Latent Dirichlet Allocation Uncovers Spectral Characteristics of Drought Stressed Plants

Understanding the adaptation process of plants to drought stress is essential in improving management practices, breeding strategies as well as engineering viable crops for a sustainable agriculture in the coming decades. Hyper-spectral imaging provides a particularly promising approach to gain such understanding since it allows to discover non-destructively spectral characteristics of plants governed primarily by scattering and absorption characteristics of the leaf internal structure and biochemical constituents. Several drought stress indices have been derived using hyper-spectral imaging. However, they are typically based on few hyper-spectral images only, rely on interpretations of experts, and consider few wavelengths only. In this study, we present the first data-driven approach to discovering spectral drought stress indices, treating it as an unsupervised labeling problem at massive scale. To make use of short range dependencies of spectral wavelengths, we develop an online variational Bayes algorithm for latent Dirichlet allocation with convolved Dirichlet regularizer. This approach scales to massive datasets and, hence, provides a more objective complement to plant physiological practices. The spectral topics found conform to plant physiological knowledge and can be computed in a fraction of the time compared to existing LDA approaches.Comment: Appears in Proceedings of the Twenty-Eighth Conference on Uncertainty in Artificial Intelligence (UAI2012

Hierarchical Convex NMF for Clustering Massive Data

We present an extension of convex-hull non-negative matrix factorization (CH-NMF) which was recently proposed as a large scale variant of convex non-negative matrix factorization or Archetypal Analysis. CH-NMF factorizes a non-negative data matrix V into two nonnegative matrix factors V ≈ W H such that the columns of W are convex combinations of certain data points so that they are readily interpretable to data analysts. There is, however, no free lunch: imposing convexity constraints on W typically prevents adaptation to intrinsic, low dimensional structures in the data. Alas, in cases where the data is distributed in a non-convex manner or consists of mixtures of lower dimensional convex distributions, the cluster representatives obtained from CH-NMF will be less meaningful. In this paper, we present a hierarchical CH-NMF that automatically adapts to internal structures of a dataset, hence it yields meaningful and interpretable clusters for non-convex datasets. This is also confirmed by our extensive evaluation on DBLP publication records of 760,000 authors, 4,000,000 images harvested from the web, and 150,000,000 votes on World of Warcraft guilds. Keywords

More Influence Means Less Work: Fast Latent Dirichlet Allocation by Influence Scheduling

There have recently been considerable advances in fast inference for (online) latent Dirichlet allocation (LDA). While it is widely recognized that the scheduling of documents in stochastic optimization and in turn in LDA may have significant consequences, this issue remains largely unexplored. Instead, practitioners schedule documents essentially uniformly at random, due perhaps to ease of implementation, and to the lack of clear guidelines on scheduling the documents. In this work, we address this issue and propose to schedule documents for an update that exert a disproportionately large influence on the topics of the corpus before less influential ones. More precisely, we justify to sample documents randomly biased towards those ones with higher norms to form mini-batches. On several real-world datasets, including 3M articles from Wikipedia and 8M from PubMed, we demonstrate that the resulting influence scheduled LDA can handily analyze massive document collections and find topic models as good or better than those found with online LDA, often at a fraction of time

Observation of plant–pathogen interaction by simultaneous hyperspectral imaging reflection and transmission measurements

Hyperspectral imaging sensors are valuable tools for plant disease detection and plant phenotyping. Reflectance properties are influenced by plant pathogens and resistance responses, but changes of transmission characteristics of plants are less described. In this study we used simultaneously recorded reflectance and transmittance imaging data of resistant and susceptible barley genotypes that were inoculated with Blumeria graminis f. sp. hordei to evaluate the added value of imaging transmission, reflection and absorption for characterisation of disease development. These datasets were statistically analysed using principal component analysis, and compared with visual and molecular disease estimation. Reflection measurement performed significantly better for early detection of powdery mildew infection, colonies could be detected 2 days before symptoms became visible in RGB images. Transmission data could be used to detect powdery mildew 2 days after symptoms becoming visible in reflection based RGB images. Additionally distinct transmission changes occurred at 580–650 nm for pixels containing disease symptoms. It could be shown that the additional information of the transmission data allows for a clearer spatial differentiation and localisation between powdery mildew symptoms and necrotic tissue on the leaf then purely reflectance based data. Thus the information of both measurement approaches are complementary: reflectance based measurements facilitate an early detection, and transmission measurements provide additional information to better understand and quantify the complex spatio-temporal dynamics of plant-pathogen interactions

Quantitative and qualitative phenotyping of disease resistance of crops by hyperspectral sensors: seamless interlocking of phytopathology, sensors, and machine learning is needed!

