http://54xushuo.net/wiki/ 2026-05-24T07:03:46+08:00 http://54xushuo.net/wiki/ http://54xushuo.net/wiki/lib/tpl/dokuwiki/images/favicon.ico text/html 2022-11-24T13:00:16+08:00 http://54xushuo.net/wiki/doku.php?id=zh:notes:at_credit&rev=1669266016&do=diff AT Model armed with Authorship Credit Allocation Scheme Requirements * Scikit-Multilearn * geniass * geniatagger * MySQL * Matlab Citation Information * Shuo Xu, Ling Li, Congcong Wang, Xin An, and Guancan Yang, 2022. An Improved Author-Topic (AT) Model with Authorship Credit Allocation Schemes. Journal of Information Science. * Shuo Xu, Ling Li, Liyuan Hao, Xin An, and Guancan Yang, 2021. text/html 2022-06-30T11:28:17+08:00 http://54xushuo.net/wiki/doku.php?id=zh:notes:atot_credit&rev=1656559697&do=diff AT Model armed with Authorship Credit Requirements * Scikit-Multilearn * geniass * geniatagger * MySQL * Matlab Citation Information To be added later. Create Database The database SQL file: synthetic_biology.sql. This database consists of the following tables: author, cited_author text/html 2023-03-23T07:42:42+08:00 http://54xushuo.net/wiki/doku.php?id=zh:notes:centos_mysql_pwd&rev=1679528562&do=diff Reset the Password of MySQL in the CentOS Stop mysql Service > systemctl stop mysqld.service Set the Environment Option > systemctl set-environment MYSQLD_OPTS="--skip-grant-tables" Login as root without Password > systemctl start mysqld.service > mysql -uroot text/html 2022-06-30T11:31:33+08:00 http://54xushuo.net/wiki/doku.php?id=zh:notes:centos_mysql_remote&rev=1656559893&do=diff CentOS环境下设置MySQL的远程访问 安装了MySQL默认是拒绝远程连接的。 设置MySQL库的远程访问密码 首先进入数据库，使用系统数据库mysql。 mysql -u root -p mysql 接着对系统数据库的root账户设置远程访问的密码，与本地的root访问密码并不冲突。 text/html 2022-11-08T07:33:47+08:00 http://54xushuo.net/wiki/doku.php?id=zh:notes:common_specialty&rev=1667864027&do=diff Commonality and Specialty Detection Citation Information Shuo Xu, Ling Li, Xin An, Liyuan Hao, and Guancan Yang, 2021. An Approach for Detecting the Commonality and Specialty between Scientific Publications and Patents. Scientometrics, Vol. 126, No. 9, pp. 7445-7475. Requirements * geniass * geniatagger * MySQL * MATLAB * VOSviewer Create Database The database SQL file: text/html 2023-03-14T17:27:16+08:00 http://54xushuo.net/wiki/doku.php?id=zh:notes:cord19_entity&rev=1678786036&do=diff Cord-19-Related Entity Annotation Citation Information * 徐硕，张萌萌，枊力元，王聪聪，孙睿，李怡琳，徐金楠，安欣，2023. 新冠领域溯源类论文筛选及全文实体标注研究. 农业图书情报学报. * Dataset reference: <https://www.semanticscholar.org/cord19> * CORD-19 (Version: 2020-03-13) * Medline/PubMed Full Text * Named Entity Recognition * EvidenceMiner Create Database text/html 2025-12-19T20:55:03+08:00 http://54xushuo.net/wiki/doku.php?id=zh:notes:disruptive_index&rev=1766148903&do=diff Disruptive Index Calculation Citation Information * Shuo Xu, Congcong Wang, Xin An, Yunkang Deng, and Jianhua Liu, 2025. Do OpenCitations and Dimensions Serve as an Alternative to Web of Science for Calculating Disruption Indexes? Journal of Informetrics, Vol. 19, No. 3, pp. 101685. * Shuo Xu, Congcong Wang, Xin An, and Jianhua Liu, 2025. CrossDI: A Comprehensive Dataset Crossing Three Databases for Calculating Disruption Indexes. Scientific Data text/html 