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Foundation models in molecular biology

Biophysics Reports 2024年第3期10卷 135-151页

作者： Yunda Si Jiawei Zou Yicheng Gao Guohui Chuai Qi Liu Luonan Chen Key Laboratory of Systems Health Science of Zhejiang Province School of Life Science Hangzhou Institute for Advanced Study University of Chinese Academy of Sciences Chinese Academy of Sciences Shanghai Institute of Biochemistry and Cell Biology Center for Excellence in Molecular Cell Science Chinese Academy of Sciences University of Chinese Academy of Sciences Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine Shanghai East Hospital Frontier Science Center for Stem Cell Research Bioinformatics Department School of Life Sciences and Technology Tongji University Shanghai Research Institute for Intelligent Autonomous Systems

Determining correlations between molecules at various levels is an important topic in molecular biology. Large language models have demonstrated a remarkable ability to capture correlations from large amounts of data in the field of natural language processing as well as image generation, and correlations captured from data using large language models can also be applicable to solving a wide range of specific tasks, hence large language models are also referred to as foundation models. The massive amount of data that exists in the field of molecular biology provides an excellent basis for the development of foundation models, and the recent emergence of foundation models in the field of molecular biology has really pushed the entire field forward. We summarize the foundation models developed based on RNA sequence data, DNA sequence data, protein sequence data, single-cell transcriptome data, and spatial transcriptome data respectively, and further discuss the research directions for the development of foundation models in molecular biology.

关键词： Transcriptome Molecular biology Foundation models

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Variant selection map of external load during Ni_(4)Ti_(3) precipitation in nitinol:a theoretical and phase field study

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Acta Mechanica Sinica 2024年第7期40卷 19-28页

作者： Xuewei Zhou Tianlong Zhang Li Cheng Xusheng Yang Jiaming Zhu School of Civil Engineering Shandong UniversityJinan 250061China Department of Mechanical Engineering Hong Kong University of Science and TechnologyHong KongChina State Key Laboratory of Ultra-precision Machining Technology Department of Industrial and Systems EngineeringThe Hong Kong Polytechnic UniversityHong KongChina Shenzhen Research Institute of Shandong University Shenzhen 518057China Institute of Materials Intelligent Technology Shenyang 110004China

The morphology of Ni_(4)Ti_(3) precipitates is important in tuning the martensitic transformation(MT)behavior and mechanical properties of *** ageing is effective in engineering the morphology of Ni_(4)Ti_(3) precipitates due to the variant selection effect of external load which is still *** this work,maps of variant selection effect of external load applied along all crystallographic directions are obtained by using a combination of theoretical analyses and phase field *** is found that maps produced by uniaxial tension and uniaxial compression are quite *** number and types of Ni_(4)Ti_(3) variants preferred by external load vary as the loading direction ***,factors influencing the strength of variant selection effect are *** work provides insights on understanding the Ni_(4)Ti_(3) precipitation process and sheds light on the engineering of morphology of Ni_(4)Ti_(3) precipitates for desired mechanical and functional properties.

关键词： Ni_(4)Ti_(3) Variant selection NiTi alloy Phase field model Precipitation morphology

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Multi-agent Deep Reinforcement Learning Based Multi-objective Charging Control for Electric Vehicle Charging Station 7th

Multi-agent Deep Reinforcement Learning Based Multi-objectiv...

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7th Chinese Conference on Swarm Intelligence and Cooperative Control, CCSICC 2023

作者： Gong, Jiabao Fu, Weiming Kang, Yu Qin, Jiahu Xiao, Feng Department of Automation University of Science and Technology of China Hefei230027 China State Key Laboratory of Alternate Electrical Power System with Renewable Energy Sources School of Control and Computer Engineering North China Electric Power University Beijing102206 China

ISBN: (纸本)9789819733279

This paper proposes a multi-agent deep reinforcement learning (MADRL) based algorithm for charging control of multiple electric vehicles (EVs) in an electric vehicle charging station (EVCS) with dynamic operations. By taking the uncertainties of EV users’ behaviors and charging prices into consideration, a Markov game with multiple objectives is first established, where the individual objective of reducing EV charging costs and the collective objective of mitigating charging load fluctuations are both studied. Then, a multi-agent actor-double-critic (MAADC) algorithm with a unified advantage actor-critic framework is proposed, where two advantage functions are designed as the local and global critics, and the integrated actor is employed to balance the learning towards the individual and collective objectives. The simulation results obtained in a delicately built EVCS environment show the effectiveness of MAADC. © The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2024.

关键词： Reinforcement learning

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Regional Scanning Strategy of UAV Cluster Platform for Mobile Emergency Broadcasting

Regional Scanning Strategy of UAV Cluster Platform for Mobil...