Determination and characterization of resistance reactions of crops against fungal pathogens are essential to select resistant genotypes. In plant breeding, phenotyping of genotypes is realized by time consuming and expensive visual plant ratings. During resistance reactions and during pathogenesis plants initiate different structural and biochemical defence mechanisms, which partly affect the optical properties of plant organs. Recently, intensive research has been conducted to develop innovative optical methods for an assessment of compatible and incompatible plant pathogen interaction. These approaches, combining classical phytopathology or microbiology with technology driven methods — such as sensors, robotics, machine learning, and artificial intelligence — are summarized by the term digital phenotyping. In contrast to common visual rating, detection and assessment methods, optical sensors in combination with advanced data analysis methods are able to retrieve pathogen induced changes in the physiology of susceptible or resistant plants non-invasively and objectively. Phenotyping disease resistance aims different tasks. In an early breeding step, a qualitative assessment and characterization of specific resistance action is aimed to link it, for example, to a genetic marker. Later, during greenhouse and field screening, the assessment of the level of susceptibility of different genotypes is relevant. Within this review, recent advances of digital phenotyping technologies for the detection of subtle resistance reactions and resistance breeding are highlighted and methodological requirements are critically discusse

Monitoring wound healing in a 3D wound model by hyperspectral imaging and efficient clustering.

Wound healing is a complex and dynamic process with different distinct and overlapping phases from homeostasis, inflammation and proliferation to remodelling. Monitoring the healing response of injured tissue is of high importance for basic research and clinical practice. In traditional application, biological markers characterize normal and abnormal wound healing. Understanding functional relationships of these biological processes is essential for developing new treatment strategies. However, most of the present techniques (in vitro or in vivo) include invasive microscopic or analytical tissue sampling. In the present study, a non-invasive alternative for monitoring processes during wound healing is introduced. Within this context, hyperspectral imaging (HSI) is an emerging and innovative non-invasive imaging technique with different opportunities in medical applications. HSI acquires the spectral reflectance of an object, depending on its biochemical and structural characteristics. An in-vitro 3-dimensional (3-D) wound model was established and incubated without and with acute and chronic wound fluid (AWF, CWF), respectively. Hyperspectral images of each individual specimen of this 3-D wound model were assessed at day 0/5/10 in vitro, and reflectance spectra were evaluated. For analysing the complex hyperspectral data, an efficient unsupervised approach for clustering massive hyperspectral data was designed, based on efficient hierarchical decomposition of spectral information according to archetypal data points. It represents, to the best of our knowledge, the first application of an advanced Data Mining approach in context of non-invasive analysis of wounds using hyperspectral imagery. By this, temporal and spatial pattern of hyperspectral clusters were determined within the tissue discs and among the different treatments. Results from non-invasive imaging were compared to the number of cells in the various clusters, assessed by Hematoxylin/Eosin (H/E) staining. It was possible to correlate cell quantity and spectral reflectance during wound closure in a 3-D wound model in vitro

Non-negative matrix factorization for the near real-time interpretation of absorption effects in elemental distribution images acquired by X-ray fluorescence Imaging

Elemental distribution images acquired by imaging X-ray fluorescence Analysis can contain high degrees of redundancy and weakly discernible correlations. In this article near real-time non-negative matrix factorization (NMF) is described for the analysis of a number of data sets acquired from samples of a bi-modal Ti-6Al-6V-2Sn alloy. NMF was used for the first time to reveal absorption artefacts in the elemental distribution images of the samples, where two phases of the alloy, namely � and �, were in superposition. The findings and interpretation of the NMF results were confirmed by Monte Carlo simulation of the layered alloy system. Furthermore, it is shown how the simultaneous factorization of several stacks of elemental distribution images provides uniform basis vectors and consequently simplifies the interpretation of the representation