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  • Journal article
    Johnston I, Hoffmann T, Greenbury S, Cominetti O, Jallow M, Kwiatkowski D, Barahona M, Jones N, Casals-Pascual Cet al., 2019,

    Precision identification of high-risk phenotypes and progression pathways in severe malaria without requiring longitudinal data

    , npj Digital Medicine, Vol: 2, ISSN: 2398-6352

    More than 400,000 deaths from severe malaria (SM) are reported every year, mainly in African children. The diversity of clinical presentations associated with SM indicates important differences in disease pathogenesis that require specific treatment, and this clinical heterogeneity of SM remains poorly understood. Here, we apply tools from machine learning and model-based inference to harness large-scale data and dissect the heterogeneity in patterns of clinical features associated with SM in 2904 Gambian children admitted to hospital with malaria. This quantitative analysis reveals features predicting the severity of individual patient outcomes, and the dynamic pathways of SM progression, notably inferred without requiring longitudinal observations. Bayesian inference of these pathways allows us assign quantitative mortality risks to individual patients. By independently surveying expert practitioners, we show that this data-driven approach agrees with and expands the current state of knowledge on malaria progression, while simultaneously providing a data-supported framework for predicting clinical risk.

  • Conference paper
    AlAttar A, Rouillard L, Kormushev P, 2019,

    Autonomous air-hockey playing cobot using optimal control and vision-based Bayesian tracking

    , Towards Autonomous Robotic Systems, Publisher: Springer, ISSN: 0302-9743

    This paper presents a novel autonomous air-hockey playing collaborative robot (cobot) that provides human-like gameplay against human opponents. Vision-based Bayesian tracking of the puck and striker are used in an Analytic Hierarchy Process (AHP)-based probabilistic tactical layer for high-speed perception. The tactical layer provides commands for an active control layer that controls the Cartesian position and yaw angle of a custom end effector. The active layer uses optimal control of the cobot’s posture inside the task nullspace. The kinematic redundancy is resolved using a weighted Moore-Penrose pseudo-inversion technique. Experiments with human players show high-speed human-like gameplay with potential applications in the growing field of entertainment robotics.

  • Conference paper
    Falck F, Larppichet K, Kormushev P, 2019,

    DE VITO: A dual-arm, high degree-of-freedom, lightweight, inexpensive, passive upper-limb exoskeleton for robot teleoperation

    , TAROS: Annual Conference Towards Autonomous Robotic Systems, Publisher: Springer, ISSN: 0302-9743

    While robotics has made significant advances in perception, planning and control in recent decades, the vast majority of tasks easily completed by a human, especially acting in dynamic, unstructured environments, are far from being autonomously performed by a robot. Teleoperation, remotely controlling a slave robot by a human operator, can be a realistic, complementary transition solution that uses the motion intelligence of a human in complex tasks while exploiting the robot’s autonomous reliability and precision in less challenging situations.We introduce DE VITO, a seven degree-of-freedom, dual-arm upper-limb exoskeleton that passively measures the pose of a human arm. DE VITO is a lightweight, simplistic and energy-efficient design with a total material cost of at least an order of magnitude less than previous work. Given the estimated human pose, we implement both joint and Cartesian space kinematic control algorithms and present qualitative experimental results on various complex manipulation tasks teleoperating Robot DE NIRO, a research platform for mobile manipulation, that demonstrate the functionality of DE VITO. We provide the CAD models, open-source code and supplementary videos of DE VITO at http://www.imperial.ac.uk/robot-intelligence/robots/de_vito/.

  • Journal article
    Schaub MT, Delvenne JC, Lambiotte R, Barahona Met al., 2019,

    Multiscale dynamical embeddings of complex networks

    , Physical Review E, Vol: 99, Pages: 062308-1-062308-18, ISSN: 1539-3755

    Complex systems and relational data are often abstracted as dynamical processes on networks. To understand, predict, and control their behavior, a crucial step is to extract reduced descriptions of such networks. Inspired by notions from control theory, we propose a time-dependent dynamical similarity measure between nodes, which quantifies the effect a node-input has on the network. This dynamical similarity induces an embedding that can be employed for several analysis tasks. Here we focus on (i) dimensionality reduction, i.e., projecting nodes onto a low-dimensional space that captures dynamic similarity at different timescales, and (ii) how to exploit our embeddings to uncover functional modules. We exemplify our ideas through case studies focusing on directed networks without strong connectivity and signed networks. We further highlight how certain ideas from community detection can be generalized and linked to control theory, by using the here developed dynamical perspective.

