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Alberto d'Onofrio

Publications and source records attributed to Alberto d'Onofrio.

At least 19 recordsLinked to original sources

Understanding and inverse design of implicit bias in stochastic learning: a geometric perspective

Can we design a model such that its stochastic training favours a desired class of solutions without enforcing an explicit penalty? Under suitable conditions, the interplay between symmetries of a model's weight parametrization and stochastic training favours particular solutions, inducing an implicit bias. Building on this mechanism, we develop a framework for inverse-designing such biases by constructing novel parametrizations and their associated symmetries. We show how holomorphic functions make this construction and calculation simple and explicit. Specifically, we introduce a new parametrization that biases learned weights toward the binary values $\{-1,+1\}$. Numerical experiments confirm the theoretical predictions. They also show that our parametrization reproduces the same preference induced by an explicitly regularized model without adding a penalty to the training loss.

cs.LG↗

A systematic review of COVID-19 epidemic models with endogenous human behaviour. What's next?

Human behaviour and epidemic dynamics are intertwined, yet accounting for this feedback remains one of the key challenges of epidemiological modelling. The COVID-19 pandemic was an opportunity to overcome the traditional limitations of the field, raising expectations that data-informed endogenous approaches to behaviour modelling would advance substantially. To quantify the progresses made, we conducted a systematic review of SARS-CoV-2 transmission models endogenously including human behaviour in response to epidemic dynamics. The COVID-19 pandemic saw great strides in terms of the expanded use of empirical data in epi-behavioural modelling. However, it also showed shortcomings with respect to limited use of behavioural empirical data, lack of innovation in model structure, and limited engagement with other disciplines and decision-makers. Overall, our results suggest that identifying priorities in model design and behavioural data, building an adequate data collection infrastructure, leveraging on AI advancements, and fostering interdisciplinarity are strategies of utmost importance for pandemic preparedness.

physics.soc-ph↗

Frequency maps reveal the correlation between Adversarial Attacks and Implicit Bias

Despite their impressive performance in classification tasks, neural networks are known to be vulnerable to adversarial attacks, subtle perturbations of the input data designed to deceive the model. In this work, we investigate the correlation between these perturbations and the implicit bias of neural networks trained with gradient-based algorithms. To this end, we analyse a representation of the network's implicit bias through the lens of the Fourier transform. Specifically, we identify unique fingerprints of implicit bias and adversarial attacks by calculating the minimal, essential frequencies needed for accurate classification of each image, as well as the frequencies that drive misclassification in its adversarially perturbed counterpart. This approach enables us to uncover and analyse the correlation between these essential frequencies, providing a precise map of how the network's biases align or contrast with the frequency components exploited by adversarial attacks. To this end, among other methods, we use a newly introduced technique capable of detecting nonlinear correlations between high-dimensional datasets. Our results provide empirical evidence that the network bias in Fourier space and the target frequencies of adversarial attacks are highly correlated and suggest new potential strategies for adversarial defence.

cs.LG↗

Optimal epidemic control by social distancing and vaccination of an infection structured by time since infection: the covid-19 case study

Motivated by the issue of COVID-19 mitigation, in this work we tackle the general problem of optimally controlling an epidemic outbreak of a communicable disease structured by time since exposure, by the aid of two types of control instruments namely, social distancing and vaccination by a vaccine at least partly effective in protecting from infection. Effective vaccines are assumed to be made available only in a subsequent period of the epidemic so that - in the first period - epidemic control only relies on social distancing, as it happened for the COVID-19 pandemic. By our analyses, we could prove the existence of (at least) one optimal control pair, we derived first-order necessary conditions for optimality, and proved some useful properties of such optimal solutions. A worked example provides a number of further insights on the relationships between key control and epidemic parameters.

q-bio.PE↗

Machine Learning Catalysis of Quantum Tunneling

Optimizing the probability of quantum tunneling between two states, while keeping the resources of the underlying physical system constant, is a task of key importance due to its critical role in various applications. We show that, by applying Machine Learning techniques when the system is coupled to an ancilla, one optimizes the parameters of both the ancillary component and the coupling, ultimately resulting in the maximization of the tunneling probability. We provide illustrative examples for the paradigmatic scenario involving a two-mode system and a two-mode ancilla in the presence of several interacting particles. Physically, the increase of the tunneling probability is rooted in the decrease of the two-well asymmetry due to the coherent oscillations induced by the coupling to the ancilla. We also argue that the enhancement of the tunneling probability is not hampered by weak coupling to noisy environments.

