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Developments and applications of the OPTIMADE API for materials discovery, design, and data exchange

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arXiv 2024年

作者： Evans, Matthew L. Bergsma, Johan Merkys, Andrius Andersen, Casper W. Andersson, Oskar B. Beltrán, Daniel Blokhin, Evgeny Boland, Tara M. Balderas, Rubén Castañeda Choudhary, Kamal Díaz, Alberto Díaz García, Rodrigo Domínguez Eckert, Hagen Eimre, Kristjan Montero, María Elena Fuentes Krajewski, Adam M. Mortensen, Jens Jørgen Duarte, José Manuel Nápoles Pietryga, Jacob Qi, Ji de Jesús Trejo Carrillo, Felipe Vaitkus, Antanas Yu, Jusong Zettel, Adam de Castro, Pedro Baptista Carlsson, Johan Cerqueira, Tiago F.T. Divilov, Simon Hajiyani, Hamidreza Hanke, Felix Jose, Kevin Oses, Corey Riebesell, Janosh Schmidt, Jonathan Winston, Donald Xie, Christen Yang, Xiaoyu Bonella, Sara Botti, Silvana Curtarolo, Stefano Draxl, Claudia Cobas, Luis Edmundo Fuentes Hospital, Adam Liu, Zi-Kui Marques, Miguel A.L. Marzari, Nicola Morris, Andrew J. Ong, Shyue Ping Orozco, Modesto Persson, Kristin A. Thygesen, Kristian S. Wolverton, Chris Scheidgen, Markus Toher, Cormac Conduit, Gareth J. Pizzi, Giovanni Gražulis, Saulius Rignanese, Gian-Marco Armiento, Rickard Chemin des Étoiles 8 Louvain-la-Neuve1348 Belgium Matgenix SRL 185 Rue Armand Bury Gozée6534 Belgium École Polytechnique Fédérale de Lausanne Avenue de Forel 3 Lausanne1015 Switzerland Institute of Biotechnology Life Sciences Center Vilnius University Sauletekio av. 7 VilniusLT-10257 Lithuania SINTEF P.O. Box 4760 Torgarden TrondheimNO-7465 Norway Materials Design and Informatics unit Department of Physics Chemistry and Biology Linköping University Sweden Baldiri i Reixac 10-12 Barcelona08028 Spain Tilde Materials Informatics Straßmannstraße 25 Berlin10249 Germany Materials Platform for Data Science Sepapaja 6 Tallinn15551 Estonia Computational Atomic-Scale Materials Design Technical University of Denmark Kgs. Lyngby Denmark Av. Miguel de Cervantes 120 Complejo Industrial Chihuahua Chihuahua Chih. 31136 Mexico Material Measurement Laboratory National Institute of Standards and Technology GaithersburgMD20899 United States Department of Mechanical Engineering and Materials Science Duke University DurhamNC27708 United States Center for Extreme Materials Duke University DurhamNC27708 United States École Polytechnique Fédérale de Lausanne Lausanne1015 Switzerland Universidad Autónoma de Chihuahua Facultad de Ciencias Quimicas Chihuahua31125 Mexico Department of Materials Science and Engineering The Pennsylvania State University University ParkPA16802 United States Department of Materials Science and Engineering Northwestern University EvanstonIL60208 United States Department of NanoEngineering University of California 9500 Gilman Drive La Jolla San DiegoCA92093-0448 United States National Institute for Materials Science 1-2-1 Sengen Ibaraki Tsukuba305-0047 Japan Dassault Systèmes Germany GmbH Am Kabellager 11-13 Cologne51063 Germany CFisUC Department of Physics University of Coimbra Rua Larga Coimbra3004-516 Portugal Dassault Systèmes 22 Science Park CB4 0FJ United Kingdom Theory of Condensed Matter Cavendis

The Open Databases Integration for Materials Design (OPTIMADE) application programming interface (API) empowers users with holistic access to a growing federation of databases, enhancing the accessibility and discoverability of materials and chemical data. Since the first release of the OPTIMADE specification (v1.0), the API has undergone significant development, leading to the v1.2 release, and has underpinned multiple scientific studies. In this work, we highlight the latest features of the API format, accompanying software tools, and provide an update on the implementation of OPTIMADE in contributing materials databases. We end by providing several use cases that demonstrate the utility of the OPTIMADE API in materials research that continue to drive its ongoing development. © 2024, CC BY.

