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TransMut: a program to predict HLA-I peptide binding and optimize mutated peptides for vaccine design by the Transformer-derived self-attention model

Research Square

引用

Research Square 2021年

作者： Chu, Yanyi Zhang, Yan Wang, Qiankun Zhang, Lingfeng Wang, Xuhong Wang, Yanjing Wang, Jianmin Jiang, Xue Salahub, Dennis Russell Xiong, Yi Wei, Dong-Qing State Key Laboratory of Microbial Metabolism Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances Joint International Research Laboratory of Metabolic & Developmental Sciences School of Life Sciences and Biotechnology Shanghai Jiao Tong University Shanghai200030 China Department of Chemistry CMS - Centre for Molecular Simulation IQST - Institute for Quantum Science and Technology University of Calgary 2500 University Drive NW CalgaryABT2N 1N4 Canada Department of Clinical Oncology The University of Hong Kong-Shenzhen Hospital Shenzhen China School of Electrical Engineering and Computer Science University of Ottawa 75 Laurier Ave. OttawaONK1N 6N5 Canada The Ministry of Education Key Laboratory of System control and information processing Department of Automation School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai200030 China Integrative Biotechnology & Translational Medicine Yonsei University Incheon21983 Korea Republic of Peng Cheng Laboratory Vanke Cloud City Phase I Building 8 Xili Street Nanshan District Guangdong Shenzhen518055 China

Computational prediction of the interaction between human leukocyte antigen (HLA) and peptide (pHLA) can speed up epitope screening and vaccine design. Here, we develop the TransMut framework composed of TransPHLA for pHLA binding prediction and AOMP for mutated peptide optimization, which can be generalized to any binding and mutation task of biomolecules. Firstly, TransPHLA is developed by using a Transformer-derived self-attention model to predict pHLA binding, which is significantly superior to 11 previous methods on pHLA binding prediction, neoantigen and human papilloma virus vaccine identification. For vaccine design, the AOMP program is then developed to automatically optimize mutated peptides to search for mutant peptides with higher affinity to the target HLA and with high homology to the source peptide. Among 3660 non-binding pHLAs, 3630 were successfully mutated. Of these, 94% were verified by the IEDB recommended method, and 88% have homology higher than 80% to the source peptide. © 2021, CC BY.

关键词： Peptides

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Quantum hamiltonian identification with classical colored measurement noise

arXiv

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arXiv 2019年

作者： Tan, Lingyu Dong, Daoyi Li, Dewei Xue, Shibei Department of Automation Shanghai Jiao Tong University Key Laboratory of System Control and Information Processing Ministry of Education of China Shanghai200240 China School of Engineering and Information Technology University of New South Wales CanberraACT2600 Australia

In this paper, we present a Hamiltonian identification method for a closed quantum system whose time trace observables are measured with colored measurement noise. The dynamics of the quantum system are described by a Liouville equation which can be converted to a coherence vector representation. Since the measurement process is disturbed by classical colored noise, we introduce an augmented system model to describe the total dynamics, where the classical colored noise is parameterized. Based on the augmented system model as well as the measurement data, we can find a realization of the quantum system with unknown parameters by employing an Eigenstate Realization Algorithm. The unknown parameters can be identified using a transfer-function-based technique. An example of a two-qubit system with colored measurement noise is demonstrated to verify the effectiveness of our method. Copyright © 2019, The Authors. All rights reserved.

关键词： Quantum optics

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A study on rotate vector reducer performance degradation based on acoustic emission techniques

A study on rotate vector reducer performance degradation bas...

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2019 IEEE International Conference on Robotics and Biomimetics, ROBIO 2019

作者： An, Haibo Liang, Wei Ding, Xiaojian Zhang, Yinlong Tan, Jindong State Key Laboratory of Robotics Chinese Academy of Sciences Shenyang110016 China Key Laboratory of Networked Control Systems Shenyang Institute of Automation Chinese Academy of Sciences Shenyang110016 China Institutes for Robotics and Intelligent Manufacturing Chinese Academy of Sciences Shenyang110016 China University of Chinese Academy of Sciences Beijing100049 China Shenyang Institute of Automation Guangzhou Chinese Academy of Sciences Guangzhou511548 China Fifth Electronic Institute of MIIT Guangzhou510610 China Department of Mechanical Aerospace and Biomedical Engineering University of Tennessee KonxvilleTN37996 United States

