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Modern deep learning in bioinformatics

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Journal of Molecular Cell Biology 2020年第11期12卷 823-827页

作者： Haoyang Li Shuye Tian Yu Li qiming fang Renbo Tan Yijie Pan Chao Huang Ying Xu Xin Gao Cancer Systems Biology Center The China-Japan Union HospitalJilin UniversityChangchun 130033China MOE Key Laboratory of Symbolic Computation and Knowledge Engineering College of Computer Science and TechnologyJilin UniversityChangchun 130012China Department of Biology Southern University of Science and TechnologyShenzhen 518055China Computational Bioscience Research Center(CBRC) Computer Electrical and Mathematical Sciences and Engineering(CEMSE)DivisionKing Abdullah University of Science and Technology(KAUST)Thuwal 23955Saudi Arabia School of Computer Science and Technology Hangzhou Dianzi UniversityHangzhou 310018China Ningbo Institute of Information Technology Application Chinese Academy of SciencesNingbo 315040China Computational Systems Biology Lab Department of Biochemistry and Molecular Biology and Institute of BioinformaticsUniversity of GeorgiaAthensGA 30602USA

Deep learning(DL)has shown explosive growth in its application to bioinformatics and has demonstrated thrillingly promising power to mine the complex relationship hidden in large-scale biological and biomedical data.A number of comprehensive reviews have been published on such applications,ranging from high-level reviews with future perspectives to those mainly serving as tutorials.

关键词： has such she

Forecasting traffic flows in irregular regions with multi-graph

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Frontiers of Information Technology & Electronic Engineering 2021年第9期22卷 1179-1193页

作者： Dewen SENG Fanshun LV Ziyi LIANG Xiaoying SHI qiming fang School of Computer Science and Technology Hangzhou DianziUniversityHangzhou 310018China

The prediction of regional traffic flows is important for traffic control and management in an intelligent traffic *** the help of deep neural networks,the convolutional neural network or residual neural network,which can be applied only to regular grids,is adopted to capture the spatial dependence for flow ***,the obtained regions are always irregular considering the road network and administrative boundaries;thus,dividing the city into grids is inaccurate for *** this paper,we propose a new model based on multi-graph convolutional network and gated recurrent unit(MGCN-GRU)to predict traffic flows for irregular ***,we first construct heterogeneous inter-region graphs for a city to reflect the rela-tionships among *** each graph,nodes represent the irregular regions and edges represent the relationship types between ***,we propose a multi-graph convolutional network to fuse different inter-region graphs and additional *** GRU is further used to capture the temporal dependence and to predict future traffic *** results based on three real-world large-scale datasets(public bicycle system dataset,taxi dataset,and dockless bike-sharing dataset)show that our MGCN-GRU model outperforms a variety of existing methods.

关键词： Traffic flow prediction Multi-graph convolutional network Gated recurrent unit Irregular regions

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稀疏图的k-frugal列表染色

同济大学学报（自然科学版） 2022年第12期50卷 1825-1832页

作者：房启明张莉同济大学数学科学学院上海200092

图G的k-frugal列表色数一般记作ch_(k)(G),关于稀疏的k-frugal列表色数上界,有以下3个结论:∀k≥3,如果图G满足mad(G)<3-a(其中0 详细信息

图G的k-frugal列表色数一般记作ch_(k)(G),关于稀疏的k-frugal列表色数上界,有以下3个结论:∀k≥3,如果图G满足mad(G)<3-a(其中0

关键词：图论染色最大平均度平面图围长

4R-TPUT:结构化对等网络中的高效top-k查询算法

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清华大学学报（自然科学版） 2014年第4期54卷 480-484页

