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Prediction of σ54 promoters in prokaryotes based on SVM–Adaboost

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Prediction of σ54 promoters in prokaryotes based on SVM–Ad...

Chinese Automation Congress (CAC)

作者： Yongxian Fan Qingqi Zhu Chengwei Lv Xianyong Pan School of Computer and Information Security Guilin University of Electronic Technology Guilin Guangxi Key Laboratory of System Control and Information Processing Ministry of Education of China Institute of Image Processing and Pattern Recognition Shanghai Jiao Tong University Shanghai China

σ 54 promoters are responsible for transcriptional carbon and nitrogen in prokaryotes. However, it is costly and difficult by experimental identification of them, especially in the postgenomic era with avalanche of sequencing data. Thus, it is imperative to develop efficiently and rapidly computational algorithms to identify the σ 54 promoters. In this study, a novel predictor named SVM-Adaboost was developed to predict σ 54 promoters from sequences alone, it used the Adaboost algorithm as the core, and support vector machine (SVM) as weak base predictors. SVM-Adaboost integrated SVM predictors to construct a more powerful and robust ensemble predictor. In SVM-Adaboost, we used pseudo k-tuple nucleotide composition method to encode DNA sequences, and then a feature selection method was used to further select the discriminate features for subsequent classification. We strictly evaluate the SVM-Adaboost on a constructed gold-standard σ 54 promoter dataset using ten-fold cross validation 100 times, and achieved an average accuracy of 96.06%.

关键词： DNA Support vector machines Feature extraction Training Prediction algorithms Benchmark testing Computational modeling

SoccerNet 2023 Challenges Results

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arXiv 2023年

作者： Cioppa, Anthony Giancola, Silvio Somers, Vladimir Magera, Floriane Zhou, Xin Mkhallati, Hassan Deliège, Adrien Held, Jan Hinojosa, Carlos Mansourian, Amir M. Miralles, Pierre Barnich, Olivier De Vleeschouwer, Christophe Alahi, Alexandre Ghanem, Bernard Van Droogenbroeck, Marc Kamal, Abdullah Maglo, Adrien Clapés, Albert Abdelaziz, Amr Xarles, Artur Orcesi, Astrid Scott, Atom Liu, Bin Lim, Byoungkwon Chen, Chen Deuser, Fabian Yan, Feng Yu, Fufu Shitrit, Gal Wang, Guanshuo Choi, Gyusik Kim, Hankyul Guo, Hao Fahrudin, Hasby Koguchi, Hidenari Ardö, Håkan Salah, Ibrahim Yerushalmy, Ido Muhammad, Iftikar Uchida, Ikuma Be'ery, Ishay Rabarisoa, Jaonary Lee, Jeongae Fu, Jiajun Yin, Jianqin Xu, Jinghang Nang, Jongho Denize, Julien Li, Junjie Zhang, Junpei Kim, Juntae Synowiec, Kamil Kobayashi, Kenji Zhang, Kexin Habel, Konrad Nakajima, Kota Jiao, Licheng Ma, Lin Wang, Lizhi Wang, Luping Li, Menglong Zhou, Mengying Nasr, Mohamed Abdelwahed, Mohamed Liashuha, Mykola Falaleev, Nikolay Oswald, Norbert Jia, Qiong Pham, Quoc-Cuong Song, Ran Hérault, Romain Peng, Rui Chen, Ruilong Liu, Ruixuan Baikulov, Ruslan Fukushima, Ryuto Escalera, Sergio Lee, Seungcheon Chen, Shimin Ding, Shouhong Someya, Taiga Moeslund, Thomas B. Li, Tianjiao Shen, Wei Zhang, Wei Li, Wei Dai, Wei Luo, Weixin Zhao, Wending Zhang, Wenjie Yang, Xinquan Ma, Yanbiao Joo, Yeeun Zeng, Yingsen Gan, Yiyang Zhu, Yongqiang Zhong, Yujie Ruan, Zheng Li, Zhiheng Huang, Zhijian Meng, Ziyu Belgium Saudi Arabia Sportradar Norway UCLouvain Belgium EPFL Switzerland EVS Broadcast Equipment Belgium Baidu Research United States Belgium Sharif University of Technology Iran Footovision France Zewail City of Science Technology and Innovation Egypt Université Paris-Saclay CEA France Universitat de Barcelona Spain Computer Vision Center Spain Nagoya University Japan Research Center for Applied Mathematics and Machine Intelligence Zhejiang Lab China AIBrain United States OPPO Research Institute China Germany Meituan China Tencent Youtu Lab China Amazon Prime Video Sport United States Sogang University Korea Republic of The University of Tokyo Japan Spiideo Sweden University of Tsukuba Japan School of Artificial Intelligence Beijing University of Posts and Telecommunications China Normandie Univ INSA Rouen LITIS France Shanghai Jiao Tong University China Key Laboratory of Intelligent Perception and Image Understanding The Ministry of Education Xidian University China NASK - National Research Institute Poland Robo Space China Tongji University China Sportlight Technology United Kingdom School of Control Science and Engineering Shandong University China lRomul Russia Aalborg University Denmark Turing AI Cultures GmbH Germany Information Systems Technology and Design Singapore University of Technology and Design Singapore Sun Yat-sen University China

