Improving clustering by imposing network information

See allHide authors and affiliations

Science Advances  07 Aug 2015:
Vol. 1, no. 7, e1500163
DOI: 10.1126/sciadv.1500163


Cluster analysis is one of the most popular data analysis tools in a wide range of applied disciplines. We propose and justify a computationally efficient and straightforward-to-implement way of imposing the available information from networks/graphs (a priori available in many application areas) on a broad family of clustering methods. The introduced approach is illustrated on the problem of a noninvasive unsupervised brain signal classification. This task is faced with several challenging difficulties such as nonstationary noisy signals and a small sample size, combined with a high-dimensional feature space and huge noise-to-signal ratios. Applying this approach results in an exact unsupervised classification of very short signals, opening new possibilities for clustering methods in the area of a noninvasive brain-computer interface.

  • time series analysis
  • finite element method
  • unsupervised classification
  • clustering
  • graph
  • Network
  • regularization
  • EEG
  • Neuroscience


Clustering can be considered as one of the most important learning and data analysis methods in a large variety of applied disciplines. The general aim of clustering is in assigning a set of objects into groups, such that the degree of association—the “similarity”—becomes maximized between members of the same group/cluster and minimized between members of different groups/clusters. The concept of similarity is—in most cases—realized via a distance function on the data space. A wide variety of different algorithms have been developed for special topics, each of them based on a diverse notion of what constitutes a cluster, thus using different induction principles for the clustering procedures. Consequently, the application of even slightly different algorithms may result in very deviating outcomes, even applied to the same data under the same conditions (14). Because the choice of “the best possible” clustering algorithm highly depends on the individual data set and the intended use of the results, clustering algorithms are developing just as dynamically as technical capabilities are evolving. In particular, the new possibilities offered by high-performance computing technologies give rise to exciting advances in the ability of researchers to use cluster modeling to analyze huge and complete data sets, from climate/weather research (5, 6), economics and finance (7, 8), computational biology, biophysics/bioinformatics (9, 10), and neuroscience (11, 12).

Most often in data analysis, the available information is only a series of U (experimental) observations X = x(1), …, x(U), without a detailed knowledge about the underlying model x(u) = f (θ(u)) and its parameters θ(u). Inference of the “optimal” parameters in a wide range of data analysis approaches is mostly achieved by minimizing the appropriate fitness function:Embedded Image(1)It is measuring the quality of the model for describing the given data sequence X by calculating the sum of distances g(x(u), θ(u)) between the model’s prediction [obtained from the parameter values θ(u)] and the analyzed data x(u). However, if only one data sequence X is available and the parameter θ is allowed to change with u in an arbitrary way, the respective minimization problem will simply not have enough data X to estimate all of the values of θ(u) and will result in what is called “overfitting.”

Assuming Embedded Image (with Embedded Image and γi(u) ≥ 0 for all i and u), clustering algorithms can also be formulated and implemented as a minimization with respect to (wrt.) Θ = (θ1, …, θK) and Γ = (γ1, …, γK) of the so-called clustering functional Lα, taking the form (13, 14):Embedded Image(2)where T is a vector transposition operation, {gi}u = g(x(u), θi) are the row vectors of cluster distances, {γi}u = γi(u) are the row vectors of cluster affiliations [that is, γi(u) is the probability for data point u to be from cluster i], and α ≥ 1 is a fixed scalar exponent called the fuzzyfier (14, 15), allowing for the assignment of observed data points to more than one cluster (soft clustering) if α > 1.

It can be demonstrated (please see section 1 in the Supplementary Text for a detailed proof) that Lαl, that is, that a wide range of clustering algorithms in their minimizational formulation (Eq. 2) represent methods for minimizing the upper bound Lα of the more general fitness function l. This means that by doing clustering, one is implicitly finding an approximate piecewise homogeneous solution of the more general and heterogeneous (that is, with parameters θ being dependent on u) data analysis problem (Eq. 1).

