On Recursive Edit Distance Kernels with Application to Time Series Classification

This paper proposes some extensions to the work on kernels dedicated to string or time series global alignment based on the aggregation of scores obtained by local alignments. The extensions we propose allow to construct, from classical recursive definition of elastic distances, recursive edit distance (or time-warp) kernels that are positive definite if some sufficient conditions are satisfied. The sufficient conditions we end-up with are original and weaker than those proposed in earlier works, although a recursive regularizing term is required to get the proof of the positive definiteness as a direct consequence of the Haussler's convolution theorem. The classification experiment we conducted on three classical time warp distances (two of which being metrics), using Support Vector Machine classifier, leads to conclude that, when the pairwise distance matrix obtained from the training data is \textit{far} from definiteness, the positive definite recursive elastic kernels outperform in general the distance substituting kernels for the classical elastic distances we have tested.Comment: 14 page

Discrete Elastic Inner Vector Spaces with Application in Time Series and Sequence Mining

This paper proposes a framework dedicated to the construction of what we call discrete elastic inner product allowing one to embed sets of non-uniformly sampled multivariate time series or sequences of varying lengths into inner product space structures. This framework is based on a recursive definition that covers the case of multiple embedded time elastic dimensions. We prove that such inner products exist in our general framework and show how a simple instance of this inner product class operates on some prospective applications, while generalizing the Euclidean inner product. Classification experimentations on time series and symbolic sequences datasets demonstrate the benefits that we can expect by embedding time series or sequences into elastic inner spaces rather than into classical Euclidean spaces. These experiments show good accuracy when compared to the euclidean distance or even dynamic programming algorithms while maintaining a linear algorithmic complexity at exploitation stage, although a quadratic indexing phase beforehand is required.Comment: arXiv admin note: substantial text overlap with arXiv:1101.431

Graphs in machine learning: an introduction

Graphs are commonly used to characterise interactions between objects of interest. Because they are based on a straightforward formalism, they are used in many scientific fields from computer science to historical sciences. In this paper, we give an introduction to some methods relying on graphs for learning. This includes both unsupervised and supervised methods. Unsupervised learning algorithms usually aim at visualising graphs in latent spaces and/or clustering the nodes. Both focus on extracting knowledge from graph topologies. While most existing techniques are only applicable to static graphs, where edges do not evolve through time, recent developments have shown that they could be extended to deal with evolving networks. In a supervised context, one generally aims at inferring labels or numerical values attached to nodes using both the graph and, when they are available, node characteristics. Balancing the two sources of information can be challenging, especially as they can disagree locally or globally. In both contexts, supervised and un-supervised, data can be relational (augmented with one or several global graphs) as described above, or graph valued. In this latter case, each object of interest is given as a full graph (possibly completed by other characteristics). In this context, natural tasks include graph clustering (as in producing clusters of graphs rather than clusters of nodes in a single graph), graph classification, etc. 1 Real networks One of the first practical studies on graphs can be dated back to the original work of Moreno [51] in the 30s. Since then, there has been a growing interest in graph analysis associated with strong developments in the modelling and the processing of these data. Graphs are now used in many scientific fields. In Biology [54, 2, 7], for instance, metabolic networks can describe pathways of biochemical reactions [41], while in social sciences networks are used to represent relation ties between actors [66, 56, 36, 34]. Other examples include powergrids [71] and the web [75]. Recently, networks have also been considered in other areas such as geography [22] and history [59, 39]. In machine learning, networks are seen as powerful tools to model problems in order to extract information from data and for prediction purposes. This is the object of this paper. For more complete surveys, we refer to [28, 62, 49, 45]. In this section, we introduce notations and highlight properties shared by most real networks. In Section 2, we then consider methods aiming at extracting information from a unique network. We will particularly focus on clustering methods where the goal is to find clusters of vertices. Finally, in Section 3, techniques that take a series of networks into account, where each network i

Times series averaging from a probabilistic interpretation of time-elastic kernel

