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Many complex flows such as those arising from ocean plastics in geophysics or moving cells in biology are characterized by sparse and noisy trajectory datasets. We introduce techniques for identifying Lagrangian Coherent Structures (LCSs) of hyperbolic and elliptic nature in such datasets. Hyperbolic LCSs, which represent surfaces with maximal attraction or repulsion over a finite amount of time, are computed through a regularized least-squares approximation of the flow map gradient. Elliptic LCSs, which identify regions of coherent motion such as vortices and jets, are extracted using DBSCAN - a popular data clustering algorithm - combined with a systematic approach to choose parameters. We deploy these methods on various benchmark analytical flows and real-life experimental datasets ranging from oceanography to biology and show that they yield accurate results, despite sparse and noisy data. We also provide a lightweight computational implementation of these techniques as a user-friendly and straightforward Python code., Comment: 26 pages, 12 figures

The key component in forecasting demand and consumption of resources in a supply network is an accurate prediction of real-valued time series. Indeed, both service interruptions and resource waste can be reduced with the implementation of an effective forecasting system. Significant research has thus been devoted to the design and development of methodologies for short term load forecasting over the past decades. A class of mathematical models, called Recurrent Neural Networks, are nowadays gaining renewed interest among researchers and they are replacing many practical implementation of the forecasting systems, previously based on static methods. Despite the undeniable expressive power of these architectures, their recurrent nature complicates their understanding and poses challenges in the training procedures. Recently, new important families of recurrent architectures have emerged and their applicability in the context of load forecasting has not been investigated completely yet. In this paper we perform a comparative study on the problem of Short-Term Load Forecast, by using different classes of state-of-the-art Recurrent Neural Networks. We test the reviewed models first on controlled synthetic tasks and then on different real datasets, covering important practical cases of study. We provide a general overview of the most important architectures and we define guidelines for configuring the recurrent networks to predict real-valued time series., Comment: Springer Briefs in Computer Science (ISBN 978-3-319-70338-1), 2017

In this work we present a novel recurrent neural network architecture designed to model systems characterized by multiple characteristic timescales in their dynamics. The proposed network is composed by several recurrent groups of neurons that are trained to separately adapt to each timescale, in order to improve the system identification process. We test our framework on time series prediction tasks and we show some promising, preliminary results achieved on synthetic data. To evaluate the capabilities of our network, we compare the performance with several state-of-the-art recurrent architectures.

Recent developments in integrated photonics technology are opening the way to the fabrication of complex linear optical interferometers. The application of this platform is ubiquitous in quantum information science, from quantum simulation to quantum metrology, including the quest for quantum supremacy via the boson sampling problem. Within these contexts, the capability to learn efficiently the unitary operation of the implemented interferometers becomes a crucial requirement. In this letter we develop a reconstruction algorithm based on a genetic approach, which can be adopted as a tool to characterize an unknown linear optical network. We report an experimental test of the described method by performing the reconstruction of a 7-mode interferometer implemented via the femtosecond laser writing technique. Further applications of genetic approaches can be found in other contexts, such as quantum metrology or learning unknown general Hamiltonian evolutions., Comment: 5 pages, 3 figures + 3 pages, 1 figure Supplementary Information

In this paper, we propose a novel data-driven approach for removing trends (detrending) from nonstationary, fractal and multifractal time series. We consider real-valued time series relative to measurements of an underlying dynamical system that evolves through time. We assume that such a dynamical process is predictable to a certain degree by means of a class of recurrent networks called Echo State Network (ESN), which are capable to model a generic dynamical process. In order to isolate the superimposed (multi)fractal component of interest, we define a data-driven filter by leveraging on the ESN prediction capability to identify the trend component of a given input time series. Specifically, the (estimated) trend is removed from the original time series and the residual signal is analyzed with the multifractal detrended fluctuation analysis procedure to verify the correctness of the detrending procedure. In order to demonstrate the effectiveness of the proposed technique, we consider several synthetic time series consisting of different types of trends and fractal noise components with known characteristics. We also process a real-world dataset, the sunspot time series, which is well-known for its multifractal features and has recently gained attention in the complex systems field. Results demonstrate the validity and generality of the proposed detrending method based on ESNs., Comment: Revised version

In this paper, we study long-term correlations and multifractal properties elaborated from time series of three-phase current signals coming from an industrial electric arc furnace plant. Implicit sinusoidal trends are suitably detected by considering the scaling of the fluctuation functions. Time series are then filtered via a Fourier-based analysis, removing hence such strong periodicities. In the filtered time series we detected long-term, positive correlations. The presence of positive correlations is in agreement with the typical V--I characteristic (hysteresis) of the electric arc furnace, providing thus a sound physical justification for the memory effects found in the current time series. The multifractal signature is strong enough in the filtered time series to be effectively classified as multifractal.

