Link Prediction: A Graphical Model Approach

We consider the problem of link prediction in networks whose edge structure may vary (sufficiently slowly) over time. This problem, with applications in many important areas including social networks, has two main variants: the first, known as positive link prediction or PLP consists in estimating the appearance of a link in the network. The second, known as negative link prediction or NLP consists in estimating the disappearance of a link in the network. We propose a data-driven approach to estimate the appearance/disappearance of edges. Our solution is based on a regularized optimization problem for which we prove existence and uniqueness of the optimal solution

Properties of Healthcare Teaming Networks as a Function of Network Construction Algorithms

Network models of healthcare systems can be used to examine how providers collaborate, communicate, refer patients to each other. Most healthcare service network models have been constructed from patient claims data, using billing claims to link patients with providers. The data sets can be quite large, making standard methods for network construction computationally challenging and thus requiring the use of alternate construction algorithms. While these alternate methods have seen increasing use in generating healthcare networks, there is little to no literature comparing the differences in the structural properties of the generated networks. To address this issue, we compared the properties of healthcare networks constructed using different algorithms and the 2013 Medicare Part B outpatient claims data. Three different algorithms were compared: binning, sliding frame, and trace-route. Unipartite networks linking either providers or healthcare organizations by shared patients were built using each method. We found that each algorithm produced networks with substantially different topological properties. Provider networks adhered to a power law, and organization networks to a power law with exponential cutoff. Censoring networks to exclude edges with less than 11 shared patients, a common de-identification practice for healthcare network data, markedly reduced edge numbers and greatly altered measures of vertex prominence such as the betweenness centrality. We identified patterns in the distance patients travel between network providers, and most strikingly between providers in the Northeast United States and Florida. We conclude that the choice of network construction algorithm is critical for healthcare network analysis, and discuss the implications for selecting the algorithm best suited to the type of analysis to be performed.Comment: With links to comprehensive, high resolution figures and networks via figshare.co

The stability of transient relationships

In contrast to long-term relationships, far less is known about the temporal evolution of transient relationships, although these constitute a substantial fraction of people’s communication networks. Previous literature suggests that ratings of relationship emotional intensity decay gradually until the relationship ends. Using mobile phone data from three countries (US, UK, and Italy), we demonstrate that the volume of communication between ego and its transient alters does not display such a systematic decay, instead showing a lack of any dominant trends. This means that the communication volume of egos to groups of similar transient alters is stable. We show that alters with longer lifetimes in ego’s network receive more calls, with the lifetime of the relationship being predictable from call volume within the first few weeks of first contact. This is observed across all three countries, which include samples of egos at different life stages. The relation between early call volume and lifetime is consistent with the suggestion that individuals initially engage with a new alter so as to evaluate their potential as a tie in terms of homophily

Mining Time-aware Actor-level Evolution Similarity for Link Prediction in Dynamic Network

Topological evolution over time in a dynamic network triggers both the addition and deletion of actors and the links among them. A dynamic network can be represented as a time series of network snapshots where each snapshot represents the state of the network over an interval of time (for example, a minute, hour or day). The duration of each snapshot denotes the temporal scale/sliding window of the dynamic network and all the links within the duration of the window are aggregated together irrespective of their order in time. The inherent trade-off in selecting the timescale in analysing dynamic networks is that choosing a short temporal window may lead to chaotic changes in network topology and measures (for example, the actors’ centrality measures and the average path length); however, choosing a long window may compromise the study and the investigation of network dynamics. Therefore, to facilitate the analysis and understand different patterns of actor-oriented evolutionary aspects, it is necessary to define an optimal window length (temporal duration) with which to sample a dynamic network. In addition to determining the optical temporal duration, another key task for understanding the dynamics of evolving networks is being able to predict the likelihood of future links among pairs of actors given the existing states of link structure at present time. This phenomenon is known as the link prediction problem in network science. Instead of considering a static state of a network where the associated topology does not change, dynamic link prediction attempts to predict emerging links by considering different types of historical/temporal information, for example the different types of temporal evolutions experienced by the actors in a dynamic network due to the topological evolution over time, known as actor dynamicities. Although there has been some success in developing various methodologies and metrics for the purpose of dynamic link prediction, mining actor-oriented evolutions to address this problem has received little attention from the research community. In addition to this, the existing methodologies were developed without considering the sampling window size of the dynamic network, even though the sampling duration has a large impact on mining the network dynamics of an evolutionary network. Therefore, although the principal focus of this thesis is link prediction in dynamic networks, the optimal sampling window determination was also considered

Inference of gene regulation from expression datasets

The development of high throughput techniques and the accumulation of large scale gene expression data provide researchers great opportunities to more efficiently solve important but complex biological problems, such as reconstruction of gene regulatory networks and identification of miRNA-target interactions. In the past decade, many algorithms have been developed to address these problems. However, prediction and simulation of gene expression data have not yet received as much attention. In this study, we present a model based on stepwise multiple linear regression (SMLR) that can be applied for prediction and simulation of gene expression, as well as reconstruction of gene regulatory networks by analysis of time-series gene expression data, and we present its application in analysis of paired miRNA-mRNA expression data.Ph.D., Biomedical Engineering -- Drexel University, 201