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MedComm - Future Medicine 2022年第2期1卷

作者： Yang, Bo Li, Kan Zhong, Xiuqin Zou, Jun Center for Clinical Translational Innovations Molecular Medicine Research Center West China Biomedical Big Data Center State Key Laboratory of Biotherapy West China Hospital West China School of Medicine Sichuan University Chengdu China Department of Pharmacy Chengdu Seventh People's Hospital The Affiliated Tumor Hospital of Chengdu Medical College Chengdu China School of Computer Science and Engineering University of Electronic Science and Technology of China Chengdu China

The field of deep learning has witnessed dramatic and rapid progress in the past several years, largely driven by the availability of massive datasets and increased computational power. Although promising advances have been made, the implementation of deep learning in drug design is still in the vigorously developing stage. Here we summarize the frontiers and emerging applications of deep learning in drug design. We provide the background of deep learning and the architecture of several important deep neural networks for drug design and discovery, including convolutional neural networks, recurrent neural networks, transformer, deep auto-encoder, generative adversarial networks, graph neural networks, and flow-based neural networks. We give some examples of tasks for which these different deep neural networks are suitable. The successful employment of deep learning in drug design and discussing its further opportunities are reviewed, such as molecular representation, drug-likeness prediction, de novo molecular generation, ligand-protein interaction prediction, reaction, and retrosynthetic prediction. Current challenges and further possibilities are proposed to help accelerate the progress of the field, such as model interpretation, the requirement for large quantities of training datasets, hyperparameters tuning, and open source. © 2022 The Authors. MedComm – Future Medicine published by John Wiley & Sons Australia, Ltd on behalf of Sichuan International Medical Exchange & Promotion Association (SCIMEA).

关键词： artificial intelligence deep learning drug design machine learning

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CMR×Recon: An open cardiac MRI dataset for the competition of accelerated image reconstruction

arXiv

引用

arXiv 2023年

作者： Wang, Chengyan Lyu, Jun Wang, Shuo Qin, Chen Guo, Kunyuan Zhang, Xinyu Yu, Xiaotong Li, Yan Wang, Fanwen Jin, Jianhua Shi, Zhang Xu, Ziqiang Tian, Yapeng Hua, Sha Chen, Zhensen Liu, Meng Sun, Mengting Kuang, Xutong Wang, Kang Wang, Haoran Li, Hao Chu, Yinghua Yang, Guang Bai, Wenjia Zhuang, Xiahai Wang, He Qin, Jing Qu, Xiaobo Human Phenome Institute Fudan University Shanghai China School of Nursing The Hong Kong Polytechnic University Hong Kong Digital Medical Research Center School of Basic Medical Sciences Fudan University Shanghai China Department of Electrical and Electronic Engineering & I-X Imperial College London United Kingdom Department of Electronic Science Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance National Institute for Data Science in Health and Medicine Institute of Artificial Intelligence Xiamen University Xiamen China Department of Radiology Ruijin Hospital Shanghai Jiao Tong University School of Medicine Shanghai China Department of Bioengineering/˜Imperial-X Imperial College London United Kingdom School of Data Science Fudan University Shanghai China Department of Radiology Zhongshan Hospital Fudan University Shanghai China School of Health Science and Engineering University of Shanghai for Science and Technology Shanghai China Department of Computer Science The University of Texas Dallas United States Department of Cardiovascular Medicine Ruijin Hospital Lu Wan Branch Shanghai Jiao Tong University School of Medicine Shanghai China Institute of Science and Technology for Brain-Inspired Intelligence Fudan University Shanghai200433 China Simens Healthineers Ltd. China Department of Brain Sciences Imperial College London London United Kingdom Department of Computing Imperial College London London United Kingdom

