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arXiv 2022年

作者： Wei, Jingxuan Chen, Yang Li, Ying Li, Wei Xie, Junsheng Lee, Chengkuo Novoselov, Kostya S. Qiu, Cheng-Wei Department of Electrical and Computer Engineering National University of Singapore Singapore117583 Singapore CAS Key Laboratory of Mechanical Behaviour and Design of Materials Department of Precision Machinery and Precision Instrumentation University of Science and Technology of China Hefei230026 China Interdisciplinary Center for Quantum Information State Key Laboratory of Modern Optical Instrumentation ZJU-Hangzhou Global Scientific and Technological Innovation Center Zhejiang University Hangzhou310027 China International Joint Innovation Center Key Lab of Advanced Micro/Nano Electronic Devices & Smart Systems of Zhejiang Zhejiang University Haining314400 China GPL Photonics Lab State Key Laboratory of Applied Optics Changchun Institute of Optics Fine Mechanics and Physics Chinese Academy of Sciences Changchun130033 China Center for Intelligent Sensors and MEMS National University of Singapore Singapore117608 Singapore Institute for Functional Intelligent Materials National University of Singapore Singapore117544 Singapore

Free-space circularly polarized light (CPL) detection, requiring polarizers and waveplates, has been well established, while such spatial degree of freedom is unfortunately absent in integrated on-chip optoelectronics. So far, those reported filterless CPL photodetectors suffer from the intrinsic small discrimination ratio, vulnerability to the non-CPL field components, and low responsivity. Here, we report a distinct paradigm of geometric photodetectors in mid-infrared exhibiting colossal discrimination ratio, close-to-perfect CPL-specific response, a zero-bias responsivity of 392 V/W at room temperature, and a detectivity of ellipticity down to 0.03o Hz−1/2. Our approach employs plasmonic nanostructures array with judiciously designed symmetry, assisted by graphene ribbons to electrically read their near-field optical information. This geometry-empowered recipe for infrared photodetectors provides a robust, direct, strict, and high-quality solution to on-chip filterless CPL detection and unlocks new opportunities for integrated functional optoelectronic devices. Copyright © 2022, The Authors. All rights reserved.

关键词： Photodetectors

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Next-generation smart homes: CO2 monitoring with Matter protocol to support indoor air quality

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Internet of Things (The Netherlands) 2025年 32卷

作者： Mota, Afonso Serôdio, Carlos Briga-Sá, Ana Valente, Antonio Department of Engineering School of Sciences and Technology Universidade de Trás-os-Montes e Alto Douro (UTAD) Vila Real 5000-801 Portugal Center ALGORITMI Universidade do Minho Campus de Azurém Guimarães 4800-058 Portugal CQ-VR (Center of Chemistry of Vila Real) Universidade de Trás-os-Montes e Alto Douro Vila Real 5000-801 Portugal CRIIS (Centre for Robotics in Industry and Intelligent Systems) INESC-TEC—Institute for Systems and Computer Engineering Technology and Science Campus da FEUP Porto 4200-465 Portugal

Humans spend most of their time indoors, where air quality and comfort are crucial to health and well-being. Elevated CO2 levels in buildings can reduce cognitive function, discomfort, and health issues. Indoor CO2 monitoring has emerged as a key focus in the literature, particularly in residential buildings, as it can play a vital role in helping to maintain adequate ventilation rates. The growing smart home market demands seamless integration and control, which are essential for implementing IAQ sensing devices. However, interoperability barriers between platforms and devices continue to hinder smart home adoption. To address these challenges, Matter protocol is starting to appear in the market. In this work, a wireless CO2 sensor is developed based on ESP32-C6 and SCD40 and integrated into a created Matter-enabled ecosystem formed with the Home Assistant open-source platform. The utilized hardware and software enable the usage of two different wireless communication technologies, WiFi and Thread, enhancing compatibility. The study highlights the rapid and seamless onboarding of the developed CO2 monitoring device into smart home ecosystems using the Matter protocol. As a result, once the device is successfully added to the ecosystem, the measurements can be accessed and analyzed through a mobile application, forming an IoT environment.

