) 'Cooperation dynamics in dynamical networks with history-based decisions.' PLoS One, 17(11) pp. e0275909-e0275909.
Waites, W., Cavaliere, M., Danos, V., Datta, R., Eggo, R.M., Hallett, T.B., Manheim, D., Panovska-Griffiths, J., Russell, T.W., Zarnitsyna, V.I. (2022) 'Compositional modelling of immune response and virus transmission dynamics.' Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 380(2233) pp. 20210307-20210307.
García-Victoria, P., Cavaliere, M., Gutiérrez-Naranjo, M.A., Cárdenas-Montes, M. (2022) 'Evolutionary game theory in a cell: A membrane computing approach.' Information Sciences, 589pp. 580-594.
Waites, W., Cavaliere, M., Manheim, D., Panovska-Griffiths, J., Danos, V. (2021) 'Rule-based epidemic models.' Journal of Theoretical Biology, 530pp. 110851-110851.
Miles, A.L., Cavaliere, M. (2021) 'Opinion diversity and the resilience of cooperation in dynamical networks.' Mathematics, 9(15)
Dokmegang, J., Yap, M.H., Han, L., Cavaliere, M., Doursat, R. (2021) 'Computational modelling unveils how epiblast remodelling and positioning rely on trophectoderm morphogenesis during mouse implantation..' PLoS One, 16(7)
Dokmegang, J., Nguyen, H., Kardash, E., Savy, T., Cavaliere, M., Peyriéras, N., Doursat, R. (2021) 'Quantification of cell behaviors and computational modelling show that cell directional behaviors drive zebrafish pectoral fin morphogenesis.' Bioinformatics, 37(18) pp. 2946-2954.
Dong, J., Stachowicz, M., Zhang, G., Cavaliere, M., Rong, H., Paul, P. (2021) 'Automatic Design of Spiking Neural P Systems Based on Genetic Algorithms.' International Journal of Unconventional Computing, 16(2-3) pp. 201-216.
Yang, G., Cavaliere, M., Zhu, C., Perc, M. (2021) 'Strategically positioning cooperators can facilitate the contagion of cooperation.' Scientific Reports, 11(1)
Yang, G., Csikász-Nagy, A., Waites, W., Xiao, G., Cavaliere, M. (2020) 'Information Cascades and the Collapse of Cooperation.' Scientific Reports, 10(1)
Yang, G., Cavaliere, M., Zhu, C., Perc, M. (2020) 'Ranking the invasions of cheaters in structured populations.' Scientific Reports, 10(1)
Yang, G., Benko, T.P., Cavaliere, M., Huang, J., Perc, M. (2019) 'Identification of influential invaders in evolutionary populations.' Scientific Reports, 9pp. 1-12.
Cavaliere, M., Alfonso, R.P. (2018) 'Editorial: Preface.' Natural Computing, 17(4) pp. 759-759.
Waites, W., Misirli, G., Cavaliere, M., Danos, V., Wipat, A. (2018) 'A Genetic Circuit Compiler: Generating Combinatorial Genetic Circuits with Web Semantics and Inference.' ACS Synthetic Biology,
Waites, W., Cavaliere, M., Cachat, E., Danos, V., Davies, J.A. (2018) 'An information-theoretic measure for patterning in epithelial tissues.' IEEE Access, 6pp. 40302-40312.
Cavaliere, M., Feng, S., Soyer, O.S., Jiménez, J.I. (2017) 'Cooperation in microbial communities and their biotechnological applications.' Environmental Microbiology, 19(8) pp. 2949-2963.
Moreno-Fenoll, C., Cavaliere, M., Martínez-García, E., Poyatos, J.F. (2017) 'Eco-evolutionary feedbacks can rescue cooperation in microbial populations.' Scientific Reports, 7
Cavaliere, M., Yang, G., Danos, V., Dakos, V. (2016) 'Detecting the Collapse of Cooperation in Evolving Networks.' Scientific Reports, 6
Misirli, G., Cavaliere, M., Waites, W., Pocock, M., Madsen, C., Gilfellon, O., Honorato-Zimmer, R., Zuliani, P., Danos, V., Wipat, A. (2015) 'Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization.' Bioinformatics, 32(6) pp. 908-917.