Cardiac magnetic resonance imaging (CMR) has emerged as a valuable diagnostic tool for cardiac diseases. However, a limitation of CMR is its slow imaging speed, which causes patient discomfort and introduces artifacts in the images. There has been growing interest in deep learning-based CMR imaging algorithms that can reconstruct high-quality images from highly under-sampled k-space data. However, the development of deep learning methods requires large training datasets, which have not been publicly available for CMR. To address this gap, we released a dataset that includes multi-contrast, multi-view, multi-slice and multi-coil CMR imaging data from 300 subjects. Imaging studies include cardiac cine and mapping sequences. Manual segmentations of the myocardium and chambers of all the subjects are also provided within the dataset. Scripts of state-of-the-art reconstruction algorithms were also provided as a point of reference. Our aim is to facilitate the advancement of state-of-the-art CMR image reconstruction by introducing standardized evaluation criteria and making the dataset freely accessible to the research community. researchers can access the dataset at https://***/#!Synapse:syn51471091/wiki/. Copyright © 2023, The Authors. All rights reserved.

关键词： Image reconstruction

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Cryogenic quasi-static embedded DRAM for energy-efficient compute-in-memory applications

arXiv

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arXiv 2023年

作者： Shu, Yuhao Zhang, Hongtu Sun, Hao Zhang, Mengru Zhao, Wenfeng Deng, Qi Tang, Zhidong Yuan, Yumeng Hu, Yongqi Gu, Yu Kou, Xufeng Ha, Yajun School of Information Science and Technology ShanghaiTech University Shanghai China Shanghai Institute of Microsystem and Information Technology Chinese Academy of Sciences Shanghai China School of Electronic Electrical and Communication Engineering University of Chinese Academy of Sciences Beijing China State Key Laboratory of Integrated Chip and System Frontier Institute of Chip and System Fudan University Shanghai China State Key Laboratory of ASIC and System School of Microelectronics Fudan University Shanghai China Department of Electrical and Computer Engineering Binghamton University SUNY BinghamtonNY United States Shanghai Advanced Research Institute Chinese Academy of Sciences Shanghai China Shanghai Engineering Research Center of Energy Efficient and Custom AI IC Shanghai China

Compute-in-memory (CIM) presents an attractive approach for energy-efficient computing in data-intensive applications. However, the development of suitable memory designs to achieve high-performance CIM remains a challenging task. Here, we propose a cryogenic quasi-static embedded DRAM to address the logic-memory mismatch of CIM. Guided by the re-calibrated cryogenic device model, the designed four-transistor bit-cell achieves full-swing data storage, low power consumption, and extended retention time at cryogenic temperatures. Combined with the adoption of cryogenic write bitline biasing technique and readout circuitry optimization, our 4Kb cryogenic eDRAM chip demonstrates a 1.37×106 times improvement in retention time, while achieving a 75 times improvement in retention variability, compared to room-temperature operation. Moreover, it also achieves outstanding power performance with a retention power of 112 fW and a dynamic power of 108 µW at 4.2 K, which can be further decreased by 7.1% and 13.6% using the dynamic voltage scaling technique. This work reveals the great potential of cryogenic CMOS for high-density data storage and lays a solid foundation for energy-efficient CIM implementations. Copyright © 2023, The Authors. All rights reserved.

关键词： Computation theory

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NLP in FinTech applications: Past, Present and Future

arXiv

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arXiv 2020年

作者： Chen, Chung-Chi Huang, Hen-Hsen Chen, Hsin-Hsi Department of Computer Science and Information Engineering National Taiwan University Taiwan Department of Computer Science National Chengchi University Taiwan MOST Joint Research Center for AI Technology All Vista Healthcare Taiwan

Financial Technology (FinTech) is one of the worldwide rapidly-rising topics in the past five years according to the statistics of FinTech from Google Trends. In this position paper, we focus on the researches applying natural language processing (NLP) technologies in the finance domain. Our goal is to indicate the position we are now and provide the blueprint for future researches. We go through the application scenarios from three aspects including Know Your Customer (KYC), Know Your Product (KYP), and Satisfy Your Customer (SYC). Both formal documents and informal textual data are analyzed to understand corporate customers and personal customers. Furthermore, we talk over how to dynamically update the features of products from the prospect and the risk points of view. Finally, we discuss satisfying the customers in both B2C and C2C business models. After summarizing the past and the recent challenges, we highlight several promising future research directions in the trend of FinTech and the open finance tendency. Copyright © 2020, The Authors. All rights reserved.

