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A Contact-Explicit Covid-19 Epidemic and Response Assessment Model [article]

Wayne M Getz, Ludovica Luisa-Vissat, Richard Salter
2020 medRxiv   pre-print
We formulate a refined SEIR epidemic model that explicitly includes a contact class C that either thwarts pathogen invasion and returns to the susceptible class S or progresses successively through a latent class L, a presymptomatic/asymptomatic class A, and a symptomatic class I. Individuals in both A and I may go directly to an immune class V, and in I to a dead class D. Upon this SCLAIV formulation we impose a set of drivers that can be used to develop policy to manage current Covid-19 and
more » ... milar type disease outbreaks. These drivers include surveillance, social distancing (rate and efficacy), social relaxation, quarantining (linked to contact tracing), patient treatment/isolation and vaccination processes that can either be a non-negative constant or an s-shaped switching curve. The latter are defined in terms of onset and switching times, initial and final values, and abruptness of switching. We built a Covid-19 NMB-DASA web app to generate both deterministic and stochastic solutions to our SCLAIV and drivers model and use incidence and mortality data to provide both maximum-likelihood frequentist and Bayesian fitting of parameters. In the context of South African and English Covid-19 incidence data we demonstrate how to both identify and evaluate the role of drivers in ongoing outbreaks. In particular, we show that early social distancing in South Africa likely averted around 80,000 observed cases (actual number is double if only half the case are observed) during the months of June and July. We also demonstrated that incidence rates in South Africa will increase to between a conservative estimate of 15 and 30 thousand observed cases per day (again, actual number considerably higher) by the end of August if stronger social distancing measures are not effected during July and August, 2020. On different a note, we show that comparably good local optimal fits of the English data using surveillance, social distancing and social relaxation drivers can represent very different kinds of outbreaks---one with close to 90% and another with under 8% immune individuals. This latter result provides a cautionary tale of why fitting SEIR-like models to incidence or prevalence data can be extremely problematic when not anchored by other critical measures, such as levels of immunity in the population. Our presentation illustrates how our Covid-19 web app can be used by individuals without any programming skills to carry out forensic and scenario analyses in spatially contained populations such as small countries or metropolitan areas.
doi:10.1101/2020.07.16.20155812 fatcat:rdrw2j7nfnev3ppkhecpyueiga

Simulation and Analysis of Animal Movement Paths using Numerus Model Builder [article]

Wayne Getz, Ludovica Luisa Vissat, Richard Salter
2019 biorxiv/medrxiv   pre-print
Animal movement paths are represented by point-location time series called relocation data. How well such paths can be simulated, when the rules governing movement depend on the internal state of individuals and environmental factors (both local and, when memory is involved, global) remains an open question. To answer this, we formulate and test models able to capture the essential statistics of multiphase versions of such paths (viz., movement-phase-specific step-length and turning-angle
more » ... variances, auto-correlation, and cross correlation values), as well as broad scale movement patterns. The latter may include patchy coverage of the landscape, as well as the existence of home-range boundaries and gravitational centers-of-movement (e.g., centered around nests). Here we present a Numerus Model Builder implementation of two kinds of models: a high-frequency, multi-mode, biased, correlated random walk designed to simulate real movement data at a scale that permits simulation and identification of path segments that range from minutes to days; and a model that uses statistics extracted from relocation data---either empirical or simulated---to construct movement modes and phases at subhourly to daily scales. We evaluate how well our derived statistical movement model captures patterns produced by our more detailed simulation model as a way to evaluate how well derived statistical movement models may capture patterns occurring in empirical data.
doi:10.1101/2019.12.15.876987 fatcat:dct6zkz26vdevlnmegzuj7bnw4

Simulation Platforms to Support Teaching and Research in Epidemiological Dynamics [article]

Wayne Marcus Getz, Richard Salter, Ludovica Luisa Vissat
2022 medRxiv   pre-print
Ludovica Luisa Vissat: Was involved with the R implementation, ran R examples, checked all mathematical and RAMP coding components, and helped edit the final text..  ...  Getz, W.M., Salter, R., Luisa Vissat, L., Horvitz, N., 2021a. A versatile web app for identifying the drivers of covid-19 epidemics. Journal of Translational Medicine 19, 1-20.  ...  , Salter, Luisa Vissat, Koopman and Simon, 2021b) ).  ... 
doi:10.1101/2022.02.09.22270752 fatcat:ybge4tixo5e3lmcm6lnegvpatm