Xu, Z., Cavaliere, M., An, P., Vrudhula, S., Cao, Y. (2014) 'The stochastic loss of spikes in spiking neural P systems: Design and implementation of reliable arithmetic circuits.' Fundamenta Informaticae, 134pp. 183-200.
Csikász-Nagy, A., Escudero, L.M., Guillaud, M., Sedwards, S., Baum, B., Cavaliere, M. (2013) 'Cooperation and competition in the dynamics of tissue architecture during homeostasis and tumorigenesis.' Seminars in Cancer Biology, 23(4) pp. 293-298.
Cavaliere, M., Poyatos, J.F. (2013) 'Plasticity facilitates sustainable growth in the commons.' Journal of the Royal Society Interface, 10(81)
Cavaliere, M., Sedwards, S., Tarnita, C.E., Nowak, M.A., Csikász-Nagy, A. (2012) 'Prosperity is associated with instability in dynamical networks.' Journal of Theoretical Biology, 299pp. 126-138.
Bernardini, F., Brijder, R., Cavaliere, M., Franco, G., Hoogeboom, H.J., Rozenberg, G. (2011) 'On aggregation in multiset-based self-assembly of graphs.' Natural Computing, 10pp. 17-38.
Cavaliere, M., Leupold, P. (2011) 'Computing by observing: Simple systems and simple observers.' Theoretical Computer Science, 412pp. 113-123.
Calude, C.S., Cavaliere, M., Mardare, R. (2011) 'An observer-based de-quantisation of Deutsch’s algorithm.' International Journal of Foundations of Computer Science, 22pp. 191-201.
Cavaliere, M., Ibarra, O.H., Pǎun, G., Egecioglu, O., Ionescu, M., Woodworth, S. (2009) 'Asynchronous spiking neural P systems.' Theoretical Computer Science, 410pp. 2352-2364.
Mazza, T., Cavaliere, M. (2009) 'Cell Cycle and Tumor Growth in Membrane Systems with Peripheral Proteins.' Electronic Notes in Theoretical Computer Science, 227pp. 127-141.
Cavaliere, M., Jonoska, N., Leupold, P. (2009) 'DNA splicing: Computing by observing.' Natural Computing, 8pp. 157-170.
Mardare, R., Cavaliere, M., Sedwards, S. (2008) 'A logical characterization of robustness, mutants and species in colonies of agents.' International Journal of Foundations of Computer Science, 19pp. 1199-1221.
Brijder, R., Cavaliere, M., Riscos-Núñez, A., Rozenberg, G., Sburlan, D. (2008) 'Membrane systems with proteins embedded in membranes.' Theoretical Computer Science, 404pp. 26-39.
Cavaliere, M., Sedwards, S. (2008) 'Decision problems in membrane systems with peripheral proteins, transport and evolution.' Theoretical Computer Science, 404pp. 40-51.
Cavaliere, M., Mura, I. (2008) 'Experiments on the reliability of stochastic spiking neural P systems.' Natural Computing, 7pp. 453-470.
Cavaliere, M., Mardare, R., Sedwards, S. (2008) 'A multiset-based model of synchronizing agents: Computability and robustness.' Theoretical Computer Science, 391pp. 216-238.
Cavaliere, M., Sedwards, S. (2007) 'Membrane Systems with Peripheral Proteins: Transport and Evolution.' Electronic Notes in Theoretical Computer Science, 171pp. 37-53.
Brijder, R., Cavaliere, M., Riscos-Núñez, A., Rozenberg, G., Sburlan, D. (2007) 'Membrane Systems with Marked Membranes.' Electronic Notes in Theoretical Computer Science, 171pp. 25-36.
Cavaliere, M., Freund, R., Oswald, M., Sburlan, D. (2007) 'Multiset random context grammars, checkers, and transducers.' Theoretical Computer Science, 372pp. 136-151.
Cavaliere, M., Leupold, P. (2006) 'Observation of string-rewriting systems.' Fundamenta Informaticae, 74pp. 447-462.
