Structural centrality measures are often used to approximate or predict dynamical influence in a network. The recently proposed Expected Force of Infection (ExF) measures the entropy of all potential transmission paths starting at a node, effectively characterizing a node's role in epidemic diffusion processes. However, this promising metric has seen limited adoption mainly due to an inefficient formulation and the lack of an open-source implementation. In this paper, we present a novel cluster-centric, parallel algorithm enhancing ExF's efficiency and scalability. Compared to the simple parallel version of the original formulation of the ExF our efficient, open-source GPU implementation enables key nodes detection at previously intractable scales, with speed-ups of up to 300 x on networks with up to 44 million edges. Leveraging on our algorithm, we compare the ExF with other well-known centrality metrics, upon six real and synthetic contact networks. The ExF emerges as the best of the considered metrics in a few, important tasks: it predicts the likelihood of a global epidemic and its diffusion speed, based on the centrality of the seed node; and it predicts how many other infections will occur as a consequence, in some sense, of a specific node having caught the disease.

The importance of the immune system (IS) in tuberculosis (TB) drug development is often underestimated because of the intricate nature of experiments and the specialized knowledge needed. In vitro and animal studies fall short in replicating the intricate reactions of the human IS to drugs and infections. In this study, we present our initial efforts in employing an in silico approach to comprehend how an individual’s IS impacts the efficacy of therapy, particularly in managing mycobacterium tuberculosis (Mtb) infection and minimizing the risk of relapse. We employed a well-established agent-based IS simulator called C-IMMSIM. We conducted simulations to investigate the long-term outcomes of TB disease in a virtual cohort infected with Mtb over a 50-year period. Our simulations revealed that individuals with competent IS showed a high success rate in containing Mtb infection. Furthermore, to better understand the dynamic interactions between Mtb and the IS, we deliberately introduced specific IS deficiencies, thus successfully inducing short-term relapses and mortality. These results confirm the model’s ability to elucidate the mechanisms underlying the interactions between Mtb and the IS.

Abstract Tor is an open source software that allows accessing various kinds of resources, known as hidden services, while guaranteeing sender and receiver anonymity. Tor relies on a free, worldwide, overlay network, managed by volunteers, that works according to the principles of onion routing in which messages are encapsulated in layers of encryption, analogous to layers of an onion. The Tor Web is the set of web resources that exist on the Tor network, and Tor websites are part of the so-called dark web. Recent research works have evaluated Tor security, its evolution over time, and its thematic organization. Nevertheless, limited information is available about the structure of the graph defined by the network of Tor websites, not to be mistaken with the network of nodes that supports the onion routing. The limited number of entry points that can be used to crawl the network, makes the study of this graph far from being simple. In the present paper we analyze two graph representations of the Tor Web and the relationship between contents and structural features, considering three crawling datasets collected over a five-month time frame. Among other findings, we show that Tor consists of a tiny strongly connected component, in which link directories play a central role, and of a multitude of services that can (only) be reached from there. From this viewpoint, the graph appears inefficient. Nevertheless, if we only consider mutual connections, a more efficient subgraph emerges, that is, probably, the backbone of social interactions in Tor.

In silico trials are emerging as a valuable tool for improving both study design and outcomes. A key component of this process is the definition of a virtual cohort, i.e., a set of virtual patients with plausible physiological characteristics (covariates). Building on the NHANES study (2017-2020), we developed a statistical model to infer immunological parameters and a technique to generate a population of plausible immunological virtual patients. A thorough statistical analysis showed that the most appropriate model to represent our data is a conditional multivariate model. Compared to others, it is able to reproduce asymmetric distributions more accurately and is therefore more suitable in cases where there is no prior knowledge of the relationships between covariates. Our analysis also demonstrates the inter-variability and inter-dependence of the different covariates of interest. For example, age has a negative impact on the number of lymphocytes and, surprisingly, ethnicity has a minor influence on the other immunological covariates.

Network-based ranking methods (e.g., centrality analysis) have found extensive use in systems biology and network medicine for the prediction of essential proteins, for the prioritization of drug targets candidates in the treatment of several pathologies and in biomarker discovery, and for human disease genes identification. We here studied the connectivity of the human protein-protein interaction network (i.e., the interactome) to find the nodes whose removal has the heaviest impact on the network, i.e., maximizes its fragmentation. Such nodes are known as Critical Nodes (CNs). Specifically, we implemented a Critical Node Heuristic (CNH) and compared its performance against other four heuristics based on well known centrality measures. To better understand the structure of the interactome, the CNs' role played in the network, and the different heuristics' capabilities to grasp biologically relevant nodes, we compared the sets of nodes identified as CNs by each heuristic with two experimentally validated sets of essential genes, i.e., the genes whose removal impact on a given organism's ability to survive. Our results show that classical centrality measures (i.e., closeness centrality, degree) found more essential genes with respect to CNH on the current version of the human interactome, however the removal of such nodes does not have the greatest impact on interactome connectivity, while, interestingly, the genes identified by CNH show peculiar characteristics both from the topological and the biological point of view. Finally, even if a relevant fraction of essential genes is found via the classical centrality measures, the same measures seem to fail in identifying the whole set of essential genes, suggesting once again that some of them are not central in the network, that there may be biases in the current interaction data, and that different, combined graph theoretical and other techniques should be applied for their discovery.

The exploration and analysis of Web graphs has flourished in the recent past, producing a large number of relevant and interesting research results. However, the unique characteristics of the Tor network demand for specific algorithms to explore and analyze it. Tor is an anonymity network that allows offering and accessing various Internet resources while guaranteeing a high degree of provider and user anonymity. So far the attention of the research community has focused on assessing the security of the Tor infrastructure. Most research work on the Tor network aimed at discovering protocol vulnerabilities to de-anonymize users and services, while little or no information is available about the topology of the Tor Web graph or the relationship between pages' content and topological structure. With our work we aim at addressing such lack of information. We describe the topology of the Tor Web graph measuring both global and local properties by means of well-known metrics that require due to the size of the network, high performance algorithms. We consider three different snapshots obtained by extensively crawling Tor three times over a 5 months time frame. Finally we present a correlation analysis of pages' semantics and topology, discussing novel insights about the Tor Web organization and its content. Our findings show that the Tor graph presents some of the characteristics of social and surface web graphs, along with a few unique peculiarities.

Tor hidden services allow offering and accessing various Internet resources while guaranteeing a high degree of provider and user anonymity. So far, most research work on the Tor network aimed at discovering protocol vulnerabilities to de-anonymize users and services. Other work aimed at estimating the number of available hidden services and classifying them. Something that still remains largely unknown is the structure of the graph defined by the network of Tor services. In this paper, we describe the topology of the Tor graph (aggregated at the hidden service level) measuring both global and local properties by means of well-known metrics. We consider three different snapshots obtained by extensively crawling Tor three times over a 5 months time frame. We separately study these three graphs and their shared “stable” core. In doing so, other than assessing the renowned volatility of Tor hidden services, we make it possible to distinguish time dependent and structural aspects of the Tor graph. Our findings show that, among other things, the graph of Tor hidden services presents some of the characteristics of social and surface web graphs, along with a few unique peculiarities, such as a very high percentage of nodes having no outbound links.

We present the results obtained by using an evolution of our CUDA-based solution for the exploration, via a breadth first search, of large graphs. This latest version exploits at its best the features of the Kepler architecture and relies on a combination of techniques to reduce both the number of communications among the GPUs and the amount of exchanged data. The final result is a code that can visit more than 800 billion edges in a second by using a cluster equipped with 4,096 Tesla K20X GPUs.