arXiv subjects

Andrea Pugliese

Publications and source records attributed to Andrea Pugliese.

16 recordsLinked to original sources

arXiv2026

PesTwin: A modular agent-based framework for pest and vector population control

Species-specific pest and vector control strategies, including the sterile insect technique, Wolbachia-based interventions, and genetic control technologies, offer powerful alternatives to broad-spectrum chemical control, with applications ranging from targeted crop protection to large-scale disease control. Among these, genetic control technologies are advancing rapidly, but the pace of technological development is outstripping the modelling tools needed to predict outcomes, guide technology design and its implementation, compare alternative strategies across different use settings, and support regulatory and operational decision-making. Here we present PesTwin, an agent-based modelling framework for simulating genetic control technologies across species, ecological settings, and deployment strategies within a common computational environment. PesTwin captures stochastic demographic effects, species-specific life-history traits, heterogeneous dispersal, and temporal variation in resource availability and infestation pressure. We validate PesTwin against published laboratory cage data from four genetic control systems, drawn from three studies, in two insect species, showing close agreement between predicted and observed population trajectories, including their replicate-to-replicate variability. We then illustrate how the same validated models extend beyond the cage to spatially explicit, field-scale scenarios, using PesTwin to explore how the timing, density and spatial placement of releases shape suppression and spread across heterogeneous landscapes. By making genetic control systems testable in silico before they are built or released, PesTwin can shorten the path from laboratory construct to field intervention: informing which constructs to prioritise, how to design the experiments that test them, where and when to release, and what evidence is needed to evaluate them.

q-bio.PE↗

arXiv2026

A model for mosquito-borne epidemic outbreaks with information-dependent protective behaviour

We investigate a model for a mosquito-borne epidemic in which human hosts may adopt protective behaviour against vector bites in response to information on both past and current disease prevalence. Assuming that mosquitoes can also feed on non-competent hosts (i.e.\ hosts that do not contribute to disease transmission), we first revisit existing results and show that behaviour-driven protection may either decrease or increase the basic reproduction number, depending on the interaction between behavioural response, host composition, and transmission parameters. Assuming that opinion dynamics evolves on a much faster time scale than disease transmission, we then apply Geometric Singular Perturbation Theory to effectively reduce the original two-group model to a model for a homogeneous host population. The reduced system enables a detailed investigation of the impact of information-induced behavioural changes on the transient dynamics of the epidemic, including scenarios in which protective measures lead to outbreaks with low attack rates. Our analysis shows that behavioural responses may either facilitate epidemic control or prolong disease persistence, potentially generating recurrent damped epidemic waves. Numerical simulations are provided to illustrate and support the analytical findings.

q-bio.PE↗

arXiv2026

PesTwin: a biology-informed Digital Twin for enabling precision farming

In a context of growing agricultural demand and new challenges related to food security and accessibility, boosting agricultural productivity is more important than ever. Reducing the damage caused by invasive insect species is a crucial lever to achieve this objective. In support of these challenges, and in line with the principles of precision agriculture and Integrated Pest Management (IPM), an innovative simulation framework is presented, aiming to become the digital twin of a pest invasion. Through a flexible rule-based approach of the Agent-Based Modeling (ABM) paradigm, the framework supports the fine-tuning of the main ecological interactions of the pest with its crop host and the environment. Forecasting insect infestation in realistic scenarios, considering both spatial and temporal dimensions, is made possible by integrating heterogeneous data sources: pest biodata collected in the laboratory, environmental data from weather stations, and GIS data of a real crop field. In this study, an application to the global pest of soft fruit, the invasive fruit fly Drosophila suzukii, also known as Spotted Wing Drosophila (SWD), is presented.

q-bio.QM↗

arXiv2026

To trace or not to trace: analytical insights from network-based contact-tracing models