Most of the existent clustering methods can be formulated as the optimization of Eq. 2, differing only in the choices of α and the distance function g(x(u), θi). If, for example, α = 1 and g(x(u), θi) = ||x(u) − θi||2, then minimization of Eq. 2 is the task performed by the classical k-means algorithm (16). Also, other classical methods of data analysis and machine learning (for example, multilinear statistical regression, Gaussian mixture models, and hidden Markov models) can be derived as special cases of the above optimizational formulation by choosing specific model distance functions and additional constraints (16). In other words, clustering can be treated as an inverse problem that can become expressed and solved as a minimization—or a maximization—problem.

Computationally, the procedure of finding a minimum of Lα wrt. Θ and Γ in all of the clustering algorithms is implemented iteratively, by a consecutive repetition of the two following steps:

View this table:

It is straightforward to verify that for any initial choice of Γ or Θ, iterative repetition of these two steps will lead to a monotonic minimization of Lα and convergence to some local minimum of Lα (13). The obtained final estimates of Γ and Θ for different local minima can then be compared with respect to their values of Lα to identify the most optimal clustering of the data sequence X - corresponding to the smallest value of the respective clustering functional from Eq. 2.

One of the central problems of virtually all state-of-the-art clustering approaches lies in the fact that the related optimization problem is generally nonconvex (may have various local minima) and nonrobust or, in mathematical terms, ill-posed, meaning that tiny changes in the start conditions or in the tuning parameters of the algorithm might result in large changes in the answer. As mentioned above, the latter issue may arise due to the high number of unknowns in relation to the known parameters. Therefore, the results may heavily depend on the choice of the initialization, or tuning parameter sets, thus involving the risk of overfitting and frequently making the clustering results nonreproducible even on the same computer with the same set of user-defined tuning parameters (16).

This drawback becomes even more apparent when dealing with high-dimensional data, where most of the existing methods can fail due to the various problems of popular distance metrics deployed in clustering algorithms. To overcome the above-mentioned issue of nonrobustness, a frequently deployed strategy is to add some additional information or assumptions to the problem. In mathematical terms, this strategy is called regularization. Herewith, the nonrobust problem can be transformed into a robust one (17). Tikhonov regularization (18) and LASSO regularization (19) are prominent examples in the context of, for example, spline interpolation and parametric regression problems in data analysis and statistics.


The central methodological contribution of this manuscript is in finding and justifying a computationally efficient and easy-to-implement way of imposing additional information—given in the form of a graph or a network—on clustering algorithms.

The main idea is based on the insight that the data index u can be brought in a relation to the respective node in some network or graph G = (E, V ), with edges E and vertices V, U = |V|. This graph G is equipped with some graph-related variation measure ||θ(·)||G, for example, with Embedded Image squared Euclidean norm of the parameter θ variation on the graph G. In this expression, W is a matrix of weights, with elements Wu,v being, for example, inverse-proportional to the Euclidean length of a minimal path connecting vertices u and v on the graph G. This graph G and the variation measure ||·||G are assumed to be underlying the measurement process and to be known a priori.

Then, inserting the clustering assumption Embedded Image from above into ||θ(·)||G, we obtainEmbedded Image(3)where Embedded Image is some (unknown) constant, ||θi|| is a Euclidean norm for cluster parameters θi and DG = P − 2W + Q (with diagonal matrices Puu ≡ Σv|(v,u)∈E Wv,u and Quu ≡ Σv|(u,v)∈E Wu,v; please see chapter 1.2 of the Supplementary Text for a detailed derivation). To give a concrete example, when dealing with problems of time series analysis, index u is denoting the time index of every particular data point, and the underlying graph G is a linear graph shown in Fig. 1A. Then, kernel weight W can be defined as Wu,v = 1 (for ||uv|| = 1) and Wu,v = 0 (for ||uv|| ≠ 1), and the resulting DG will be a tridiagonal positive semidefinite symmetric Laplacian matrix. This case will be particularly important in a context of time series clustering methods considered below.