关键词： Electronic data interchange

Nearest neighborhood-based deep clustering for source data-absent unsupervised domain adaptation

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arXiv 2021年

作者： Tang, Song Yang, Yan Ma, Zhiyuan Hendrich, Norman Zeng, Fanyu Ge, Shuzhi Sam Zhang, Changshui Zhang, Jianwei The Institute of Machine Intelligence University of Shanghai for Science and Technology Shanghai China The State Key Laboratory of Electronic Thin Films and Integrated Devices University of Electronic Science and Technology of China Chengdu China Group Department of Informatics Universität Hamburg Hamburg Germany The Institute of Machine Intelligence University of Shanghai for Science and Technology Shanghai China The State Key Lab. for Novel Software Technology Nanjing University Nanjing China The Engineering Research Center of Wideband Wireless Communication Technology Ministry of Education Nanjing University of Posts and Telecommunications Nanjing China The Department of Electrical and Computer Engineering National University of Singapore Singapore Singapore The Department of Automation Tsinghua University Beijing China

In the classic setting of unsupervised domain adaptation (UDA), the labeled source data are available in the training phase. However, in many real-world scenarios, owing to some reasons such as privacy protection and information security, the source data is inaccessible, and only a model trained on the source domain is available. This paper proposes a novel deep clustering method for this challenging task. Aiming at the dynamical clustering at feature-level, we introduce extra constraints hidden in the geometric structure between data to assist the process. Concretely, we propose a geometry-based constraint, named semantic consistency on the nearest neighborhood (SCNNH), and use it to encourage robust clustering. To reach this goal, we construct the nearest neighborhood for every target data and take it as the fundamental clustering unit by building our objective on the geometry. Also, we develop a more SCNNH-compliant structure with an additional semantic credibility constraint, named semantic hyper-nearest neighborhood (SHNNH). After that, we extend our method to this new geometry. Extensive experiments on three challenging UDA datasets indicate that our method achieves state-of-the-art results. The proposed method has significant improvement on all datasets (as we adopt SHNNH, the average accuracy increases by over 3.0% on the large-scaled dataset). Code is available at https://***/tntek/N2DCX. Copyright © 2021, The Authors. All rights reserved.

关键词： Semantics

Interaction embeddings for prediction and explanation in knowledge graphs

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arXiv 2019年

作者： Zhang, Wen Paudel, Bibek Zhang, Wei Bernstein, Abraham Chen, Huajun College of Computer Science Zhejiang University China Department of Informatics University of Zürich Zürich Switzerland Alibaba Group AZFT Joint Lab of Knowledge Engine China College of Computer Science Zhejiang University AZFT Joint Lab of Knowledge Engine

Knowledge graph embedding aims to learn distributed representations for entities and relations, and is proven to be effective in many applications. Crossover interactions - bi-directional effects between entities and relations - help select related information when predicting a new triple, but haven't been formally discussed before. In this paper, we propose CrossE, a novel knowledge graph embedding which explicitly simulates crossover interactions. It not only learns one general embedding for each entity and relation as most previous methods do, but also generates multiple triple specific embeddings for both of them, named interaction embeddings. We evaluate embeddings on typical link prediction tasks and find that CrossE achieves state-of-the-art results on complex and more challenging datasets. Furthermore, we evaluate embeddings from a new perspective - giving explanations for predicted triples, which is important for real applications. In this work, an explanation for a triple is regarded as a reliable closed-path between the head and the tail entity. Compared to other baselines, we show experimentally that CrossE, benefiting from interaction embeddings, is more capable of generating reliable explanations to support its predictions. Copyright © 2019, The Authors. All rights reserved.

关键词： Knowledge graph

Knowledge Mapping System Implementation in Knowledge Management: A Systematic Literature Review 3

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Knowledge Mapping System Implementation in Knowledge Managem...

