Staff within the Department of Computer Science have research interests in Visualization, Interaction & Computer Graphics (with a particular focus on Medical Graphics), Cyber Security and Discrete Optimisation.

Recent Submissions

  • Visualization for Epidemiological Modelling: Challenges, Solutions, Reflections & Recommendations

    Dykes, Jason; Abdul-Rahman, Alfie; Archambault, Daniel; Bach, Benjamin; Borgo, Rita; Chen, Min; Enright, Jessica; Fang, Hui; Firat, Elif E.; Freeman, Euan; et al.
    We report on an ongoing collaboration between epidemiological modellers and visualization researchers by documenting and reflecting upon knowledge constructs – a series of ideas, approaches and methods taken from existing visualization research and practice – deployed and developed to support modelling of the COVID-19 pandemic. Structured independent commentary on these efforts is synthesized through iterative reflection to develop: evidence of the effectiveness and value of visualization in this context; open problems upon which the research communities may focus; guidance for future activity of this type; and recommendations to safeguard the achievements and promote, advance, secure and prepare for future collaborations of this kind. In describing and comparing a series of related projects that were undertaken in unprecedented conditions, our hope is that this unique report, and its rich interactive supplementary materials, will guide the scientific community in embracing visualization in its observation, analysis and modelling of data as well as in disseminating findings. Equally we hope to encourage the visualization community to engage with impactful science in addressing its emerging data challenges. If we are successful, this showcase of activity may stimulate mutually beneficial engagement between communities with complementary expertise to address problems of significance in epidemiology and beyond.
  • A survey of modern deep learning based object detection models

    Zaidi, Syed Sahil Abbas; Ansari, Mohammad Samar; Aslam, Asra; Kanwal, Nadia; Asghar, Mamoona; Lee, Brian; Technological University of the Shannon; University of Chester; National University of Ireland; Keele University; Lahore College for Women University (Elsevier, 2022-03-08)
    Object Detection is the task of classification and localization of objects in an image or video. It has gained prominence in recent years due to its widespread applications. This article surveys recent developments in deep learning based object detectors. Concise overview of benchmark datasets and evaluation metrics used in detection is also provided along with some of the prominent backbone architectures used in recognition tasks. It also covers contemporary lightweight classification models used on edge devices. Lastly, we compare the performances of these architectures on multiple metrics.
  • Immersive Virtual Reality for the Cognitive Rehabilitation of Stroke Survivors

    Chatterjee, Kausik; Buchanan, Alastair; Cottrell, Katy; Hughes, Sara; Day, Thomas W.; John, Nigel W.; Countess of Chester Hospital NHS Foundation Trust; Cadscan Limited; University of Chester (IEEE, 2022-03-10)
    We present the results of a double-blind phase 2b randomized control trial that used a custom built virtual reality environment for the cognitive rehabilitation of stroke survivors. A stroke causes damage to the brain and problem solving, memory and task sequencing are commonly affected. The brain can recover to some extent, however, and stroke patients have to relearn how to carry out activities of daily living. We have created an application called VIRTUE to enable such activities to be practiced using immersive virtual reality. Gamification techniques enhance the motivation of patients such as by making the level of difficulty of a task increase over time. The design and implementation of VIRTUE is described together with the results of the trial conducted within the Stroke Unit of a large hospital. We report on the safety and acceptability of VIRTUE. We have also observed particular benefits of VR treatment for stroke survivors that experienced more severe cognitive impairment, and an encouraging reduction in time spent in the hospital for all patients that received the VR treatment.
  • LevelEd SR: A Substitutional Reality Level Design Workflow

    Beever, Lee; John, Nigel W.; University of Chester
    Virtual reality (VR) and augmented reality (AR) have continued to increase in popularity over the past decade. However, there are still issues with how much space is required for room-scale VR and experiences are still lacking from haptic feedback. We present LevelEd SR, a substitutional reality level design workflow that combines AR and VR systems and is built for consumer devices. The system enables passive haptics through the inclusion of physical objects from within a space into a virtual world. A validation study (17 participants) has produced quantitative data that suggests players benefit from passive haptics in entertainment VR games with an improved game experience and increased levels of presence. Including objects, such as real-world furniture that is paired with a digital proxy in the virtual world, also opens up more spaces to be used for room-scale VR. We evaluated the workflow and found that participants were accepting of the system, rating it positively using the System Usability Scale questionnaire and would want to use it again to experience substitutional reality.
  • Application of Virtual Reality and Electrodermal Activity for the Detection of Cognitive Impairments

