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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

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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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Privacy-preserving medical treatment system through nondeterministic finite automata

arXiv

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arXiv 2020年

作者： Yang, Yang Deng, Robert H. Liu, Ximeng Wu, Yongdong Weng, Jian Zheng, Xianghan Rong, Chunming School of Information Systems Singapore Management University Singapore College of Mathematics and Computer Science Fuzhou University Fujian China State Key Laboratory of Integrated Services Networks Xidian University 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 School of Information Systems Singapore Management University Singapore Singapore Department of Computer Science Jinan University Guangdong China College of Mathematics and Computer Science Fuzhou University Fujian China Department of Electronic Engineering and Computer Science University of Stavanger Norway MingByte Technology Qingdao China

In this paper, we propose a privacy-preserving medical treatment system using nondeterministic finite automata (NFA), hereafter referred to as P-Med, designed for the remote medical environment. P-Med makes use of the nondeterministic transition characteristic of NFA to flexibly represent the medical model, which includes illness states, treatment methods and state transitions caused by exerting different treatment methods. A medical model is encrypted and outsourced to the cloud to deliver telemedicine services. Using P-Med, patient-centric diagnosis and treatment can be made on-the-fly while protecting the confidentiality of a patient's illness states and treatment recommendation results. Moreover, a new privacy-preserving NFA evaluation method is given in P-Med to get a confidential match result for the evaluation of an encrypted NFA and an encrypted data set, which avoids the cumbersome inner state transition determination. We demonstrate that P-Med realizes treatment procedure recommendation without privacy leakage to unauthorized parties. We conduct extensive experiments and analyses to evaluate efficiency. Copyright © 2020, The Authors. All rights reserved.

关键词： Diseases

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Continuous control set nonlinear model predictive control of reluctance synchronous machines

arXiv

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arXiv 2019年

作者： Zanelli, Andrea Kullick, Julian Eldeeb, Hisham Frison, Gianluca Hackl, Christoph Diehl, Moritz Systems Control and Optimization Laboratory Department of Microsystems Engineering University of Freiburg Freiburg Germany Research Group Control of Renewable Energy Systems Munich School of Engineering Technical University of Munich Munich Germany IAV GmbH Munich Germany Department of Electrical Engineering and Information Technology Munich University of Applied Sciences Munich Germany Systems Control and Optimization Laboratory Department of Microsystems Engineering Department of Mathematics University of Freiburg Freiburg Germany

In this paper we describe the design and implementation of a current controller for a reluctance synchronous machine based on continuous set nonlinear model predictive control. A simplified experimentally identified grey box model of the flux linkage map is employed in a tracking formulation which is implemented using the high-performance framework for nonlinear model predictive control acados. The resulting controller is validated in simulation and deployed on a dSPACE real-time system connected with a physical reluctance synchronous machine. Experimental results are presented where the proposed implementation can reach sampling times in the range typical for electrical drives and outperforms state-of-the-art classical control strategies. Copyright © 2019, The Authors. All rights reserved.

关键词： Nonlinear systems

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Systematic Resource Allocation in Cloud RAN with Caching as a Service under Two Timescales

Systematic Resource Allocation in Cloud RAN with Caching as ...

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作者： Tang, Jianhua Quek, Tony Q. S. Chang, Tsung-Hui Shim, Byonghyo Hunan Provincial Key Laboratory of Intelligent Computing and Language Information Processing College of Information Science and Engineering Hunan Normal University Changsha410081 China Institute of New Media and Communications Department of Electrical and Computer Engineering Seoul National University Seoul08826 Korea Republic of Information Systems Technology and Design Pillar Singapore University of Technology and Design Singapore487372 Singapore Department of Electronic Engineering Kyung Hee University Yongin17104 Korea Republic of School of Science and Engineering Chinese University of Hong Kong Shenzhen518172 China Shenzhen Research Institute of Big Data Shenzhen518172 China Department of Electrical and Computer Engineering Institute of New Media and Communications Seoul National University Seoul08826 Korea Republic of

Recently, cloud radio access network (C-RAN) with caching as a service (CaaS) was proposed to merge the functionalities of communication, computing, and caching (CCC) together. In this paper, we dissect the interactions of CCC in C-RAN with CaaS from two dimensions: physical resource dimension and time dimension. In the physical resource dimension, we identify how to segment the baseband unit (BBU) pool resources (i.e., computation and storage) into different types of virtual machines (VMs). In the time dimension, we address how the long-term resource segmentation in the BBU pool impacts on the short-term transmit beamforming at the remote radio heads. We formulate the problem as a stochastic mixed-integer nonlinear programming (SMINLP) to minimize the system cost, including the server cost, VM cost and wireless transmission cost. After a series of approximation, including sample average approximation, successive convex approximation, and semidefinite relaxation, the SMINLP is approximated as a global consensus problem. The alternating direction method of multipliers (ADMM) is utilized to obtain the solution in a parallel fashion. Simulation results verify the convergence of our proposed algorithm, and also confirm that the proposed scheme is more cost-saving than that without considering the integration of CCC. © 1972-2012 IEEE.

