arXiv subjects

Justin M. Calabrese

Publications and source records attributed to Justin M. Calabrese.

At least 19 recordsLinked to original sources

arXiv2026

How animal movement influences wildlife-vehicle collision risk: a mathematical framework for range-resident species

Wildlife-vehicle collisions (WVC) threaten both biodiversity and human safety worldwide. Despite empirical efforts to characterize the major determinants of WVC risk and optimize mitigation strategies, we still lack a theoretical framework linking traffic, landscape, and individual movement features to collision risk. Here, we introduce such a framework by leveraging recent advances in movement ecology and reaction-diffusion stochastic processes with partially absorbing boundaries. Focusing on range-resident terrestrial mammals -- responsible for most fatal WVCs -- we model interactions with a single linear road and derive exact expressions for key survival statistics, including mean collision time and road-induced lifespan reduction. These quantities are expressed in terms of measurable parameters, such as traffic intensity or road width, and movement parameters that can be robustly estimated from relocation data, such as home-range crossing times, home-range sizes, or distance between home-range center and road. Therefore, our work provides an effective theoretical framework integrating movement and road ecology, laying the foundation for data-driven, evidence-based strategies to mitigate WVCs and promote safer, more sustainable transportation networks.

q-bio.PE↗

arXiv2025

Stable Trajectory Clustering: An Efficient Split and Merge Algorithm

Clustering algorithms fundamentally group data points by characteristics to identify patterns. Over the past two decades, researchers have extended these methods to analyze trajectories of humans, animals, and vehicles, studying their behavior and movement across applications. \noindent This paper presents whole-trajectory clustering and sub-trajectory clustering algorithms based on DBSCAN line segment clustering, which encompasses two key events: split and merge of line segments. The events are utilized to capture object movement history based on the average Euclidean distance between line segments. In this framework, whole-trajectory clustering considers entire entities' trajectories, whereas sub-trajectory clustering employs a sliding window model to identify local similarity patterns. Many existing trajectory clustering algorithms respond to temporary anomalies in data by splitting trajectories, which often obscures otherwise consistent clustering patterns and leads to less reliable insights. To address this, we introduce the stable trajectory clustering algorithm, which leverages the mean absolute deviation concept to demonstrate that selective omission of transient deviations not only preserves the integrity of clusters but also improves their stability and interpretability. We evaluate all proposed algorithms on real trajectory datasets to illustrate their effectiveness and sensitivity to parameter variations.

cs.LG↗

arXiv2025

Range residency determines how movement persistence shapes encounter rates

Encounters between individuals link movement behavior to population-level processes such as predation and disease transmission. For many animal species, movement can be modeled as a multiscale stochastic process, dominated by directional persistence at short time scales and range residency at long time scales. Their separate effects on encounters are well understood: range residency can raise or lower encounter rates depending on home-range overlap, whereas moving with higher directional persistence systematically increases them. However, how directional persistence and range residency jointly determine encounters remains unknown. We present an analytical encounter theory for movement models that combine both features. In this framework, we derive a threshold in home-range overlap above which directional persistence diminishes, rather than enhances, encounters. At shorter time scales, attraction toward the home-range center displaces individual locations, altering encounter rates even when range residency is not measurable in movement tracks. Movement models fitted to short tracks can therefore describe trajectories accurately yet under- or overestimate the encounters derived from those trajectories, depending on home range spatial configuration. Encounter rates are a more demanding target for inference than movement parameters themselves.

q-bio.PE↗

arXiv2025

Ergodicity shapes inference in biological reactions driven by a latent trajectory

