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Interpretable and Explainable Machine Learning for Materials Science and Chemistry

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

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Kinematic alterations after two high-intensity intermittent training protocols in endurance runners

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Journal of Sport and Health Science 2019年第5期8卷 442-449页

作者： felipe García-Pinillos Alejandro Molina-Molina juan A.Párraga-Montilla Pedro A.Latorre-Román Department of Corporal Expression University of JaenJaen 23071Spain Human Lab Sport and Health University Institute(iMUDS)Granada 18007Spain

Purpose:This study aimed to evaluate running kinematic characteristics during the early and late stages of 2 high-intensity intermittent training(HIIT)protocols with similar external load but different average running pace,as well as to compare the fatigue-induced changes during both HIIT protocols at a kinematic ***:Eighteen endurance runners were tested on a track on 2 occasions:10 runs of 400 m with 90-120 s recovery between running bouts(10 × 400 m),and 40 runs of 100 m with 25-30 s recovery between running bouts(40 × 100 m).Heart rate was monitored during both protocols;blood lactate accumulation and rate of perceived exertion were recorded after both exercises.A high-speed camera was used to measure sagittalplane kinematics at the first and last runs during both HIIT *** dependent variables were spatial-temporal parameters(step length and contact and flight time),joint angles during support(relative angles of the hip,knee,and ankle),and foot strike ***:High levels of exhaustion were reached by the athletes during both workouts(blood lactate accumulation>12 mmol/L,rate of perceived exertion>15;peak heart rate(HRpeak)>176 bpm).A within-protocol paired t test(first *** run)revealed no significant changes(p≥0.05)in kinematic variables during any of the HIIT sessions.A between-protocol comparison with the first run of each protocol revealed the effect of running speed on kinematics:+2.44 km/h during the 40 × 100 m:shorter contact and flight time(p<0.01)and longer step length(p= 0.001);greater hip flexion(p = 0.031)and ankle extension(p = 0.001)at initial contact;smaller knee and ankle flexion(p<0.001)at midstance;and greater hip extension at toe-off(p<0.001).Conclusion:HIIT sessions including runs for 15-90 s and performed at intensity above the velocity associated with maximal oxygen uptake did not consistently perturb the running kinematics of trained endurance runners.

关键词： Biomechanics Fatigue-induced Runners Running Training Two-dimensional

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Early-onset colorectal cancer:A separate subset of colorectal cancer

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World Journal of Gastroenterology 2014年第46期20卷 17288-17296页

作者： Irene Osorio Silla Daniel Rueda Yolanda Rodríguez juan Luis García felipe de la Cruz Vigo José Perea Department of Surgery 12 de Octubre University HospitalMadrid 28041Spain Molecular Biology Laboratory 12 de Octubre University HospitalMadrid 28041Spain Department of Pathology 12 de Octubre University HospitalMadrid 28041Spain Centre for Cancer Research Medical University of SalamancaSalamanca 37008Spain

Colorectal cancer(CRC)has a great impact on the world *** increasing frequency,CRC is described according to the presenting phenotype,based on its molecular *** of CRC tumors according to their genetic and/or epigenetic alterations is not only important for establishing the molecular bases of the disease,but also for predicting patient outcomes and developing more individualized ***-onset CRC is a heterogeneous disease,with a strong familial component,although the disease is sporadic in an important proportion of *** molecular alterations appear to contribute to the apparent heterogeneity of the early-onset population and subgroups can be distinguished with distinct histopathologic and familial ***,compared with late-onset CRC,there are characteristicsthat suggest that early-onset CRC may have a different molecular *** purpose of this review was to analyze the current state of knowledge about earlyonset CRC with respect to clinicopathologic,familial and molecular ***,these features make it increasingly clear that this subset of CRC may be a separate disease,although it has much in common with late-onset CRC.

关键词： Chromosomal instability CpG island methylator phenotype Early-onset colorectal cancer Lynch syndrome Microsatellite instability

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Rectal cancer treatment: improving the picture

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World Journal of Gastroenterology 2007年第44期13卷 5805-5812页

作者： juan A diaz-Gonzalez Leire Arbea Javier Aristu Department of Oncology Clinica Universitaria Universtity of Navarra Pamplona 31080 Spain

Multidisciplinary approach for rectal cancer treatment is currently well defined. Nevertheless, new and promising advances are enriching the portrait. Since the US NIH Consensus in the early 90's some new characters have been added. A bird's-eye view along the last decade shows the main milestones in the development of rectal cancer treatment protocols. New drugs, in combination with radiotherapy are being tested to increase response and tumor control outcomes. However, therapeutic intensity is often associated with toxicity. Thus, innovative strategies are needed to create a better-balanced therapeutic ratio. Molecular targeted therapies and improved technology for delivering radiotherapy respond to the need for accuracy and precision in rectal cancer treatment.

