Alessia Annibale

Reader in Disordered Systems
Department of Mathematics, Strand campus, London WC2R 2LS
Room S4.02.1, Strand campus,

Institute of Mathematical and Molecular Biomedicine
Room HB4.3N, Hodgkin Bldg, Guy's campus, London WC2R

Email: alessia.annibale (followed by @kcl.ac.uk)

TEACHING

Postgraduate

• 7CCMCS07   Research Methods and Advanced Topics in Complex Systems   (2022-present)
• 7CCMCS04   Dynamical Analysis of Complex Systems   (from 2011 to 2020)
• 7CCMCS02   Theory of Complex Networks   (in 2017/18)
• 7CCMNE04   Advanced Topics in Non-equilibrium systems   (in 2014/15)
• 7CCM451A   Neural Networks   (from 2007 to 2010)

Undergraduate

• 6CCMCS05   Mathematical Biology   (2022-present)
• 4CCM131A/5CCM131B   Introduction to Dynamical Systems   (from 2007 to 2017)
• 6CCMCS02   Theory of Complex Networks   (in 2017/18)

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PUBLICATIONS/PREPRINTS

• L Gamberi, A Annibale, P Vivo
     Price of Information in games of chance: a Statistical Physics approach (2024)
     Physical Review Reserach 6, 033250    Journal link   preprint
  

• Carles Martorell, Rubén Calvo, Alessia Annibale, and Miguel A. Muñoz
     Dynamically selected steady states and criticality in non-reciprocal networks (2024)
     Chaos, Solitons and Fractals, 182 (2024) 114809    Link

• Linda Albanese, Andrea Alessandrelli, Alessia Annibale, Adriano Barra
     Replica Symmetry Breaking in Supervised and Unsupervised Hebbian networks (2024)
     J. Phys. A: Math. Theor. 57 165003   Journal link   Preprint

• Gyeong-Gyun Ha, Izaak Neri, Alessia Annibale
     Clustering coefficients for networks with higher order interactions (2024)
     Chaos, Solitons and Fractals, 34(4):043102 (2024)    Link

• L Albanese, A Alessandrelli, A Barra, A Annibale
     About the de Almeida-Thouless line in neural networks (2024)
     Physica A 633 (2024) 129372    Link

• Evan Tzanis, Pierpaolo Vivo, Yanik-Pascal Förster, Luca Gamberi, Alessia Annibale
     Graphie: A network-based visual interface for UK's Primary Legislation (2023);
     F1000Research 2023, 12:236   Journal Link  preprint

• Vladimir Koskin, Adam Kells, Joe Clayton, Alexander K. Hartmann, Alessia Annibale, and Edina Rosta
     Variational Kinetic Clustering of Complex Networks ;  
     J. Chem. Phys. 158, 104112 (2023)   journal link

• Luca Gamberi, Pierpaolo Vivo, Yanik-Pascal Förster, Evan Tzanis and Alessia Annibale
     Rationalizing systematic discrepancies between election outcomes and opinion polls (2022);   preprint
     J. Stat. Mech. (2022) 123403 (selected by JSTAT Scientific Directors for the Highlights collection)

• Christian John Hurry, Alexander Mozeika, Alessia Annibale
     Dynamics of sparse Boolean networks with multi-node and self-interactions (2022) ;   preprint
     J. Phys. A: Math. Theor. 55 415003   journal link

• Yanik-Pascal Förster, Alessia Annibale, Luca Gamberi, Evan Tzanis, Pierpaolo Vivo
    Information retrieval and structural complexity of legal trees (2022);   preprint
     J. Phys. Complex. 3 035008   journal link

• G Torrisi, R. Kühn, A Annibale
     Uncovering the non-equilibrium stationary properties in sparse Boolean networks (2022);   preprint
     J. Stat. Mech. (2022) 053303

