Because most complex genetic diseases are caused by defects of cell signaling, illuminating a signaling cascade is essential for understanding their mechanisms. We present three novel computational algorithms to reconstruct signaling networks between a starting protein and an ending protein using genome-wide protein-protein interaction (PPI) networks and gene ontology (GO) annotation data. A signaling network is represented as a directed acyclic graph in a merged form of multiple linear pathways. An advanced semantic similarity metric is applied for weighting PPIs as the preprocessing of all three methods. The first algorithm repeatedly extends the list of nodes based on path frequency towards an ending protein. The second algorithm repeatedly appends edges based on the occurrence of network motifs which indicate the link patterns more frequently appearing in a PPI network than in a random graph. The last algorithm uses the information propagation technique which iteratively updates edge orientations based on the path strength and merges the selected directed edges. Our experimental results demonstrate that the proposed algorithms achieve higher accuracy than previous methods when they are tested on well-studied pathways of S. cerevisiae. Furthermore, we introduce an interactive web application tool, called P-Finder, to visualize reconstructed signaling networks.

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Abstract. The number of electric vehicles (EVs) has been rapidly increasing over the last decade, motivated by the effort to decrease greenhouse gas emissions and the fast development of battery technology. This trend challenges distribution grids since EVs will bring significant stress if the charging of many EVs is not coordinated. Among the many strategies to cope with this challenge, next-day EV energy demand forecasting plays a key role. Existing studies have focused on predicting the next-day energy demand of EVs on the aggregated and individual levels. However, these studies have not yet extensively considered individual user mobility behaviors, which exhibit a high level of predictability. In this study, we consider several mobility features of individual users when forecasting the next-day energy demand of individual EVs. Three types of quantile regression models are used to generate probabilistic forecasts of energy demand, particularly the next-day energy consumption and parking duration. Based on the prediction results, two time-shifting smart charging strategies are designed: unidirectional and bidirectional smart charging. These two strategies are compared with an uncontrolled charging baseline to evaluate their financial benefits and peak-shaving effects. Our results show that human mobility features can partially improve the prediction of next-day individual EV energy demand. Additionally, users and distribution grids can benefit from smart charging strategies both financially and technically.

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