Fig. 1 An example of the imposed network and a cluster model discrimination.

(A) Imposed (linear) graph: a priori persistency assumption for the underlying dynamics in time. (B) Comparing information content of EEG clusterings: graphs of the AIC values for K = 1 to 3 as a function of the regularization constant ϵ2.

Deploying Eq. 3 as an additional constraint in the minimization of the original clustering problem (Eq. 2), one gets a possibility of a “guided” search for parameters θ(·)—based on their differences measured in terms of the a priori available graph/network information G. More specifically, choosing large values of Embedded Image will result in those possible solutions of the original clustering problem that are very different wrt. parameters θ on the neighboring nodes of the graph G. Decreasing the value of Embedded Image will provide parameters that are more and more “close” in terms of the a priori available information G. Finally, setting Embedded Image to zero will result in stationary/homogeneous estimates, that is, in the parameters θ that are equal for all of the graph G nodes and, thereby, for all of the data points u. Formulated as an additional assumption, Eq. 3 basically means that we expect any two different nodes u and v of the graph G (that are not “too far away” from each other in a sense of the underlying graph distance measure) to have not “too different” values of unknown parameters θ(u) and θ(v).

It turns out that from numerical/computational points of view, instead of directly deploying Eq. 3 as an additional inequality constraint, it is more advantageous to use its equivalent formulation—when the confined term from Eq. 3 is added as a penalty term to the original clustering problem formulation (Eq. 2):Embedded Image(4)and subject to the original constraints Embedded Image, γi ≥ 0. Penalty factor ϵ2 can then be interpreted as the level of our confidence in the a priori network/graph information G: if ϵ2 is large, then the impact of the a priori information on the overall solution will be strong; if ϵ2 is very small or zero, then we essentially solve the original clustering problem (Eq. 2) and information about G does not play any significant role. Systematic strategies for automated and user-independent choice of ϵ2 and K will be introduced below.

The main theoretical/conceptual advantage of this problem formulation (Eq. 4) can be revealed after making an observation that the right-hand side of the obtained functional is essentially a log-likelihood formulation of the Bayes theorem: with the second term being a log-likelihood of the prior distribution in the space of clustering parameters (that becomes Gaussian if one fixes either Γ or Θ) and with the first term keeping the form of the original clustering functional (Eq. 2) as a posterior log-likelihood [It is interesting to observe that the direct application of Bayes theorem to the original clustering problem (Eq. 2), assuming the independence of Γ or Θ and a priori Gaussianity for both of them, would result in two separate quadratic terms for Θ and for Γ in the right-hand side of Eq. 4, that is, in Embedded Image. In contrast, we obtain a fourth-order log-likelihood term that is derived from an assumption (Eq. 3) and does not require or impose a priori conditional independence of Γ and Θ.]. In another words, increasing the value of the user-defined tunable parameter ϵ2 would decrease the variance/uncertainty of cluster parameters Γ or Θ, making this transformed clustering problem well posed and robust, that is, less and less dependent on small changes of algorithmic parameters and on fluctuations in the analyzed data X.

Moreover, it is straightforward to validate (please see chapter 2 of the Supplementary Text for the detailed derivation) that this regularized clustering problem represents an upper bound for problems 1 and 2.Embedded Image(5)that is, the ill-posed data analysis problem (Eq. 1) (and the clustering problem in Eq. 2) can be both approximately solved through a minimization of the well-posed problem (Eq. 4).

The transformed problem (Eq. 4) can now be solved by a slight modification of the classical clustering algorithm explained above:

View this table:

It is easy to prove that the iterative repetition of these two convex minimization steps will monotonically converge to a local minimum of Lϵ,α.

Step ii of this modified clustering algorithm represents the main computational bottleneck because it requires a numerical solution of a large QP problem. If the a priori graph/network information is available in the form of an undirected graph G, the corresponding matrices DG will be symmetric. If DG are also sparse, then we can take advantage of the highly efficient linear solvers for sparse banded matrices implemented, for example, in high-performance software libraries such as (Sca)LAPAK (20, 21) or FLAME (22). However, the computational complexity in this case will still scale as Embedded Image(Up) (with p > 2), limiting the overall applicability of this methodology to relatively small data sets.

