Survey-scale discovery-based research processes: Evaluating a bespoke visualisation environment for astronomical survey data

Next generation astronomical surveys naturally pose challenges for human-centred visualisation and analysis workflows that currently rely on the use of standard desktop display environments. While a significant fraction of the data preparation and analysis will be taken care of by automated pipelines, crucial steps of knowledge discovery can still only be achieved through various level of human interpretation. As the number of sources in a survey grows, there is need to both modify and simplify repetitive visualisation processes that need to be completed for each source. As tasks such as per-source quality control, candidate rejection, and morphological classification all share a single instruction, multiple data (SIMD) work pattern, they are amenable to a parallel solution. Selecting extragalactic neutral hydrogen (HI) surveys as a representative example, we use system performance benchmarking and the visual data and reasoning (VDAR) methodology from the field of information visualisation to evaluate a bespoke comparative visualisation environment: the encube visual analytics framework deployed on the 83 Megapixel Swinburne Discovery Wall. Through benchmarking using spectral cube data from existing HI surveys, we are able to perform interactive comparative visualisation via texture-based volume rendering of 180 three-dimensional (3D) data cubes at a time. The time to load a configuration of spectral cubes scale linearly with the number of voxels, with independent samples of 180 cubes (8.4 Gigavoxels or 34 Gigabytes) each loading in under 5 minutes. We show that parallel comparative inspection is a productive and time-saving technique which can reduce the time taken to complete SIMD-style visual tasks currently performed at the desktop by at least two orders of magnitude, potentially rendering some labour-intensive desktop-based workflows obsolete.Comment: 21 pages, 10 figures, Accepted for publication in the Publications of the Astronomical Society of Australi

Sequential Manipulation Planning on Scene Graph

We devise a 3D scene graph representation, contact graph+ (cg+), for efficient sequential task planning. Augmented with predicate-like attributes, this contact graph-based representation abstracts scene layouts with succinct geometric information and valid robot-scene interactions. Goal configurations, naturally specified on contact graphs, can be produced by a genetic algorithm with a stochastic optimization method. A task plan is then initialized by computing the Graph Editing Distance (GED) between the initial contact graphs and the goal configurations, which generates graph edit operations corresponding to possible robot actions. We finalize the task plan by imposing constraints to regulate the temporal feasibility of graph edit operations, ensuring valid task and motion correspondences. In a series of simulations and experiments, robots successfully complete complex sequential object rearrangement tasks that are difficult to specify using conventional planning language like Planning Domain Definition Language (PDDL), demonstrating the high feasibility and potential of robot sequential task planning on contact graph.Comment: 8 pages, 6 figures. Accepted by IROS 202

Semantic Driven Approach for Rapid Application Development in Industrial Internet of Things

