Virtual

Nonuniform Ellipticity is a classical topic in PDE, and regularity of solutions to nonuniformly elliptic and parabolic equations has been studied at length. I will present some recent results in this direction, including the solution to the longstanding issue of the validity of Schauder estimates in the nonuniformly elliptic case obtained in collaboration with Cristiana De Filippis. 

A metapopulation model, composed of subpopulations and pairwise connections, is a particle-network framework for epidemic dynamics study. Individuals are well-mixed within each subpopulation and migrate from one subpopulation to another, obeying a given mobility rule. While different mobility rules in metapopulation models have been studied, few efforts have been made to compare the effects of simple (i.e., unbiased) random walks and more complex mobility rules. In this talk, we study susceptible-infectious-susceptible (SIS) dynamics in a metapopulation model, in which individuals obey a second-order parametric random-walk mobility rule called the node2vec. We transform the node2vec mobility rule to a first-order Markov chain whose state space is composed of the directed edges and then derive the epidemic threshold. We find that the epidemic threshold is larger for various networks when individuals avoid frequent backtracking or visiting a neighbor of the previously visited subpopulation than when individuals obey the simple random walk. The amount of change in the epidemic threshold induced by the node2vec mobility is generally not as significant as, but is sometimes comparable with, the one induced by the change in the diffusion rate for individuals.

arXiv links: https://arxiv.org/abs/2006.04904 and https://arxiv.org/abs/2106.08080

In this talk we will show the application of (multilayer) network science to a wide spectrum of problems related to the ongoing COVID-19 pandemic, ranging from the molecular to the societal scale. Specifically, we will discuss our recent results about how network analysis: i) has been successfully applied to virus-host protein-protein interactions to unravel the systemic nature of SARS-CoV-2 infection; ii) has been used to gain insights about the potential role of non-compliant behavior in spreading of COVID-19; iii) has been crucial to assess the infodemic risk related to the simultaneous circulation of reliable and unreliable information about COVID-19.

References:

Assessing the risks of "infodemics" in response to COVID-19 epidemics
R. Gallotti, F. Valle, N. Castaldo, P. Sacco, M. De Domenico, Nature Human Behavior 4, 1285-1293 (2020)

CovMulNet19, Integrating Proteins, Diseases, Drugs, and Symptoms: A Network Medicine Approach to COVID-19
N. Verstraete, G. Jurman, G. Bertagnolli, A. Ghavasieh, V. Pancaldi, M. De Domenico, Network and Systems Medicine 3, 130 (2020)

Multiscale statistical physics of the pan-viral interactome unravels the systemic nature of SARS-CoV-2 infections
A. Ghavasieh, S. Bontorin, O. Artime, N. Verstraete, M. De Domenico, Communications Physics 4, 83 (2021)

Individual risk perception and empirical social structures shape the dynamics of infectious disease outbreaks
V. D'Andrea, R. Gallotti, N. Castaldo, M. De Domenico, To appear in PLOS Computational Biology (2022)

In the first part of the seminar I will introduce shallow neural-networks from a statistical-mechanics perspective, focusing on simple cases and on a naive scenario where information to be learnt is structureless. Then, inspired by biological information processing, I will enrich this framework by accounting for structured datasets and by making the network able to perform challenging tasks like generalization or even "taking a nap”. Results presented are both analytical and numerical.

Identifying novel drug-target interactions (DTI) is a critical and rate limiting step in drug discovery. While deep learning models have been proposed to accelerate the identification process, we show that state-of-the-art models fail to generalize to novel (i.e., never-before-seen) structures. We first unveil the mechanisms responsible for this shortcoming, demonstrating how models rely on shortcuts that leverage the topology of the protein-ligand bipartite network, rather than learning the node features. Then, we introduce AI-Bind, a pipeline that combines network-based sampling strategies with unsupervised pre-training, allowing us to limit the annotation imbalance and improve binding predictions for novel proteins and ligands. We illustrate the value of AI-Bind by predicting drugs and natural compounds with binding affinity to SARS-CoV-2 viral proteins and the associated human proteins. We also validate these predictions via auto-docking simulations and comparison with recent experimental evidence. Overall, AI-Bind offers a powerful high-throughput approach to identify drug-target combinations, with the potential of becoming a powerful tool in drug discovery.

arXiv link: https://arxiv.org/abs/2112.13168

Many applications involve non-Euclidean data, where exploiting Riemannian geometry can deliver algorithms that are computationally superior to standard nonlinear programming approaches. This observation has resulted in an increasing interest in Riemannian methods in the optimization and machine learning community. In this talk, we consider the problem of optimizing a function on a Riemannian manifold subject to convex constraints. We introduce Riemannian Frank-Wolfe (RFW) methods, a class of projection-free algorithms for constrained geodesically convex optimization. To understand the algorithm’s efficiency, we discuss (1) its iteration complexity, (2) the complexity of computing the Riemannian gradient and (3) the complexity of the Riemannian “linear” oracle (RLO), a crucial subroutine at the heart of the algorithm. We complement our theoretical results with an empirical comparison of RFW against state-of-the-art Riemannian optimization methods. Joint work with Suvrit Sra (MIT).

There's an idea going back at least to Kirchberger in 1902 that since the only operations we can ultimately compute are +, -, *, and /, all of numerical computation must reduce to rational functions.  I've been looking into this idea and it has led in some interesting directions.

The use of heuristics to assess the convergence and compress the output of Markov chain Monte Carlo can be sub-optimal in terms of the empirical approximations that are produced. Here we consider the problem of retrospectively selecting a subset of states, of fixed cardinality, from the sample path such that the approximation provided by their empirical distribution is close to optimal. A novel method is proposed, based on greedy minimisation of a kernel Stein discrepancy, that is suitable for problems where heavy compression is required. Theoretical results guarantee consistency of the method and its effectiveness is demonstrated in the challenging context of parameter inference for ordinary differential equations. Software is available in the Stein Thinning package in Python, R and MATLAB.

Supersymmetric gauge theories in five dimensions, although power counting non-renormalizable, are known to be in some cases UV completed by a superconformal field theory. Many tools, such as M-theory compactification and pq-web constructions, were used in recent years in order to deepen our understanding of these theories. This framework gives us a concrete way in which we can try to search for additional IR conformal field theory via deformations of these well-known superconformal fixed points. Recently, the authors of 2001.00023 proposed a supersymmetry breaking mass deformation of the E_1theory which, at weak gauge coupling, leads to pure SU(2) Yang-Mills and which was conjectured to lead to an interacting CFT at strong coupling. During this talk, I will provide an explicit geometric construction of the deformation using brane-web techniques and show that for large enough gauge coupling a global symmetry is spontaneously broken and the theory enters a new phase which, at infinite coupling, displays an instability. The Yang-Mills and the symmetry broken phases are separated by a phase transition. Quantum corrections to this analysis are discussed, as well as possible outlooks. Based on arXiv: 2109.02662.

A topological insulator has anomalous boundary spectrum which completely fills up gaps in the bulk spectrum. This ``topologically protected’’ spectral property is a physical manifestation of coarse geometry and index theory ideas. Special examples involve spectral flow and gerbes, related to Hamiltonian anomalies, and they arise experimentally in quantum Hall systems, time-reversal invariant mod-2 insulators, and shallow-water waves.