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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

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

Strategies for farmers and policy makers to control nitro-gen losses whilst maintaining crop production

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Science China(Life Sciences) 2005年第z2期48卷 710-719页

作者： keith W.t.Goulding Agriculture and the Environment Division Rothamsted Research HarpendenHertfordshireAL5 2JQUK

the nitrogen (N) cycle is essentially 'leaky'. the losses of small amounts of nitrate to waters and of ammonia and nitrous oxide to the atmosphere are a part of the global biogeo-chemical N cycle. However, intensive agricultural production, industry and vehicle use have more than doubled the amount of 'reactive' N in the environment, resulting in eutrophication, ecosystem change and health concerns. Research has identified agricultural practices that cause large losses of N and, in some cases, developed solutions. this paper discusses the problems of maintaining productivity while reducing N losses, compares conventional with low input (integrated) and organic farming systems, and discusses wider options. It also looks at the need to integrate studies on N with other environmental impacts, set in the context of the whole farm system, to provide truly sustainable agricultural systems.

关键词： Nitrogen cycle, farm systems, best management, environmental impact, productivity.

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

Prostate-associated gene 4 （PAGE4）, an intrinsically disordered cancer/testis antigen, is a novel therapeutic target for prostate cancer

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Asian Journal of Andrology 2016年第5期18卷 695-703页

作者： Prakash Kulkarni A keith Dunker keith Weninge John Orban Institute for Bioscience and Biotechnology Research University of Maryland Rockville MD 20850 USA Center for Computational Biology and Bioinformatics Department of Biochemistry and Molecular Biology Indiana University School of Medicine and Informatics Indianapolis IN 46202 USA Department of Physics North Carolina State University Raleigh NC 27695 USA Department of Chemistry and Biochemistry University of Maryland College Park MD 20742 USA.

Prostate-associated gene 4 （PAGE4） is a remarkably prostate-specific Cancer/testis Antigen that is highly upregulated in the human fetal prostate and its diseased states but not in the adult normal gland. PAGE4 is an intrinsically disordered protein （IDP） that functions as a stress-response protein to suppress reactive oxygen species as well as prevent DNA damage. In addition, PAGE4 is also a transcriptional regulator that potentiates transactivation by the oncogene c-Jun, c-Jun forms the AP-1 complex by heterodimerizing with members of the Fos family and plays an important role in the development and pathology of the prostate gland, underscoring the importance of the PAGE4/c-Jun interaction. HIPK1, also a component of the stress-response pathway, phosphorylates PAGE4 at t51 which is critical for its transcriptional activity. Phosphorylation induces conformational and dynamic switching in the PAGE4 ensemble leading to a new cellular function. Finally, bioinformatics evidence suggests that the PAGE4 mRNA could be alternatively spliced resulting in four potential isoforms of the polypeptide alluding to the possibility of a range of conformational ensembles with latent functions. Considered together, the data suggest that PAGE4 may represent the first molecular link between stress and prostate cancer （PCa）. thus, pharmacologically targeting PAGE4 may be a novel opportunity for treating and managing patients with PCa, especially patients with low-risk disease.

关键词： prostate-associated Gene 4 cancer/testis antigen intrinsically disordered protein prostate cancer c-Jun AP-1 proteininteraction networks homeodomain-interacting protein 1

Systematic review with meta-analysis on transplantation for alcohol-related liver disease:Very low evidence of improved outcomes

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World Journal of Gastroenterology 2019年第13期25卷 1628-1639页

作者： Nicole t Shen Cristina Londono Stephanie Gold Ashley Wu keith C Mages Robert S Jr Brown Department of Medicine Division of Gastroenterology and Hepatology Weill Cornell Medicine New York Department of Medicine Weill Cornell Medical College New York Department of Medicine Division of Internal Medicine Weill Cornell Medicine New York Department of Medicine Weill Cornell Medical College Samuel J. Wood Library and C.V. Starr Biomedical Information Center New York