The evolution of IoT has revolutionized industrial automation. Industrial devices at every level such as field devices, control devices, enterprise level devices etc., are connected to the Internet, where they can be accessed easily. It has significantly changed the way applications are developed on the industrial automation systems. It led to the paradigm shift where novel IoT application development tools such as Node-RED can be used to develop complex industrial applications as IoT orchestrations. However, in the current state, these applications are bound strictly to devices from specific vendors and ecosystems. They cannot be re-used with devices from other vendors and platforms, since the applications are not semantically interoperable. For this purpose, it is desirable to use platform-independent, vendor-neutral application templates for common automation tasks. However, in the current state in Node-RED such reusable and interoperable application templates cannot be developed. The interoperability problem at the data level can be addressed in IoT, using Semantic Web (SW) technologies. However, for an industrial engineer or an IoT application developer, SW technologies are not very easy to use. In order to enable efficient use of SW technologies to create interoperable IoT applications, novel IoT tools are required. For this purpose, in this paper we propose a novel semantic extension to the widely used Node-RED tool by introducing semantic definitions such as iot.schema.org semantic models into Node-RED. The tool guides a non-expert in semantic technologies such as a device vendor, a machine builder to configure the semantics of a device consistently. Moreover, it also enables an engineer, IoT application developer to design and develop semantically interoperable IoT applications with minimal effort. Our approach accelerates the application development process by introducing novel semantic application templates called Recipes in Node-RED. Using Recipes, complex application development tasks such as skill matching between Recipes and existing things can be automated.We will present the approach to perform automated skill matching on the Cloud or on the Edge of an automation system. We performed quantitative and qualitative evaluation of our approach to test the feasibility and scalability of the approach in real world scenarios. The results of the evaluation are presented and discussed in the paper.Die Entwicklung des Internet der Dinge (IoT) hat die industrielle Automatisierung revolutioniert. Industrielle Geräte auf allen Ebenen wie Feldgeräte, Steuergeräte, Geräte auf Unternehmensebene usw. sind mit dem Internet verbunden, wodurch problemlos auf sie zugegriffen werden kann. Es hat die Art und Weise, wie Anwendungen auf industriellen Automatisierungssystemen entwickelt werden, deutlich verändert. Es führte zum Paradigmenwechsel, wo neuartige IoT Anwendungsentwicklungstools, wie Node-RED, verwendet werden können, um komplexe industrielle Anwendungen als IoT-Orchestrierungen zu entwickeln. Aktuell sind diese Anwendungen jedoch ausschließlich an Geräte bestimmter Anbieter und Ökosysteme gebunden. Sie können nicht mit Geräten anderer Anbieter und Plattformen verbunden werden, da die Anwendungen nicht semantisch interoperabel sind. Daher ist es wünschenswert, plattformunabhängige, herstellerneutrale Anwendungsvorlagen für allgemeine Automatisierungsaufgaben zu verwenden. Im aktuellen Status von Node-RED können solche wiederverwendbaren und interoperablen Anwendungsvorlagen jedoch nicht entwickelt werden. Diese Interoperabilitätsprobleme auf Datenebene können im IoT mithilfe von Semantic Web (SW) -Technologien behoben werden. Für Ingenieure oder Entwickler von IoT-Anwendungen sind SW-Technologien nicht sehr einfach zu verwenden. Zur Erstellung interoperabler IoT-Anwendungen sind daher neuartige IoT-Tools erforderlich. Zu diesem Zweck schlagen wir eine neuartige semantische Erweiterung des weit verbreiteten Node-RED-Tools vor, indem wir semantische Definitionen wie iot.schema.org in die semantischen Modelle von NODE-Red einführen. Das Tool leitet einen Gerätehersteller oder Maschinebauer, die keine Experten in semantische Technologien sind, an um die Semantik eines Geräts konsistent zu konfigurieren. Darüber hinaus ermöglicht es auch einem Ingenieur oder IoT-Anwendungsentwickler, semantische, interoperable IoT-Anwendungen mit minimalem Aufwand zu entwerfen und entwicklen Unser Ansatz beschleunigt die Anwendungsentwicklungsprozesse durch Einführung neuartiger semantischer Anwendungsvorlagen namens Rezepte für Node-RED. Durch die Verwendung von Rezepten können komplexe Anwendungsentwicklungsaufgaben wie das Abgleichen von Funktionen zwischen Rezepten und vorhandenen Strukturen automatisiert werden. Wir demonstrieren Skill-Matching in der Cloud oder am Industrial Edge eines Automatisierungssystems. Wir haben dafür quantitative und qualitative Bewertung unseres Ansatzes durchgeführt, um die Machbarkeit und Skalierbarkeit des Ansatzes in realen Szenarien zu testen. Die Ergebnisse der Bewertung werden in dieser Arbeit vorgestellt und diskutiert