Many natural phenomena are quantified by counts of observable events, from the annihilation of quasiparticles in a lattice to predator-prey encounters on a landscape to spikes in a neural network. These events are triggered at random intervals, when an underlying, often unobserved and therefore latent, dynamical system occupies a set of reactive states within its phase space. We show how the ergodicity of this latent dynamical system, i.e. existence of a well-behaved limiting stationary distribution, constrains the statistics of the reaction counts. This formulation makes explicit the conditions under which the counting process approaches a limiting Poisson process, a subject of debate in the application of counting processes to different fields. We show that the overdispersal relative to this limit encodes properties of the latent trajectory through its hitting times. These results set bounds on how information about a latent process can be inferred from a local detector, which we explore for two biophysical scenarios. First, in estimating an animal's activity level by how often it crosses a detector, we show how the mean count can fail to give any information on movement parameters, which are encoded in higher order moments. Second, we show how the variance of the inter-reaction time sets a fundamental limit on how precisely the size of a population of trajectories can be inferred by a detector, vastly generalizing the Berg-Purcell limit for chemosensation. Overall, we develop a flexible theoretical framework to quantify inter-event time distributions in reaction-diffusion systems that clarifies existing debates in the literature and explicitly shows which properties of latent processes can be inferred from observed reactions.

cond-mat.stat-mech↗

arXiv2024

Pulsed interactions unify reaction-diffusion and spatial nonlocal models for biological pattern formation

The emergence of a spatially-organized population distribution depends on the dynamics of the population and mediators of interaction (activators and inhibitors). Two broad classes of models have been used to investigate when and how self-organization is triggered, namely, reaction-diffusion and spatially nonlocal models. Nevertheless, these models implicitly assume smooth propagation scenarios, neglecting that individuals many times interact by exchanging short and abrupt pulses of the mediating substance. A recently proposed framework advances in the direction of properly accounting for these short-scale fluctuations by applying a coarse-graining procedure on the pulse dynamics. In this paper, we generalize the coarse-graining procedure and apply the extended formalism to new scenarios in which mediators influence individuals' reproductive success or their motility. We show that, in the slow- and fast-mediator limits, pulsed interactions recover, respectively, the reaction-diffusion and nonlocal models, providing a mechanistic connection between them. Furthermore, at each limit, the spatial stability condition is qualitatively different, leading to a timescale-induced transition where spatial patterns emerge as mediator dynamics becomes sufficiently fast.

q-bio.PE↗

arXiv2024

Movement bias in asymmetric landscapes and its impact on population distribution and critical habitat size

Ecologists have long investigated how demographic and movement parameters determine the spatial distribution and critical habitat size of a population. However, most models oversimplify movement behavior, neglecting how landscape heterogeneity influences individual movement. We relax this assumption and introduce a reaction-advection-diffusion equation that describes population dynamics when individuals exhibit space-dependent movement bias toward preferred regions. Our model incorporates two types of these preferred regions: a high-quality habitat patch, termed `habitat', which is included to model avoidance of degraded habitats like deforested regions; and a preferred location, such as a chemoattractant source or a watering hole, that we allow to be asymmetrically located with respect to habitat edges. In this scenario, the critical habitat size depends on both the relative position of the preferred location and the movement bias intensities. When preferred locations are near habitat edges, the critical habitat size can decrease when diffusion increases, a phenomenon called the drift paradox. Also, ecological traps arise when the habitat overcrowds due to excessive attractiveness or the preferred location is near a low-quality region. Our results highlight the importance of species-specific movement behavior and habitat preference as drivers of population dynamics in fragmented landscapes and, therefore, in the design of protected areas.

q-bio.PE↗

arXiv2023

Test Center Location Problem: A bi-objective Model and Algorithms

The optimal placement of healthcare facilities, including the placement of diagnostic test centers, plays a pivotal role in ensuring efficient and equitable access to healthcare services. However, the emergence of unique complexities in the context of a pandemic, exemplified by the COVID-19 crisis, has necessitated the development of customized solutions. This paper introduces a bi-objective integer linear programming model designed to achieve two key objectives: minimizing average travel time for individuals visiting testing centers and maximizing an equitable workload distribution among testing centers. To address this problem, we propose a customized local search algorithm based on the Voronoi diagram. Additionally, we employ an $ε$-constraint approach, which leverages the Gurobi solver. We rigorously examine the effectiveness of the model and the algorithms through numerical experiments and demonstrate their capability to identify Pareto-optimal solutions. We show that while the Gurobi performs efficiently in small-size instances, our proposed algorithm outperforms it in large-size instances of the problem.

