Publications from our Researchers

Several of our current PhD candidates and fellow researchers at the Data Science Institute have published, or in the proccess of publishing, papers to present their research.  

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  • Journal article
    Quilodrán-Casas C, Silva VS, Arcucci R, Heaney CE, Guo Y, Pain CCet al., 2021,

    Digital twins based on bidirectional LSTM and GAN for modelling COVID-19

    The outbreak of the coronavirus disease 2019 (COVID-19) has now spreadthroughout the globe infecting over 100 million people and causing the death ofover 2.2 million people. Thus, there is an urgent need to study the dynamics ofepidemiological models to gain a better understanding of how such diseasesspread. While epidemiological models can be computationally expensive, recentadvances in machine learning techniques have given rise to neural networks withthe ability to learn and predict complex dynamics at reduced computationalcosts. Here we introduce two digital twins of a SEIRS model applied to anidealised town. The SEIRS model has been modified to take account of spatialvariation and, where possible, the model parameters are based on official virusspreading data from the UK. We compare predictions from a data-correctedBidirectional Long Short-Term Memory network and a predictive GenerativeAdversarial Network. The predictions given by these two frameworks are accuratewhen compared to the original SEIRS model data. Additionally, these frameworksare data-agnostic and could be applied to towns, idealised or real, in the UKor in other countries. Also, more compartments could be included in the SEIRSmodel, in order to study more realistic epidemiological behaviour.

  • Journal article
    Balaban G, Halliday B, Bradley P, Bai W, Nygaard S, Owen R, Hatipoglu S, Ferreira ND, Izgi C, Tayal U, Corden B, Ware J, Pennell D, Rueckert D, Plank G, Rinaldi CA, Prasad SK, Bishop Met al., 2021,

    Late-gadolinium enhancement interface area and electrophysiological simulations predict arrhythmic events in non-ischemic dilated cardiomyopathy patients

    , JACC: Clinical Electrophysiology, Vol: 7, Pages: 238-249, ISSN: 2405-5018

    BACKGROUND: The presence of late-gadolinium enhancement (LGE) predicts life threatening ventricular arrhythmias in non-ischemic dilated cardiomyopathy (NIDCM); however, risk stratification remains imprecise. LGE shape and simulations of electrical activity may be able to provide additional prognostic information.OBJECTIVE: This study sought to investigate whether shape-based LGE metrics and simulations of reentrant electrical activity are associated with arrhythmic events in NIDCM patients.METHODS: CMR-LGE shape metrics were computed for a cohort of 156 NIDCM patients with visible LGE and tested retrospectively for an association with an arrhythmic composite end-point of sudden cardiac death and ventricular tachycardia. Computational models were created from images and used in conjunction with simulated stimulation protocols to assess the potential for reentry induction in each patient’s scar morphology. A mechanistic analysis of the simulations was carried out to explain the associations. RESULTS: During a median follow-up of 1611 [IQR 881-2341] days, 16 patients (10.3%) met the primary endpoint. In an inverse probability weighted Cox regression, the LGE-myocardial interface area (HR:1.75; 95% CI:1.24-2.47; p=0.001), number of simulated reentries (HR: 1.4; 95% CI: 1.23-1.59; p<0.01) and LGE volume (HR:1.44; 95% CI:1.07-1.94; p=0.02) were associated with arrhythmic events. Computational modeling revealed repolarisation heterogeneity and rate-dependent block of electrical wavefronts at the LGE-myocardial interface as putative arrhythmogenic mechanisms directly related to LGE interface area.CONCLUSION: The area of interface between scar and surviving myocardium, as well as simulated reentrant activity, are associated with an elevated risk of major arrhythmic events in NIDCM patients with LGE and represent novel risk predictors.