By deploying the method of Lagrange multipliers, it can be shown that in a particular case of hard clustering (that is, when α = 1), one can find an explicit analytical solution of this problem:Embedded Image(6)that also satisfies the optimization constraints γi ≥ 0 and Σi γi = 1. Please see chapter 3 of the Supplementary Text for a detailed derivation of this solution.

This result (Eq. 6) is particularly important in the context of the so-called finite element method family of time series clustering methods with bounded variation of the model parameters (FEM-BV) (23, 24). This method family represents a special case of the introduced graph-regularized clustering framework, when the underlying graph is linear (representing the time axis) with graph distances only being localized to consider/measure the nearest neighbor interactions in time. In this situation, the graph distance matrix DG will be a Laplacian matrix, that is, it will be tridiagonal and positive-semidefinite, meaning that its inverse can be expressed analytically—through the eigenvectors and eigenfunctions of Laplace operator in one dimension. This result allows to reduce the overall computational complexity of step ii in FEM-BV clustering methods from Embedded Image(Up) (with p > 2) to Embedded Image(U). The inverse of DG in this tridiagonal case can be analytically precomputed once and then reused with Eq. 6 every time when step ii of the FEM-BV clustering is performed. This resolves the main current computational bottleneck of the FEM-BV methods of the time series analysis, allowing us to address the analysis of a much longer time series than what is currently possible with these methods.

Choosing an optimal setting for the clustering algorithm

Because the outcome of clustering is highly dependent on the specific choice of the number of clusters K, regularization constant ϵ2, and fuzzier α (as well as on the choice of the distance measure on the graph G), another challenge is in choosing all of these parameters and settings in some “optimal” way. Several ways of choosing optimal clustering parameters have been discussed in the literature (23, 24). In the situations when the distance function g can be interpreted in the probabilistic sense—for example, as a log-likelihood of some distribution—information criteria can be used to identify/discriminate the optimal parameter setting for clustering algorithms (16, 25). This is done in a sense of “Occam’s razor” principle: information-theoretic tools such as Akaike (AIC) and Bayes information criteria can be used to find the clusterings that are simultaneously most qualitative (in terms of minimizing the value of L in Eq. 2 or 4) and simple (in terms of the low number of clusters and/or other tunable parameters). However, this information-theoretic approach is limited to situations when g has an explicit probabilistic interpretation, that is, has a form of the parametric (for example, Gaussian) log-likelihood. It is not the case in situations when g simply measures some geometric distance (for example, an Euclidean distance between the points for standard k-means clustering) that is not a priori-interpretable as some log-likelihood associated with some assumed parametric probability measure (for example, Gaussian). In (16), it was presented how to select the optimal clustering models in a non-parametric way, without a priori parametric probabilistic assumptions on underlying measures. As was demonstrated in information theory (26), nonparametric exponential distributions represent the family of maximum entropy distributions for the given scalar valued process time series. That is, max log-likelihood fitting of these exponential distributions to the available data would result in the posterior identification of the most likely and least-biased (that is, the simplest) random process that has the highest affinity to produce such an output as the one that is observed. The main idea of the respective nonparametric model selection approach is based on the posterior maximum log-likelihood fitting of a sequence of such nonparametric exponential family distributionsEmbedded Image(7)(for various k) to the scalar sequence of the posterior clustering model errors Embedded Image, obtained from regularized clustering problem (Eq. 4) for various combinations of ϵ, K, α. Then, the log-likelihood of the identified nonparametric process (Eq. 7) can be plugged into the information criterion to obtain the most informative model. This modified AIC (mAIC) [please see section 3 of (16) for more details] will be, in the following text, applied to compare different clustering results and to identify the optimal combination of clustering parameters K, k, ϵ2, and α, resulting in the procedure that is free of any user-defined tunable parameters.