关键词： Sales

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Prediction of oral food challenge outcomes via ensemble learning

引用

Informatics in Medicine Unlocked 2023年 36卷

作者： Zhang, Justin Lee, Deborah Jungles, Kylie Shaltis, Diane Najarian, Kayvan Ravikumar, Rajan Sanders, Georgiana Gryak, Jonathan Department of Electrical and Computer Engineering University of Michigan Ann Arbor MI United States Department of Internal Medicine University of Michigan Ann Arbor MI United States Department of Pediatrics University of Michigan Ann Arbor MI United States Department of Computational Medicine and Bioinformatics University of Michigan Ann Arbor MI United States Michigan Institute for Data Science University of Michigan Ann Arbor MI United States Department of Emergency Medicine University of Michigan Ann Arbor MI United States Department of Computer Science and Engineering University of Michigan Ann Arbor MI United States Max Harry Weil Institute for Critical Care Research and Innovation University of Michigan Ann Arbor MI United States Mary H. Weiser Food Allergy Center University of Michigan Ann Arbor MI United States Department of Computer Science Queens College City University of New York New York NY United States

Oral Food Challenges (OFCs) are essential to accurately diagnosing food allergy due to the limitations of existing clinical testing. However, some patients are hesitant to undergo OFCs, while those willing suffer from limited access to allergists in rural/community healthcare settings. Despite its success in predicting patient outcomes in other clinical settings, few applications of machine learning to food allergy have been developed. Thus, in this study, we seek to leverage machine learning methodologies for OFC outcome prediction. Retrospective data was gathered from 1,112 patients who collectively underwent a total of 1,284 OFCs, and consisted of clinical factors including serum-specific Immunoglobulin E (IgE), total IgE, skin prick tests (SPTs), comorbidities, sex, and age. Using these features, multiple machine learning models were constructed to predict OFC outcomes for three common allergens: peanut, egg, and milk. The best performing model for each allergen was an ensemble of random forest (egg) or Learning Using Concave and Convex Kernels (LUCCK) (peanut, milk) models, which achieved an Area under the Curve (AUC) of 0.91, 0.96, and 0.94, in predicting OFC outcomes for peanut, egg, and milk, respectively. Moreover, all such models had sensitivity and specificity values ≥89%. Model interpretation via SHapley Additive exPlanations (SHAP) indicates that specific IgE, along with wheal and flare values from SPTs, are highly predictive of OFC outcomes. The results of this analysis suggest that ensemble learning has the potential to predict OFC outcomes and reveal relevant clinical factors for further study. © 2022 The Author(s)

关键词： Ensemble learning Learning Using Concave and Convex Kernels Machine learning Oral food challenges SHAP

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Corrigendum to “Molecular subtypes classification of breast cancer in DCE-MRI using deep features” [Expert Syst. Appl. 236 (2024) 121371]

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Expert Systems with applications 2025年 270卷

作者： Ali M. Hasan Noor K.N. Al-Waely Hadeel K. Aljobouri Hamid A. Jalab Rabha W. Ibrahim Farid Meziane College of Medicine Al-Nahrain University Baghdad Iraq Biomedical Engineering Department College of Engineering Al-Nahrain University Iraq Faculty of Computer Science and Information Technology University of Malaya 50603 Kuala Lumpur Malaysia Information and Communication Technology Research Group Scientific Research Center Al-Ayen University Nile Street 64001 Thi-Qar Iraq Department of Computer Science and Mathematics Lebanese American University Beirut 1102 2801 Lebanon Near East University Mathematics Research Center Department of Mathematics Near East Boulevard PC: 99138 Nicosia/Mersin 10 Turkey Data Science Research Centre School of Computing and Engineering University of Derby United Kingdom

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Blockchain-Based Participant Selection for Federated Learning 2nd

Blockchain-Based Participant Selection for Federated Learnin...

