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RESEARCH PAPER · Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences · 2016

Big data need big theory too

Peter V. Coveney, Edward R. Dougherty, Roger Highfield

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Big data need big theory tooOriginalBridging the gaps at the physics–chemistry–biology interface38Francis Bacon, Karl Popper, Michael Polanyi, and Modern Experimental Biology0Genetic studies of alcohol dependence in the context of the addiction cycle156Gene expression profiling in the human alcoholic brain52The Importance of Nutrition in a Conceptual Framework of Frailty Syndrome8Identicação de sistemas neurais com redes bayesianas dinâmicas e transferência de entropia0Big Data to Big Knowledge for Next Generation Medicine: A Data Science Roadmap0The Role of Multiscale Protein Dynamics in Antigen Presentation and T Lymphocyte Recognition10Single-Subject Studies in Translational Nutrition Research76Big Data approaches in social and behavioral science: four key trade-offs and a call for integration40Natural and Artificial Intelligence in Neurosurgery: A Systematic Review264Compressibility, Laws of Nature, Initial Conditions and Complexity2Evidence amalgamation, plausibility, and cancer research13Statistical physics and representations in real and artificial neural networks23Clinical judgement in the era of big data and predictive analytics59MetaQSAR: An Integrated Database Engine to Manage and Analyze Metabolic Data36Chemistry0Big Data in Computational Toxicology: Challenges and Opportunities10Developing WHO guidelines: Time to formally include evidence from mathematical modelling studies51Big data framework for students' academic performance prediction: A systematic literature review17Go to field, look around, measure and then run models15Uncertainty Quantification in Alchemical Free Energy Methods70Adaptive multiscale predictive modelling57Opportunities and challenges for big data ornithology81Projection-based model reduction: Formulations for physics-based machine learning372Prediction of Chemical Reactions Using Statistical Models of Chemical Knowledge4Prediction of Chemical Reactions Using Statistical Models of Chemical Knowledge0A Review of Machine Learning Applications to Coastal Sediment Transport and Morphodynamics222Mathematical models of tumor cell proliferation: A review of the literature159Quantifying the value of surveillance data for improving model predictions of lymphatic filariasis elimination13Big Data in Head and Neck Cancer64Theoretical underpinnings of research in strategic marketing: a commentary20On the Ethics of Biodiversity Models, Forecasts and Scenarios5Ensemble-Based Replica Exchange Alchemical Free Energy Methods: The Effect of Protein Mutations on Inhibitor Binding36Big Data in Discourse0Hope, hype and harms of Big Data16Three Problems with Big Data and Artificial Intelligence in Medicine111Toward a Predictive Hierarchical Multiscale Modeling Approach for Energetic Materials17Big Data: From Forecasting to Mesoscopic Understanding. Meta-Profiling as Complex Systems7Big data: the end of the scientific method?91Multiscale modelling, simulation and computing: from the desktop to the exascale19Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers130Using non-invasive stimulation of the undamaged brain to guide the identification of lesion sites that predict language outcome after stroke0Big data: The end of the scientific method?56The 2019 mathematical oncology roadmap215Introduction to Mathematical Oncology41Machine learning's feet of clay10Mesoscopic simulations at the physics-chemistry-biology interface48Complexity and integration. A philosophical analysis of how cancer complexity can be faced in the era of precision medicine7The future of laboratory medicine: Navigating between technology and professionalism8The Nature of Organizing: A Relational Approach to Understanding Business Sustainability31A Systematic Review on Big Data Analytics Frameworks for Higher Education - Tools and Algorithms16Improving palliative care with machine learning and routine data: a rapid review26TRANSPORT MODELING WITH A PURPOSE: HOW URBAN SYSTEMS DESIGN CAN BRIDGE THE GAPS BETWEEN MODELING, PLANNING, AND DESIGN11Through the Looking Glass0Retailing and retailing research in the age of big data analytics199Factoring a 2 x 2 contingency table10The Human Ecological Perspective and Biopsychosocial Medicine27An integrative methodology based on protein-protein interaction networks for identification and functional annotation of disease-relevant genes applied to channelopathies10Deep Learning for Deep Chemistry: Optimizing the Prediction of Chemical Patterns181A Model of Growth Trajectory Bifurcation in Animals Ontogeny2El voto vigilado. Influencia y control electoral en las hermandades de Huelva durante el Antiguo Régimen0Bayesian Estimation of the Shape Parameters of Mcdonald Generalized Beta-Binomial Distribution0Big-data driven approaches in materials science: A survey20Computational inference in mathematical biology: Methodological developments and applications1Fairness von KI-Algorithmen1Redundancy and Complexity Metrics for Big Data Classification: Towards Smart Data40Revisiting the Concept of Human Disease3The Pixelated Person – Humanity in the Grip of Algorithmic Personalisation1Thermal field prediction for laser scanning paths in laser aided additive manufacturing by physics-based machine learning181Development of Supervised Learning Predictive Models for Highly Non-linear Biological, Biomedical, and General Datasets23Toward Data Sense-Making in Digital Health Communication Research: Why Theory Matters in the Age of Big Data26From digital hype to analogue reality: Universal simulation beyond the quantum and exascale eras8Rediscovery of natural compounds acting via multitarget recognition and noncanonical pharmacodynamical actions22Monte Carlo science15Pre-Drilling Production Forecasting of Parent and Child Wells Using a 2-Segment Decline Curve Analysis (DCA) Method Based on an Analytical Flow-Cell Model Scaled by a Single Type Well6Hidden theorizing in big data analytics: With a reference to tourism