2026-04-18T14:14:34+08:00 http://54xushuo.net/wiki/doku.php?id=zh:notes:drugbank&rev=1776492874&do=diff DrugBank Dataset Construction with Extended Information Citation Information * Shuo Xu, Zhen Liu, and Xin An, 2026. Interactions among Organizations from Science, Technology, and Industry on the basis of Percolation Theory: Case Study of Pharmaceutical Industry. Scientometrics. * Shuo Xu, Zhen Liu, Xin An, 2025. STInt: An Integrated Dataset Covering Science, Technology and Industry Information in the Pharmaceutical Field. Scientific Data, Vol. 12, pp. 1056. Dataset * Shuo Xu, Zhen Liu, Xin … text/html 2024-06-24T10:05:02+08:00 http://54xushuo.net/wiki/doku.php?id=zh:notes:education&rev=1719194702&do=diff Mapping Technological Trajectories in the Education Domain Citation Information * Shuo Xu, Congcong Wang, Xin An, Liyuan Hao, and Guancan Yang, 2024. A Novel Developmental Trajectory Discovery Approach by Integrating Main Path Analysis and Intermediacy. Journal of Information Science, Vol. 50, No. 3, pp. 651-672. * Requirements * DTM * Pajek Dataset text/html 2025-07-23T15:11:09+08:00 http://54xushuo.net/wiki/doku.php?id=zh:notes:electric_power&rev=1753254669&do=diff Data Construction for Electric Power Domain Requirements * OpenNLP 1.9.2 * BioC Data Sources * Web of Science: Scientific Publications in English * PatStat: Patents in English Create Database The database SQL file: electric_power.sql. Web of Science Project: text/html 2022-01-28T09:12:20+08:00 http://54xushuo.net/wiki/doku.php?id=zh:notes:emerging_topics_detection&rev=1643332340&do=diff Emerging Research Topics Detection Citation Information Shuo Xu, Liyuan Hao, Xin An, Guancan Yang, and Feifei Wang, 2019. Emerging Research Topics Detection with Multiple Machine Learning Models. Journal of Informetrics, Vol. 13, No. 4, pp. 100983. Requirements * DTM * scikit-Learn * nltk * jbibtext Dataset * Search stragegy * TS = (gene edit*) or TS = (crispr)) text/html 2022-06-30T11:33:14+08:00 http://54xushuo.net/wiki/doku.php?id=zh:notes:exponential_family&rev=1656559994&do=diff Exponential Family The exponential family of distributions over , given parameters , is defined to be the set of distributions of the form where may be scalar or vector, and may be discrete or continuous. Here are called the natural parameters of the distribution, and text/html 2022-01-26T10:39:18+08:00 http://54xushuo.net/wiki/doku.php?id=zh:notes:huang_river&rev=1643164758&do=diff Gap Analysis on the Huang River Domain Citation Information To be added later. Dataset The dataset comes form the Web of Science (WoS). Here, we include all publications of the document type Article, Article; Proceedings Paper, Proceedings Paper, text/html 2022-01-27T08:23:19+08:00 http://54xushuo.net/wiki/doku.php?id=zh:notes:important_citation&rev=1643242999&do=diff Important citations identification by exploiting generative model into discriminative model Citation Information Xin An, Xin Sun, Shuo Xu, Liyuan Hao, and Jinghong Li, 2021. Important Citations Identification by Exploiting Generative Model into Discriminative Model. Journal of Information Science. Requirements * Python 3 * pandas * text/html 2022-11-08T07:35:59+08:00 