引用

2nd International Conference on Blockchain and Trustworthy Systems, Blocksys 2020

作者： Zhang, Keshan Huang, Huawei Guo, Song Zhou, Xiaocong School of Data and Computer Science Sun Yat-Sen University Guangzhou China National Engineering Research Center of Digital Life Sun Yat-Sen University Guangzhou China Department of Computing The Hong Kong Polytechnic University Kowloon Hong Kong Shenzhen Research Institute The Hong Kong Polytechnic University Kowloon Hong Kong

ISBN: (纸本)9789811592126

Federated Learning (FL) advocates training a global model using a large-scale of distributed devices such that the collaborative model training can be benefited from the rich local datasets, while preserving the privacy of local training dataset in each participant. This is because only the training results, i.e., the updated model parameters and model weights are needed to report to the FL server for aggregation in each round of FL-training. However, during the model transmission of the original FL protocol, there is no security guarantee towards the training results. Thus, every step during model uploading phase can be attacked by malicious attackers. To address such threat, we propose a new federated learning architecture by taking the advantages of blockchain into account. The proposed architecture includes two-phase design. The first phase is a numerical evaluation, which can prevent the malicious devices from being selected. For the second phase, we devise a participant-selection algorithm that enables the FL server to select the appropriate group of devices for each round of FL-training. We believe that our study can shed new light on the joint research of blockchain and federated learning. © 2020, Springer Nature Singapore Pte Ltd.

关键词： Blockchain

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The Multi-modality Cell Segmentation Challenge: Towards Universal Solutions

arXiv

引用

arXiv 2023年

作者： Ma, Jun Xie, Ronald Ayyadhury, Shamini Ge, Cheng Gupta, Anubha Gupta, Ritu Gu, Song Zhang, Yao Lee, Gihun Kim, Joonkee Lou, Wei Li, Haofeng Upschulte, Eric Dickscheid, Timo de Almeida, José Guilherme Wang, Yixin Han, Lin Yang, Xin Labagnara, Marco Gligorovski, Vojislav Scheder, Maxime Rahi, Sahand Jamal Kempster, Carly Pollitt, Alice Espinosa, Leon Mignot, Tâm Middeke, Jan Moritz Eckardt, Jan-Niklas Li, Wangkai Li, Zhaoyang Cai, Xiaochen Bai, Bizhe Greenwald, Noah F. Van Valen, David Weisbart, Erin Cimini, Beth A. Cheung, Trevor Brück, Oscar Bader, Gary D. Wang, Bo Peter Munk Cardiac Centre University Health Network TorontoON Canada Department of Laboratory Medicine and Pathobiology University of Toronto TorontoON Canada Vector Institute TorontoON Canada Department of Molecular Genetics University of Toronto TorontoON Canada Donnelly Centre University of Toronto TorontoON Canada Princess Margaret Cancer Centre University Health Network TorontoON Canada School of Medicine and Pharmacy Ocean University of China Qingdao China New Delhi India Laboratory Oncology Dr. BRA-IRCH All India Institute of Medical Sciences New Delhi India Department of Image Reconstruction Nanjing Anke Medical Technology Co. Ltd. Nanjing China Shanghai Artificial Intelligence Laboratory Shanghai China Graduate School of AI KAIST Seoul Korea Republic of Shenzhen Research Institute of Big Data Shenzhen China Shenzhen China Helmholtz AI Research Center Jülich Jülich Germany Faculty of Mathematics and Natural Sciences Institute of Computer Science Heinrich Heine University Düsseldorf Düsseldorf Germany Hinxton United Kingdom Champalimaud Foundation - Centre for the Unknown Lisbon Portugal Department of Bioengineering Stanford University Palo AltoCA United States Tandon School of Engineering New York University New YorkNY United States School of Biomedical Engineering Health Science Center Shenzhen University Shenzhen China Lausanne Switzerland School of Biological Sciences University of Reading Reading United Kingdom Laboratoire de Chimie Bactérienne CNRS Université Aix Marseille UMR Institut de Microbiologie de la Méditerranée Marseille France Department of Internal Medicine I University Hospital Dresden Technical University Dresden Dresden Germany Else Kroener Fresenius Center for Digital Health Technical University Dresden Dresden Germany Department of Automation University of Science and Technology of China Hefei China Institute of Advanced Technology University of Science and Technology of China Hefei Chi

