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課程名稱 |
生醫資料探勘
BIOMEDICAL DATA MINING |
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開課學期 |
99-1 |
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授課對象 |
生命科學院 基因體與系統生物學學位學程 |
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授課教師 |
陳倩瑜 |
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課號 |
BME5419 |
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課程識別碼 |
631 U9470 |
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班次 |
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學分 |
3 |
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全/半年 |
半年 |
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必/選修 |
選修 |
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上課時間 |
星期二6,7,8(13:20~16:20) |
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上課地點 |
知203 |
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備註 |
合適本學程學生選修。
總人數上限：40人 |
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Ceiba 課程網頁 |
http://ceiba.ntu.edu.tw/991BioDataMining |
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課程簡介影片 |
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核心能力關聯 |
核心能力與課程規劃關聯圖 |
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課程大綱
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課程概述 |
此一課程在於介紹資料探勘之演算法應用於生醫相關之研究，包括資料正規化/特徵選取/資料分群/資料分類/序列特徵探勘。 |
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課程目標 |
使學生獲得從事生醫資料分析必須之基礎能力 |
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課程要求 |
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預期每週課後學習時數 |
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Office Hours |
每週一 13:00~14:00
每週二 13:00~14:00 |
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指定閱讀 |
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參考書目 |
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評量方式
(僅供參考) |
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No. |
項目 |
百分比 |
說明 |
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1. |
期中考 |
30% |
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2. |
期末專題 |
20% |
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3. |
隨堂報告 |
20% |
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4. |
作業 |
30% |
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週次 |
日期 |
單元主題 |
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第1週 |
09/14 |
Introduction |
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第2週 |
09/21 |
Data Preprocessing |
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第3週 |
09/28 |
Data clustering (I) |
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第4週 |
10/05 |
Data clustering (II), Comprehensive Identification of Cell Cycle-regulated Genes of the Yeast Saccharomyces cerevisiae by Microarray Hybridization (Molecular Biology of the Cell, 1998) |
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第5週 |
10/12 |
Cluster analysis and display of genome-wide expression patterns (PNAS, 1998) (家誠, 孟軒, 俞州) [feature selection, univariate analysis, SAM] Significance analysis of microarrays applied to the ionizing radiation response, PNAS, 2001; Statistical significance for genomewide studies, PNAS, 2003 |
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第6週 |
10/19 |
Molecular Classification of Cancer: Class Discovery and Class Prediction by Gene Expression Monitoring (Science, 1999 ) (曙詮, 翊安, 意儒) [data clustering, SOM, feature selection, univariate analysis] |
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第7週 |
10/26 |
Data classification, Statistical methods for identifying yeast cell cycle
transcription factors (PNAS, 2005) (宗廷, 慶和, 品翔) |
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第8週 |
11/02 |
Two-way ANOVA, Data classification, ChIP-data |
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第9週 |
11/09 |
Data classification, Knowledge-based analysis of microarray gene expression data by using support vector machines (PNAS, 2000) (品蒨, 承恩, 健合) |
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第10週 |
11/16 |
Midterm |
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第11週 |
11/23 |
SVM (short comments), Mining association rules, Pattern mining, Predicting Gene Expression from Sequence (Cell, 2004) (家全, 之儀, 陸 彤) Predicting Gene Expression from Sequence: A Reexamination (PLoS computational biology, 2007) |
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第12週 |
11/30 |
Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment (Science, 1993) |
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第13週 |
12/07 |
EM clustering, Discovering Gapped Binding Sites of Yeast Transcription Factors (PNAS, 2008) (永軒, 昶志, 豐伃) |
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第14週 |
12/14 |
Discussions on topics of final projects [Project examples: 1. Cross-generation and Cross-laboratory Predictions of Affymetrix Microarrays by Rank-based Methods, 2. Statistical identification of gene association by CID in application of constructing ER regulatory network] |
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第15週 |
12/21 |
因出國開會停課一次 |
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第16週 |
12/28 |
Introduction to next-generation sequencing (邀請電機系盧奕璋教授前來給予演講) |
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第17週 |
01/04 |
RNA-Seq, DEGsea: an R package for identifying differentially expressed genes from RNA-seq data (Bioinformatics, 2010) (宜萍, 康育) [Proposal for final project] |
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第18週 |
01/11 |
ChIP-Seq, Genome-wide identification of in vivo protein–DNA binding sites from ChIP-Seq data (NAR, 2008) (柏均, 鈺喬) |
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第19週 |
01/18 |
Final project presentation |
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