关键词： Integer programming

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Machine learning in the air

arXiv

引用

arXiv 2019年

作者： Gundüz, Deniz De Kerret, Paul Sidiropoulos, Nicholas D. Gesbert, David Murthy, Chandra Van Der Schaar, Mihaela Information Processing and Communications Laboratory Department of Electrical and Electronics Engineering Imperial College London London United Kingdom Communication Systems Department EURECOM Sophia Antipolis France Department of Electrical and Computer Engineering University of Virginia Charlottesville VA United States Department of Electrical and Computer Engineering Indian Institute of Science Bangalore India

Thanks to the recent advances in processing speed and data acquisition and storage, machine learning (ML) is penetrating every facet of our lives, and transforming research in many areas in a fundamental manner. Wireless communications is another success story - ubiquitous in our lives, from handheld devices to wearables, smart homes, and automobiles. While recent years have seen a flurry of research activity in exploiting ML tools for various wireless communication problems, the impact of these techniques in practical communication systems and standards is yet to be seen. In this paper, we review some of the major promises and challenges of ML in wireless communication systems, focusing mainly on the physical layer. We present some of the most striking recent accomplishments that ML techniques have achieved with respect to classical approaches, and point to promising research directions where ML is likely to make the biggest impact in the near future. We also highlight the complementary problem of designing physical layer techniques to enable distributed ML at the wireless network edge, which further emphasizes the need to understand and connect ML with fundamental concepts in wireless communications. Copyright © 2019, The Authors. All rights reserved.

关键词： Intelligent buildings

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Robust Semi-Global Leaderless Consensus and Containment control of Identical Linear systems with Imperfect Actuators

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Journal of systems Science & Complexity 2018年第1期31卷 69-86页

作者： SHI Liangren ZHAO Zhiyun LIN Zongli Department of Automation Shanghai Jiao Tong University and Key Laboratory of System Control and Information Processing of Ministry of Education Shanghai 200240 China Key Laboratory of Advanced Control and Optimization for Chemical Processes (East China University of Science and Technology) Ministry of Education Shanghai 200237 China Charles L. Brown Department of Electrical and Computer Engineering University of Virginia P.O. Box 400743 Charlottesville VA 22904-4743 USA

This paper investigates both the robust semi-global leaderless consensus problem and the robust semi-global containment control problem for a group of identical linear systems with imperfect actuators. The imperfect actuators are characterized by nonlinearities such as saturation and dead zone and there input output relationships are not precisely known. The dynamics of follower agents are also affected by the input additive disturbances. Low-and-high gain feedback consensus protocols are constructed to solve these problems. More specifically, it is shown that robust semi-global leaderless consensus can be achieved over a connected undirected graph and robust semi-global containment control can be achieved when each follower agent has access to the information of at least one leader agent. Numerical simulation illustrates the theoretical results.

关键词： Consensus containment control dead zone leaderless consensus multi-agent systems saturation

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Stochastic Link Flow Model for Signalized Traffic Networks with Uncertainty in Demand

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IFAC-PapersOnLine 2018年第9期51卷 458-463页

作者： Lin, S. Pan, T.L. Lam, W.H.K. Zhong, R.X. Schutter, B. De School of Computer and Control Engineering University of Chinese Academy of Sciences Key Laboratory of System Control and Information Processing Ministry of Education BeijingShanghai China Department of Civil and Structural Engineering The Hong Kong Polytechnic University Hong KongSAR Hong Kong School of Engineering Sun Yat-Sen University Guangzhou China Delft Center for Systems and Control Delft University of Technology Delft Netherlands

In order to investigate the stochastic features in urban traffic dynamics, we propose a Stochastic Link Flow Model (SLFM) for signalized traffic networks with demand uncertainties. In the proposed model, the link traffic state is described using four different link state modes, and the probability for each link state mode is determined based on the stochastic link states. The SLFM model is expressed as a finite mixture approximation of the link state probabilities and the dynamic link flow models for all the four link state modes. Using data from microscopic traffic simulator SUMO, we illustrate that the proposed model can provide a reliable estimation of the link traffic states, and as well as good estimations on the link state uncertainties propagating within a signalized traffic network. © 2018

关键词： Stochastic models Routers Stochastic systems Street traffic control Traffic signals Vehicle actuated signals Demand uncertainty Finite mixtures Stochastic features Stochastic traffic Traffic networks Traffic simulators Uncertainty in demand Urban traffic networks