    Patient, Rebecca; Ghali, Fawaz; Kolivand, Hoshang; Hurst, William; John, Nigel W.; Liverpool John Moores; Wageningen University; University of Chester (IEEE, 2022-03-01)
    Mild Cognitive Impairment (MCI) is a definition of the diagnosis of early memory loss and disorientation. This study aims to identify people’s symptoms through technology. However, machine learning (ML) can classify Cognitive Normal (CN) and Mild Cognitive Impairment (MCI) and Early Mild Cognitive Impairment (EMCI) using standard assessments from the Alzheimer’s Disease Neuroimaging Initiative (ADNI); Montreal Cognitive (MoCA), Mini-Mental State Examination (MMSE), Functional Activities Questionnaire (FAQ). Consequently, a Multilayer Perceptron (MLP) model was assembled into tables; MCI vs CN, MCI vs EMCI, and CN vs MCI. Additionally, an MLP model was developed for CN vs MCI vs EMCI. As a result, of advanced model performance, a cascade 3-path categorisation approach was created. Similarly, the exploitation of meta-analysis indicated a combination of MLP models (MCI vs CN, MCI vs EMCI, and CN vs MCI) with an overall accuracy within an acceptable limit. In addition, better results were found when assessments were combined rather than individually. Furthermore, applying class weights and probability thresholds could improve the MLP framework by performance achieving a balanced specificity and sensitivity ratio. Altering class weights and probability thresholds when training the MLP neuro network model, the sensitivity and Accuracy could be progressed further. In conclusion, ML, VR and electrodermal activity are constrained. Introducing the possibility of activity-based applications to enhance innovative solutions for cognitive impairment diagnosis and treatment.
  • Virtual reality training in cardiopulmonary resuscitation in schools

    Rees, Nigel; John, Nigel W.; Beever, Lee; Vaughan, Neil; Powell, C; Fletcher, A; Welsh Ambulance Services NHS Trust; Swansea University; University of Chester; University of Exeter; British Heart Foundation; London School of Hygiene & Tropical Medicine (Mark Allen Healthcare, 2021-09-11)
    UK average survival from Out of Hospital Cardiac Arrest (OHCA) survival is around 8.6%, which is significantly lower than other high performing countries with survival rates of over 20%. A cardiac arrest victim is 2–4 times more likely to survive OHCA with bystander CPR provision. Mandatory Teaching CPR to children in school is acknowledged to be the most effective way to reach the entire population and improving the bystander CPR rate and is endorsed by the World Health Organization (WHO) “Kids Save Lives” statement. Despite this, Wales is yet to follow other home nations by including CPR training as a mandatory within the school’s curriculum. In this paper, we explore the role of teaching CPR to schoolchildren and report on the development by Computer scientists at the University of Chester and the Welsh Ambulance Services NHS Trust (WAST) of VCPR, a virtual environment to help teach the procedure. VCPR was developed in three stages: identifying requirements and specifications; development of a prototype; and management—development of software, further funding and exploring opportunities for commercialisation. We describe the opportunities in Wales to skill up the whole population over time in CPR and present our Virtual reality (VR) technology is emerging as a powerful for teaching CPR in schools.
  • Talos: a prototype Intrusion Detection and Prevention system for profiling ransomware behaviour

    Wood, Ashley; Eze, Thaddeus; Speakman, Lee; University of Chester (Academic Conferences International, 2021-06-24)
    Abstract: In this paper, we profile the behaviour and functionality of multiple recent variants of WannaCry and CrySiS/Dharma, through static and dynamic malware analysis. We then analyse and detail the commonly occurring behavioural features of ransomware. These features are utilised to develop a prototype Intrusion Detection and Prevention System (IDPS) named Talos, which comprises of several detection mechanisms/components. Benchmarking is later performed to test and validate the performance of the proposed Talos IDPS system and the results discussed in detail. It is established that the Talos system can successfully detect all ransomware variants tested, in an average of 1.7 seconds and instigate remedial action in a timely manner following first detection. The paper concludes with a summarisation of our main findings and discussion of potential future works which may be carried out to allow the effective detection and prevention of ransomware on systems and networks.
  • An Endoscope Interface for Immersive Virtual Reality