Application example

As explained in Materials and Methods, the FEM-BV family of time series clustering methods represents a particular case of the introduced graph-regularized clustering methodology, with the graph G being a linear graph and matrix DG being tridiagonal. Application of the methodology in this situation to various test systems, comparison to standard clustering methods, and machine learning approaches can be found, for example, in the review paper (16).

In the following text, we illustrate the potential of the presented methodology for time series analysis (that is, imposing the linear graph G as in the case of FEM-BV methods) and exploiting the new possibilities provided by the formulation (Eq. 4) and, especially, by the obtained analytical solution (Eq. 6). We consider analysis and unsupervised classification of electroencephalography (EEG) data—an application area with currently very limited use of unsupervised approaches such as clustering. For example, EEG data analysis in the rapidly developing area of brain-computer interface (BCI) (27, 28) is usually performed by (semi-)supervised methods such as independent component analysis (ICA), linear discriminant analysis (LDA), support vector machines (SVMs), decision trees, or artificial neural networks (ANN) [for review, please see (2931)]. The BCI technology enables people to communicate with their environment or to activate and control certain devices solely by using the brain’s neural activity. Herewith, it opens a perspective for restoring motor ability or communication to severely disabled and paralyzed people as well as for ill individuals who experience significant physical limitations such as amyotrophic lateral sclerosis, locked-in syndrome, or other severe neuromuscular disorders (3234). The benefits and accuracy of such a prosthetic system in the so-called noninvasive setting, however, heavily depend on correct recognition of patterns within the recorded signal as well as an unerring classification of the executed signals. This task is hampered by serious challenges: in contrast to the excellent (millisecond) temporal resolution of EEG, the spatial information of the neuronal activity is rather poor (resolution of centimeters).

The observable information, the so-called electroencephalogram, is the summed activity of about 106 to 108 neurons lying in the vicinity of the electrodes (35) being recorded and condensed by a comparatively tiny number of electrodes (normally between 64 and 128). This signal is also characterized by a poor signal-to-noise ratio and high uncertainty because scull, skin, and hair are damping and skewing the electromagnetic waves (36). Furthermore, the measured signal reflects both the intrinsic neuronal activity within the cerebral cortex as well as the nerve impulses received from subcortical structures and the sense receptors. Such a signal is by its nature nonstationary and nonlinear, which makes the analysis and classification of the underlying signal patterns very difficult. Systematically missing data and unresolved scales may result in a problem of nonstationarity (37, 38), which may lead to biased results when using the most common state-of-the-art classifiers in BCI research (ICA, LDA, SVMs, or ANN) that are all based on some form of intrinsic stationarity assumptions (38, 39).

Although a wide range of these classifiers have been successfully applied to several important problems such as the noninvasive identification of epileptic patterns, almost all of the classifications of (imaginary) left/right hand or foot movements, or classification of emotions (2931), given the inter- and intrapersonal variations in EEG as well as the poor signal-to-noise ratio—require very long data sets for the initial training to obtain satisfactory performance. In addition, from the mathematical/computational perspective, they are based on a priori assumptions concerning the distance metric (mostly chosen to be Euclidean) and/or the probabilistic assumptions (for example, Gaussianity and independence). In practical applications, however, there is no guarantee that these necessary assumptions can be fulfilled a priori. For this purpose, as a practical illustration of the clustering methodology is introduced in this article, we are presenting a way of using nonparametric clustering approaches to enable classification of high-dimensional experimental EEG data without initial training or a priori probabilistic assumptions on the nature of the data. As will be demonstrated below on a particular set of EEG data, this procedure leads to a very accurate unsupervised classification of very short nonstationary and noisy EEG signals.