Cell segmentation is a critical step for quantitative single-cell analysis in microscopy images. Existing cell segmentation methods are often tailored to specific modalities or require manual interventions to specify hyper-parameters in different experimental settings. Here, we present a multi-modality cell segmentation benchmark, comprising over 1500 labeled images derived from more than 50 diverse biological experiments. The top participants developed a Transformer-based deep-learning algorithm that not only exceeds existing methods but can also be applied to diverse microscopy images across imaging platforms and tissue types without manual parameter adjustments. This benchmark and the improved algorithm offer promising avenues for more accurate and versatile cell analysis in microscopy imaging. © 2023, CC BY-NC-ND.

关键词： Deep learning

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A systematic collection of medical image datasets for deep learning

arXiv

引用

arXiv 2021年

作者： Li, Johann Zhu, Guangming Hua, Cong Feng, Mingtao Bennamoun, Basheer Li, Ping Lu, Xiaoyuan Song, Juan Shen, Peiyi Xu, Xu Mei, Lin Zhang, Liang Shah, Syed Afaq Ali Bennamoun, Mohammed School of Computer Science and Technology Xidian University China School of Medicine University of Notre Dame Australia Data and Virtual Research Room Shanghai Broadband Network Center China Third Research Institute of The Ministry of Public Security China Discipline of Information Technology Media and Communications Murdoch University Australia Department of Computer Science and Software Engineering University of Western Australia Australia

The astounding success made by artificial intelligence (ai) in healthcare and other fields proves that ai can achieve human-like performance. However, success always comes with challenges. Deep learning algorithms are data-dependent and require large datasets for training. The lack of data in the medical imaging field creates a bottleneck for the application of deep learning to medical image analysis. Medical image acquisition, annotation, and analysis are costly, and their usage is constrained by ethical restrictions. They also require many resources, such as human expertise and funding. That makes it difficult for non-medical researchers to have access to useful and large medical data. Thus, as comprehensive as possible, this paper provides a collection of medical image datasets with their associated challenges for deep learning research. We have collected information of around three hundred datasets and challenges mainly reported between 2013 and 2020 and categorized them into four categories: head & neck, chest & abdomen, pathology & blood, and "others". Our paper has three purposes: 1) to provide a most up to date and complete list that can be used as a universal reference to easily find the datasets for clinical image analysis, 2) to guide researchers on the methodology to test and evaluate their methods’ performance and robustness on relevant datasets, 3) to provide a "route" to relevant algorithms for the relevant medical topics, and challenge leaderboards. © 2021, CC BY-NC-SA.

