Trading contact tracing efficiency for finding patient zero.

As the COVID-19 pandemic has demonstrated, identifying the origin of a pandemic remains a challenging task. The search for patient zero may benefit from the widely-used and well-established toolkit of contact tracing methods, although this possibility has not been explored to date. We fill this gap by investigating the prospect of performing the source detection task as part of the contact tracing process, i.e., the possibility of tuning the parameters of the process in order to pinpoint the origin of the infection. To this end, we perform simulations on temporal networks using a recent diffusion model that recreates the dynamics of the COVID-19 pandemic. We find that increasing the budget for contact tracing beyond a certain threshold can significantly improve the identification of infected individuals but has diminishing returns in terms of source detection. Moreover, disease variants of higher infectivity make it easier to find the source but harder to identify infected individuals. Finally, we unravel a seemingly-intrinsic trade-off between the use of contact tracing to either identify infected nodes or detect the source of infection. This trade-off suggests that focusing on the identification of patient zero may come at the expense of identifying infected individuals.

Learning PDE to Model Self-Organization of Matter.

A self-organization hydrodynamic process has recently been proposed to partially explain the formation of femtosecond laser-induced nanopatterns on Nickel, which have important applications in optics, microbiology, medicine, etc. Exploring laser pattern space is difficult, however, which simultaneously (i) motivates using machine learning (ML) to search for novel patterns and (ii) hinders it, because of the few data available from costly and time-consuming experiments. In this paper, we use ML to predict novel patterns by integrating partial physical knowledge in the form of the Swift-Hohenberg (SH) partial differential equation (PDE). To do so, we propose a framework to learn with few data, in the absence of initial conditions, by benefiting from background knowledge in the form of a PDE solver. We show that in the case of a self-organization process, a feature mapping exists in which initial conditions can safely be ignored and patterns can be described in terms of PDE parameters alone, which drastically simplifies the problem. In order to apply this framework, we develop a second-order pseudospectral solver of the SH equation which offers a good compromise between accuracy and speed. Our method allows us to predict new nanopatterns in good agreement with experimental data. Moreover, we show that pattern features are related, which imposes constraints on novel pattern design, and suggest an efficient procedure of acquiring experimental data iteratively to improve the generalization of the learned model. It also allows us to identify the limitations of the SH equation as a partial model and suggests an improvement to the physical model itself.

Modelling digital and manual contact tracing for COVID-19. Are low uptakes and missed contacts deal-breakers?

Comprehensive testing schemes, followed by adequate contact tracing and isolation, represent the best public health interventions we can employ to reduce the impact of an ongoing epidemic when no or limited vaccine supplies are available and the implications of a full lockdown are to be avoided. However, the process of tracing can prove feckless for highly-contagious viruses such as SARS-CoV-2. The interview-based approaches often miss contacts and involve significant delays, while digital solutions can suffer from insufficient adoption rates or inadequate usage patterns. Here we present a novel way of modelling different contact tracing strategies, using a generalized multi-site mean-field model, which can naturally assess the impact of manual and digital approaches alike. Our methodology can readily be applied to any compartmental formulation, thus enabling the study of more complex pathogen dynamics. We use this technique to simulate a newly-defined epidemiological model, SEIR-T, and show that, given the right conditions, tracing in a COVID-19 epidemic can be effective even when digital uptakes are sub-optimal or interviewers miss a fair proportion of the contacts.

Epidemic contact tracing via communication traces.

Traditional contact tracing relies on knowledge of the interpersonal network of physical interactions, where contagious outbreaks propagate. However, due to privacy constraints and noisy data assimilation, this network is generally difficult to reconstruct accurately. Communication traces obtained by mobile phones are known to be good proxies for the physical interaction network, and they may provide a valuable tool for contact tracing. Motivated by this assumption, we propose a model for contact tracing, where an infection is spreading in the physical interpersonal network, which can never be fully recovered; and contact tracing is occurring in a communication network which acts as a proxy for the first. We apply this dual model to a dataset covering 72 students over a 9 month period, for which both the physical interactions as well as the mobile communication traces are known. Our results suggest that a wide range of contact tracing strategies may significantly reduce the final size of the epidemic, by mainly affecting its peak of incidence. However, we find that for low overlap between the face-to-face and communication interaction network, contact tracing is only efficient at the beginning of the outbreak, due to rapidly increasing costs as the epidemic evolves. Overall, contact tracing via mobile phone communication traces may be a viable option to arrest contagious outbreaks.

Temporal analysis of motif mixtures using Dirichlet processes.

In this paper, we present a new model for unsupervised discovery of recurrent temporal patterns (or motifs) in time series (or documents). The model is designed to handle the difficult case of multivariate time series obtained from a mixture of activities, that is, our observations are caused by the superposition of multiple phenomena occurring concurrently and with no synchronization. The model uses nonparametric Bayesian methods to describe both the motifs and their occurrences in documents. We derive an inference scheme to automatically and simultaneously recover the recurrent motifs (both their characteristics and number) and their occurrence instants in each document. The model is widely applicable and is illustrated on datasets coming from multiple modalities, mainly videos from static cameras and audio localization data. The rich semantic interpretation that the model offers can be leveraged in tasks such as event counting or for scene analysis. The approach is also used as a mean of doing soft camera calibration in a camera network. A thorough study of the model parameters is provided and a cross-platform implementation of the inference algorithm will be made publicly available.