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Mem Brain: An Easy-to-Use Online Webserver for Transmembrane Protein Structure Prediction

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Nano-Micro Letters 2018年第1期10卷 12-19页

作者： Xi Yin Jing Yang Feng Xiao Yang Yang Hong-Bin Shen Institute of Image Processing and Pattern Recognition Shanghai Jiao Tong University Key Laboratory of System Control and Information Processing Ministry of Education of China Department of Computer Science Shanghai Jiao Tong University Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering

Membrane proteins are an important kind of proteins embedded in the membranes of cells and play crucial roles in living organisms, such as ion channels,transporters, receptors. Because it is difficult to determinate the membrane protein's structure by wet-lab experiments,accurate and fast amino acid sequence-based computational methods are highly desired. In this paper, we report an online prediction tool called Mem Brain, whose input is the amino acid sequence. Mem Brain consists of specialized modules for predicting transmembrane helices, residue–residue contacts and relative accessible surface area of a-helical membrane proteins. Mem Brain achieves aprediction accuracy of 97.9% of ATMH, 87.1% of AP,3.2 ± 3.0 of N-score, 3.1 ± 2.8 of C-score. Mem BrainContact obtains 62%/64.1% prediction accuracy on training and independent dataset on top L/5 contact prediction,respectively. And Mem Brain-Rasa achieves Pearson correlation coefficient of 0.733 and its mean absolute error of13.593. These prediction results provide valuable hints for revealing the structure and function of membrane *** Brain web server is free for academic use and available at ***/bioinf/Mem Brain/.

关键词： Transmembrane a-helices Structure prediction Machine learning Contact map prediction Relative accessible surface area

BoostTree and BoostForest for Ensemble Learning

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arXiv 2020年

作者： Zhao, Changming Wu, Dongrui Huang, Jian Yuan, Ye Zhang, Hai-Tao Peng, Ruimin Shi, Zhenhua Key Laboratory of the Ministry of Education for Image Processing and Intelligent Control School of Artificial Intelligence and Automation Huazhong University of Science and Technology Wuhan China Shenzhen Huazhong University of Science and Technology Research Institute Shenzhen China The Autonomous Intelligence Unmanned Systems Engineering Research Center of Ministry of Education of China The State Key Lab of Digital Manufacturing Equipment and Technology Wuhan China

Bootstrap aggregating (Bagging) and boosting are two popular ensemble learning approaches, which combine multiple base learners to generate a composite model for more accurate and more reliable performance. They have been widely used in biology, engineering, healthcare, etc. This paper proposes BoostForest, which is an ensemble learning approach using BoostTree as base learners and can be used for both classification and regression. BoostTree constructs a tree model by gradient boosting. It increases the randomness (diversity) by drawing the cut-points randomly at node splitting. BoostForest further increases the randomness by bootstrapping the training data in constructing different BoostTrees. BoostForest generally outperformed four classical ensemble learning approaches (Random Forest, Extra-Trees, XGBoost and LightGBM) on 35 classification and regression datasets. Remarkably, BoostForest tunes its parameters by simply sampling them randomly from a parameter pool, which can be easily specified, and its ensemble learning framework can also be used to combine many other base learners. Copyright © 2020, The Authors. All rights reserved.

关键词： Classification (of information)

EEG-Based Brain-Computer Interfaces Are Vulnerable to Backdoor Attacks

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arXiv 2020年

作者： Meng, Lubin Huang, Jian Zeng, Zhigang Jiang, Xue Yu, Shan Jung, Tzyy-Ping Lin, Chin-Teng Chavarriaga, Ricardo Wu, Dongrui Ministry of Education Key Laboratory of Image Processing and Intelligent Control School of Artificial Intelligence and Automation Huazhong University of Science and Technology Wuhan China Brainnetome Center National Laboratory of Pattern Recognition Institute of Automation Chinese Academy of Sciences Beijing China La Jolla CA United States Center for Advanced Neurological Engineering Institute of Engineering in Medicine Ucsd La Jolla CA United States Centre of Artificial Intelligence Faculty of Engineering and Information Technology University of Technology Sydney Australia Zhaw DataLab Zürich University of Applied Sciences Winterthur8401 Switzerland

Research and development of electroencephalogram (EEG) based brain-computer interfaces (BCIs) have advanced rapidly, partly due to deeper understanding of the brain and wide adoption of sophisticated machine learning approaches for decoding the EEG signals. However, recent studies have shown that machine learning algorithms are vulnerable to adversarial attacks. This article proposes to use narrow period pulse for poisoning attack of EEG-based BCIs, which is implementable in practice and has never been considered before. One can create dangerous backdoors in the machine learning model by injecting poisoning samples into the training set. Test samples with the backdoor key will then be classified into the target class specified by the attacker. What most distinguishes our approach from previous ones is that the backdoor key does not need to be synchronized with the EEG trials, making it very easy to implement. The effectiveness and robustness of the backdoor attack approach is demonstrated, highlighting a critical security concern for EEG-based BCIs and calling for urgent attention to address it. Copyright © 2020, The Authors. All rights reserved.

