Superconducting radio-frequency cavity fault classification using machine learning at Jefferson Laboratory

We report on the development of machine learning models for classifying C100 superconducting radio-frequency (SRF) cavity faults in the Continuous Electron Beam Accelerator Facility (CEBAF) at Jefferson Lab. CEBAF is a continuous-wave recirculating linac utilizing 418 SRF cavities to accelerate electrons up to 12 GeV through 5-passes. Of these, 96 cavities (12 cryomodules) are designed with a digital low-level RF system configured such that a cavity fault triggers waveform recordings of 17 RF signals for each of the 8 cavities in the cryomodule. Subject matter experts (SME) are able to analyze the collected time-series data and identify which of the eight cavities faulted first and classify the type of fault. This information is used to find trends and strategically deploy mitigations to problematic cryomodules. However manually labeling the data is laborious and time-consuming. By leveraging machine learning, near real-time (rather than post-mortem) identification of the offending cavity and classification of the fault type has been implemented. We discuss performance of the ML models during a recent physics run. Results show the cavity identification and fault classification models have accuracies of 84.9% and 78.2%, respectively.Comment: 20 pages, 10 figures submitted to Physical Review Accelerators and Beam

Hypothesis Testing For Network Data in Functional Neuroimaging

In recent years, it has become common practice in neuroscience to use networks to summarize relational information in a set of measurements, typically assumed to be reflective of either functional or structural relationships between regions of interest in the brain. One of the most basic tasks of interest in the analysis of such data is the testing of hypotheses, in answer to questions such as "Is there a difference between the networks of these two groups of subjects?" In the classical setting, where the unit of interest is a scalar or a vector, such questions are answered through the use of familiar two-sample testing strategies. Networks, however, are not Euclidean objects, and hence classical methods do not directly apply. We address this challenge by drawing on concepts and techniques from geometry, and high-dimensional statistical inference. Our work is based on a precise geometric characterization of the space of graph Laplacian matrices and a nonparametric notion of averaging due to Fr\'echet. We motivate and illustrate our resulting methodologies for testing in the context of networks derived from functional neuroimaging data on human subjects from the 1000 Functional Connectomes Project. In particular, we show that this global test is more statistical powerful, than a mass-univariate approach. In addition, we have also provided a method for visualizing the individual contribution of each edge to the overall test statistic.Comment: 34 pages. 5 figure

MINET a fast Network LP Solver

In comparison with already existing software for the solution of network type linear programming problems. MINET gives a possibility of very flexible pricing that can be further fitted to the special structure of the network and using a suitable interface, it can reflect the need for changing the network structure

Clustering in the Big Data Era: methods for efficient approximation, distribution, and parallelization

Data clustering is an unsupervised machine learning task whose objective is to group together similar items. As a versatile data mining tool, data clustering has numerous applications, such as object detection and localization using data from 3D laser-based sensors, finding popular routes using geolocation data, and finding similar patterns of electricity consumption using smart meters.The datasets in modern IoT-based applications are getting more and more challenging for conventional clustering schemes. Big Data is a term used to loosely describe hard-to-manage datasets. Particularly, large numbers of data points, high rates of data production, large numbers of dimensions, high skewness, and distributed data sources are aspects that challenge the classical data processing schemes, including clustering methods. This thesis contributes to efficient big data clustering for distributed and parallel computing architectures, representative of the processing environments in edge-cloud computing continuum. The thesis also proposes approximation techniques to cope with certain challenging aspects of big data.Regarding distributed clustering, the thesis proposes MAD-C, abbreviating Multi-stage Approximate Distributed Cluster-Combining. MAD-C leverages an approximation-based data synopsis that drastically lowers the required communication bandwidth among the distributed nodes and achieves multiplicative savings in computation time, compared to a baseline that centrally gathers and clusters the data. The thesis shows MAD-C can be used to detect and localize objects using data from distributed 3D laser-based sensors with high accuracy. Furthermore, the work in the thesis shows how to utilize MAD-C to efficiently detect the objects within a restricted area for geofencing purposes.Regarding parallel clustering, the thesis proposes a family of algorithms called PARMA-CC, abbreviating Parallel Multistage Approximate Cluster Combining. Using approximation-based data synopsis, PARMA-CC algorithms achieve scalability on multi-core systems by facilitating parallel execution of threads with limited dependencies which get resolved using fine-grained synchronization techniques. To further enhance the efficiency, PARMA-CC algorithms can be configured with respect to different data properties. Analytical and empirical evaluations show PARMA-CC algorithms achieve significantly higher scalability than the state-of-the-art methods while preserving a high accuracy.On parallel high dimensional clustering, the thesis proposes IP.LSH.DBSCAN, abbreviating Integrated Parallel Density-Based Clustering through Locality-Sensitive Hashing (LSH). IP.LSH.DBSCAN fuses the process of creating an LSH index into the process of data clustering, and it takes advantage of data parallelization and fine-grained synchronization. Analytical and empirical evaluations show IP.LSH.DBSCAN facilitates parallel density-based clustering of massive datasets using desired distance measures resulting in several orders of magnitude lower latency than state-of-the-art for high dimensional data.In essence, the thesis proposes methods and algorithmic implementations targeting the problem of big data clustering and applications using distributed and parallel processing. The proposed methods (available as open source software) are extensible and can be used in combination with other methods

