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Distributed representations of atoms and materials for machine learning

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npj Computational Materials 2022年第1期8卷 415-423页

作者： Luis M.Antunes Ricardo Grau-Crespo keith t.butler Department of Chemistry University of ReadingWhiteknightsReadingRG66DXUK SciML Scientific Computing DepartmentRutherford Appleton LaboratoryHarwellOX110QXUK

the use of machine learning is becoming increasingly common in computational materials *** build effective models of the chemistry of materials,useful machine-based representations of atoms and their compounds are *** derive distributed representations of compounds from their chemical formulas only,via pooling operations of distributed representations of *** compound representations are evaluated on ten different tasks,such as the prediction of formation energy and band gap,and are found to be competitive with existing benchmarks that make use of structure,and even superior in cases where only composition is ***,we introduce an approach for learning distributed representations of atoms,named SkipAtom,which makes use of the growing information in materials structure databases.

关键词： representations operations competitive

Interpretable and Explainable Machine Learning for Materials Science and Chemistry

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Accounts of Materials Research 2022年第6期3卷 597-607页

作者： Felipe Oviedo Juan Lavista Ferres tonio Buonassisi keith t.butler Massachusetts Institute of technology CambridgeMassachusetts 02139United States Microsoft AI for Good Research Lab RedmondWashington 98052United States SciML Scientific Computing DepartmentRutherford Appleton LaboratoryDidcot OX110DU.K. Department of Chemistry University of ReadingReading RG66ADU.K.

Machine learning has become a common and powerful tool in materials *** more data become available,with the use of high-performance computing and high-throughput experimentation,machine learning has proven potential to accelerate scientific research and technology *** the uptake of data-driven approaches for materials science is at an exciting,early stage,to realize the true potential of machine learning models for successful scientific discovery,they must have qualities beyond purely predictive *** predictions and inner workings of models should provide a certain degree of explainability by human experts,permitting the identification of potential model issues or limitations,building trust in model predictions,and unveiling unexpected correlations that may lead to scientific *** this work,we summarize applications of interpretability and explainability techniques for materials science and chemistry and discuss how these techniques can improve the outcome of scientific *** start by defining the fundamental concepts of interpretability and explainability in machine learning and making them less abstract by providing examples in the *** show how interpretability in scientific machine learning has additional constraints compared to general *** upon formal definitions in machine learning,we formulate the basic trade-offs among the explainability,completeness,and scientific validity of model explanations in scientific *** the context of these trade-offs,we discuss how interpretable models can be constructed,what insights they provide,and what drawbacks they *** present numerous examples of the application of interpretable machine learning in a variety of experimental and simulation studies,encompassing first-principles calculations,physicochemical characterization,materials development,and integration into complex *** discuss the varied impacts and uses of interpretabiltiy in these cases

关键词： explain purely insight

A deep convolutional neural network for real-time full profile analysis of big powder diffraction data

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npj Computational Materials 2021年第1期7卷 671-679页

作者： Hongyang Dong keith t.butler Dorota Matras Stephen W.t.Price Yaroslav Odarchenko Rahul Khatry Andrew thompson Vesna Middelkoop Simon D.M.Jacques Andrew M.Beale Antonis Vamvakeros Department of Chemistry University College London20 Gordon StreetLondon WC1H 0AJUnited Kingdom SciML Scientific Computer DivisionSTFCRutherford Appleton LaboratoryHarwell OX110QXUnited Kingdom Finden Limited Merchant House5 East St Helens StreetAbingdon OX145EGUnited Kingdom National Physical Laboratory Hampton RoadTeddington TW110LWUnited Kingdom Flemish Institute for technological Research VITO NVBoeretang 200Mol 2400Belgium Research Complex at Harwell Rutherford Appleton LaboratoryHarwell Science and Innovation CampusDidcotOX110FA OxfordshireUnited Kingdom Present address:Diamond Light Source Harwell Science and Innovation CampusDidcotOxfordshire OX110DEUnited Kingdom Present address:the Faraday Institution Quad OneHarwell Science and Innovation CampusOX110RA OxfordshireUnited Kingdom