Contact tracing is one of the most important control measures deployed during epidemics. Relying on the identification of contacts of known infected individuals, it necessitates a network perspective. Although pairwise models have been used extensively to study contact tracing, their analysis typically depends on a decoupling assumption-most commonly that contact tracing operates on a much faster timescale than disease transmission. Furthermore, contact tracing models often assume that all infected individuals become contact tracing-triggering, which is unrealistic given partial compliance to treatment. We relax both of these restrictive assumptions and provide a full analytical characterisation of the epidemic threshold in the pairwise mean-field model. Our analysis uses a fast-variables approach that captures the rapid early stabilisation of key network quantities. Inspired by mechanisms from social adoption dynamics, we introduce triplewise contact tracing in which an infected individual can be traced not only through direct contact with a single tracing-triggering neighbor (pairwise tracing), but also indirectly when connected to two tracing-triggering nodes simultaneously. For pure pairwise and pure triplewise contact tracing, we derive analytical expressions for critical contact tracing levels and demonstrate that when many infected individuals bypass treatment, the epidemic can become uncontrollable. When both contact tracing mechanisms operate together, we map out their combined contribution and relative impact on epidemic control. This unified framework yields rigorous and tractable threshold conditions for contact tracing dynamics on networks, extending the applicability of pairwise models beyond the fast-tracing regime and providing new insight into the interplay between disease progression, partial treatment compliance, and higher-order tracing processes.

physics.soc-ph↗

arXiv2026

SEIR models with host heterogeneity: theoretical aspects and applications to seasonal influenza dynamics

Population heterogeneity is a key factor in epidemic dynamics, influencing both transmission and final epidemic size. While heterogeneity is often modelled through age structure, spatial location, or contact patterns, differences in host susceptibility have recently gained attention, particularly during the COVID-19 pandemic. Building on the framework of Diekmann and Inaba (Journal of Mathematical Biology, 2023), we focus on the special case of SEIR epidemic models, assuming that at the epidemic start there is no pre-existing immunity. Under two distinct assumptions linking susceptibility and infectiousness, one obtains a closed system of 3 ODEs, which can be easily simulated and for which some analytical results are obtained. In particular, we proved that heterogeneity in susceptibility reduces the epidemic final size compared to homogeneous models with the same basic reproduction number $R_0$. We specialised in the case where susceptibility is distributed according to a gamma or extended Beta distribution, showing how the epidemic final size depends on the variance of the distribution. In the case of a gamma-distributed susceptibility, the resulting model consists of a system of ODEs with just one parameter more than the classical SEIR model; this makes it practical for fitting epidemic data. We illustrate its use by fitting data on seasonal influenza in Italy, and comparing the results to those obtained with simple SEIR models with pre-existing immunity.

q-bio.PE↗

arXiv2025

On the effectiveness of odor-baited traps on mosquito-borne infections

The host's odor serves as a critical biological tracking signal in the host-seeking process of mosquitoes, and its heterogeneity significantly influences the transmission of mosquito-borne diseases. In this study, we propose a mosquito-borne disease model incorporating odor-baited traps to examine the impact of odor on disease transmission. Following recent experimental evidence, we also assume that infected humans are more attractive than susceptible or recovered ones. The value of the basic reproduction number, $R_0$, depends on the attractiveness of traps, adjusted relative to infected individuals; the dependence on the relative attractiveness of susceptibles is non-monotone, suggesting that there exists an optimal mosquito preference that maximizes disease transmission. When $R_0>1$, there exists an endemic equilibrium which, under certain conditions, is proved to be globally stable. An endemic equilibrium may also exist when $R_0 < 1$, due to a backward bifurcation occurring when infected humans incur significant mortality. The phenomenon of backward bifurcation is reduced when odor-baited traps are more abundant. Analytical results and simulations show that deploying traps and enhancing their lethality for mosquitoes can help reduce disease prevalence and the risk of an outbreak. However, the attenuation of odor in highly attractive traps may lead to a rebound in the epidemic, especially when the traps gradually lose their attractiveness compared to susceptible hosts.

q-bio.PE↗

arXiv2025

Defending a City from Multi-Drone Attacks: A Sequential Stackelberg Security Games Approach

To counter an imminent multi-drone attack on a city, defenders have deployed drones across the city. These drones must intercept/eliminate the threat, thus reducing potential damage from the attack. We model this as a Sequential Stackelberg Security Game, where the defender first commits to a mixed sequential defense strategy, and the attacker then best responds. We develop an efficient algorithm called S2D2, which outputs a defense strategy. We demonstrate the efficacy of S2D2 in extensive experiments on data from 80 real cities, improving the performance of the defender in comparison to greedy heuristics based on prior works. We prove that under some reasonable assumptions about the city structure, S2D2 outputs an approximate Strong Stackelberg Equilibrium (SSE) with a convenient structure.

