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  • Conference paper
    Cully A, 2021,

    Multi-Emitter MAP-Elites: Improving quality, diversity and convergence speed with heterogeneous sets of emitters

    , Genetic and Evolutionary Computation Conference (GECCO)

    Quality-Diversity (QD) optimisation is a new family of learning algorithmsthat aims at generating collections of diverse and high-performing solutions.Among those algorithms, MAP-Elites is a simple yet powerful approach that hasshown promising results in numerous applications. In this paper, we introduce anovel algorithm named Multi-Emitter MAP-Elites (ME-MAP-Elites) that improvesthe quality, diversity and convergence speed of MAP-Elites. It is based on therecently introduced concept of emitters, which are used to drive thealgorithm's exploration according to predefined heuristics. ME-MAP-Elitesleverages the diversity of a heterogeneous set of emitters, in which eachemitter type is designed to improve differently the optimisation process.Moreover, a bandit algorithm is used to dynamically find the best emitter setdepending on the current situation. We evaluate the performance ofME-MAP-Elites on six tasks, ranging from standard optimisation problems (in 100dimensions) to complex locomotion tasks in robotics. Our comparisons againstMAP-Elites and existing approaches using emitters show that ME-MAP-Elites isfaster at providing collections of solutions that are significantly morediverse and higher performing. Moreover, in the rare cases where no fruitfulsynergy can be found between the different emitters, ME-MAP-Elites isequivalent to the best of the compared algorithms.

  • Journal article
    Mersmann S, Stromich L, Song F, Wu N, Vianello F, Barahona M, Yaliraki Set al., 2021,

    ProteinLens: a web-based application for the analysis of allosteric signalling on atomistic graphs of biomolecules

    , Nucleic Acids Research, ISSN: 0305-1048
  • Journal article
    Rago A, Cocarascu O, Bechlivanidis C, Lagnado D, Toni Fet al., 2021,

    Argumentative Explanations for Interactive Recommendations

    , Artificial Intelligence, ISSN: 0004-3702
  • Conference paper
    Cyras K, Rago A, Emanuele A, Baroni P, Toni Fet al., 2021,

    Argumentative XAI: A Survey

    , The 30th International Joint Conference on Artificial Intelligence (IJCAI-21)
  • Journal article
    Cyras K, Heinrich Q, Toni F, 2021,

    Computational complexity of flat and generic assumption-based argumentation, with and without probabilities

    , Artificial Intelligence, Vol: 293, Pages: 1-36, ISSN: 0004-3702

    Reasoning with probabilistic information has recently attracted considerable attention in argumentation, and formalisms of Probabilistic Abstract Argumentation (PAA), Probabilistic Bipolar Argumentation (PBA) and Probabilistic Structured Argumentation (PSA) have been proposed. These foundational advances have been complemented with investigations on the complexity of some approaches to PAA and PBA, but not to PSA. We study the complexity of an existing form of PSA, namely Probabilistic Assumption-Based Argumentation (PABA), a powerful, implemented formalism which subsumes several forms of PAA and other forms of PSA. Specifically, we establish membership (general upper bounds) and completeness (instantiated lower bounds) of reasoning in PABA for the class FP#P (of functions with a #P-oracle for counting the solutions of an NP problem) with respect to newly introduced probabilistic verification, credulous and sceptical acceptance function problems under several ABA semantics. As a by-product necessary to establish PABA complexity results, we provide a comprehensive picture of the ABA complexity landscape (for both flat and generic, possibly non-flat ABA) for the classical decision problems of verification, existence, credulous and sceptical acceptance under those ABA semantics.

  • Journal article
    Qian Y, Expert P, Panzarasa P, Barahona Met al., 2021,

    Geometric graphs from data to aid classification tasks with Graph Convolutional Networks

    , Patterns, Vol: 2, Pages: 100237-100237, ISSN: 2666-3899
  • Journal article
    Peach RL, Arnaudon A, Schmidt JA, Palasciano HA, Bernier NR, Jelfs KE, Yaliraki SN, Barahona Met al., 2021,

