141 research outputs found
A network inference method for large-scale unsupervised identification of novel drug-drug interactions
Characterizing interactions between drugs is important to avoid potentially
harmful combinations, to reduce off-target effects of treatments and to fight
antibiotic resistant pathogens, among others. Here we present a network
inference algorithm to predict uncharacterized drug-drug interactions. Our
algorithm takes, as its only input, sets of previously reported interactions,
and does not require any pharmacological or biochemical information about the
drugs, their targets or their mechanisms of action. Because the models we use
are abstract, our approach can deal with adverse interactions,
synergistic/antagonistic/suppressing interactions, or any other type of drug
interaction. We show that our method is able to accurately predict
interactions, both in exhaustive pairwise interaction data between small sets
of drugs, and in large-scale databases. We also demonstrate that our algorithm
can be used efficiently to discover interactions of new drugs as part of the
drug discovery process
Missing and spurious interactions and the reconstruction of complex networks
Network analysis is currently used in a myriad of contexts: from identifying
potential drug targets to predicting the spread of epidemics and designing
vaccination strategies, and from finding friends to uncovering criminal
activity. Despite the promise of the network approach, the reliability of
network data is a source of great concern in all fields where complex networks
are studied. Here, we present a general mathematical and computational
framework to deal with the problem of data reliability in complex networks. In
particular, we are able to reliably identify both missing and spurious
interactions in noisy network observations. Remarkably, our approach also
enables us to obtain, from those noisy observations, network reconstructions
that yield estimates of the true network properties that are more accurate than
those provided by the observations themselves. Our approach has the potential
to guide experiments, to better characterize network data sets, and to drive
new discoveries
Predicting human preferences using the block structure of complex social networks
With ever-increasing available data, predicting individuals' preferences and
helping them locate the most relevant information has become a pressing need.
Understanding and predicting preferences is also important from a fundamental
point of view, as part of what has been called a "new" computational social
science. Here, we propose a novel approach based on stochastic block models,
which have been developed by sociologists as plausible models of complex
networks of social interactions. Our model is in the spirit of predicting
individuals' preferences based on the preferences of others but, rather than
fitting a particular model, we rely on a Bayesian approach that samples over
the ensemble of all possible models. We show that our approach is considerably
more accurate than leading recommender algorithms, with major relative
improvements between 38% and 99% over industry-level algorithms. Besides, our
approach sheds light on decision-making processes by identifying groups of
individuals that have consistently similar preferences, and enabling the
analysis of the characteristics of those groups
Detection of node group membership in networks with group overlap
Most networks found in social and biochemical systems have modular
structures. An important question prompted by the modularity of these networks
is whether nodes can be said to belong to a single group. If they cannot, we
would need to consider the role of "overlapping communities." Despite some
efforts in this direction, the problem of detecting overlapping groups remains
unsolved because there is neither a formal definition of overlapping community,
nor an ensemble of networks with which to test the performance of group
detection algorithms when nodes can belong to more than one group. Here, we
introduce an ensemble of networks with overlapping groups. We then apply three
group identification methods--modularity maximization, k-clique percolation,
and modularity-landscape surveying--to these networks. We find that the
modularity-landscape surveying method is the only one able to detect
heterogeneities in node memberships, and that those heterogeneities are only
detectable when the overlap is small. Surprisingly, we find that the k-clique
percolation method is unable to detect node membership for the overlapping
case.Comment: 12 pages, 6 figures. To appear in Euro. Phys. J
Modularity from Fluctuations in Random Graphs and Complex Networks
The mechanisms by which modularity emerges in complex networks are not well
understood but recent reports have suggested that modularity may arise from
evolutionary selection. We show that finding the modularity of a network is
analogous to finding the ground-state energy of a spin system. Moreover, we
demonstrate that, due to fluctuations, stochastic network models give rise to
modular networks. Specifically, we show both numerically and analytically that
random graphs and scale-free networks have modularity. We argue that this fact
must be taken into consideration to define statistically-significant modularity
in complex networks.Comment: 4 page
Early-career factors largely determine the future impact of prominent researchers: evidence across eight scientific fields
Abstract Can we help predict the future impact of researchers using early-career factors? We analyze early-career factors of the world’s 100 most prominent researchers across 8 scientific fields and identify four key drivers in researchers’ initial career: working at a top 25 ranked university, publishing a paper in a top 5 ranked journal, publishing most papers in top quartile (high-impact) journals and co-authoring with other prominent researchers in their field. We find that over 95% of prominent researchers across multiple fields had at least one of these four features in the first 5 years of their career. We find that the most prominent scientists who had an early career advantage in terms of citations and h-index are more likely to have had all four features, and that this advantage persists throughout their career after 10, 15 and 20 years. Our findings show that these few early-career factors help predict researchers’ impact later in their careers. Our research thus points to the need to enhance fairness and career mobility among scientists who have not had a jump start early on
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