  • Journal article
    Moriconi R, Kumar KSS, Deisenroth MP, 2020,

    High-dimensional Bayesian optimization with projections using quantile Gaussian processes

    , Optimization Letters, ISSN: 1862-4472
  • Journal article
    Warren L, Clarke J, Arora S, Barahona M, Arebi N, Darzi Aet al., 2019,

    Transitions of care across hospital settings in patients with inflammatory bowel disease

    , World Journal of Gastroenterology, Vol: 25, Pages: 2122-2132, ISSN: 1007-9327

    BACKGROUNDInflammatory bowel disease (IBD) is a chronic, inflammatory disorder characterised by both intestinal and extra-intestinal pathology. Patients may receive both emergency and elective care from several providers, often in different hospital settings. Poorly managed transitions of care between providers can lead to inefficiencies in care and patient safety issues. To ensure that the sharing of patient information between providers is appropriate, timely, accurate and secure, effective data-sharing infrastructure needs to be developed. To optimise inter-hospital data-sharing for IBD patients, we need to better understand patterns of hospital encounters in this group.AIMTo determine the type and location of hospital services accessed by IBD patients in England.METHODSThis was a retrospective observational study using Hospital Episode Statistics, a large administrative patient data set from the National Health Service in England. Adult patients with a diagnosis of IBD following admission to hospital were followed over a 2-year period to determine the proportion of care accessed at the same hospital providing their outpatient IBD care, defined as their ‘home provider’. Secondary outcome measures included the geographic distribution of patient-sharing, regional and age-related differences in accessing services, and type and frequency of outpatient encounters.RESULTSOf 95055 patients accessed hospital services on 1760156 occasions over a 2-year follow-up period. The proportion of these encounters with their identified IBD ‘home provider’ was 73.3%, 87.8% and 83.1% for accident and emergency, inpatient and outpatient encounters respectively. Patients living in metropolitan centres and younger patients were less likely to attend their ‘home provider’ for hospital services. The most commonly attended specialty services were gastroenterology, general surgery and ophthalmology.CONCLUSIONTransitions of care between secondary care sett

  • Journal article
    Bertone G, Deisenroth MP, Kim JS, Liem S, de Austri RR, Welling Met al., 2019,

    Accelerating the BSM interpretation of LHC data with machine learning

    , PHYSICS OF THE DARK UNIVERSE, Vol: 24, ISSN: 2212-6864
  • Journal article
    Kuntz J, Thomas P, Stan G-B, Barahona Met al., 2019,

    The exit time finite state projection scheme: bounding exit distributions and occupation measures of continuous-time Markov chains

    , SIAM Journal on Scientific Computing, Vol: 41, Pages: A748-A769, ISSN: 1064-8275

    We introduce the exit time finite state projection (ETFSP) scheme, a truncation- based method that yields approximations to the exit distribution and occupation measure associated with the time of exit from a domain (i.e., the time of first passage to the complement of the domain) of time-homogeneous continuous-time Markov chains. We prove that: (i) the computed approximations bound the measures from below; (ii) the total variation distances between the approximations and the measures decrease monotonically as states are added to the truncation; and (iii) the scheme converges, in the sense that, as the truncation tends to the entire state space, the total variation distances tend to zero. Furthermore, we give a computable bound on the total variation distance between the exit distribution and its approximation, and we delineate the cases in which the bound is sharp. We also revisit the related finite state projection scheme and give a comprehensive account of its theoretical properties. We demonstrate the use of the ETFSP scheme by applying it to two biological examples: the computation of the first passage time associated with the expression of a gene, and the fixation times of competing species subject to demographic noise.