ISBN: (纸本)9781728163215

This paper presents a performance degradation analysis for rotate vector (RV) reducer using acoustic emission (AE) techniques. Unlike the AE signals from fixed gear reducer that are steady and have unchanged route, the AE signals from RV reducer have variant propagation paths and strengths. This work investigates the kinematics model using AE techniques to solve the inherent issues of RV reducer performance degradation analysis, such as signal variabilities and inappropriate thresholds. Firstly, the propagation path of AE signals within the crankshaft is developed. Secondly, the attenuation trend of AE signals is exponentially formulated based on the corresponding propagation curve. The proposed method has been evaluated on the developed RV reducer platform. AE signals were collected under various working conditions, i.e., four abrasion states with eight types of loads and five rotation speeds. The experimental analysis on typical parameters (e.g., signal energies) proves the effectiveness and accuracy of the developed method based on AE techniques. © 2019 IEEE.

关键词： Crankshafts

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Observation of anti-Klein tunneling of chiral phonons

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Science Bulletin 2025年

作者： Li, Hongzhu Liu, Yang Ding, Qian Yang, Tianzhi Han, Chenglin He, Mengxin Jiang, Jian-Hua Li, Ying Department of Mechanics Tianjin University Tianjin 300072 China School of Physical Science and Technology & Collaborative Innovation Center of Suzhou Nano Science and Technology Soochow University Suzhou 215006 China School of Mechanical Engineering and Automation Northeastern University Shenyang 110819 China School of Biomedical Engineering Division of Life Sciences and Medicine University of Science and Technology of China Hefei 230026 China Suzhou Institute for Advanced Research University of Science and Technology of China Suzhou 215123 China School of Physical Sciences University of Science and Technology of China Hefei 230026 China State Key Laboratory of Extreme Photonics and Instrumentation Zhejiang Key Laboratory of Intelligent Electromagnetic Control and Advanced Electronic Zhejiang University Hangzhou 310027 China International Joint Innovation Center The Electromagnetics Academy at Zhejiang University Zhejiang University Haining 314400 China

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Challenges and solutions in automotive powertrain systems

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Journal of control and Decision 2018年第1期5卷 61-93页

作者： Tielong Shen Mingxin Kang Jinwu Gao Jiangyan Zhang Yuhu Wu Department of Engineering and Applied Sciences Sophia UniversityTokyoJapan State Key Laboratory of Synthetical Automation for Process Industries Northeastern UniversityShenyangP.R.China State Key Laboratory of Automobile Simulation and Control Jilin UniversityChangchunP.R.China College of Mechanical and Electronic Engineering Dalian Minzu UniversityDalianP.R.China School of Control Science and Engineering Dalian University of TechnologyDalianP.R.China

Automotive powertrain mainly consisting of combustion engine,motor and battery(*** for hybrid powertrain)is a very complicated integration system,and the research on the automotive powertrain control techniques remains hot-spot in past *** paper proposes some challenging issues and control solutions of automotive powertrain system from the perspective of the dynamic system *** typical characteristics of automotive powertrain system are analysed for control development,and the several control applications using model-based and model-free control design are demonstrated with sufficient experimental *** addition,some open issues for future powertrain control development are summarised.

关键词： Model-based control model-free control combustion engine automotive powertrain control technology

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Analysis of Indoor Exclusion Zone in Nuclear Power Plant Environments

Analysis of Indoor Exclusion Zone in Nuclear Power Plant Env...

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2018 IEEE International Workshop on Electromagnetics: Applications and Student Innovation Competition, iWEM 2018

作者： Park, Jong-Eon Youn, Sangwoon Choo, Hosung Choo, Jaeyul Metamaterial Electronic Device Research Center Hongik University Seoul Korea Republic of School of Electronic and Electrical Engineering Hongik University Seoul Korea Republic of Department of Instrumentation Control and Electrical System Korea Institute of Nuclear Safety Daejeon Korea Republic of

This article investigates the indoor exclusion zones (EZs) according to room dimensions and compares them with the free space EZs. Fluctuations in the received power level with respect to the distance for various path... 详细信息

ISBN: (纸本)9781538648346

关键词： Nuclear power plants

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Feedback control of a non-Markovian single qubit system 11

Feedback control of a non-Markovian single qubit system

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2017 11th Asian control Conference, ASCC 2017

作者： Xue, Shibei Nguyen, Thien Petersen, Ian R. Department of Automation Shanghai Jiao Tong University Key Laboratory of System Control and Information Processing Ministry of Education of China Shanghai200240 China Research School of Engineering Australian National University CanberraACT2600 Australia

ISBN: (纸本)9781509015733

In this paper, we utilize a feedback strategy to stabilize a single qubit in a non-Markovian environment with a Lorentzian spectrum. The non-Markovian single qubit is represented in an augmented system model, where an ancillary system is introduced as the internal mode of the environment to generate Lorentzian noise. The density matrix of the single qubit can be estimated by using an augmented-system-based quantum stochastic master equation. Then a feedback controller can be driven by the estimates to stabilize the qubit in a target state. Simulations show the feedback strategy can provide effective control of the non-Markovian single qubit. © 2017 IEEE.