• DT Robson, ACW Baas, A Annibale
    Reproducing size distributions of swarms of barchan dunes on Mars and Earth using a mean-field model (2022)
    Physica A: Statistical Mechanics and its Applications, 128042 ; journal link

• C. Hurry, A. Mozeika, A Annibale
     Vaccination with partial transmission and social distancing on contact networks    preprint
    J. Stat. Mech. (2022) 033302; journal link

• Yanik-Pascal Förster, Luca Gamberi, Evan Tzanis, Pierpaolo Vivo, Alessia Annibale
    Exact and Approximate Mean First Passage Times on Trees and other Necklace Structures: a Local Equilibrium Approach    preprint
    J. Phys. A: Math. Theor. 55 115001 (2022);   journal link

• G Torrisi, A Annibale, R. Kühn
     Unlocking heterogeneity of node activation in Boolean networks through dynamical programming (2021);   preprint
     Phys. Rev. E 104, 045313;   journal link

• DT Robson, ACW Baas, A Annibale
    A combined model of aggregation, fragmentation, and exchange processes: insights from analytical calculations (2021)   preprint
     J. Stat. Mech. (2021) 053203;  journal link

• L Gamberi, YP Förster, E Tzanis, A Annibale, P Vivo
    Maximal modularity and the optimal size of parliaments (2021)    preprint
     Scientific Reports, 11, 14452 (2021);   journal link

• CJ Hurry, A Mozeika, A Annibale
     Modelling the interplay between the CD4+/CD8+ T-cell ratio and the expression of MHC-I in tumours (2021);  
     Journal of Mathematical Biology, 83, 2 (2021)   journal link

• F Sicard, V Koskin, A Annibale, E Rosta
    Assessing Position-Dependent Diffusion from Biased Simulations and Markov State Model Analysis (2020);   preprint
    J. Chem. Theory Comput 2021, 17, 4, 2022−2033 journal link

• Giuseppe Torrisi, Reimer Kühn, Alessia Annibale
     Percolation on the gene regulatory network (2020);  preprint
     J. Stat. Mech. (2020) 083501   journal link

• A Kells, V. Koskin E Rosta, A Annibale
     Correlation functions, mean first passage times and the Kemeny constant (2020)
     J. Chem. Phys. 152, 104108 (2020) journal link

• R Hannam, R, Kühn, A Annibale
     Percolation in Gene Regulatory Networks and its role in sustaining life (2019)
     J. Phys. A: Math. Theor. 52 334002   (Invited contribution to Disordered serendipity: a glassy path to discovery) journal link

• A Kells, ZE Mihalka, A Annibale, E Rosta
     Mean First Passage Times in Variational Coarse Graining using Markov State Models (2019)
     J. Chem. Phys. 150, 134107   (Editor's pick)   journal link

• A Annibale, LA Dziobek-Garrett, H Tari
     The role of the T-helper/T-suppressor ratio on the adaptive immune response: a dynamical model (2018)
     J. Phys. A: Math. Theor. 51 505602   preprint

• A Kells, A Annibale, E Rosta
     Limiting relaxation times from Markov state models (2018)
     J. Chem. Phys. 149, 072324   journal link

• E Agliari, A Annibale, A Barra, ACC Coolen, D Tantari
     Retrieving an infinite number of patterns in a spin glass model of immune network (2017)
     European Physics Letters 117:28003, (Editor's choice 2017)   journal link

• R Hannam, A Annibale, R Kuehn
     Cell reprogramming modelled as transitions in a hierarchy of cell cycles (2017)
     J. Phys. A: Math. Theor. 50 425601, (Journal of Physics A Highlights of 2017) preprint

• ACC Coolen, A Annibale, ES Roberts
     Generating randomg networks and graphs (2017)
     Oxford University Press, ISBN: 9780198709893

• Silvia Bartolucci, Alexander Mozeika, Alessia Annibale
     The role of idiotypic interactions in the adaptive immune system: a belief-propagation approach (2016)
     J. Stat. Mech. (2016) 083402 ,   preprint