cs.MA↗

arXiv2025

A multi-season epidemic model with random genetic drift and transmissibility

We consider a model for an influenza-like disease, in which, between seasons, the virus makes a random genetic drift $δ$, (reducing immunity by the factor $δ$) and obtains a new random transmissibility $τ$ (closely related to $R_0$). Given the immunity status at the start of season $k$: $\textbf{p}^{(k)}$, describing community distribution of years since last infection, and their associated immunity levels $\boldsymbolι^{(k)}$, the outcome of the epidemic season $k$, characterized by the effective reproduction number $R_e^{(k)}$ and the fractions infected in the different immunity groups $\textbf{z}^{(k)}$, is determined by the random pair $(δ_k, τ_k)$. It is shown that the immunity status $(\textbf{p}^{(k)}, \boldsymbolι^{(k)})$, is an ergodic Markov chain, which converges to a stationary distribution $\bar π(\cdot) $. More analytical progress is made for the case where immunity only lasts for one season. We then characterize the stationary distribution of $p_1^{(k)}$, being identical to $z^{(k-1)}$. Further, we also characterize the stationary distribution of $(R_e^{(k)}, z^{(k)})$, and the conditional distribution of $z^{(k)}$ given $R_e^{(k)}$. The effective reproduction number $R_e^{(k)}$ is closely related to the initial exponential growth rate $ρ^{(k)}$ of the outbreak, a quantity which can be estimated early in the epidemic season. As a consequence, this conditional distribution may be used for predicting the final size of the epidemic based on its initial growth and immunity status.

math.PR↗

arXiv2025

Multi-Object Active Search and Tracking by Multiple Agents in Untrusted, Dynamically Changing Environments

This paper addresses the problem of both actively searching and tracking multiple unknown dynamic objects in a known environment with multiple cooperative autonomous agents with partial observability. The tracking of a target ends when the uncertainty is below a threshold. Current methods typically assume homogeneous agents without access to external information and utilize short-horizon target predictive models. Such assumptions limit real-world applications. We propose a fully integrated pipeline where the main contributions are: (1) a time-varying weighted belief representation capable of handling knowledge that changes over time, which includes external reports of varying levels of trustworthiness in addition to the agents; (2) the integration of a Long Short Term Memory-based trajectory prediction within the optimization framework for long-horizon decision-making, which reasons in time-configuration space, thus increasing responsiveness; and (3) a comprehensive system that accounts for multiple agents and enables information-driven optimization. When communication is available, our strategy consolidates exploration results collected asynchronously by agents and external sources into a headquarters, who can allocate each agent to maximize the overall team's utility, using all available information. We tested our approach extensively in simulations against baselines, and in robustness and ablation studies. In addition, we performed experiments in a 3D physics based engine robot simulator to test the applicability in the real world, as well as with real-world trajectories obtained from an oceanography computational fluid dynamics simulator. Results show the effectiveness of our method, which achieves mission completion times 1.3 to 3.2 times faster in finding all targets, even under the most challenging scenarios where the number of targets is 5 times greater than that of the agents.

cs.RO↗

arXiv2023

A geometric analysis of the SIRS model with secondary infections

We propose a compartmental model for a disease with temporary immunity and secondary infections. From our assumptions on the parameters involved in the model, the system naturally evolves in three time scales. We characterize the equilibria of the system and analyze their stability. We find conditions for the existence of two endemic equilibria, for some cases in which $\mathcal{R}_0 < 1$. Then, we unravel the interplay of the three time scales, providing conditions to foresee whether the system evolves in all three scales, or only in the fast and the intermediate ones. We conclude with numerical simulations and bifurcation analysis, to complement our analytical results.

math.DS↗

arXiv2021

Evolutionary dynamics in an SI epidemic model with phenotype-structured susceptible compartment

