Automatic Analysis and Validation of the Chemical Literature

ThesisMethods to automatically extract and validate data from the chemical literature in legacy formats to machine-understandable forms are examined. The work focuses of three types of data: analytical data reported in articles, computational chemistry output files and crystallographic information files (CIFs). It is shown that machines are capable of reading and extracting analytical data from the current legacy formats with high recall and precision. Regular expressions cannot identify chemical names with high precision or recall but non-deterministic methods perform significantly better. The lack of machine-understandable connection tables in the literature has been identified as the major issue preventing molecule-based data-driven science being performed in the area. The extraction of data from computational chemistry output files using parser-like approaches is shown to be not generally possible although such methods work well for input files. A hierarchical regular expression based approach can parse > 99:9% of the output files correctly although significant human input is required to prepare the templates. CIFs may be parsed with extremely high recall and precision, contain connection tables and the data is of high quality. The comparison of bond lengths calculated by two computational chemistry programs show good agreement in general but structures containing specific moieties cause discrepancies. An initial protocol for the high-throughput geometry optimisation of molecules extracted from the CIFs is presented and the refinement of this protocol is discussed. Differences in bond length between calculated and experimentally determined values from the CIFs of less than 0.03 Angstrom are shown to be expected by random error. The final protocol is used to find high-quality structures from crystallography which can be reused for further science.Unilever Centre for Molecular Science Informatic

The Rocketbox Library and the Utility of Freely Available Rigged Avatars

As part of the open sourcing of the Microsoft Rocketbox avatar library for research and academic purposes, here we discuss the importance of rigged avatars for the Virtual and Augmented Reality (VR, AR) research community. Avatars, virtual representations of humans, are widely used in VR applications. Furthermore many research areas ranging from crowd simulation to neuroscience, psychology, or sociology have used avatars to investigate new theories or to demonstrate how they influence human performance and interactions. We divide this paper in two main parts: the first one gives an overview of the different methods available to create and animate avatars. We cover the current main alternatives for face and body animation as well introduce upcoming capture methods. The second part presents the scientific evidence of the utility of using rigged avatars for embodiment but also for applications such as crowd simulation and entertainment. All in all this paper attempts to convey why rigged avatars will be key to the future of VR and its wide adoption

An incremental approach for real-time Big Data visual analytics

In the age of Big Data, the real-time interactive visualization is a challenge due to latency of executing calculation over terabytes (even, petabytes) datasets. The execution of an operation has to finish before its outcome is displayed, which would be an issue in those scenarios where low-latency responses are required. To address such a requirement, this paper introduces a new approach for real-time visualization of extremely large data-at-rest as well as data-in-motion by showing intermediate results as soon as they become available. This should allow the data analyst to take decisions in real-time

3D-based Advanced Machine Service Support

In the face of today's unpredictable and fluctuating global market, there have been trends in industry towards wider adoption of more advanced and flexible new generation manufacturing systems. These have brought about new challenges to manufacturing equipment builders/suppliers in respect of satisfying ever-increasing customers' requirements for such advanced manufacturing systems. To stay competitive, in addition to supplying high quality equipment, machine builders/suppliers must also be capable of providing their customers with cost-effective, efficient and comprehensive service support, throughout the equipment's lifecycle. This research study has been motivated by the relatively unexplored potential of integrating 3D virtual technology with various machine service support tools/techniques to address the aforementioned challenges. The hypothesis formulated for this study is that a 3D-based virtual environment can be used as an integration platform to improve service support for new generation manufacturing systems. In order to ensure the rigour of the study, it has been initiated with a two-stage (iterative) literature review, consisting of: a preliminary review for the identification of practical problems/main issues related to the area of machine service support and in-depth reviews for the identification of research problems/questions and potential solutions. These were then followed by iterations of intensive research activities, consisting of: requirements identification, concept development, prototype implementation, testing and exploration, reflection and feedback. The process has been repeated and revised continuously until satisfactory results, required for answering the identified research problems/questions, were obtained. The main focus of this study is exploring how a 3D-based virtual environment can be used as an integration platform for supporting a more cost-effective and comprehensive strategy for improving service support for new generation manufacturing systems. One of the main outcomes of this study is the proposal of a conceptual framework for a novel 3D-based advanced machine service support strategy and a reference architecture for a corresponding service support system, for allowing machine builders/suppliers to: (1) provide more cost-effective remote machine maintenance support, and (2) provide more efficient and comprehensive extended service support during the equipment's life cycle. The proposed service support strategy advocates the tight integration of conventional (consisting of mainly machine monitoring, diagnostics, prognostics and maintenance action decision support) and extended (consisting of mainly machine re-configuration, upgrade and expansion support) service support functions. The proposed service support system is based on the integration of a 3D-based virtual environment with the equipment control system, a re-configurable automated service support system, coupled with a maintenance-support-tool/strategy support environment and an equipment re-configuration/upgrade/expansion support environment, in a network/lntenet framework. The basic concepts, potential benefits and limitations of the proposed strategy/ system have been explored via a prototype based on a laboratory-scale test bed. The prototype consists of a set of integrated modular network-ready software tools consisting of: (1) an integrated 20/30 visualisation and analysis module, (2) support tools library modules, (3) communication modules and (4) a set of modular and re-configurable automated data logging, maintenance and re-configuration support modules. A number of test cases based on various machine service support scenarios, have been conducted using the prototype. The experimentation has shown the potential and feasibility (technical implementation aspects) of the proposed 3D-based approach. This research study has made an original contribution to knowledge in the field of machine service support. It has contributed a novel approach of using a 3D-based virtual environment as an integration platform for improving the capability of machine builders/suppliers in providing more cost-effective and comprehensive machine service support for complex new generation manufacturing systems. Several important findings have resulted from this work in particular with respect to how various 20/30 visualisation environments are integrated with machine service support tools/techniques for improving service support for complex manufacturing systems. A number of aspects have also been identified for future work

