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Identification and Prediction of key Nucleotide Sites Using Machine Learning in Bioinformatics: A Brief Overview

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Identification and Prediction of Key Nucleotide Sites Using ...

IEEE International Conference on Big Data and Cloud computing (BdCloud)

作者： Jianhua Cai Leyi Wei Kun Zeng Guobao Xiao Fujian Provincial Key Laboratory of Information Processing and Intelligent Control Minjiang University Fuzhou P.R. China College of Mathematics and Computer Science Fuzhou University Fuzhou P.R. China College of Intelligence and Computing Tianjin University Tianjin P.R. China

ISBN: (数字)9781728143286

ISBN: (纸本)9781728143293

Nowadays, the burgeon of machine learning has promoted its wide application in various fields. In Bioinformatics, machine learning computational method has become an indispensable part. Its efficiency and simplicity break the expensive and inefficient barriers of previous experimental methods. This article briefly reviews the application and development of machine learning in identifying and predicting key nucleotide sites (such as 6mA, 5mC, 4mC, etc.) in DNA or RNA. Among them, supervised learning is one of the main methods to this work. Its wide application has provided great convenience for the development of identification and prediction of key nucleotides in Bioinformatics.

关键词： Bioinformatics Feature extraction Machine learning Predictive models Computational modeling DNA Prediction algorithms

AIROGS: ARTIFICIAL intelligence FOR ROBUST GLAUCOMA SCREENING CHALLENGE

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arXiv 2023年

作者： De Vente, Coen Vermeer, Koenraad A. Jaccard, Nicolas Wang, He Sun, Hongyi Khader, Firas Truhn, Daniel Aimyshev, Temirgali Zhanibekuly, Yerkebulan Le, Tien-Dung Galdran, Adrian Ballester, Miguel Ángel González Carneiro, Gustavo Devika, R.G. Hrishikesh, P.S. Puthussery, Densen Liu, Hong Yang, Zekang Kondo, Satoshi Kasai, Satoshi Wang, Edward Durvasula, Ashritha Heras, Jónathan Zapata, Miguel Ángel Araújo, Teresa Aresta, Guilherme Bogunović, Hrvoje Arikan, Mustafa Lee, Yeong Chan Cho, Hyun Bin Choi, Yoon Ho Qayyum, Abdul Razzak, Imran Van Ginneken, Bram Lemij, Hans G. Sánchez, Clara I. Group Informatics Institute Universiteit Van Amsterdam Noord-Holland Amsterdam Netherlands The Department of Biomedical Engineering and Physics Amsterdam Umc Locatie Amc Noord-Holland Amsterdam Netherlands Department of Radiology and Nuclear Medicine Radboudumc Gelderland Nijmegen Netherlands The Rotterdam Ophthalmic Institute Rotterdam Eye Hospital Rotterdam Netherlands Project Orbis International Inc. New York United States The Peking Union Medical College Hospital Beijing China The Xuanwu Hospital Capital Medical University Beijing100053 China The Tsinghua University Beijing China The Department of Diagnostic and Interventional Radiology University Hospital Aachen Aachen Germany Cmc Technologies Llp Nur-Sultan Kazakhstan Kbc Belgium Universitat Pompeu Fabra Barcelona Spain The Australian Institute for Machine Learning Aiml University of Adelaide Australia Icrea Barcelona Spain The Centre for Vision Speech and Signal Processing University of Surrey United Kingdom The College of Engineering Trivandrum India Founding Minds Software India The Institute of Computing Technology Chinese Academy of Sciences China The Muroran Institute of Technology Japan The Niigata University of Health and Welfare Japan The Schulich School of Medicine and Dentistry University of Western Ontario London Canada The Department of Mathematics and Computer Science University of la Rioja Spain Hospital Vall Hebron Passeig Roser 126 Sant Cugat del Vallès Barcelona08195 Spain UPRetina Barcelona Spain The Christian Doppler Laboratory for Artificial Intelligence in Retina Department of Ophthalmology and Optometry Medical University of Vienna Vienna Austria The Institute of Ophthalmology University College London London United Kingdom The Research Institute for Future Medicine Samsung Medical Center Seoul Korea Republic of Sungkyunkwan University Samsung Medical Center Seoul Korea Republic of The Department of Artificial Intelligence and Informatics Mayo Clinic Jacks

