Exploring variability in medical imaging

Although recent successes of deep learning and novel machine learning techniques improved the perfor- mance of classification and (anomaly) detection in computer vision problems, the application of these methods in medical imaging pipeline remains a very challenging task. One of the main reasons for this is the amount of variability that is encountered and encapsulated in human anatomy and subsequently reflected in medical images. This fundamental factor impacts most stages in modern medical imaging processing pipelines. Variability of human anatomy makes it virtually impossible to build large datasets for each disease with labels and annotation for fully supervised machine learning. An efficient way to cope with this is to try and learn only from normal samples. Such data is much easier to collect. A case study of such an automatic anomaly detection system based on normative learning is presented in this work. We present a framework for detecting fetal cardiac anomalies during ultrasound screening using generative models, which are trained only utilising normal/healthy subjects. However, despite the significant improvement in automatic abnormality detection systems, clinical routine continues to rely exclusively on the contribution of overburdened medical experts to diagnosis and localise abnormalities. Integrating human expert knowledge into the medical imaging processing pipeline entails uncertainty which is mainly correlated with inter-observer variability. From the per- spective of building an automated medical imaging system, it is still an open issue, to what extent this kind of variability and the resulting uncertainty are introduced during the training of a model and how it affects the final performance of the task. Consequently, it is very important to explore the effect of inter-observer variability both, on the reliable estimation of model’s uncertainty, as well as on the model’s performance in a specific machine learning task. A thorough investigation of this issue is presented in this work by leveraging automated estimates for machine learning model uncertainty, inter-observer variability and segmentation task performance in lung CT scan images. Finally, a presentation of an overview of the existing anomaly detection methods in medical imaging was attempted. This state-of-the-art survey includes both conventional pattern recognition methods and deep learning based methods. It is one of the first literature surveys attempted in the specific research area.Open Acces

Auditory Displays and Assistive Technologies: the use of head movements by visually impaired individuals and their implementation in binaural interfaces

Visually impaired people rely upon audition for a variety of purposes, among these are the use of sound to identify the position of objects in their surrounding environment. This is limited not just to localising sound emitting objects, but also obstacles and environmental boundaries, thanks to their ability to extract information from reverberation and sound reflections- all of which can contribute to effective and safe navigation, as well as serving a function in certain assistive technologies thanks to the advent of binaural auditory virtual reality. It is known that head movements in the presence of sound elicit changes in the acoustical signals which arrive at each ear, and these changes can improve common auditory localisation problems in headphone-based auditory virtual reality, such as front-to-back reversals. The goal of the work presented here is to investigate whether the visually impaired naturally engage head movement to facilitate auditory perception and to what extent it may be applicable to the design of virtual auditory assistive technology. Three novel experiments are presented; a field study of head movement behaviour during navigation, a questionnaire assessing the self-reported use of head movement in auditory perception by visually impaired individuals (each comparing visually impaired and sighted participants) and an acoustical analysis of inter-aural differences and cross- correlations as a function of head angle and sound source distance. It is found that visually impaired people self-report using head movement for auditory distance perception. This is supported by head movements observed during the field study, whilst the acoustical analysis showed that interaural correlations for sound sources within 5m of the listener were reduced as head angle or distance to sound source were increased, and that interaural differences and correlations in reflected sound were generally lower than that of direct sound. Subsequently, relevant guidelines for designers of assistive auditory virtual reality are proposed

