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Toward a unified information framework for cell atlas assembly

National Science Review 2022年第3期9卷 7-10页

作者： Sijie Chen Yanting Luo Haoxiang Gao Fanhong Li Jiaqi Li Yixin Chen Renke You Hairong Lv Kui Hua Rui Jiang Xuegong Zhang Bioinformatics Division of BNRIST and Department of Automation MOE Key Lab of BioinformaticsTsinghua University Fuzhou Institute of Data Technology School of Medicine Tsinghua University School of Life Sciences Center for Synthetic and Systems Biology Tsinghua University

Cells are the basic structural and functional unit of the human body. Virtually all cells of a human body possess the same genome, but they exhibit colorful heterogeneities in phenotypes and *** heterogeneities includ...

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NFDI4Energy Task Area 4: FAIR data for Energy System Research

NFDI4Energy Task Area 4: FAIR Data for Energy System Researc...

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2023 Designing Futures: Zukunfte gestalten, INFORMATIK 2023 - 2023 Designing Futures: Shaping the Future, INFORMATIK 2023

作者： Wein, Amanda Reinkensmeier, Jan Weidlich, Anke Lilliestam, Johan Hagenmeyer, Veit Richter, Mascha Auer, Sören Nieße, Astrid Lehnhoff, Sebastian OFFIS E.V. RandD Division Energy Escherweg 2 Oldenburg26121 Germany Friedrichstr. 39 Freiburg79110 Germany Friedrich-Alexander-Universität Erlangen-Nörnberg Lehrstuhl for Sustainability Transition Policy Lange Gasse 20 Nörnberg90403 Germany Karlsruhe Institute of Technology Institute for Automation and Applied Informatics Kaiserstr. 89 Karlsruhe76131 Germany Reiner Lemoine Institut GGmbH Research Unit Transformation of Energy Systems Rudower Chaussee 12 Berlin12489 Germany Technische Informationsbibliothek Data Science and Digital Libraries Research Group Welfengarten 1 B Hannover30167 Germany Carl von Ossietzky Universität Oldenburg Department for Informatik Ammerländer Heerstr. 114-118 Oldenburg26129 Germany

ISBN: (纸本)9783885797319

The NFDI4Energy consortium will create a research data infrastructure for energy system research, emphasizing the openness and FAIRness of data and models in this research domain. Within the consortium, Task Area 4 focuses on the development of resources and services that will provide a semantic layer for the overall platform built by NFDI4Energy. The team of this Task Area will produce artifacts including a domain ontology, metadata standards, a knowledge graph, a Persistent Identifier service, and integration infrastructure to join these artifacts to the NFDI4Energy platform. © 2023 Gesellschaft fur Informatik (GI). All rights reserved.

关键词： Metadata

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Optimizing Carbon Emissions in Green Logistics for Time-Dependent Routing

SSRN

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SSRN 2024年

作者： Liu, Yiming Yu, Yang Roberto, Baldacci Tang, Jiafu Sun, Wei State Key Laboratory of Synthetic Automation for Process Industries Institute of Intelligent Data and Systems Engineering Northeastern University Shenyang110819 China Dalian University of Technology School of Economics and Management Liaoning Dalian116024 China Division of Engineering Management and Decision Sciences College of Science and Engineering Hamad Bin Khalifa University Qatar Foundation P.O. Box 34110 Doha Qatar College of Management Science and Engineering Dongbei University of Finance and Economics Shahekou Dalian116026 China Business School Liaoning University Shenyang110316 China

This paper considers a green vehicle routing problem termed the time-dependent green vehicle routing problem with time windows (TDGVRPTW). The TDGVRPTW is an extension of the green vehicle routing problem with time windows in green logistics. It considers time-dependent vehicle speed and aims to minimize carbon emissions. Since the travel times and carbon emissions between locations depend on the departure time from the starting location, optimizing carbon emissions requires determining the optimal departure times from both the depot and customers. This paper presents a branch-price-and-cut (BPC) algorithm to solve the TDGVRPTW. The problem is formulated based on a set-partitioning model. To solve the pricing problem associated with the set-partitioning model, we first define backward non-dominated time-dependent arcs and optimal timed routes. We also introduce three types of routes, forward, backward, and patchwork optimal timed routes, and analyze their characteristics. Then, we introduce a method to adjust the times in backward and patchwork optimal timed routes from the latest to the earliest. We prove that this method guarantees correctness and effectively reduces complexity. We propose a bidirectional labeling algorithm to generate routes. The pricing problem employs state-of-the-art techniques, including limited memory subset row cuts (lm-SRCs), ng-route relaxation, and bucket graphs to enhance the algorithm’s efficiency. The BPC algorithm is tested on a set of instances derived from benchmark instances in the literature. The results demonstrate the effectiveness of the proposed algorithm in solving the TDGVRPTW. © 2024, The Authors. All rights reserved.