关键词： CO2 Espressif Indoor air quality Interoperability IoT Matter Smart home

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Retrospective for the dynamic sensorium competition for predicting large-scale mouse primary visual cortex activity from videos 24

Retrospective for the dynamic sensorium competition for pred...

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Proceedings of the 38th International Conference on Neural Information Processing systems

作者： Polina Turishcheva Paul G. Fahey Michaela Vystrčilová Laura Hansel Rachel Froebe Kayla Ponder Yongrong Qiu Konstantin F. Willeke Mohammad Bashiri Ruslan Baikulov Yu Zhu Lei Ma Shan Yu Tiejun Huang Bryan M. Li Wolf De Wulf Nina Kudryashova Matthias H. Hennig Nathalie L. Rochefort Arno Onken Eric Wang Zhiwei Ding Andreas S. Tolias Fabian H. Sinz Alexander S. Ecker Institute of Computer Science and Campus Institute Data Science University of Göttingen Germany Department of Neuroscience & Center for Neuroscience and Artificial Intelligence Baylor College of Medicine Houston Texas and Department of Ophthalmology Byers Eye Institute Stanford University School of Medicine Stanford CA and Stanford Bio-X Stanford University Stanford CA and Wu Tsai Neurosciences Institute Stanford University Stanford CA Department of Neuroscience & Center for Neuroscience and Artificial Intelligence Baylor College of Medicine Houston Texas Institute of Computer Science and Campus Institute Data Science University of Göttingen Germany and Department of Ophthalmology Byers Eye Institute Stanford University School of Medicine Stanford CA and Stanford Bio-X Stanford University Stanford CA and Wu Tsai Neurosciences Institute Stanford University Stanford CA Institute of Computer Science and Campus Institute Data Science University of Göttingen Germany and International Max Planck Research School for Intelligent Systems Tübingen Germany and Institute for Bioinformatics and Medical Informatics Tübingen University Germany lRomul Russia Institute of Automation Chinese Academy of Sciences China and Beijing Academy of Artificial Intelligence China Beijing Academy of Artificial Intelligence China Institute of Automation Chinese Academy of Sciences China The Alan Turing Institute UK and School of Informatics University of Edinburgh UK School of Informatics University of Edinburgh UK Centre for Discovery Brain Sciences University of Edinburgh UK and Simons Initiative for the Developing Brain University of Edinburgh UK Department of Neuroscience & Center for Neuroscience and Artificial Intelligence Baylor College of Medicine Houston Texas and Department of Ophthalmology Byers Eye Institute Stanford University School of Medicine Stanford CA and Stanford Bio-X Stanford University Stanford CA and Wu Tsai Neurosciences Institute Stanford University Stanf

ISBN: (纸本)9798331314385

Understanding how biological visual systems process information is challenging because of the nonlinear relationship between visual input and neuronal responses. Artificial neural networks allow computational neuroscientists to create predictive models that connect biological and machine vision. Machine learning has benefited tremendously from benchmarks that compare different models on the same task under standardized conditions. However, there was no standardized benchmark to identify state-of-the-art dynamic models of the mouse visual system. To address this gap, we established the SENSORIUM 2023 Benchmark Competition with dynamic input, featuring a new large-scale dataset from the primary visual cortex of ten mice. This dataset includes responses from 78,853 neurons to 2 hours of dynamic stimuli per neuron, together with behavioral measurements such as running speed, pupil dilation, and eye movements. The competition ranked models in two tracks based on predictive performance for neuronal responses on a held-out test set: one focusing on predicting in-domain natural stimuli and another on out-of-distribution (OOD) stimuli to assess model generalization. As part of the NeurIPS 2023 Competition Track, we received more than 160 model submissions from 22 teams. Several new architectures for predictive models were proposed, and the winning teams improved the previous state-of-the-art model by 50%. Access to the dataset as well as the benchmarking infrastructure will remain online at ***.