Understanding, Analysis, and Handling of Software Architecture Erosion

Architecture erosion occurs when a software system's implemented architecture diverges from the intended architecture over time. Studies show erosion impacts development, maintenance, and evolution since it accumulates imperceptibly. Identifying early symptoms like architectural smells enables managing erosion through refactoring. However, research lacks comprehensive understanding of erosion, unclear which symptoms are most common, and lacks detection methods. This thesis establishes an erosion landscape, investigates symptoms, and proposes identification approaches. A mapping study covers erosion definitions, symptoms, causes, and consequences. Key findings: 1) "Architecture erosion" is the most used term, with four perspectives on definitions and respective symptom types. 2) Technical and non-technical reasons contribute to erosion, negatively impacting quality attributes. Practitioners can advocate addressing erosion to prevent failures. 3) Detection and correction approaches are categorized, with consistency and evolution-based approaches commonly mentioned.An empirical study explores practitioner perspectives through communities, surveys, and interviews. Findings reveal associated practices like code review and tools identify symptoms, while collected measures address erosion during implementation. Studying code review comments analyzes erosion in practice. One study reveals architectural violations, duplicate functionality, and cyclic dependencies are most frequent. Symptoms decreased over time, indicating increased stability. Most were addressed after review. A second study explores violation symptoms in four projects, identifying 10 categories. Refactoring and removing code address most violations, while some are disregarded.Machine learning classifiers using pre-trained word embeddings identify violation symptoms from code reviews. Key findings: 1) SVM with word2vec achieved highest performance. 2) fastText embeddings worked well. 3) 200-dimensional embeddings outperformed 100/300-dimensional. 4) Ensemble classifier improved performance. 5) Practitioners found results valuable, confirming potential.An automated recommendation system identifies qualified reviewers for violations using similarity detection on file paths and comments. Experiments show common methods perform well, outperforming a baseline approach. Sampling techniques impact recommendation performance

MatNexus: A Comprehensive Text Mining and Analysis Suite for Materials Discover

MatNexus is a specialized software for the automated collection, processing, and analysis of text from scientific articles. Through an integrated suite of modules, the MatNexus facilitates the retrieval of scientific articles, processes textual data for insights, generates vector representations suitable for machine learning, and offers visualization capabilities for word embeddings. With the vast volume of scientific publications, MatNexus stands out as an end-to-end tool for researchers aiming to gain insights from scientific literature in material science, making the exploration of materials, such as the electrocatalyst examples we show here, efficient and insightful.Comment: 15 pages, 6 figures, submission to Software

By how much can closed-loop frameworks accelerate computational materials discovery?

The implementation of automation and machine learning surrogatization within closed-loop computational workflows is an increasingly popular approach to accelerate materials discovery. However, the scale of the speedup associated with this paradigm shift from traditional manual approaches remains an open question. In this work, we rigorously quantify the acceleration from each of the components within a closed-loop framework for material hypothesis evaluation by identifying four distinct sources of speedup: (1) task automation, (2) calculation runtime improvements, (3) sequential learning-driven design space search, and (4) surrogatization of expensive simulations with machine learning models. This is done using a time-keeping ledger to record runs of automated software and corresponding manual computational experiments within the context of electrocatalysis. From a combination of the first three sources of acceleration, we estimate that overall hypothesis evaluation time can be reduced by over 90%, i.e., achieving a speedup of $\sim$$10\times$. Further, by introducing surrogatization into the loop, we estimate that the design time can be reduced by over 95%, i.e., achieving a speedup of $\sim$$15$-$20\times$. Our findings present a clear value proposition for utilizing closed-loop approaches for accelerating materials discovery.Comment: added Supplementary Informatio

An integrated approach to high integrity software verification.

