Epidemic mitigation by statistical inference from contact tracing data.

Contact tracing is an essential tool to mitigate the impact of a pandemic, such as the COVID-19 pandemic. In order to achieve efficient and scalable contact tracing in real time, digital devices can play an important role. While a lot of attention has been paid to analyzing the privacy and ethical risks of the associated mobile applications, so far much less research has been devoted to optimizing their performance and assessing their impact on the mitigation of the epidemic. We develop Bayesian inference methods to estimate the risk that an individual is infected. This inference is based on the list of his recent contacts and their own risk levels, as well as personal information such as results of tests or presence of syndromes. We propose to use probabilistic risk estimation to optimize testing and quarantining strategies for the control of an epidemic. Our results show that in some range of epidemic spreading (typically when the manual tracing of all contacts of infected people becomes practically impossible but before the fraction of infected people reaches the scale where a lockdown becomes unavoidable), this inference of individuals at risk could be an efficient way to mitigate the epidemic. Our approaches translate into fully distributed algorithms that only require communication between individuals who have recently been in contact. Such communication may be encrypted and anonymized, and thus, it is compatible with privacy-preserving standards. We conclude that probabilistic risk estimation is capable of enhancing the performance of digital contact tracing and should be considered in the mobile applications.

Eribulin in brain metastases of breast cancer: outcomes of the EBRAIM prospective observational trial.

Background: Eribulin shows some activity in controlling brain metastasis in breast cancer. Methods: This observational, multicenter study evaluated brain disease control rates, survival and safety in patients with brain metastatic breast cancer treated with eribulin in clinical practice. Results: A total of 34 patients were enrolled (mean age 49 years, 91% with visceral metastases) and 29 were evaluable for brain disease. Fourteen achieved disease control and showed a longer time without progression: 10 months (95% CI: 2.3-17.7) versus 4 months (95% CI: 3.3-4.7) in the control group (p = 0.029). Patients with clinical benefits at 6 months had longer survival. Leukopenia and neutropenia were the most frequent grade 3-4 toxicities. Conclusion: Eribulin confirms its effectiveness in patients with brain metastatic breast cancer. Further studies on larger cohorts are needed to confirm the results.

Loop Corrections in Spin Models through Density Consistency.

Computing marginal distributions of discrete or semidiscrete Markov random fields (MRFs) is a fundamental, generally intractable problem with a vast number of applications in virtually all fields of science. We present a new family of computational schemes to approximately calculate the marginals of discrete MRFs. This method shares some desirable properties with belief propagation, in particular, providing exact marginals on acyclic graphs, but it differs with the latter in that it includes some loop corrections; i.e., it takes into account correlations coming from all cycles in the factor graph. It is also similar to the adaptive Thouless-Anderson-Palmer method, but it differs with the latter in that the consistency is not on the first two moments of the distribution but rather on the value of its density on a subset of values. The results on finite-dimensional Isinglike models show a significant improvement with respect to the Bethe-Peierls (tree) approximation in all cases and with respect to the plaquette cluster variational method approximation in many cases. In particular, for the critical inverse temperature ß_{c} of the homogeneous hypercubic lattice, the expansion of (dß_{c})^{-1} around d=∞ of the proposed scheme is exact up to d^{-4} order, whereas the latter two are exact only up to d^{-2} order.

Copycat perceptron: Smashing barriers through collective learning.

We characterize the equilibrium properties of a model of y coupled binary perceptrons in the teacher-student scenario, subject to a suitable cost function, with an explicit ferromagnetic coupling proportional to the Hamming distance between the students' weights. In contrast to recent works, we analyze a more general setting in which thermal noise is present that affects each student's generalization performance. In the nonzero temperature regime, we find that the coupling of replicas leads to a bend of the phase diagram towards smaller values of α: This suggests that the free entropy landscape gets smoother around the solution with perfect generalization (i.e., the teacher) at a fixed fraction of examples, allowing standard thermal updating algorithms such as Simulated Annealing to easily reach the teacher solution and avoid getting trapped in metastable states as happens in the unreplicated case, even in the computationally easy regime of the inference phase diagram. These results provide additional analytic and numerical evidence for the recently conjectured Bayes-optimal property of Replicated Simulated Annealing for a sufficient number of replicas. From a learning perspective, these results also suggest that multiple students working together (in this case reviewing the same data) are able to learn the same rule both significantly faster and with fewer examples, a property that could be exploited in the context of cooperative and federated learning.

Inference in conditioned dynamics through causality restoration.

Estimating observables from conditioned dynamics is typically computationally hard. While obtaining independent samples efficiently from unconditioned dynamics is usually feasible, most of them do not satisfy the imposed conditions and must be discarded. On the other hand, conditioning breaks the causal properties of the dynamics, which ultimately renders the sampling of the conditioned dynamics non-trivial and inefficient. In this work, a Causal Variational Approach is proposed, as an approximate method to generate independent samples from a conditioned distribution. The procedure relies on learning the parameters of a generalized dynamical model that optimally describes the conditioned distribution in a variational sense. The outcome is an effective and unconditioned dynamical model from which one can trivially obtain independent samples, effectively restoring the causality of the conditioned dynamics. The consequences are twofold: the method allows one to efficiently compute observables from the conditioned dynamics by averaging over independent samples; moreover, it provides an effective unconditioned distribution that is easy to interpret. This approximation can be applied virtually to any dynamics. The application of the method to epidemic inference is discussed in detail. The results of direct comparison with state-of-the-art inference methods, including the soft-margin approach and mean-field methods, are promising.

Microsatellite Characterization and Panel Selection for Brown Bear (Ursus arctos) Population Assessment.

An assessment of the genetic diversity and structure of a population is essential for designing recovery plans for threatened species. Italy hosts two brown bear populations, Ursus arctos marsicanus (Uam), endemic to the Apennines of central Italy, and Ursus arctos arctos (Uaa), in the Italian Alps. Both populations are endangered and occasionally involved in human-wildlife conflict; thus, detailed management plans have been in place for several decades, including genetic monitoring. Here, we propose a simple cost-effective microsatellite-based protocol for the management of populations with low genetic variation. We sampled 22 Uam and 22 Uaa individuals and analyzed a total of 32 microsatellite loci in order to evaluate their applicability in individual identification. Based on genetic variability estimates, we compared data from four different STR marker sets, to evaluate the optimal settings in long-term monitoring projects. Allelic richness and gene diversity were the highest for the Uaa population, whereas depleted genetic variability was noted for the Uam population, which should be regarded as a conservation priority. Our results identified the most effective STR sets for the estimation of genetic diversity and individual discrimination in Uam (9 loci, PIC 0.45; PID 2.0 × 10-5), and Uaa (12 loci, PIC 0.64; PID 6.9 × 10-11) populations, which can easily be utilized by smaller laboratories to support local governments in regular population monitoring. The method we proposed to select the most variable markers could be adopted for the genetic characterization of other small and isolated populations.