Potential Applications of Class Frequency Distributions of Maximal Repeats

Potential Applications using the Class Frequency
Distribution of Maximal Repeats
from Tagged Sequential data.
Jing-Doo Wang (王經篤)
Associate Professor
Asia University, Taiwan.
第八屆台灣 Hadoop 社群年會 HadoopCon 2016
中央研究院人文社會科學館 (2016.9.10)

簡介
• 現職:
– 亞洲大學資訊工程系副教授
• 最高學歷:
– 中正大學資訊工程所博士
• 專長
– 文字挖掘(Text Mining)-Maximal Repeat Extraction
– 生物資訊(Bioinformatics)、
– 雲端計算(Cloud Computing)、
– 類別架構模糊度之評估(Class Structure Ambiguity
Evaluation)

亞洲現代美術館
http://www.asia.edu.tw/main_1.php?yard/yard_01_09

Asia University Hospital
亞洲大學附屬醫院(2016.8.1)
http://www.auh.org.tw/web/index.php

精準醫療
(Precision Medicine)
• 臨床醫學 (中國醫大醫院+亞大附屬醫院)
• 基因體定序(Next Generation Sequencing)
• 生物資訊(亞洲大學)
http://newjust.masterlink.com.tw/HotPr
oduct/HTML/img/GetImg.xdjpng?A=PA3
14-1b.png

大數據研究中心
（一）建置本校大數據研究設備。
（二）整合精準醫療相關資料庫。
（三）執行有關大數據之學術交流、研究發展與
產學事宜。
（四）執行有關大數據之推廣服務相關事宜。

學士後第二專長學士學位學程
申請學校：亞洲大學
新設學程：學士後巨量資料處理與分析學程

Outline
• Introduction
• Pattern History For Trend Analysis
• Product Traceability for Quality Monitoring
• Mining for Distinctive Pattern (Biomarker)
from Genomic Sequences
• Future Works

9
“xabcyiiizabcqabcyrxar”
• ab
• bc
• abc
• abcy
Not Maximal repeat Pattern
Maximal Repeat Pattern
Yes
Yes

Why use “Maximal Repeats ”
as features?
• Dictionary
– How to identify new words or phrases?
– e.g. “just do it”, “洪荒之力”。
• N-gram
– 2-gram, 3-gram,…,5-grams. (Google Ngram viewer)
– The value of “N” is limited.
• Maximal Repeat
– The length of maximal repeat is variable.

Journal of Supercomputing,
72(8), pp. 3236-3260,April 2016

專利概念圖
一個最大重複樣式抽取與計算
出現次數分布表格之方法

Patent Application Serial Number
(US 15/208,994)( 申請中)
• Wang, Ching-Tu. Method for Extracting Maximal
Repeat Patterns and Computing Frequency
Distribution Tables. Patent Application Serial
Number 15/208,994. 13 July 2016.
• 申請美國發明專利PA
– 所有權:王經篤
– 發明人:王經篤

The flowchart of Maximal Repeat
Extraction via MapReduce

Boundary Verification
(Left&Right)

Pattern History for Trend Analysis
Jing-Doo Wang (王經篤)
Associate Professor
Asia University, Taiwan.
2016/9/12 19FSKD 20'11
Sequential Data + Timestamp

Experimental Results
• Download the abstracts of articles in PubMed
from 1990~2014.(25 years)
2016/9/12 21FSKD 20'11

PubMed
(1990~2014)(25 years)
The abstracts and titles of
14,473,242 articles
=>about 12 GB
2016/9/12 22FSKD 20'11

The Abstracts and Titles of PubMed
Articles (1990~2014)(12GB)
6 PCs=> 5 hours

The History of a Significant Pattern
顯要樣式歷史
The history of a significant pattern is the
frequency distribution of that pattern over
equally spaced time intervals.
25

Significant Pattern
(顯要樣式)
• A significant pattern is one maximal repeat of
consecutive words within texts.
26
(Length=1) TDP-43
(Length=1)SARS
(Length=1)H1N1
(Length=5)non-small cell lung cancer (NSCLC)
(Length=6)75 g oral glucose tolerance test
(Length=6)4 x 4 Latin square design
(Length=7)2 x 2 factorial arrangement of treatments
(Length=9)the National Institute of Child Health and Human Development
(Length=10)patients with squamous cell carcinoma of the head and neck
(Length=11)anomalous origin of the left coronary artery from the pulmonary artery
(Length=12)Pregnancy and Childbirth Group trials register and the Cochrane Controlled Trials Regist
(Length=13)the European Organization for Research and Treatment of Cancer Quality of Life Questi

The History of the “HINI”
27

(50,75,100) g Oral Glucose
Tolerance Test
2016/9/12 FSKD 20'11 28

The (goal, aim, purpose) of this study
2016/9/12 FSKD 20'11 29
aim
goal
purpose

Archaeology
(考古學)
https://zh.wikipedia.org/wiki/%E8%80%83%E5%8F%A4%E5%AD%A6

On-Line.
– PubMed (Medicine Articles)(1990-2014)
– CNA (Central News Agent)(中央社新聞)(1990-1996)
– 中華民國專利(1950~2009)(中華民國專利文件)
Potential Works. 法院判決案例 (Judicial Systems)
– (Studies that allow closer examination of legal texts)
– 全國碩博士論文
– 中央圖書館
– 中華明國專利(Patents)
– 小說
– 金庸小說全集
– Harry Potter(哈力波特)
– Shakespeare
– 九把刀
– Blogs.
– News.
Text Archaeology
(文件考古學)
圖:https://www.google.com.tw/search

