High-Performance Modelling and Simulation for Big Data Applications

This open access book was prepared as a Final Publication of the COST Action IC1406 “High-Performance Modelling and Simulation for Big Data Applications (cHiPSet)“ project. Long considered important pillars of the scientific method, Modelling and Simulation have evolved from traditional discrete numerical methods to complex data-intensive continuous analytical optimisations. Resolution, scale, and accuracy have become essential to predict and analyse natural and complex systems in science and engineering. When their level of abstraction raises to have a better discernment of the domain at hand, their representation gets increasingly demanding for computational and data resources. On the other hand, High Performance Computing typically entails the effective use of parallel and distributed processing units coupled with efficient storage, communication and visualisation systems to underpin complex data-intensive applications in distinct scientific and technical domains. It is then arguably required to have a seamless interaction of High Performance Computing with Modelling and Simulation in order to store, compute, analyse, and visualise large data sets in science and engineering. Funded by the European Commission, cHiPSet has provided a dynamic trans-European forum for their members and distinguished guests to openly discuss novel perspectives and topics of interests for these two communities. This cHiPSet compendium presents a set of selected case studies related to healthcare, biological data, computational advertising, multimedia, finance, bioinformatics, and telecommunications

High-Performance Modelling and Simulation for Big Data Applications

This open access book was prepared as a Final Publication of the COST Action IC1406 “High-Performance Modelling and Simulation for Big Data Applications (cHiPSet)“ project. Long considered important pillars of the scientific method, Modelling and Simulation have evolved from traditional discrete numerical methods to complex data-intensive continuous analytical optimisations. Resolution, scale, and accuracy have become essential to predict and analyse natural and complex systems in science and engineering. When their level of abstraction raises to have a better discernment of the domain at hand, their representation gets increasingly demanding for computational and data resources. On the other hand, High Performance Computing typically entails the effective use of parallel and distributed processing units coupled with efficient storage, communication and visualisation systems to underpin complex data-intensive applications in distinct scientific and technical domains. It is then arguably required to have a seamless interaction of High Performance Computing with Modelling and Simulation in order to store, compute, analyse, and visualise large data sets in science and engineering. Funded by the European Commission, cHiPSet has provided a dynamic trans-European forum for their members and distinguished guests to openly discuss novel perspectives and topics of interests for these two communities. This cHiPSet compendium presents a set of selected case studies related to healthcare, biological data, computational advertising, multimedia, finance, bioinformatics, and telecommunications

Biometrics

Biometrics-Unique and Diverse Applications in Nature, Science, and Technology provides a unique sampling of the diverse ways in which biometrics is integrated into our lives and our technology. From time immemorial, we as humans have been intrigued by, perplexed by, and entertained by observing and analyzing ourselves and the natural world around us. Science and technology have evolved to a point where we can empirically record a measure of a biological or behavioral feature and use it for recognizing patterns, trends, and or discrete phenomena, such as individuals' and this is what biometrics is all about. Understanding some of the ways in which we use biometrics and for what specific purposes is what this book is all about

Dynamic Volume Rendering of Functional Medical Data on Dissimilar Hardware Platforms