The SoccerNet 2023 challenges were the third annual video understanding challenges organized by the SoccerNet team. For this third edition, the challenges were composed of seven vision-based tasks split into three main themes. The first theme, broadcast video understanding, is composed of three high-level tasks related to describing events occurring in the video broadcasts: (1) action spotting, focusing on retrieving all timestamps related to global actions in soccer, (2) ball action spotting, focusing on retrieving all timestamps related to the soccer ball change of state, and (3) dense video captioning, focusing on describing the broadcast with natural language and anchored timestamps. The second theme, field understanding, relates to the single task of (4) camera calibration, focusing on retrieving the intrinsic and extrinsic camera parameters from images. The third and last theme, player understanding, is composed of three low-level tasks related to extracting information about the players: (5) re-identification, focusing on retrieving the same players across multiple views, (6) multiple object tracking, focusing on tracking players and the ball through unedited video streams, and (7) jersey number recognition, focusing on recognizing the jersey number of players from tracklets. Compared to the previous editions of the SoccerNet challenges, tasks (2-3-7) are novel, including new annotations and data, task (4) was enhanced with more data and annotations, and task (6) now focuses on end-to-end approaches. More information on the tasks, challenges, and leader-boards are available on https://***. Baselines and development kits can be found on https://***/SoccerNet. © 2023, CC BY.

关键词： Computer vision

Recommendations on Designing Practical Interval Type-2 Fuzzy Systems

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arXiv 2019年

作者： Wu, Dongrui Mendel, Jerry M. 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 Wuhan430074 China Ming Hsieh Department of Electrical Engineering University of Southern California Los AngelesCA United States College of Artificial Intelligence Tianjin Normal University Tianjin China

Interval type-2 (IT2) fuzzy systems have become increasingly popular in the last 20 years. They have demonstrated superior performance in many applications. However, the operation of an IT2 fuzzy system is more complex than that of its type-1 counterpart. There are many questions to be answered in designing an IT2 fuzzy system: Should singleton or non-singleton fuzzifier be used? How many membership functions (MFs) should be used for each input? Should Gaussian or piecewise linear MFs be used? Should Mamdani or Takagi-Sugeno-Kang (TSK) inference be used? Should minimum or product t-norm be used? Should type-reduction be used or not? How to optimize the IT2 fuzzy system? These questions may look overwhelming and confusing to IT2 beginners. In this paper we recommend some representative starting choices for an IT2 fuzzy system design, which hopefully will make IT2 fuzzy systems more accessible to IT2 fuzzy system designers. Copyright © 2019, The Authors. All rights reserved.

关键词： Membership functions

In Vitro Fertilization (IVF) cumulative pregnancy rate prediction from basic patient characteristics

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arXiv 2019年

作者： Zhang, Bo Cui, Yuqi Wang, Meng Li, Jingjing Jin, Lei Wu, Dongrui Reproductive Medicine Center Tongji Hospital Tongji Medical College Huazhong University of Science and Technology Wuhan Hubei430030 China 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 Hubei430074 China