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2023 IEEE International Symposium on Broadband Multimedia systems and Broadcasting, BMSB 2023

作者： Guo, Lingfeng Xiong, Jian Zhou, Jun Liu, Bo Shanghai Jiao Tong University Department of Electronic Engineering Shanghai China Beijing University of Posts and Telecommunications State Key Laboratory of Networking and Switching Technology China University of Technology Sydney School of Computer Science UltimoNSW Australia

ISBN: (纸本)9798350321524

With the development of release and retrieval technology for unmanned air vehicles (UAVs), the aerial cluster platform composed of carrier aircraft and multiple rotor UAVs can be used as a new approach for mobile emergency broadcasting operations. It indicates that we can resolve the paradoxical relationship between limited endurance of UAVs and large scale mission area. This paper proposes a region scanning strategy based on the aerial UAV cluster platform. The system can achieve all-region broadcasting in disaster ares, as well as audio and video collection for disaster assessment and emergency rescue. © 2023 IEEE.

关键词： Broadcasting

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Bi-level Optimal Planning of Voltage Regulator in Distribution systems Considering Maximization of Incentive-based Photovoltaic Energy Integration

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CSEE Journal of Power and Energy systems 2023年第6期9卷 2008-2017页

作者： Xu Xu Youwei Jia Chun Sing Lai Minghao Wang Zhao Xu Department of Electrical and Electronic Engineering Southern University of Science and TechnologyShenzhenChina Department of Electrical Engineering The Hong Kong Polytechnic UniversityHung HomHong Kong SARChina Department of Electrical and Electronic Engineering University Key Laboratory of Advanced Wireless Communications of Guangdong ProvinceSouthern University of Science and TechnologyShenzhen 515100China Department of Electronic and Computer Engineering Brunel Institute of Power SystemsBrunel University LondonLondonUB83PH United Kingdom Department of Electrical Engineering Shenzhen Research InstituteThe Hong Kong Polytechnic UniversityHung HomHong Kong SARChina

This paper focuses on optimal voltage regulator(VR)planning to maximize the photovoltaic(PV)energy integration in distribution *** describe the amount of dynamic PV energy that can be integrated into the power system,the concept of PV accommodation capability(PVAC)is introduced and modeled with *** proposed planning model is formulated as a Benders decomposition based bi-level stochastic optimization *** the upper-level problem,VR planning decisions and PVAC are determined via mixed integer linear programming(MILP)before considering *** in the lower-level problem,the feasibility of first-level results is checked by critical network constraints(*** magnitude constraints and line capacity constraints)under uncertainties considered by time-varying loads and PV *** this paper,these uncertainties are represented in the form of operational scenarios,which are generated by the Gaussian copula theory and reduced by a well-studied backward-reduction *** modified IEEE 33-node distribution grid is utilized to verify the effectiveness of the proposed *** results demonstrate that a PV energy integration can be significantly enhanced after optimal voltage regulator planning.

关键词： Bi-level stochastic optimization problem critical network constraints photovoltaic energy integration uncertainties voltage regulator planning

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A Dynamics-Constrained Rapid Path-Planning Method for Shipping in Arctic Waters 34th

A Dynamics-Constrained Rapid Path-Planning Method for Shippi...

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34th International Ocean and Polar Engineering Conference, ISOPE 2024

作者： Sun, Youguo Wu, Da Zhang, Jinfen Lang, Xiao Ringsberg, Jonas W. Mao, Wengang Cui, Meng State Key Laboratory of Maritime Technology and Safety Wuhan University of Technology Wuhan China National Engineering Research Center for Water Transport Safety Wuhan University of Technology Wuhan China Intelligent Transportation Systems Research Center Wuhan University of Technology Wuhan China Department of Mechanics and Maritime Sciences Chalmers University of Technology Gothenburg Sweden Marine Design and Research Institute of China Shanghai China

ISBN: (纸本)9781880653784

The challenge of Arctic sea ice environments is crucial for Arctic shipping. To address this concern, we propose an innovative method for ship path planning to enhance navigation safety and efficiency in Arctic waters. Firstly, a 3D risk grid map for path planning is developed based on POLARIS. The JPS algorithm searchesfor key nodes on the 2D layers sliced from the 3D risk grid map with given risk values. Secondly, key nodes indicating different risk values are pruned to form a roadmap for path-finding. Then, the Dijkstra algorithm is employed to find the reference path yielding the lowest navigation risk from the roadmap. Finally, the ship's trajectory is optimized through optimal control to guarantee the ship's maneuver feasibility. Experiments are carried out to demonstrate the performance of the optimized trajectory, and the outcomes validate the proposed method, demonstrating its capability of rapidly planning safe and executable paths for Arctic shipping. © 2024 by the International Society of Offshore and Polar Engineers (ISOPE).

关键词： Motion planning

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A Formal Specification Approach to Specify Pet's House System Using Z - Notations

A Formal Specification Approach to Specify Pet's House Syste...