http://54xushuo.net/wiki/doku.php?id=zh:notes:important_citation_semi&rev=1667864159&do=diff Important Citations Identification with Semi-Supervised Classification Model Citation information Xin An, Xin Sun, and Shuo Xu, 2022. Important Citations Identification with Semi-Supervised Classification Model. Scientometrics, Vol. 127, No. 11, pp. 6533-6555. Requirements * Python3 * Sklearn * matplotlib, pandas, numpy, nltk, re, xlrd, xlwt text/html 2022-06-30T11:35:00+08:00 http://54xushuo.net/wiki/doku.php?id=zh:notes:install_brat&rev=1656560100&do=diff 安装brat 参考：<http://brat.nlplab.org/> 系统环境 CentOS 5.8（64 bits） 下载并安装brat > wget http://weaver.nlplab.org/~brat/releases/brat-v1.3_Crunchy_Frog.tar.gz > tar xzf brat-v1.3_Crunchy_Frog.tar.gz > rm -f brat-v1.3_Crunchy_Frog.tar.gz > cd brat-v1.3_Crunchy_Frog > ./install.sh -u text/html 2022-06-30T11:32:19+08:00 http://54xushuo.net/wiki/doku.php?id=zh:notes:install_brown&rev=1656559939&do=diff Install Brown Word Clustering Tool source: <https://github.com/percyliang/brown-cluster> Operation System CentOS 5.8（64 bits） Install gcc By default, gcc is not installed in CentOS. > yum install gcc-c++ Download and Install > wget https://github.com/percyliang/brown-cluster/archive/master.zip > unzip master > mv brown-cluster-master brown-cluster > rm -f master.zip > cd brown-cluster > make text/html 2020-08-28T15:31:29+08:00 http://54xushuo.net/wiki/doku.php?id=zh:notes:install_dokuwiki&rev=1598599889&do=diff Install Dokuwiki Operation System CentOS 5.8（64 bits） Install PHP > yum list php > yum install php.x86_64 Download dokuwiki Apache的默认安装路径在/var/www/html > wget -P /var/www/html/ https://download.dokuwiki.org/src/dokuwiki/dokuwiki-stable.tgz > cd /var/www/html > tar zxvf dokuwiki-stable.tgz > mv dokuwiki-2017-02-19b dokuwiki text/html 2022-01-28T08:30:59+08:00 http://54xushuo.net/wiki/doku.php?id=zh:notes:install_dtm&rev=1643329859&do=diff Install DTM source：<https://github.com/blei-lab/dtm> Operation System CentOS 5.8（64 bits） Install gsl and gflags > yum install gsl-devel > yum install gcc-c++ > yum install gflags-devel Download and Install > wget https://github.com/blei-lab/dtm/archive/master.zip > unzip master.zip > mv dtm-master dtm > cd dtm/dtm > make text/html 2022-06-30T11:30:18+08:00 http://54xushuo.net/wiki/doku.php?id=zh:notes:install_genia&rev=1656559818&do=diff How to install geniass and geniatagger Operation System CentOS 6.8 (64 bits) Install g++ and ruby > yum install gcc-c++ > yum install ruby Install geniass source: <http://www.nactem.ac.uk/y-matsu/geniass/> > wget http://www.nactem.ac.uk/y-matsu/geniass/geniass-1.00.tar.gz > tar xvzf geniass-1.00.tar.gz > rm -f geniass-1.00.tar.gz > cd geniass > make text/html 2022-06-30T11:28:21+08:00 http://54xushuo.net/wiki/doku.php?id=zh:notes:install_infomap&rev=1656559701&do=diff Install Infomap source: <https://www.mapequation.org/> Requirements * gcc Download Infomap > wget https://github.com/mapequation/infomap/archive/v1.1.3.zip > unzip v1.1.3.zip > mv infomap-1.1.3 infomap > rm -f v1.1.3.zip Make > cd infomap > make > ./Infomap -h # an example > mkdir out > ./Infomap ninetriangles.net out --ftree --clu -N 5 text/html 2023-07-30T17:38:47+08:00 