Search for: All records

As hyperscalers such as Google, Microsoft, and Amazon play an increasingly important role in today's Internet, they are also capable of manipulating probe packets that traverse their privately owned and operated backbones. As a result, standard traceroute-based measurement techniques are no longer a reliable means for assessing network connectivity in these global-scale cloud provider infrastructures. In response to these developments, we present a new empirical approach for elucidating connectivity in these private backbone networks. Our approach relies on using only lightweight (i.e., simple, easily interpretable, and readily available) measurements, but requires applying heavyweight mathematical techniques for analyzing these measurements. In particular, we describe a new method that uses network latency measurements and relies on concepts from Riemannian geometry (i.e., Ricci curvature) to assess the characteristics of the connectivity fabric of a given network infrastructure. We complement this method with a visualization tool that generates a novel manifold view of a network's delay space. We demonstrate our approach by utilizing latency measurements from available vantage points and virtual machines running in datacenters of three large cloud providers to study different aspects of connectivity in their private backbones and show how our generated manifold views enable us to expose and visualize critical aspects of this connectivity.

 

The main premise of this work is that since large cloud providers can and do manipulate probe packets that traverse their privately owned and operated backbones, standard traceroute-based measurement techniques are no longer a reliable means for assessing network connectivity in large cloud provider infrastructures. In response to these developments, we present a new empirical approach for elucidating private connectivity in today's Internet. Our approach relies on using only "light-weight" ( i.e., simple, easily-interpretable, and readily available) measurements, but requires applying a "heavy-weight" or advanced mathematical analysis. In particular, we describe a new method for assessing the characteristics of network path connectivity that is based on concepts from Riemannian geometry ( i.e., Ricci curvature) and also relies on an array of carefully crafted visualizations ( e.g., a novel manifold view of a network's delay space). We demonstrate our method by utilizing latency measurements from RIPE Atlas anchors and virtual machines running in data centers of three large cloud providers to (i) study different aspects of connectivity in their private backbones and (ii) show how our manifold-based view enables us to expose and visualize critical aspects of this connectivity over different geographic scales. 

Abstract Motivation Mapping genetic interactions (GIs) can reveal important insights into cellular function and has potential translational applications. There has been great progress in developing high-throughput experimental systems for measuring GIs (e.g. with double knockouts) as well as in defining computational methods for inferring (imputing) unknown interactions. However, existing computational methods for imputation have largely been developed for and applied in baker’s yeast, even as experimental systems have begun to allow measurements in other contexts. Importantly, existing methods face a number of limitations in requiring specific side information and with respect to computational cost. Further, few have addressed how GIs can be imputed when data are scarce. Results In this article, we address these limitations by presenting a new imputation framework, called Extensible Matrix Factorization (EMF). EMF is a framework of composable models that flexibly exploit cross-species information in the form of GI data across multiple species, and arbitrary side information in the form of kernels (e.g. from protein–protein interaction networks). We perform a rigorous set of experiments on these models in matched GI datasets from baker’s and fission yeast. These include the first such experiments on genome-scale GI datasets in multiple species in the same study. We find that EMF models that exploit side and cross-species information improve imputation, especially in data-scarce settings. Further, we show that EMF outperforms the state-of-the-art deep learning method, even when using strictly less data, and incurs orders of magnitude less computational cost. Availability Implementations of models and experiments are available at: https://github.com/lrgr/EMF. Supplementary information Supplementary data are available at Bioinformatics online. 

Predicting election outcomes is of considerable interest to candidates, political scientists, and the public at large. We propose the use of Web browsing history as a new indicator of candidate preference among the electorate, one that has potential to overcome a number of the drawbacks of election polls. However, there are a number of challenges that must be overcome to effectively use Web browsing for assessing candidate preference—including the lack of suitable ground truth data and the heterogeneity of user populations in time and space. We address these challenges, and show that the resulting methods can shed considerable light on the dynamics of voters’ candidate preferences in ways that are difficult to achieve using polls. 

Network propagation has been widely used for nearly 20 years to predict gene functions and phenotypes. Despite the popularity of this approach, little attention has been paid to the question of provenance tracing in this context, e.g., determining how much any experimental observation in the input contributes to the score of every prediction.

We design a network propagation framework with 2 novel components and apply it to predict human proteins that directly or indirectly interact with SARS-CoV-2 proteins. First, we trace the provenance of each prediction to its experimentally validated sources, which in our case are human proteins experimentally determined to interact with viral proteins. Second, we design a technique that helps to reduce the manual adjustment of parameters by users. We find that for every top-ranking prediction, the highest contribution to its score arises from a direct neighbor in a human protein-protein interaction network. We further analyze these results to develop functional insights on SARS-CoV-2 that expand on known biology such as the connection between endoplasmic reticulum stress, HSPA5, and anti-clotting agents.

We examine how our provenance-tracing method can be generalized to a broad class of network-based algorithms. We provide a useful resource for the SARS-CoV-2 community that implicates many previously undocumented proteins with putative functional relationships to viral infection. This resource includes potential drugs that can be opportunistically repositioned to target these proteins. We also discuss how our overall framework can be extended to other, newly emerging viruses.