In the last 30 years, medical imaging has become one of the most used diagnostic tools in the medical profession. Computed Tomography (CT) and Magnetic Resonance Imaging (MRI) technologies have become widely adopted because of their ability to capture the human body in a non-invasive manner. A volumetric dataset is a series of orthogonal 2D slices captured at a regular interval, typically along the axis of the body from the head to the feet. Volume rendering is a computer graphics technique that allows volumetric data to be visualized and manipulated as a single 3D object. Iso-surface rendering, image splatting, shear warp, texture slicing, and raycasting are volume rendering methods, each with associated advantages and disadvantages. Raycasting is widely regarded as the highest quality renderer of these methods. Originally, CT and MRI hardware was limited to providing a single 3D scan of the human body. The technology has improved to allow a set of scans capable of capturing anatomical movements like a beating heart. The capturing of anatomical data over time is referred to as functional imaging. Functional MRI (fMRI) is used to capture changes in the human body over time. While fMRI’s can be used to capture any anatomical data over time, one of the more common uses of fMRI is to capture brain activity. The fMRI scanning process is typically broken up into a time consuming high resolution anatomical scan and a series of quick low resolution scans capturing activity. The low resolution activity data is mapped onto the high resolution anatomical data to show changes over time. Academic research has advanced volume rendering and specifically fMRI volume rendering. Unfortunately, academic research is typically a one-off solution to a singular medical case or set of data, causing any advances to be problem specific as opposed to a general capability. Additionally, academic volume renderers are often designed to work on a specific device and operating system under controlled conditions. This prevents volume rendering from being used across the ever expanding number of different computing devices, such as desktops, laptops, immersive virtual reality systems, and mobile computers like phones or tablets. This research will investigate the feasibility of creating a generic software capability to perform real-time 4D volume rendering, via raycasting, on desktop, mobile, and immersive virtual reality platforms. Implementing a GPU-based 4D volume raycasting method for mobile devices will harness the power of the increasing number of mobile computational devices being used by medical professionals. Developing support for immersive virtual reality can enhance medical professionals’ interpretation of 3D physiology with the additional depth information provided by stereoscopic 3D. The results of this research will help expand the use of 4D volume rendering beyond the traditional desktop computer in the medical field. Developing the same 4D volume rendering capabilities across dissimilar platforms has many challenges. Each platform relies on their own coding languages, libraries, and hardware support. There are tradeoffs between using languages and libraries native to each platform and using a generic cross-platform system, such as a game engine. Native libraries will generally be more efficient during application run-time, but they require different coding implementations for each platform. The decision was made to use platform native languages and libraries in this research, whenever practical, in an attempt to achieve the best possible frame rates. 4D volume raycasting provides unique challenges independent of the platform. Specifically, fMRI data loading, volume animation, and multiple volume rendering. Additionally, real-time raycasting has never been successfully performed on a mobile device. Previous research relied on less computationally expensive methods, such as orthogonal texture slicing, to achieve real-time frame rates. These challenges will be addressed as the contributions of this research. The first contribution was exploring the feasibility of generic functional data input across desktop, mobile, and immersive virtual reality. To visualize 4D fMRI data it was necessary to build in the capability to read Neuroimaging Informatics Technology Initiative (NIfTI) files. The NIfTI format was designed to overcome limitations of 3D file formats like DICOM and store functional imagery with a single high-resolution anatomical scan and a set of low-resolution anatomical scans. Allowing input of the NIfTI binary data required creating custom C++ routines, as no object oriented APIs freely available for use existed. The NIfTI input code was built using C++ and the C++ Standard Library to be both light weight and cross-platform. Multi-volume rendering is another challenge of fMRI data visualization and a contribution of this work. fMRI data is typically broken into a single high-resolution anatomical volume and a series of low-resolution volumes that capture anatomical changes. Visualizing two volumes at the same time is known as multi-volume visualization. Therefore, the ability to correctly align and scale the volumes relative to each other was necessary. It was also necessary to develop a compositing method to combine data from both volumes into a single cohesive representation. Three prototype applications were built for the different platforms to test the feasibility of 4D volume raycasting. One each for desktop, mobile, and virtual reality. Although the backend implementations were required to be different between the three platforms, the raycasting functionality and features were identical. Therefore, the same fMRI dataset resulted in the same 3D visualization independent of the platform itself. Each platform uses the same NIfTI data loader and provides support for dataset coloring and windowing (tissue density manipulation). The fMRI data can be viewed changing over time by either animation through the time steps, like a movie, or using an interface slider to “scrub” through the different time steps of the data. The prototype applications data load times and frame rates were tested to determine if they achieved the real-time interaction goal. Real-time interaction was defined by achieving 10 frames per second (fps) or better, based on the work of Miller [1]. The desktop version was evaluated on a 2013 MacBook Pro running OS X 10.12 with a 2.6 GHz Intel Core i7 processor, 16 GB of RAM, and a NVIDIA GeForce GT 750M graphics card. The immersive application was tested in the C6 CAVE™, a 96 graphics node computer cluster comprised of NVIDIA Quadro 6000 graphics cards running Red Hat Enterprise Linux. The mobile application was evaluated on a 2016 9.7” iPad Pro running iOS 9.3.4. The iPad had a 64-bit Apple A9X dual core processor with 2 GB of built in memory. Two different fMRI brain activity datasets with different voxel resolutions were used as test datasets. Datasets were tested using both the 3D structural data, the 4D functional data, and a combination of the two. Frame rates for the desktop implementation were consistently above 10 fps, indicating that real-time 4D volume raycasting is possible on desktop hardware. The mobile and virtual reality platforms were able to perform real-time 3D volume raycasting consistently. This is a marked improvement for 3D mobile volume raycasting that was previously only able to achieve under one frame per second [2]. Both VR and mobile platforms were able to raycast the 4D only data at real-time frame rates, but did not consistently meet 10 fps when rendering both the 3D structural and 4D functional data simultaneously. However, 7 frames per second was the lowest frame rate recorded, indicating that hardware advances will allow consistent real-time raycasting of 4D fMRI data in the near future