关键词： Electroencephalography

Tiny noise, big mistakes: Adversarial perturbations induce errors in Brain-Computer Interface spellers

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arXiv 2020年

作者： Zhang, Xiao Wu, Dongrui Ding, Lieyun Luo, Hanbin Lin, Chin-Teng Jung, Tzyy-Ping Chavarriaga, Ricardo Ministry of Education Key Laboratory of Image Processing and Intelligent Control School of Artificial Intelligence and Automation Huazhong University of Science and Technology Wuhan430074 China School of Civil Engineering and Mechanics Huazhong University of Science and Technology Wuhan430074 China Centre of Artificial Intelligence Faculty of Engineering and Information Technology University of Technology Sydney Sydney2007 Australia La Jolla CA92093 United States Center for Advanced Neurological Engineering Institute of Engineering in Medicine UCSD La Jolla CA92093 United States ZHAW DataLab Zürich University of Applied Sciences Winterthur8401 Switzerland

An electroencephalogram (EEG) based brain-computer interface (BCI) speller allows a user to input text to a computer by thought. It is particularly useful to severely disabled individuals, e.g., amyotrophic lateral sclerosis patients, who have no other effective means of communication with another person or a computer. Most studies so far focused on making EEG-based BCI spellers faster and more reliable;however, few have considered their security. This study, for the first time, shows that P300 and steady-state visual evoked potential BCI spellers are very vulnerable, i.e., they can be severely attacked by adversarial perturbations, which are too tiny to be noticed when added to EEG signals, but can mislead the spellers to spell anything the attacker wants. The consequence could range from merely user frustration to severe misdiagnosis in clinical applications. We hope our research can attract more attention to the security of EEG-based BCI spellers, and more broadly, EEG-based BCIs, which has received little attention before. Copyright © 2020, The Authors. All rights reserved.

关键词： Electroencephalography

Target characterization and scattering power decomposition for full and compact polarimetric SAR data

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TechRxiv

TechRxiv 2019年

作者： Dey, Subhadip Bhattacharya, Avik Ratha, Debanshu Mandal, Dipankar Frery, Alejandro C. The Microwave Remote Sensing Lab Center of Studies in Resources Engineering Indian Institute of Technology Bombay India The Universidade Federal de Alagoas Maceió Brazil The Key Lab of Intelligent Perception and Image Understanding of the Ministry of Education Xidian University Xi'an China

In radar polarimetry, incoherent target decomposition techniques help extract scattering information from polarimetric SAR data. This is achieved either by fitting appropriate scattering models or by optimizing the received wave intensity through the diagonalization of the coherency (or covariance) matrix. As such, the received wave information depends on the received antenna configuration. Additionally, a polarimetric descriptor that is independent of the received antenna configuration might provide additional information which is missed by the individual elements of the coherency matrix. This implies that existing target characterization techniques might neglect this information. In this regard, we suitably utilize the 2D and 3D Barakat degree of polarization which is independent of the received antenna configuration to obtain distinct polarimetric information for target characterization. In this study, we introduce new roll-invariant scattering-type parameters for both full-polarimetric (FP) and compact-polarimetric (CP) SAR data. These new parameters jointly use the information of the 2D and 3D Barakat degree of polarization and the elements of the coherency (or covariance) matrix. We use these new scattering-type parameters, which provide equivalent information as the Cloude α for FP SAR data and the ellipticity parameter χ for CP SAR data, to characterize various targets adequately. Additionally, we appropriately utilize these new scattering-type parameters to obtain unique non-model based three-component scattering power decomposition techniques. We obtain the even-bounce, and the odd-bounce scattering powers by modulating the total polarized power by a proper geometrical factor derived using the new scattering-type parameters for FP and CP SAR data. The diffused scattering power is obtained as the depolarized fraction of the total power. Moreover, due to the nature of its formulation, the decomposition scattering powers are nonnegative and roll-invariant whi

关键词： Polarimeters

Micro Channel for Analyzing Mechanical Adaption of Cancer Cell

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Micro Channel for Analyzing Mechanical Adaption of Cancer Ce...