关键词： Travel time

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uniLIVER: a human liver cell atlas for data-driven cellular state mapping

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Journal of Genetics and Genomics 2025年

作者： Wu, Yanhong Fan, Yuhan Miao, Yuxin Li, Yuman Du, Guifang Chen, Zeyu Diao, Jinmei Chen, Yu-Ann Ye, Mingli You, Renke Chen, Amin Chen, Yixin Li, Wenrui Guo, Wenbo Dong, Jiahong Zhang, Xuegong Wang, Yunfang Gu, Jin MOE Key Lab of Bioinformatics BNRIST Bioinformatics Division Department of Automation Tsinghua University Beijing 100084 China Hepato-Pancreato-Biliary Center Beijing Tsinghua Changgung Hospital Tsinghua University Beijing 102218 China Clinical Translational Science Center Beijing Tsinghua Changgung Hospital Tsinghua University Beijing 102218 China Fuzhou Institute of Data Technology Fujian Fuzhou 350207 China Center for Synthetic and Systems Biology School of Life Sciences and School of Medicine Tsinghua University Beijing 100084 China

The liver performs several vital functions such as metabolism, toxin removal, and glucose storage through the coordination of various cell types. With the recent breakthrough of the single-cell/single-nucleus RNA-seq (sc/snRNA-seq) techniques, there is a great opportunity to establish a reference cell map of the liver at single-cell resolution with transcriptome-wise features. In this study, we build a unified liver cell atlas uniLIVER (http://***/database/uniliver) by integrative analysis of a large-scale sc/snRNA-seq data collection of normal human liver with 331,125 cells and 79 samples from 6 datasets. Moreover, we introduce LiverCT, a novel machine learning based method for mapping any query dataset to the liver reference map by introducing the definition of “variant” cellular states analogy to the sequence variants in genomic analysis. Applying LiverCT on liver cancer datasets, we find that the “deviated” states of T cells are highly correlated with the stress pathway activities in hepatocellular carcinoma, and the enrichments of tumor cells with the hepatocyte-cholangiocyte “intermediate” states significantly indicate poor prognosis. Besides, we find that the tumor cells of different patients have different zonation tendencies and this zonation tendency is also significantly associated with the prognosis. This reference atlas mapping framework can also be extended to any other tissues. © 2025 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China

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Label Informed Contrastive Pretraining for Node Importance Estimation on Knowledge Graphs

arXiv

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arXiv 2024年

作者： Zhang, Tianyu Hou, Chengbin Jiang, Rui Zhang, Xuegong Zhou, Chenghu Tang, Ke Lv, Hairong The Ministry of Education Key Laboratory of Bioinformatics Bioinformatics Division Beijing National Research Center for Information Science and Technology Department of Automation Tsinghua University Beijing100084 China The School of Computer Science and Engineering Fuyao Institute of Technology Fuzhou350109 China The State Key Laboratory of Resources and Environmental Information Systems Institute of Geographic Sciences and Natural Resources Research Chinese Academy of Sciences Beijing100101 China The Department of Computer Science and Engineering Southern University of Science and Technology Shenzhen518055 China The Fuzhou Institute of Data Technology Fuzhou350200 China

Node Importance Estimation (NIE) is a task of inferring importance scores of the nodes in a graph. Due to the availability of richer data and knowledge, recent research interests of NIE have been dedicating to knowledge graphs for predicting future or missing node importance scores. Existing state-of-the-art NIE methods train the model by available labels, and they consider every interested node equally before training. However, the nodes with higher importance often require or receive more attention in real-world scenarios, e.g., people may care more about the movies or webpages with higher importance. To this end, we introduce Label Informed ContrAstive Pretraining (LICAP) to the NIE problem for being better aware of the nodes with high importance scores. Specifically, LICAP is a novel type of contrastive learning framework that aims to fully utilize the continuous labels to generate contrastive samples for pretraining embeddings. Considering the NIE problem, LICAP adopts a novel sampling strategy called top nodes preferred hierarchical sampling to first group all interested nodes into a top bin and a non-top bin based on node importance scores, and then divide the nodes within top bin into several finer bins also based on the scores. The contrastive samples are generated from those bins, and are then used to pretrain node embeddings of knowledge graphs via a newly proposed Predicate-aware Graph Attention Networks (PreGAT), so as to better separate the top nodes from non-top nodes, and distinguish the top nodes within top bin by keeping the relative order among finer bins. Extensive experiments demonstrate that the LICAP pretrained embeddings can further boost the performance of existing NIE methods and achieve the new state-of-the-art performance regarding both regression and ranking metrics. The source code for reproducibility is available at https://***/zhangtia16/LICAP Copyright © 2024, The Authors. All rights reserved.