Multimodal assessment of neonatal pain

Pain assessment is critical to prevent suffering and harm in infants admitted to the neonatal care unit. As pain is a subjective experience, its assessment in nonverbal infants relies on surrogate measures. Current infant pain assessment tools that are based on behaviour and autonomic nervous system measurements lack face validity — they are unlikely to reflect pain in all its dimensions. In recent years, EEG-derived measures of pain have been developed in late preterm and term infants. Multimodal tools which include these cerebral measurements are conceptually more appropriate to measure pain. Yet, their use is still limited to specific research applications. This thesis focuses on outstanding questions that need to be addressed in order to advance the development of multimodal pain assessment tools that incorporate cerebral measurements. In the first part of this thesis, I focus on the characterisation of preterm infants’ noxious-evoked responses and their development. Across several modalities, premature infants have dampened or altered responsiveness compared to term infants, and it is uncertain if these responses can be reliably discriminated from tactile-evoked responses. In particular, a discriminative pattern of noxious-evoked EEG activity that is present in term infants, is unlikely to be present in preterm infants. In addition, it is unclear how noxious-evoked responses, especially brainderived responses, change with age. In this thesis, I use a classification model to show that infants aged 28–40 weeks postmenstrual age display discriminable multimodal responses to a noxious clinical procedure and a tactile control procedure, and I provide examples of how a such a model could be used in clinical trials of analgesics. I show that noxious-evoked responses change magnitude and morphology across this age range, and that discriminative brain activity emerges in early prematurity. In the second part of this thesis, I focus on improving the neuroscientific validity of a noxious-evoked EEG response measured at the cot-side, as the spatial neural correlates of these responses are still poorly understood. I present an EEG-fMRI pilot study to investigate the spatial neural correlates of inter-individual differences in noxious-evoked EEG responses and provide recommendations for a larger follow-up study. Overall, this thesis provides a characterisation of infants’ noxious-evoked responses and their development across multiple modalities, a crucial next step in improving multimodal neonatal pain assessment

Fear Classification using Affective Computing with Physiological Information and Smart-Wearables

Mención Internacional en el título de doctorAmong the 17 Sustainable Development Goals proposed within the 2030 Agenda and adopted by all of the United Nations member states, the fifth SDG is a call for action to effectively turn gender equality into a fundamental human right and an essential foundation for a better world. It includes the eradication of all types of violence against women. Focusing on the technological perspective, the range of available solutions intended to prevent this social problem is very limited. Moreover, most of the solutions are based on a panic button approach, leaving aside the usage and integration of current state-of-the-art technologies, such as the Internet of Things (IoT), affective computing, cyber-physical systems, and smart-sensors. Thus, the main purpose of this research is to provide new insight into the design and development of tools to prevent and combat Gender-based Violence risky situations and, even, aggressions, from a technological perspective, but without leaving aside the different sociological considerations directly related to the problem. To achieve such an objective, we rely on the application of affective computing from a realist point of view, i.e. targeting the generation of systems and tools capable of being implemented and used nowadays or within an achievable time-frame. This pragmatic vision is channelled through: 1) an exhaustive study of the existing technological tools and mechanisms oriented to the fight Gender-based Violence, 2) the proposal of a new smart-wearable system intended to deal with some of the current technological encountered limitations, 3) a novel fear-related emotion classification approach to disentangle the relation between emotions and physiology, and 4) the definition and release of a new multi-modal dataset for emotion recognition in women. Firstly, different fear classification systems using a reduced set of physiological signals are explored and designed. This is done by employing open datasets together with the combination of time, frequency and non-linear domain techniques. This design process is encompassed by trade-offs between both physiological considerations and embedded capabilities. The latter is of paramount importance due to the edge-computing focus of this research. Two results are highlighted in this first task, the designed fear classification system that employed the DEAP dataset data and achieved an AUC of 81.60% and a Gmean of 81.55% on average for a subjectindependent approach, and only two physiological signals; and the designed fear classification system that employed the MAHNOB dataset data achieving an AUC of 86.00% and a Gmean of 73.78% on average for a subject-independent approach, only three physiological signals, and a Leave-One-Subject-Out configuration. A detailed comparison with other emotion recognition systems proposed in the literature is presented, which proves that the obtained metrics are in line with the state-ofthe- art. Secondly, Bindi is presented. This is an end-to-end autonomous multimodal system leveraging affective IoT throughout auditory and physiological commercial off-theshelf smart-sensors, hierarchical multisensorial fusion, and secured server architecture to combat Gender-based Violence by automatically detecting risky situations based on a multimodal intelligence engine and then triggering a protection protocol. Specifically, this research is focused onto the hardware and software design of one of the two edge-computing devices within Bindi. This is a bracelet integrating three physiological sensors, actuators, power monitoring integrated chips, and a System- On-Chip with wireless capabilities. Within this context, different embedded design space explorations are presented: embedded filtering evaluation, online physiological signal quality assessment, feature extraction, and power consumption analysis. The reported results in all these processes are successfully validated and, for some of them, even compared against physiological standard measurement equipment. Amongst the different obtained results regarding the embedded design and implementation within the bracelet of Bindi, it should be highlighted that its low power consumption provides a battery life to be approximately 40 hours when using a 500 mAh battery. Finally, the particularities of our use case and the scarcity of open multimodal datasets dealing with emotional immersive technology, labelling methodology considering the gender perspective, balanced stimuli distribution regarding the target emotions, and recovery processes based on the physiological signals of the volunteers to quantify and isolate the emotional activation between stimuli, led us to the definition and elaboration of Women and Emotion Multi-modal Affective Computing (WEMAC) dataset. This is a multimodal dataset in which 104 women who never experienced Gender-based Violence that performed different emotion-related stimuli visualisations in a laboratory environment. The previous fear binary classification systems were improved and applied to this novel multimodal dataset. For instance, the proposed multimodal fear recognition system using this dataset reports up to 60.20% and 67.59% for ACC and F1-score, respectively. These values represent a competitive result in comparison with the state-of-the-art that deal with similar multi-modal use cases. In general, this PhD thesis has opened a new research line within the research group under which it has been developed. Moreover, this work has established a solid base from which to expand knowledge and continue research targeting the generation of both mechanisms to help vulnerable groups and socially oriented technology.Programa de Doctorado en Ingeniería Eléctrica, Electrónica y Automática por la Universidad Carlos III de MadridPresidente: David Atienza Alonso.- Secretaria: Susana Patón Álvarez.- Vocal: Eduardo de la Torre Arnan