BACKGROUND Alcohol-related liver disease(ALD) is a leading cause of liver failure and indication for liver transplantation that arises in the setting of alcohol use disorder(AUD). Previous reviews of transplantation for ALD are limited in scope of outcomes and type of ALD studied. A comprehensive systematic review could improve use of transplantation in ALD and improve future research. We hypothesize that while transplanting ALD may improve mortality and relapse,findings will be limited by pre-specified causes of heterogeneity-assessment and treatment of AUD, definition of ALD, spectrum of ALD studied, assessment and rates of relapse, and study quality and *** to optimize liver transplantation for ALD, understanding existing research to guide future research, we conducted a systematic review with *** We conducted a systematic review, comparing liver transplant to no-transplant in patients with ALD, with a primary outcome of both short-and long-term mortality and relapse. We performed a comprehensive search of MEDLINE,EMBASE, Web of Science, and the Cochrane Library databases for peer-reviewed journal articles comparing use of liver transplant in ALD to no-transplant. two reviewers independently conducted screening, full text review, and data extraction according to the PRISMA guidelines. We report the quality of the evidence according to the GRADE *** We analyzed data from 10 studies. Of 1332 participants, 34.2%(456/1332) had undergone liver transplantation, while 65.8%(876/1332) had not. While random effects meta-analysis suggested transplant in comparison to no-transplant had an association of reduced mortality that did not reach statistical significance, relative risk(RR) = 0.51(0.25-1.05), but not relapse risk, RR = 0.52(0.18-1.53), significant heterogeneity limited these findings. When restricted to prospective data,transplant compared to no-transplant significantly reduced mortality, RR = 0.25(0.13-0.46, P < 0.01), and relap

关键词： Alcohol-related hepatitis Alcohol-related cirrhosis Alcohol use disorder Liver transplantation Standardization

Impact of a national basic skills in colonoscopy course on trainee performance: An interrupted time series analysis

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World Journal of Gastroenterology 2020年第23期26卷 3283-3292页

作者： keith Siau James Hodson John t Anderson Roland Valori Geoff Smith Paul Hagan Marietta Iacucci Paul Dunckley Joint Advisory Group on Gastrointestinal Endoscopy Royal College of PhysiciansLondon NW14LEUnited Kingdom NIHR Biomedical Research Centre University of BirminghamBirmingham B152TTUnited Kingdom Institute of translational Medicine University Hospitals BirminghamBirmingham B152TTUnited Kingdom Department of Gastroenterology Gloucestershire Hospitals NHSFTCheltenham GL537ANUnited Kingdom Department of Gastroenterology Imperial College NHS Foundation TrustLondon NW14LEUnited Kingdom Endoscopy Department Derby Royal HospitalDerby GL13NNUnited Kingdom

BACKGROUND the Joint Advisory Group on Gastrointestinal Endoscopy basic skills in colonoscopy(BSC) course was introduced in 2009 to improve colonoscopy training within the United Kingdom, but its impact on trainee performance is *** to assess whether attendance of the BSC could improve colonoscopy *** trainees awarded colonoscopy certification between 2011-2016 were stratified into 3 groups according to pre-course procedure count( 140).Study outcomes, comprising the unassisted caecal intubation rate(CIR) and the performance indicator of colonic intubation(PICI), were studied over the 50 procedures pre and post-course. Interrupted time series analyses were performed to detect step-change changes attributable to the *** A total of 369 trainees with pre-course procedure counts of 140(n = 130) were included. Over the 50 pre-course procedures,significant linear improvements in CIR were found, with average increases of 4.2,3.6 and 1.7 percentage points(pp) per 10 procedures performed in the 140 groups respectively(all P the t step-change improvement in CIR, increasing from 46% in the last pre-course procedure, to 51% in the first procedure post-course(P = 0.005). the CIR step-change was not significant in the 70-140(68% to 71%;P = 0.239) or > 140(86% to 87%;P = 0.354) groups. For PICI, significant step-change improvements were seen in all three groups, with average increases of 5.6 pp(P ttendance of the BSC was associated with a significant step-change improvement in PICI, regardless of prior procedural experience. However, CIR data suggest that the optimal timing of course attendance appears to be at earlier stages of training(< 70 procedures).

关键词： Colonoscopy training Course Competency development Skills Endoscopy