Cavaliere, M., Deufemia, V. (2006) 'Further results on time-free P systems.' International Journal of Foundations of Computer Science, 17pp. 69-89.
Cavaliere, M., Sburlan, D. (2005) 'Time and synchronization in membrane systems.' Fundamenta Informaticae, 64pp. 65-77.
Ardelean, I.I., Cavaliere, M., Sburlan, D. (2005) 'Computing using signals: From cells to P systems.' Soft Computing, 9pp. 631-639.
Cavaliere, M., Genova, D. (2004) 'P systems with symport/antiport of rules.' Journal of Universal Computer Science, 10pp. 540-558.
Cavaliere, M., Leupold, P. (2004) 'Evolution and observation - A non-standard way to generate formal languages.' Theoretical Computer Science, 321pp. 233-248.
Ardelean, I.I., Cavaliere, M. (2003) 'Modelling biological processes by using a probabilistic P system software.' Natural Computing, 2pp. 173-197.
Cavaliere, M., Jonoska, N. (2003) 'Forbidding and enforcing in membrane computing.' Natural Computing, 2pp. 215-228.
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Conference papers
Cavaliere, M., Sanchez, A. (2017) 'The evolutionary resilience of distributed cellular computing.' In 17th International Conference on Membrane Computing (CMC 2016). 10105 LNCS. Valencia, Spain, 25/7/2016 - 29/7/2016. Springer, pp. 3-15.
Cavaliere, M. (2008) 'Computing by observing: A brief survey.' 5028 LNCS. pp. 110-119.
Cavaliere, M., Egecioglu, O., Ibarra, O.H., Ionescu, M., Pǎun, G., Woodworth, S. (2008) 'Asynchronous spiking neural P systems: Decidability and undecidability.' 4848 LNCS. pp. 246-255.
Cavaliere, M., Mardare, R. (2006) 'Partial knowledge in membrane systems: A logical approach.' 4361 LNCS. pp. 279-297.
Brijder, R., Cavaliere, M., Riscos-Núñez, A., Rozenberg, G., Sburlan, D. (2006) 'Membrane systems with external control.' 4361 LNCS. pp. 215-232.
Cavaliere, M., Jonoska, N., Leupold, P. (2006) 'Recognizing DNA splicing.' 3892 LNCS. pp. 12-26.
Cavaliere, M., Frisco, P., Hoogeboom, H.J. (2006) 'Computing by only observing.' 4036 LNCS. pp. 304-314.
Cavaliere, M., Sedwards, S. (2006) 'Modelling cellular processes using membrane systems with peripheral and integral proteins.' 4210 LNBI. pp. 108-126.
Cavaliere, M., Jonoska, N., Yogev, S., Piran, R., Keinan, E., Seeman, N.C. (2005) 'Biomolecular implementation of computing devices with unbounded memory.' 3384. pp. 35-49.
Alhazov, A., Cavaliere, M. (2005) 'Computing by observing bio-systems: The case of sticker systems.' 3384. pp. 1-13.
Cavaliere, M., Leupold, P. (2005) 'Evolution and observation: A non-standard way to accept formal languages.' 3354. pp. 153-163.
Cavaliere, M., Ionescu, M., Ishdorj, T.O. (2005) 'Inhibiting/de-inhibiting rules in P systems.' 3365. pp. 224-238.
Cavaliere, M., Sburlan, D. (2005) 'Time-independent P systems.' 3365. pp. 239-258.
Alhazov, A., Cavaliere, M. (2004) 'Proton pumping P systems.' 2933. pp. 1-18.
Cavaliere, M., Leupold, P. (2004) 'Evolution and observation: A new way to look at membrane systems.' 2933. pp. 70-87.
Cavaliere, M. (2003) 'Evolution-communication P systems.' 2597. pp. 134-145.
Enguix, G.B., Cavaliere, M., Ceterchi, R., Gramatovici, R., Martín-Vide, C. (2003) 'An application of dynamic P systems: Generating context-free languages.' 2597. pp. 90-106.