关键词： Rectal cancer Chemoradiotherapy Intensitymodulated radiation therapy Molecular targeted therapy

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Genome-Wide Survey and Evolutionary Analysis of Trypsin Proteases in Apicomplexan Parasites

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Genomics, Proteomics & Bioinformatics 2010年第2期8卷 103-112页

作者： Aylan Farid Arenas juan felipe Osorio-Méndez Andres Julian Gutierrez Jorge E. Gomez-Marin Grupo de Parasitología Molecular (GEPAMOL) Centro de Investigaciones BiomédicasUniversidad del QuindíoArmeniaColombia

Apicomplexa are an extremely diverse group of unicellular organisms that infect humans and other animals. Despite the great advances in combating infectious diseases over the past century, these parasites still have a tremendous social and economic burden on human societies, particularly in tropical and subtropical regions of the world. Proteases from apicomplexa have been characterized at the molecular and cellular levels, and central roles have been proposed for proteases in diverse processes. In this work, 16 new genes encoding for trypsin proteases are identified in 8 apicomplexan genomes by a genome-wide survey. Phylogenetic analysis suggests that these genes were gained through both intracellutar gene transfer and vertical gene transfer. Identification, characterization and understanding of the evolutionary origin of protease-mediated processes are crucial to increase the knowledge and improve the strategies for the development of novel chemotherapeutic agents and vaccines.

关键词： Apicomplexa trypsin endosymbiotic gene transfer

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Mantle derived crystal-poor rhyolitic ignimbrites:Eruptive mechanism from geochemical and geochronological data of the Piedra Parada caldera,Southern Argentina

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Geoscience Frontiers 2018年第5期9卷 1529-1553页

作者： Eugenio Aragon Antonio Castro juan diaz-Alvarado Lucio Pinotti Fernando D'eramo Manuel Demartis Jorge Coniglio Irene Hernando Carmen Rodriguez Centro de Investigaciones Geológicas(UNLP-CONICET) 1 N^o 644(1900)La PlataBuenos AiresArgentina Departamento de Geología Universidad de Huelva21071 HuelvaSpain Departamento de Geología Universidad de AtacamaCopayapu 485CopiapóChile Departamento de Geología Universidad Nacional de Río Cuarto(UNRC-CONICET)Ruta 36 km 601Río CuartoCórdobaArgentina

Trace elements, isotopic modeling and U-Th-Pb SHRIMP zircon age constraints are used to reconstruct the eruption history and magmatic processes of the Piedra Parada Caldera. In the early Eocene, the crystal-poor Barda Colorada ignimbrite(BCI), having >>15% micro-porphyritic crystals with respect to magmatic components, erupted a volume estimated in more than 300 km^3. The Piedra Parada caldera is located in the Patagonian Andes foreland, at the southern end of the calderas field of the Pilcaniyeu Volcanic Belt(PVB). This belt is related to an extensional tectonic setting as a result of the collision of the Farallon-Aluk ridge with South America, which enabled the development of a transform ocean/continental plate margin followed by the detachment of the Aluk plate and the opening of a slab window. The BCI extra-caldera Plateau is a >100 m thick deposit, having a lower unit with high silica(Si O_2> 76 wt.%),potassium poor rhyolitic composition(trondhjemitic like magma), and an upper unit with normal to high potassium rhyolitic composition(granitic like magma). A trace elements modeling of the BCI units shows that the BCI lower and upper units did not evolve from fractionation or immiscibility in the shallow magma reservoir. The BCI also have a primitive isotopic signature(initial87 Sr/86 Sr =0.7031-0.7049 and ε_(Nd)= +3.4 to +3.65). Thus, tectonic, compositional and isotopic constraints suggest the fast ascent of high silica magmas to a shallow reservoir, and point to an upper mantle origin for these rhyolitic magmas in a transitional(Orogenic-Anorogenic) tectono-magmatic setting. U-Th-Pb SHRIMP zircon crystallization ages of the Syn-caldera stage BCI units(56 -51.5 Ma) show a protracted life of 5 Ma for this caldera reservoir. The age of 52.9 ± 0.3 Ma is considered the best fit for the possible maximum age for the caldera collapse. The Late-caldera magmatism has trachyandesitic and rhyolitic *** trace element modeling suggests that these rhyolites evolv