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Passive Quadrupedal Gait Synchronization for Extra Robotic Legs Using a Dynamically Coupled Double Rimless Wheel Model

arXiv

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arXiv 2020年

作者： Gonzalez, Daniel J. Harry Asada, H. Robotics Research Center Department of Electrical Engineering and Computer Science United States Military Academy West PointNY10996 United States d’Arbeloff Laboratory for Information Systems and Technology Department of Mechanical Engineering Massachusetts Institute of Technology CambridgeMA02139 United States

The Extra Robotic Legs (XRL) system is a robotic augmentation worn by a human operator consisting of two articulated robot legs that walk with the operator and help bear a heavy backpack payload. It is desirable for the Human-XRL quadruped system to walk with the rear legs lead the front by 25% of the gait period, minimizing the energy lost from foot impacts while maximizing balance stability. Unlike quadrupedal robots, the XRL cannot command the human’s limbs to coordinate quadrupedal locomotion. Using a pair of Rimless Wheel models, it is shown that the systems coupled with a spring and damper converge to the desired 25% phase difference. A Poincaré return map was generated using numerical simulation to examine the convergence properties to different coupler design parameters, and initial conditions. The Dynamically Coupled Double Rimless Wheel system was physically realized with a spring and dashpot chosen from the theoretical results, and initial experiments indicate that the desired synchronization properties may be achieved within several steps using this set of passive components alone. Copyright © 2020, The Authors. All rights reserved.

关键词： Exoskeleton (robotics)

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GardnerNet: An Interpretable Deep Learning Model for Quantitative Human Blastocyst Evaluation - A Retrospective Model Development and Validation Study

SSRN

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SSRN 2024年

作者： Liu, Hang Chen, Longbin Shan, Guanqiao Sun, Chen Liao, Hongqing Lu, Changfu Zhang, Shuoping Dong, Shaonan Xu, Xinxin Yan, Qiuyun Gong, Fei Zhang, Zhuoran Dai, Changsheng Chen, Wenyuan Song, Haocong Chen, Lei Sun, Haixiang Wang, Shanshan Lin, Ge Sun, Yu Gu, Yifan Department of Mechanical and Industrial Engineering University of Toronto 5 King’s College Road TorontoONM5S 3G8 Canada Institute of Reproductive and Stem Cell Engineering School of Basic Medical Science Central South University 172 Tongzipo Road Hunan Province Changsha China Hengyang Nanhua-Xinghui Reproductive Health Hospital 30 Jiefang Road Hunan Province Hengyang China The second Affiliated Hospital Hengyang Medical School University of South China 30 Jiefang Road Hunan Province Hengyang City China Reproductive & Genetic Hospital of CITIC-Xiangya 567 Tongzipo Road Hunan Province Changsha China NHC Key Laboratory of Human Stem Cell and Reproductive Engineering School of Basic Medical Science Central South University 172 Tongzipo Road Hunan Province Changsha China Clinical Research Center for Reproduction and Genetics in Hunan Province Reproductive & Genetic Hospital of CITIC-Xiangya 567 Tongzipo Road Hunan Province Changsha China School of Science and Engineering The Chinese University of Hong Kong-Shenzhen 2001 Longxiang Boulevard Longgang District Shenzhen China Institute of Robotics and Intelligent Systems Dalian University of Technolgy 2 Linggong Road Liaoning Province Dalian China Department of Computer Science University of Toronto 40 St George Street TorontoONM5S 2E4 Canada Center for Reproductive Medicine and Obstetrics and Gynecology Nanjing Drum Tower Hospital Nanjing University Medical School 321 Zhongshan Road Jiangsu Province Nanjing China National Engineering and Research Center of Human Stem Cell 8 Luyun Road Jiangsu Province Changsha China Department of Electrical and Computer Engineering 10 King’s College Road TorontoONM5S 3G8 Canada Institute of Biomedical Engineering University of Toronto 164 College Street TorontoONM5S 3G9 Canada

