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

Deep constrained clustering applied to satellite image time series

International audienceThe advent of satellite imagery is generating an unprecedented amount of remote sensing images. Current satellites now achieve frequent revisits and high mission availability and provide series of images of the Earth captured at different dates that can be seen as time series. Analyzing satellite image time series allows to perform continuous wide range Earth observation with applications in agricultural mapping , environmental disaster monitoring, etc. However, the lack of large quantity of labeled data generally prevents from easily applying supervised methods. On the contrary, unsupervised methods do not require expert knowledge but sometimes provide poor results. In this context, constrained clustering, which is a class of semi-supervised learning algorithms , is an alternative and offers a good trade-off of supervision. In this paper, we explore the use of constraints with deep clustering approaches to process satellite image time series. Our experimental study relies on deep embedded clustering and the deep constrained framework using pairwise constraints (must-link and cannot-link). Experiments on a real dataset composed of 11 satellite images show promising results and open many perspectives for applying deep constrained clustering to satellite image time series

Comparison of optical sensors discrimination ability using spectral libraries

In remote sensing, the ability to discriminate different land covers or material types is directly linked with the spectral resolution and sampling provided by the optical sensor. Previous studies showed that the spectral resolution is a critical issue, especially in complex environment. In spite of the increasing availability of hyperspectral data, multispectral optical sensors onboard various satellites are acquiring everyday a massive amount of data with a relatively poor spectral resolution (i.e. usually about 4 to 7 spectral bands). These remotely sensed data are intensively used for Earth observation regardless of their limited spectral resolution. In this paper, we studied seven of these optical sensors: Pleiades, QuickBird, SPOT5, Ikonos, Landsat TM, Formosat and Meris. This study focuses on the ability of each sensor to discriminate different materials according to its spectral resolution. We used four different spectral libraries which contains around 2500 spectra of materials and land covers with a fine spectral resolution. These spectra were convolved with the Relative Spectral Responses (RSR) of each sensor to create spectra at the sensors’ resolutions. Then, these reduced spectra were compared using separability indexes (Divergence, Transformed divergence, Bhattacharyya, Jeffreys-Matusita) and machine learning tools. In the experiments, we highlighted that the spectral bands configuration could lead to important differences in classification accuracy according to the context of application (e.g. urban area)

Constrained Distance Based Clustering for Satellite Image Time-Series

International audienceThe advent of high-resolution instruments for time-series sampling poses added complexity for the formal definition of thematic classes in the remote sensing domain-required by supervised methods-while unsupervised methods ignore expert knowledge and intuition. Constrained clustering is becoming an increasingly popular approach in data mining because it offers a solution to these problems, however, its application in remote sensing is relatively unknown. This article addresses this divide by adapting publicly available constrained clustering implementations to use the dynamic time warping (DTW) dissimilarity measure, which is sometimes used for time-series analysis. A comparative study is presented, in which their performance is evaluated (using both DTW and Euclidean distances). It is found that adding constraints to the clustering problem results in an increase in accuracy when compared to unconstrained clustering. The output of such algorithms are homogeneous in spatially defined regions. Declarative approaches and k-Means based algorithms are simple to apply, requiring little or no choice of parameter values. Spectral methods, however, require careful tuning, which is unrealistic in a semi-supervised setting, although they offer the highest accuracy. These conclusions were drawn from two applications: crop clustering using 11 multi-spectral Landsat images non-uniformly sampled over a period of eight months in 2007; and tree-cut detection using 10 NDVI Sentinel-2 images non-uniformly sampled between 2016 and 2018

Stain unmixing in brightfield multiplexed immunohistochemistry

Automated image analysis of multiplexed brightfield immunohistochemistry assays is a challenging objective. One central task of the analysis is the robust identification of the different stains in the image, called stain unmixing. Stain unmixing strongly depends on the method of image acquisition. Currently available multispectral cameras enable color unmixing of single fields of view (FoV), selected by matter experts (e.g. pathologists). Beyond the individual FoV approach, there is an increasing need to process larger regions or whole histopathological sections (whole slide imaging; WSI). Rapid color deconvolution in WSI is a challenge that is only partially solved. We propose a method based on a multilayer perceptron to compute dye-specific stain layers for chromogenic red and brown labeling in WSI

Vers une approche collaborative segmentation-classification pour l'analyse d'images de télédétection

National audienceL'interprétation automatique d'images de télédétection à très haute résolution spatiale est une tâche complexe. Les approches d'analyse d'images orientée objets sont couramment utilisées afin de résoudre ce problème ; mais leurs résultats dépendent fortement sur la segmentation d'images. Or, il n'existe pas de méthode de segmentation universelle permettant d'isoler correctement les différents objets à extraire. Nous proposons ici un cadre formel de collaboration entre un segmenteur et un classeur pour améliorer conjointement la segmentation et la classification pour une classe thématique donnée