1,424 research outputs found
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
Exact Mean Computation in Dynamic Time Warping Spaces
Dynamic time warping constitutes a major tool for analyzing time series. In
particular, computing a mean series of a given sample of series in dynamic time
warping spaces (by minimizing the Fr\'echet function) is a challenging
computational problem, so far solved by several heuristic and inexact
strategies. We spot some inaccuracies in the literature on exact mean
computation in dynamic time warping spaces. Our contributions comprise an exact
dynamic program computing a mean (useful for benchmarking and evaluating known
heuristics). Based on this dynamic program, we empirically study properties
like uniqueness and length of a mean. Moreover, experimental evaluations reveal
substantial deficits of state-of-the-art heuristics in terms of their output
quality. We also give an exact polynomial-time algorithm for the special case
of binary time series
Novel modeling of task versus rest brain state predictability using a dynamic time warping spectrum: comparisons and contrasts with other standard measures of brain dynamics
Dynamic time warping, or DTW, is a powerful and domain-general sequence alignment method for computing a similarity measure. Such dynamic programming-based techniques like DTW are now the backbone and driver of most bioinformatics methods and discoveries. In neuroscience it has had far less use, though this has begun to change. We wanted to explore new ways of applying DTW, not simply as a measure with which to cluster or compare similarity between features but in a conceptually different way. We have used DTW to provide a more interpretable spectral description of the data, compared to standard approaches such as the Fourier and related transforms. The DTW approach and standard discrete Fourier transform (DFT) are assessed against benchmark measures of neural dynamics. These include EEG microstates, EEG avalanches, and the sum squared error (SSE) from a multilayer perceptron (MLP) prediction of the EEG time series, and simultaneously acquired FMRI BOLD signal. We explored the relationships between these variables of interest in an EEG-FMRI dataset acquired during a standard cognitive task, which allowed us to explore how DTW differentially performs in different task settings. We found that despite strong correlations between DTW and DFT-spectra, DTW was a better predictor for almost every measure of brain dynamics. Using these DTW measures, we show that predictability is almost always higher in task than in rest states, which is consistent to other theoretical and empirical findings, providing additional evidence for the utility of the DTW approach
Summarizing a set of time series by averaging: From Steiner sequence to compact multiple alignment
AbstractSummarizing a set of sequences is an old topic that has been revived in the last decade, due to the increasing availability of sequential datasets. The definition of a consensus object is on the center of data analysis issues, since it crystallizes the underlying organization of the data.Dynamic Time Warping (DTW) is currently the most relevant similarity measure between sequences for a large panel of applications, since it makes it possible to capture temporal distortions. In this context, averaging a set of sequences is not a trivial task, since the average sequence has to be consistent with this similarity measure.The Steiner theory and several works in computational biology have pointed out the connection between multiple alignments and average sequences. Taking inspiration from these works, we introduce the notion of compact multiple alignment, which allows us to link these theories to the problem of summarizing under time warping. Having defined the link between the multiple alignment and the average sequence, the second part of this article focuses on the scan of the space of compact multiple alignments in order to provide an average sequence of a set of sequences. We propose to use a genetic algorithm based on a specific representation of the genotype inspired by genes. This representation of the genotype makes it possible to consistently paint the fitness landscape.Experiments carried out on standard datasets show that the proposed approach outperforms existing methods
Faster and more accurate classification of time series by exploiting a novel dynamic time warping averaging algorithm
A concerted research effort over the past two decades has heralded significant improvements in both the efficiency and effectiveness of time series classification. The consensus that has emerged in the community is that the best solution is a surprisingly simple one. In virtually all domains, the most accurate classifier is the nearest neighbor algorithm with dynamic time warping as the distance measure. The time complexity of dynamic time warping means that successful deployments on resource-constrained devices remain elusive. Moreover, the recent explosion of interest in wearable computing devices, which typically have limited computational resources, has greatly increased the need for very efficient classification algorithms. A classic technique to obtain the benefits of the nearest neighbor algorithm, without inheriting its undesirable time and space complexity, is to use the nearest centroid algorithm. Unfortunately, the unique properties of (most) time series data mean that the centroid typically does not resemble any of the instances, an unintuitive and underappreciated fact. In this paper we demonstrate that we can exploit a recent result by Petitjean et al. to allow meaningful averaging of “warped” time series, which then allows us to create super-efficient nearest “centroid” classifiers that are at least as accurate as their more computationally challenged nearest neighbor relatives. We demonstrate empirically the utility of our approach by comparing it to all the appropriate strawmen algorithms on the ubiquitous UCR Benchmarks and with a case study in supporting insect classification on resource-constrained sensors
Dynamic Time Warping Averaging of Time Series Allows Faster and More Accurate Classification
Recent years have seen significant progress in improving both the efficiency and effectiveness of time series classification. However, because the best solution is typically the Nearest Neighbor algorithm with the relatively expensive Dynamic Time Warping as the distance measure, successful deployments on resource constrained devices remain elusive. Moreover, the recent explosion of interest in wearable devices, which typically have limited computational resources, has created a growing need for very efficient classification algorithms. A commonly used technique to glean the benefits of the Nearest Neighbor algorithm, without inheriting its undesirable time complexity, is to use the Nearest Centroid algorithm. However, because of the unique properties of (most) time series data, the centroid typically does not resemble any of the instances, an unintuitive and underappreciated fact. In this work we show that we can exploit a recent result to allow meaningful averaging of 'warped' times series, and that this result allows us to create ultra-efficient Nearest 'Centroid' classifiers that are at least as accurate as their more lethargic Nearest Neighbor cousins
Diffeomorphic Transformations for Time Series Analysis: An Efficient Approach to Nonlinear Warping
The proliferation and ubiquity of temporal data across many disciplines has
sparked interest for similarity, classification and clustering methods
specifically designed to handle time series data. A core issue when dealing
with time series is determining their pairwise similarity, i.e., the degree to
which a given time series resembles another. Traditional distance measures such
as the Euclidean are not well-suited due to the time-dependent nature of the
data. Elastic metrics such as dynamic time warping (DTW) offer a promising
approach, but are limited by their computational complexity,
non-differentiability and sensitivity to noise and outliers. This thesis
proposes novel elastic alignment methods that use parametric \& diffeomorphic
warping transformations as a means of overcoming the shortcomings of DTW-based
metrics. The proposed method is differentiable \& invertible, well-suited for
deep learning architectures, robust to noise and outliers, computationally
efficient, and is expressive and flexible enough to capture complex patterns.
Furthermore, a closed-form solution was developed for the gradient of these
diffeomorphic transformations, which allows an efficient search in the
parameter space, leading to better solutions at convergence. Leveraging the
benefits of these closed-form diffeomorphic transformations, this thesis
proposes a suite of advancements that include: (a) an enhanced temporal
transformer network for time series alignment and averaging, (b) a
deep-learning based time series classification model to simultaneously align
and classify signals with high accuracy, (c) an incremental time series
clustering algorithm that is warping-invariant, scalable and can operate under
limited computational and time resources, and finally, (d) a normalizing flow
model that enhances the flexibility of affine transformations in coupling and
autoregressive layers.Comment: PhD Thesis, defended at the University of Navarra on July 17, 2023.
277 pages, 8 chapters, 1 appendi
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