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Analysis and experimental demonstration of orthant-symmetric four-dimensional 7 bit/4D-sym modulation for optical fiber communication

arXiv

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arXiv 2020年

作者： Chen, Bin Alvarado, Alex van der Heide, Sjoerd van den Hout, Menno Hafermann, Hartmut Okonkwo, Chigo The School of Computer Science and Information Engineering Hefei University of Technology Hefei China Eindhoven University of Technology Eindhoven5600 MB Netherlands The Information and Communication Theory Lab Signal Processing Systems Group Department of Electrical Engineering Eindhoven University of Technology Eindhoven5600 MB Netherlands The High Capacity Optical Transmission Laboratory Eindhoven University of Technology Eindhoven5600 MB Netherlands The Optical Communication Technology Lab Paris Research Center Huawei Technologies France SASU Boulogne-Billancourt92100 France

We propose a new four-dimensional orthant-symmetric 128-ary modulation format (4D-OS128) with a spectral efficiency of 7 bit/4D-sym. The proposed format fills the gap between polarization-multiplexed 8- and 16-ary quadrature-amplitude modulation (PM-8QAM and PM-16QAM). Numerical simulations show that 4D-OS128 outperforms two well-studied 4D geometrically-shaped modulation formats: 128SP-16QAM and 7b4D-2A8PSK by up to 0.65 dB for bit-interleaved coded modulation at the same spectral efficiency. These gains are experimentally demonstrated in a 11×233 Gbit/s wavelength division multiplexing (WDM) transmission system operating at 5.95 bit/4D-sym over 6000 km and 9000 km for both EDFA-only and hybrid amplification scenarios, respectively. A reach increase of 15% is achieved with respect to 128-ary set-partitioning 16QAM. Furthermore, the proposed 4D-OS128 is also compared to D4 lattice-based constellation, 16QAM and probabilistically-shaped 16QAM with finite blocklength via simulation. © 2020, CC BY.

关键词： Quadrature amplitude modulation

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Predicting Network controllability Robustness: A Convolutional Neural Network Approach

arXiv

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arXiv 2019年

作者： Lou, Yang He, Yaodong Wang, Lin Chen, Guanrong The Department of Electrical Engineering City University of Hong Kong Hong Kong The Department of Automation Shanghai Jiao Tong University Shanghai 200240 China The Key Laboratory of System Control and Information Processing Ministry of Education Shanghai 200240 China

Network controllability measures how well a networked system can be controlled to a target state, and its robustness reflects how well the system can maintain the controllability against malicious attacks by means of node-removals or edge-removals. The measure of network controllability is quantified by the number of external control inputs needed to recover or to retain the controllability after the occurrence of an unexpected attack. The measure of the network controllability robustness, on the other hand, is quantified by a sequence of values that record the remaining controllability of the network after a sequence of attacks. Traditionally, the controllability robustness is determined by attack simulations, which is computationally time consuming. In this paper, a method to predict the controllability robustness based on machine learning using a convolutional neural network is proposed, motivated by the observations that 1) there is no clear correlation between the topological features and the controllability robustness of a general network, 2) the adjacency matrix of a network can be regarded as a gray-scale image, and 3) the convolutional neural network technique has proved successful in image processing without human intervention. Under the new framework, a fairly large number of training data generated by simulations are used to train a convolutional neural network for predicting the controllability robustness according to the input network-adjacency matrices, without performing conventional attack simulations. Extensive experimental studies were carried out, which demonstrate that the proposed framework for predicting controllability robustness of different network configurations is accurate and reliable with very low overheads. © 2019, CC BY.

关键词： Complex networks

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Towards optimal robustness of network controllability: An empirical necessary condition

arXiv

引用

arXiv 2019年

作者： Lou, Yang Wang, Lin Tsang, Kim Fung Chen, Guanrong Department of Electrical Engineering City University of Hong Kong Hong Kong Department of Automation Shanghai Jiao Tong University Shanghai200240 China Key Laboratory of System Control and Information Processing Ministry of Education Shanghai200240 China

To better understand the correlation between network topological features and the robustness of network controllability in a general setting, this paper suggests a practical approach to searching for optimal network topologies with given numbers of nodes and edges. Since theoretical analysis is impossible at least in the present time, exhaustive search based on optimization techniques is employed, firstly for a group of small-sized networks that are realistically workable, where exhaustive means 1) all possible network structures with the given numbers of nodes and edges are computed and compared, and 2) all possible node-removal sequences are considered. An empirical necessary condition (ENC) is observed from the results of exhaustive search, which shrinks the search space to quickly find an optimal solution. ENC shows that the maximum and minimum in- and out-degrees of an optimal network structure should be almost identical, or within a very narrow range, i.e., the network should be extremely homogeneous. Edge rectification towards the satisfaction of the ENC is then designed and evaluated. Simulation results on large-sized synthetic and real-world networks verify the effectiveness of both the observed ENC and the edge rectification scheme. As more operations of edge rectification are performed, the network is getting closer to exactly satisfying the ENC, and consequently the robustness of the network controllability is enhanced towards optimum. Copyright © 2019, The Authors. All rights reserved.

关键词： controllability

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