As a data source, we take the EEG Motor Movement/Imagery Dataset from (40), which was created using the BCI2000 instrumentation system (28) ( This data set consists of more than 1500 1- and 2-min EEG recordings obtained from 109 volunteers. Subjects performed different motor/imagery tasks while 64-channel EEG activity was recorded with electrodes positioned according to the international 10-10 system. Each subject performed—besides other experimental runs—the two 1-min baseline runs (one with eyes opened, one with eyes closed) when the basic activity of the brain is being measured. In the following, we will only focus on these baseline measurements. These measurements for opened and closed eyes are similar to such an extent that standard unsupervised methods (as will be seen later) are not able to distinguish between them.

The experiment is undertaken as follows: the subject (without any external disturbance) is sitting for 1 min with closed eyes and for another minute with opened eyes. Each of the two investigated experiments (baseline “eyes opened” and baseline “eyes closed”) has 64 dimensions (due to the 64 electrodes), with U = 9760 measurements per minute (which makes a demand interval of about 160 Hz). Thus, for every experimental run, we have to deal with a matrix in R64×U. To ensure the comparability of different EEG data sets and applicability of Euclidean distance measure, a series of preprocessing steps (including differencing, embedding, and dimension reduction of the embedded signal) has been performed (please see the section “Preprocessing” in the Supplementary Text for the explicit description of the data preprocessing protocol). For a distance measure g to be deployed in the clustering, we choose a measure associated with the principal components analysis (PCA), that is, the Euclidean distanceEmbedded Imagebetween the n-dimensional data points x(u) and their orthogonal projections on the d-dimensional (d < n) locally linear manifold ΘiRn×d correspondent to the cluster i. For more details on PCA-induced clustering, please refer to (16, 23). Next, we choose an appropriate initial information/assumptions that can be imposed on the clustering of the EEG data. We choose a very mild assumption that the underlying essential dynamics (captured as the temporal change of the low-dimensional manifold Embedded Image) is a persistent and slowly varying process in time. Then, the a priori graph G is a linear time graph, and a matrix of weights W can be chosen, for example, as Embedded Image (with σ < 0, please see Fig. 1A).


We tested the methodology for this particular choice of distance measure g and weight matrix W with the first 20 subjects of the original data set. We achieved an exact and unsupervised classification of opened and closed eyes measurements for all of the cases with the measurement fragments that were down to 7 seconds short. We will show exemplarily results for the subject Nr. 1. Figure 1B demonstrates the mAIC curves for models with K = 1, 2, 3 clusters as a function of the regularization constant ϵ2. The overall minimum is attained at the position K = 2, ϵ2 ≥ 105. As can be seen from Fig. 1B, from the viewpoint of information theory, the optimal solution of clustering problems obtained with standard unregularized clustering methods (such as k-means and hierarchical clustering algorithms) is attained for K = 1, and allows no distinction between the two states (that is, between opened and closed eyes), and is inferior in terms of information contents to the solution of the regularized problem (Eq. 4) for a given set of data. By introducing regularization, the overall minimum is attained with two clusters (K = 2), where one cluster only corresponds to the opened eyes and the second to the closed. Both experiments are correctly classified to their respective manifolds and can be visualized by plotting the cluster affiliation function γ for the optimal result (please see fig. S1). The two identified attractive manifolds—each of which is characteristic for one experiment—can be visualized by plotting the first three dimensions (out of the 300 most significant dimensions) that were detected during the data reprocessing via PCA. Figure 2 gives an impression of the dynamics of the two systems in phase space. Both dynamic systems are essentially nonlinear oscillators. Although they behave similarly, one can see that the orientation of the planes in which the oscillations take place is different. These principal attractor manifolds are approximated and distinguished via linear projectors Θi deployed in our PCA-based regularized clustering procedure. However, because the dynamics are geared into each other, standard algorithms are incapable of correctly solving this clustering problem. This result demonstrates that deploying the manifold-based clustering combined with a priori persistency assumption for the underlying dynamics allows us to use the respective structure of the manifold as a classifier to determine whether the unlabeled short measurement belongs to a subject with opened or closed eyes. New data can be projected on the manifolds and (by means of proximity) assigned to one of them. Standard PCA clustering [with Embedded Image but without the graph-induced regularization] was, in contrast, not able to detect the two manifolds and proposed a common basis manifold for the two situations. That is, graph-induced regularization introduced in this paper appears to be essential for the correct unsupervised classification of these data sequences.