  • Journal article
    Xiong Z, Xia Q, Hu Z, Huang N, Bian C, Zheng Y, Vesal S, Ravikumar N, Maier A, Yang X, Heng P-A, Ni D, Li C, Tong Q, Si W, Puybareau E, Khoudli Y, Geraud T, Chen C, Bai W, Rueckert D, Xu L, Zhuang X, Luo X, Jia S, Sermesant M, Liu Y, Wang K, Borra D, Masci A, Corsi C, de Vente C, Veta M, Karim R, Preetha CJ, Engelhardt S, Qiao M, Wang Y, Tao Q, Nunez-Garcia M, Camara O, Savioli N, Lamata P, Zhao Jet al., 2021,

    A global benchmark of algorithms for segmenting the left atrium from late gadolinium-enhanced cardiac magnetic resonance imaging

    , Medical Image Analysis, Vol: 67, Pages: 1-14, ISSN: 1361-8415

    Segmentation of medical images, particularly late gadolinium-enhanced magnetic resonance imaging (LGE-MRI) used for visualizing diseased atrial structures, is a crucial first step for ablation treatment of atrial fibrillation. However, direct segmentation of LGE-MRIs is challenging due to the varying intensities caused by contrast agents. Since most clinical studies have relied on manual, labor-intensive approaches, automatic methods are of high interest, particularly optimized machine learning approaches. To address this, we organized the 2018 Left Atrium Segmentation Challenge using 154 3D LGE-MRIs, currently the world's largest atrial LGE-MRI dataset, and associated labels of the left atrium segmented by three medical experts, ultimately attracting the participation of 27 international teams. In this paper, extensive analysis of the submitted algorithms using technical and biological metrics was performed by undergoing subgroup analysis and conducting hyper-parameter analysis, offering an overall picture of the major design choices of convolutional neural networks (CNNs) and practical considerations for achieving state-of-the-art left atrium segmentation. Results show that the top method achieved a Dice score of 93.2% and a mean surface to surface distance of 0.7 mm, significantly outperforming prior state-of-the-art. Particularly, our analysis demonstrated that double sequentially used CNNs, in which a first CNN is used for automatic region-of-interest localization and a subsequent CNN is used for refined regional segmentation, achieved superior results than traditional methods and machine learning approaches containing single CNNs. This large-scale benchmarking study makes a significant step towards much-improved segmentation methods for atrial LGE-MRIs, and will serve as an important benchmark for evaluating and comparing the future works in the field. Furthermore, the findings from this study can potentially be extended to other imaging datasets and modalitie

  • Conference paper
    Afzali J, Casas CQ, Arcucci R, 2021,

    Latent GAN: Using a Latent Space-Based GAN for Rapid Forecasting of CFD Models

    , Pages: 360-372, ISSN: 0302-9743

    The focus of this study is to simulate realistic fluid flow, through Machine Learning techniques that could be utilised in real-time forecasting of urban air pollution. We propose a novel Latent GAN architecture which looks at combining an AutoEncoder with a Generative Adversarial Network to predict fluid flow at the proceeding timestep of a given input, whilst keeping computational costs low. This architecture is applied to tracer flows and velocity fields around an urban city. We present a pair of AutoEncoders capable of dimensionality reduction of 3 orders of magnitude. Further, we present a pair of Generator models capable of performing real-time forecasting of tracer flows and velocity fields. We demonstrate that the models, as well as the latent spaces generated, learn and retain meaningful physical features of the domain. Despite the domain of this project being that of computational fluid dynamics, the Latent GAN architecture is designed to be generalisable such that it can be applied to other dynamical systems.