• A Annibale, ACC Coolen, N. Planell-Morrell
     Quantifying noise in mass spectrometry and yeast two-hybrid protein interaction detection experiments (2015)
     J. R. Soc. Interface 12(110):0573,   preprint

• S Bartolucci, A Annibale
     A dynamical model of the adaptive immune system: effects of cells promiscuity, antigens and B-B interactions (2015)
     J. Stat. Mech. (2015) P08017,   preprint

• A Annibale, O Courtney
     The two-star model: exact solution in the sparse regime and condensation transition (2015)
     J. Phys. A: Math. Theor. 48 (2015) 365001,   link

• S Sook Chung, A Pandini, A Annibale, ACC Coolen, N S Thomas, F Fraternali
     Bridging Topological and Functional Information in Protein Interaction Networks by Short Loops Profiling (2015)
     Scientific Reports 5:8540   journal link

• P Sollich, D Tantari, A Annibale, A Barra
     Extensive Parallel Processing on Scale-Free Networks (2014)
     Phys. Rev. Lett. 113 (23), 238106   journal link

• S Bartolucci, A Annibale
     Associative networks with diluted patterns: dynamical analysis at low and medium load (2014)
     J. Phys. A: Math. Theor. 47 415001 (on the Front Cover)     preprint

• E Roberts, A Annibale, ACC Coolen
     Controlled Markovian dynamics of graphs: unbiased algorithms for the generation of random graphs with controlled topological properties in Nonlinear Maps and their Applications (2014)
     Springer Proceedings in Mathematical and Statistics Volume 57 pp25-34 (pdf)

• C Gracio, ACC Coolen, A Annibale
     Cycle Statistics in Complex Networks and Ihara's Zeta Function in Nonlinear Maps and their Applications (2014)
     Springer Proceedings in Mathematical and Statistics Volume 57 pp81-94

• E Agliari, A Annibale, A Barra, ACC Coolen, D Tantari
     Immune networks: multi-tasking capabilities near saturation (2013)
     J. Phys. A: Math. Theor: 46 (41) 2013, (IOP Select: Highlights 2013)   preprint

• E Agliari, A Annibale, A Barra, ACC Coolen, D Tantari
     Immune networks: multi-tasking capabilities at medium load (2013)
     J. Phys. A: Math. Theor: 46 (33) 2013, (News item on "Insights")   preprint

• ES Roberts, A Annibale, ACC Coolen
     Tailored Random Graph Ensembles (2013)
     Journal of Physics Conference Series 410 012097

• ACC Coolen, F Fraternali, A Annibale, LP Fernandes, J Kleinjung
     Modelling biological networks via tailored random graphs (2011)
     in Handbook of statistical systems biology  ISBN: 978-0-470-71086-9   (pdf)

• A Annibale, ACC Coolen
     What you see is not what you get: how sampling affects macroscopic features of biological networks (2011)
     Interface Focus 2011, 1(6) , (on the Front Cover)   (pdf)

• A Annibale, ACC Coolen, G Bianconi
     Network resilience against intelligent attacks constrained by degree dependent node removal cost (2010)
     J. Phys. A: Math. Theor: 43 (39) 2010,   arXiv:1005.4283

• LP Fernandes, A Annibale, J Kleinjung, ACC Coolen and F Fraternali
     Protein networks reveal detection bias and species consistency when viewed through information-theoretic glasses (2010)
     PLoSONE 5(8) e12083 (2010),   (pdf)

• A Annibale, ACC Coolen, LP Fernandes, F Fraternali, J Kleinjung
     Tailored graph ensembles as proxies or null models for real networks I: tools for quantifying structure (2009)
     J. Phys. A: Math. Theor. 42 485001 (Top 10% most dowloaded of the quarter)  arXiv:0908.1759