3rd International Conference on Information Management and Technology, ICIMTech 2018

作者： Hakim, Shidiq Al Sensuse, Dana Indra Faculty of Computer Science University of Indonesia Depok Research Center for Informatics Cibinong Indonesia Faculty of Computer Science University of Indonesia E-Government and E-Business Research Lab Depok Indonesia

ISBN: (纸本)9781538658215

Knowledge mapping has been studied widely in knowledge management context, but the terminology ofknowledge map system (KMSs) is not been much studied and it needs to identify state the art KMSs topic from a literature review to propose the future research. The method refers to the systematic literature reviewas guidelines from Kitchenham, this research gathers, synthesizes, and analyses some paper based on keyword 'knowledge map system' or 'knowledge mapping system' and 'knowledge management', where it published from 2008 until 2017 on four international electronic databases and using predefined review protocol. We obtained 9 articles used in this study and find that most design systems use customized with some computational *** scope is still a lot of focus on enterprise and virtual community, accordingly it needs to be developed further system for the country aspublic services and also validation method that combines elements of content and software. © 2018 IEEE.

关键词： Knowledge management

Reconfigurable Intelligent Computational Surfaces: When Wave Propagation Control Meets Computing

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arXiv 2022年

作者： Yang, Bo Cao, Xuelin Xu, Jindan Huang, Chongwen Alexandropoulos, George C. Dai, Linglong Debbah, Mérouane Poor, H. Vincent Yuen, Chau The Engineering Product Development Pillar Singapore University of Technology and Design Singapore487372 Singapore The College of Information Science and Electronic Engineering Zhejiang Provincial Key Lab of information processing communication and networking Zhejiang University Hangzhou310007 China International Joint Innovation Center Zhejiang University Haining314400 China The Department of Informatics and Telecommunications National and Kapodistrian University of Athens Athens15784 Greece The Technology Innovation Institute Masdar City Abu Dhabi9639 United Arab Emirates The Department of Electronic Engineering Tsinghua University Beijing100084 China CentraleSupelec University Paris-Saclay Gif-sur-Yvette91192 France Department of Electrical and Computer Engineering Princeton University NJ United States

The envisioned sixth-generation (6G) of wireless networks will involve an intelligent integration of communications and computing, thereby meeting the urgent demands of diverse applications. To realize the concept of the smart radio environment, reconfigurable intelligent surfaces (RISs) are a promising technology for offering programmable propagation of impinging electromagnetic signals via external control. However, the purely reflective nature of conventional RISs induces significant challenges in supporting computation-based applications, e.g., wave-based calculation and signal processing. To fulfil future communication and computing requirements, new materials are needed to complement the existing technologies of metasurfaces, enabling further diversification of electronics and their applications. In this event, we introduce the concept of reconfigurable intelligent computational surface (RICS), which is composed of two reconfigurable multifunctional layers: the ‘reconfigurable beamforming layer’ which is responsible for tunable signal reflection, absorption, and refraction, and the ‘intelligence computation layer’ that concentrates on metamaterials-based computing. By exploring the recent trends on computational metamaterials, RICSs have the potential to make joint communication and computation a reality. We further demonstrate two typical applications of RICSs for performing wireless spectrum sensing and secrecy signal processing. Future research challenges arising from the design and operation of RICSs are finally highlighted. Copyright © 2022, The Authors. All rights reserved.

关键词： Metamaterials

A Support Infrastructure for Machine Learning at the Edge in Smart City Surveillance

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A Support Infrastructure for Machine Learning at the Edge in...

IEEE Symposium on computers and Communications (ISCC)

作者： Paolo Bellavista Periklis Chatzimisios Luca Foschini Marianna Paradisioti Domenico Scotece Department of Computer Science and Engineering University of Bologna Bologna BO Italy Department of Informatics Alexander TEI of Thessaloniki CSSN Research Lab Thessaloniki Greece

Nowadays, the massive usage of mobile and IoT applications generate large amounts of data. Due to several reasons, including latency and bandwidth, it is not practical to send all generated data to the cloud. Recent standardization efforts, namely, Fog computing and the Multi-access Edge Computing (MEC), provide an extension of Cloud computing storage and network resources placed in a geographically distributed manner at the edge of the network closer to mobiles and IoT devices. These paradigms allow low latency, high bandwidth, and location-based awareness. In this paper, we present an infrastructure to support distributed Machine Learning (ML) by enabling edge devices to collaboratively learn a shared model while keeping local knowledge stored at the edge of the network. In addition, we claim the possibility of improving the model through the cloud that acts as a supervisor of the system that contains the global knowledge of the entire system through the integration of local edge models. We describe our architectural proposal and analyze a case study, namely video streaming processing for face recognition, deployed in a collaborative edge network. Finally, we report experimental results that show the potential advantages of using our approach instead of ML algorithms completely expected at the cloud infrastructure.