Computer software is developed through software engineering. At its most precise, software engineering involves mathematical rigour as formal methods. High integrity software is associated with safety critical and security critical applications, where failure would bring significant costs. The development of high integrity software is subject to stringent standards, prescribing best practises to increase quality. Typically, these standards will strongly encourage or enforce the application of formal methods. The application of formal methods can entail a significant amount of mathematical reasoning. Thus, the development of automated techniques is an active area of research. The trend is to deliver increased automation through two complementary approaches. Firstly, lightweight formal methods are adopted, sacrificing expressive power, breadth of coverage, or both in favour of tractability. Secondly, integrated solutions are sought, exploiting the strengths of different technologies to increase automation. The objective of this thesis is to support the production of high integrity software by automating an aspect of formal methods. To develop tractable techniques we focus on the niche activity of verifying exception freedom. To increase effectiveness, we integrate the complementary technologies of proof planning and program analysis. Our approach is investigated by enhancing the SPARK Approach, as developed by Altran Praxis Limited. Our approach is implemented and evaluated as the SPADEase system. The key contributions of the thesis are summarised below: • Configurable and Sound - Present a configurable and justifiably sound approach to software verification. • Cooperative Integration - Demonstrate that more targeted and effective automation can be achieved through the cooperative integration of distinct technologies. • Proof Discovery - Present proof plans that support the verification of exception freedom. • Invariant Discovery - Present invariant discovery heuristics that support the verification of exception freedom. • Implementation as SPADEase - Implement our approach as SPADEase. • Industrial Evaluation - Evaluate SPADEase against both textbook and industrial subprograms

Regulation of human pancreas hormone secretion by autonomic innervation

Diabetes mellitus is a silent killer doing away with one person every 10 seconds. We speak of diabetes when the organism cannot control the right level of glucose in the blood. The hormones insulin and glucagon secreted by the islets of Langerhans are the major players maintaining glucose homeostasis. In the living organism, the function of the islets is orchestrated by their interaction with other organs through the vasculature and with the nervous system. Most of our current knowledge of islet biology has been obtained by using mouse models, but caution is needed, as mice are not simply small humans. Indeed, recent studies have revealed that the cell composition and architecture of the human islet are different from that of mouse islets. Thus, other important features such as nervous regulation of islet function may also be different. The work in this thesis aimed to identify the role of innervation for islet function. Our hypothesis is that autonomic and paracrine signals are involved in islet function and that the relative role of these components varies among species. To identify the sympathetic and parasympathetic components of innervation as well as their cellular targets we used immunohistochemical staining of human and mouse pancreatic sections. In contrast to mouse, human islets are devoid of parasympathetic innervation. Instead, human alpha cells possess the machinery for exocytosis of acetylcholine, the major parasympathetic neurotransmitter. Our findings suggest that human islets depend less on neural cholinergic input than mouse islets. Alpha cells secrete acetylcholine as a paracrine signal priming the human beta cell to respond optimally to subsequent increases in glucose concentration. In addition, noradrenergic fibers contact few endocrine cells in the human islet and preferentially innervate smooth muscle cells of the islet vasculature. This suggests that sympathetic innervation regulates hormone secretion by controlling the blood flow rather than modulating endocrine cell function directly. By taking advantage of our recently developed noninvasive anterior chamber of the eye imaging platform we were able to study the role of innervation in the maintenance of glucose homeostasis in vivo. We studied the process of reinnervation and revascularization of intraocular islet grafts and showed that islets orchestrate the process of engraftment to restore their original microenvironment. Islet grafts from two different mouse strains and human xenografts showed innervation patterns similar to those in pancreatic sections in situ. Islet grafts displayed the characteristic fenestrae of the pancreatic vascular endothelium independently of the origin of the new vessels. In addition, the model allowed controlling the fraction of the graft vasculature that is contributed by the donor islet endothelial cells to the point that the original donor vasculature of the islet is restored. Recording graft function while manipulating the eye’s neural input through the pupillary light reflex revealed functional differences in parasympathetic innervation between the two mouse strains. The eye platform also allowed us to follow cell dynamics during immune responses, which will enable investigations aimed at clarifying the role of innervation in the pathogenesis of autoimmune diabetes. To study human islet biology in vivo we further adopted the eye model by transplanting human islets into the eye of diabetic immune compromised mice. Human xenografts reversed diabetes and tightly controlled plasma glucose concentrations. Moreover, our results provided the first real time monitoring of revascularization and blood flow inside human islets and graft function could be modulated by local drug administration. Our findings establish a “humanized” mouse model to investigate human islet biology in vivo that will allow addressing how nervous input affects endocrine function or blood flow in human islets. The physiological relevance of the anterior chamber of the eye model is further underscored by the therapeutic potential as a novel transplantation site to treat type 1 diabetic patients