Time Series Classification in Dissimilarity Spaces

Abstract. Time series classification in the dissimilarity space combines the advantages of the dynamic time warping and the rich mathematical structure of Euclidean spaces. We applied dimension reduction using PCA followed by support vector learning on dissimilarity representations to 43 UCR datasets. Results indicate that time series classification in dissimilarity space has potential to complement the state-of-the-art

Classifying sequences by the optimized dissimilarity space embedding approach: a case study on the solubility analysis of the E. coli proteome

We evaluate a version of the recently-proposed classification system named Optimized Dissimilarity Space Embedding (ODSE) that operates in the input space of sequences of generic objects. The ODSE system has been originally presented as a classification system for patterns represented as labeled graphs. However, since ODSE is founded on the dissimilarity space representation of the input data, the classifier can be easily adapted to any input domain where it is possible to define a meaningful dissimilarity measure. Here we demonstrate the effectiveness of the ODSE classifier for sequences by considering an application dealing with the recognition of the solubility degree of the Escherichia coli proteome. Solubility, or analogously aggregation propensity, is an important property of protein molecules, which is intimately related to the mechanisms underlying the chemico-physical process of folding. Each protein of our dataset is initially associated with a solubility degree and it is represented as a sequence of symbols, denoting the 20 amino acid residues. The herein obtained computational results, which we stress that have been achieved with no context-dependent tuning of the ODSE system, confirm the validity and generality of the ODSE-based approach for structured data classification.Comment: 10 pages, 49 reference

Ranking and significance of variable-length similarity-based time series motifs

The detection of very similar patterns in a time series, commonly called motifs, has received continuous and increasing attention from diverse scientific communities. In particular, recent approaches for discovering similar motifs of different lengths have been proposed. In this work, we show that such variable-length similarity-based motifs cannot be directly compared, and hence ranked, by their normalized dissimilarities. Specifically, we find that length-normalized motif dissimilarities still have intrinsic dependencies on the motif length, and that lowest dissimilarities are particularly affected by this dependency. Moreover, we find that such dependencies are generally non-linear and change with the considered data set and dissimilarity measure. Based on these findings, we propose a solution to rank those motifs and measure their significance. This solution relies on a compact but accurate model of the dissimilarity space, using a beta distribution with three parameters that depend on the motif length in a non-linear way. We believe the incomparability of variable-length dissimilarities could go beyond the field of time series, and that similar modeling strategies as the one used here could be of help in a more broad context.Comment: 20 pages, 10 figure