quant-ph↗

Catalysis of quantum tunneling by ancillary system learning

Given the key role that quantum tunneling plays in a wide range of applications, a crucial objective is to maximize the probability of tunneling from one quantum state/level to another, while keeping the resources of the underlying physical system fixed. In this work, we demonstrate that an effective solution to this challenge can be achieved by coupling the tunneling system with an ancillary system of the same kind. By utilizing machine learning techniques, the parameters of both the ancillary system and the coupling can be optimized, leading to the maximization of the tunneling probability. We provide illustrative examples for the paradigmatic scenario involving a two-mode system and a two-mode ancilla with arbitrary couplings and in the presence of several interacting particles. Importantly, the enhancement of the tunneling probability appears to be minimally affected by noise and decoherence in both the system and the ancilla.

quant-ph↗

Local Search, Semantics, and Genetic Programming: a Global Analysis

Geometric Semantic Geometric Programming (GSGP) is one of the most prominent Genetic Programming (GP) variants, thanks to its solid theoretical background, the excellent performance achieved, and the execution time significantly smaller than standard syntax-based GP. In recent years, a new mutation operator, Geometric Semantic Mutation with Local Search (GSM-LS), has been proposed to include a local search step in the mutation process based on the idea that performing a linear regression during the mutation can allow for a faster convergence to good-quality solutions. While GSM-LS helps the convergence of the evolutionary search, it is prone to overfitting. Thus, it was suggested to use GSM-LS only for a limited number of generations and, subsequently, to switch back to standard geometric semantic mutation. A more recently defined variant of GSGP (called GSGP-reg) also includes a local search step but shares similar strengths and weaknesses with GSM-LS. Here we explore multiple possibilities to limit the overfitting of GSM-LS and GSGP-reg, ranging from adaptive methods to estimate the risk of overfitting at each mutation to a simple regularized regression. The results show that the method used to limit overfitting is not that important: providing that a technique to control overfitting is used, it is possible to consistently outperform standard GSGP on both training and unseen data. The obtained results allow practitioners to better understand the role of local search in GSGP and demonstrate that simple regularization strategies are effective in controlling overfitting.

cs.NE↗

A geometric analysis of the impact of large but finite switching rates on vaccination evolutionary games

In contemporary society, social networks accelerate decision dynamics causing a rapid switch of opinions in a number of fields, including the prevention of infectious diseases by means of vaccines. This means that opinion dynamics can nowadays be much faster than the spread of epidemics. Hence, we propose a Susceptible-Infectious-Removed epidemic model coupled with an evolutionary vaccination game embedding the public health system efforts to increase vaccine uptake. This results in a global system ``epidemic model + evolutionary game''. The epidemiological novelty of this work is that we assume that the switching to the strategy ``pro vaccine'' depends on the incidence of the disease. As a consequence of the above-mentioned accelerated decisions, the dynamics of the system acts on two different scales: a fast scale for the vaccine decisions and a slower scale for the spread of the disease. Another, and more methodological, element of novelty is that we apply Geometrical Singular Perturbation Theory (GSPT) to such a two-scale model and we then compare the geometric analysis with the Quasi-Steady-State Approximation (QSSA) approach, showing a criticality in the latter. Later, we apply the GSPT approach to the disease prevalence-based model already studied in (Della Marca and d'Onofrio, Comm Nonl Sci Num Sim, 2021) via the QSSA approach by considering medium-large values of the strategy switching parameter.

q-bio.PE↗

Spatio-temporal chaos and clustering induced by nonlocal information and vaccine hesitancy in the SIR epidemic model

Human behavior, and in particular vaccine hesitancy, is a critical factor for the control of childhood infectious disease. Here we propose a spatio-temporal behavioral epidemiology model where the vaccine propensity depends on information that is non-local in space and in time. The properties of the proposed model are analysed under different hypotheses on the spatio-temporal kernels tuning the vaccination response of individuals. As a main result, we could numerically show that vaccine hesitancy induces the onset of many dynamic patterns of relevance for epidemiology. In particular we observed: behavior-modulated patterns and spatio-temporal chaos. This is the first known example of human behavior-induced spatio-temporal chaos in statistical physics of vaccination. Patterns and spatio-temporal chaos are difficult to deal with, from the Public Health viewpoint, hence showing that vaccine hesitancy can cause them could be of interest. Additionally, we propose a new simple heuristic algorithm to estimate the Maximum Lyapunov Exponent.