A relative-motion method for parsing spatio-temporal behaviour of dyads using GPS relocation data [article]

Ludovica Luisa Vissat, Jason Blackburn, Wayne Marcus Getz
2021 bioRxiv   pre-print
In this paper, we introduce a novel method for classifying and computing the frequencies of movement modes of intra and interspecific dyads, focusing in particular on distance-mediated approach, retreat, following and side by side movement modes. Besides distance, the method includes factors such as sex, age, time of day, or season that cause frequencies of movement modes to deviate from random. We demonstrate and validate our method using both simulated and empirical data. Our simulated data
more » ... re obtained from a relative-motion, biased random-walk (RM-BRW) model with attraction and repulsion circumferences. Our empirical data were GPS relocation time series collected from African elephants in Etosha National Park, Namibia. The simulated data were primarily used to validate our method while the empirical data analysis were used to illustrate the types of behavioral assessment that our methodology reveals. Our methodology facilitates automated, observer-bias-free analysis of the locomotive interactions of dyads using GPS relocation data, which is becoming increasingly ubiquitous as telemetry and related technologies improve. Our method should open up a whole new vista of behavioral-interaction type analyses to movement and behavioral ecologists.
doi:10.1101/2021.01.04.425238 fatcat:twpgm2vifjdrncz63cxyyimlaq

Characterization of Israeli COVID-19 Outbreak Drivers and Forecasting Using a Versatile Web App [article]

Wayne M. Getz, Richard Salter, Nir Horvitz, Ludovica Luisa Vissat
2020 medRxiv   pre-print
Richard Salter and Ludovica Luisa Vissat were responsible for the MCMC simulations and the material on this in the SM. Nir Horvitz scrapped data from the web.  ... 
doi:10.1101/2020.08.06.20155804 fatcat:tyjikdv4bzg5hklfcud4wmbakm

Finding Optimal Timetables for Edinburgh Bus Routes

Ludovica Luisa Vissat, Allan Clark, Stephen Gilmore
2015 Electronical Notes in Theoretical Computer Science  
The authors thank Luca Bortolussi for arranging Ludovica Luisa Vissat's visit to the Laboratory for Foundations of Computer Science in Edinburgh where this work was done, and for his suggestion to use  ... 
doi:10.1016/j.entcs.2014.12.018 fatcat:vsv7fngrkbegterp6ehyp7xaf4

A versatile web app for identifying the drivers of COVID-19 epidemics

Wayne M. Getz, Richard Salter, Ludovica Luisa Vissat, Nir Horvitz
2021 Journal of Translational Medicine  
Acknowledgements Ludovica Luisa Vissat thanks Michalis Michaelides and Sally Paganin for providing useful guidance for the MCMC procedure.  ... 
doi:10.1186/s12967-021-02736-2 pmid:33726787 fatcat:zqkia7s4zvakxbg65gtkxwcd2e

Appendeces from A runtime alterable epidemic model with genetic drift, waning immunity and vaccinations

Wayne M. Getz, Richard Salter, Ludovica Luisa Vissat, James S. Koopman, Carl P. Simon
2021 figshare.com  
This file contains Appendices A and B referred to in the main text
doi:10.6084/m9.figshare.17004881.v1 fatcat:elzve5by2nayho526h563e7rne

