arXiv subjects

Pejman Rohani

Publications and source records attributed to Pejman Rohani.

6 recordsLinked to original sources

arXiv2025

Topolow: Force-Directed Euclidean Embedding of Dissimilarity Data with Robustness Against Non-Metricity and Sparsity

The problem of embedding a set of objects into a low-dimensional Euclidean space based on a matrix of pairwise dissimilarities is fundamental in data analysis, machine learning, and statistics. However, the assumptions of many standard analytical methods are violated when the input dissimilarities fail to satisfy metric or Euclidean axioms. We present the mathematical and statistical foundations of Topolow, a physics-inspired, gradient-free optimization framework for such embedding problems. Topolow is conceptually related to force-directed graph drawing algorithms but is fundamentally distinguished by its goal of quantitative metric reconstruction. It models objects as particles in a physical system, and its novel optimization scheme proceeds through sequential, stochastic pairwise interactions, which circumvents the need to compute a global gradient and provides robustness against convergence to local optima, especially for sparse data. Topolow maximizes the likelihood under a Laplace error model, robust to outliers and heterogeneous errors, and properly handles censored data. Crucially, Topolow does not require the input dissimilarities to be metric, making it a robust solution for embedding non-metric measurements into a valid Euclidean space, thereby enabling the use of standard analytical tools. We demonstrate the superior performance of Topolow compared to standard Multidimensional Scaling (MDS) methods in reconstructing the geometry of sparse and non-Euclidean data. This paper formalizes the algorithm, first introduced as Topolow in the context of antigenic mapping in (Arhami and Rohani, 2025) (open access), with emphasis on its metric embedding and mathematical properties for a broader audience. The general-purpose function Euclidify is available in the R package topolow.

cs.CG↗

arXiv2025

Physics-informed deep learning for infectious disease forecasting

Accurate forecasting of contagious diseases is critical for public health policymaking and pandemic preparedness. We propose a new infectious disease forecasting model based on physics-informed neural networks (PINNs), an emerging scientific machine learning approach. By embedding a compartmental model into the loss function, our method integrates epidemiological theory with data, helping to prevent model overfitting. We further enhance the model with a sub-network that accounts for covariates such as mobility and cumulative vaccine doses, which influence the transmission rate. Using state-level COVID-19 data from California, we demonstrate that the PINN model accurately predicts cases, deaths, and hospitalizations, aligning well with existing benchmarks. Notably, the PINN model outperforms naive baseline forecasts and several sequence deep learning models, including Recurrent Neural Networks (RNNs), Long Short-Term Memory (LSTM) networks, Gated Recurrent Units (GRUs), and Transformers. It also achieves performance comparable to a sophisticated Gaussian infection state forecasting model that combines compartmental dynamics, a data observation model, and parameter regression. However, the PINN model features a simpler structure and is easier to implement. In summary, we systematically evaluate the PINN model's ability to forecast infectious disease dynamics, demonstrating its potential as an efficient computational tool to strengthen forecasting capabilities.

cs.LG↗

arXiv2021

Optimal non-pharmaceutical intervention policy for Covid-19 epidemic via neuroevolution algorithm

National responses to the Covid-19 pandemic varied markedly across countries, from business-as-usual to complete shutdowns. Policies aimed at disrupting the viral transmission cycle and preventing the healthcare system from being overwhelmed, simultaneously exact an economic toll. We developed a intervention policy model that comprised the relative human, economic and healthcare costs of non-pharmaceutical epidemic intervention and arrived at the optimal strategy using the neuroevolution algorithm. The proposed model finds the minimum required reduction in contact rates to maintain the burden on the healthcare system below the maximum capacity. We find that such a policy renders a sharp increase in the control strength at the early stages of the epidemic, followed by a steady increase in the subsequent ten weeks as the epidemic approaches its peak, and finally control strength is gradually decreased as the population moves towards herd immunity. We have also shown how such a model can provide an efficient adaptive intervention policy at different stages of the epidemic without having access to the entire history of its progression in the population. This work emphasizes the importance of imposing intervention measures early and provides insights into adaptive intervention policies to minimize the economic impacts of the epidemic without putting an extra burden on the healthcare system.

q-bio.PE↗

arXiv2020

Nonlinear dynamic analysis of an epidemiological model for COVID-19 including public behavior and government action

This paper is concerned with nonlinear modeling and analysis of the COVID-19 pandemic currently ravaging the planet. There are two objectives: to arrive at an appropriate model that captures the collected data faithfully, and to use that as a basis to explore the nonlinear behavior. We use a nonlinear SEIR (Susceptible, Exposed, Infectious & Removed) transmission model with added behavioral and government policy dynamics. We develop a genetic algorithm technique to identify key model parameters employing COVID19 data from South Korea. Stability, bifurcations and dynamic behavior are analyzed. Parametric analysis reveals conditions for sustained epidemic equilibria to occur. This work points to the value of nonlinear dynamic analysis in pandemic modeling and demonstrates the dramatic influence of social and government behavior on disease dynamics.

q-bio.PE↗

arXiv2015

Avoidable errors in the modeling of outbreaks of emerging pathogens, with special reference to Ebola

As an emergent infectious disease outbreak unfolds, public health response is reliant on information on key epidemiological quantities, such as transmission potential and serial interval. Increasingly, transmission models fit to incidence data are used to estimate these parameters and guide policy. Some widely-used modeling practices lead to potentially large errors in parameter estimates and, consequently, errors in model-based forecasts. Even more worryingly, in such situations, confidence in parameter estimates and forecasts can itself be far over-estimated, leading to the potential for large errors that mask their own presence. Fortunately, straightforward and computationally inexpensive alternatives exist that avoid these problems. Here, we first use a simulation study to demonstrate potential pitfalls of the standard practice of fitting deterministic models to cumulative incidence data. Next, we demonstrate an alternative based on stochastic models fit to raw data from an early phase of 2014 West Africa Ebola Virus Disease outbreak. We show not only that bias is thereby reduced, but that uncertainty in estimates and forecasts is better quantified and that, critically, lack of model fit is more readily diagnosed. We conclude with a short list of principles to guide the modeling response to future infectious disease outbreaks.

q-bio.PE↗

arXiv2014

The interaction of regional and local in the dynamics of the coffee rust disease

A simple mean field model is proposed that captures the two scales of dynamic processes involved in the spread of the coffee rust disease. At a local level the state variable is the fraction of coffee plants on an average farm that are infested with the disease and at the regional level the state variable is the fraction of farms that are infested with the disease. These two levels are interactive with one another in obvious ways, producing qualitatively interesting results. Specifically there are three distinct outcomes: disease disappears, disease is potentially persistent, and disease is inevitably persistent. The basic structure of the model generates the potential for tipping point behavior due to the presence of a blue sky bifurcation, suggesting that the emergence of epizootics of the disease may be unpredictable.

q-bio.PE↗