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Tumor type classification and candidate cancer-specific biomarkers discovery via semi-supervised learning

Biophysics Reports 2023年第2期9卷 57-66页

作者： Peng Chen Zhenlei Li Zhaolin Hong Haoran Zheng Rong Zeng School of Computer Science and Technology University of Science and Technology of China Anhui Key Laboratory of Software Engineering in Computing and Communication University of Science and Technology of China Department of Systems Biology University of Science and Technology of China CAS Key Laboratory of Systems Biology Shanghai Institute of Biochemistry and Cell Biology Center for Excellence in Molecular Cell Science Chinese Academy of Sciences School of Life Science and Technology ShanghaiTech University

Identifying cancer-related differentially expressed genes provides significant information for diagnosing tumors, predicting prognoses, and effective treatments. Recently, deep learning methods have been used to perform gene differential expression analysis using microarray-based high-throughput gene profiling and have achieved good results. In this study, we proposed a new robust multiple-datasetsbased semi-supervised learning model, MSSL, to perform tumor type classification and candidate cancer-specific biomarkers discovery across multiple tumor types and multiple datasets, which addressed the following long-lasting obstacles:(1) the data volume of the existing single dataset is not enough to fully exert the advantages of deep learning;(2) a large number of datasets from different research institutions cannot be effectively used due to inconsistent internal variances and low quality;(3) relatively uncommon cancers have limited effects on deep learning methods. In our article, we applied MSSL to The Cancer Genome Atlas(TCGA) and the Gene Expression Comprehensive Database(GEO) pan-cancer normalized-level3 RNA-seq data and got 97.6% final classification accuracy, which had a significant performance leap compared with previous approaches. Finally, we got the ranking of the importance of the corresponding genes for each cancer type based on classification results and validated that the top genes selected in this way were biologically meaningful for corresponding tumors and some of them had been used as biomarkers, which showed the efficacy of our method.

关键词： Deep learning Tumor type classification Cancer-specific biomarkers MSSL

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Fast fourier transform based ip traffic classification system for SIPTO at H(e)NB

Fast fourier transform based ip traffic classification syste...

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2012 7th International ICST Conference on communications and Networking in China, CHINACOM 2012

作者： Han, Lin Huang, Liusheng Hu, Qian Han, Xue Shi, Jinglin School of Software and Engineering University of Science and Technology of China Suzhou China Wireless Communication Technology Research Center Institute of Computing Technology Chinese Academy of Sciences China Beijing Key Laboratory of Mobile Computing and Pervasive Device China Beijing Sylincom Technologies Co. Ltd. China

ISBN: (纸本)9781467326995

3GPP has recently introduced LIPA(Local IP Access) and SIPTO(Selected IP Traffic Offload) to offload traffic from the core network, which brings new challenge to on-line traffic classification, because of the large amount of data and the difference of mobile network from wired network, such as high bit error rates(BER) and temporary disconnections. Therefore, other proposed schemes which aim at ether LIPA at H(e)NB or SIPTO at macro network could not get high accuracy and high speed at the same time, and traffic classification methodologies in wired IP network are not applicable. This paper proposes a fast fourier transform(FFT) based IP traffic classification system for SIPTO at H(e)NB, which focuses on classifying each packet at H(e)NB by extracting the application layer payload pattern using FFT. Pattern extraction and classification using machine learning algorithms are simulated, and results show that our system outperforms existing methods by offering about 3%-6% improvement in classification accuracy with about 7% time. Simulation of SIPTO shows good reduction of press to the core network and low false rates. © 2012 IEEE.

关键词： Fast Fourier transforms

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Neighborhood-based distributed topological hole detection algorithm in sensor networks

Neighborhood-based distributed topological hole detection al...

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IET International Conference on Wireless Mobile and Multimedia Networks Proceedings, ICWMMN 2006

作者： Kun, Bi Naijie, Gu Kun, Tu Wanli, Dong Dept. of Comput. Sci. and Technol. Univ. of Sci. and Technol. of China Hefei Anhui 230027 China Anhui Province Key Laboratory of Software in Computing and Communication Hefei Anhui 230027 China

ISBN: (纸本)0863416446

Topological holes in sensor networks usually indicate the region where nodes are depleted or not dense enough due to kinds of reasons. In this paper, we study the problem of detecting topological holes in wireless sensor networks. Those sensor nodes have no geographic location information and have a limited communication range. We present a novel distributed topological holes detection algorithm which is based purely on the logical communication topology graph. By exchanging information with its 1-hop and 2-hop neighbors, each node can independently decide whether it is on the boundary of a hole. Those boundary sensor nodes together could describe the region of the topological hole. Experimental results show that our distributed algorithm is effective in exploiting those characteristics of those nodes on the boundaries of holes. And thus it could identify those holes in sensor networks of moderate node densities.