关键词： Knowledge graph

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Biomedical data and AI

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Science China Life Sciences 2025年第5期68卷 1536-1540页

作者： Hao Xu Shibo Zhou Zefeng Zhu Vincenzo Vitelli Liangyi Chen Ziwei Dai Ning Yang Luhua Lai Shengyong Yang Sergey Ovchinnikov Zhuoran Qiao Sirui Liu Chen Song Jianfeng Pei Han Wen Jianfeng Feng Yaoyao Zhang Zhengwei Xie Yang-Yu Liu Zhiyuan Li Fulai Jin Hao Li Mohammad Lotfollahi Xuegong Zhang Ge Yang Shihua Zhang Ge Gao Pulin Li Qi Liu Jing-Dong Jackie Han Peking-Tsinghua Center for Life Sciences (CLS) Academy for Advanced Interdisciplinary StudiesPeking University Center for Quantitative Biology (CQB) Academy for Advanced Interdisciplinary StudiesPeking University Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program Academy for Advanced Interdisciplinary StudiesPeking University Department of Physics University of Chicago School of Life Sciences Southern University of Science and Technology Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies College of Chemistry and Molecular Engineering Peking University Department of Biotherapy Cancer Center and State Key Laboratory of BiotherapyWest China HospitalSichuan University Department of Biology Massachusetts Institute of Technology Lambic Therapeutics Inc. Changping Laboratory Al for Science Institute Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence Fudan University Department of Obstetrics and Gynecology West China Second University HospitalSichuan University Peking University International Cancer Institute and Peking University-Yunnan Baiyao International Medical Institute and State Key Laboratory of Natural and Biomimetic Drugs Department of Molecular and Cellular PharmacologySchool of Pharmaceutical SciencesPeking University Health Science CenterPeking University Channing Division of Network Medicine Department of MedicineBrigham and Women's Hospital and Harvard Medical School Center for Artificial Intelligence and Modeling the Carl R.Woese Institute for Genomic BiologyUniversity of Illinois Urbana-Champaign Department of Genetics and Genome Sciences School of Medicine and Department of Computer and Data Sciences and Department of Population and Quantitative Health SciencesCase Western Reserve University Department of Biochemistry and Biophysics University of California Sanger Institute Department of Automation Tsinghua University State Key Laboratory of Multimodal Artificial Intelligence Systems I

The development of artificial intelligence(AI) and the mining of biomedical data complement each other. From the direct use of computer vision results to analyze medical images for disease screening, to now integrating biological knowledge into models and even accelerating the development of new AI based on biological discoveries, the boundaries of both are constantly expanding, and their connections are becoming closer.

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NTIRE 2023 Challenge on Efficient Super-Resolution: Methods and Results

NTIRE 2023 Challenge on Efficient Super-Resolution: Methods ...

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2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition Workshops, CVPRW 2023