The early detection of glaucoma is essential in preventing visual impairment. Artificial intelligence (AI) can be used to analyze color fundus photographs (CFPs) in a cost-effective manner, making glaucoma screening more accessible. While AI models for glaucoma screening from CFPs have shown promising results in laboratory settings, their performance decreases significantly in realworld scenarios due to the presence of out-of-distribution and low-quality images. To address this issue, we propose the Artificial intelligence for Robust Glaucoma Screening (AIROGS) challenge. This challenge includes a large dataset of around 113,000 images from about 60,000 patients and 500 different screening centers, and encourages the development of algorithms that are robust to ungradable and unexpected input data. We evaluated solutions from 14 teams in this paper, and found that the best teams performed similarly to a set of 20 expert ophthalmologists and optometrists. The highest-scoring team achieved an area under the receiver operating characteristic curve of 0.99 (95% CI: 0.98-0.99) for detecting ungradable images on-the-fly. Additionally, many of the algorithms showed robust performance when tested on three other publicly available datasets. These results demonstrate the feasibility of robust AI-enabled glaucoma screening. Copyright © 2023, The Authors. All rights reserved.

关键词： Diagnosis

Recent Developments in Service Function Chaining (SFC) and Network Slicing in Backhaul and Metro Networks in Support of 5G

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Recent Developments in Service Function Chaining (SFC) and N...

International Conference on Transparent Optical Networks

作者： Adrian Farrel Key Laboratory of Intelligent Computing and Signal Processing Ministry of Education School of Electrical Engineering and Automation Anhui University Hefei China

In this invited paper we examine the role of Service Function Chaining (SFC) and Network Slicing in providing support for emerging 5G services as data is carried across backhaul and metro networks. The way in which backhaul and metro networks are managed and operated affects the ability of those networks to support a wide range of services that will be enabled by 5G connectivity. Those services will place exacting demands on the bandwidth, delay bounds, and jitter delivered to users, but may vary significantly over relatively short time periods. SFC and Network Slicing offer opportunities for software-driven coordination of network resources to marshal them so as to best deliver the network behaviour that will support the demands of the services. We present the latest proposals towards standardisation of SFC and Network Slicing in the Internet Engineering Task Force (IETF) and discuss how these concepts are applied in optical networks through the Metro-Haul project.

关键词： 5G mobile communication Network slicing Multiprotocol label switching Integrated optics Routing Optical fiber networks Network function virtualization

Analysis of mutual inductance between non-coaxial rectangular coils with rectangular cross-section

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Analysis of mutual inductance between non-coaxial rectangula...

2017 International Applied Computational Electromagnetics Society Symposium in China, ACES-China 2017

作者： Pan, Wenlong Song, Kaihong Key Laboratory of Intelligent Computing and Signal Processing Ministry of Education Anhui University China

ISBN: (纸本)9780996007856

Magnetic coupling resonance wireless power transmission is a new technology to realize the wireless transmission of energy by means of high frequency coupling resonance between the coils. The variation of the coupling coil size and the relative position will change the mutual inductance between the windings, which will finally affect the characteristics of the infinite power transmission system. Using rectangular coil with rectangular cross-section as the analysis object, to research the calculation method of mutual inductance between non-coaxial rectangular coils, by subdividing and summation method to deduce the theory formula of the mutual inductance, to support wireless power transmission which consists of rectangular coils. In all cases, the formula programming calculation, the FEM software simulation and the experimental measurement results are consistent, which proves the correctness of the calculation method. © 2017 Applied Computational Electromagnetics Society.

