Characterization of complex networks: A survey of measurements

Each complex network (or class of networks) presents specific topological features which characterize its connectivity and highly influence the dynamics of processes executed on the network. The analysis, discrimination, and synthesis of complex networks therefore rely on the use of measurements capable of expressing the most relevant topological features. This article presents a survey of such measurements. It includes general considerations about complex network characterization, a brief review of the principal models, and the presentation of the main existing measurements. Important related issues covered in this work comprise the representation of the evolution of complex networks in terms of trajectories in several measurement spaces, the analysis of the correlations between some of the most traditional measurements, perturbation analysis, as well as the use of multivariate statistics for feature selection and network classification. Depending on the network and the analysis task one has in mind, a specific set of features may be chosen. It is hoped that the present survey will help the proper application and interpretation of measurements.Comment: A working manuscript with 78 pages, 32 figures. Suggestions of measurements for inclusion are welcomed by the author

Path Similarity Analysis: a Method for Quantifying Macromolecular Pathways

Diverse classes of proteins function through large-scale conformational changes; sophisticated enhanced sampling methods have been proposed to generate these macromolecular transition paths. As such paths are curves in a high-dimensional space, they have been difficult to compare quantitatively, a prerequisite to, for instance, assess the quality of different sampling algorithms. The Path Similarity Analysis (PSA) approach alleviates these difficulties by utilizing the full information in 3N-dimensional trajectories in configuration space. PSA employs the Hausdorff or Fr\'echet path metrics---adopted from computational geometry---enabling us to quantify path (dis)similarity, while the new concept of a Hausdorff-pair map permits the extraction of atomic-scale determinants responsible for path differences. Combined with clustering techniques, PSA facilitates the comparison of many paths, including collections of transition ensembles. We use the closed-to-open transition of the enzyme adenylate kinase (AdK)---a commonly used testbed for the assessment enhanced sampling algorithms---to examine multiple microsecond equilibrium molecular dynamics (MD) transitions of AdK in its substrate-free form alongside transition ensembles from the MD-based dynamic importance sampling (DIMS-MD) and targeted MD (TMD) methods, and a geometrical targeting algorithm (FRODA). A Hausdorff pairs analysis of these ensembles revealed, for instance, that differences in DIMS-MD and FRODA paths were mediated by a set of conserved salt bridges whose charge-charge interactions are fully modeled in DIMS-MD but not in FRODA. We also demonstrate how existing trajectory analysis methods relying on pre-defined collective variables, such as native contacts or geometric quantities, can be used synergistically with PSA, as well as the application of PSA to more complex systems such as membrane transporter proteins.Comment: 9 figures, 3 tables in the main manuscript; supplementary information includes 7 texts (S1 Text - S7 Text) and 11 figures (S1 Fig - S11 Fig) (also available from journal site

Animating the development of Social Networks over time using a dynamic extension of multidimensional scaling

The animation of network visualizations poses technical and theoretical challenges. Rather stable patterns are required before the mental map enables a user to make inferences over time. In order to enhance stability, we developed an extension of stress-minimization with developments over time. This dynamic layouter is no longer based on linear interpolation between independent static visualizations, but change over time is used as a parameter in the optimization. Because of our focus on structural change versus stability the attention is shifted from the relational graph to the latent eigenvectors of matrices. The approach is illustrated with animations for the journal citation environments of Social Networks, the (co-)author networks in the carrying community of this journal, and the topical development using relations among its title words. Our results are also compared with animations based on PajekToSVGAnim and SoNIA

Recurrent Neural Networks For Accurate RSSI Indoor Localization

This paper proposes recurrent neuron networks (RNNs) for a fingerprinting indoor localization using WiFi. Instead of locating user's position one at a time as in the cases of conventional algorithms, our RNN solution aims at trajectory positioning and takes into account the relation among the received signal strength indicator (RSSI) measurements in a trajectory. Furthermore, a weighted average filter is proposed for both input RSSI data and sequential output locations to enhance the accuracy among the temporal fluctuations of RSSI. The results using different types of RNN including vanilla RNN, long short-term memory (LSTM), gated recurrent unit (GRU) and bidirectional LSTM (BiLSTM) are presented. On-site experiments demonstrate that the proposed structure achieves an average localization error of $0.75$ m with $80\%$ of the errors under $1$ m, which outperforms the conventional KNN algorithms and probabilistic algorithms by approximately $30\%$ under the same test environment.Comment: Received signal strength indicator (RSSI), WiFi indoor localization, recurrent neuron network (RNN), long shortterm memory (LSTM), fingerprint-based localizatio