Multimodal Approach for Big Data Analytics and Applications

The thesis presents multimodal conceptual frameworks and their applications in improving the robustness and the performance of big data analytics through cross-modal interaction or integration. A joint interpretation of several knowledge renderings such as stream, batch, linguistics, visuals and metadata creates a unified view that can provide a more accurate and holistic approach to data analytics compared to a single standalone knowledge base. Novel approaches in the thesis involve integrating multimodal framework with state-of-the-art computational models for big data, cloud computing, natural language processing, image processing, video processing, and contextual metadata. The integration of these disparate fields has the potential to improve computational tools and techniques dramatically. Thus, the contributions place multimodality at the forefront of big data analytics; the research aims at mapping and under- standing multimodal correspondence between different modalities. The primary contribution of the thesis is the Multimodal Analytics Framework (MAF), a collaborative ensemble framework for stream and batch processing along with cues from multiple input modalities like language, visuals and metadata to combine benefits from both low-latency and high-throughput. The framework is a five-step process: Data ingestion. As a first step towards Big Data analytics, a high velocity, fault-tolerant streaming data acquisition pipeline is proposed through a distributed big data setup, followed by mining and searching patterns in it while data is still in transit. The data ingestion methods are demonstrated using Hadoop ecosystem tools like Kafka and Flume as sample implementations. Decision making on the ingested data to use the best-fit tools and methods. In Big Data Analytics, the primary challenges often remain in processing heterogeneous data pools with a one-method-fits all approach. The research introduces a decision-making system to select the best-fit solutions for the incoming data stream. This is the second step towards building a data processing pipeline presented in the thesis. The decision-making system introduces a Fuzzy Graph-based method to provide real-time and offline decision-making. Lifelong incremental machine learning. In the third step, the thesis describes a Lifelong Learning model at the processing layer of the analytical pipeline, following the data acquisition and decision making at step two for downstream processing. Lifelong learning iteratively increments the training model using a proposed Multi-agent Lambda Architecture (MALA), a collaborative ensemble architecture between the stream and batch data. As part of the proposed MAF, MALA is one of the primary contributions of the research.The work introduces a general-purpose and comprehensive approach in hybrid learning of batch and stream processing to achieve lifelong learning objectives. Improving machine learning results through ensemble learning. As an extension of the Lifelong Learning model, the thesis proposes a boosting based Ensemble method as the fourth step of the framework, improving lifelong learning results by reducing the learning error in each iteration of a streaming window. The strategy is to incrementally boost the learning accuracy on each iterating mini-batch, enabling the model to accumulate knowledge faster. The base learners adapt more quickly in smaller intervals of a sliding window, improving the machine learning accuracy rate by countering the concept drift. Cross-modal integration between text, image, video and metadata for more comprehensive data coverage than a text-only dataset. The final contribution of this thesis is a new multimodal method where three different modalities: text, visuals (image and video) and metadata, are intertwined along with real-time and batch data for more comprehensive input data coverage than text-only data. The model is validated through a detailed case study on the contemporary and relevant topic of the COVID-19 pandemic. While the remainder of the thesis deals with text-only input, the COVID-19 dataset analyzes both textual and visual information in integration. Post completion of this research work, as an extension to the current framework, multimodal machine learning is investigated as a future research direction