math.OC↗

arXiv2023

Personnel Scheduling and Testing Strategy during Pandemics: The case of COVID-19

Efficient personnel scheduling plays a significant role in matching workload demand in organizations. However, staff scheduling is sometimes affected by unexpected events, such as the COVID-19 pandemic, that disrupt regular operations. Since infectious diseases like COVID-19 transmit mainly through close contact with individuals, an efficient way to prevent the spread is by limiting the number of on-site employees in the workplace along with regular testing. Thus, determining an optimal scheduling and testing strategy that meets the organization's goals and prevents the spread of the virus is crucial during disease outbreaks. In this paper, we formulate these challenges in the framework of two Mixed Integer Non-linear Programming (MINLP) models. The first model aims to derive optimal staff occupancy and testing strategies to minimize the risk of infection among employees, while the second model aims at only optimal staff occupancy under a random testing strategy. To solve the problems expressed in the models, we propose a canonical genetic algorithm as well as two commercial solvers. Using both real and synthetic contact networks of employees, our results show that following the recommended occupancy and testing strategy reduces the risk of infection 25\%--60\% under different scenarios.

math.OC↗

arXiv2022

Estimating cross-border mobility from the difference in peak-timing: A case study in Poland-Germany border regions

Human mobility contributes to the fast spatio-temporal propagation of infectious diseases. During an outbreak, monitoring the infection situation on either side of an international border is very crucial as there is always a higher risk of disease importation associated with cross-border migration. Mechanistic models are effective tools to investigate the consequences of cross-border mobility on disease dynamics and help in designing effective control strategies. However, in practice, due to the unavailability of cross-border mobility data, it becomes difficult to propose reliable, model-based strategies. In this study, we propose a method for estimating cross-border mobility flux between any pair of regions that share an international border from the observed difference in the timing of the infection peak in each region. Assuming the underlying disease dynamics is governed by a Susceptible-Infected-Recovered (SIR) model, we employ stochastic simulations to obtain the maximum likelihood cross-border mobility estimate for any pair of regions where the difference in peak time can be measured. We then investigate how the estimate of cross-border mobility flux varies depending on the disease transmission rate, which is a key epidemiological parameter. We further show that the uncertainty in mobility flux estimates decreases for higher disease transmission rates and larger observed differences in peak timing. Finally, as a case study, we apply the method to some selected regions along the Poland-Germany border which are directly connected through multiple modes of transportation and quantify the cross-border fluxes from the COVID-19 cases data during the period $20^{\rm th}$ February $2021$ to $20^{\rm th}$ June $2021$.

q-bio.PE↗

arXiv2022

Integrating theory and experiments to link local mechanisms and ecosystem-level consequences of vegetation patterns in drylands

Self-organized spatial patterns of vegetation are frequent in drylands and, because pattern shape correlates with water availability, they have been suggested as important indicators of ecosystem health. However, the mechanisms underlying pattern emergence remain unclear. Some theories hypothesize that patterns could result from a water-mediated scale-dependent feedback (SDF) whereby interactions favoring plant growth dominate at short distances and growth-inhibitory interactions dominate in the long range. However, we know little about how the presence of a focal plant affects the fitness of its neighbors as a function of the inter-individual distance, which is expected to be highly ecosystem-dependent. This lack of empirical knowledge and system dependency challenge the relevance of SDF as a unifying theory for vegetation pattern formation. Assuming that plant interactions are always inhibitory and only their intensity is scale-dependent, alternative theories also recover the typical vegetation patterns observed in nature. Importantly, although these alternative hypotheses lead to visually indistinguishable patterns, they predict contrasting desertification dynamics, which questions the potential use of vegetation patterns as ecosystem-state indicators. To help resolve this issue, we first review existing theories for vegetation self-organization and their conflicting predictions about desertification dynamics. Second, we discuss potential empirical tests via manipulative experiments to identify pattern-forming mechanisms and link them to specific desertification dynamics. A comprehensive view of models, the mechanisms they intend to capture, and experiments to test them in the field will help to better understand both how patterns emerge and improve predictions on the fate of the ecosystems where they form.