Tens of millions of women suffer from infertility worldwide each year. In vitro fertilization (IVF) is the best choice for many such patients. However, IVF is expensive, time-consuming, and both physically and emotionally demanding. The first question that a patient usually asks before the IVF is how likely she will conceive, given her basic medical examination information. This paper proposes three approaches to predict the cumulative pregnancy rate after multiple oocyte pickup cycles. Experiments on 11,190 patients showed that first clustering the patients into different groups and then building a support vector machine model for each group can achieve the best overall performance. Our model could be a quick and economic approach for reliably estimating the cumulative pregnancy rate for a patient, given only her basic medical examination information, well before starting the actual IVF procedure. The predictions can help the patient make optimal decisions on whether to use her own oocyte or donor oocyte, how many oocyte pickup cycles she may need, whether to use embryo frozen, etc. They will also reduce the patient's cost and time to pregnancy, and improve her quality of life. Copyright © 2019, The Authors. All rights reserved.

关键词： Obstetrics

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

RFBLS: A robust rough fuzzy broad learning system with local neighborhood structure

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Neurocomputing 2025年 647卷

作者： Yonghe Chu Yanlong Guo Peng Li Weiping Ding Witold Pedrycz Heling Cao School of Artificial Intelligence and Computer Science Nantong University Nantong 226019 China College of Information Science and Engineering Henan University of Technology Zhengzhou 450001 China Key Laboratory of Grain Information Processing and Control(Henan University of Technology) Ministry of Education Zhengzhou 450001 China Centre for Complexity Science Henan University of Technology Zhengzhou 450001 China Department of Electrical and Computer Engineering University of Alberta Edmonton AB T6G 2R3 Canada Institute of Systems Engineering Macau University of Science and Technology Macau SAR Taipa 999078 China Research Center of Performance and Productivity Analysis Istinye University Istanbul Turkiye

As an extension of random vector functional link neural network (RVFLNN), the broad learning system (BLS) has gradually been applied in various fields due to its advantages of simple network structure, rapid training, and fast model updating. Despite its remarkable achievements, there are still some difficulties and challenges that restrict its further application in practical tasks. In BLS, all samples equally contribute to constructing the optimal classification boundary. However, when training samples contain noise or outliers, it will result in the obtained classification boundary not being the true optimal classification boundary. In other words, BLS is sensitive to noise points or outliers. To address it, we propose a robust rough fuzzy broad learning system with local neighborhood structure (RFBLS). In RFBLS, fuzzy sets are utilized by associating a membership degree with each sample. This incorporation ensures diverse contributions of different samples during the minimization of the objective function. Samples with noise or outliers are assigned smaller weights, effectively eliminating the influence of noise and outlier samples in the learning process. We employ the rough set theory to explore the influence-decision degree of each conditional attribute on the decision attribute, aiming to eliminate the impact of redundant or interfering features. Subsequently, we comprehensively consider the distance between samples and class centers, as well as the local neighborhood structure relationship between samples. Initially, we calculate the initial membership degree of each sample based on the distance to class centers. Then, utilizing fuzzy K-nearest neighbors, we calculate and rank the membership degrees of K nearest neighbors for each sample. These rankings are then weighted with the initial membership degree, achieving the fusion of relationships and membership degree calculations between samples. Finally, extensive comparative experiments are conducted on var

关键词： Broad learning system Fuzzy theory K-nearest neighbors Neighborhood rough sets

Attention to refine through multi-scales for semantic segmentation

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arXiv 2018年

作者： Yang, Shiqi Peng, Gang Key Laboratory of Ministry of Education for Image Processing and Intelligence Control School of Automation Huazhong University of Science and Technology Wuhan China

This paper proposes a novel attention model for semantic segmentation, which aggregates multi-scale and context features to refine prediction. Specifically, the skeleton convolutional neural network framework takes in multiple different scales inputs, by which means the CNN can get representations in different scales. The proposed attention model will handle the features from different scale streams respectively and integrate them. Then location attention branch of the model learns to softly weight the multi-scale features at each pixel location. More- over, we add an recalibrating branch, parallel to where location attention comes out, to recalibrate the score map per class. We achieve quite com- petitive results on PASCAL VOC 2012 and ADE20K datasets, which surpass baseline and related works. Copyright © 2018, The Authors. All rights reserved.

关键词： Semantic Segmentation

Model Predictive control for Human Following Rehabilitation Robot

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Model Predictive Control for Human Following Rehabilitation ...