State of the art of audio- and video based solutions for AAL

Working Group 3. Audio- and Video-based AAL ApplicationsIt is a matter of fact that Europe is facing more and more crucial challenges regarding health and social care due to the demographic change and the current economic context. The recent COVID-19 pandemic has stressed this situation even further, thus highlighting the need for taking action. Active and Assisted Living (AAL) technologies come as a viable approach to help facing these challenges, thanks to the high potential they have in enabling remote care and support. Broadly speaking, AAL can be referred to as the use of innovative and advanced Information and Communication Technologies to create supportive, inclusive and empowering applications and environments that enable older, impaired or frail people to live independently and stay active longer in society. AAL capitalizes on the growing pervasiveness and effectiveness of sensing and computing facilities to supply the persons in need with smart assistance, by responding to their necessities of autonomy, independence, comfort, security and safety. The application scenarios addressed by AAL are complex, due to the inherent heterogeneity of the end-user population, their living arrangements, and their physical conditions or impairment. Despite aiming at diverse goals, AAL systems should share some common characteristics. They are designed to provide support in daily life in an invisible, unobtrusive and user-friendly manner. Moreover, they are conceived to be intelligent, to be able to learn and adapt to the requirements and requests of the assisted people, and to synchronise with their specific needs. Nevertheless, to ensure the uptake of AAL in society, potential users must be willing to use AAL applications and to integrate them in their daily environments and lives. In this respect, video- and audio-based AAL applications have several advantages, in terms of unobtrusiveness and information richness. Indeed, cameras and microphones are far less obtrusive with respect to the hindrance other wearable sensors may cause to one’s activities. In addition, a single camera placed in a room can record most of the activities performed in the room, thus replacing many other non-visual sensors. Currently, video-based applications are effective in recognising and monitoring the activities, the movements, and the overall conditions of the assisted individuals as well as to assess their vital parameters (e.g., heart rate, respiratory rate). Similarly, audio sensors have the potential to become one of the most important modalities for interaction with AAL systems, as they can have a large range of sensing, do not require physical presence at a particular location and are physically intangible. Moreover, relevant information about individuals’ activities and health status can derive from processing audio signals (e.g., speech recordings). Nevertheless, as the other side of the coin, cameras and microphones are often perceived as the most intrusive technologies from the viewpoint of the privacy of the monitored individuals. This is due to the richness of the information these technologies convey and the intimate setting where they may be deployed. Solutions able to ensure privacy preservation by context and by design, as well as to ensure high legal and ethical standards are in high demand. After the review of the current state of play and the discussion in GoodBrother, we may claim that the first solutions in this direction are starting to appear in the literature. A multidisciplinary 4 debate among experts and stakeholders is paving the way towards AAL ensuring ergonomics, usability, acceptance and privacy preservation. The DIANA, PAAL, and VisuAAL projects are examples of this fresh approach. This report provides the reader with a review of the most recent advances in audio- and video-based monitoring technologies for AAL. It has been drafted as a collective effort of WG3 to supply an introduction to AAL, its evolution over time and its main functional and technological underpinnings. In this respect, the report contributes to the field with the outline of a new generation of ethical-aware AAL technologies and a proposal for a novel comprehensive taxonomy of AAL systems and applications. Moreover, the report allows non-technical readers to gather an overview of the main components of an AAL system and how these function and interact with the end-users. The report illustrates the state of the art of the most successful AAL applications and functions based on audio and video data, namely (i) lifelogging and self-monitoring, (ii) remote monitoring of vital signs, (iii) emotional state recognition, (iv) food intake monitoring, activity and behaviour recognition, (v) activity and personal assistance, (vi) gesture recognition, (vii) fall detection and prevention, (viii) mobility assessment and frailty recognition, and (ix) cognitive and motor rehabilitation. For these application scenarios, the report illustrates the state of play in terms of scientific advances, available products and research project. The open challenges are also highlighted. The report ends with an overview of the challenges, the hindrances and the opportunities posed by the uptake in real world settings of AAL technologies. In this respect, the report illustrates the current procedural and technological approaches to cope with acceptability, usability and trust in the AAL technology, by surveying strategies and approaches to co-design, to privacy preservation in video and audio data, to transparency and explainability in data processing, and to data transmission and communication. User acceptance and ethical considerations are also debated. Finally, the potentials coming from the silver economy are overviewed.publishedVersio

The University Defence Research Collaboration In Signal Processing

This chapter describes the development of algorithms for automatic detection of anomalies from multi-dimensional, undersampled and incomplete datasets. The challenge in this work is to identify and classify behaviours as normal or abnormal, safe or threatening, from an irregular and often heterogeneous sensor network. Many defence and civilian applications can be modelled as complex networks of interconnected nodes with unknown or uncertain spatio-temporal relations. The behavior of such heterogeneous networks can exhibit dynamic properties, reflecting evolution in both network structure (new nodes appearing and existing nodes disappearing), as well as inter-node relations. The UDRC work has addressed not only the detection of anomalies, but also the identification of their nature and their statistical characteristics. Normal patterns and changes in behavior have been incorporated to provide an acceptable balance between true positive rate, false positive rate, performance and computational cost. Data quality measures have been used to ensure the models of normality are not corrupted by unreliable and ambiguous data. The context for the activity of each node in complex networks offers an even more efficient anomaly detection mechanism. This has allowed the development of efficient approaches which not only detect anomalies but which also go on to classify their behaviour