Background: Selecting the blastocyst with the highest potential for live birth from a cohort is crucial for the success of in vitro fertilization (IVF). While the Gardner and Schoolcraft morphological grading system, commonly known as the Gardner grading system, is widely used by embryologists worldwide, blastocysts having similar or the same inner cell mass (ICM) and trophectoderm (TE) grades cause challenges for embryologists in decision-making. Furthermore, human assessment is subjective and inconsistent in predicting which blastocysts have higher potential to result in live birth. This study aims to develop an interpretable, quantitative method aligned with the Gardner grading system, providing continuous scores that correlate with live birth outcomes, thereby assisting embryologists in improving blastocyst selection. Methods: In this retrospective study, we developed GardnerNet, an interpretable deep learning model that outputs expansion degree grade and continuous scores quantifying a blastocyst's ICM morphology and TE morphology, based on the Gardner grading system. The continuous ICM and TE scores were calculated by weighting each base grade's predicted probability and summing the predicted probabilities. To represent each blastocyst's overall potential for live birth, we combined the ICM and TE scores using their odds ratios (ORs) for live birth. We further assessed the correlation between the ICM score, TE score, and the OR-combined score (adjusted for expansion degree) with live birth rates by applying GardnerNet to blastocysts with known live birth outcomes. To test its generalizability, we also applied GardnerNet to an external IVF institution, accounting for variations in imaging conditions, live birth rates, and embryologists' experience levels. Findings: GardnerNet was developed using data from 2760 blastocysts with majority-voted grades for expansion degree, ICM, and TE. The model achieved mean area under the receiver operating characteristic curve

关键词： Risk assessment

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Cryogenic in-memory computing using tunable chiral edge states

arXiv

引用

arXiv 2022年

作者： Liu, Yuting Lee, Albert Qian, Kun Zhang, Peng He, Haoran Ren, Zheyu Cheung, Shun Kong Li, Yaoyin Zhang, Xu Ma, Zichao Xiao, Zhihua Yu, Guoqiang Wang, Xin Liu, Junwei Wang, Zhongrui Wang, Kang L. Shao, Qiming Department of Electronic and Computer Engineering The Hong Kong University of Science and Technology Clear Water Bay Kowloon 999077 Hong Kong School of Material Science and Engineering Harbin Institute of Technology Shenzhen518055 China Device Research Laboratory Department of Electrical and Computer Engineering University of California Los AngelesCA90095 United States IAS Center for Quantum Technologies The Hong Kong University of Science and Technology Hong Kong Department of Electrical and Electronic Engineering The University of Hong Kong Pokfulam Road 999077 Hong Kong Department of Physics The Hong Kong University of Science and Technology Clear Water Bay Kowloon 999077 Hong Kong Beijing National Laboratory for Condensed Matter Physics Institute of Physics University of Chinese Academy of Sciences Chinese Academy of Sciences Beijing100190 China Department of Physics The City University of Hong Kong 999077 Hong Kong Guangdong-Hong Kong-Macao Joint Laboratory for Intelligent Micro-Nano Optoelectronic Technology The Hong Kong University of Science and Technology Hong Kong ACCESS AI Chip Center for Emerging Smart Systems InnoHK Centers Hong Kong Science Park Hong Kong