http://54xushuo.net/wiki/doku.php?id=zh:notes:install_mysql&rev=1690709927&do=diff Install MySQL Server on CentOS 8 Source: <https://www.cyberciti.biz/faq/how-to-install-mysql-server-on-centos-8-linux/> To update CentOS system to apply security updates and fixes on Linux system using the yum or dnf command. > yum update > dnf update Install MySQL 8 Server The CentOS 8 box comes with MySQL 8 server package. text/html 2022-06-30T11:30:22+08:00 http://54xushuo.net/wiki/doku.php?id=zh:notes:install_parscit&rev=1656559822&do=diff How to install ParsCit Reference：<https://github.com/knmnyn/parscit>，<http://parscit.comp.nus.edu.sg/index.html> Operation System CentOS 6.8 (64 bits) Upgrade Perl > wget https://www.cpan.org/src/5.0/perl-5.30.0.tar.gz > tar -zxvf perl-5.30.0.tar.gz > rm -f perl-5.30.0.tar.gz > cd perl-5.30.0 > ./Configure -des -Dprefix=/usr/local/perl -Dusethreads -Uversiononly > make > make install # redirect link > mv /usr/bin/perl /usr/bin/perl.bak > ln -s /usr/local/perl/bin/perl /usr/bin/perl # To … text/html 2023-04-24T13:49:11+08:00 http://54xushuo.net/wiki/doku.php?id=zh:notes:install_pgd&rev=1682315351&do=diff Install PGD source: <https://github.com/nkahmed/PGD> Operation System Ubuntu 22.04（64 bits） Install gcc > apt update > apt install build-essential > gcc --version Download PGD > wget https://github.com/nkahmed/PGD/archive/refs/heads/master.zip > unzip -q master.zip > mv PGD-master PGD text/html 2022-01-27T08:23:11+08:00 http://54xushuo.net/wiki/doku.php?id=zh:notes:install_python3-pip&rev=1643242991&do=diff Install Python3-pip Operation System CentOS 7.6 (64 bits) Requirements * Python 3 Install Dependencies > yum -y install zlib-devel bzip2-devel openssl-devel ncurses-devel sqlite-devel readline-devel tk-devel gdbm-devel db4-devel libpcap-devel xz-devel text/html 2022-06-30T11:30:08+08:00 http://54xushuo.net/wiki/doku.php?id=zh:notes:install_python3.7&rev=1656559808&do=diff Install Python 3.7 Operation System CentOS 6.8 (64 bits), CentOS 7.6 (64 bits) Install libffi-devel and zlib-devel # If this library is not installed ahead, the following exception will be raised. # ModuleNotFoundError: No module named '_ctypes' > yum install libffi-devel # If this library is not installed ahead, the following error will appear. # zipimport.ZipImportError: can't decompress data; zlib not available > yum install zlib-devel # This library should be installed ahead. # Oth… text/html 2019-08-16T16:24:00+08:00 http://54xushuo.net/wiki/doku.php?id=zh:notes:install_pytorch&rev=1565943840&do=diff Install PyTorch Operation System CentOS 7.6 (64 bits) Install Python 3.7 How to Install Python 3.7 Install Anaconda > wget https://repo.anaconda.com/archive/Anaconda3-2019.07-Linux-x86_64.sh > chmod u+x Anaconda3-2019.07-Linux-x86_64.sh > ./Anaconda3-2019.07-Linux-x86_64.sh > rm -f Anaconda3-2019.07-Linux-x86_64.sh text/html 2022-01-27T08:23:04+08:00 http://54xushuo.net/wiki/doku.php?id=zh:notes:install_scikit-learn&rev=1643242984&do=diff Install scikit-learn Operation System CentOS 7.6 (64 bits) Requirements * Python 3 * Python3-pip Add a Directory to PATH # append a line to profile > vim /etc/profile > PATH=/usr/local/python3.7.4/bin:$PATH > source /etc/profile > echo $PATH Install scikit-learn text/html 2022-06-30T11:34:14+08:00 http://54xushuo.net/wiki/doku.php?id=zh:notes:install_svinet&rev=1656560054&do=diff Install svinet source: <https://github.com/premgopalan/svinet> Operation System CentOS 5.8（64 bits） Install gsl, gcc-c++ and unzip > yum install gsl-devel > yum install gcc-c++ > yum install unzip Download svinet > wget https://github.com/premgopalan/svinet/archive/master.zip > unzip master.zip > mv svinet-master svinet > rm -f master.zip text/html 2026-04-28T12:00:14+08:00 http://54xushuo.net/wiki/doku.php?id=zh:notes:math_softwares&rev=1777348814&do=diff Math Software Dataset Construction Citation Information * Data Sources * zbMATH * Web of Science * English Wikipedia * Word Embedding: GloVe Create Database The database SQL file: math_software.sql. zbMATH Web of Science Project: WoSImporter Preprocess Articles text/html 2022-06-30T11:27:21+08:00 http://54xushuo.net/wiki/doku.php?id=zh:notes:ml2s_svm&rev=1656559641&do=diff ML$^2$S-SVM: Multi-Label Least-Squares Support Vector Machine Classifiers Requirements Matlab toolbox: ML2S-SVM, MTLSSVM Citation Information Shuo Xu and Xin An, 2019. ML2S-SVM: Multi-Label Least-Squares Support Vector Machine Classifiers. The Electronic Library, Vol. 37, No. 6, pp. 1040-1058. Parameter Turing & Model Running with ML$^2$S-SVM text/html 2024-09-12T20:51:27+08:00 http://54xushuo.net/wiki/doku.php?id=zh:notes:multi-label-covid&rev=1726145487&do=diff Multi-Label Topic Classification for COVID-19 Literature Citation Information * Shuo Xu, Yuefu Zhang, Liang Chen, and Xin An, 2024. Is Metadata of Articles about COVID-19 enough for Multi-Label Topic Classification Task? Database, Vol. 2024, pp. baae106. Dataset * Qingyu Chen, Alexis Allot, Robert Leaman, Rezarta Islamaj, Jingcheng Du, Li Fang, Kai Wang, Shuo Xu, Yuefu Zhang, Parsa Bagherzadeh, Sabine Bergler, Aakash Bhatnagar, Nidhir Bhavsar, Yung-Chun Chang, Sheng-Jie Lin, Wentai Tang, Hon… text/html 2022-10-20T17:20:34+08:00 http://54xushuo.net/wiki/doku.php?id=zh:notes:mysql_backup_restore&rev=1666257634&do=diff Backup and Restore MySQL Database Backup One Database > mysqldump -uusername -ppassword databasename > database-backup.sql Backup Multiple Tables in a Database > mysqldump -uusername -ppassword databasename specific_table1 specific_table2 > database-backup.sql text/html 2022-01-27T08:23:31+08:00 http://54xushuo.net/wiki/doku.php?id=zh:notes:patent_similarity&rev=1643243011&do=diff An Improved Patent Similarity Measurement Citation Information Xin An, Jinghong Li, Shuo Xu, Liang Chen, and Wei Sun, 2021. An Improved Patent Similarity Measurement based on Entities and Semantic Relations. Journal of Informetrics, Vol. 15, No. 2, pp. 101135. Requirements * Python 3模块： * Pandas: pip install pandas text/html 2020-08-28T21:02:06+08:00 http://54xushuo.net/wiki/doku.php?id=zh:notes:rel_type_tng&rev=1598619726&do=diff Semantic Relation Extraction Aware of N-Gram Features from Unstructured Biomedical Text Citation Information Zheng Wang, Shuo Xu, and Lijun Zhu, 2018. Semantic Relation Extraction Aware of N-Gram Features from Unstructured Biomedical Text. Journal of Biomedical Informatics, Vol. 86, pp. 59-70. Requirements * JDK 1.8 + * Maven * text/html 2022-06-30T11:26:39+08:00 http://54xushuo.net/wiki/doku.php?id=zh:notes:running_jate2&rev=1656559599&do=diff Running JATE2.0 (Embedded mode) source: <https://github.com/ziqizhang/jate> download JATE2.0 <https://github.com/ziqizhang/jate/releases> jate-2.0-beta.1-jar-with-dependencies.jar clone and download JATE2.0 把solr-testbed拷贝到与以上jar包在同一个目录下，然后创建某个文件夹，把自己的数据放在那个文件夹中，最后运行下面的命令即可。 