Analysis of Spatio-temporal Properties of Stochastic Systems Using TSTL

Ludovica Luisa Vissat, Michele Loreti, Laura Nenzi, Jane Hillston, Glenn Marion
2019 ACM Transactions on Modeling and Computer Simulation  
In this article, we present Three-Valued spatio-temporal Logic (TSTL), which enriches the available spatiotemporal analysis of properties expressed in Signal spatio-temporal Logic (SSTL), to give further insight into the dynamic behavior of systems. Our novel analysis starts from the estimation of satisfaction probabilities of given SSTL properties and allows the analysis of their temporal and spatial evolution. Moreover, in our verification procedure, we use a three-valued approach to include
more » ... he intrinsic and unavoidable uncertainty related to the simulation-based statistical evaluation of the estimates; this can be also used to assess the appropriate number of simulations to use depending on the analysis needs. We present the syntax and three-valued semantics of TSTL and specific extended monitoring algorithms to check the validity of TSTL formulas. We introduce a reliability requirement for TSTL monitoring and an automatic procedure to verify it. Two case studies demonstrate how TSTL broadens the application of spatio-temporal logics in realistic scenarios, enabling analysis of threat monitoring and privacy preservation based on spatial stochastic population models.
doi:10.1145/3326168 fatcat:tvufyaer4befvmgw5mj2vh3i64

Adaptive vaccination may be needed to extirpate COVID-19: Results from a runtime-alterable strain-drift and waning-immunity model [article]

Wayne M Getz, Richard Salter, Ludovica Luisa Vissat, James S Koopman, Carl P Simon
2021 medRxiv   pre-print
We developed an elaborated susceptible-infected-recovered (SIR) individual-based model (IBM) with pathogen strain drift, waning and cross immunity, implemented as a novel Java Runtime-Alterable-Model Platform (J-RAMP). This platform allows parameter values, process formulations, and scriptable runtime drivers to be easily added at the start of simulation. It includes facility for integration into the R statistical and other data analysis platforms. We selected a set of parameter values and
more » ... ss descriptions relevant to the current COVID-19 pandemic. These include pathogen-specific shedding, environmental persistence, host transmission and mortality, within-host pathogen mutation and replication, adaptive social distancing, and time dependent vaccine rate and strain valency specifications. Our simulations illustrate that if waning immunity outpaces vaccination rates, then vaccination rollouts may fail to contain the most transmissible strains. Our study highlights the need for adaptive vaccination rollouts, which depend on reliable real-time monitoring and surveillance of strain proliferation and reinfection data needed to ensure that vaccines target emerging strains and constrain escape mutations. Together with such data, our platform has the potential to inform the design of vaccination programs that extirpate rather than exacerbate local outbreaks. Finally, our RAMP concept promotes the development of highly flexible models that can be easily shared among researchers and policymakers not only addressing healthcare crises, but other types of environmental crises as well.
doi:10.1101/2021.06.07.21258504 fatcat:nr3r3risknb7rghlbmlwoiebve

Three-Valued Spatio-Temporal Logic: A Further Analysis on Spatio-Temporal Properties of Stochastic Systems [chapter]

Ludovica Luisa Vissat, Michele Loreti, Laura Nenzi, Jane Hillston, Glenn Marion
2017 Lecture Notes in Computer Science  
In this paper we present Three-Valued Spatio-Temporal Logic (TSTL), which enriches the available spatio-temporal analysis of properties expressed in Signal Spatio-Temporal Logic (SSTL), to give further insight into the dynamic behaviour of systems. Our novel analysis starts from the estimation of satisfaction probabilities of given SSTL properties and allows the analysis of their temporal and spatial evolution. Moreover, in our verification procedure, we use a three-valued approach to include
more » ... e intrinsic and unavoidable uncertainty related to the simulation-based statistical evaluation of the estimates; this can be also used to assess the appropriate number of simulations to use depending on the analysis needs. We present the syntax and three-valued semantics of TSTL and a specific extended monitoring algorithm to check the validity of TSTL formulas. We conclude with two case studies that demonstrate how TSTL broadens the application of spatio-temporal logics in realistic scenarios, enabling analysis of threat monitoring and control programmes based on spatial stochastic population models.
doi:10.1007/978-3-319-66335-7_22 fatcat:32ywregwgrcsvjvdydksyf5c74