We present Parameter Quantification Network(PQ-Net),a regression deep convolutional neural network providing quantitative analysis of powder X-ray diffraction patterns from multi-phase *** network is tested against simulated and experimental datasets of increasing complexity with the last one being an X-ray diffraction computed tomography dataset of a multi-phase Ni-Pd/CeO_(2)-ZrO_(2)/Al_(2)O_(3) catalytic material system consisting of ca.20,000 diffraction *** is shown that the network predicts accurate scale factor,lattice parameter and crystallite size maps for all phases,which are comparable to those obtained through full profile analysis using the Rietveld method,also providing a reliable uncertainty measure on the *** main advantage of PQNet is its ability to yield these results orders of magnitude faster showing its potential as a tool for real-time diffraction data analysis during in situ/operando experiments.

关键词： network powder analysis

Symptom presentation and evolution in the first 48 hours after injury are associated with return to play after concussion in elite Rugby Union

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Journal of Sport and Health Science 2024年第3期13卷 387-397页

作者： Ross tucker Matt Cross keith Stokes Lindsay Starling Rosy Hyman Simon Kemp Stephen West Martin Raftery Eanna Falvey James Brown Institute of Sport and Exercise Medicine(ISEM) Department of ExerciseUniversity of StellenboschTygerberg 7505South Africa World Rugby Ltd. Dublin D02 AE93Ireland Premiership Rugby London SW1V 1PXUK Centre for Health and Injury and Illness Prevention in SportUniversity of BathClaverton Down BA27AYUK UK Collaborating Centre on Injury and Illness Prevention in Sport(UKCCIIS) University of BathClaverton Down BA27AYUK Rugby Football Union London TW27BAUK London School of tropical Medicine London WC1E 7HTUK Sport Injury Prevention Research Centre Faculty of KinesiologyUniversity of CalgaryCalgary T2N 1N4Canada Department of Medicine School of Medicine and HealthUniversity College CorkCork T12 EC8PIreland Carnegie Applied Rugby Research(CARR)centre Carnegie School of SportLeeds Beckett UniversityLeeds LS63QSUK

Background:Return to play(RtP)in elite rugby is managed using a 6-stage graduated RtP protocol,which can result in clearance to play within 1 week of *** aimed to explore how symptom,cognitive,and balance presentation and evolution during concussion screens 2 h(head injury assessment(HIA2)and 48 h(HIA3)after injury were associated with time to RtP)to identify whether a more conservative graduated RtP may be ***:A retrospective cohort study was conducted in 380 concussed rugby players from elite men’s rugby over 3 consecutive *** were classified as shorter or longer returns,depending on whether RtP occurred within 7 days(allowing them to be considered to play the match 1 week after injury)or longer than 8 days,***,cognitive,and balance performance during screens was assessed relative to baseline(normal or abnormal)and to the preceding screen(improving or worsening).Associations between sub-test abnormalities and RtP time were explored using odds ratios(OR,longer ***).Median day absence was compared between players with abnormal or worsening results and those whose results were normal or ***:Abnormal symptom results during screens 2 h and 48 h after concussion were associated with longer return time(HIA2:OR=2.21,95%confidence interval(95%CI):1.39-3.50;HIA3:OR=3.30,95%CI:1.89-5.75).Worsening symptom number or severity from the time of injury to 2 h and 48 h post-injury was associated with longer return(HIA2:OR=2.49,95%CI:1.36-4.58;HIA3:OR=3.34,95%CI:1.10-10.15).Median days absence was greater in players with abnormal symptom results at both HIA2 and *** and balance performance were not associated with longer return and did not affect median days ***:Symptom presentation and evolution within 48 h of concussion were associated with longer RtP *** may guide a more conservative approach to RtP,while still adhering to individualized concussion management principles.