关键词： Face recognition Training

Modeling eye gaze velocity trajectories using GANs with spectral loss for enhanced fidelity

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Scientific reports 2025年第1期15卷 19929页

作者： Shailendra Bhandari Pedro Lencastre Rujeena Mathema Alexander Szorkovszky Anis Yazidi Pedro G Lind Department of Computer Science OsloMet - Oslo Metropolitan University P.O. Box 4 St. Olavs plass N-0130 Oslo Norway. shailendra.bhandari@oslomet.no. OsloMet Artificial Intelligence Lab Pilestredet 52 N-0166 Oslo Norway. shailendra.bhandari@oslomet.no. Department of Computer Science OsloMet - Oslo Metropolitan University P.O. Box 4 St. Olavs plass N-0130 Oslo Norway. OsloMet Artificial Intelligence Lab Pilestredet 52 N-0166 Oslo Norway. Simula Research Laboratory Numerical Analysis and Scientific Computing Oslo 0164 Norway. Department of Informatics University of Oslo Oslo Norway. School of Economics Innovation and Technology Kristiania University of Applied Sciences Kirkegata 24-26 N-0153 Oslo Norway.

Accurate modeling of eye gaze dynamics is essential for advancement in human-computer interaction, neurological diagnostics, and cognitive research. Traditional generative models like Markov models often fail to capture the complex temporal dependencies and distributional nuance inherent in eye gaze trajectories data. This study introduces a Generative Adversarial Network (GAN) framework employing Long Short-Term Memory (LSTM) and Convolutional Neural Network (CNN) generators and discriminators to generate high-fidelity synthetic eye gaze velocity trajectories. We conducted a comprehensive evaluation of four GAN architectures: CNN-CNN, LSTM-CNN, CNN-LSTM, and LSTM-LSTM-trained under two conditions: using only adversarial loss ([Formula: see text]) and using a weighted combination of adversarial and spectral losses. Our findings reveal that the LSTM-CNN architecture trained with this new loss function exhibits the closest alignment to the real data distribution, effectively capturing both the distribution tails and the intricate temporal dependencies. The inclusion of spectral regularization significantly enhances the GANs' ability to replicate the spectral characteristics of eye gaze movements, leading to a more stable learning process and improved data fidelity. Comparative analysis with a Hidden Markov Model (HMM) optimized to four hidden states further highlights the advantages of the LSTM-CNN GAN. Statistical metrics show that the HMM-generated data significantly diverges from the real data in terms of mean, standard deviation, skewness, and kurtosis. In contrast, the LSTM-CNN model closely matches the real data across these statistics, affirming its capacity to model the complexity of eye gaze dynamics effectively. These results position the spectrally regularized LSTM-CNN GAN as a robust tool for generating synthetic eye gaze velocity data with high fidelity. Its ability to accurately replicate both the distributional and temporal properties of real data holds

关键词： Eye-gaze trajectories Generative Adversarial Networks Hidden Markov Models Stochastic Processes

Ontologizing Health Systems Data at Scale: Making Translational Discovery a Reality