In this paper we present a generative model for protein contact networks. The soundness of the proposed model is investigated by focusing primarily on mesoscopic properties elaborated from the spectra of the graph Laplacian. To complement the analysis, we study also classical topological descriptors, such as statistics of the shortest paths and the important feature of modularity. Our experiments show that the proposed model results in a considerable improvement with respect to two suitably chosen generative mechanisms, mimicking with better approximation real protein contact networks in terms of diffusion properties elaborated from the Laplacian spectra. However, as well as the other considered models, it does not reproduce with sufficient accuracy the shortest paths structure. To compensate this drawback, we designed a second step involving a targeted edge reconfiguration process. The ensemble of reconfigured networks denotes improvements that are statistically significant. As a byproduct of our study, we demonstrate that modularity, a well-known property of proteins, does not entirely explain the actual network architecture characterizing protein contact networks. In fact, we conclude that modularity, intended as a quantification of an underlying community structure, should be considered as an emergent property of the structural organization of proteins. Interestingly, such a property is suitably optimized in protein contact networks together with the feature of path efficiency., Comment: 18 pages, 67 references

The multifractal detrended fluctuation analysis of time series is able to reveal the presence of long-range correlations and, at the same time, to characterize the self-similarity of the series. The rich information derivable from the characteristic exponents and the multifractal spectrum can be further analyzed to discover important insights about the underlying dynamical process. In this paper, we employ multifractal analysis techniques in the study of protein contact networks. To this end, initially a network is mapped to three different time series, each of which is generated by a stationary unbiased random walk. To capture the peculiarities of the networks at different levels, we accordingly consider three observables at each vertex: the degree, the clustering coefficient, and the closeness centrality. To compare the results with suitable references, we consider also instances of three well-known network models and two typical time series with pure monofractal and multifractal properties. The first result of notable interest is that time series associated to proteins contact networks exhibit long-range correlations (strong persistence), which are consistent with signals in-between the typical monofractal and multifractal behavior. Successively, a suitable embedding of the multifractal spectra allows to focus on ensemble properties, which in turn gives us the possibility to make further observations regarding the considered networks. In particular, we highlight the different role that small and large fluctuations of the considered observables play in the characterization of the network topology.

We propose a multi-agent algorithm able to automatically discover relevant regularities in a given dataset, determining at the same time the set of configurations of the adopted parametric dissimilarity measure yielding compact and separated clusters. Each agent operates independently by performing a Markovian random walk on a suitable weighted graph representation of the input dataset. Such a weighted graph representation is induced by the specific parameter configuration of the dissimilarity measure adopted by the agent, which searches and takes decisions autonomously for one cluster at a time. Results show that the algorithm is able to discover parameter configurations that yield a consistent and interpretable collection of clusters. Moreover, we demonstrate that our algorithm shows comparable performances with other similar state-of-the-art algorithms when facing specific clustering problems.

In this paper, we study the structure and dynamical properties of protein contact networks with respect to other biological networks, together with simulated archetypal models acting as probes. We consider both classical topological descriptors, such as the modularity and statistics of the shortest paths, and different interpretations in terms of diffusion provided by the discrete heat kernel, which is elaborated from the normalized graph Laplacians. A principal component analysis shows high discrimination among the network types, either by considering the topological and heat kernel based vector characterizations. Furthermore, a canonical correlation analysis demonstrates the strong agreement among those two characterizations, providing thus an important justification in terms of interpretability for the heat kernel. Finally, and most importantly, the focused analysis of the heat kernel provides a way to yield insights on the fact that proteins have to satisfy specific structural design constraints that the other considered networks do not need to obey. Notably, the heat trace decay of an ensemble of varying-size proteins denotes subdiffusion, a peculiar property of proteins.