design research52Review: Energy efficiency evaluation of complex petrochemical industries65Integrating remote sensing and jurisdictional observation networks to improve the resolution of ecological management3Machine Learning Requires Probability and Statistics [Perspectives]1Beyond Screen Time: Identity Development in the Digital Age231Incorporating Physical Knowledge Into Machine Learning for Planetary Space Physics27Formidable females redux: male social integration into female networks and the value of dynamic multilayer networks12Application of Systems Engineering Principles and Techniques in Biological Big Data Analytics: A Review14Microstructure-informed probability-driven point-particle model for hydrodynamic forces and torques in particle-laden flows70Computational medicine, present and the future: obstetrics and gynecology perspective11Continuous-domain assignment flows15A Study on The Limits and Potential of Machine Predictions from a Human-Big Data-Machine Interaction Perspective2Structural dynamics simulation using a novel physics-guided machine learning method134Machine learning for digital soil mapping: Applications, challenges and suggested solutions731Computational biomedicine. Part 1: molecular medicine4Rapid, accurate, precise and reproducible ligand–protein binding free energy prediction153Methodological problems of big data and artificial intelligence in the medical specialists training3Integrating Quantitative Assays with Biologically Based Mathematical Modeling for Predictive Oncology32Evaluating patient-specific neoadjuvant regimens for breast cancer via a mathematical model constrained by quantitative magnetic resonance imaging data58Towards integration of 64Cu-DOTA-trastuzumab PET-CT and MRI with mathematical modeling to predict response to neoadjuvant therapy in HER2 + breast cancer34Hybrid Modeling: Towards the Next Level of Scientific Computing in Engineering4Rapid Bayesian Inference for Expensive Stochastic Models3Application of artificial intelligence in the dental field: A literature review28Big Data32Blue Chips and White Collars: Whose Data Science Is It?3Review of Deep Learning Algorithms in Computational biochemistry7Towards Accountability for Machine Learning Datasets: Practices from Software Engineering and Infrastructure274Pandemic Drugs at Pandemic Speed: Infrastructure for Accelerating COVID-19 Drug Discovery with Hybrid Machine Learning- and Physics-based Simulations on High Performance Computers38The imperative of physics-based modeling and inverse theory in computational science123When we can trust computers (and when we can't)26Is Computational Oceanography Coming of Age?16Risk management focusing on the best practices of data security systems for healthcare19Artificial Intelligence in Drug Design: Algorithms, Applications, Challenges and Ethics70Combinatorial enumeration of stereo, chiral and position isomers of polysubstituted halocarbons: applications to machine learning of proton and 35Cl NMR spectroscopy of halocarbons5Scaling digital twins from the artisanal to the industrial226Futures-oriented drugs policy research: Events, trends, and speculating on what might become22Relevance in the Renormalization Group and in Information Theory21Data Analysis will not Result in Knowledge Production about Sepsis0Integrating explanation and prediction in computational social science361Ensembles Are Required to Handle Aleatoric and Parametric Uncertainty in Molecular Dynamics Simulation55The machine-learned radii of atoms8A Reflection on Learning from Data: Epistemology Issues and Limitations3Snapshot Wisconsin: networking community scientists and remote sensing to improve ecological monitoring and management20Computational studies of protein–drug binding affinity changes upon mutations in the drug target56Theory, evidence, policy, and practice of medicine0A fast and efficient deep learning procedure for tracking droplet motion in dense microfluidic emulsions24Why Probability isn’t Magic1Artificial Intelligence, Chaos, Prediction and Understanding in Science15Why can we detect lianas from space?6Personalization of medical treatments in oncology: time for rethinking the disease concept to improve individual outcomes25Miasmas, mental models and preventive public health: some philosophical reflections on science in the COVID-19 pandemic20The COVID-19 pandemic: when science collided with politics, culture and the human imagination1Digital medicine and the curse of dimensionality340Rapid Bayesian Inference for Expensive Stochastic Models15Statistical Physics through the Lens of Real-Space Mutual Information21Artificial intelligence applications in radiotherapy0Chemistry0Complexity and Integration0Digital Health Research and Health Data Pools1Personalized Treatments: Where Patient’s History and Biological Background Meet2Philosophy of Computing1Zero Sales Resistance: The Dark Side of Big Data and Artificial Intelligence12Hybrid modeling: towards the next level of scientific computing in engineering50Artificial intelligence in the field of economics67Large Scale Study of Ligand–Protein Relative Binding Free Energy Calculations: Actionable Predictions from Statistically Robust Protocols33A Unified Neural Network Framework for Extended Redundancy Analysis3Machine Learning in Computational Chemistry1Análisis y diseño de técnicas de preprocesamiento de instancias escalables para problemas no balanceados en Big Data0Foreword to the Special Issue in honour of Prof. Luigi Preziosi “Nonlinear mechanics: The driving force of modern applied and industrial mathematics”2On the Integration of Fundamental Knowledge about Degradation Processes into Data-Driven Diagnostics and Prognostics Using Theory-Guided Data Science9Machine learning, artificial intelligence, and chemistry: How smart algorithms are reshaping simulation and the laboratory35MRI-Based Digital Models Forecast Patient-Specific Treatment Responses to Neoadjuvant Chemotherapy in Triple-Negative Breast Cancer74Exploring the potential of in silico machine learning tools for the prediction of acute Daphnia magna nanotoxicity32Experimental radiation oncology. A real evolution towards a precision therapy?0