q-bio.PE↗

arXiv2022

A scalable pipeline for COVID-19: the case study of Germany, Czechia and Poland

Throughout the coronavirus disease 2019 (COVID-19) pandemic, decision makers have relied on forecasting models to determine and implement non-pharmaceutical interventions (NPI). In building the forecasting models, continuously updated datasets from various stakeholders including developers, analysts, and testers are required to provide precise predictions. Here we report the design of a scalable pipeline which serves as a data synchronization to support inter-country top-down spatiotemporal observations and forecasting models of COVID-19, named the where2test, for Germany, Czechia and Poland. We have built an operational data store (ODS) using PostgreSQL to continuously consolidate datasets from multiple data sources, perform collaborative work, facilitate high performance data analysis, and trace changes. The ODS has been built not only to store the COVID-19 data from Germany, Czechia, and Poland but also other areas. Employing the dimensional fact model, a schema of metadata is capable of synchronizing the various structures of data from those regions, and is scalable to the entire world. Next, the ODS is populated using batch Extract, Transfer, and Load (ETL) jobs. The SQL queries are subsequently created to reduce the need for pre-processing data for users. The data can then support not only forecasting using a version-controlled Arima-Holt model and other analyses to support decision making, but also risk calculator and optimisation apps. The data synchronization runs at a daily interval, which is displayed at https://www.where2test.de.

cs.DB↗

arXiv2022

Modeling COVID-19 optimal testing strategies in long-term care facilities: An optimization-based approach

Long-term care facilities have been widely affected by the COVID-19 pandemic. Retirement homes are particularly vulnerable due to the higher mortality risk of infected elderly individuals. Once an outbreak occurs, suppressing the spread of the virus in retirement homes is challenging because the residents are in contact with each other, and isolation measures cannot be widely enforced. Regular testing strategies, on the other hand, have been shown to effectively prevent outbreaks in retirement homes. However, high frequency testing may consume substantial staff working time, which results in a trade-off between the time invested in testing, and the time spent providing essential care to residents. Thus, developing an optimal testing strategy is crucial to proactively detect infections while guaranteeing efficient use of limited staff time in these facilities. Although numerous efforts have been made to prevent the virus from spreading in long-term care facilities, this is the first study to develop testing strategies based on formal optimization methods. This paper proposes two novel optimization models for testing schedules. The models aim to minimize the risk of infection in retirement homes, considering the trade-off between the probability of infection and staff workload. We employ a probabilistic approach in conjunction with the optimization models, to compute the risk of infection, including contact rates, incidence status, and the probability of infection of the residents. To solve the models, we propose an enhanced local search algorithm by leveraging the symmetry property of the optimal solution. We perform several experiments with realistically sized instances and show that the proposed approach can derive optimal testing strategies.

math.OC↗

arXiv2022

Optimal Workplace Occupancy Strategies during the COVID-19 Pandemic

During the COVID-19 pandemic, many organizations (e.g. businesses, companies, government facilities, etc.) have attempted to reduce infection risk by employing partial home office strategies. However, working from home can also reduce productivity for certain types of work and particular employees. Over the long term, many organizations therefore face a need to balance infection risk against productivity. Motivated by this trade-off, we model this situation as a bi-objective optimization problem and propose a practical approach to find trade-off (Pareto optimal) solutions. We present a new probabilistic framework to compute the expected number of infected employees as a function of key parameters including: the incidence level in the neighborhood of the organization, the COVID-19 transmission rate, the number of employees, the percentage of vaccinated employees, the testing frequency, and the contact rate among employees. We implement the model and the optimization algorithm and perform several numerical experiments with different parameter settings. Furthermore, we provide an online application based on the models and algorithms developed in this paper, which can be used to identify the optimal workplace occupancy rate for real-world organizations.