关键词： Brain injury Concussion management General return to play Medical management

tree structure and diversity shape the biomass of primary temperate mountain forests

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Forest Ecosystems 2024年第4期11卷 568-579页

作者： Dheeraj Ralhan Ruffy Rodrigo Heather keith Annemiek Irene Stegehuis Jakob Pavlin Yumei Jiang Milos Rydval Juliana Nogueira Alexandre Fruleux Marek Svitok Martin Mikolas Daniel Kozak Martin Dusatko Pavel Janda Oleh Chaskovsky Catalin-Constantin Roibu Miroslav Svoboda Czech University of Life Sciences Prague Faculty of Forestry and Wood SciencesKamycka 129Suchdol16521 Praha 6Czech Republic Department of Forest Science Biliran Province State UniversityBiliran6549Philippines Griffith Climate Action Beacon Griffith UniversityParklands DriveSouthportGold CoastQueensland4222Australia Laboratoire de Geologie IPSLCNRSUMR 8538Ecole Normale SuperieurePSL UniversityParisFrance Univ.Lille Institut Mines-TelecomUniv.ArtoisJuniaULR 4515LGCgELaboratoire de Genie Civil et Geo-EnvironnementF-59000LilleFrance Department of Biology and General Ecology Faculty of Ecology and Environmental SciencesTechnical University in ZvolenMasaryka 2496001ZvolenSlovakia Institute of Forest Management Ukrainian National Forestry UniversityLvivUkraine Forest Biometrics Laboratory–Faculty of Forestry Stefan Cel Mare University of SuceavaUniversitații Street Number.13Suceava720229Romania

Primary forests are spatially diverse terrestrial ecosystems with unique characteristics,being naturally regenerative and heterogeneous,which supports the stability of their carbon storage through the accumulation of live and dead ***,little is known about the interactions between biomass stocks,tree genus diversity and structure across a temperate montane primary ***,we investigated the relationship between tree structure(variability in basal area and tree size),genus-level diversity(abundance,tree diversity)and biomass stocks in temperate primary mountain forests across Central and Eastern *** used inventory data from726 permanent sample plots from mixed beech and spruce across the Carpathian *** used nonlinear regression to analyse the spatial variability in forest biomass,structure,and genus-level diversity and how they interact with plot-level tree age,disturbances,temperature and *** found that the combined effects of genus and structural indices were important for addressing the variability in biomass across different spatial *** processes in disturbance regimes and uneven tree age support forest hete rogeneity and the accumulation of live and dead biomass through the natural regeneration,growth and decay of the forest *** complexities in basal area index,supporte d by genus-level abundance,positively influence total biomass stocks,which was modulated by tree age and *** forests showed higher tree density and basal area than mixed beech forests,though mixed beech still contributes significantly to biomass across *** heterogeneity was strongly influenced by complexities in forest composition(tree genus diversity,structure).We addressed the importance of primary forests as stable carbon stores,achieved through structure and *** such ecosystems is critical for ensuring the stability of the primary forest,carbon store and biodiversity into the future.

关键词： Biodiversity indicators Biomass carbon stock Ecosystem functioning Forest composition Primary forest structure tree size distribution

EZH2 inhibitors promote β-like cell regeneration in young and adult type 1 diabetes donors

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Signal transduction and targeted therapy 2024年第2期9卷 679-692页

作者： keith Al-Hasani Safiya Naina Marikar Harikrishnan Kaipananickal Scott Maxwell Jun Okabe Ishant Khurana thomas Karagiannis Julia J.Liang Lina Mariana thomas Loudovaris thomas Kay Assam El-Osta Epigenetics in Human Health and Disease Program Baker Heart and Diabetes Institute75 Commercial RoadMelbourne 3004 VICAustralia Department of Diabetes Central Clinical SchoolMonash UniversityMelbourne 3004 VICAustralia Epigenetics in Human Health and Disease Laboratory Central Clinical SchoolMonash UniversityMelbourne 3004 VICAustralia School of Science STEM CollegeRMIT UniversityMelbourne 3001 VICAustralia Immunology and Diabetes Unit St Vincent’s Institute of Medical ResearchFitzroy 3065 VICAustralia Department of Medicine and therapeutics The Chinese University of Hong KongSha TinHong Kong SAR Hong Kong Institute of Diabetes and Obesity Prince of Wales HospitalThe Chinese University of Hong Kong3/F Lui Che Woo Clinical Sciences Building30-32-Ngan Shing StreetSha TinHong Kong SAR Li Ka Shing Institute of Health Sciences The Chinese University of Hong KongSha TinHong Kong SAR Biomedical Laboratory Science Department of TechnologyFaculty of HealthUniversity College CopenhagenCopenhagenDenmark