作者： Li, Yawei Zhang, Yulun Timofte, Radu Van Gool, Luc Yu, Lei Li, Youwei Li, Xinpeng Jiang, Ting Wu, Qi Han, Mingyan Lin, Wenjie Jiang, Chengzhi Luo, Jinting Fan, Haoqiang Liu, Shuaicheng Wang, Yucong Cai, Minjie Li, Mingxi Zhang, Yuhang Fan, Xian-Jun Sheng, Yankai Mao, Yanyu Zhang, Nihao Wang, Qian Zheng, Mingjun Sun, Long Pan, Jinshan Dong, Jiangxin Tang, Jinhui Yang, Zhongbao Wang, Yan Pan, Erlin Cai, Qixuan Dai, Xinan Zhussip, Magauiya Kalyazin, Nikolay Vyal, Dmitry Zou, Xueyi Yan, Youliang Chung, Heaseo Zhang, Jin Yu, Gaocheng Zhang, Feng Wang, Hongbin Liao, Bohao Du, Zhibo Wu, Yu-Liang Shi, Gege Peng, Long Wang, Yang Cao, Yang Zha, Zhengjun Huang, Zhi-Kai Chen, Yi-Chung Chiang, Yuan-Chun Yang, Hao-Hsiang Chen, Wei-Ting Chang, Hua-En Chen, I-Hsiang Hsieh, Chia-Hsuan Kuo, Sy-Yen Liu, Xin Pan, Jiahao Yu, Hongyuan Yu, Weichen Ge, Lin Dong, Jiahua Zou, Yajun Wu, Zhuoyuan Han, Binnan Zhang, Xiaolin Zhang, Heng Yin, Xuanwu Zuo, Kunlong Deng, Weijian Yuan, Hongjie Lu, Zengtong Ouyang, Mingyu Ma, Wenzhuo Liu, Nian Zheng, Hanyou Zhang, Yuantong Zhang, Junxi Chen, Zhenzhong Gendy, Garas Sabor, Nabil Hou, Jingchao He, Guanghui Zhu, Yurui Wang, Xi Fu, Xueyang Zha, Zheng-Jun Yin, Daheng Liu, Mengyang Chen, Baijun Li, Ao Luo, Lei Jin, Kangjun Zhu, Ce Zhang, Xiaoming Xie, Chengxing Li, Linze Meng, Haiteng Zhang, Tianlin Li, Tianrui Zhao, Xiaole Zhang, Zhao Li, Baiang Zheng, Huan Zhao, Suiyi Gao, Yangcheng Ren, Jiahuan Hu, Kang Shi, Jingpeng Wu, Zhijian Huang, Dingjiang Zhu, Jinchen Li, Hui Xv, Qianru Liu, Tianle Weng, Shizhuang Wu, Gang Jiang, Junpeng Liu, Xianming Jiang, Junjun Zhang, Mingjian Hu, Jing Wu, Chengxu Fan, Qinrui Feng, Chengming Luo, Ziwei Hu, Shu Lyu, Siwei Wu, Xi Wang, Xin Computer Vision Lab ETH Zurich Switzerland Computer Vision Lab University of Würzburg Germany Megvii Technology China MicroBT China College of Computer Science and Electronic Engineering Hunan University China Attrsense Xian University of Posts and Telecommunications Xi'an China National Engineering Laboratory for Cyber Event Warning and Control Technologies China Nanjing University of Science and Technology China Nankai University China University of Electronic Science and Technology of China China Tianjin University China Noah's Ark Lab Huawei Technologies McMaster University Canada Espresomedia Korea Republic of AntGroup China University of Science and Technology of China China Department of Electrical Engineering National Taiwan University Taiwan Graduate Institute of Communication Engineering National Taiwan University Taiwan Graduate Institute of Electronics Engineering National Taiwan University Taiwan ServiceNow United States China Mobile Research Institute China Chongqing University of Technology China Multimedia Department Xiaomi Inc. China Institute of Automation Chinese Academy of Sciences China Shenyang Institute of Automation Chinese Academy of Sciences China School of Information and Communication Engineering Communication University of China China Smart Classroom Division Ruijie Networks Co. Ltd. China School of Remote Sensing and Information Engineering Wuhan University China Micro-Nano Electronics Department Shanghai Jiao Tong University Shanghai200240 China Electrical Engineering Department Faculty of Engineering Assiut University Assiut71516 Egypt Southeast University China University of Electronic Science and Technology of China Chengdu China Chongqing University of Posts and Telecommunications Chongqing China Information Technology Co. Ltd Hangzhou China Southwest Jiaotong University China National Space Science Center Chinese Academy of Science China Hefei University of Technology Hefei China Anhui University China Fried Ric

ISBN: (纸本)9798350302493

This paper reviews the NTIRE 2023 challenge on efficient single-image super-resolution with a focus on the proposed solutions and results. The aim of this challenge is to devise a network that reduces one or several aspects such as runtime, parameters, FLOPs, activations, memory footprint, and depth of RFDN while at least maintaining the PSNR of 29.00dB on DIV2K validation datasets. The challenge had 272 registered participants, and 35 teams made valid submissions. They gauge the state-of-the-art for efficient single-image super-resolution. © 2023 IEEE.

关键词： Optical resolving power

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Blockchain-Based Incentive Announcement System for Internet of Vehicles

Blockchain-Based Incentive Announcement System for Internet ...