MELA: Modelling in Ecology with Location Attributes

Ludovica Luisa Vissat, Jane Hillston, Glenn Marion, Matthew J. Smith
2016 Electronic Proceedings in Theoretical Computer Science  
Ecology studies the interactions between individuals, species and the environment. The ability to predict the dynamics of ecological systems would support the design and monitoring of control strategies and would help to address pressing global environmental issues. It is also important to plan for efficient use of natural resources and maintenance of critical ecosystem services. The mathematical modelling of ecological systems often includes nontrivial specifications of processes that
more » ... the birth, death, development and movement of individuals in the environment, that take into account both biotic and abiotic interactions. To assist in the specification of such models, we introduce MELA, a process algebra for Modelling in Ecology with Location Attributes. Process algebras allow the modeller to describe concurrent systems in a high-level language. A key feature of concurrent systems is that they are composed of agents that can progress simultaneously but also interact - a good match to ecological systems. MELA aims to provide ecologists with a straightforward yet flexible tool for modelling ecological systems, with particular emphasis on the description of space and the environment. Here we present four example MELA models, illustrating the different spatial arrangements which can be accommodated and demonstrating the use of MELA in epidemiological and predator-prey scenarios.
doi:10.4204/eptcs.227.6 fatcat:6jjwsdtdgvftnf2syuuoewuom4

Automatic verification of reliability requirements of spatio-temporal analysis using Three-Valued Spatio-Temporal Logic

Ludovica Luisa Vissat, Jane Hillston, Michele Loreti, Laura Nenzi
2017 Proceedings of the 11th EAI International Conference on Performance Evaluation Methodologies and Tools - VALUETOOLS 2017  
In this paper we present the recently introduced Three-Valued Spatio-Temporal Logic (TSTL), which extends the available spatiotemporal analysis of stochastic systems, and an automatic procedure to verify whether this analysis satisfies given reliability requirements. The novel spatio-temporal logic TSTL enriches the analysis of properties expressed in Signal Spatio-Temporal Logic (SSTL), providing further insight into the dynamic behaviour of systems. Starting from the estimated satisfaction
more » ... babilities of given SSTL properties, it enables the analysis of their temporal and spatial evolution. We use a three-valued approach in our verification procedure to include the uncertainty associated with the simulation-based statistical method used to estimate the satisfaction probabilities. In relation to this aspect, we introduce a reliability specification for the TSTL analysis and we present a specific algorithm to automatically assess whether it is satisfied by the evaluation of TSTL formulas. CCS CONCEPTS • Theory of computation → Verification by model checking;
doi:10.1145/3150928.3150961 dblp:conf/valuetools/VissatHLN17 fatcat:f47q33aiijcnnog3ygni43cdym

A runtime alterable epidemic model with genetic drift, waning immunity and vaccinations

Wayne M Getz, Richard Salter, Ludovica Luisa Vissat, James S Koopman, Carl P Simon
2021
We present methods for building a Java Runtime-Alterable-Model Platform (RAMP) of complex dynamical systems. We illustrate our methods by building a multivariant SEIR (epidemic) RAMP. Underlying our RAMP is an individual-based model that includes adaptive contact rates, pathogen genetic drift, waning and cross-immunity. Besides allowing parameter values, process descriptions and scriptable runtime drivers to be easily modified during simulations, our RAMP can used within R-Studio and other
more » ... tational platforms. Process descriptions that can be runtime altered within our SEIR RAMP include pathogen variant-dependent host shedding, environmental persistence, host transmission and within-host pathogen mutation and replication. They also include adaptive social distancing and adaptive application of vaccination rates and variant-valency of vaccines. We present simulation results using parameter values and process descriptions relevant to the current COVID-19 pandemic. Our results suggest that if waning immunity outpaces vaccination rates, then vaccination rollouts may fail to contain the most transmissible variants, particularly if vaccine valencies are not adapted to deal with escape mutations. Our SEIR RAMP is designed for easy use by others. More generally, our RAMP concept facilitates construction of highly flexible complex systems models of all types, which can then be easily shared as stand-alone application programs.
doi:10.1098/rsif.2021.0648 pmid:34814729 pmcid:PMC8611333 fatcat:ffjb5e3rrzg35d5awclpiiwvru

An Analysis Pathway for the Quantitative Evaluation of Public Transport Systems [chapter]

Stephen Gilmore, Mirco Tribastone, Andrea Vandin
2014 Lecture Notes in Computer Science  
The authors thank Allan Clark and Ludovica Luisa Vissat for the work in [7] which provided the model parameters for the present paper.  ... 
doi:10.1007/978-3-319-10181-1_5 fatcat:x437hd5rozabfnilhguowr73ta