Adaptive user interfaces for mobile map-based visualisation

Mobile devices today frequently serve as platforms for the visualisation of map-based data. Despite the obvious advantages, mobile map-based visualisation (MMV) systems are often difficult to design and use. Limited screen space, resource constraints and awkward interaction mechanisms are among the many problems with which designers and users have to contend. Adaptive user interfaces (AUIs), which adapt to the individual user, represent a possible means of addressing the problems of MMV. Adaptive MMV systems are, however, generally designed in an ad-hoc fashion, making the benefits achieved difficult to replicate. In addition, existing models for adaptive MMV systems are either conceptual in nature or only address a subset of the possible input variables and adaptation effects. The primary objective of this research was to develop and evaluate an adaptive MMV system using a model-based approach. The Proteus Model was proposed to support the design of MMV systems which adapt in terms of information, visualisation and user interface in response to the user‟s behaviour, tasks and context. The Proteus Model describes the architectural, interface, data and algorithm design of an adaptive MMV system. A prototype adaptive MMV system, called MediaMaps, was designed and implemented based on the Proteus Model. MediaMaps allows users to capture, location-tag, organise and visualise multimedia on their mobile phones. Information adaptation is performed through the use of an algorithm to assist users in sorting media items into collections based on time and location. Visualisation adaptation is performed by adapting various parameters of the map-based visualisations according to user preferences. Interface adaptation is performed through the use of adaptive lists. An international field study of MediaMaps was conducted in which participants were required to use MediaMaps on their personal mobile phones for a period of three weeks. The results of the field study showed that high levels of accuracy were achieved by both the information and interface adaptations. High levels of user satisfaction were reported, with participants rating all three forms of adaptation as highly useful. The successful implementation of MediaMaps provides practical evidence that the model-based design of adaptive MMV systems is feasible. The positive results of the field study clearly show that the adaptations implemented were highly accurate and that participants found these adaptations to be useful, usable and easy to understand. This research thus provides empirical evidence that the use of AUIs can provide significant benefits for the visualisation of map-based information on mobile devices

Bayesian image restoration and bacteria detection in optical endomicroscopy

Optical microscopy systems can be used to obtain high-resolution microscopic images of tissue cultures and ex vivo tissue samples. This imaging technique can be translated for in vivo, in situ applications by using optical fibres and miniature optics. Fibred optical endomicroscopy (OEM) can enable optical biopsy in organs inaccessible by any other imaging systems, and hence can provide rapid and accurate diagnosis in a short time. The raw data the system produce is difficult to interpret as it is modulated by a fibre bundle pattern, producing what is called the “honeycomb effect”. Moreover, the data is further degraded due to the fibre core cross coupling problem. On the other hand, there is an unmet clinical need for automatic tools that can help the clinicians to detect fluorescently labelled bacteria in distal lung images. The aim of this thesis is to develop advanced image processing algorithms that can address the above mentioned problems. First, we provide a statistical model for the fibre core cross coupling problem and the sparse sampling by imaging fibre bundles (honeycomb artefact), which are formulated here as a restoration problem for the first time in the literature. We then introduce a non-linear interpolation method, based on Gaussian processes regression, in order to recover an interpretable scene from the deconvolved data. Second, we develop two bacteria detection algorithms, each of which provides different characteristics. The first approach considers joint formulation to the sparse coding and anomaly detection problems. The anomalies here are considered as candidate bacteria, which are annotated with the help of a trained clinician. Although this approach provides good detection performance and outperforms existing methods in the literature, the user has to carefully tune some crucial model parameters. Hence, we propose a more adaptive approach, for which a Bayesian framework is adopted. This approach not only outperforms the proposed supervised approach and existing methods in the literature but also provides computation time that competes with optimization-based methods

High-resolution imaging beneath the Santorini volcano

Volcanoes are surface expressions of much deeper magmatic systems, inaccessible to direct observation. Constraining the geometry and physical properties of these systems, in particular detecting high melt fraction (magma) reservoirs, is key to managing a volcanic hazard and understanding fundamental processes that lead to the formation of continents. Unfortunately, unambiguous evidence of magma reservoirs has not yet been provided due to the limited resolving power of the geophysical methods used so far. Here, a high-resolution imaging technique called full-waveform inversion was applied to study the magmatic system beneath the Santorini volcanic field, one of the most volcanically and seismically active regions of Europe. Quality-controlled inversion of 3d wide-angle, multi-azimuth ocean-bottom seismic data revealed a previously undetected high melt fraction reservoir 3 km beneath the Kolumbo volcano, a centre of microseismic and hydrothermal activity of the field. To enable the above method to handle land data, two major algorithmic improvements were added to the high-performance inversion code. First, to simulate instrument response of land seismometers, a pressure-velocity conversion has been implemented in a way that ensures reciprocity of the discretised 2nd-order acoustic wave equation. Second, the immersed-boundary method, originally developed for computational fluid dynamics, was implemented to simulate the wave-scattering off the irregular topography of the Santorini caldera. These advancements can be readily used to provide a higher-resolution image of the melt reservoir beneath the Santorini caldera already detected by means of travel-time tomography.Open Acces