At the light of regularized dynamic time warping kernels, this paper reconsider the concept of time elastic centroid (TEC) for a set of time series. From this perspective, we show first how TEC can easily be addressed as a preimage problem. Unfortunately this preimage problem is ill-posed, may suffer from over-fitting especially for long time series and getting a sub-optimal solution involves heavy computational costs. We then derive two new algorithms based on a probabilistic interpretation of kernel alignment matrices that expresses in terms of probabilistic distributions over sets of alignment paths. The first algorithm is an iterative agglomerative heuristics inspired from the state of the art DTW barycenter averaging (DBA) algorithm proposed specifically for the Dynamic Time Warping measure. The second proposed algorithm achieves a classical averaging of the aligned samples but also implements an averaging of the time of occurrences of the aligned samples. It exploits a straightforward progressive agglomerative heuristics. An experimentation that compares for 45 time series datasets classification error rates obtained by first near neighbors classifiers exploiting a single medoid or centroid estimate to represent each categories show that: i) centroids based approaches significantly outperform medoids based approaches, ii) on the considered experience, the two proposed algorithms outperform the state of the art DBA algorithm, and iii) the second proposed algorithm that implements an averaging jointly in the sample space and along the time axes emerges as the most significantly robust time elastic averaging heuristic with an interesting noise reduction capability. Index Terms-Time series averaging Time elastic kernel Dynamic Time Warping Time series clustering and classification

Time Series Cluster Kernel for Learning Similarities between Multivariate Time Series with Missing Data

Similarity-based approaches represent a promising direction for time series analysis. However, many such methods rely on parameter tuning, and some have shortcomings if the time series are multivariate (MTS), due to dependencies between attributes, or the time series contain missing data. In this paper, we address these challenges within the powerful context of kernel methods by proposing the robust \emph{time series cluster kernel} (TCK). The approach taken leverages the missing data handling properties of Gaussian mixture models (GMM) augmented with informative prior distributions. An ensemble learning approach is exploited to ensure robustness to parameters by combining the clustering results of many GMM to form the final kernel. We evaluate the TCK on synthetic and real data and compare to other state-of-the-art techniques. The experimental results demonstrate that the TCK is robust to parameter choices, provides competitive results for MTS without missing data and outstanding results for missing data.Comment: 23 pages, 6 figure

Distance Metric Learning using Graph Convolutional Networks: Application to Functional Brain Networks

Evaluating similarity between graphs is of major importance in several computer vision and pattern recognition problems, where graph representations are often used to model objects or interactions between elements. The choice of a distance or similarity metric is, however, not trivial and can be highly dependent on the application at hand. In this work, we propose a novel metric learning method to evaluate distance between graphs that leverages the power of convolutional neural networks, while exploiting concepts from spectral graph theory to allow these operations on irregular graphs. We demonstrate the potential of our method in the field of connectomics, where neuronal pathways or functional connections between brain regions are commonly modelled as graphs. In this problem, the definition of an appropriate graph similarity function is critical to unveil patterns of disruptions associated with certain brain disorders. Experimental results on the ABIDE dataset show that our method can learn a graph similarity metric tailored for a clinical application, improving the performance of a simple k-nn classifier by 11.9% compared to a traditional distance metric.Comment: International Conference on Medical Image Computing and Computer-Assisted Interventions (MICCAI) 201

A review on distance based time series classification

Time series classification is an increasing research topic due to the vast amount of time series data that is being created over a wide variety of fields. The particularity of the data makes it a challenging task and different approaches have been taken, including the distance based approach. 1-NN has been a widely used method within distance based time series classification due to its simplicity but still good performance. However, its supremacy may be attributed to being able to use specific distances for time series within the classification process and not to the classifier itself. With the aim of exploiting these distances within more complex classifiers, new approaches have arisen in the past few years that are competitive or which outperform the 1-NN based approaches. In some cases, these new methods use the distance measure to transform the series into feature vectors, bridging the gap between time series and traditional classifiers. In other cases, the distances are employed to obtain a time series kernel and enable the use of kernel methods for time series classification. One of the main challenges is that a kernel function must be positive semi-definite, a matter that is also addressed within this review. The presented review includes a taxonomy of all those methods that aim to classify time series using a distance based approach, as well as a discussion of the strengths and weaknesses of each method.TIN2016-78365-

Neural Networks for Complex Data

Artificial neural networks are simple and efficient machine learning tools. Defined originally in the traditional setting of simple vector data, neural network models have evolved to address more and more difficulties of complex real world problems, ranging from time evolving data to sophisticated data structures such as graphs and functions. This paper summarizes advances on those themes from the last decade, with a focus on results obtained by members of the SAMM team of Universit\'e Paris