• ACC Coolen, A De Martino, A Annibale
     Constrained Markovian dynamics of random graphs (2009)
     J. Stat. Phys. 136 (2009), 1035-1067 , arXiv:0905.4155

• A Annibale, P Sollich
     Dynamic heterogeneities in critical coarsening: Exact results for correlation and response fluctuations in finite-sized spherical models (2009)
     J Stat Mech P02064 (2009), arXiv:0811.3168

• A Annibale, P Sollich
     Fluctuation-dissipation relations in critical coarsening: crossover from unmagnetized to magnetized initial states (2008)
     J.Phys.A: Math.Theor: 41 (2008) 135001 (IOP Select)  arXiv:0801.1381

• A Annibale, P Sollich
     Spin, bond and global fluctuation-dissipation relations in the non-equilibrium spherical ferromagnet,
     J.Phys.A: Math.Gen: 39 (2006) 2853-2907 arXiv:cond-mat/0510731

• A Annibale, G Gualdi, A Cavagna
     Coexistence of supersymmetirc and supersymmetry-breaking states in spherical spin-glasses,
     J.Phys.A: Math.Gen: 37 (2004) 11311-11320 arXiv:cond-mat/0406466

• A Annibale, A Cavagna, I Giardina, G Parisi, E Trevigne
     The role of the Becchi-Rouet-Stora-Tyutin supersymmetry in the calculation of the complexity for the Sherrington-Kirkpatrick model,
     J.Phys.A: Math.Gen.36 (2003) 10937 arXiv:cond-mat/0307465

• A Annibale, A Cavagna, I Giardina, G Parisi
     Supersymmetric quenched complexity in the Sherrington-Kirkpatrick model,
     Phys.Rev.E 68, 061103 (2003) arXiv:cond-mat/0304698

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RECENT PRESENTATIONS

• "Dynamically selected steady states and criticality in non-reciprocal networks", Stochastic Models and Experiments in Ecology and Biology, L' Aquila, Italy, 28-31 May (2024)

• "Replica symmetry breaking in information processing systems", From Machine-Learning Theory to Driven Complex Systems and back, CECAM-HQ-EPFL, Lausanne, Switzerland, 22-24 May (2024)

• "Two types of criticality in neural network rate models: mapping to equilibrium phase transitions", Laboratoire de Physique Theorique et Modeles Statistiques Seminar Serie, Paris-Saclay, 20 February 2024

• "Replica Symmetry Breaking in Neural Networks", Theory and Methods Challenge Fortnight, Alan Turing Institute, London, 9 October 2023

• "Mathematicians against gene-regulatory networks", Disordered Systems Days at King's College London: a two day workshop to celebrate Reimer Kuehn, King's College London, 6 September 2023

• "Dynamical analysis of sparse Boolean networks", Sigma-Phi International Conference on Statistical Physics, Chania-Crete-Greece, 10-14 July 2023

• "Modelling cellular attractors in gene-regulatory networks", Workshop Physics-informed machine learning -- Explainable artificial intelligence via glassy statistical mechanics and biologically-inspired computing, Alan Turing Institute, 23 January 2023

• "Non-equilibrium dynamics of Sparse Boolean Networks", SEMPS18: A one-day Workshop on Out-of-Equilibrium Dynamics, City, University of London, 16 November 2022

• "Dynamics of Gene Regulatory Networks: dealing with sparsity and cooperativity out of equilibrium", Seminar Series of the Institute of Theoretical and Computational Physics, University of Granada, 14 June 2022

• "Statistical Mechanics perspectives on Cell Differentiation and Reprogramming", Chimera Seminar Series, Sapienza University of Rome, 16 March 2022

• "Non-equilibrium dynamics of Sparse Boolean Networks", Chimera Seminar Series, Sapienza University of Rome, 16 February 2022

• " Gene expression: insights from Neural networks and graph theoretical approaches " Seminar in Physics of Machine Learning and Complex Systems, Radboud University, Nijmegen, 6 October 2021

