EpiSpec: A formal specification language for parameterized agent-based models against epidemiological ground truth

Building complex computational models of the spread of epidemics is a problem that has seen renewed interest in recent years. Such models are being used for understanding real-time disease evolution prediction and are also proving useful in the prevention, monitoring and control of contagious diseases. There is a pressing need to ensure reliability of epidemiological models since they are widely used in safety-critical applications. In this paper, we present a new spatio-temporal specification language, EpiSpec, for describing detailed properties of agent-based computational epidemiological models. We describe the formal syntax of EpiSpec and demonstrate its use by describing various spatio-temporal properties related to disease evolution, and propose the use of statistical model checking as an algorithmic technique for verification and validation of large computational epidemiological models.

[1]  Alberto Policriti,et al.  Model building and model checking for biochemical processes , 2007, Cell Biochemistry and Biophysics.

[2]  Stephan Merz,et al.  Model Checking , 2000 .

[3]  G. Naber.  The geometry of Minkowski spacetime : an introduction to the mathematics of the special theory of relativity , 1992 .

[4]  Madhav V. Marathe,et al.  Computational epidemiology , 2013, CACM.

[5]  Sanjit A. Seshia,et al.  Beaver: Engineering an Efficient SMT Solver for Bit-Vector Arithmetic , 2009, CAV.

[6]  G. An,et al.  Agent‐based models in translational systems biology , 2009, Wiley interdisciplinary reviews. Systems biology and medicine.

[7]  Roberto Giacobazzi,et al.  Verification, Model Checking, and Abstract Interpretation , 2013, Lecture Notes in Computer Science.

[8]  Axel Legay,et al.  A Bayesian Approach to Model Checking Biological Systems , 2009, CMSB.

[9]  Susmit Jha,et al.  Decision procedure based discovery of rare behaviors in Stochastic Differential Equation models of biological systems , 2012, 2012 IEEE 2nd International Conference on Computational Advances in Bio and medical Sciences (ICCABS).

[10]  Declan Butler,et al.  When Google got flu wrong , 2013, Nature.

[11]  Håkan L. S. Younes,et al.  Probabilistic Verification of Discrete Event Systems Using Acceptance Sampling , 2002, CAV.

[12]  Jon Parker,et al.  A Distributed Platform for Global-Scale Agent-Based Models of Disease Transmission , 2011, TOMC.

[13]  S. K. Jha,et al.  Quantifying Uncertainty in Epidemiological Models , 2012, 2012 ASE/IEEE International Conference on BioMedical Computing (BioMedCom).

[14]  Sumit Kumar Jha.  Model validation and discovery for complex stochastic system , 2010 .

[15]  S. Varadhan.  Large Deviations and Applications , 1984 .

[16]  Grigore Rosu,et al.  Monitoring Algorithms for Metric Temporal Logic Specifications , 2004, RV@ETAPS.

[17]  Tu Bao Ho,et al.  Visualization Support for User-Centered Model Selection in Knowledge Discovery and Data Mining , 2001, Int. J. Artif. Intell. Tools.

[18]  S Greenland,et al.  Modeling and variable selection in epidemiologic analysis. , 1989, American journal of public health.

[19]  Dino Mandrioli,et al.  Modeling time in computing: A taxonomy and a comparative survey , 2008, CSUR.

[20]  A. Ramanathan,et al.  Verification of Compartmental Epidemiological Models Using Metamorphic Testing, Model Checking and Visual Analytics , 2012, 2012 ASE/IEEE International Conference on BioMedical Computing (BioMedCom).

[21]  Sumit Kumar Jha,et al.  Exploring behaviors of stochastic differential equation models of biological systems using change of measures , 2012, BMC Bioinformatics.

[22]  A. Prasad Sistla,et al.  Timely monitoring of partially observable stochastic systems , 2014, HSCC.

[23]  Thomas Hérault,et al.  Approximate Probabilistic Model Checking , 2004, VMCAI.

[24]  R. Kessler,et al.  The genetic epidemiology of bulimia nervosa. , 1991, The American journal of psychiatry.

[25]  Susmit Jha,et al.  Parameter discovery for stochastic biological models against temporal behavioral specifications using an SPRT based Metric for simulated annealing , 2012, 2012 IEEE 2nd International Conference on Computational Advances in Bio and medical Sciences (ICCABS).

[26]  R. Khan,et al.  Sequential Tests of Statistical Hypotheses. , 1972 .

[27]  Marta Z. Kwiatkowska,et al.  PRISM 4.0: Verification of Probabilistic Real-Time Systems , 2011, CAV.