关键词： Parallel algorithms

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Zone routing protocol based on energy consumption

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Jisuanji Gongcheng/Computer Engineering 2006年第12期32卷 117-118+135页

作者： Zhai, Weifeng Gu, Naijie Zhang, Jianming Department of Computer Science and Technology University of Science and Technology of China Hefei 230027 China Anhui Province Key Laboratory of Computing and Communication Software Hefei 230027 China

A zone routing protocol based on the energy consumption speed of nodes in mobile Adhoc networks is presented. A route select parameter computed by residual lifetime of nodes and hop count of route is used to be selected the best route, the nodes that have more energy have more probability of chosen. The mechanism can balance the energy consumption of node and prolong network's life. Simulation result comparing with zone routing protocol in NS-2 shows EZRP has less number of death nodes, lower routing overhead, and longer lifetime of network.

关键词： Energy consumption EZRP Hybrid routing protocol MANET

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Accelerating vehicle detection in low-altitude airborne urban video

Accelerating vehicle detection in low-altitude airborne urba...

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International Conference on Image and Graphics

作者： Cao, Xianbin Lin, Renjun Yan, Pingkun Li, Xuelong Anhui Province Key Laboratory of Software In Computing and Communication School of Computer Science and Technology University of Science and Technology of China Hefei 230027 Anhui China Xi'an Institute of Optics and Precision Mechanics Chinese Academy of Sciences Xi'an 710119 Shaanxi China

ISBN: (纸本)9780769545417

The limitation of the existing methods of traffic data collection is that they rely on techniques that are strictly local in nature. The airborne system in unmanned aircrafts provides the advantages of wider view angle and higher mobility. However, detecting vehicles in airborne videos is a challenging task because of the scene complexity and platform movement. Most of the techniques used in stationary platforms cannot perform well in this situation. A new and efficient method based on Bayes model is proposed in this paper. This method can be divided into two stages, attention focus extraction and vehicle classification. Experimental results demonstrated that, compared with other representative algorithms, our method obtained better performance with higher detection rate, lower false positive rate and faster detection speed. © 2011 IEEE.

关键词： Extraction

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A qualitative modeling and simulation method based on cloud model

A qualitative modeling and simulation method based on cloud ...

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2013 5th International Conference on Modeling, Simulation and Applied Optimization, ICMSAO 2013

作者： Shao, Chenxi Sun, Kelu Zhenzhong, Shao Computer Science and Technology Dept. University of Science and Technology of China Hefei 230027 China Anhui Province Key Laboratory of Software in Computing and Communication Hefei 230027 China Jianghuai Automobile Co. Ltd. Hefei 230022 China

ISBN: (纸本)9781467358149

Qualitative simulation is effective methods processing incomplete knowledge, how to represent qualitative knowledge and reduce spurious behaviors is its research emphasis. Contraposing the limitations of existing methods representing qualitative knowledge and filtering spurious behaviors, an approach is proposed to qualitatively model and simulate on the basis of normal cloud model. In this research, the cloud numeric characteristics and cloud measurement are introduced into this approach;consequently, it can more accurately assess the qualitative knowledge, and expand the variables expression and quantity space;meanwhile, it is constructed the means of modeling and simulation by adopting more amply portraying the system status, more intuitively transforming status and more accurately filtering spurious behaviors. Furthermore, in simulation algorithm, cloud measurement indices are employed to significantly select the successor status which can not be determined by existing constraint means. The results of simulation example demonstrate that our approach effectively improves the ability to filter spurious behaviors, and it is a feasible method. © 2013 IEEE.

关键词： Cloud computing

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Scheduling aircraft landing based on clonal selection algorithm and receding horizon control

Scheduling aircraft landing based on clonal selection algori...