作者：方启明杨广文清华大学计算机科学与技术系北京100084 杭州电子科技大学计算机学院杭州310018

top-k查询要求查找出最符合需求的前k个结果,是对等网络中的重要数据处理技术。该文研究了结构化对等网络中数据在各节点上垂直划分的精确top-k查询处理,在3通信回合的三阶段阈值(TPUT)算法基础上提出了4回合阈值算法4R-TPUT。它由下界... 详细信息

top-k查询要求查找出最符合需求的前k个结果,是对等网络中的重要数据处理技术。该文研究了结构化对等网络中数据在各节点上垂直划分的精确top-k查询处理,在3通信回合的三阶段阈值(TPUT)算法基础上提出了4回合阈值算法4R-TPUT。它由下界估计、剪枝和结果查找3个阶段组成,通过在TPUT的下界估计阶段增加一个通信回合来获取更多的数据信息以得到更准确的top-k下界估计和剪枝阈值,从而减少查询处理过程中的数据访问和传输量。实验表明:4R-TPUT相比于TPUT较大幅度降低了数据传输量,减小了查询响应时间,是一种更高效的top-k查询算法。

关键词：对等网络 top-k查询 TPUT 4R-TPUT

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基于依存语义注意力的词对上下位关系识别

华中科技大学学报（自然科学版） 2022年第5期50卷 33-38页

作者：徐小良戴乾杰方启明杭州电子科技大学计算机学院浙江杭州310018

针对现有上下位关系识别方法未能充分挖掘利用词对共现句中上下位关系语义的问题,提出一种基于依存语义注意力的词对上下位关系识别方法.利用词对共现句最短依存路径的路径向量训练Softmax分类器进行上下位关系识别,引入依存语义注意力... 详细信息

针对现有上下位关系识别方法未能充分挖掘利用词对共现句中上下位关系语义的问题,提出一种基于依存语义注意力的词对上下位关系识别方法.利用词对共现句最短依存路径的路径向量训练Softmax分类器进行上下位关系识别,引入依存语义注意力机制,构建最短依存路径的注意力权重向量和路径评价函数,更细粒度挖掘和表示不同词和不同路径对上下位关系语义的不同贡献,从而更充分利用精细语义特征实现更准确的上下位关系识别.结果表明:相比HypeNet和NPM等代表性方法,本方法在中文和英文实验数据集上的识别准确率分别可提高2.0%和1.3%,且识别性能更稳定.

关键词：上下位关系识别注意力机制语义特征词向量路径向量

滇中地区坡耕地红黏土离散元仿真模型参数标定与试验

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农业机械学报 2024年第9期55卷 185-193,285页

作者：果霖方启明李明飞王智王灿张立芸云南农业大学机电工程学院昆明650201 西安石油大学机械工程学院西安710065

适用于山区坡耕地的耕整地机械在优化设计过程中缺乏准确的离散元仿真模型参数,制约了机具的设计改进。以滇中地区坡耕地红黏土为研究对象,结合无侧限抗压强度试验和离散元仿真方法,建立了基于EEPA模型和Bonding模型的无侧限抗压强度试... 详细信息

适用于山区坡耕地的耕整地机械在优化设计过程中缺乏准确的离散元仿真模型参数,制约了机具的设计改进。以滇中地区坡耕地红黏土为研究对象,结合无侧限抗压强度试验和离散元仿真方法,建立了基于EEPA模型和Bonding模型的无侧限抗压强度试验仿真模型,并对仿真模型中的相关参数进行标定。试验中土样断裂的最大轴向压力平均值为431.19 N。以最大轴向压力为响应值设计Plackett-Burman试验、Steepest Ascent试验和Box-Behnken试验来确定离散元仿真模型参数,并通过试验来验证仿真的可靠性。Bonding模型单位面积法向刚度X1为3.14×10^(8)N/m^(3)、临界法向应力X_(3)为53175.4 Pa、EEPA模型接触塑性比X_(6)为0.31824。在该参数组合下进行验证仿真,其最大轴向压力与试验的相对误差仅为1.71%,并且Bond键的断裂面与试验相比较为符合。仿真与试验所得到的数据基本一致,说明该参数组合可靠,可为后续红黏土的离散元仿真提供理论依据。