β-cells are a type of endocrine cell found in pancreatic islets that synthesize,store and release *** type 1 diabetes(t1D),t-cells of the immune system selectively destroy the insulin-producingβ-*** of these cells leads to a lifelong dependence on exogenous insulin administration for ***,there is an urgent need to identify novel therapies that stimulateβ-cell growth and induceβ-cell *** and others have shown that pancreatic ductal progenitor cells are a promising source for regeneratingβ-cells for t1D owing to their inherent differentiation *** transcriptional suppression is refractory to exocrine reaction and tightly controls the regenerative potential by the EZH2 *** the present study,we show that transient stimulation of exocrine cells,derived from juvenile and adult t1D donors to the FDAapproved EZH2 inhibitors GSK126 and tazemetostat(taz)influence a phenotypic shift towards aβ-like cell *** transition from repressed to permissive chromatin states are dependent on bivalent H3K27me3 and H3K4me3 chromatin *** EZH2 is fundamental toβ-cell regenerative *** pancreatic ductal cells exhibit insulin production and secretion in response to a physiological glucose challenge ex *** pre-clinical studies underscore the potential of small molecule inhibitors as novel modulators of ductal progenitor differentiation and a promising new approach for the restoration ofβ-like cell function.

关键词： EZH2 struction inhibitors

Inflammation in Mental Disorders:Is the Microbiota the Missing Link?

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Neuroscience Bulletin 2020年第9期36卷 1071-1084页

作者： Sophie Ouabbou Ying He keith butler Ming tsuang Department of Psychiatry and National Clinical Research Center for Mental Disordersand Hunan Key Laboratory of Psychiatry and Mental HealthThe Second Xiangya Hospital of Central South UniversityChangshaHunan 410011China Human Microbiome Research Program Faculty of MedicineUniversity of Helsinki00290 HelsinkiFinland Cellular and Molecular Biology Research Centre University of Costa RicaSan Jose´11501Costa Rica Center for Behavioral Genomics Department of PsychiatryInstitute for Genomic MedicineUniversity of California San DiegoLa JollaCA 92093USA Harvard Institute of Psychiatric Epidemiology and Genetics Harvard School of Public HealthBostonMA 02115USA

Research suggests that inflammation is important in the pathophysiology of mental *** addition,a growing body of evidence has led to the concept of the microbiota-gut-brain *** understand the potential interactions,we begin by exploring the liaison between the immune system and mental disorders,then we describe the evidence that the microbiota impact the immune response in the developing ***,we review the literature that has documented microbiome alterations in major mental *** end with a summary of therapeutic applications,ranging from psycho-biotics to immunomodulatory drugs that could affect the microbiotagut-brain axis,and potential treatments to alleviate the adverse effects of antipsycho *** conclude that there is promising evidence to support the position that the microbiota plays an important role in the immunological pathophysiology of mental disorders with an emphasis on psychotic disorders and mood ***,more research is needed to elucidate the mechanisms.

关键词： Mental disorder Microbiota Immunology Neurodevelopment

How completely are randomized controlled trials of non-pharmacological interventions following concussion reported? A systematic review

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Journal of Sport and Health Science 2024年第4期13卷 537-547页

