31,332 research outputs found
Going the distance for protein function prediction: a new distance metric for protein interaction networks
Due to an error introduced in the production process, the x-axes in the first panels of Figure 1 and Figure 7 are not formatted correctly. The correct Figure 1 can be viewed here: http://dx.doi.org/10.1371/annotation/343bf260-f6ff-48a2-93b2-3cc79af518a9In protein-protein interaction (PPI) networks, functional similarity is often inferred based on the function of directly interacting proteins, or more generally, some notion of interaction network proximity among proteins in a local neighborhood. Prior methods typically measure proximity as the shortest-path distance in the network, but this has only a limited ability to capture fine-grained neighborhood distinctions, because most proteins are close to each other, and there are many ties in proximity. We introduce diffusion state distance (DSD), a new metric based on a graph diffusion property, designed to capture finer-grained distinctions in proximity for transfer of functional annotation in PPI networks. We present a tool that, when input a PPI network, will output the DSD distances between every pair of proteins. We show that replacing the shortest-path metric by DSD improves the performance of classical function prediction methods across the board.MC, HZ, NMD and LJC were supported in part by National Institutes of Health (NIH) R01 grant GM080330. JP was supported in part by NIH grant R01 HD058880. This material is based upon work supported by the National Science Foundation under grant numbers CNS-0905565, CNS-1018266, CNS-1012910, and CNS-1117039, and supported by the Army Research Office under grant W911NF-11-1-0227 (to MEC). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript
Role-similarity based functional prediction in networked systems: Application to the yeast proteome
We propose a general method to predict functions of vertices where: 1. The
wiring of the network is somehow related to the vertex functionality. 2. A
fraction of the vertices are functionally classified. The method is influenced
by role-similarity measures of social network analysis. The two versions of our
prediction scheme is tested on model networks were the functions of the
vertices are designed to match their network surroundings. We also apply these
methods to the proteome of the yeast Saccharomyces cerevisiae and find the
results compatible with more specialized methods
Hoodsquare: Modeling and Recommending Neighborhoods in Location-based Social Networks
Information garnered from activity on location-based social networks can be
harnessed to characterize urban spaces and organize them into neighborhoods. In
this work, we adopt a data-driven approach to the identification and modeling
of urban neighborhoods using location-based social networks. We represent
geographic points in the city using spatio-temporal information about
Foursquare user check-ins and semantic information about places, with the goal
of developing features to input into a novel neighborhood detection algorithm.
The algorithm first employs a similarity metric that assesses the homogeneity
of a geographic area, and then with a simple mechanism of geographic
navigation, it detects the boundaries of a city's neighborhoods. The models and
algorithms devised are subsequently integrated into a publicly available,
map-based tool named Hoodsquare that allows users to explore activities and
neighborhoods in cities around the world.
Finally, we evaluate Hoodsquare in the context of a recommendation
application where user profiles are matched to urban neighborhoods. By
comparing with a number of baselines, we demonstrate how Hoodsquare can be used
to accurately predict the home neighborhood of Twitter users. We also show that
we are able to suggest neighborhoods geographically constrained in size, a
desirable property in mobile recommendation scenarios for which geographical
precision is key.Comment: ASE/IEEE SocialCom 201
A Survey on Graph Kernels
Graph kernels have become an established and widely-used technique for
solving classification tasks on graphs. This survey gives a comprehensive
overview of techniques for kernel-based graph classification developed in the
past 15 years. We describe and categorize graph kernels based on properties
inherent to their design, such as the nature of their extracted graph features,
their method of computation and their applicability to problems in practice. In
an extensive experimental evaluation, we study the classification accuracy of a
large suite of graph kernels on established benchmarks as well as new datasets.
We compare the performance of popular kernels with several baseline methods and
study the effect of applying a Gaussian RBF kernel to the metric induced by a
graph kernel. In doing so, we find that simple baselines become competitive
after this transformation on some datasets. Moreover, we study the extent to
which existing graph kernels agree in their predictions (and prediction errors)
and obtain a data-driven categorization of kernels as result. Finally, based on
our experimental results, we derive a practitioner's guide to kernel-based
graph classification
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