关键词： Computer software

Controlling The Uncertain Time-Delayed Lipschitz Nonlinear System: The Finite-time Non-fragile Design Approach

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Controlling The Uncertain Time-Delayed Lipschitz Nonlinear S...

第30届中国控制与决策会议

作者： Longfang Li Qilong Ai Shuping He School of Electrical Engineering and Automation Anhui University Key Laboratory of Intelligent Computing & Signal Processing Ministry of Education Anhui University

The finite-time non-fragile H controller design problem of a class of Lipschitz nonlinear systems with uncertainties and time-delays is studied. The objective is to design a suitable non-fragile controller which makes the Lipschitz nonlinear system be finite-time bounded and satisfies the given H performance index. By choosing a proper Lyapunov function and using linear matrix inequalities, a sufficient condition for the existence of finite-time non-fragile H controller is given and proved. Then, the designed method is described as an optimization one. Finally, the effectiveness and feasibility of the proposed design method is illustrated by the simulation result.

关键词： finite-time bounded Lipschitz nonlinear systems uncertain non-fragile H∞ controller

A New User Grouping and Power Allocation Scheme for Downlink Non-orthogonal Multiple Access Systems

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Journal of Physics: Conference Series 2019年第1期1284卷

作者： Yin Wang Xiaohui Li Wenwu Wang Gongquan Zhang Hongwei Zhang Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education Anhui University Hefei 230039 China

In this paper, we propose a new user grouping and power allocation scheme based on beamforming for downlink non-orthogonal multiple access systems. The proposed user grouping scheme can effectively reduce the interference from the other user and other beams as well, and can effectively improve the weak user rate especially when the SNR is not large. In addition, a power allocation scheme that can maximize the sum capacity while satisfying a certain fairness index is proposed. From the simulation results, the user grouping and power allocation method proposed in this paper can not only improve the overall system throughput performance, but also improve the fairness of weak users.

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Nonlinearity in the dark: Broadband terahertz generation with extremely high efficiency

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arXiv 2019年

作者： Fang, Ming Shen, Nian-Hai Sha, Wei E.I. Huang, Zhixiang Koschny, Thomas Soukoulis, Costas M. Ames Laboratory U.S. DOE and Department of Physics and Astronomy Iowa State University AmesIA50011 United States Key Laboratory of Intelligent Computing and Signal Processing Ministry of Education Anhui University Hefei230039 China Key Laboratory of Micro-nano Electronic Devices and Smart Systems of Zhejiang Province College of Information Science and Electronic Engineering Zhejiang University Hangzhou310027 China FORTH Heraklion Crete71110 Greece

Plasmonic metamaterials and metasurfaces offer new opportunities in developing high performance terahertz emitters/detectors beyond the limitations of conventional nonlinear materials. However, simple meta-atoms for second-order nonlinear applications encounter fundamental trade-offs in the necessary symmetry-breaking and local-field enhancement due to radiation damping that is inherent to the operating resonant mode and cannot be controlled separately. Here we present a novel concept that eliminates this restriction obstructing the improvement of terahertz generation efficiency in nonlinear metasurfaces based on metallic nano-resonators. This is achieved by combing a resonant dark-state metasurface, which locally drives nonlinear SRRs in the near field, with a specific spatial symmetry that enables destructive interference of the radiating linear moments of the SRRs, and perfect absorption via simultaneous electric and magnetic critical coupling of the pump radiation to the dark mode. Our proposal allows eliminating linear radiation damping, while maintaining constructive interference and effective radiation of the nonlinear components. We numerically demonstrate a giant second-order nonlinear susceptibility ∼ 10−11 m/V, one order improvement compared to previously reported split-ring-resonator metasurface, and correspondingly, two orders of magnitude enhanced terahertz energy extraction should be expected with our configuration under the same conditions. Our study offers a paradigm of high efficiency tunable nonlinear meta-devices and paves the way to revolutionary terahertz technologies and optoelectronic nanocircuitry. Copyright © 2019, The Authors. All rights reserved.