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16th IEEE International Conference on Advanced Infocomm technology, ICAIT 2024

作者： Khalid, Nibtal Ahmed, Irfan Mahmood, Jabar Ali, Qasim Abid, Saman Batool, Khadija University of Sialkot Department of Computer Science Sialkot Pakistan School of Cyber Science and Technology College of Computer Science and Technology Zhejiang University State Key Laboratory of Blockchain Hangzhou China

ISBN: (纸本)9798350391497

The formal method (FM) is an innovative method that employs mathematical notations to describe explicit and precise requirements. This makes it possible to find errors and conflicts early in the software development process. To improve quality, the Z concept can assist with system specifications, design, and testing. A formal Specifications of a pet system is presented in this paper using the Z specification language. The complicated pet system is in charge of maintaining information about pets, owners, and numerous components of their care. We demonstrate how the requirements of the pet system, including its functionality, data structures, and behavior, can be specified using Z. In this specification, we aim to highlight the benefits of using formal methods to ensure the accuracy and reliability of complex systems and to show how valuable they are in system design and development. Formal approaches are advantageous not just for mission-critical systems, but also in commercial and business-oriented applications, since they could significantly decrease development time, verification, and maintenance costs. These results will serve as motivation for formal approaches. © 2024 IEEE.

关键词： Formal specification

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A Formal Specification Approach to Specify Pet's House System Using Z - Notations

A Formal Specification Approach to Specify Pet's House Syste...

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International Conference on Advanced Infocomm technology (ICAIT)

作者： Nibtal Khalid Irfan Ahmed Jabar Mahmood Qasim Ali Saman Abid Khadija Batool Department of Computer Science University of Sialkot Sialkot Pakistan State Key Laboratory of Blockchain School of Cyber Science and Technology College of Computer Science and Technology Zhejiang University Hangzhou China

ISBN: (数字)9798350391497

ISBN: (纸本)9798350391503

关键词： Frequency modulation Costs System performance computer bugs Software Maintenance Specification languages Formal specifications Testing Software development management

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On-chip topological nanophotonic devices

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Chip 2022年第4期1卷 1-21页

作者： Cui-Cui Lu Hong-Yi Yuan Hong-Yu Zhang Wen Zhao Nian-En Zhang Yan-Ji Zheng Sayed Elshahat Yong-Chun Liu Key Laboratory of Advanced Optoelectronic Quantum Architecture and Mea-surements of Ministry of Education Beijing Key Laboratory of Nanophotonics and Ultrafine Optoelectronic SystemsSchool of PhysicsBeijing Institute of TechnologyBeijing 100081China State Key Laboratory of Low-Dimensional Quantum Physics Department of PhysicsFrontier Science Center for Quantum InformationTsinghua UniversityBeijing 100084China

On-chip topological nanophotonic devices,which take photons as in-formation carriers with topological protection during light propaga-tion,have great application potential in the next generation photonic *** topological photonic states enable the nanophotonic de-vices to be robust and stable,immune to scattering even with imper-fect *** development,opportunities and challenges of the on-chip topological nanophotonic devices have attracted great atten-tion of scholars,and desired to be *** this review,topologi-cal devices were introduced in the order of functionalities on an in-tegrated photonic chip,*** light source,topological light waveguiding,topological light division and selection,topological light manipulation and topological light ***,we gave out-looks for predicting and promoting the performances of on-chip topo-logical nanophotonic devices from the angles of non-Hermitian sys-tems,non-Abelian topology,metasurfaces,intelligent algorithms and multiple functional topological nanophotonic *** review provides rich knowledge about on-chip topological nanophotonic *** insights in this paper will spark inspiration and inspire new thinking for the realization of topological photonic chips.

关键词： Topological photonics Nanophotonic devices Photonic chip

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A Synchronous Parallel Method with Parameters Communication Prediction for Distributed Machine Learning 19th

A Synchronous Parallel Method with Parameters Communication...

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19th EAI International Conference on Collaborative Computing: Networking, Applications and Worksharing, CollaborateCom 2023

作者： Zeng, Yanguo Xue, Meiting Xu, Peiran Shi, Yukun Zeng, Kaisheng Zhang, Jilin Yue, Lupeng School of Computer Science and Technology Hangzhou Dianzi University Hangzhou310018 China Key Laboratory for Modeling and Simulation of Complex Systems Ministry of Education Hangzhou310018 China Data Security Governance Zhejiang Engineering Research Center Hangzhou310018 China National University of Defense Technology Changsha China School of Cyberspace HangZhou Dianzi University Hangzhou China Department of Computer Science and Technology Tsinghua University Beijing China

ISBN: (纸本)9783031545306

With the development of machine learning technology in various fields, such as medical care, smart manufacturing, etc., the data has exploded. It is a challenge to train a deep learning model for different application domains with large-scale data and limited resources of a single device. The distributed machine-learning technology, which uses a parameter server and multiple clients to train a model collaboratively, is an excellent method to solve this problem. However, it needs much communication between different devices with limited communication resources. The stale synchronous parallel method is a mainstream communication method to solve this problem, but it always leads to high synchronization delay and low computing efficiency as the inappropriate delay threshold value set by the user based on experience. This paper proposes a synchronous parallel method with parameters communication prediction for distributed machine learning. It predicts the optimal timing for synchronization, which can solve the problem of long synchronization waiting time caused by the inappropriate threshold settings in the stale synchronous parallel method. Moreover, it allows fast nodes to continue local training while performing global synchronization, which can improve the resource utilization of work nodes. Experimental results show that compared with the delayed synchronous parallel method, the training time and quality, and resource usage of our method are both significantly improved. © ICST Institute for computer sciences, Social Informatics and Telecommunications Engineering 2024.

关键词： Forecasting

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