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IEEE International Conference on Big data and Cloud Computing (BdCloud)

作者： Yang Yang Jialiang Chen Xianghan Zheng Ximeng Liu Wenzhong Guo Hairong Lv College of Mathematics and Computer Science Fuzhou University Fuzhou China Guangxi Key Laboratory of Cryptography and Information Security Guangnxi China Guangdong Provincial Key Laboratory of Data Security and Privacy Protection Guangzhou China Fujian Provincial Key Laboratory of Information Processing and Intelligent Control (Minjiang University) Fuzhou China Ministry of Education Key Laboratory of Bioinformatics Bioinformatics Division and Center for Synthetic and Systems Biology Beijing National Research Center for Information Science and TechnologyDepartment of Automation Tsinghua University Beijing China

ISBN: (数字)9781728143286

ISBN: (纸本)9781728143293

With the rapid development of computation and communication technologies, the traditional vehicle ad hoc networks (VANETs) are changing to Internet of vehicle (IoV). Vehicular announcement networks in IoV have been widely used in the communication of vehicles. Generally, we need to solve two problems while establishing a vehicular announcement system. First, we need to protect user's privacy when broadcasting the message. Second, participants usually lack the enthusiasm to reply to the announcement. To solve these two problems, we propose a novel blockchain-based incentive announcement system that not only allows participants to anonymously announce their message on the blockchain in a non-trusted environment, but also motivates witnesses to respond to the request of the traffic information with incentive mechanism. Meanwhile, traffic messages and signatures in our system are tamper-resistant, which are recorded on the blockchain. According to the security and performance analysis, it shows that our system is privacy-preserving and efficient in computation cost.

关键词： Blockchain Privacy Smart contracts Authentication Internet Remuneration Hash functions

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Modeling the causal regulatory network by integrating chromatin accessibility and transcriptome data

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National Science Review 2016年第2期3卷 240-251页

作者： Yong Wang Rui Jiang Wing Hung Wong Department of Statistics Department of Biomedical Data ScienceBio-X ProgramStanford University Academy of Mathematics and Systems Science National Center for Mathematics and Interdisciplinary SciencesChinese Academy of Sciences MOE Key Laboratory of Bioinformatics Bioinformatics Division and Center for Synthetic and Systems BiologyTNLISTDepartment of AutomationTsinghua University

Cell packs a lot of genetic and regulatory information through a structure known as chromatin,*** is wrapped around histone proteins and is tightly packed in a remarkable *** express a gene in a specific coding region,the chromatin would open up and DNA loop may be formed by interacting enhancers and ***,the mediator and cohesion complexes,sequence-specific transcription factors,and RNA polymerase Ⅱ are recruited and work together to elaborately regulate the expression *** is in pressing need to understand how the information,about when,where,and to what degree genes should be expressed,is embedded into chromatin structure and gene regulatory *** to large consortia such as Encyclopedia of DNA Elements(ENCODE) and Roadmap Epigenomic projects,extensive data on chromatin accessibility and transcript abundance are available across many tissues and cell *** rich data offer an exciting opportunity to model the causal regulatory ***,we will review the current experimental approaches,foundational data,computational problems,interpretive frameworks,and integrative models that will enable the accurate interpretation of regulatory ***,we will discuss the efforts to organize,analyze,model,and integrate the DNA accessibility data,transcriptional data,and functional genomic regions *** believe that these efforts will eventually help us understand the information flow within the cell and will influence research directions across many fields.

关键词： gene regulatory network open chromatin DNA accessibility transcription factor colocalization statistical model data integration

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The Unique Challenges of Testing Specialized Network-Based data Acquisition systems

The Unique Challenges of Testing Specialized Network-Based D...

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International Automatic Testing Conference, AUTOTESTCON

作者： Stephen A. Kilpatrick Todd A. Newton Automation and Data Systems Division Southwest Research Institute® San Antonio TX USA

The increasing speeds and decreasing prices of network equipment have spurred much interest in applying networks to many different types of systems. A wide range of network protocols and tools already exist making its application attractive. Over the last decade, there has been a noticeable shift to introduce Internet Protocol (IP) networks into new areas such as data acquisition systems. These modern network-based test systems are composed of a large number of recognizable devices such as switches, routers, and recorders. While these networks contain components familiar to most, common enterprise network test tools are not always sufficient to test these specialized systems. Typically, these specialized network-centric data systems require tighter timing accuracies, shorter latency windows, and little to no acceptable packet loss. The unique features of IP networks present testing challenges that must be addressed to provide reliable verification of the data acquisition system. Packet latency, delay, jitter, and loss are all factors that must be accounted for. Intentionally introducing these types of impairments to the data system are essential in any full, end-toend system test. It is not only important to produce these types of errors, but to mimic the conditions that will exist in the real system and reliably reproduce them at any time. This paper describes the shortcomings of those common network tools for testing specialized network-based data acquisition systems and the custom workarounds that were necessary to provide the test capabilities that we required. We will share some of our lessons learned from real-life examples of testing specialized network equipment for a flight-test data acquisition system that would apply to any network-centric data system. The paper will also describe a portion of our lab setup that allows us to rapidly reconfigure test networks and deploy custom simulation tools to support multiple types of data acquisition systems simultane

关键词： Protocols data acquisition Software Generators IP networks System testing

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