  • Conference paper
    Amendola M, Arcucci R, Mottet L, Casas CQ, Fan S, Pain C, Linden P, Guo YKet al., 2021,

    Data Assimilation in the Latent Space of a Convolutional Autoencoder

    , Pages: 373-386, ISSN: 0302-9743

    Data Assimilation (DA) is a Bayesian inference that combines the state of a dynamical system with real data collected by instruments at a given time. The goal of DA is to improve the accuracy of the dynamic system making its result as real as possible. One of the most popular technique for DA is the Kalman Filter (KF). When the dynamic system refers to a real world application, the representation of the state of a physical system usually leads to a big data problem. For these problems, KF results computationally too expensive and mandates to use of reduced order modeling techniques. In this paper we proposed a new methodology we called Latent Assimilation (LA). It consists in performing the KF in the latent space obtained by an Autoencoder with non-linear encoder functions and non-linear decoder functions. In the latent space, the dynamic system is represented by a surrogate model built by a Recurrent Neural Network. In particular, an Long Short Term Memory (LSTM) network is used to train a function which emulates the dynamic system in the latent space. The data from the dynamic model and the real data coming from the instruments are both processed through the Autoencoder. We apply the methodology to a real test case and we show that the LA has a good performance both in accuracy and in efficiency.

  • Journal article
    Arcucci R, Zhu J, Hu S, Guo Y-Ket al., 2021,

    Deep Data Assimilation: Integrating Deep Learning with Data Assimilation

  • Journal article
    Andersen MM, Schjoedt U, Price H, Rosas FE, Scrivner C, Clasen Met al., 2020,

    Playing with fear: a field study in recreational horror

    , Psychological Science, Vol: 31, Pages: 1497-1510, ISSN: 0956-7976

    Haunted attractions are illustrative examples of recreational fear in which people voluntarily seek out frightening experiences in pursuit of enjoyment. We present findings from a field study at a haunted-house attraction where visitors between the ages of 12 and 57 years (N = 110) were equipped with heart rate monitors, video-recorded at peak scare points during the attraction, and asked to report on their experience. Our results show that enjoyment has an inverted-U-shaped relationship with fear across repeated self-reported measures. Moreover, results from physiological data demonstrate that the experience of being frightened is a linear function of large-scale heart rate fluctuations, whereas there is an inverted-U-shaped relationship between participant enjoyment and small-scale heart rate fluctuations. These results suggest that enjoyment is related to forms of arousal dynamics that are “just right.” These findings shed light on how fear and enjoyment can coexist in recreational horror.

  • Journal article
    Ruiz LGB, Pegalajar MC, Arcucci R, Molina-Solana Met al., 2020,

    A time-series clustering methodology for knowledge extraction in energy consumption data

    , Expert Systems with Applications, Vol: 160, ISSN: 0957-4174

    In the Energy Efficiency field, the incorporation of intelligent systems in cities and buildings is motivated by the energy savings and pollution reduction that can be attained. To achieve this goal, energy modelling and a better understanding of how energy is consumed are fundamental factors. As a result, this study proposes a methodology for knowledge acquisition in energy-related data through Time-Series Clustering (TSC) techniques. In our experimentation, we utilize data from the buildings at the University of Granada (Spain) and compare several clustering methods to get the optimum model, in particular, we tested k-Means, k-Medoids, Hierarchical clustering and Gaussian Mixtures; as well as several algorithms to obtain the best grouping, such as PAM, CLARA, and two variants of Lloyd’s method, Small and Large. Thus, our methodology can provide non-trivial knowledge from raw energy data. In contrast to previous studies in this field, not only do we propose a clustering methodology to group time series straightforwardly, but we also present an automatic strategy to search and analyse energy periodicity in these series recursively so that we can deepen granularity and extract information at different levels of detail. The results show that k-Medoids with PAM is the best approach in virtually all cases, and the Squared Euclidean distance outperforms the rest of the metrics.