Fig. 2 Visualization of the two identified manifolds.

Revealing the essential spatiotemporal dynamics

With the help of the identified manifolds and their affiliated eigenvectors (constituting the columns of cluster projector matrices Θi), essential components of the underlying dynamical system can now be extracted from the available short, nonstationary, and noisy EEG time series. For this purpose, the experimental data are projected on the identified linear attractor manifolds Θi. Spectral analysis for the embedded projections of original EEG data on the dominant manifold dimensions (that is, on different columns of Θi as resulting from the regularized clustering) reveals the well-known α, β, γ, and μ waves of the brain (please see fig. S2). In contrast to the standard procedures of obtaining these signals (that involve a very long measurement series and a careful selection of points on the head where these measurements are performed), in the context of the presented methodology, these brain waves can be obtained from the full original EEG with a very short (down to 7 seconds) measurement length. In the next step, we are going to examine the spatiotemporal dynamics of these brain wave patterns. For this purpose, the snapshots of eigenvectors are visualized over a schematic representation of the head (indicating the positions and numbers of electrodes according to the international 10-10 system). Because of the embedding during the preprocessing, this visualization of embedded eigenvectors (representing the dominant manifold components) results in spatiotemporal animations of the essential dimensions of the underlying dynamics that can be extracted from the two identified clusters. A selection of these animations is provided as movies S1 to S8. A couple of snapshots from movies S1 (animating the most dominant attractor dimension for the experiment with opened eyes) and S2 (animating the most dominant attractor dimension for the experiment with closed eyes) are exemplarily presented in Fig. 3. The left column of Fig. 3 presents a series of snapshots taken from movie S1. These snapshots capture the dynamics in the most dominant manifold dimension (that is, the first column of the obtained Θi in the respective cluster) for the experiment with opened eyes. This dominant dynamics—a spatiotemporal oscillation—takes place in the anterior part of the brain: most evident frontally and propagating into the central (and even posterior) regions of the brain. These spatial characteristics (together with the observation of fig. S2) allow to conclude that the observed dominant pattern reflects a combination of rhythmical β activity [which is usually encountered over the frontal and central brain regions (41)] and γ waves [mainly observed in the visual cortex (42, 43)]. Furthermore, the movie reveals that the main spatiotemporal dynamics for the EEG with opened eyes can be explained by a traveling wave oscillating between the frontal and the posterior regions of the brain. This dynamic is hidden in the very noisy EEG signal and can be uncovered by the presented cluster analysis methodology.

Fig. 3 Snapshots of the spatiotemporal dynamics of the most dominant eigenvectors.

(A, C, E, and G) Several time instances of the extracted dominant wave pattern for the EEG with opened eyes. (B, D, F, and H) Snapshots for the dominant EEG pattern with closed eyes at the same time points. Red color stands for the positive component of the oscillation, and blue color for the negative component. Snapshots are taken in both experiments at time points t = 0.0 s (A and B), 0.018443 s (C and D), 0.043033 s (E and F), and 0.061475 s (G and H).

Entirely different dominant spatiotemporal dynamics are revealed in the situation with closed eyes (right column of Fig. 3): the oscillations are clearly located in the posterior half of the head only propagating to a minor degree into central areas (please see in addition movie S2 for the full animation). This pattern may be dedicated to the α rhythm, which is usually found over occipital, parietal, and posterior temporal regions of the brain (41, 44). The animations of higher components (4, 7, and 10) for both experiments are provided by additional movies S3 to S8.