关键词： Mantle derived rhyolite Crystal-poor ignimbrite Bimodal volcanism Slab window volcanism K poor-rhyolite

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Numerical and experimental investigation to design a novel morphing airfoil for performance optimization

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Propulsion and Power Research 2023年第1期12卷 83-103页

作者： Kiumars Khani Aminjan Maryam Ghodrat Milad Heidari Pooyan Rahmanivahid Shayan Naghdi Khanachah Mira Chitt juan Pablo Escobedo-diaz Faculty of Aerospace Malek Ashtar University of TechnologyTehran 1774-15875Iran School of Engineering and Information Technology University of New South Wales CanberraCanberraACT 2610Australia Mechanical Engineering Department Global College of Engineering and Technology(GCET)P.O.Box 2546 CPO Ruwi 112MuscatSultanate of Oman School of Industrial Engineering Iran University of Science and TechnologyTehran 16846-13114Iran

Optimizing flying objects’wing performance has attracted a significant attention in the last few *** this article,some of the main mechanisms for changing the geometry of the wing were investigated and a new mechanism is proposed to improve the aerodynamic performance of the airplane *** designs have been simulated and analyzed from both aerodynamic and control points of *** aerodynamic simulations using CFD methods,two airfoils of NACA series 6 with specifications 65-212 and 65-2012 were *** results indicated that both airfoils used have a better performance compared to others in a certain range of the angle of ***,a new mechanism is proposed to change the wing geometry to optimize its *** the proposed mechanism,the structures of airfoils and wings consist of two fixed and moving parts,which can change their geometry with the help of a control *** fixed part has a grooved track,and as the moving part moves in the direction of the grooves,the curvature of the upper and lower parts of the wing *** design control circuit includes an angle sensor,a micro controller,and a *** CFD results are entered into the micro controller as *** any moment,the micro controller receives the angle data from the angle sensor and by comparing them with the CFD data,and issuing a command to the servomotor,it situates the wing curvature in the optimal state at all *** built mechanism was tested at an attack angle of 0°and 25°.The results showed that the different parts of the mechanism work with very high precision and put the geometric shape of the wing in an optimal state in a completely intelligent *** should be noted that the average error in test for t/c and Xt/c was 15.3% and 9%,respectively.

关键词： Morphing airfoil Lift force Optimization Computational fluid dynamics Micro controller Angle sensor

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Tibolone modulates neuronal plasticity through regulating Tau, GSK3β/Akt/PI3K pathway and CDK5 p35/p25 complexes in the hippocampus of aged male mice

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Neural Regeneration Research 2017年第4期12卷 588-595页

作者： Teresa Neri-Gomez Judith Espinosa-Raya Sofia diaz Cintra Julia Segura-Uribe Sandra Orozco-Suarez juan Manuel Gallardo Christian Guerra-Araiza Unidad de Investigación Médica en Farmacología Hospital de Especialidades Centro Médico Nacional Siglo XXI Instituto Mexicano del Seguro Social Ciudad de México México Laboratorio de Farmacología Conductual Escuela Superior de Medicina Instituto Politécnico Nacional Plan de San Luis y Díaz Mirón Col. Sto. Tomás Ciudad de México México Departamento de Neurobiología del Desarrollo y Neurofisiología Instituto de Neurobiología Universidad Nacional Autónoma de México Campus Juriquilla Querétaro Querétaro México Enfermedades Neurológicas (Neurological Diseases) Hospital de Especialidades Centro Médico Nacional Siglo XXI Instituto Mexicano del Seguro Social Ciudad de México México Enfermedades Nefrológicas (Kidney Diseases) Hospital de Especialidades Centro Medico Nacional Siglo XXI Instituto Mexicano del Seguro Social Ciudad de Mexico Mexico