Cryogenic electronics have become essential in reducing the number of input/output ports to the quantum chips and generating multiplexed reading and control pulses for scalable quantum computation 1-5. A demanding request for cryogenic electronics is to support efficient machine learning algorithms, which have been proven effective for essential quantum computation tasks such as quantum error correction and quantum control 6,7. However, current digital cryogenic electronics suffer from the von Neumann bottleneck, where the physical separation of computation and memory units causes a huge amount of energy and delay when processing data-intensive programs. Energy-efficient hardware implementation of machine learning algorithms for quantum computation requires nonvolatile and electrically-programmable devices, memristors, working at cryogenic temperatures that enable in-memory computing 8,9. Magnetic topological insulators are promising candidates due to their tunable magnetic order by electrical currents with high energy efficiency 10-15. Here, we utilize magnetic topological insulators as memristors (termed magnetic topological memristors) and introduce a chiral edge state-based cryogenic in-memory computing scheme. On the one hand, the chiral edge state can be tuned from left-handed to right-handed chirality through spin-momentum locked topological surface current injection. On the other hand, the chiral edge state exhibits giant and bipolar anomalous Hall resistance, which facilitates the electrical readout. The memristive switching and reading of the chiral edge state exhibit high energy efficiency, high stability, and low stochasticity. We achieve high accuracy in a proof-of-concept classification task using four magnetic topological memristors. Furthermore, our algorithm-level and circuit-level simulations of large-scale neural networks based on magnetic topological memristors demonstrate a software-level accuracy and lower energy consumption for image recogniti

关键词： Topology

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The Dynamic Sensorium competition for predicting large-scale mouse visual cortex activity from videos

arXiv

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arXiv 2023年

作者： Turishcheva, Polina Fahey, Paul G. Hansel, Laura Froebe, Rachel Ponder, Kayla Vystrčilová, Michaela Willeke, Konstantin F. Bashiri, Mohammad Wang, Eric Ding, Zhiwei Tolias, Andreas S. Sinz, Fabian H. Ecker, Alexander S. Qiur, Yongrong Institute of Computer Science and Campus Institute Data Science University of Göttingen Germany Department of Neuroscience Baylor College of Medicine HoustonTX United States Center for Neuroscience and Artificial Intelligence Baylor College of Medicine HoustonTX United States Department of Ophthalmology Byers Eye Institute Stanford University School of Medicine StanfordCA United States Stanford Bio-X Stanford University StanfordCA United States Wu Tsai Neurosciences Institute Stanford University StanfordCA United States International Max Planck Research School for Intelligent Systems University of Tübingen Germany Institute for Bioinformatics and Medical Informatics University of Tübingen Germany Department of Electrical Engineering Stanford University StanfordCA United States Max Planck Institute for Dynamics and Self-Organization Göttingen Germany

Understanding how biological visual systems process information is challenging due to the complex nonlinear relationship between neuronal responses and high-dimensional visual input. Artificial neural networks have already improved our understanding of this system by allowing computational neuroscientists to create predictive models and bridge biological and machine vision. During the Sensorium 2022 competition, we introduced benchmarks for vision models with static input (i.e. images). However, animals operate and excel in dynamic environments, making it crucial to study and understand how the brain functions under these conditions. Moreover, many biological theories, such as predictive coding, suggest that previous input is crucial for current input processing. Currently, there is no standardized benchmark to identify state-of-the-art dynamic models of the mouse visual system. To address this gap, we propose the Sensorium 2023 Benchmark Competition with dynamic input (https://***/). This competition includes the collection of a new large-scale dataset from the primary visual cortex of ten mice, containing responses from over 78,000 neurons to over 2 hours of dynamic stimuli per neuron. Participants in the main benchmark track will compete to identify the best predictive models of neuronal responses for dynamic input (i.e. video). We will also host a bonus track in which submission performance will be evaluated on out-of-domain input, using withheld neuronal responses to dynamic input stimuli whose statistics differ from the training set. Both tracks will offer behavioral data along with video stimuli. As before, we will provide code, tutorials, and strong pre-trained baseline models to encourage participation. We hope this competition will continue to strengthen the accompanying Sensorium benchmarks collection as a standard tool to measure progress in large-scale neural system identification models of the entire mouse visual hierarchy and