  • Journal article
    Zhong Q, Fan X, Luo X, Toni Fet al., 2019,

    An explainable multi-attribute decision model based on argumentation

    , Expert Systems with Applications, Vol: 117, Pages: 42-61, ISSN: 0957-4174

    We present a multi-attribute decision model and a method for explaining the decisions it recommends based on an argumentative reformulation of the model. Specifically, (i) we define a notion of best (i.e., minimally redundant) decisions amounting to achieving as many goals as possible and exhibiting as few redundant attributes as possible, and (ii) we generate explanations for why a decision is best or better than or as good as another, using a mapping between the given decision model and an argumentation framework, such that best decisions correspond to admissible sets of arguments. Concretely, natural language explanations are generated automatically from dispute trees sanctioning the admissibility of arguments. Throughout, we illustrate the power of our approach within a legal reasoning setting, where best decisions amount to past cases that are most similar to a given new, open case. Finally, we conduct an empirical evaluation of our method with legal practitioners, confirming that our method is effective for the choice of most similar past cases and helpful to understand automatically generated recommendations.

  • Journal article
    Bello G, Dawes T, Duan J, Biffi C, Simoes Monteiro de Marvao A, Howard L, Gibbs S, Wilkins M, Cook S, Rueckert D, O'Regan Det al., 2019,

    Deep learning cardiac motion analysis for human survival prediction

    , Nature Machine Intelligence, Vol: 1, Pages: 95-104, ISSN: 2522-5839

    Motion analysis is used in computer vision to understand the behaviour of moving objects in sequences of images. Optimizing the interpretation of dynamic biological systems requires accurate and precise motion tracking as well as efficient representations of high-dimensional motion trajectories so that these can be used for prediction tasks. Here we use image sequences of the heart, acquired using cardiac magnetic resonance imaging, to create time-resolved three-dimensional segmentations using a fully convolutional network trained on anatomical shape priors. This dense motion model formed the input to a supervised denoising autoencoder (4Dsurvival), which is a hybrid network consisting of an autoencoder that learns a task-specific latent code representation trained on observed outcome data, yielding a latent representation optimized for survival prediction. To handle right-censored survival outcomes, our network used a Cox partial likelihood loss function. In a study of 302 patients, the predictive accuracy (quantified by Harrell’s C-index) was significantly higher (P = 0.0012) for our model C = 0.75 (95% CI: 0.70–0.79) than the human benchmark of C = 0.59 (95% CI: 0.53–0.65). This work demonstrates how a complex computer vision task using high-dimensional medical image data can efficiently predict human survival.

  • Conference paper
    Arulkumaran K, Cully A, Togelius J, 2019,

    AlphaStar: an evolutionary computation perspective

    , The Genetic and Evolutionary Computation Conference 2019, Publisher: ACM

    In January 2019, DeepMind revealed AlphaStar to the world—thefirst artificial intelligence (AI) system to beat a professional playerat the game of StarCraft II—representing a milestone in the progressof AI. AlphaStar draws on many areas of AI research, includingdeep learning, reinforcement learning, game theory, and evolution-ary computation (EC). In this paper we analyze AlphaStar primar-ily through the lens of EC, presenting a new look at the systemandrelating it to many concepts in the field. We highlight some ofitsmost interesting aspects—the use of Lamarckian evolution,com-petitive co-evolution, and quality diversity. In doing so,we hopeto provide a bridge between the wider EC community and one ofthe most significant AI systems developed in recent times.

  • Journal article
    Baroni P, Rago A, Toni F, 2019,

    From fine-grained properties to broad principles for gradual argumentation: A principled spectrum

    , International Journal of Approximate Reasoning, Vol: 105, Pages: 252-286, ISSN: 0888-613X

    The study of properties of gradual evaluation methods in argumentation has received increasing attention in recent years, with studies devoted to various classes of frameworks/ methods leading to conceptually similar but formally distinct properties in different contexts. In this paper we provide a novel systematic analysis for this research landscape by making three main contributions. First, we identify groups of conceptually related properties in the literature, which can be regarded as based on common patterns and, using these patterns, we evidence that many further novel properties can be considered. Then, we provide a simplifying and unifying perspective for these groups of properties by showing that they are all implied by novel parametric principles of (either strict or non-strict) balance and monotonicity. Finally, we show that (instances of) these principles (and thus the group, literature and novel properties that they imply) are satisfied by several quantitative argumentation formalisms in the literature, thus confirming the principles' general validity and utility to support a compact, yet comprehensive, analysis of properties of gradual argumentation.