    HCGA: Highly comparative graph analysis for network phenotyping

    , Patterns, Vol: 2, Pages: 100227-100227, ISSN: 2666-3899

    <jats:title>A<jats:sc>bstract</jats:sc></jats:title><jats:p>Networks are widely used as mathematical models of complex systems across many scientific disciplines, not only in biology and medicine but also in the social sciences, physics, computing and engineering. Decades of work have produced a vast corpus of research characterising the topological, combinatorial, statistical and spectral properties of graphs. Each graph property can be thought of as a feature that captures important (and some times overlapping) characteristics of a network. In the analysis of real-world graphs, it is crucial to integrate systematically a large number of diverse graph features in order to characterise and classify networks, as well as to aid network-based scientific discovery. In this paper, we introduce HCGA, a framework for highly comparative analysis of graph data sets that computes several thousands of graph features from any given network. HCGA also offers a suite of statistical learning and data analysis tools for automated identification and selection of important and interpretable features underpinning the characterisation of graph data sets. We show that HCGA outperforms other methodologies on supervised classification tasks on benchmark data sets whilst retaining the interpretability of network features. We also illustrate how HCGA can be used for network-based discovery through two examples where data is naturally represented as graphs: the clustering of a data set of images of neuronal morphologies, and a regression problem to predict charge transfer in organic semiconductors based on their structure. HCGA is an open platform that can be expanded to include further graph properties and statistical learning tools to allow researchers to leverage the wide breadth of graph-theoretical research to quantitatively analyse and draw insights from network data.</jats:p>

  • Journal article
    Myall AC, Peach RL, Wei├če AY, Davies F, Mookerjee S, Holmes A, Barahona Met al., 2021,

    Network memory in the movement of hospital patients carrying drug-resistant bacteria

    , Applied Network Science, ISSN: 2364-8228

    Hospitals constitute highly interconnected systems that bring into contact anabundance of infectious pathogens and susceptible individuals, thus makinginfection outbreaks both common and challenging. In recent years, there hasbeen a sharp incidence of antimicrobial-resistance amongsthealthcare-associated infections, a situation now considered endemic in manycountries. Here we present network-based analyses of a data set capturing themovement of patients harbouring drug-resistant bacteria across three largeLondon hospitals. We show that there are substantial memory effects in themovement of hospital patients colonised with drug-resistant bacteria. Suchmemory effects break first-order Markovian transitive assumptions andsubstantially alter the conclusions from the analysis, specifically on noderankings and the evolution of diffusive processes. We capture variable lengthmemory effects by constructing a lumped-state memory network, which we then useto identify overlapping communities of wards. We find that these communities ofwards display a quasi-hierarchical structure at different levels of granularitywhich is consistent with different aspects of patient flows related to hospitallocations and medical specialties.

  • Journal article
    Zheng JX, Pawar S, Goodman DFM, 2021,

    Further towards unambiguous edge bundling: Investigating power-confluentdrawings for network visualization

    , IEEE Transactions on Visualization and Computer Graphics, Vol: 27, Pages: 2244-2249, ISSN: 1077-2626

    Bach et al. [1] recently presented an algorithm for constructing confluentdrawings, by leveraging power graph decomposition to generate an auxiliaryrouting graph. We identify two problems with their method and offer a singlesolution to solve both. We also classify the exact type of confluent drawingsthat the algorithm can produce as 'power-confluent', and prove that it is asubclass of the previously studied 'strict confluent' drawing. A descriptionand source code of our implementation is also provided, which additionallyincludes an improved method for power graph construction.

  • Journal article
    Maes A, Barahona M, Clopath C, 2021,

    Learning compositional sequences with multiple time scales through a hierarchical network of spiking neurons

  • Journal article
    Kuntz J, Thomas P, Stan G-B, Barahona Met al., 2021,

    Stationary distributions of continuous-time Markov chains: a review of theory and truncation-based approximations

    , SIAM Review, ISSN: 0036-1445

    Computing the stationary distributions of a continuous-time Markov chaininvolves solving a set of linear equations. In most cases of interest, thenumber of equations is infinite or too large, and cannot be solved analyticallyor numerically. Several approximation schemes overcome this issue by truncatingthe state space to a manageable size. In this review, we first give acomprehensive theoretical account of the stationary distributions and theirrelation to the long-term behaviour of the Markov chain, which is readilyaccessible to non-experts and free of irreducibility assumptions made instandard texts. We then review truncation-based approximation schemes payingparticular attention to their convergence and to the errors they introduce, andwe illustrate their performance with an example of a stochastic reactionnetwork of relevance in biology and chemistry. We conclude by elaborating oncomputational trade-offs associated with error control and some open questions.

  • Conference paper
    Lauren S, Belardinelli F, Toni F, 2020,

    Aggregating Bipolar Opinions

    , 20th International Conference on Autonomous Agents and Multiagent Systems
  • Conference paper
    Kotonya N, Toni F, 2020,

    Explainable Automated Fact-Checking: A Survey

    , Barcelona. Spain, 28th International Conference on Computational Linguistics (COLING 2020), Publisher: International Committee on Computational Linguistics, Pages: 5430-5443

    A number of exciting advances have been made in automated fact-checkingthanks to increasingly larger datasets and more powerful systems, leading toimprovements in the complexity of claims which can be accurately fact-checked.However, despite these advances, there are still desirable functionalitiesmissing from the fact-checking pipeline. In this survey, we focus on theexplanation functionality -- that is fact-checking systems providing reasonsfor their predictions. We summarize existing methods for explaining thepredictions of fact-checking systems and we explore trends in this topic.Further, we consider what makes for good explanations in this specific domainthrough a comparative analysis of existing fact-checking explanations againstsome desirable properties. Finally, we propose further research directions forgenerating fact-checking explanations, and describe how these may lead toimprovements in the research area.v

