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Register a new userDifferentiating resting brain states using ordinal symbolic analysis
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Symbolic methods of analysis are valuable tools for investigating complex time-dependent signals. In particular, the ordinal method defines sequences of symbols according to the ordering in which values appear in a time series. This method has been shown to yield useful information, even when applied to signals with large noise contamination. Here we use ordinal analysis to investigate the transition between eyes closed (EC) and eyes open (EO) resting states. We analyze two {EEG} datasets (with 71 and 109 healthy subjects) with different recording conditions (sampling rates and the number of electrodes in the scalp). Using as diagnostic tools the permutation entropy, the entropy computed from symbolic transition probabilities, and an asymmetry coefficient (that measures the asymmetry of the likelihood of the transitions between symbols) we show that ordinal analysis applied to the raw data distinguishes the two brain states. In both datasets, we find that the EO state is characterized by higher entropies and lower asymmetry coefficient, as compared to the EC state. Our results thus show that these diagnostic tools have the potential for detecting and characterizing changes in time-evolving brain states.
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We extracted and processed abstract data from the SFN annual meeting abstracts during the period 2001-2006, using techniques and software from natural language processing, database management, and data visualization and analysis. An important first step in the process was the application of data cleaning and disambiguation methods to construct a unified database, since the data were too noisy to be of full utility in the raw form initially available. The resulting co-author graph in 2006, for example, had 39,645 nodes (with an estimated 6% error rate in our disambiguation of similar author names) and 13,979 abstracts, with an average of 1.5 abstracts per author, 4.3 authors per abstract, and 5.96 collaborators per author (including all authors on shared abstracts). Recent work in related areas has focused on reputational indices such as highly cited papers or scientists and journal impact factors, and to a lesser extent on creating visual maps of the knowledge space. In contrast, there has been relatively less work on the demographics and community structure, the dynamics of the field over time to examine major research trends and the structure of the sources of research funding. In this paper we examined each of these areas in order to gain an objective overview of contemporary neuroscience. Some interesting findings include a high geographical concentration of neuroscience research in north eastern United States, a surprisingly large transient population (60% of the authors appear in only one out of the six studied years), the central role played by the study of neurodegenerative disorders in the neuroscience community structure, and an apparent growth of behavioral/systems neuroscience with a corresponding shrinkage of cellular/molecular neuroscience over the six year period.
Since Bandt and Pompes seminal work, permutation entropy has been used in several applications and is now an essential tool for time series analysis. Beyond becoming a popular and successful technique, permutation entropy inspired a framework for mapping time series into symbolic sequences that triggered the development of many other tools, including an approach for creating networks from time series known as ordinal networks. Despite the increasing popularity, the computational development of these methods is fragmented, and there were still no efforts focusing on creating a unified software package. Here we present ordpy, a simple and open-source Python module that implements permutation entropy and several of the principal methods related to Bandt and Pompes framework to analyze time series and two-dimensional data. In particular, ordpy implements permutation entropy, Tsallis and Renyi permutation entropies, complexity-entropy plane, complexity-entropy curves, missing ordinal patterns, ordinal networks, and missing ordinal transitions for one-dimensional (time series) and two-dimensional (images) data as well as their multiscale generalizations. We review some theoretical aspects of these tools and illustrate the use of ordpy by replicating several literature results.
We consider the evolution of a network of neurons, focusing on the asymptotic behavior of spikes dynamics instead of membrane potential dynamics. The spike response is not sought as a deterministic response in this context, but as a conditional probability : Reading out the code consists of inferring such a probability. This probability is computed from empirical raster plots, by using the framework of thermodynamic formalism in ergodic theory. This gives us a parametric statistical model where the probability has the form of a Gibbs distribution. In this respect, this approach generalizes the seminal and profound work of Schneidman and collaborators. A minimal presentation of the formalism is reviewed here, while a general algorithmic estimation method is proposed yielding fast convergent implementations. It is also made explicit how several spike observables (entropy, rate, synchronizations, correlations) are given in closed-form from the parametric estimation. This paradigm does not only allow us to estimate the spike statistics, given a design choice, but also to compare different models, thus answering comparative questions about the neural code such as : are correlations (or time synchrony or a given set of spike patterns, ..) significant with respect to rate coding only ? A numerical validation of the method is proposed and the perspectives regarding spike-train code analysis are also discussed.
EEG is a non-invasive technique for recording brain bioelectric activity, which has potential applications in various fields such as human-computer interaction and neuroscience. However, there are many difficulties in analyzing EEG data, including its complex composition, low amplitude as well as low signal-to-noise ratio. Some of the existing methods of analysis are based on feature extraction and machine learning to differentiate the phase of schizophrenia that samples belong to. However, medical research requires the use of machine learning not only to give more accurate classification results, but also to give the results that can be applied to pathological studies. The main purpose of this study is to obtain the weight values as the representation of influence of each frequency band on the classification of schizophrenia phases on the basis of a more effective classification method using the LES feature extraction, and then the weight values are processed and applied to improve the accuracy of machine learning classification. We propose a method called weight-voting to obtain the weights of sub-bands features by using results of classification for voting to fit the actual categories of EEG data, and using weights for reclassification. Through this method, we can first obtain the influence of each band in distinguishing three schizophrenia phases, and analyze the effect of band features on the risk of schizophrenia contributing to the study of psychopathology. Our results show that there is a high correlation between the change of weight of low gamma band and the difference between HC, CHR and FES. If the features revised according to weights are used for reclassification, the accuracy of result will be improved compared with the original classifier, which confirms the role of the band weight distribution.
Approaches for mapping time series to networks have become essential tools for dealing with the increasing challenges of characterizing data from complex systems. Among the different algorithms, the recently proposed ordinal networks stand out due to its simplicity and computational efficiency. However, applications of ordinal networks have been mainly focused on time series arising from nonlinear dynamical systems, while basic properties of ordinal networks related to simple stochastic processes remain poorly understood. Here, we investigate several properties of ordinal networks emerging from random time series, noisy periodic signals, fractional Brownian motion, and earthquake magnitude series. For ordinal networks of random series, we present an approach for building the exact form of the adjacency matrix, which in turn is useful for detecting non-random behavior in time series and the existence of missing transitions among ordinal patterns. We find that the average value of a local entropy, estimated from transition probabilities among neighboring nodes of ordinal networks, is more robust against noise addition than the standard permutation entropy. We show that ordinal networks can be used for estimating the Hurst exponent of time series with accuracy comparable with state-of-the-art methods. Finally, we argue that ordinal networks can detect sudden changes in Earth seismic activity caused by large earthquakes.
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