We present an SI epidemic model whereby a continuous variable captures variability in proliferative potential and resistance to infection among susceptibles. The occurrence of heritable, spontaneous changes in these phenotype and the presence of a fitness trade-off between resistance to infection and proliferative potential are incorporated into the model. The model comprises an ODE for the number of infected individuals that is coupled with a partial integrodifferential equation for the population density of susceptibles through an integral term. The expression for the basic reproduction number $\mathcal{R}_0$ is derived, the disease-free and endemic equilibrium of the model are characterised and a threshold theorem is proved. Analytical results are integrated with numerical simulations of a calibrated version of the model based on the results of artificial selection experiments in a host-parasite system. The results of our mathematical study disentangle the impact of different evolutionary parameters on the spread of infectious diseases and the consequent phenotypic adaption of susceptible individuals. In particular, these results provide a theoretical basis for the observation that infectious diseases exerting stronger selective pressures on susceptibles and being characterised by higher infection rates are more likely to spread. Moreover, our results indicate that spontaneous phenotypic changes in proliferative potential and resistance to infection can either promote or prevent the spread of diseases depending on the strength of selection acting on susceptible individuals prior to infection. Finally, we demonstrate that, when an endemic equilibrium is established, higher levels of resistance to infection and lower degrees of phenotypic heterogeneity are to be expected in the presence of infections which are characterised by lower rates of death and exert stronger selective pressures.

q-bio.PE↗

arXiv2021

SUIHTER: A new mathematical model for COVID-19. Application to the analysis of the second epidemic outbreak in Italy

The COVID-19 epidemic is the last of a long list of pandemics that have affected humankind in the last century. In this paper, we propose a novel mathematical epidemiological model named SUIHTER from the names of the seven compartments that it comprises: susceptible uninfected individuals (S), undetected (both asymptomatic and symptomatic) infected (U), isolated (I), hospitalized (H), threatened (T), extinct (E), and recovered (R). A suitable parameter calibration that is based on the combined use of least squares method and Markov Chain Monte Carlo (MCMC) method is proposed with the aim of reproducing the past history of the epidemic in Italy, surfaced in late February and still ongoing to date, and of validating SUIHTER in terms of its predicting capabilities. A distinctive feature of the new model is that it allows a one-to-one calibration strategy between the model compartments and the data that are daily made available from the Italian Civil Protection. The new model is then applied to the analysis of the Italian epidemic with emphasis on the second outbreak emerged in Fall 2020. In particular, we show that the epidemiological model SUIHTER can be suitably used in a predictive manner to perform scenario analysis at national level.

q-bio.PE↗

arXiv2020

A geometric analysis of the SIRS epidemiological model on a homogeneous network

We study a fast-slow version of an SIRS epidemiological model on homogeneous graphs, obtained through the application of the moment closure method. We use GSPT to study the model, taking into account that the infection period is much shorter than the average duration of immunity. We show that the dynamics occurs through a sequence of fast and slow flows, that can be described through 2-dimensional maps that, under some assumptions, can be approximated as 1-dimensional maps. Using this method, together with numerical bifurcation tools, we show that the model can give rise to periodic solutions, differently from the corresponding model based on homogeneous mixing.

math.DS↗

arXiv2020

Inferring the COVID-19 infection curve in Italy

Aim of this manuscript is to show a simple method to infer the time-course of new COVID-19 infections (the most important information in order to establish the effect of containment strategies) from available aggregated data, such as number of deaths and hospitalizations. The method, that was used for HIV-AIDS and was named `back-calculation', relies on good estimates of the distribution of the delays between infection and the observed events; assuming that the epidemic follows a simple SIR model with a known generation interval, we can then estimate the parameters that define the time-varying contact rate through maximum likelihood. We show the application of the method to data from Italy and several of its region; it is found that $R_0$ had decreased consistently below 1 around March 20, and in the beginning of April it was between 0.5 and 0.8 in the whole Italy and in most regions.

q-bio.PE↗

arXiv2020

A geometric analysis of the SIR, SIRS and SIRWS epidemiological models

We study fast-slow versions of the SIR, SIRS, and SIRWS epidemiological models. The multiple time scale behavior is introduced to account for large differences between some of the rates of the epidemiological pathways. Our main purpose is to show that the fast-slow models, even though in nonstandard form, can be studied by means of Geometric Singular Perturbation Theory (GSPT). In particular, without using Lyapunov's method, we are able to not only analyze the stability of the endemic equilibria but also to show that in some of the models limit cycles arise. We show that the proposed approach is particularly useful in more complicated (higher dimensional) models such as the SIRWS model, for which we provide a detailed description of its dynamics by combining analytic and numerical techniques.

math.DS↗

arXiv2006

Path Summaries and Path Partitioning in Modern XML Databases

We study the applicability of XML path summaries in the context of current-day XML databases. We find that summaries provide an excellent basis for optimizing data access methods, which furthermore mixes very well with path-partitioned stores. We provide practical algorithms for building and exploiting summaries, and prove its benefits through extensive experiments.

cs.DB↗