IEEE Workshop on Advanced Robotics and its Social Impacts, ARSO

作者： Shihao Yan Jing Tao Jian Huang Anshun Xue the 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 Ministry of Civil Affairs of the People's Republic of China National Research Center for Rehabilitation Technical Aids Beijing China the Beijing Advanced Innovation Center of Intelligent Robots and Systems Beijing China

A new type of rehabilitation robot that can follow the user side-by-side is designed for aiding the elderly and disabled. The Human Following Rehabilitation Robot (HFRR) consists of a metal armrest, a set of sensors and a differential mobile base. By predicting the user's speed in the future through the user's current walking speed and the preset path, the problem of human following side-by-side is converted to a problem of keeping a certain lateral distance from the predicted trajectory. Linearizing the tracking error model, the nonholonomic mobile robot (NMR) can maintain a certain lateral distance from the trajectory by using Model Predictive control (MPC) and then follow the user side-by-side. The simulation and experimental results show the proposed controller can obtain good performance in this problem.

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A Mixed-attention Network for Automated Interventricular Septum Segmentation in Bright-blood Myocardial T2* MRI Relaxometry in Thalassemia

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Academic radiology 2025年

作者： Xiaofeng Wu Hangyu Wang Zeluan Chen Songsong Sun Zifeng Lian Xinyuan Zhang Peng Peng Yanqiu Feng School of Biomedical Engineering Southern Medical University Guangzhou 510000 China (X.W. H.W. Z.C. S.S. Z.L. X.Z. Y.F.) Guangdong Provincial Key Laboratory of Medical Image Processing & Guangdong Province Engineering Laboratory for Medical Imaging and Diagnostic Technology Southern Medical University Guangzhou 510000 China (X.W. H.W. Z.C. S.S. Z.L. X.Z. Y.F.) Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence & Key Laboratory of Mental Health of the Ministry of Education Southern Medical University Guangzhou 510000 China (X.W. H.W. Z.C. S.S. Z.L. X.Z. Y.F.). Department of Radiology The First Affiliated Hospital of Guangxi Medical University Nanning 530021 China (P.P.) NHC Key Laboratory of Thalassemia Medicine and Guangxi Key laboratory of Thalassemia Research Nanning Guangxi China (P.P.). Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence & Key Laboratory of Mental Health of the Ministry of Education Southern Medical University Guangzhou 510000 China (X.W. H.W. Z.C. S.S. Z.L. X.Z. Y.F.) Department of Radiology Shunde Hospital Southern Medical University (The First People's Hospital of Shunde Foshan) Foshan China (Y.F.). Electronic address: foree@***.

RATIONALE AND OBJECTIVES:This study develops a deep-learning method for automatic segmentation of the interventricular septum (IS) in MR images to measure myocardial T2* and estimate cardiac iron deposition in patients with thalassemia. MATERIALS AND METHODS:This retrospective study used multiple-gradient-echo cardiac MR scans from 419 thalassemia patients to develop and evaluate the segmentation network. The network was trained on 1.5 T images from Center 1 and evaluated on 3.0 T unseen images from Center 1, all data from Center 2, and the CHMMOTv1 dataset. Model performance was assessed using five metrics, and T2* values were obtained by fitting the network output. Bland-Altman analysis, coefficient of variation (CoV), and regression analysis were used to evaluate the consistency between automatic and manual methods. RESULTS:MA-BBIsegNet achieved a Dice of 0.90 on the internal test set, 0.85 on the external test set, and 0.81 on the CHMMOTv1 dataset. Bland-Altman analysis showed mean differences of 0.08 (95% LoA: -2.79 ∼ 2.63) ms (internal), 0.29 (95% LoA: -4.12 ∼ 3.54) ms (external) and 0.19 (95% LoA: -3.50 ∼ 3.88) ms (CHMMOTv1), with CoV of 8.9%, 6.8%, and 9.3%. Regression analysis yielded r values of 0.98 for the internal and CHMMOTv1 datasets, and 0.99 for the external dataset (p < 0.05). CONCLUSION:The IS segmentation network based on multiple-gradient-echo bright-blood images yielded T2* values that were in strong agreement with manual measurements, highlighting its potential for the efficient, non-invasive monitoring of myocardial iron deposition in patients with thalassemia.

关键词： Automatic segmentation Bright-blood myocardial images Magnetic resonance imaging Myocardial iron overload T2* measurement