physics.soc-ph↗

Feedback control of social distancing for COVID-19 via elementary formulae

Social distancing has been enacted in order to mitigate the spread of COVID-19. Like many authors, we adopt the classic epidemic SIR model, where the infection rate is the control variable. Its differential flatness property yields ele mentary closed-form formulae for open-loop social distancing scenarios, where, for instance, the increase of the number of uninfected people may be taken into account. Those formulae might therefore be useful to decision makers. A feedback loop stemming from model-free control leads to a remarkable robustness with respect to severe uncertainties and mismatches. Although an identification procedure is presented, a good knowledge of the recovery rate is not necessary for our control strategy.

eess.SY↗

A behavioural modelling approach to assess the impact of COVID-19 vaccine hesitancy

In this paper we introduce a compartmental epidemic model describing the transmission of the COVID-19 disease in presence of non-mandatory vaccination. The model takes into account the hesitancy and refusal of vaccination. To this aim, we employ the information index, which mimics the idea that individuals take their decision on vaccination based not only on the present but also on the past information about the spread of the disease. Theoretical analysis and simulations show clearly as a voluntary vaccination can certainly reduce the impact of the disease but it is unable to eliminate it. We also show how the information-related parameters affect the dynamics of the disease. In particular, the hesitancy and refusal of vaccination is better contained in case of large information coverage and small memory characteristic time. Finally, the possible influence of seasonality is also investigated.

q-bio.PE↗

Modeling the effects of information-dependent vaccination behavior on meningitis transmission

We propose a mathematical model to investigate the effects of information-dependent vaccination behavior on meningitis transmission. The information is represented by means of information index as early proposed in (d'Onofrio et al., Theor. pop. biol., 2007). We perform a qualitative analysis based on stability theory, focusing to the global stability of the disease free equilibrium (DFE) and the related transcritical bifurcation taking place at the threshold for the DFE. Finally, we assess the role of epidemiological and information parameters in the model dynamics through numerical simulations. Our simulations suggests that the impact of the human behavior critically depend on the average information delay. For example, it can induce recurrent epidemics, provided that transfer rate from the carrier to the infectious state is over a threshold. Otherwise, the endemic equilibrium is (at least) locally stable.

q-bio.PE↗

Lyapunov stability of an SIRS epidemic model with varying population

In this paper we consider an SIRS epidemic model under a general assumption of density-dependent mortality. We prove the global stability of the disease-free equilibrium and propose a Lyapunov function that allows to demonstrate the global stability of the (unique) endemic state under broad conditions.

math.DS↗

Statistical physics of vaccination

Historically, infectious diseases caused considerable damage to human societies, and they continue to do so today. To help reduce their impact, mathematical models of disease transmission have been studied to help understand disease dynamics and inform prevention strategies. Vaccination - one of the most important preventive measures of modern times - is of great interest both theoretically and empirically. And in contrast to traditional approaches, recent research increasingly explores the pivotal implications of individual behavior and heterogeneous contact patterns in populations. Our report reviews the developmental arc of theoretical epidemiology with emphasis on vaccination, as it led from classical models assuming homogeneously mixing (mean-field) populations and ignoring human behavior, to recent models that account for behavioral feedback and/or population spatial/social structure. Many of the methods used originated in statistical physics, such as lattice and network models, and their associated analytical frameworks. Similarly, the feedback loop between vaccinating behavior and disease propagation forms a coupled nonlinear system with analogs in physics. We also review the new paradigm of digital epidemiology, wherein sources of digital data such as online social media are mined for high-resolution information on epidemiologically relevant individual behavior. Armed with the tools and concepts of statistical physics, and further assisted by new sources of digital data, models that capture nonlinear interactions between behavior and disease dynamics offer a novel way of modeling real-world phenomena, and can help improve health outcomes. We conclude the review by discussing open problems in the field and promising directions for future research.

physics.soc-ph↗

Gene switching rate determines response to extrinsic perturbations in a transcriptional network motif