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11th International IEEE Conference on Intelligent Transportation Systems, ITSC 2008

作者： Jia, Xiaolan Cao, Xianbin Guo, Yuanping Qiao, Hong Zhang, Jun University of Science and Technology of China Anhui Province Key Laboratory of Software in Computing and Communication Hefei 230026 China Institute of Automation Chinese Academy of Sciences Beijing 100080 China School of Electronic and Information Engineering Beihang University Beijing 100083 China

ISBN: (纸本)9781424421121

The task of Aircraft Landing Scheduling (ALS) is to give a landing sequence and landing times for a given set of aircrafts where many constraints must be satisfied. ALS is an NP-hard problem with large-scale and multi-constraint characteristics, thus it is hard to find optimal solution efficiently. In this paper, a hybrid algorithm of Clonal Selection Algorithm (CSA) and Receding Horizon Control (RHC) was proposed for ALS problem. In details, constrained CSA based on infeasibility degree (IFD) schedules aircrafts in current receding horizon, and then RHC repeats that optimization procedure using excellent gene segment spread (EGSS) until all aircrafts have landed. Comparative experiments show that the CSA-RHC hybrid algorithm is able to obtain an optimal landing sequence and landing times rapidly and effectively. © 2008 IEEE.

关键词： Computational complexity

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NURBS model for chaotic time series

NURBS model for chaotic time series

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2011 3rd International Conference on Computer Research and Development, ICCRD 2011

作者： Shao, Chenxi Xiao, Lipeng Department of Computer Science and Technology University of Science and Technology of China Hefei China Department of Modern Physics Nonlinear Science Center University of Science and Technology of China Hefei China Anhui Province Key Laboratory of Software in Computing and Communication Hefei China

ISBN: (纸本)9781612848372

NURBS method is extensively used in the field of Geometric Modeling. Since the original NURBS method does not have time factor, it can not display the huge advantage in the dynamics field. In this article, inspired by the segmented nature of basis functions, we propose a time factor method which can be directly applied in reconstruction of missing data, with remarkable performance in matching the original data. This work does not only give an expression of chaotic time series, but also highlights a possible way for the challenge in reconstruction of missing data. © 2011 IEEE.

关键词： Time series

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Fault diagnosis design based on qualitative simulation

Fault diagnosis design based on qualitative simulation

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2012 3rd International Conference on Intelligent Control and Information Processing, ICICIP 2012

作者： Shao, Chenxi Shao, Zhenzhong Zhang, Juntao Bai, Fanzhou College of Computer Science and Technology University of Science and Technology of China Hefei 230026 China Anhui Province Key Laboratory of Software in Computing and Communication Hefei Anhui 230027 China Jianghuai Automobile Co. Ltd. Hefei 230022 China

ISBN: (纸本)9781457721427

Based on the QSIM reasoning of Kuipers, comparative constraint is presented to reduce the diagnosis space. The transfer regulation of qualitative constrain is used in the simulation and reasoning of system diagnosis. This arithmetic takes observed faulty state as the beginning, to diagnosis the discrepancy of variable and location of the causation according to the transfer regulation of qualitative constraint, reasons from faulty diagnosed to examine the result and delete the redundancy of diagnosis result. In the example of Condensation refrigeration system, the constraint relation is built according to qualitative difference equation. Aim at the bad efficiency of refrigeration, the mixture of air or Freon superfluously is diagnosed as the result faulty source, is consistent with the factual system. © 2012 IEEE.

关键词： Fault detection

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KLT feature based vehicle detection and tracking in airborne videos

KLT feature based vehicle detection and tracking in airborne...

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International Conference on Image and Graphics

作者： Cao, Xianbin Lan, Jinhe Yan, Pingkun Li, Xuelong Anhui Province Key Laboratory of Software In Computing and Communication School of Computer Science and Technology University of Science and Technology of China Hefei 230027 Anhui China Xi'an Institute of Optics and Precision Mechanics Chinese Academy of Sciences Xi'an 710119 Shaanxi China

ISBN: (纸本)9780769545417

Airborne vehicle detection and tracking systems equipped on unmanned aerial vehicles (UAVs) are difficult to develop because of factors like UAV motion, scene complexity and so on. In this paper, we propose a new framework of multi-motion layer analysis to detect and track moving vehicles in airborne platform. Moving vehicles are firstly detected by registration and temporal differencing to establish motion layers. After motion layers are constructed, they are maintained over time for tracking vehicles. All vehicles are tracked by maintaining their corresponding motion layers. Our experimental results showed that compared with other previous algorithms, our method can achieve better results in terms of detection and tracking performance. © 2011 IEEE.

关键词： Antennas

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