  • Journal article
    Altuncu MT, Mayer E, Yaliraki SN, Barahona Met al., 2019,

    From free text to clusters of content in health records: An unsupervised graph partitioning approach

    , Applied Network Science, Vol: 4, ISSN: 2364-8228

    Electronic Healthcare records contain large volumes of unstructured data in different forms. Free text constitutes a large portion of such data, yet this source of richly detailed information often remains under-used in practice because of a lack of suitable methodologies to extract interpretable contentin a timely manner. Here we apply network-theoretical tools to the analysis of free text in Hospital Patient Incident reports in the English National Health Service, to find clusters of reports in an unsupervised manner and at different levels of resolution based directly on the free text descriptions contained within them. To do so, we combine recently developed deep neural network text-embedding methodologies based on paragraph vectors with multi-scale Markov Stability community detection applied to a similarity graph of documents obtained from sparsified text vector similarities. We showcase the approach with the analysis of incident reports submitted in Imperial College Healthcare NHS Trust, London. The multiscale community structure reveals levels of meaning with different resolution in the topics of the dataset, as shown by relevant descriptive terms extracted from thegroups of records, as well as by comparing a posteriori against hand-coded categories assigned by healthcare personnel. Our content communities exhibit good correspondence with well-defined hand-coded categories, yet our results also provide further medical detail in certain areas as well asrevealing complementary descriptors of incidents beyond the external classification. We also discuss how the method can be used to monitor reports over time and across different healthcare providers, and to detect emerging trends that fall outside of pre-existing categories.

  • Conference paper
    Kotonya N, Toni F, 2019,

    Gradual Argumentation Evaluation for Stance Aggregation in Automated Fake News Detection

    , 6th Workshop on Argument Mining (ArgMining), Publisher: ASSOC COMPUTATIONAL LINGUISTICS-ACL, Pages: 156-166
  • Journal article
    Kormushev P, Ugurlu B, Caldwell DG, Tsagarakis NGet al., 2019,

    Learning to exploit passive compliance for energy-efficient gait generation on a compliant humanoid

    , Autonomous Robots, Vol: 43, Pages: 79-95, ISSN: 1573-7527

    Modern humanoid robots include not only active compliance but also passive compliance. Apart from improved safety and dependability, availability of passive elements, such as springs, opens up new possibilities for improving the energy efficiency. With this in mind, this paper addresses the challenging open problem of exploiting the passive compliance for the purpose of energy efficient humanoid walking. To this end, we develop a method comprising two parts: an optimization part that finds an optimal vertical center-of-mass trajectory, and a walking pattern generator part that uses this trajectory to produce a dynamically-balanced gait. For the optimization part, we propose a reinforcement learning approach that dynamically evolves the policy parametrization during the learning process. By gradually increasing the representational power of the policy parametrization, it manages to find better policies in a faster and computationally efficient way. For the walking generator part, we develop a variable-center-of-mass-height ZMP-based bipedal walking pattern generator. The method is tested in real-world experiments with the bipedal robot COMAN and achieves a significant 18% reduction in the electric energy consumption by learning to efficiently use the passive compliance of the robot.

  • Journal article
    Eyerich K, Brown S, Perez White B, Tanaka RJ, Bissonette R, Dhar S, Bieber T, Hijnen DJ, Guttman-Yassky E, Irvine A, Thyssen JP, Vestergaard C, Werfel T, Wollenberg A, Paller A, Reynolds NJet al., 2019,

    Human and computational models of atopic dermatitis: A review and perspectives by an expert panel of the International Eczema Council

    , Journal of Allergy and Clinical Immunology, Vol: 143, Pages: 36-45, ISSN: 0091-6749