It is well-known that gene activation/deactivation dynamics may be a major source of randomness in genetic networks, also in the case of large concentrations of the transcription factors. In this work, we investigate the effect of realistic extrinsic noises acting on gene deactivation in a common network motif - the positive feedback of a transcription factor on its own synthesis - under a variety of settings, i.e., distinct cellular types, distribution of proteins and properties of the external perturbations. At variance with standard models where the perturbations are Gaussian unbounded, we focus here on bounded extrinsic noises to better mimic biological reality. Our results suggest that the gene switching velocity is a key parameter to modulate the response of the network. Simulations suggest that, if the gene switching is fast and many proteins are present, an irreversible noise-induced first order transition is observed as a function of the noise intensity. If noise intensity is further increased a second order transition is also observed. When gene switching is fast, a similar scenario is observed even when few proteins are present, provided that larger cells are considered, which is mainly influenced by noise autocorrelation. On the contrary, if the gene switching is slow, no fist order transitions are observed. In the concluding remarks possible implications of the irreversible transitions for cellular differentiation are briefly discussed.

q-bio.MN↗

A general framework for modeling tumor-immune system competition and immunotherapy: mathematical analysis and biomedical inferences

In this work we propose and investigate a family of models, which admits as particular cases some well known mathematical models of tumor-immune system interaction, with the additional assumption that the influx of immune system cells may be a function of the number of cancer cells. Constant, periodic and impulsive therapies (as well as the non-perturbed system) are investigated both analytically for the general family and, by using the model by Kuznetsov et al. (V. A. Kuznetsov, I. A. Makalkin, M. A. Taylor and A. S. Perelson. Nonlinear dynamics of immunogenic tumors: Parameter estimation and global bifurcation analysis. Bulletin of Mathematical Biology 56(2): 295-321, (1994)), via numerical simulations. Simulations seem to show that the shape of the function modeling the therapy is a crucial factor only for very high values of the therapy period $T$, whereas for realistic values of $T$, the eradication of the cancer cells depends on the mean values of the therapy term. Finally, some medical inferences are proposed.

q-bio.TO↗

Fractal growth of tumors and other cellular populations: Linking the mechanistic to the phenomenological modeling and vice versa

In this paper we study and extend the mechanistic mean field theory of growth of cellular populations proposed by Mombach et al in (Mombach J. C. M. et al., Europhysics Letter, 59 (2002) 923) (MLBI model), and we demonstrate that the original model and our generalizations lead to inferences of biological interest. In the first part of this paper, we show that the model in study is widely general since it admits, as particular cases, the main phenomenological models of cellular growth. In the second part of this work, we generalize the \emph{MLBI} model to a wider family of models by allowing the cells to have a generic unspecified biologically plausible interaction. Then, we derive a relationship between this generic microscopic interaction function and the growth rate of the corresponding macroscopic model. Finally, we propose to use this relationship in order to help the investigation of the biological plausibility of phenomenological models of cancer growth.

q-bio.TO↗

A non-linear mathematical model of cell turnover, differentiation and tumorigenesis in the intestinal crypt

We present a development of a model of the relationship between cells in three compartments of the intestinal crypt: stem cells, semi-differentiated cells and fully differentiated cells. Stem and semi-differentiated cells may divide to self-renew, undergo programmed death or progress to semi-differentiated and fully differentiated cells respectively. The probabilities of each of these events provide the most important parameters of the model. Fully differentiated cells do not divide, but a proportion undergoes programmed death in each generation. Our previous models showed that failure of programmed death - for example, in tumorigenesis - could lead either to exponential growth in cell numbers or to growth to some plateau. Our new models incorporate plausible fluctuation in the parameters of the model and introduce non-linearity by assuming that the parameters depend on the numbers of cells in each state of differentiation. We find that the model is characterized by bifurcation between increase in cell numbers to stable equilibrium or 'explosive' exponential growth; in a restricted number of cases, there may be multiple stable equilibria. Fluctuation in cell numbers undergoing programmed death, for example caused by tissue damage, generally makes exponential growth more likely, as long as the size of the fluctuation exceeds a certain critical value for a sufficiently long period of time. In most cases, once exponential growth has started, this process is irreversible. In some circumstances, exponential growth is preceded by a long plateau phase, of variable duration, mimicking equilibrium: thus apparently self-limiting lesions may not be so in practice.

q-bio.TO↗