关键词： Deep learning

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Paddy rice methane emissions across Monsoon Asia

引用

Remote Sensing of Environment 2023年 284卷

作者： Ouyang, Zutao Jackson, Robert B. McNicol, Gavin Fluet-Chouinard, Etienne Runkle, Benjamin R.K. Papale, Dario Knox, Sara H. Cooley, Sarah Delwiche, Kyle B. Feron, Sarah Irvin, Jeremy Andrew Malhotra, Avni Muddasir, Muhammad Sabbatini, Simone Alberto, Ma. Carmelita R. Cescatti, Alessandro Chen, Chi-Ling Dong, Jinwei Fong, Bryant N. Guo, Haiqiang Hao, Lu Iwata, Hiroki Jia, Qingyu Ju, Weimin Kang, Minseok Li, Hong Kim, Joon Reba, Michele L. Nayak, Amaresh Kumar Roberti, Debora Regina Ryu, Youngryel Swain, Chinmaya Kumar Tsuang, Benjei Xiao, Xiangming Yuan, Wenping Zhang, Geli Zhang, Yongguang Department of Earth System Science Stanford University StanfordCA United States Woods Institute for the Environment Stanford University StanfordCA United States Precourt Institute for Energy Stanford University StanfordCA United States Department of Earth and Environmental Sciences University of Illinois Chicago ChicagoIL United States Department of Biological and Agricultural Engineering University of Arkansas FayettevilleAR United States University of Tuscia Viterbo Italy IAFES division Viterbo Italy Department of Geography The University of British Columbia VancouverBC Canada Department of Geography University of Oregon EugeneOR United States Department of Environmental Science Policy And Management UC Berkeley BerkeleyCA United States Campus Fryslan University of Groningen Groningen Netherlands Department of Computer Science Stanford University StanfordCA United States Department of Geography University of Zurich Zurich Switzerland International Rice Research Institute Laguna Philippines Ispra Italy Taiwan Agricultural Research Institute Taichung Wufeng Taiwan Institute of Geographic Sciences and Natural Resources Research Chinese Academy of Sciences Beijing China USDA ARS Delta Water Management Research Unit JonesboroAR United States Fudan University Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering and Coastal Ecosystems Research Station of the Yangtze River Estuary Shanghai China / Jiangsu Key Laboratory of Agricultural Meteorology Nanjing University of Information Science and Technology Nanjing China Department of Environmental Science Shinshu University Matsumoto Japan China Meteorological Administration Institute of Atmospheric Environment Shenyang China International Institute for Earth System Sciences Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application Nanjing University Jiangsu Nanjing210023 China National Center for AgroM

Although rice cultivation is one of the most important agricultural sources of methane (CH4) and contributes ∼8% of total global anthropogenic emissions, large discrepancies remain among estimates of global CH4 emissions from rice cultivation (ranging from 18 to 115 Tg CH4 yr−1) due to a lack of observational constraints. The spatial distribution of paddy-rice emissions has been assessed at regional-to-global scales by bottom-up inventories and land surface models over coarse spatial resolution (e.g., > 0.5°) or spatial units (e.g., agro-ecological zones). However, high-resolution CH4 flux estimates capable of capturing the effects of local climate and management practices on emissions, as well as replicating in situ data, remain challenging to produce because of the scarcity of high-resolution maps of paddy-rice and insufficient understanding of CH4 predictors. Here, we combine paddy-rice methane-flux data from 23 global eddy covariance sites and MODIS remote sensing data with machine learning to 1) evaluate data-driven model performance and variable importance for predicting rice CH4 fluxes;and 2) produce gridded up-scaling estimates of rice CH4 emissions at 5000-m resolution across Monsoon Asia, where ∼87% of global rice area is cultivated and ∼ 90% of global rice production occurs. Our random-forest model achieved Nash-Sutcliffe Efficiency values of 0.59 and 0.69 for 8-day CH4 fluxes and site mean CH4 fluxes respectively, with land surface temperature, biomass and water-availability-related indices as the most important predictors. We estimate the average annual (winter fallow season excluded) paddy rice CH4 emissions throughout Monsoon Asia to be 20.6 ± 1.1 Tg yr−1 for 2001–2015, which is at the lower range of previous inventory-based estimates (20–32 CH4 Tg yr−1). Our estimates also suggest that CH4 emissions from paddy rice in this region have been declining from 2007 through 2015 following declines in both paddy-rice growing area and emission rates per unit

关键词： Climate change

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