  • Journal article
    Cyras K, Oliveira T, Karamlou M, Toni Fet al.,

    Assumption-based argumentation with preferences and goals for patient-centric reasoning with interacting clinical guidelines

    , Argument and Computation, ISSN: 1946-2166

    A paramount, yet unresolved issue in personalised medicine is that of automated reasoning with clinical guidelines in multimorbidity settings. This entails enabling machines to use computerised generic clinical guideline recommendations and patient-specific information to yield patient-tailored recommendations where interactions arising due to multimorbidities are resolved. This problem is further complicated by patient management desiderata, in particular the need to account for patient-centric goals as well as preferences of various parties involved. We propose to solve this problem of automated reasoning with interacting guideline recommendations in the context of a given patient by means of computational argumentation. In particular, we advance a structured argumentation formalism ABA+G (short for Assumption-Based Argumentation with Preferences (ABA+) and Goals) for integrating and reasoning with information about recommendations, interactions, patient’s state, preferences and prioritised goals. ABA+G combines assumption-based reasoning with preferences and goal-driven selection among reasoning outcomes. Specifically, we assume defeasible applicability of guideline recommendations with the general goal of patient well-being, resolve interactions (conflicts and otherwise undesirable situations) among recommendations based on the state and preferences of the patient, and employ patient-centered goals to suggest interaction-resolving, goal-importance maximising and preference-adhering recommendations. We use a well-established Transition-based Medical Recommendation model for representing guideline recommendations and identifying interactions thereof, and map the components in question, together with the given patient’s state, prioritised goals, and preferences over actions, to ABA+G for automated reasoning. In this, we follow principles of patient management and establish corresponding theoretical properties as well as illustrate our approach in realis

  • Conference paper
    Liu S, Lin Z, Wang Y, Jianming Z, Perazzi F, Johns Eet al., 2020,

    Shape adaptor: a learnable resizing module

    , European Conference on Computer Vision 2020, Publisher: Springer Verlag, Pages: 661-677, ISSN: 0302-9743

    We present a novel resizing module for neural networks: shape adaptor, a drop-in enhancement built on top of traditional resizing layers, such as pooling, bilinear sampling, and strided convolution. Whilst traditional resizing layers have fixed and deterministic reshaping factors, our module allows for a learnable reshaping factor. Our implementation enables shape adaptors to be trained end-to-end without any additional supervision, through which network architectures can be optimised for each individual task, in a fully automated way. We performed experiments across seven image classification datasets, and results show that by simply using a set of our shape adaptors instead of the original resizing layers, performance increases consistently over human-designed networks, across all datasets. Additionally, we show the effectiveness of shape adaptors on two other applications: network compression and transfer learning.

  • Journal article
    Bai W, Suzuki H, Huang J, Francis C, Wang S, Tarroni G, Guitton F, Aung N, Fung K, Petersen SE, Piechnik SK, Neubauer S, Evangelou E, Dehghan A, O'Regan DP, Wilkins MR, Guo Y, Matthews PM, Rueckert Det al., 2020,

    A population-based phenome-wide association study of cardiac and aortic structure and function

    , Nature Medicine, Vol: 26, Pages: 1654-1662, ISSN: 1078-8956

    Differences in cardiac and aortic structure and function are associated with cardiovascular diseases and a wide range of other types of disease. Here we analyzed cardiovascular magnetic resonance images from a population-based study, the UK Biobank, using an automated machine-learning-based analysis pipeline. We report a comprehensive range of structural and functional phenotypes for the heart and aorta across 26,893 participants, and explore how these phenotypes vary according to sex, age and major cardiovascular risk factors. We extended this analysis with a phenome-wide association study, in which we tested for correlations of a wide range of non-imaging phenotypes of the participants with imaging phenotypes. We further explored the associations of imaging phenotypes with early-life factors, mental health and cognitive function using both observational analysis and Mendelian randomization. Our study illustrates how population-based cardiac and aortic imaging phenotypes can be used to better define cardiovascular disease risks as well as heart–brain health interactions, highlighting new opportunities for studying disease mechanisms and developing image-based biomarkers.