IEEE International Conference on Cyborg and Bionic Systems (CBS)

作者： Pengyun Li Xiaoming Liu Xiaoqing Tang Masaru Kojima Jian Huang Qiang Huang Tatsuo Arai Beijing Advanced Innovation Center for Intelligent Robots and Systems and the Intelligent Robotics Institute School of Mechatronical Engineering Beijing Institute of Technology Beijing China Osaka University 1-3 Machikaneyama Toyonaka Osaka Japan Key Laboratory of Ministry of Education for Image Processing and Intelligent Control the School of Artificial Intelligence and Automation Huazhong University of Science and Technology Wuhan China

ISBN: (数字)9781728150734

ISBN: (纸本)9781728150741

It was reported that cancer cells could biologically respond and adapt to the confined environment during migration in extracellular matrix (ECM). But it is not clearly studied that how cancer cells respond and adapt to confined environment in mechanical way. Thus, in this study, we designed and fabricated a kind of one-layer micro channel to mimic confined environment for analyzing mechanical adaption of cell. This micro channel could apply sequential mechanical stresses on a number of cells with high throughput, and the time of cells passing through five rows of micro channels were used to evaluate their adaptability to the sequential and confined space. In experiments, each cell suffered 20 times of mechanical stresses after passing through 20 squeezing channels arranged in 5 rows. We observed the sequential squeezing processes under microscope and investigated the passing time using a high-speed camera. The preliminary results indicated that cancer cells could pass through and adapt to the confined environment faster than normal cells.

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Network Resilience

arXiv 2020年

作者： Liu, Xueming Li, Daqing Ma, Manqing Szymanski, Boleslaw K. Eugene Stanley, H. Gao, Jianxi Key Laboratory of Image Information Processing and Intelligent Control School of Artificial Intelligence and Automation Huazhong University of Science and Technology Hubei Wuhan430074 China School of Reliability and Systems Engineering Beihang University Beijing100191 China College of Safety Science and Engineering Civil Aviation University of China Tianjin 300300 China Department of Computer Science Rensselaer Polytechnic Institute TroyNY12180 United States Network Science and Technology Center Rensselaer Polytechnic Institute TroyNY12180 United States Center for Polymer Studies Department of Physics Boston University BostonMA02215 United States

Many systems on our planet shift abruptly and irreversibly from the desired state to an undesired state when forced across a "tipping point". Some examples are mass extinctions within ecosystems, cascading failures in infrastructure systems, and changes in human and animal social networks. The ability to avoid such regime shifts or to recover quickly from such a non-resilient state demonstrates a system's resilience;system resilience is a quality that enables a system to adjust its activities to retain its basic functionality when errors and failures occur. In the past 50 years, attention has been paid almost exclusively to low-dimensional systems;scholars have focused on the calibration of the resilience functions of such systems and the identification of indicators of early warning signals based on two to three connected components. In recent years, taking advantage of network theory and the availability of lavish real datasets, network scientists have begun to explore real-world complex networked multidimensional systems, as well as their resilience functions and early warning indicators. This report presents a comprehensive review of resilience functions and regime shifts in complex systems in domains such as ecology, biology, society, and infrastructure. The research approach includes empirical observations, experimental studies, mathematical modeling, and theoretical analysis. We also review the definitions of some ambiguous terms, including robustness, resilience, and stability. Copyright © 2020, The Authors. All rights reserved.

关键词： Complex networks

Global Rice Multi-Class Segmentation Dataset (RiceSEG): A Comprehensive and Diverse High-Resolution RGB-Annotated images for the Development and Benchmarking of Rice Segmentation Algorithms