作者： Jacqueline Josee van Ierssel Olivia Galea Kirsten Holte Caroline Luszawski Elizabeth Jenkins Jennifer O’Neil Carolyn A Emery Rebekah Mannix Kathryn Schneider keith Owen Yeates Roger Zemek Children’s Hospital of Eastern Ontario Research Institute OttawaON K1H 8L1Canada the Centre for Health Activity and Rehabilitation ResearchUniversity of OtagoDunedin 9016New Zealand Sport Injury Prevention Research Centre Faculty of KinesiologyUniversity of CalgaryCalgaryAB T2N 1N4Canada Alberta Children’s Hospital Research Institute University of Calgary CalgaryAB T2N 1N4Canada Hotchkiss Brain Institute University of CalgaryCalgaryAB T2N 4N1Canada Department of Psychology University of CalgaryCalgaryAB T2N 1N4Canada g Faculty of MedicineUniversity of OttawaOttawaON K1H 8M5Canada School of Rehabilitation Sciences University of OttawaOttawaON K1H 8M5Canada Bruyere Research Institute OttawaON K1N 5C8Canada Departments of Pediatrics and Emergency Medicine Harvard Medical SchoolBostonMA 02115USA Departments of Pediatrics and Emergency Medicine University of OttawaOttawaON K1H 8M5Canada

Purpose:the study aimed to examine the reporting completeness of randomized controlled trials(RCts)of non-pharmacological interventions following ***:We searched MEDLINE,Embase,PsycInfo,CINAHL,and Web of Science up to May *** reviewers independently screened studies and assessed reporting completeness using the template for Intervention Description and Replication(tIDieR),Consensus on Exercise Reporting template(CERt),and international Consensus on therapeutic Exercise aNd training(i-CONtENt)*** information was sought my study authors where reporting was *** of bias(ROB)was assessed with the Cochrane ROB-2 *** examining non-pharmacological interventions following ***:We included 89 RCts(n=53 high ROB)examining 11 different interventions for concussion:sub-symptom threshold aerobic exercise,cervicovestibular therapy,physical/cognitive rest,vision therapy,education,psychotherapy,hyperbaric oxygen therapy,transcranial magnetic stimulation,blue light therapy,osteopathic manipulation,and head/neck *** scores were:tIDieR 9/12(75%;interquartile range(IQR)=5;range:5-12),CERt 17/19(89%;IQR=2;range:10-19),and i-CONtENt 6/7(86%;IQR=1;range:5-7).Percentage of studies completely reporting all items was tIDieR 35%(31/89),CERt 24%(5/21),and i-CONtENt 10%(2/21).Studies were more completely reported after publication of tIDieR(t_(87)=2.08;p=0.04)and CERt(t_(19)=2.72;p=0.01).Reporting completeness was not strongly associated with journal impact factor(tIDieR:rs=0.27;p=0.01;CERt:r_(s)=-0.44;p=0.06;i-CONtENt:r_(s)=-0.17;p=0.48)or ROB(tIDieR:rs=0.11;p=0.31;CERt:rs=0.04;p=0.86;i-CONtENt:rs=0.12;p=0.60).Conclusion:RCts of non-pharmacological interventions following concussion demonstrate moderate to good reporting completeness,but are often missing key components,particularly modifications,motivational strategies,and qualified *** completeness improved after tIDieR and CERt publication,but p

关键词： Concussion Intervention Randomized controlled trial Systematic review

ROBUStNESS OF EQUILIBRIA IN tHE GRAPH MODEL FOR CONFLICt RESOLUtION

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Journal of Systems Science and Systems Engineering 2015年第4期24卷 450-465页

作者： Yasser t.Matbouli D.Marc Kilgour keith W.Hipel Department of Industrial Engineering King Abdulaziz University Department of Systems Design Engineering University of Waterloo Department of Mathematics Wilfrid Laurier University Centre for International Governance Innovation(CIGI)

A novel approach for assessing the robustness of an equilibrium in conflict resolution is presented. Roughly, an equilibrium is robust if it is resilient, or resistant to deviation. Robustness assessment is based on a new concept called Level of Freedom, which evaluates the relative freedom of a decision maker to escape an equilibrium. Resolutions of a conflict can be affected by changes in decision makers＇ preferences, which may destabilize an equilibrium, causing the conflict to evolve. Hence, a conflict may become long-term and thereby continue to evolve, even after reaching an equilibrium. the new robustness measure is used to rank equilibria based on robustness, to facilitate distinguishing equiiibria that are relatively sustainable. An absolutely robust equilibrium is a special case in which the level of freedom is at an absolute minimum for each individual stability definition.

关键词： Robustness equilibria level of freedom conflict evolution graph model