Learning from Multi-Class Imbalanced Big Data with Apache Spark

With data becoming a new form of currency, its analysis has become a top priority in both academia and industry, furthering advancements in high-performance computing and machine learning. However, these large, real-world datasets come with additional complications such as noise and class overlap. Problems are magnified when with multi-class data is presented, especially since many of the popular algorithms were originally designed for binary data. Another challenge arises when the number of examples are not evenly distributed across all classes in a dataset. This often causes classifiers to favor the majority class over the minority classes, leading to undesirable results as learning from the rare cases may be the primary goal. Many of the classic machine learning algorithms were not designed for multi-class, imbalanced data or parallelism, and so their effectiveness has been hindered. This dissertation addresses some of these challenges with in-depth experimentation using novel implementations of machine learning algorithms using Apache Spark, a distributed computing framework based on the MapReduce model designed to handle very large datasets. Experimentation showed that many of the traditional classifier algorithms do not translate well to a distributed computing environment, indicating the need for a new generation of algorithms targeting modern high-performance computing. A collection of popular oversampling methods, originally designed for small binary class datasets, have been implemented using Apache Spark for the first time to improve parallelism and add multi-class support. An extensive study on how instance level difficulty affects the learning from large datasets was also performed

Quelques extensions des level sets et des graph cuts et leurs applications à la segmentation d'images et de vidéos

Image processing techniques are now widely spread out over a large quantity of domains: like medical imaging, movies post-production, games... Automatic detection and extraction of regions of interest inside an image, a volume or a video is challenging problem since it is a starting point for many applications in image processing. However many techniques were developed during the last years and the state of the art methods suffer from some drawbacks: The Level Sets method only provides a local minimum while the Graph Cuts method comes from Combinatorial Community and could take advantage of the specificity of image processing problems. In this thesis, we propose two extensions of the previously cited methods in order to soften or remove these drawbacks. We first discuss the existing methods and show how they are related to the segmentation problem through an energy formulation. Then we introduce stochastic perturbations to the Level Sets method and we build a more generic framework: the Stochastic Level Sets (SLS). Later we provide a direct application of the SLS to image segmentation that provides a better minimization of energies. Basically, it allows the contours to escape from local minimum. Then we propose a new formulation of an existing algorithm of Graph Cuts in order to introduce some interesting concept for image processing community: like initialization of the algorithm for speed improvement. We also provide a new approach for layer extraction from video sequence that retrieves both visible and hidden layers in it.Les techniques de traitement d'image sont maintenant largement répandues dans une grande quantité de domaines: comme l'imagerie médicale, la post-production de films, les jeux... La détection et l'extraction automatique de régions d'intérêt à l'intérieur d'une image, d'un volume ou d'une vidéo est réel challenge puisqu'il représente un point de départ pour un grand nombre d'applications en traitement d'image. Cependant beaucoup de techniques développées pendant ces dernières années et les méthodes de l'état de l'art souffrent de quelques inconvénients: la méthode des ensembles de niveaux fournit seulement un minimum local tandis que la méthode de coupes de graphe vient de la communauté combinatoire et pourrait tirer profit de la spécificité des problèmes de traitement d'image. Dans cette thèse, nous proposons deux prolongements des méthodes précédemment citées afin de réduire ou enlever ces inconvénients. Nous discutons d'abord les méthodes existantes et montrons comment elles sont liées au problème de segmentation via une formulation énergétique. Nous présentons ensuite des perturbations stochastiques a la méthode des ensembles de niveaux et nous établissons un cadre plus générique: les ensembles de niveaux stochastiques (SLS). Plus tard nous fournissons une application directe du SLS à la segmentation d'image et montrons qu'elle fournit une meilleure minimisation des énergies. Fondamentalement, il permet aux contours de s'échapper des minima locaux. Nous proposons ensuite une nouvelle formulation d'un algorithme existant des coupes de graphe afin d'introduire de nouveaux concepts intéressant pour la communauté de traitement d'image: comme l'initialisation de l'algorithme pour l'amélioration de vitesse. Nous fournissons également une nouvelle approche pour l'extraction de couches d'une vidéo par segmentation du mouvement et qui extrait à la fois les couches visibles et cachées présentes

Parallel distributed-memory particle methods for acquisition-rate segmentation and uncertainty quantifications of large fluorescence microscopy images