Data-Driven Framework for Understanding & Modeling Ride-Sourcing Transportation Systems

Ride-sourcing transportation services offered by transportation network companies (TNCs) like Uber and Lyft are disrupting the transportation landscape. The growing demand on these services, along with their potential short and long-term impacts on the environment, society, and infrastructure emphasize the need to further understand the ride-sourcing system. There were no sufficient data to fully understand the system and integrate it within regional multimodal transportation frameworks. This can be attributed to commercial and competition reasons, given the technology-enabled and innovative nature of the system. Recently, in 2019, the City of Chicago the released an extensive and complete ride-sourcing trip-level data for all trips made within the city since November 1, 2018. The data comprises the trip ends (pick-up and drop-off locations), trip timestamps, trip length and duration, fare including tipping amounts, and whether the trip was authorized to be shared (pooled) with another passenger or not. Therefore, the main goal of this dissertation is to develop a comprehensive data-driven framework to understand and model the system using this data from Chicago, in a reproducible and transferable fashion. Using data fusion approach, sociodemographic, economic, parking supply, transit availability and accessibility, built environment and crime data are collected from open sources to develop this framework. The framework is predicated on three pillars of analytics: (1) explorative and descriptive analytics, (2) diagnostic analytics, and (3) predictive analytics. The dissertation research framework also provides a guide on the key spatial and behavioral explanatory variables shaping the utility of the mode, driving the demand, and governing the interdependencies between the demand’s willingness to share and surge price. Thus, the key findings can be readily challenged, verified, and utilized in different geographies. In the explorative and descriptive analytics, the ride-sourcing system’s spatial and temporal dimensions of the system are analyzed to achieve two objectives: (1) explore, reveal, and assess the significance of spatial effects, i.e., spatial dependence and heterogeneity, in the system behavior, and (2) develop a behavioral market segmentation and trend mining of the willingness to share. This is linked to the diagnostic analytics layer, as the revealed spatial effects motivates the adoption of spatial econometric models to analytically identify the ride-sourcing system determinants. Multiple linear regression (MLR) is used as a benchmark model against spatial error model (SEM), spatially lagged X (SLX) model, and geographically weighted regression (GWR) model. Two innovative modeling constructs are introduced deal with the ride-sourcing system’s spatial effects and multicollinearity: (1) Calibrated Spatially Lagged X Ridge Model (CSLXR) and Calibrated Geographically Weighted Ridge Regression (CGWRR) in the diagnostic analytics layer. The identified determinants in the diagnostic analytics layer are then fed into the predictive analytics one to develop an interpretable machine learning (ML) modeling framework. The system’s annual average weekday origin-destination (AAWD OD) flow is modeled using the following state-of-the-art ML models: (1) Multilayer Perceptron (MLP) Regression, (2) Support Vector Machines Regression (SVR), and (3) Tree-based ensemble learning methods, i.e., Random Forest Regression (RFR) and Extreme Gradient Boosting (XGBoost). The innovative modeling construct of CGWRR developed in the diagnostic analytics is then validated in a predictive context and is found to outperform the state-of-the-art ML models in terms of testing score of 0.914, in comparison to 0.906 for XGBoost, 0.84 for RFR, 0.89 for SVR, and 0.86 for MLP. The CGWRR exhibits outperformance as well in terms of the root mean squared error (RMSE) and mean average error (MAE). The findings of this dissertation partially bridge the gap between the practice and the research on ride-sourcing transportation systems understanding and integration. The empirical findings made in the descriptive and explorative analytics can be further utilized by regional agencies to fill practice and policymaking gaps on regulating ride-sourcing services using corridor or cordon toll, optimally allocating standing areas to minimize deadheading, especially during off-peak periods, and promoting the ride-share willingness in disadvantage communities. The CGWRR provides a reliable modeling and simulation tool to researchers and practitioners to integrate the ride-sourcing system in multimodal transportation modeling frameworks, simulation testbed for testing long-range impacts of policies on ride-sourcing, like improved transit supply, congestions pricing, or increased parking rates, and to plan ahead for similar futuristic transportation modes, like the shared autonomous vehicles