• " Gene regulatory networks versus Neural networks and Bipartite Graphs: what we can learn on cellular (re)programming? " Statistical Physics and Complexity Seminar Series, University of Edinburgh, 23 June 2021

• " Variational coarse-graining and Mean First Passage Times in Markov State Models " Warwick Centre for Predictive Modelling, 11 May 2020

• " Quantifying sampling bias in protein interaction networks " Symposium on Networks and Machine Learning in Biology, Francis Crick Institute, 3 February 2020

• " Modelling Gene Expression Dynamics via Neural Networks and Bipartite Boolean Graphs " University of Leeds - Non-linear Applied Dynamics Seminar Series, 3 December 2019

• " A mathematical perspective on cellular reprogramming "Image and Data - Analysis, Research and Translation, The Francis Crick Institute, 2 September 2019

• " A statistical physics view of cellular (re)programming ", Computational Approaches in Mathematical Biology, Dundee, 17 May 2019

• " Markov State models: Limiting relaxation time and Dimensionality Reduction ", ZIF Wokshop, Bielefeld, 4-9 March 2019 (pdf)

• " Modelling cellular gene expression via neural networks and bipartite graphs ", The Cambridge University Mathematical Society, 22th February 2019

• " Cell differentiation and reprogramming: insights from neural networks and graph theoretical approaches ", Disordered serendipity: a glassy path to discovery, Sapienza University (Rome), 20th September 2018

• " Cell reprogramming modelled as transitions in a hierarchy of cell cycles " Northumbria University (Newcastle), 18th April 2018

• " The role of the T-helper/T-regulator lymphocyte ratio on the adaptive immune system ", Mathematical Innovation for Biomedicine one-day meeting, 13th September 2017

• "Quantifying Noise in Y2H and Mass-spectrometry Datasets: A Mathematical Approach ", 7th Annual World Congress of Molecular and Cell Biology, 26 April 2017, Xi'An

• "Cell differentiation modelled as transitions in a hierarchy of cell cycles ", The Crick Institute London - Computational and Physical Biology Workshop 5 Dec 2016

• "Protein interaction networks and biology: towards a connection?", NIMR (National Institute for Medical Research), London, 11 Feb 2015 (pdf)

• "Immune system: multi-tasking capabilities near the saturation regime", University of Birmingham, 20 Oct 2013

• "Immune networks: multi-tasking capabilities near saturation" (pdf)   One-day workshop on Modelling the Complexity of the Immune System,
  A satellite of the European Conference on Complex Systems (ECCS'13), Barcelona, World Trade Center, 19 September 2013

• "Modelling biological networks via tailored random graphs: a study of sampling", Queen's Mary University London, 17 January 2013

• "Protein Interaction Networks via tailored random graph ensembles: a study of sampling" (pdf)   Workshop on interdisciplinary Complex Adaptive Networks and Systems (iCANS), King's College London, 15 June 2012

• "Modelling biological networks via tailored random graphs", University College London, Intelligent Systems Seminars, 23 Apr 2012 (pdf)

• "Effects of sampling on macroscopic features of biological networks", Symposium of Synthetic and Systems Biology, Imperial College London, 16 Nov 2011 (pdf)

• "Network resilience against intelligent attacks" (pdf)   EMBO Cancer Proteomics Conference, the Burlington Hotel, Dublin, 20-23 June 2011

• "Network resilience against intelligent attacks", Randall Regtreat, University of Chichester, 1-3 September 2010

• "Quantifying and comparing complexity of cellular networks", University College Dublin, 15-17 June 2009

• "Signaling networks and random graphs", King's College London, 26 June 2009 The key role of mathematics in 21st century biology and medicine

• "Cellular networks: structure beyond degree statistics", King's College London, 26 May 2009

• "Fluctuation-dissipation relations and heterogeneities in coarsening systems", The University of Manchester, 22 October 2008

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ORGANISED EVENTS