    John, Nigel W.; Day, Thomas W.; Wardle, Terrence; University of Chester
    This is a work in progress paper that describes a novel endoscope interface designed for use in an immersive virtual reality surgical simulator. We use an affordable off the shelf head mounted display to recreate the operating theatre environment. A hand held controller has been adapted so that it feels like the trainee is holding an endoscope controller with the same functionality. The simulator allows the endoscope shaft to be inserted into a virtual patient and pushed forward to a target position. The paper describes how we have built this surgical simulator with the intention of carrying out a full clinical study in the near future.
  • ParaVR: A Virtual Reality Training Simulator for Paramedic Skills maintenance

    Rees, Nigel; Dorrington, Keith; Rees, Lloyd; Day, Thomas W; Vaughan, Neil; John, Nigel W; Welsh Ambulance Services NHS Trust, University of Chester
    Background, Virtual Reality (VR) technology is emerging as a powerful educational tool which is used in medical training and has potential benefits for paramedic practice education. Aim The aim of this paper is to report development of ParaVR, which utilises VR to address skills maintenance for paramedics. Methods Computer scientists at the University of Chester and the Welsh Ambulance Services NHS Trust (WAST) developed ParaVR in four stages: 1. Identifying requirements and specifications 2. Alpha version development, 3. Beta version development 4. Management: Development of software, further funding and commercialisation. Results Needle Cricothyrotomy and Needle Thoracostomy emerged as candidates for the prototype ParaVR. The Oculus Rift head mounted display (HMD) combined with Novint Falcon haptic device was used, and a virtual environment crafted using 3D modelling software, ported (a computing term meaning transfer (software) from one system or machine to another) onto Oculus Go and Google cardboard VR platform. Conclusion VR is an emerging educational tool with the potential to enhance paramedic skills development and maintenance. The ParaVR program is the first step in our development, testing, and scaling up of this technology.
  • LevelEd VR: A virtual reality level editor and workflow for virtual reality level design

    Beever, Lee; Pop, Serban W.; John, Nigel W.; University of Chester
    Virtual reality entertainment and serious games popularity has continued to rise but the processes for level design for VR games has not been adequately researched. Our paper contributes LevelEd VR; a generic runtime virtual reality level editor that supports the level design workflow used by developers and can potentially support user generated content. We evaluated our LevelEd VR application and compared it to an existing workflow of Unity on a desktop. Our current research indicates that users are accepting of such a system, and it has the potential to be preferred over existing workflows for VR level design. We found that the primary benefit of our system is an improved sense of scale and perspective when creating the geometry and implementing gameplay. The paper also contributes some best practices and lessons learned from creating a complex virtual reality tool, such as LevelEd VR.
  • Formal Verification of Astronaut-Rover Teams for Planetary Surface Operations

    Webster, Matt; Dennis, Louise A; Dixon, Clare; Fisher, Michael; Stocker, Richard; Sierhuis, Maarten; University of Liverpool; University of Chester; Ejenta, inc.
    This paper describes an approach to assuring the reliability of autonomous systems for Astronaut-Rover (ASRO) teams using the formal verification of models in the Brahms multi-agent modelling language. Planetary surface rovers have proven essential to several manned and unmanned missions to the moon and Mars. The first rovers were tele- or manuallyoperated, but autonomous systems are increasingly being used to increase the effectiveness and range of rover operations on missions such as the NASA Mars Science Laboratory. It is anticipated that future manned missions to the moon and Mars will use autonomous rovers to assist astronauts during extravehicular activity (EVA), including science, technical and construction operations. These ASRO teams have the potential to significantly increase the safety and efficiency of surface operations. We describe a new Brahms model in which an autonomous rover may perform several different activities including assisting an astronaut during EVA. These activities compete for the autonomous rovers “attention’ and therefore the rover must decide which activity is currently the most important and engage in that activity. The Brahms model also includes an astronaut agent, which models an astronauts predicted behaviour during an EVA. The rover must also respond to the astronauts activities. We show how this Brahms model can be simulated using the Brahms integrated development environment. The model can then also be formally verified with respect to system requirements using the SPIN model checker, through automatic translation from Brahms to PROMELA (the input language for SPIN). We show that such formal verification can be used to determine that mission- and safety critical operations are conducted correctly, and therefore increase the reliability of autonomous systems for planetary rovers in ASRO teams.
  • Towards Cyber-User Awareness: Design and Evaluation