关键词：滇中地区红黏土离散元无侧限抗压强度试验参数标定

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面向P2P搜索的可定制聚焦网络爬虫

华中科技大学学报（自然科学版） 2007年第S2期35卷 148-152页

作者：方启明杨广文武永卫朱安平郑纬民清华大学计算机科学与技术系清华信息科学与技术国家实验室北京100084

提出了一种可定制聚焦网络爬虫技术.该技术采用简单的主题描述方法提高网络爬虫的可定制性,利用基于站点页面链接结构的链接导航技术实现对主题信息的高效抓取,通过配置文件实施定制,从而构建一个资源消耗小、数据采集准确性高、可控性... 详细信息

提出了一种可定制聚焦网络爬虫技术.该技术采用简单的主题描述方法提高网络爬虫的可定制性,利用基于站点页面链接结构的链接导航技术实现对主题信息的高效抓取,通过配置文件实施定制,从而构建一个资源消耗小、数据采集准确性高、可控性强的轻量级聚焦网络爬虫,以满足P2P搜索的需求.文中进一步提出一种增量更新和批量更新相结合的网络爬虫数据更新机制,这种混合更新机制降低了增量更新的实现复杂性,相比批量更新具有更小的资源消耗,实验表明采用这种机制能达到较高的数据新鲜度和召回率.

关键词： P2P搜索聚焦网络爬虫链接导航增量更新批量更新

1×4 MMI Splitter Based on Rib SOI Waveguide

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Chinese Journal of Lasers 2000年第6期 46-51页

作者： Supported by the National Natural Science Foundation of China under grant No.69896260 and No.69990540.WEI Hongzhen 1 YU Jinzhong 1 LIU Zhongli 2 Wang qiming 1 fang Changshui 3 ( 1 State Key Laboratory on Integrated optoelectronics, Institu

In this paper, a 1×4 MMI splitter based on silicon on insulator (SOI) by effective index method and guide mode method is designed. The fabrication tolerance was analyzed. The device was fabricated and near field outp... 详细信息

关键词： SOI multimode interference splitter integrated opt?

A Novel Dynamic Stretching Solution to Eliminate Saturation Effect in NDVI and Its Application in Drought Monitoring

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Chinese Geographical Science 2012年第6期22卷 683-694页

作者： LIU fang QIN qiming ZHAN Zhiming School of Earth and Space Science Peking University Beijing 100871 China Satellite Environment Center Ministry of Environmental Protection Beijing 100094 China

The normalized difference vegetation index(NDVI) is one of the key input variables for developing drought ***,the NDVI quickly saturates in high vegetation surfaces,and thus,the generalization of a drought index over different ecosystems becomes a *** paper presents a novel,dynamic stretching algorithm to overcome the saturation effect in NDVI.A scaling transformation function to eliminate saturation effects when the vegetation fraction(VF) is large is *** range adjustment is conducted using three coefficients,namely,the normalization factor(a),the stretching range controlling factor(m),and the stretching size controlling factor(e).The results show that the stretched NDVI(S-NDVI) is more sensitive to vegetation fraction than NDVI when the VF is large,ranging from 0.75 to ***,the saturation effect in NDVI is effectively removed by using the *** analysis suggests that there is a good linear correlation between the S-NDVI and the leaf area index(LAI).At the same time,the proposed S-NDVI significantly reduces or even eliminates the saturation effect over high biomass.A comparative analysis is performed between drought indices derived from NDVI and S-NDVI,*** the experiment,reflectance data from the moderate resolution imaging spectroradiometer(MODIS) products and in-situ observation data from the meteorological sites at a regional scale are *** this study,the coefficient of determination(R2) of the stretched drought index(S-DI) is above 0.5,indicating the reliability of the proposed algorithm with surface soil moisture ***,the S-DI is suggested to be used as a drought index in extended regions,thus regional heterogeneity should be taken into account when applying stretching method.

关键词： drought monitoring saturation effect scaling transformation NDVI MODIS remote sensing