    Atopic dermatitis (AD) is a prevalent disease worldwide and is associated with systemic comorbidities representing a significant burden on patients, their families, and society. Therapeutic options for AD remain limited, in part because of a lack of well-characterized animal models. There has been increasing interest in developing experimental approaches to study the pathogenesis of human AD in vivo, in vitro, and in silico to better define pathophysiologic mechanisms and identify novel therapeutic targets and biomarkers that predict therapeutic response. This review critically appraises a range of models, including genetic mutations relevant to AD, experimental challenge of human skin in vivo, tissue culture models, integration of “omics” data sets, and development of predictive computational models. Although no one individual model recapitulates the complex AD pathophysiology, our review highlights insights gained into key elements of cutaneous biology, molecular pathways, and therapeutic target identification through each approach. Recent developments in computational analysis, including application of machine learning and a systems approach to data integration and predictive modeling, highlight the applicability of these methods to AD subclassification (endotyping), therapy development, and precision medicine. Such predictive modeling will highlight knowledge gaps, further inform refinement of biological models, and support new experimental and systems approaches to AD.

  • Conference paper
    Cyras K, Domínguez J, Karamlou A, Prociuk D, Curcin V, Delaney B, Toni F, Chalkidou K, Darzi Aet al., 2019,

    ROAD2H: Learning Decision Support System for Low- and Middle-Income Countries.

    , Publisher: AMIA
  • Journal article
    Cocarascu O, Toni F, 2018,

    Combining deep learning and argumentative reasoning for the analysis of social media textual content using small datasets

    , Computational Linguistics, Vol: 44, Pages: 833-858, ISSN: 0891-2017

    The use of social media has become a regular habit for many and has changed the way people interact with each other. In this article, we focus on analysing whether news headlines support tweets and whether reviews are deceptive by analysing the interaction or the influence that these texts have on the others, thus exploiting contextual information. Concretely, we define a deep learning method for Relation-based Argument Mining to extract argumentative relations of attack and support. We then use this method for determining whether news articles support tweets, a useful task in fact-checking settings, where determining agreement towards a statement is a useful step towards determining its truthfulness. Furthermore we use our method for extracting Bipolar Argumentation Frameworks from reviews to help detect whether they are deceptive. We show experimentally that our method performs well in both settings. In particular, in the case of deception detection, our method contributes a novel argumentative feature that, when used in combination with other features in standard supervised classifiers, outperforms the latter even on small datasets.

  • Journal article
    Clarke JM, Warren LR, Arora S, Barahona M, Darzi AWet al., 2018,

    Guiding interoperable electronic health records through patient-sharing networks.

    , NPJ digital medicine, Vol: 1, Pages: 65-65, ISSN: 2398-6352

    Effective sharing of clinical information between care providers is a critical component of a safe, efficient health system. National data-sharing systems may be costly, politically contentious and do not reflect local patterns of care delivery. This study examines hospital attendances in England from 2013 to 2015 to identify instances of patient sharing between hospitals. Of 19.6 million patients receiving care from 155 hospital care providers, 130 million presentations were identified. On 14.7 million occasions (12%), patients attended a different hospital to the one they attended on their previous interaction. A network of hospitals was constructed based on the frequency of patient sharing between hospitals which was partitioned using the Louvain algorithm into ten distinct data-sharing communities, improving the continuity of data sharing in such instances from 0 to 65-95%. Locally implemented data-sharing communities of hospitals may achieve effective accessibility of clinical information without a large-scale national interoperable information system.

  • Conference paper
    Dutordoir V, Salimbeni HR, Hensman J, Deisenroth MPet al., 2018,

    Gaussian process conditional density estimation

    , Advances in Neural Information Processing Systems, Publisher: Neural Information Processing Systems Conference

    Conditional Density Estimation (CDE) models deal with estimating conditional distributions. The conditions imposed on the distribution are the inputs of the model. CDE is a challenging task as there is a fundamental trade-off between model complexity, representational capacity and overfitting. In this work, we propose to extend the model's input with latent variables and use Gaussian processes (GP) to map this augmented input onto samples from the conditional distribution. Our Bayesian approach allows for the modeling of small datasets, but we also provide the machinery for it to be applied to big data using stochastic variational inference. Our approach can be used to model densities even in sparse data regions, and allows for sharing learned structure between conditions. We illustrate the effectiveness and wide-reaching applicability of our model on a variety of real-world problems, such as spatio-temporal density estimation of taxi drop-offs, non-Gaussian noise modeling, and few-shot learning on omniglot images.

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