cs.DS↗

arXiv2019

How range residency and long-range perception change encounter rates

Encounter rates link movement strategies to intra- and inter-specific interactions, and therefore translate individual movement behavior into higher-level ecological processes. Indeed, a large body of interacting population theory rests on the law of mass action, which can be derived from assumptions of Brownian motion in an enclosed container with exclusively local perception. These assumptions imply completely uniform space use, individual home ranges equivalent to the population range, and encounter dependent on movement paths actually crossing. Mounting empirical evidence, however, suggests that animals use space non-uniformly, occupy home ranges substantially smaller than the population range, and are often capable of nonlocal perception. Here, we explore how these empirically supported behaviors change pairwise encounter rates. Specifically, we derive novel analytical expressions for encounter rates under Ornstein-Uhlenbeck motion, which features non-uniform space use and allows individual home ranges to differ from the population range. We compare OU-based encounter predictions to those of Reflected Brownian Motion, from which the law of mass action can be derived. For both models, we further explore how the interplay between the scale of perception and home range size affects encounter rates. We find that neglecting realistic movement and perceptual behaviors can systematically bias encounter rate predictions.

q-bio.PE↗

arXiv2016

Online games: a novel approach to explore how partial information influences human random searches

Many natural processes rely on optimizing the success ratio of a search process. We use an experimental setup consisting of a simple online game in which players have to find a target hidden on a board, to investigate the how the rounds are influenced by the detection of cues. We focus on the search duration and the statistics of the trajectories traced on the board. The experimental data are explained by a family of random-walk-based models and probabilistic analytical approximations. If no initial information is given to the players, the search is optimized for cues that cover an intermediate spatial scale. In addition, initial information about the extension of the cues results, in general, in faster searches. Finally, strategies used by informed players turn into non-stationary processes in which the length of each displacement evolves to show a well-defined characteristic scale that is not found in non-informed searches.

physics.bio-ph↗

arXiv2014

Minimal mechanisms for vegetation patterns in semiarid regions

The minimal ecological requirements for formation of regular vegetation patterns in semiarid systems have been recently questioned. Against the general belief that a combination of facilitative and competitive interactions is necessary, recent theoretical studies suggest that, under broad conditions, nonlocal competition among plants alone may induce patterns. In this paper, we review results along this line, presenting a series of models that yield spatial patterns when finite-range competition is the only driving force. A preliminary derivation of this type of model from a more detailed one that considers water-biomass dynamics is also presented. Keywords: Vegetation patterns, nonlocal interactions

q-bio.PE↗

arXiv2014

A maximum-entropy description of animal movement

We introduce a class of maximum-entropy states that naturally includes within it all of the major continuous-time stochastic processes that have been applied to animal movement, including Brownian motion, Ornstein-Uhlenbeck motion, integrated Ornstein-Uhlenbeck motion, a recently discovered hybrid of the previous models, and a new model that describes central-place foraging. We are also able to predict a further hierarchy of new models that will emerge as data quality improves to better resolve the underlying continuity of animal movement. Finally, we also show that Langevin equations must obey a fluctuation-dissipation theorem to generate processes that fall from this class of maximum-entropy distributions.

cond-mat.stat-mech↗

arXiv2014

Vegetation pattern formation in semiarid systems without facilitative mechanisms

Regular vegetation patterns in semiarid ecosystems are believed to arise from the interplay between long-range competition and facilitation processes acting at smaller distances. We show that, under rather general conditions, long-range competition alone may be enough to shape these patterns. To this end we propose a simple, general model for the dynamics of vegetation, which includes only long-range competition between plants. Competition is introduced through a nonlocal term, where the kernel function quantifies the intensity of the interaction. We recover the full spectrum of spatial structures typical of vegetation models that also account for facilitation in addition to competition.

q-bio.PE↗