    Oyinloye, Toyosi; Eze, Thaddeus; Speakman, Lee; University of Chester
    Human reliance on interconnected devices has given rise to a massive increase in cyber activities. There are about 17 billion interconnected devices in our World of about 8 billion people. Like the physical world, the cyber world is not void of entities whose activities, malicious or not, could be detrimental to other users who remain vulnerable as a result of their existence within cyberspace. Developments such as the introduction of 5G networks which advances communication speed among interconnected devices, undoubtedly proffer solutions for human living as well as adversely impacting systems. Vulnerabilities in applications embedded in devices, hardware deficiencies, user errors, are some of the loopholes that are exploited. Studies have revealed humans as weakest links in the cyber-chain, submitting that consistent implementation of cyber awareness programs would largely impact cybersecurity. Cyber-active systems have goals that compete with the implementation of cyber awareness programs, within limited resources. It is desirable to have cyber awareness systems that can be tailored around specific needs and considerations for important factors. This paper presents a system that aims to promote user awareness through a flexible, accessible, and cost-effective design. The system implements steps in a user awareness cycle, that considers human-factor (HF) and HF related root causes of cyber-attacks. We introduce a new user testing tool, adaptable for administering cybersecurity test questions for varying levels and categories of users. The tool was implemented experimentally by engaging cyber users within UK. Schemes and online documentations by UK Cybersecurity organisations were harnessed for assessing and providing relevant recommendations to participants. Results provided us with values representing each participants’ notional level of awareness which were subjected to a paired-T test for comparison with values derived in an automated assessment. This pilot study provides valuable details for projecting the efficacy of the system towards improving human influence in cybersecurity.
  • The Evolution of Ransomware Variants

    Wood, Ashley; Eze, Thaddeus
    Abstract: This paper investigates how ransomware is continuing to evolve and adapt as time progresses to become more damaging, resilient and sophisticated from one ransomware variant to another. This involves investigating how each ransomware sample including; Petya, WannaCry and CrySiS/Dharma interacts with the underlying system to implicate on both the systems functionality and its underlying data, by utilising several static and dynamic analysis tools. Our analysis shows, whilst ransomware is undoubtedly becoming more sophisticated, fundamental problems exist with its underlying encryption processes which has shown data recovery to be possible across all three samples studied whilst varying aspects of system functionality can be preserved or restored in their entirety.
  • Modelling the effects of glucagon during glucose tolerance testing

    Kelly, Ross A; Fitches, Molly J; Webb, Steven D; Pop, Serban R; Chidlow, Stewart J; Liverpool John Moores University; University of Dundee; University of Chester
    Background Glucose tolerance testing is a tool used to estimate glucose effectiveness and insulin sensitivity in diabetic patients. The importance of such tests has prompted the development and utilisation of mathematical models that describe glucose kinetics as a function of insulin activity. The hormone glucagon, also plays a fundamental role in systemic plasma glucose regulation and is secreted reciprocally to insulin, stimulating catabolic glucose utilisation. However, regulation of glucagon secretion by α-cells is impaired in type-1 and type-2 diabetes through pancreatic islet dysfunction. Despite this, inclusion of glucagon activity when modelling the glucose kinetics during glucose tolerance testing is often overlooked. This study presents two mathematical models of a glucose tolerance test that incorporate glucose-insulin-glucagon dynamics. The first model describes a non-linear relationship between glucagon and glucose, whereas the second model assumes a linear relationship. Results Both models are validated against insulin-modified and glucose infusion intravenous glucose tolerance test (IVGTT) data, as well as insulin infusion data, and are capable of estimating patient glucose effectiveness (sG) and insulin sensitivity (sI). Inclusion of glucagon dynamics proves to provide a more detailed representation of the metabolic portrait, enabling estimation of two new diagnostic parameters: glucagon effectiveness (sE) and glucagon sensitivity (δ). Conclusions The models are used to investigate how different degrees of patient glucagon sensitivity and effectiveness affect the concentration of blood glucose and plasma glucagon during IVGTT and insulin infusion tests, providing a platform from which the role of glucagon dynamics during a glucose tolerance test may be investigated and predicted.
  • In vitro and Computational Modelling of Drug Delivery across the Outer Blood-Retinal Barrier