Aging is a key risk factor for cognitive decline and age-related neurodegenerative disorders. Also, an age-related decrease in sex steroid hormones may have a negative impact on the formation of neurofibrillary tangles （NFTs）; these hormones can regulate Tau phosphorylation and the principal kinase GSK3β involved in this process. Hormone replacement therapy decreases NFTs, but it increases the risk of some types of cancer. However, other synthetic hormones such as tibolone （TIB） have been used for hormone replacement therapy. The aim of this work was to evaluate the long-term effects of TIB （0.01 mg/kg and 1mg/kg, intragastrically for 12 weeks） on the content of total and hyperphosphorylated Tau （PHF-1） proteins and the regulation of GSK3β/Akt/PI3K pathway and CDK5/p35/p25 complexes in the hippocampus of aged male mice. We observed that the content of PHF-1 decreased with TIB administration. In contrast, no changes were observed in the active form of GSK3β or PI3K. TIB decreased the expression of the total and phosphorylated form of Akt while increased that of p110 and p85. The content of CDK5 was differentially modified with TIB： it was increased at low doses and decreased at high doses. When we analyzed the content of CDK5 activators, an increase was found on p35; however, the content of p25 decreased with administration of low dose of TIB. Our results suggest a possible mechanism of action of TIB in the hippocampus of aged male mice. Through the regulation of Tau and GSK3β/Akt/PI3K pathway, and CDK5/p35/p25 complexes, TIB may modulate neuronal plasticity and regulate learning and memory processes.

关键词： nerve regeneration Tibolone hippocampus aged mice sex steroids Akt GSK3β PI3K neuralplasticity Tau neurofibrillary tangles neural regeneration

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Local and generalized height-diameter models with random parameters for mixed,uneven-aged forests in Northwestern Durango,Mexico

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Forestry Studies in China 2014年第1期16卷 41-49页

作者： Sacramento Corral-Rivas juan Gabriel lvarez-González felipe Crecente-Campo José Javier Corral-Rivas Instituto Tecnológico de EI Salto Mesa del Tecnologico s/n.Apdo.Postal No.2EI Salto P.N.34950DurangoMéxico Departamento de Ingenieria Agroforestal Universidad de Santiago de Compostela.Escuela Politécnica SuperiorCampus Universitario27002 LugoEspana lnstituto de Silvicultura e Industria de la Madera Universidad Jurez del Estado de DurangoBlvd.del Guadiana # 501.Cuidad Universitaria34160 DurangoMexico

Background:We used mixed models with random components to develop height-diameter(h-d) functions for mixed,uneven-aged stands in northwestern Durango(Mexico),considering the breast height diameter(d) and stand variables as ***:The data were obtained from 44 permanent plots used to monitor stand growth under forest management in the study ***:The generalized Bertalanffy-Richards model performed better than the other generalized models in predicting the total height of the species under *** the genera Pinus and Quercus,the models were successfully calibrated by measuring the height of a subsample of three randomly selected trees close to the mean d,whereas for species of the genera Cupressus,Arbutus and Alnus,three trees were also selected,but they are specifically the maximum,minimum and mean d ***:The presented equations represent a new tool for the evaluation and management of natural forest in the region.

关键词： Conifer and broadleaves forests h-d relationship Mixed models Calibration

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Characterization of Driving Style and the Influence of Distraction Based on Non-intrusive Driving Parameters

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Journal of Mechanics Engineering and Automation 2011年第6期1卷 413-419页

作者： felipe Jimenez juan Jose Sanchez Oscar Gomez University Institute for Automobile Research Technical University of Madrid Madrid 28031 Spain

It is difficult to model human behavior because of the variability in driving styles and driving skills. However, for some driver assistance systems, it is necessary to have knowledge of that behavior to discriminate potentially hazardous situations, such as distraction, fatigue or drowsiness. Many of the systems that look for driver distraction or drowsiness are based on intrusive means （analysis of the electroencephalogram--EEG） or highly sensitive to operating conditions and expensive equipment （eye movements analysis through artificial vision）. A solution that seeks to avoid the above drawbacks is the use of driving parameters This article presents the conclusions obtained after a set of driving simulator tests with professional drivers with two main objectives using driving variables such as speed profile, steering wheel angle, transversal position on the lane, safety distance, etc., that are available in a non-intrusive way：（1） To analyze the differences between the driving patterns of individual drivers; and （2） To analyze the effect of distraction and drowsiness on these parameters. Different scenarios have been designed, including sequences with distractions and situations that cause fatigue. The analysis of the results is carried out in time and frequency domains in order to identify situations of loss of attention and to study whether the evolution of the analyzed variables along the time could be considered independent of the driver.

关键词： ADAS (advanced driver assistance systems) driver behavior distraction driving simulator professional driver.

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