Motivation: Network alignment (NA) aims to find regions of similarities between species’ molecular networks. There exist two NA categories: local (LNA) and global (GNA). LNA finds small highly conserved network regions and produces a many-to-many node mapping. GNA finds large conserved regions and produces a one-to-one node mapping. Given the different outputs of LNA and GNA, when a new NA method is proposed, it is compared against existing methods from the same category. However, both NA categories have the same goal: to allow for transferring functional knowledge from well- to poorly-studied species between conserved network regions. So, which one to choose, LNA or GNA? To answer this, we introduce the first systematic evaluation of the two NA categories.Results: We introduce new measures of alignment quality that allow for fair comparison of the different LNA and GNA outputs, as such measures do not exist. We provide user-friendly software for efficient alignment evaluation that implements the new and existing measures. We evaluate prominent LNA and GNA methods on synthetic and real-world biological networks. We study the effect on alignment quality of using different interaction types and confidence levels. We find that the superiority of one NA category over the other is context-dependent. Further, when we contrast LNA and GNA in the application of learning novel protein functional knowledge, the two produce very different predictions, indicating their complementarity. Our results and software provide guidelines for future NA method development and evaluation.Availability and implementation: Software: http://www.nd.edu/~cone/LNA_GNAContact: tmilenko@nd.eduSupplementary information:
Supplementary data are available at Bioinformatics online.
Previous studies of seasonal effects on sleep have yielded unclear results, likely due to methodological differences and limitations in data size and/or quality. We measured the sleep habits of 216 individuals across the U.S. over four seasons for slightly over a year using objective, continuous, and unobtrusive measures of sleep and local weather. In addition, we controlled for demographics and trait-like constructs previously identified to correlate with sleep behavior. We investigated seasonal and weather effects of sleep duration, bedtime, and wake time. We found several small but statistically significant effects of seasonal and weather effects on sleep patterns. We observe the strongest seasonal effects for wake time and sleep duration, especially during the spring season: wake times are earlier, and sleep duration decreases (compared to the reference season winter). Sleep duration also modestly decreases when day lengths get longer (between the winter and summer solstice). Bedtimes and wake times tend to be slightly later as outdoor temperature increases.
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