Spatio-temporal traffic anomaly detection for urban networks

Urban road networks are often affected by disruptions such as accidents and roadworks, giving rise to congestion and delays, which can, in turn, create a wide range of negative impacts to the economy, environment, safety and security. Accurate detection of the onset of traffic anomalies, specifically Recurrent Congestion (RC) and Nonrecurrent Congestion (NRC) in the traffic networks, is an important ITS function to facilitate proactive intervention measures to reduce the level of severity of congestion. A substantial body of literature is dedicated to models with varying levels of complexity that attempt to identify such anomalies. Given the complexity of the problem, however, very less effort is dedicated to the development of methods that attempt to detect traffic anomalies using spatio-temporal features. Driven both by the recent advances in deep learning techniques and the development of Traffic Incident Management Systems (TIMS), the aim of this research is to develop novel traffic anomaly detection models that can incorporate both spatial and temporal traffic information to detect traffic anomalies at a network level. This thesis first reviews the state of the art in traffic anomaly detection techniques, including the existing methods and emerging machine learning and deep learning methods, before identifying the gaps in the current understanding of traffic anomaly and its detection. One of the problems in terms of adapting the deep learning models to traffic anomaly detection is the translation of time series traffic data from multiple locations to the format necessary for the deep learning model to learn the spatial and temporal features effectively. To address this challenging problem and build a systematic traffic anomaly detection method at a network level, this thesis proposes a methodological framework consisting of (a) the translation layer (which is designed to translate the time series traffic data from multiple locations over the road network into a desired format with spatial and temporal features), (b) detection methods and (c) localisation. This methodological framework is subsequently tested for early RC detection and NRC detection. Three translation layers including connectivity matrix, geographical grid translation and spatial temporal translation are presented and evaluated for both RC and NRC detection. The early RC detection approach is a deep learning based method that combines Convolutional Neural Networks (CNN) and Long Short-Term Memory (LSTM). The NRC detection, on the other hand, involves only the application of the CNN. The performance of the proposed approach is compared against other conventional congestion detection methods, using a comprehensive evaluation framework that includes metrics such as detection rates and false positive rates, and the sensitivity analysis of time windows as well as prediction horizons. The conventional congestion detection methods used for the comparison include Multilayer Perceptron, Random Forest and Gradient Boost Classifier, all of which are commonly used in the literature. Real-world traffic data from the City of Bath are used for the comparative analysis of RC, while traffic data in conjunction with incident data extracted from Central London are used for NRC detection. The results show that while the connectivity matrix may be capable of extracting features of a small network, the increased sparsity in the matrix in a large network reduces its effectiveness in feature learning compared to geographical grid translation. The results also indicate that the proposed deep learning method demonstrates superior detection accuracy compared to alternative methods and that it can detect recurrent congestion as early as one hour ahead with acceptable accuracy. The proposed method is capable of being implemented within a real-world ITS system making use of traffic sensor data, thereby providing a practically useful tool for road network managers to manage traffic proactively. In addition, the results demonstrate that a deep learning-based approach may improve the accuracy of incident detection and locate traffic anomalies precisely, especially in a large urban network. Finally, the framework is further tested for robustness in terms of network topology, sensor faults and missing data. The robustness analysis demonstrates that the proposed traffic anomaly detection approaches are transferable to different sizes of road networks, and that they are robust in the presence of sensor faults and missing data.Open Acces

The assessment and development of methods in (spatial) sound ecology

As vital ecosystems across the globe enter unchartered pressure from climate change industrial land use, understanding the processes driving ecosystem viability has never been more critical. Nuanced ecosystem understanding comes from well-collected field data and a wealth of associated interpretations. In recent years the most popular methods of ecosystem monitoring have revolutionised from often damaging and labour-intensive manual data collection to automated methods of data collection and analysis. Sound ecology describes the school of research that uses information transmitted through sound to infer properties about an area's species, biodiversity, and health. In this thesis, we explore and develop state-of-the-art automated monitoring with sound, specifically relating to data storage practice and spatial acoustic recording and data analysis. In the first chapter, we explore the necessity and methods of ecosystem monitoring, focusing on acoustic monitoring, later exploring how and why sound is recorded and the current state-of-the-art in acoustic monitoring. Chapter one concludes with us setting out the aims and overall content of the following chapters. We begin the second chapter by exploring methods used to mitigate data storage expense, a widespread issue as automated methods quickly amass vast amounts of data which can be expensive and impractical to manage. Importantly I explain how these data management practices are often used without known consequence, something I then address. Specifically, I present evidence that the most used data reduction methods (namely compression and temporal subsetting) have a surprisingly small impact on the information content of recorded sound compared to the method of analysis. This work also adds to the increasing evidence that deep learning-based methods of environmental sound quantification are more powerful and robust to experimental variation than more traditional acoustic indices. In the latter chapters, I focus on using multichannel acoustic recording for sound-source localisation. Knowing where a sound originated has a range of ecological uses, including counting individuals, locating threats, and monitoring habitat use. While an exciting application of acoustic technology, spatial acoustics has had minimal uptake owing to the expense, impracticality and inaccessibility of equipment. In my third chapter, I introduce MAARU (Multichannel Acoustic Autonomous Recording Unit), a low-cost, easy-to-use and accessible solution to this problem. I explain the software and hardware necessary for spatial recording and show how MAARU can be used to localise the direction of a sound to within ±10˚ accurately. In the fourth chapter, I explore how MAARU devices deployed in the field can be used for enhanced ecosystem monitoring by spatially clustering individuals by calling directions for more accurate abundance approximations and crude species-specific habitat usage monitoring. Most literature on spatial acoustics cites the need for many accurately synced recording devices over an area. This chapter provides the first evidence of advances made with just one recorder. Finally, I conclude this thesis by restating my aims and discussing my success in achieving them. Specifically, in the thesis’ conclusion, I reiterate the contributions made to the field as a direct result of this work and outline some possible development avenues.Open Acces