关键词： Feedback control

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Mitigate the obstructing effect of vehicles on the propagation of VANETs safety-related information

Mitigate the obstructing effect of vehicles on the propagati...

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作者： Huang, Rui Wu, Jing Long, Chengnian Zhu, Yanmin Li, Bo Lin, Yi-Bing Department of Automation Shanghai Jiao Tong University Key Laboratory of System Control and Information Processing Ministry of Education of China Shanghai200240 China Department of Computer Science School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai200240 China Department of Computer Science and Engineering The Hong Kong University of Science and Technology Hong Kong China Department of Computer Science and Information Engineering National Chiao Tung University Taiwan

As physical obstacles, vehicles have significant impacts on the efficient propagations of safety-related information in vehicular ad hoc networks (VANETs) by frequently obstructing the LOS links between transmitters and receivers. Obstructing effect will diminish the effective coverage of safety-related information and incur severe impact on road safety. However, this impact has not been addressed effectively. In this paper, we first present the definition of broadcast efficiency as the metric for quantizing the obstructing effect. We investigate the optimization issue for mitigating the impact of obstructing effect on the propagation of safety-related information and propose a graph theory-based optimization algorithm. For a distributed implementation of this optimization in VANETs, we further propose the maximum broadcast efficiency relaying (MBER) algorithm. MBER maximizes the effective coverage of information, meanwhile, meets delay and reliability constraints by incorporating broadcast efficiency and propagation distance in relay contention. Simulation results demonstrate that MBER promotes the effective coverage of safety-related information in VANETs with varying vehicular distribution. © 1967-2012 IEEE.

关键词： Vehicular ad hoc networks

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Low Power CMOS Thermal and Tamper Sensor for Smart Cards Protection

Low Power CMOS Thermal and Tamper Sensor for Smart Cards Pro...

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International Conference on Electromagnetics in Advanced Applications (ICEAA)

作者： Luis Q Cartagena Silvio E Barbin Department of Electronic System Engineering and Telecommunications and Control Engineering Polytechnic School of the University of Sao Paulo Brazil

ISBN: (纸本)9781538667637

In this paper, we present a new design of a tamper resistance and a temperature sensor protection in Smart Cards to prevent both, physical and security attacks in the corners of their operating temperature range. Physical attacks are used for reverse engineering and temperature attacks normally result in malfunctions in the smart card processor, allowing the access to extra information. The purpose of this design is the protection of the chip of smart cards in a temperature range of -20 °C to 120 °C, and tamper resistance with a small area and low power consumption circuit. The sensor and tamper resistance were designed in Cadence using the system on a Chip (SoC) concept, employing a standard 90 nm CMOS technology that operates on a power supply voltage of 1.2 V. The obtained results show effective protection at the corners of the -40 °C to 140 °C temperature range and V dd = 1.2 V 10%. This new circuit design can effectively work as an excellent protector against security manipulation of Smart Cards.

关键词： Temperature sensors Resistance Temperature distribution Smart cards Integrated circuits Voltage control Temperature measurement

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Contraction analysis on primal-dual gradient optimization

arXiv

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arXiv 2019年

作者： Su, Yanxu Shi, Yang Sun, Changyin School of Automation Southeast University Nanjing210096 China Key Laboratory of Measurement and Control of Complex System of Engineering Ministry of Education Southeast University Nanjing210096 China Department of Mechanical Engineering University of Victoria VictoriaBCV8W 3P6 Canada

This paper analyzes the contraction of the primaldual gradient optimization via contraction theory in the context of discrete-time updating dynamics. The contraction theory based on Riemannian manifolds is first established for convergence analysis of a convex optimization algorithm. The equality and inequality constrained optimization cases are studied, respectively. Under some reasonable assumptions, we construct the Riemannian metric to characterize a contraction region. It is shown that if the step-sizes of the updating dynamics are properly designed, the convergence rates for both cases can be obtained according to the contraction region in which the convergence can be ***, the augmented Lagrangian function which is projection free is adopted to tackle the inequality constraints. Some numerical experiments are simulated to demonstrate the effectiveness of the presented contraction analysis results on primal-dual gradient optimization algorithm. Copyright © 2019, The Authors. All rights reserved.

关键词： Convex optimization

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