  • Journal article
    Rosas FE, Mediano PAM, Jensen HJ, Seth AK, Barrett AB, Carhart-Harris RL, Bor Det al., 2020,

    Reconciling emergences: an information-theoretic approach to identify causal emergence in multivariate data

    , PLoS Computational Biology, Vol: 16, ISSN: 1553-734X

    The broad concept of emergence is instrumental in various of the most challenging open scientific questions—yet, few quantitative theories of what constitutes emergent phenomena have been proposed. This article introduces a formal theory of causal emergence in multivariate systems, which studies the relationship between the dynamics of parts of a system and macroscopic features of interest. Our theory provides a quantitative definition of downward causation, and introduces a complementary modality of emergent behaviour—which we refer to as causal decoupling. Moreover, the theory allows practical criteria that can be efficiently calculated in large systems, making our framework applicable in a range of scenarios of practical interest. We illustrate our findings in a number of case studies, including Conway’s Game of Life, Reynolds’ flocking model, and neural activity as measured by electrocorticography.

  • Journal article
    Mack J, Arcucci R, Molina-Solana M, Guo Y-Ket al., 2020,

    Attention-based Convolutional Autoencoders for 3D-Variational Data Assimilation

  • Journal article
    Rosas FE, Mediano PAM, Rassouli B, Barrett ABet al., 2020,

    An operational information decomposition via synergistic disclosure

    , Journal of Physics A: Mathematical and Theoretical, Vol: 53, Pages: 485001-485001, ISSN: 1751-8113

    Multivariate information decompositions hold promise to yield insight into complex systems, and stand out for their ability to identify synergistic phenomena. However, the adoption of these approaches has been hindered by there being multiple possible decompositions, and no precise guidance for preferring one over the others. At the heart of this disagreement lies the absence of a clear operational interpretation of what synergistic information is. Here we fill this gap by proposing a new information decomposition based on a novel operationalisation of informational synergy, which leverages recent developments in the literature of data privacy. Our decomposition is defined for any number of information sources, and its atoms can be calculated using elementary optimisation techniques. The decomposition provides a natural coarse-graining that scales gracefully with the system's size, and is applicable in a wide range of scenarios of practical interest.

  • Journal article
    Casas CQ, Arcucci R, Wu P, Pain C, Guo Y-Ket al., 2020,

    A Reduced Order Deep Data Assimilation model

    , PHYSICA D-NONLINEAR PHENOMENA, Vol: 412, ISSN: 0167-2789
  • Journal article
    Wang S, Nadler P, Arcucci R, Yang X, Li L, Huang Y, Teng Z, Guo Yet al., 2020,

    A Bayesian Updating Scheme for Pandemics: Estimating the Infection Dynamics of COVID-19

  • Journal article
    Herzog R, Mediano PAM, Rosas FE, Carhart-Harris R, Perl YS, Tagliazucchi E, Cofre Ret al., 2020,

    A mechanistic model of the neural entropy increase elicited by psychedelic drugs

    , Scientific Reports, Vol: 10, ISSN: 2045-2322

    Psychedelic drugs, including lysergic acid diethylamide and other agonists of the serotonin 2A receptor (5HT2A-R), induce drastic changes in subjective experience, and provide a unique opportunity to study the neurobiological basis of consciousness. One of the most notable neurophysiological signatures of psychedelics, increased entropy in spontaneous neural activity, is thought to be of relevance to the psychedelic experience, mediating both acute alterations in consciousness and long-term effects. However, no clear mechanistic explanation for this entropy increase has been put forward so far. We sought to do this here by building upon a recent whole-brain model of serotonergic neuromodulation, to study the entropic effects of 5HT2A-R activation. Our results reproduce the overall entropy increase observed in previous experiments in vivo, providing the first model-based explanation for this phenomenon. We also found that entropy changes were not uniform across the brain: entropy increased in some regions and decreased in others, suggesting a topographical reconfiguration mediated by 5HT2A-R activation. Interestingly, at the whole-brain level, this reconfiguration was not well explained by 5HT2A-R density, but related closely to the topological properties of the brain's anatomical connectivity. These results help us understand the mechanisms underlying the psychedelic state and, more generally, the pharmacological modulation of whole-brain activity.

  • Journal article
    D'Amore L, Murano A, Sorrentino L, Arcucci R, Laccetti Get al., 2020,

    Toward a multilevel scalable parallel Zielonka's algorithm for solving parity games


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