text/html 2024-12-09T10:18:47+08:00 http://54xushuo.net/wiki/doku.php?id=zh:notes:sentences&rev=1733710727&do=diff Several Excerpted Sentences * The procedure boils down to exploring a pattern via a spanning tree to construct a canonical form of a pattern, a useful construct to establish isomorphism without actually running a computationally intensive test. * text/html 2026-03-28T19:10:00+08:00 http://54xushuo.net/wiki/doku.php?id=zh:notes:sidebar&rev=1774696200&do=diff 科研笔记（Notes） * Math Software Dataset Construction * Scientific Data Constrution * Install PGD * Cord-19-Related Entity Annotation * Data Construction for Electric Power Domain * Disruptive Index Calculation * Backup & Restore MySQL Database * Install MySQL Server on CentOS 8 * Multi-Label Topic Classification for COVID-19 Literature * Semi-Supervised Important Citations Identification * Gap Analysis in the Huang River Domain * DrugBank Dataset Construction with Extende… text/html 2020-10-17T16:19:55+08:00 http://54xushuo.net/wiki/doku.php?id=zh:notes:techemergence&rev=1602922795&do=diff Detecting and Forecasting Emerging Technologies Citation Information Shuo Xu, Liyuan Hao, Guancan Yang, Kun Lu, and Xin An, 2021. A Topic Models based Framework for Detecting and Forecasting Emerging Technologies. Technology Forecasting and Social Change, Vol. 162, pp. 120366. Create Database The database SQL file: emergence.sql text/html 2022-06-30T11:32:40+08:00 http://54xushuo.net/wiki/doku.php?id=zh:notes:topic_extraction_mmsb&rev=1656559960&do=diff Overlapping Thematic Structures Extraction with Mixed-Membership Stochastic Blockmodel data source: Topic Extraction Challenge Citation Information Shuo Xu, Junwan Liu, Dongsheng Zhai, Xin An, Zheng Wang, and Hongshen Pang, 2018. Overlapping Thematic Structures Extraction with Mixed-Membership Stochastic Blockmodel. Scientometrics, Vol. 117, No. 1, pp. 61-84. text/html 2022-06-30T11:31:24+08:00 http://54xushuo.net/wiki/doku.php?id=zh:notes:topic_linkages2&rev=1656559884&do=diff Topic Linkages between Scientific Publications and Patents Citation Information Shuo Xu, Dongsheng Zhai, Feifei Wang, Xin An, Hongshen Pang, and Yirong Sun, 2019. A Novel Method for Topic Linkages between Scientific Publications and Patens. Journal of the Association for Information Science and Technology, Vol. 70, No. 9, pp. 1026-1042. text/html 2022-06-30T11:28:26+08:00 http://54xushuo.net/wiki/doku.php?id=zh:notes:update_gcc&rev=1656559706&do=diff Update gcc Operation System CentOS 6.8 (64 bits), CentOS 7.6 (64 bits) Download the Latest Version > wget http://ftp.gnu.org/gnu/gcc/gcc-10.2.0/gcc-10.2.0.tar.gz > tar -zxvf gcc-10.2.0.tgz > rm -f gcc-10.2.0.tgz Download the Prerequisites > cd gcc-10.2.0 > ./contrib/download_prerequisites