    Davies, Alys E; Williams, Rachel L.; Lugano, Gaia; Pop, Serban R.; Kearns, Victoria R.; University of Liverpool; University of Chester
    The ability to produce rapid, cost-effective and human-relevant data has the potential to accelerate development of new drug delivery systems. Intraocular drug delivery is an area undergoing rapid expansion due to the increase in sight-threatening diseases linked to increasing age and lifestyle factors. The outer bloodretinal barrier (OBRB) is important in this area of drug delivery, as it separates the eye from the systemic blood flow. This study reports the development of complementary in vitro and in silico models to study drug transport from silicone oil across the outer blood-retinal barrier. Monolayer cultures of a human retinal pigmented epithelium cell line, ARPE-19, were added to chambers and exposed to a controlled flow to simulate drug clearance across the OBRB. Movement of dextran molecules and release of ibuprofen from silicone oil in this model were measured. Corresponding simulations were developed using COMSOL Multiphysics computational fluid dynamics (CFD) software and validated using independent in vitro data sets. Computational simulations were able to predict dextran movement and ibuprofen release, with all of the features of the experimental release profiles being observed in the simulated data. Simulated values for peak concentrations of permeated dextran and ibuprofen released from silicone oil were within 18% of the in vitro results. This model could be used as a predictive tool of drug transport across this important tissue.
  • Self-supervised monocular image depth learning and confidence estimation

    Chen, Long; Tang, Wen; Wan, Tao Ruan; John, Nigel W.; Bournemouth University; University of Bradford; University of Chester
    We present a novel self-supervised framework for monocular image depth learning and confidence estimation. Our framework reduces the amount of ground truth annotation data required for training Convolutional Neural Networks (CNNs), which is often a challenging problem for the fast deployment of CNNs in many computer vision tasks. Our DepthNet adopts a novel fully differential patch-based cost function through the Zero-Mean Normalized Cross Correlation (ZNCC) to take multi-scale patches as matching and learning strategies. This approach greatly increases the accuracy and robustness of the depth learning. Whilst the proposed patch-based cost function naturally provides a 0-to-1 confidence, it is then used to self-supervise the training of a parallel network for confidence map learning and estimation by exploiting the fact that ZNCC is a normalized measure of similarity which can be approximated as the confidence of the depth estimation. Therefore, the proposed corresponding confidence map learning and estimation operate in a self-supervised manner and is a parallel network to the DepthNet. Evaluation on the KITTI depth prediction evaluation dataset and Make3D dataset show that our method outperforms the state-of-the-art results.
  • VRIA: A Web-based Framework for Creating Immersive Analytics Experiences

    Butcher, Peter; John, Nigel W; Ritsos, Panagiotis D.; University of Chester and Bangor University (IEEE, 2020-01-09)
    We present<VRIA>, a Web-based framework for creating Immersive Analytics (IA) experiences in Virtual Reality.<VRIA>is built upon WebVR, A-Frame, React and D3.js, and offers a visualization creation workflow which enables users, of different levels of expertise, to rapidly develop Immersive Analytics experiences for the Web. The use of these open-standards Web-based technologies allows us to implement VR experiences in a browser and offers strong synergies with popular visualization libraries, through the HTMLDocument Object Model (DOM). This makes<VRIA>ubiquitous and platform-independent. Moreover, by using WebVR’s progressive enhancement, the experiences<VRIA>creates are accessible on a plethora of devices. We elaborate on our motivation for focusing on open-standards Web technologies, present the<VRIA>creation workflow and detail the underlying mechanics of our framework. We also report on techniques and optimizations necessary for implementing Immersive Analytics experiences on the Web, discuss scalability implications of our framework, and present a series of use case applications to demonstrate the various features of <VRIA>. Finally, we discuss current limitations of our framework, the lessons learned from its development, and outline further extensions.
  • Translational Medicine: Challenges and new orthopaedic vision (Mediouni-Model)