关键词： Mammals

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Spintronic memristors for computing

arXiv

引用

arXiv 2021年

作者： Shao, Qiming Wang, Zhongrui Zhou, Yan Fukami, Shunsuke Querlioz, Damien Chua, Leon O. Department of Electronic and Computer Engineering Department of Physics Guangdong-Hong Kong-Macao Joint Laboratory for Intelligent Micro-Nano Optoelectronic Technology The Hong Kong University of Science and Technology Clear Water Bay Hong Kong Department of Electrical and Electronic Engineering The University of Hong Kong Pokfulam Road Hong Kong School of Science and Engineering The Chinese University of Hong Kong Guangdong Shenzhen518172 China Research Institute of Electrical Communication Tohoku University Sendai980-8577 Japan Université Paris-Saclay CNRS Centre de Nanosciences et de Nanotechnologies Palaiseau91120 France Department of Electrical Engineering and Computer Sciences University of California BerkeleyCA94720 United States ACCESS – AI Chip Center for Emerging Smart Systems Hong Kong Science Park Hong Kong

The ever-increasing amount of data from ubiquitous smart devices fosters data-centric and cognitive algorithms. Traditional digital computer systems have separate logic and memory units, resulting in a huge delay and energy cost for implementing these algorithms. Memristors are programmable resistors with a memory, providing a paradigm-shifting approach towards creating intelligent hardware systems to handle data-centric tasks. Spintronic nanodevices are promising choices as they are high-speed, low-power, highly scalable, robust, and capable of constructing dynamic complex systems. In this Review, we survey spintronic devices from a memristor point of view. We introduce spintronic memristors based on magnetic tunnel junctions, nanomagnet ensemble, domain walls, topological spin textures, and spin waves, which represent dramatically different state spaces. They can exhibit steady, oscillatory, stochastic, and chaotic trajectories in their state spaces, which have been exploited for in-memory logic, neuromorphic computing, stochastic and chaos computing. Finally, we discuss challenges and trends in realizing large-scale spintronic memristive systems for practical applications. © 2021, CC BY.

关键词： Stochastic systems

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Evaluation of LSTM for predicting grip strength using electromyography: a comparison of setups and methods

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Neural Computing and Applications 2025年

作者： Anam, Khairul Sudrajat, Ahmad Rizal, Naufal Ainur Intyanto, Gramandha Wega Muldayani, Wahyu Negara, Mohamad Agung Prawira Sumardi Bukhori, Saiful Gitakarma, Made Santo Castellini, Claudio Department of Electrical Engineering Universitas Jember Jl. Kalimantan 37 Jawa Timur Jember68121 Indonesia Intelligent Systems and Robotics Lab CDAST Universitas Jember Jl. Kalimantan 37 Jawa Timur Jember68121 Indonesia Faculty of Computer Science CDAST Universitas Jember Jl. Kalimantan 37 Jawa Timur Jember68121 Indonesia Department of Electronic Systems Engineering Technology Universitas Pendidikan Ganesha Jl. Udayana 11 Bali Singaraja81116 Indonesia Lab Friedrich-Alexander-Universität Erlangen-Nürnberg Nürnberger Str. 74 Bavaria Erlangen91052 Germany

Despite decades of research in prosthetics and myocontrol, using electromyography (EMG) to accurately predict the force a user grasps an object with is still a subject of investigation. Although the problem seems trivial, the optimal EMG setup, able to deliver high prediction accuracy at a minimal economic and computational cost needs to be found. In this work, we compare several EMG setups consisting of one to eight sensors and deep learning methods to find out which combination is most convenient. In particular, we compare long short-term memory (LSTM), together with a stacked autoencoder (LSTM–SAE) and an attention mechanism (LSTMATT). Our experimental results reveal that, while the best performance is attained by LSTM–SAE (coefficient of correlation 0.9867±0.0087, coefficient of determination 0.9676±0.0489, normalized root mean square error 0.048±0.0213), statistically significant differences can only be found when the number of sensors is drastically reduced, namely to 2 sensors, in which case, anyway, the performance is still close to optimal and even surpasses state-of-the-art methods. Further research will focus on testing the optimal approach and setup online on amputated users using prosthetic hardware in daily living activities. © The Author(s), under exclusive licence to Springer-Verlag London Ltd., part of Springer Nature 2025.