  • Journal article
    Russell F, Kormushev P, Vaidyanathan R, Ellison Pet al., 2020,

    The impact of ACL laxity on a bicondylar robotic knee and implications in human joint biomechanics

    , IEEE Transactions on Biomedical Engineering, Vol: 67, Pages: 2817-2827, ISSN: 0018-9294

    Objective: Elucidating the role of structural mechanisms in the knee can improve joint surgeries, rehabilitation, and understanding of biped locomotion. Identification of key features, however, is challenging due to limitations in simulation and in-vivo studies. In particular the coupling of the patello-femoral and tibio-femoral joints with ligaments and its impact on joint mechanics and movement is not understood. We investigate this coupling experimentally through the design and testing of a robotic sagittal plane model. Methods: We constructed a sagittal plane robot comprised of: 1) elastic links representing cruciate ligaments; 2) a bi-condylar joint; 3) a patella; and 4) actuator hamstrings and quadriceps. Stiffness and geometry were derived from anthropometric data. 10° - 110° squatting tests were executed at speeds of 0.1 - 0.25Hz over a range of anterior cruciate ligament (ACL) slack lengths. Results: Increasing ACL length compromised joint stability, yet did not impact quadriceps mechanical advantage and force required for squat. The trend was consistent through varying condyle contact point and ligament force changes. Conclusion: The geometry of the condyles allows the ratio of quadriceps to patella tendon force to compensate for contact point changes imparted by the removal of the ACL. Thus the system maintains a constant mechanical advantage. Significance: The investigation uncovers critical features of human knee biomechanics. Findings contribute to understanding of knee ligament damage, inform procedures for knee surgery and orthopaedic implant design, and support design of trans-femoral prosthetics and walking robots. Results further demonstrate the utility of robotics as a powerful means of studying human joint biomechanics.

  • Conference paper
    Wang K, Marsh DM, Saputra RP, Chappell D, Jiang Z, Raut A, Kon B, Kormushev Pet al., 2020,

    Design and Control of SLIDER: An Ultra-lightweight, Knee-less, Low-cost Bipedal Walking Robot

    , Las Vegas, USA, International Conference on Intelligence Robots and Systems (IROS), Pages: 3488-3495

    Most state-of-the-art bipedal robots are designedto be highly anthropomorphic and therefore possess legs withknees. Whilst this facilitates more human-like locomotion, thereare implementation issues that make walking with straight ornear-straight legs difficult. Most bipedal robots have to movewith a constant bend in the legs to avoid singularities at theknee joints, and to keep the centre of mass at a constant heightfor control purposes. Furthermore, having a knee on the legincreases the design complexity as well as the weight of the leg,hindering the robot’s performance in agile behaviours such asrunning and jumping.We present SLIDER, an ultra-lightweight, low-cost bipedalwalking robot with a novel knee-less leg design. This nonanthropomorphic straight-legged design reduces the weight ofthe legs significantly whilst keeping the same functionality asanthropomorphic legs. Simulation results show that SLIDER’slow-inertia legs contribute to less vertical motion in the centerof mass (CoM) than anthropomorphic robots during walking,indicating that SLIDER’s model is closer to the widely usedInverted Pendulum (IP) model. Finally, stable walking onflat terrain is demonstrated both in simulation and in thephysical world, and feedback control is implemented to addresschallenges with the physical robot.

  • Journal article
    AlAttar A, Kormushev P, 2020,

    Kinematic-model-free orientation control for robot manipulation using locally weighted dual quaternions

    , Robotics, Vol: 9, Pages: 1-12, ISSN: 2218-6581

    Conventional control of robotic manipulators requires prior knowledge of their kinematic structure. Model-learning controllers have the advantage of being able to control robots without requiring a complete kinematic model and work well in less structured environments. Our recently proposed Encoderless controller has shown promising ability to control a manipulator without requiring any prior kinematic model whatsoever. However, this controller is only limited to position control, leaving orientation control unsolved. The research presented in this paper extends the state-of-the-art kinematic-model-free controller to handle orientation control to manipulate a robotic arm without requiring any prior model of the robot or any joint angle information during control. This paper presents a novel method to simultaneously control the position and orientation of a robot’s end effector using locally weighted dual quaternions. The proposed novel controller is also scaled up to control three-degrees-of-freedom robots.

  • Conference paper
    Kotonya N, Toni F, 2020,

    Explainable Automated Fact-Checking for Public Health Claims

    , 2020 Conference on Empirical Methods in Natural Language Processing (EMNLP(1) 2020), Publisher: ACL

    Fact-checking is the task of verifying the veracity of claims by assessing their assertions against credible evidence. The vast major-ity of fact-checking studies focus exclusively on political claims. Very little research explores fact-checking for other topics, specifically subject matters for which expertise is required. We present the first study of explainable fact-checking for claims which require specific expertise. For our case study we choose the setting of public health. To support this case study we construct a new datasetPUBHEALTHof 11.8K claims accompanied by journalist crafted, gold standard explanations(i.e., judgments) to support the fact-check la-bels for claims1. We explore two tasks: veracity prediction and explanation generation. We also define and evaluate, with humans and computationally, three coherence properties of explanation quality. Our results indicate that,by training on in-domain data, gains can be made in explainable, automated fact-checking for claims which require specific expertise.

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