Streaming visualisation of quantitative mass spectrometry data based on a novel raw signal decomposition method

As data rates rise, there is a danger that informatics for high-throughput LC-MS becomes more opaque and inaccessible to practitioners. It is therefore critical that efficient visualisation tools are available to facilitate quality control, verification, validation, interpretation, and sharing of raw MS data and the results of MS analyses. Currently, MS data is stored as contiguous spectra. Recall of individual spectra is quick but panoramas, zooming and panning across whole datasets necessitates processing/memory overheads impractical for interactive use. Moreover, visualisation is challenging if significant quantification data is missing due to data-dependent acquisition of MS/MS spectra. In order to tackle these issues, we leverage our seaMass technique for novel signal decomposition. LC-MS data is modelled as a 2D surface through selection of a sparse set of weighted B-spline basis functions from an over-complete dictionary. By ordering and spatially partitioning the weights with an R-tree data model, efficient streaming visualisations are achieved. In this paper, we describe the core MS1 visualisation engine and overlay of MS/MS annotations. This enables the mass spectrometrist to quickly inspect whole runs for ionisation/chromatographic issues, MS/MS precursors for coverage problems, or putative biomarkers for interferences, for example. The open-source software is available from http://seamass.net/viz/

Unsupervised Learning of Artistic Styles with Archetypal Style Analysis

In this paper, we introduce an unsupervised learning approach to automatically discover, summarize, and manipulate artistic styles from large collections of paintings. Our method is based on archetypal analysis, which is an unsupervised learning technique akin to sparse coding with a geometric interpretation. When applied to deep image representations from a collection of artworks, it learns a dictionary of archetypal styles, which can be easily visualized. After training the model, the style of a new image, which is characterized by local statistics of deep visual features, is approximated by a sparse convex combination of archetypes. This enables us to interpret which archetypal styles are present in the input image, and in which proportion. Finally, our approach allows us to manipulate the coefficients of the latent archetypal decomposition, and achieve various special effects such as style enhancement, transfer, and interpolation between multiple archetypes.Comment: Accepted at NIPS 2018, Montr\'eal, Canad

Dictionary Learning for Deblurring and Digital Zoom

This paper proposes a novel approach to image deblurring and digital zooming using sparse local models of image appearance. These models, where small image patches are represented as linear combinations of a few elements drawn from some large set (dictionary) of candidates, have proven well adapted to several image restoration tasks. A key to their success has been to learn dictionaries adapted to the reconstruction of small image patches. In contrast, recent works have proposed instead to learn dictionaries which are not only adapted to data reconstruction, but also tuned for a specific task. We introduce here such an approach to deblurring and digital zoom, using pairs of blurry/sharp (or low-/high-resolution) images for training, as well as an effective stochastic gradient algorithm for solving the corresponding optimization task. Although this learning problem is not convex, once the dictionaries have been learned, the sharp/high-resolution image can be recovered via convex optimization at test time. Experiments with synthetic and real data demonstrate the effectiveness of the proposed approach, leading to state-of-the-art performance for non-blind image deblurring and digital zoom

Log-Euclidean Bag of Words for Human Action Recognition

Representing videos by densely extracted local space-time features has recently become a popular approach for analysing actions. In this paper, we tackle the problem of categorising human actions by devising Bag of Words (BoW) models based on covariance matrices of spatio-temporal features, with the features formed from histograms of optical flow. Since covariance matrices form a special type of Riemannian manifold, the space of Symmetric Positive Definite (SPD) matrices, non-Euclidean geometry should be taken into account while discriminating between covariance matrices. To this end, we propose to embed SPD manifolds to Euclidean spaces via a diffeomorphism and extend the BoW approach to its Riemannian version. The proposed BoW approach takes into account the manifold geometry of SPD matrices during the generation of the codebook and histograms. Experiments on challenging human action datasets show that the proposed method obtains notable improvements in discrimination accuracy, in comparison to several state-of-the-art methods