关键词： Deep learning

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An Open-Source Knowledge Graph Ecosystem for the Life Sciences

arXiv

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arXiv 2023年

作者： Callahan, Tiffany J. Tripodi, Ignacio J. Stefanski, Adrianne L. Cappelletti, Luca Taneja, Sanya B. Wyrwa, Jordan M. Casiraghi, Elena Matentzoglu, Nicolas A. Reese, Justin Silverstein, Jonathan C. Hoyt, Charles Tapley Boyce, Richard D. Malec, Scott A. Unni, Deepak R. Joachimiak, Marcin P. Robinson, Peter N. Mungall, Christopher J. Cavalleri, Emanuele Fontana, Tommaso Valentini, Giorgio Mesiti, Marco Gillenwater, Lucas A. Santangelo, Brook Vasilevsky, Nicole A. Hoehndorf, Robert Bennett, Tellen D. Ryan, Patrick B. Hripcsak, George Kahn, Michael G. Bada, Michael Baumgartner, William A. Hunter, Lawrence E. 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 Computer Science Department Interdisciplinary Quantitative Biology University of Colorado Boulder BoulderCO80301 United States AnacletoLab Computer Science Department University of Milan 20122 Italy Intelligent Systems Program University of Pittsburgh PittsburghPA15260 United States Department of Physical Medicine and Rehabilitation School of Medicine University of Colorado Anschutz Medical Campus AuroraCO80045 United States Division of Environmental Genomics and Systems Biology Lawrence Berkeley National Laboratory BerkeleyCA94720 United States Semanticly Ltd Athens Greece Department of Biomedical Informatics University of Pittsburgh School of Medicine PittsburghPA15206 United States Laboratory of Systems Pharmacology Harvard Medical School BostonMA02115 United States Division of Translational Informatics University of New Mexico School of Medicine AlbuquerqueNM87131 United States SIB Swiss Institute of Bioinformatics Basel Switzerland Berlin Institute of Health at Charité-Universitatsmedizin Berlin10117 Germany ELLIS European Laboratory for Learning and Intelligent Systems Germany Department of Biomedical Informatics University of Colorado School of Medicine AuroraCO80045 United States Data Collaboration Center Critical Path Institute 1840 E River Rd. Suite 100 TucsonAZ85718 United States Computer Electrical and Mathematical Sciences & Engineering Division Computational Bioscience Research Center King Abdullah University of Science and Technology Thuwal23955-6900 Saudi Arabia Department of Pediatrics University of Colorado School of Medicine AuroraCO80045 United States Janssen Research and Development RaritanNJ08869 United States Division of General Internal Medicine University of Colorado School of Medicine A

Translational research requires data at multiple scales of biological organization. Advancements in sequencing and multi-omics technologies have increased the availability of these data, but researchers face significant integration challenges. Knowledge graphs (KGs) are used to model complex phenomena, and methods exist to construct them automatically. However, tackling complex biomedical integration problems requires flexibility in the way knowledge is modeled. Moreover, existing KG construction methods provide robust tooling at the cost of fixed or limited choices among knowledge representation models. PheKnowLator (Phenotype Knowledge Translator) is a semantic ecosystem for automating the FAIR (Findable, Accessible, Interoperable, and Reusable) construction of ontologically grounded KGs with fully customizable knowledge representation. The ecosystem includes KG construction resources (e.g., data preparation APIs), analysis tools (e.g., SPARQL endpoints and abstraction algorithms), and benchmarks (e.g., prebuilt KGs and embeddings). We evaluated the ecosystem by systematically comparing it to existing open-source KG construction methods and by analyzing its computational performance when used to construct 12 large-scale KGs. With flexible knowledge representation, PheKnowLator enables fully customizable KGs without compromising performance or usability. © 2023, CC BY.

关键词： Ecosystems

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