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  1. Bridging the gaps at the physics–chemistry–biology interface

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  2. Francis Bacon, Karl Popper, Michael Polanyi, and Modern Experimental Biology

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  3. Genetic studies of alcohol dependence in the context of the addiction cycle

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  4. Gene expression profiling in the human alcoholic brain

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  5. The Importance of Nutrition in a Conceptual Framework of Frailty Syndrome

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  6. Identicação de sistemas neurais com redes bayesianas dinâmicas e transferência de entropia

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  7. Big Data to Big Knowledge for Next Generation Medicine: A Data Science Roadmap

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  8. The Role of Multiscale Protein Dynamics in Antigen Presentation and T Lymphocyte Recognition

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  9. Single-Subject Studies in Translational Nutrition Research

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  10. Big Data approaches in social and behavioral science: four key trade-offs and a call for integration

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  11. Natural and Artificial Intelligence in Neurosurgery: A Systematic Review

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  12. Compressibility, Laws of Nature, Initial Conditions and Complexity

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  13. Evidence amalgamation, plausibility, and cancer research

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  14. Statistical physics and representations in real and artificial neural networks

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  15. Clinical judgement in the era of big data and predictive analytics

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  16. MetaQSAR: An Integrated Database Engine to Manage and Analyze Metabolic Data

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  17. Chemistry

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  18. Big Data in Computational Toxicology: Challenges and Opportunities

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  19. Developing WHO guidelines: Time to formally include evidence from mathematical modelling studies

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  20. Big data framework for students' academic performance prediction: A systematic literature review

    IEEE Symposium on Computer Applications & Industrial Electronics (ISCAIE) · 2018-04-01

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  21. Go to field, look around, measure and then run models

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  22. Uncertainty Quantification in Alchemical Free Energy Methods

    Journal of Chemical Theory and Computation · 2018-04-20

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  23. Adaptive multiscale predictive modelling

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  24. Opportunities and challenges for big data ornithology

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  25. Projection-based model reduction: Formulations for physics-based machine learning

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  26. Prediction of Chemical Reactions Using Statistical Models of Chemical Knowledge

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  27. Prediction of Chemical Reactions Using Statistical Models of Chemical Knowledge

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  28. A Review of Machine Learning Applications to Coastal Sediment Transport and Morphodynamics

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  29. Mathematical models of tumor cell proliferation: A review of the literature

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  30. Quantifying the value of surveillance data for improving model predictions of lymphatic filariasis elimination

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  31. Big Data in Head and Neck Cancer

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  33. On the Ethics of Biodiversity Models, Forecasts and Scenarios

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  34. Ensemble-Based Replica Exchange Alchemical Free Energy Methods: The Effect of Protein Mutations on Inhibitor Binding

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  35. Big Data in Discourse

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  36. Hope, hype and harms of Big Data

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  40. Big data: the end of the scientific method?

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  41. Multiscale modelling, simulation and computing: from the desktop to the exascale

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  43. Using non-invasive stimulation of the undamaged brain to guide the identification of lesion sites that predict language outcome after stroke

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  44. Big data: The end of the scientific method?

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  45. The 2019 mathematical oncology roadmap

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  46. Introduction to Mathematical Oncology

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  47. Machine learning's feet of clay

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  48. Mesoscopic simulations at the physics-chemistry-biology interface

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  49. Complexity and integration. A philosophical analysis of how cancer complexity can be faced in the era of precision medicine

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  50. The future of laboratory medicine: Navigating between technology and professionalism

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