    Mediouni, Mohamed; Madiouni, Riadh; Gardner, Michael; Vaughan, Neil; University of Chester, UK
    Background: In North America and three European countries Translational Medicine (TM) funding has taken center stage as the National Institutes of Health (NIH), for example, has come to recognize that delays are common place in completing clinical trials based upon benchside advancements. Recently, there are several illustrative examples whereby the translation of research had untoward outcomes requiring immediate action. Methods: Focus more on three-dimensional (3D) simulation, biomarkers, and Artificial Intelligence may allow orthopaedic surgeons to predict the ideal practices before orthopaedic surgery. Using the best medical imaging techniques may improve the accuracy and precision of tumor resections. Results: This article is directed at the young surgeon scientist and in particular orthopaedic residents and all other junior physicians in training to help them better understand TM and position themselves in career paths and hospital systems that strive for optimal TM. It serves to hasten the movement of knowledge garnered from the benchside and move it quickly to the bedside. Conclusions: Communication is ongoing in a bidirectional format. It is anticipated that more and more medical Centers and institutions will adopt TM models of healthcare delivery.
  • An overview of self-adaptive technologies within virtual reality training

    Vaughan, Neil; Gabrys, Bogdan; Dubey, Venketesh; University of Chester
    This overview presents the current state-of-the-art of self-adaptive technologies within virtual reality (VR) training. Virtual reality training and assessment is increasingly used for five key areas: medical, industrial & commercial training, serious games, rehabilitation and remote training such as Massive Open Online Courses (MOOCs). Adaptation can be applied to five core technologies of VR including haptic devices, stereo graphics, adaptive content, assessment and autonomous agents. Automation of VR training can contribute to automation of actual procedures including remote and robotic assisted surgery which reduces injury and improves accuracy of the procedure. Automated haptic interaction can enable tele-presence and virtual artefact tactile interaction from either remote or simulated environments. Automation, machine learning and data driven features play an important role in providing trainee-specific individual adaptive training content. Data from trainee assessment can form an input to autonomous systems for customised training and automated difficulty levels to match individual requirements. Self-adaptive technology has been developed previously within individual technologies of VR training. One of the conclusions of this research is that while it does not exist, an enhanced portable framework is needed and it would be beneficial to combine automation of core technologies, producing a reusable automation framework for VR training.
  • De-smokeGCN: Generative Cooperative Networks for Joint Surgical Smoke Detection and Removal

    Chen, Long; Tang, Wen; John, Nigel W.; Wan, Tao Ruan; Zhang, Jian Jun; Bournemouth University; University of Chester; University of Bradford (IEEE XPlore, 2019-11-15)
    Surgical smoke removal algorithms can improve the quality of intra-operative imaging and reduce hazards in image-guided surgery, a highly desirable post-process for many clinical applications. These algorithms also enable effective computer vision tasks for future robotic surgery. In this paper, we present a new unsupervised learning framework for high-quality pixel-wise smoke detection and removal. One of the well recognized grand challenges in using convolutional neural networks (CNNs) for medical image processing is to obtain intra-operative medical imaging datasets for network training and validation, but availability and quality of these datasets are scarce. Our novel training framework does not require ground-truth image pairs. Instead, it learns purely from computer-generated simulation images. This approach opens up new avenues and bridges a substantial gap between conventional non-learning based methods and which requiring prior knowledge gained from extensive training datasets. Inspired by the Generative Adversarial Network (GAN), we have developed a novel generative-collaborative learning scheme that decomposes the de-smoke process into two separate tasks: smoke detection and smoke removal. The detection network is used as prior knowledge, and also as a loss function to maximize its support for training of the smoke removal network. Quantitative and qualitative studies show that the proposed training framework outperforms the state-of-the-art de-smoking approaches including the latest GAN framework (such as PIX2PIX). Although trained on synthetic images, experimental results on clinical images have proved the effectiveness of the proposed network for detecting and removing surgical smoke on both simulated and real-world laparoscopic images.

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