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arXiv 2022年

作者： Callahan, Tiffany J. Stefanski, Adrianne L. Wyrwa, Jordan M. Zeng, Chenjie Ostropolets, Anna Banda, Juan M. Baumgartner, William A. Boyce, Richard D. Casiraghi, Elena Coleman, Ben D. Collins, Janine H. Deakyne-Davies, Sara J. Feinstein, James A. Haendel, Melissa A. Lin, Asiyah Y. Martin, Blake Matentzoglu, Nicolas A. Meeker, Daniella Reese, Justin Sinclair, Jessica Taneja, Sanya B. Trinkley, Katy E. Vasilevsky, Nicole A. Williams, Andrew Zhang, Xingman A. Denny, Joshua C. Robinson, Peter N. Ryan, Patrick Hripcsak, George Bennett, Tellen D. Hunter, Lawrence E. Kahn, Michael G. Computational Bioscience Program University of Colorado Anschutz Medical Campus AuroraCO80045 United States Department of Biomedical Informatics Columbia University Irving Medical Center New YorkNY10032 United States Department of Physical Medicine and Rehabilitation School of Medicine University of Colorado Anschutz Medical Campus AuroraCO80045 United States National Human Genome Research Institute National Institutes of Health BethesdaMD20892 United States Department of Computer Science Georgia State University AtlantaGA30303 United States Department of Biomedical Informatics University of Pittsburgh School of Medicine PittsburghPA15260 United States Computer Science Università degli Studi di Milano Milan20122 Italy Division of Environmental Genomics and Systems Biology Lawrence Berkeley National Laboratory BerkeleyCA94720 United States The Jackson Laboratory for Genomic Medicine FarmingtonCT06032 United States Department of Haematology University of Cambridge Cambridge United Kingdom Department of Research Informatics & Data Science Analytics Resource Center Children’s Hospital Colorado AuroraCO80045 United States University of Colorado Anschutz School of Medicine AuroraCO80045 United States Center for Health AI University of Colorado Anschutz Medical Campus AuroraCO80045 United States Departments of Biomedical Informatics and Pediatrics University of Colorado School of Medicine AuroraCO80045 United States Semanticly Athens Greece Yale School of Medicine New HavenCT06510 United States HealthLinc ValparaisoIN46383 United States Intelligent Systems Program University of Pittsburgh PittsburghPA15260 United States Department of Family Medicine University of Colorado Anschutz School of Medicine AuroraCO80045 United States Translational and Integrative Sciences Lab University of Colorado Anschutz Medical Campus AuroraCO80045 United States Tufts Institute for Clinical Research and Health Policy Studies Tufts University Bos

Background: Common data models solve many challenges of standardizing electronic health record (EHR) data, but are unable to semantically integrate all the resources needed for deep phenotyping. Open Biological and Biomedical Ontology (OBO) Foundry ontologies provide computable representations of biological knowledge and enable the integration of heterogeneous data. However, mapping EHR data to OBO ontologies requires significant manual curation and domain expertise. Objective: We introduce OMOP2OBO, an algorithm for mapping Observational Medical Outcomes Partnership (OMOP) vocabularies to OBO ontologies. Results: Using OMOP2OBO, we produced mappings for 92,367 conditions, 8611 drug ingredients, and 10,673 measurement results, which covered 68-99% of concepts used in clinical practice when examined across 24 hospitals. When used to phenotype rare disease patients, the mappings helped systematically identify undiagnosed patients who might benefit from genetic testing. Conclusions: By aligning OMOP vocabularies to OBO ontologies our algorithm presents new opportunities to advance EHR-based deep phenotyping. © 2022, CC BY.

关键词： Ontology

Detection of Cell Nuclei using LadderNet 9

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Detection of Cell Nuclei using LadderNet

9th International Congress on Advanced Applied informatics, IIAI-AAI 2020

作者： Ando, Ren Iwahori, Yuji Fukui, Shinji Wang, Aili Bhuyan, M.K. Iwamoto, Takashi Ueda, Jun Chubu University Dept. of Computer Science Kasugai487-8501 Japan Aichi University of Education Informatics and Communication Tech. Kariya448-8542 Japan Harbin Univ. of Sci. and Tech. Higher Education Key Lab. Harbin China Indian Institute of Technology Guwahati Dept. of Electronics and Electrical Eng. Guwahati781039 India Chubu University Dept. of Biomedical Sciences Kasugai487-8501 Japan Asahikawa Medical University Center for Advanced Research and Education Asahikawa078-8510 Japan

ISBN: (纸本)9781728173979

Cytology which directly examines cells in the early detection of cancer plays an important role but this diagnosis depends on the experience and technology of a pathologist. The problem is that it takes time and the objectivity is poor. An automatic diagnosis system for pathologically diagnosing cancer is necessary to solve these problems. To classify cells into benign or malignant automatically, it is important to detect the cell nucleus from the cell image in advance. This paper proposes a new approach to detect cell nuclei for automatically using LadderNet which is a recent extension model of U-Net used in the Deep Learning Approach. © 2020 IEEE.

关键词： Cytology