2018 spring Course
<Bio-medicine Text Mining and Knowledge discovery>
研究生课程《生物医药文本挖掘和知识发现》
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Outline oWeek 1: (9th, Mar) •Chapter 0. Introduction of BioNLP and This Course •Chapter 1. First Class of Linux and Lexicon Analysis -Alex's Case(教师Slides, download here.) 数据: Brown Corpus Sample. 史志茹:《Token/Term Ratio》(Slides download here.) oWeek 2: (16th, Mar) •Chances for earning points, 3 talks (8-10 mins for each) •Chapter *. Idea of this Course •Chapter 2. R programming & Word Cloud (Slides download here) 杨晨:《Word Cloud代码详解》(Slides download here.) 郭梦瑶:《Word Cloud应用》(Slides download here.) 钱胜:《Rapidly hybrid speciation in Darwin's finches》(Slides download here.) oWeek 3: (23rd, Mar) •Chances for earning points, 3 talks (8-10 mins for each) •Chapter 3. Gene Ontology (Dataset and Text Retrieval and Ontology)(Slides download here) Suggested link: ftp://ftp.geneontology.org/go/www/GO.tools_by_type.term_enrichment.shtml Suggested paper: AgriGO-https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896167/ 付海涛:《GO富集分析》(Slides download here.) (Codes and Data download here.) 万靖:《昼夜节律的GO分析和文本挖掘》(Slides download here.) oWeek 4: (30th, Mar) •Chances for earning points, 3 talks (8-10 mins for each) •Chapter 4. Side Effect and Human Phenotype Ontology (Case study for drug repurposing) HPO disease-gene-phenotype link ref (download here). 许璇:《Psoriasis Drug repurposing》 (Slides download here.) 佟馨宇:《Case study for drug repurposing》 (Slides download here.) oWeek 5: (8th, Apr) •Chances for earning points, 3 talks (8-10 mins for each) •Chapter 5. Clinical Trial and Its R package application (Download the slides) *Chapter 5'. NER and Shell programming. (Codes for shell was distributed in class. Please cautiously use the curl command. Please...) 薛雅文:《利用shell编程实现NLP》(Slides download here.) 廖璇:《Shell programming for NER》(Slides download here.) oWeek 6: (13th, Apr) •Chances for earning points, 3 talks (8-10 mins for each) •Chapter 6‘. GloVe, a start of semantic computation. 丁可:《GloVe, Global Vectors for word representation》(Download the slides) 章胜:《Tensorflow implementation of GloVe》(Codes and data) 李桐:《GloVe思想与密码子偏好性》(Slides download here.) 周开银:《词向量对数据挖掘任务的影响》(Slides download here.) 张亚亮:《GloVe for PubMed texts》(Slides, Codes) oWeek 7: (20th, Apr) •Chances for earning points, 3 talks (8-10 mins for each) •Chapter 6. Event Extraction and Knowledge Discovery (A little bit Python coding and Parsing tree thing) Text data set 1: SE for salsalate (Download here.) Text data set 2: SE for viagra (Download here.) 毛盛强:《Event Extraction and Knowledge discovery》(Slides download here.) 王书言: 《用Metamap和Semrep发现salsalate和viagra的副作用》(Slides download here.) oWeek 8: (27th, Apr) •Chances for earning points, 2 talks (8-10 mins for each) •Conclusion Talk <History and Future of Bio Text Mining> |