Immersive analytics for oncology patient cohorts

This thesis proposes a novel interactive immersive analytics tool and methods to interrogate the cancer patient cohort in an immersive virtual environment, namely Virtual Reality to Observe Oncology data Models (VROOM). The overall objective is to develop an immersive analytics platform, which includes a data analytics pipeline from raw gene expression data to immersive visualisation on virtual and augmented reality platforms utilising a game engine. Unity3D has been used to implement the visualisation. Work in this thesis could provide oncologists and clinicians with an interactive visualisation and visual analytics platform that helps them to drive their analysis in treatment efficacy and achieve the goal of evidence-based personalised medicine. The thesis integrates the latest discovery and development in cancer patients’ prognoses, immersive technologies, machine learning, decision support system and interactive visualisation to form an immersive analytics platform of complex genomic data. For this thesis, the experimental paradigm that will be followed is in understanding transcriptomics in cancer samples. This thesis specifically investigates gene expression data to determine the biological similarity revealed by the patient's tumour samples' transcriptomic profiles revealing the active genes in different patients. In summary, the thesis contributes to i) a novel immersive analytics platform for patient cohort data interrogation in similarity space where the similarity space is based on the patient's biological and genomic similarity; ii) an effective immersive environment optimisation design based on the usability study of exocentric and egocentric visualisation, audio and sound design optimisation; iii) an integration of trusted and familiar 2D biomedical visual analytics methods into the immersive environment; iv) novel use of the game theory as the decision-making system engine to help the analytics process, and application of the optimal transport theory in missing data imputation to ensure the preservation of data distribution; and v) case studies to showcase the real-world application of the visualisation and its effectiveness

Improving Detection of DeepFakes through Facial Region Analysis in Images

\ua9 2023 by the authors. In the evolving landscape of digital media, the discipline of media forensics, which encompasses the critical examination and authentication of digital images, videos, and audio recordings, has emerged as an area of paramount importance. This heightened significance is predominantly attributed to the burgeoning concerns surrounding the proliferation of DeepFakes, which are highly realistic and manipulated media content, often created using advanced artificial intelligence techniques. Such developments necessitate a profound understanding and advancement in media forensics to ensure the integrity of digital media in various domains. Current research endeavours are primarily directed towards addressing a common challenge observed in DeepFake datasets, which pertains to the issue of overfitting. Many suggested remedies centre around the application of data augmentation methods, with a frequently adopted strategy being the incorporation of random erasure or cutout. This method entails the random removal of sections from an image to introduce diversity and mitigate overfitting. Generating disparities between the altered and unaltered images serves to inhibit the model from excessively adapting itself to individual samples, thus leading to more favourable results. Nonetheless, the stochastic nature of this approach may inadvertently obscure facial regions that harbour vital information necessary for DeepFake detection. Due to the lack of guidelines on specific regions for cutout, most studies use a randomised approach. However, in recent research, face landmarks have been integrated to designate specific facial areas for removal, even though the selection remains somewhat random. Therefore, there is a need to acquire a more comprehensive insight into facial features and identify which regions hold more crucial data for the identification of DeepFakes. In this study, the investigation delves into the data conveyed by various facial components through the excision of distinct facial regions during the training of the model. The goal is to offer valuable insights to enhance forthcoming face removal techniques within DeepFake datasets, fostering a deeper comprehension among researchers and advancing the realm of DeepFake detection. Our study presents a novel method that uses face cutout techniques to improve understanding of key facial features crucial in DeepFake detection. Moreover, the method combats overfitting in DeepFake datasets by generating diverse images with these techniques, thereby enhancing model robustness. The developed methodology is validated against publicly available datasets like FF++ and Celeb-DFv2. Both face cutout groups surpassed the Baseline, indicating cutouts improve DeepFake detection. Face Cutout Group 2 excelled, with 91% accuracy on Celeb-DF and 86% on the compound dataset, suggesting external facial features’ significance in detection. The study found that eyes are most impactful and the nose is least in model performance. Future research could explore the augmentation policy’s effect on video-based DeepFake detection