关键词： Terahertz waves

Towards real-time eyeblink detection in the wild: Dataset, theory and practices

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arXiv 2019年

作者： Hu, Guilei Xiao, Yang Cao, Zhiguo Meng, Lubin Fang, Zhiwen Zhou, Joey Tianyi Yuan, Junsong National Key Laboratory of Science and Technology on Multi-Spectral Information Processing School of Artificial Intelligence and Automation Huazhong University of Science and Technology China Guangdong Provincial Key Laboratory of Medical Image Processing School of Biomedical Engineering Southern Medical University China School of Energy and Mechanicalelectronic Engineering Hunan University of Humanities Science and Technology China Institute of High Performance Computing A∗STAR Singapore Computer Science and Engineering Department of University at Buffalo State University of New York United States

Effective and real-time eyeblink detection is of widerange applications, such as deception detection, drive fatigue detection, face anti-spoofing. Despite previous efforts, most of existing focus on addressing the eyeblink detection problem under constrained indoor conditions with relative consistent subject and environment setup. Nevertheless, towards practical applications, eyeblink detection in the wild is highly preferred, and of greater challenges. In this paper, we shed the light to this research topic. A labelled eyeblink in the wild dataset (i.e., HUST-LEBW) of 673 eyeblink video samples (i.e., 381 positives, and 292 negatives) is first established. These samples are captured from the unconstrained movies, with the dramatic variation on face attribute, head pose, illumination condition, imaging configuration, etc. Then, we formulate eyeblink detection task as a binary spatial-temporal pattern recognition problem. After locating and tracking human eyes using SeetaFace engine and KCF (Kernelized Correlation Filters) tracker respectively, a modified LSTM model able to capture the multi-scale temporal information is proposed to verify eyeblink. A feature extraction approach that reveals the appearance and motion characteristics simultaneously is also proposed. The experiments on HUSTLEBW reveal the superiority and efficiency of our approach. The comparisons with the existing state-of-the-art methods validate the advantages of our manner for eyeblink detection in the wild. Copyright © 2019, The Authors. All rights reserved.

关键词： Long short-term memory

Segmented successive cancellation list polar decoding with tailored CRC

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arXiv 2018年

作者： Zhou, Huayi Liang, Xiao Li, Liping Zhang, Zaichen You, Xiaohu Zhang, Chuan National Mobile Communications Research Laboratory Southeast University Nanjing China Key Laboratory of Intelligent Computing and Signal Processing of the MoE Anhui University Hefei China

As the first error correction codes provably achieving the symmetric capacity of binary-input discrete memory-less channels (B-DMCs), polar codes have been recently chosen by 3GPP for eMBB control channel. Among existing algorithms, CRC-aided successive cancellation list (CA-SCL) decoding is favorable due to its good performance, where CRC is placed at the end of the decoding and helps to eliminate the invalid candidates before final selection. However, the good performance is obtained with a complexity increase that is linear in list size L. In this paper, the tailored CRC-aided SCL (TCA-SCL) decoding is proposed to balance performance and complexity. Analysis on how to choose the proper CRC for a given segment is proposed with the help of virtual transform and virtual length. For further performance improvement, hybrid automatic repeat request (HARQ) scheme is incorporated. Numerical results have shown that, with the similar complexity as the state-of-the-art, the proposed TCA-SCL and HARQ-TCA-SCL schemes achieve 0.1 dB and 0.25 dB performance gain at frame error rate FER = 10-2, respectively. Finally, an efficient TCA-SCL decoder is implemented with FPGA demonstrating its advantages over CA-SCL decoder. Copyright © 2018, The Authors. All rights reserved.

关键词： Error correction