Concluding discussion

We have presented a methodology for imposing a priori graph/network information on clustering algorithms. The theoretical justification of this approach was presented, based on the derivation of a generalized graph/network-related regularization strategy, proving that it allows us to find the approximate solutions of various heterogeneous data analysis problems through upper-bound minimization and obtaining a particular analytic solution (Eq. 6). This thereby resolves a main computational bottleneck of a large family of time series clustering algorithms. The introduced approach is neither in competition with the various existing clustering methods nor is it just “yet another clustering method.” As demonstrated above, presented methodology can be implemented as a very straightforward modification of the existent clustering algorithms for solving unsupervised and nonparametric classification problems.

When applying this approach to different EEG data sets, it was shown that combining the new methodology with Taken’s theorem, data embedding, and PCA-related clustering, one can achieve the exact unsupervised classification of very short unlabeled EEG sequences. Standard clustering methods without regularization (for example, k-means, spectral clustering, and hierarchical clustering) were not able to differentiate between the two situations and suggested a common model/cluster, thus excluding the possibility for the unsupervised classification of the analyzed data. The introduced methodology operated as an exact classifier and detected two distinct clusters as the best model—each of which associated with only one of the two states. Furthermore, it was exemplified how the obtained results can be used to extract the dominant spatiotemporal dynamic patterns which are otherwise hidden in very noisy nonstationary signals. We also investigated the possibility of using the identified manifolds from one subject’s EEG to classify the signal in the EEG of another subject. However, results differ significantly across probands, implying that the analysis must be uniquely performed separately for each individual.

The presented general framework for graph-induced regularization of clustering problems is expected to become helpful in the areas where the already collected information can be represented as a graph and deployed to increase the quality of clustering results. For example, this may be done in the areas of bioinformatics (where the a priori information is put together in the form of a so-called gene ontology graph) or in geoscience (where the prior notion about scaling cascades and self-similarity can be represented as directed graphs, giving a possibility to deploy them in cluster analysis of geophysical data). A brief overview and classification of the clustering methods that can potentially profit from this methodology are given within the section “Classification of the clustering algorithms” in the Supplementary Text.


Supplementary material for this article is available at


Movie S1. Visualization of the most dominant attractor dimension over a schematic representation of the head (indicating the positions and numbers of electrodes according to the international 10-10 system) for the experiment with opened eyes.

Movie S2. Visualization of the most dominant attractor dimension over a schematic representation of the head (indicating the positions and numbers of electrodes according to the international 10-10 system) for the experiment with closed eyes.

Movie S3. Visualization of fourth eigenvector over a schematic representation of the head (indicating the positions and numbers of electrodes according to the international 10-10 system) for the experiment with opened eyes.

Movie S4. Visualization of the fourth eigenvector over a schematic representation of the head (indicating the positions and numbers of electrodes according to the international 10-10 system) for the experiment with closed eyes.

Movie S5. Visualization of the seventh eigenvector over a schematic representation of the head (indicating the positions and numbers of electrodes according to the international 10-10 system) for the experiment with opened eyes.

Movie S6. Visualization of the seventh eigenvector over a schematic representation of the head (indicating the positions and numbers of electrodes according to the international 10-10 system) for the experiment with closed eyes.

Movie S7. Visualization of the 10th eigenvector over a schematic representation of the head (indicating the positions and numbers of electrodes according to the international 10-10 system) for the experiment with opened eyes.

Movie S8. Visualization of the 10th eigenvector over a schematic representation of the head (indicating the positions and numbers of electrodes according to the international 10-10 system) for the experiment with closed eyes.

Fig. S1. Cluster affiliation function for the two identified manifolds.

Fig. S2. Spectrograms of the EEG data.

References (4584)

This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license, which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited.


Acknowledgments: Both authors contributed equally to this study. Funding: The work of S.G. and I.H. is partly funded by the Swiss National Research Foundation (grant 200021 152979), Swiss Platform for Advanced Scientific Computing, and German Research Foundation (“Mercator Fellowship” of I.H. in the CRC 1114 “Scaling Cascades in Complex Systems”). Competing interests: The authors declare that they have no competing interests.
View Abstract

Stay Connected to Science Advances

Navigate This Article