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arXiv 2025年

作者： Zhou, Junchi Wang, Haozhou Kato, Yoichiro Nampally, Tejasri Rajalakshmi, P. Balram, M. Katsura, Keisuke Lu, Hao Mu, Yue Yang, Wanneng Gao, Yangmingrui Xiao, Feng Chen, Hongtao Chen, Yuhao Li, Wenjuan Wang, Jingwen Yu, Fenghua Zhou, Jian Wang, Wensheng Hu, Xiaochun Yang, Yuanzhu Ding, Yanfeng Guo, Wei Liu, Shouyang Engineering Research Center of Plant Phenotyping Ministry of Education Jiangsu Collaborative Innovation Center for Modern Crop Production Academy for Advanced Interdisciplinary Studies Sanya Institute of Nanjing Agricultural University Nanjing Agricultural University Nanjing China Graduate School of Agricultural and Life Sciences The University of Tokyo Tokyo Japan Department of Artificial Intelligence Indian Institute of Technology Hyderabad India Department of Electrical Engineering Indian Institute of Technology Hyderabad India Institute of Biotechnology Professor Jayashankar Telangana Agricultural State University Hyderabad India Graduate School of Agriculture Kyoto University Kyoto Japan Key Laboratory of Image Processing and Intelligent Control School of Artificial Intelligence and Automation Huazhong University of Science and Technology Wuhan China National Key Laboratory of Crop Genetic Improvement National Center of Plant Gene Research Hubei Key Laboratory of Agricultural Bioinformatics Huazhong Agricultural University Wuhan China State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China the Institute of Agricultural Resources and Regional Planning Chinese Academy of Agricultural Sciences Beijing China Center for Geospatial Information Shenzhen Institutes of Advanced Technology Chinese Academy of Science Shenzhen China School of Information and Electrical Engineering Shenyang Agricultural University Shenyang China Rice Research Institute Jilin Academy of Agricultural Sciences Changchun China Institute of Crop Sciences National Key Facility for Crop Gene Resources and Genetic Improvement Chinese Academy of Agricultural Sciences Beijing China Yuan Long Ping High-Tech Agriculture Co. Ltd. Changsha China

Developing computer vision–based rice phenotyping techniques is crucial for precision field management and accelerating breeding, thereby continuously advancing rice production. Among phenotyping tasks, distinguishing image components is a key prerequisite for characterizing plant growth and development at the organ scale, enabling deeper insights into eco-physiological processes. However, due to the fine structure of rice organs and complex illumination within the canopy, this task remains highly challenging, underscoring the need for a high-quality training dataset. Such datasets are scarce, both due to a lack of large, representative collections of rice field images and the time-intensive nature of annotation. To address this gap, we established the first comprehensive multi-class rice semantic segmentation dataset, RiceSEG. We gathered nearly 50,000 high-resolution, ground-based images from five major rice-growing countries (China, Japan, India, the Philippines, and Tanzania), encompassing over 6,000 genotypes across all growth stages. From these original images, 3,078 representative samples were selected and annotated with six classes (background, green vegetation, senescent vegetation, panicle, weeds, and duckweed) to form the RiceSEG dataset. Notably, the sub-dataset from China spans all major genotypes and rice-growing environments from the northeast to the south. Both state-of-the-art convolutional neural networks and transformer-based semantic segmentation models were used as baselines. While these models perform reasonably well in segmenting background and green vegetation, they face difficulties during the reproductive stage, when canopy structures are more complex and multiple classes are involved. These findings highlight the importance of our dataset for developing specialized segmentation models for rice and other crops. The RiceSEG dataset is publicly available at ***. © 2025, CC BY.

关键词： Semantic Segmentation

Universal enzymatic numerical P systems with small number of enzymatic variables

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Science China(Information Sciences) 2018年第9期61卷 38-49页

作者： Zhiqiang ZHANG Tingfang WU ANDrei P■UN Linqiang PAN Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China School of Automation Huazhong University of Science and Technology Department of Computer Science Faculty of Mathematics and Computer ScienceUniversity of Bucharest Bioinformatics Department National Institute of Research and Development for Biological Sciences School of Electric and Information Engineering Zhengzhou University of Light Industry

Numerical P systems(for short, NP systems) are distributed and parallel computing models inspired from the structure of living cells and economics. Enzymatic numerical P systems(for short, ENP systems) are a variant of NP systems, which have been successfully applied in designing and implementing controllers for mobile robots. Since ENP systems were proved to be Turing universal, there has been much work to simplify the universal systems, where the complexity parameters considered are the number of membranes, the degrees of polynomial production functions or the number of variables used in the *** the number of enzymatic variables, which is essential for ENP systems to reach universality, has not been investigated. Here we consider the problem of searching for the smallest number of enzymatic variables needed for universal ENP systems. We prove that for ENP systems as number acceptors working in the all-parallel or one-parallel mode, one enzymatic variable is sufficient to reach universality; while for the one-parallel ENP systems as number generators, two enzymatic variables are sufficient to reach *** results improve the best known results that the numbers of enzymatic variables are 13 and 52 for the all-parallel and one-parallel systems, respectively.

关键词： bio-inspired computing numerical P system mobile robot membrane controller universality