Modern fluorescence microscopy modalities, such as light-sheet microscopy, are capable of acquiring large three-dimensional images at high data rate. This creates a bottleneck in computational processing and analysis of the acquired images, as the rate of acquisition outpaces the speed of processing. Moreover, images can be so large that they do not fit the main memory of a single computer. Another issue is the information loss during image acquisition due to limitations of the optical imaging systems. Analysis of the acquired images may, therefore, find multiple solutions (or no solution) due to imaging noise, blurring, and other uncertainties introduced during image acquisition. In this thesis, we address the computational processing time and memory issues by developing a distributed parallel algorithm for segmentation of large fluorescence-microscopy images. The method is based on the versatile Discrete Region Competition (Cardinale et al., 2012) algorithm, which has previously proven useful in microscopy image segmentation. The present distributed implementation decomposes the input image into smaller sub-images that are distributed across multiple computers. Using network communication, the computers orchestrate the collective solving of the global segmentation problem. This not only enables segmentation of large images (we test images of up to 10^10 pixels) but also accelerates segmentation to match the time scale of image acquisition. Such acquisition-rate image segmentation is a prerequisite for the smart microscopes of the future and enables online data inspection and interactive experiments. Second, we estimate the segmentation uncertainty on large images that do not fit the main memory of a single computer. We there- fore develop a distributed parallel algorithm for efficient Markov- chain Monte Carlo Discrete Region Sampling (Cardinale, 2013). The parallel algorithm provides a measure of segmentation uncertainty in a statistically unbiased way. It approximates the posterior probability densities over the high-dimensional space of segmentations around the previously found segmentation.Moderne Fluoreszenzmikroskopie, wie zum Beispiel Lichtblattmikroskopie, erlauben die Aufnahme hochaufgelöster, 3-dimensionaler Bilder. Dies führt zu einen Engpass bei der Bearbeitung und Analyse der aufgenommenen Bilder, da die Aufnahmerate die Datenverarbeitungsrate übersteigt. Zusätzlich können diese Bilder so groß sein, dass sie die Speicherkapazität eines einzelnen Computers überschreiten. Hinzu kommt der aus Limitierungen des optischen Abbildungssystems resultierende Informationsverlust während der Bildaufnahme. Bildrauschen, Unschärfe und andere Messunsicherheiten können dazu führen, dass Analysealgorithmen möglicherweise mehrere oder keine Lösung für Bildverarbeitungsaufgaben finden. Im Rahmen der vorliegenden Arbeit entwickeln wir einen verteilten, parallelen Algorithmus für die Segmentierung von speicherintensiven Fluoreszenzmikroskopie-Bildern. Diese Methode basiert auf dem vielseitigen "Discrete Region Competition" Algorithmus (Cardinale et al., 2012), der sich bereits in anderen Anwendungen als nützlich für die Segmentierung von Mikroskopie-Bildern erwiesen hat. Das hier präsentierte Verfahren unterteilt das Eingangsbild in kleinere Unterbilder, welche auf die Speicher mehrerer Computer verteilt werden. Die Koordinierung des globalen Segmentierungsproblems wird durch die Benutzung von Netzwerkkommunikation erreicht. Dies erlaubt die Segmentierung von sehr großen Bildern, wobei wir die Anwendung des Algorithmus auf Bildern mit bis zu 10^10 Pixeln demonstrieren. Zusätzlich wird die Segmentierungsgeschwindigkeit erhöht und damit vergleichbar mit der Aufnahmerate des Mikroskops. Dies ist eine Grundvoraussetzung für die intelligenten Mikroskope der Zukunft, und es erlaubt die Online-Betrachtung der aufgenommenen Daten, sowie interaktive Experimente. Wir bestimmen die Unsicherheit des Segmentierungsalgorithmus bei der Anwendung auf Bilder, deren Größe den Speicher eines einzelnen Computers übersteigen. Dazu entwickeln wir einen verteilten, parallelen Algorithmus für effizientes Markov-chain Monte Carlo "Discrete Region Sampling" (Cardinale, 2013). Dieser Algorithmus quantifiziert die Segmentierungsunsicherheit statistisch erwartungstreu. Dazu wird die A-posteriori-Wahrscheinlichkeitsdichte über den hochdimensionalen Raum der Segmentierungen in der Umgebung der zuvor gefundenen Segmentierung approximiert

A divide-and-conquer approach to geometric sampling for active learning

Active learning (AL) repeatedly trains the classifier with the minimum labeling budget to improve the current classification model. The training process is usually supervised by an uncertainty evaluation strategy. However, the uncertainty evaluation always suffers from performance degeneration when the initial labeled set has insufficient labels. To completely eliminate the dependence on the uncertainty evaluation sampling in AL, this paper proposes a divide-and-conquer idea that directly transfers the AL sampling as the geometric sampling over the clusters. By dividing the points of the clusters into cluster boundary and core points, we theoretically discuss their margin distance and {hypothesis relationship}. With the advantages of cluster boundary points in the above two properties, we propose a Geometric Active Learning (GAL) algorithm by knight's tour. Experimental studies of the two reported experimental tasks including cluster boundary detection and AL classification show that the proposed GAL method significantly outperforms the state-of-the-art baselines.Comment: This paper has been withdrawn. The first author quitted the PhD study from AAI, University of Technology Sydney. The manuscript stopped updatin