個人化學習
樣式歷史雲
http://www.tutortristar.com/topic/Internet/seminar-big-data-marketing-beckett-
20151005.html?utm_source=facebook&utm_medium=banner&utm_campaign=seminar-
bigdata-marketing

老人語言智力檢測
(重複性話語)
你吃飽了沒!
https://www.google.com.tw/search

新增語言詞彙檢測
(口頭禪)

如何收集口語?
轉換成文字?
Google’s Speech
Recognition API
Version 2

時間標籤文字+地理位置

農產品Traceability (產銷履歷)
• 農產品產銷履歷制度＝臺灣良好農業規範
實施及驗證＋履歷追溯體系
• 產銷履歷—安全、永續、資訊公開之可追溯
農產品
From: http://taft.coa.gov.tw/ct.asp?xItem=4&CtNode=206&role=C

χ α β ϒ θ φ樣式(Symbol)
序列化
(Serialization)數值(Numeric Value)
生產履歷
(Product Traceability)
樣式化
(Symbolization)
大陸惠州 /蘇州
紙本記錄自動量測機量測紙本記錄X-R管制目視管制顯微鏡量測
照片檔
紙本記錄X-R管制
Icon: http://www.freepik.com
自動量測機量測自動量測機量測

40
產銷履歷=>
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Products
(產品)
Steps(步驟)專家意見

41
特殊事件(訊號)序列
(某類別中重複出現的序列)
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專家意見

事件(訊號)序列
#****?
@****
&*******%
$**********
*****

物聯網（IoT）
http://www.indetail.com.tw/archives/2494

物聯網（IoT）+ 工業4.0=?
http://portal.stpi.narl.org.tw/index/article/10095

物聯網（IoT）+ 工業4.0
資料處理=>BigData!
www.slideshare.net

監控與異常分析
http://innobic.blogspot.tw/

單點故障
(single point of failure)
www.ontargetpartners.com

單點故障=>
具有經驗者可能解決!
www.benison.com.tw
www.youtube.com

統計分析
newgenerationresearcher.blogspot.com

統計分析觀點
• 單點故障=>單變數分析
• 多點故障=>多變數分析(multivariate analysis)
www.slideshare.net

意外(Accident)
?=多點故障(Multiple Points of Failure)
multiple points of failure
ops.fhwa.dot.gov

電影• 絕命終結站
g333773.pixnet.net maizizi.pixnet.net

(一連串事件的組合!)
=>意外
• 無法預測?
www.frillo.co.uk

Wu Gui says "There are no accidents" -
https://www.youtube.com/watch?v=Q04LPj99ZPc

人力組裝-生產線
jdzol.com.cn www.cfea.org.cn

機械人組裝-生產線
kaifangzhansb.mofcom.gov.cn

從資料處理的角度來看
這些代表了甚麼?
http://superbest.typepad.com/.a/6a00d83451b39269e20147e
25f0551970b-pisuperbest.typepad.com

每件【物品】的背後
一連串的數字(符號)
www.36dsj.com big5.xinhuanet.com

「工業4.0」吹響號角
加速資訊化與智慧化融合
提升「智造」競爭力
http://tw.digiwin.biz/newsListDetail_6828.html

天下武功，無堅不破，唯快不破！
chuansong.me
dannylun.blogspot.com

62
物聯網(IoT) vs. 產銷履歷(Traceability)
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Products
(產品)
Steps(步驟)

63
物聯網(IoT) vs. 產銷履歷(Traceability)
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Products
(產品)
Steps(步驟)
blog.tianya.cn news.hxsd.com

Traceability (產銷履歷)
P1 => S1, S2, S3, S4, S5, S6, S7, S8, S9, S10
P2 => S1, S2, S3, S4, S5, S6, S7, S8, S9, S10
P3 => S1, S2, S3, S4, S5, S6, S7, S8, S9, S10
P4 => S1, S2, S3, S4, S5, S6, S7, S8, S9, S10
P5 => S1, S2, S3, S4, S5, S6, S7, S8, S9, S10
P6 => S1, S2, S3, S4, S5, S6, S7, S8, S9, S10
…
…
…
P99 => S1, S2, S3, S4, S5, S6, S7, S8, S9, S10
P100=> S1, S2, S3, S4, S5, S6, S7, S8, S9, S10
100
Products
(產品)
10 Steps(步驟)

Traceability (產銷履歷)(1)
…[S3] [S4] [S5]…

P1 => S1, S2, S3, S4, S5, S6, S7, S8, S9, S10
P2 => S1, S2, S3, S4, S5, S6, S7, S8, S9, S10
P3 => S1, S2, S3, S4
P4 => S1, S2, S3, S4, S5, S6, S7, S8, S9, S10
P5 => S1, S2, S3, S4, S5, S6, S7, S8, S9, S10
P6 => S1, S2, S3, S4, S5, S6, S7, S8, S9, S10
…
…
…
P99 => S1, S2, S3, S4, S5, S6, S7, S8, S9, S10
P100=> S1, S2, S3, S4, S5, S6, S7, S8, S9, S10
Detect Abnormal
(發現異常)
www.publicdomainpictures.net

…[S3] [S4] [S5]…

P1 => S1, S2, S3, S4, S5, S6, S7, S8, S9, S10
P2 => S1, S2, S3, S4, S5, S6, S7, S8, S9, S10
P3 => S1, S2, S3, S4, S5, S6, S7, S8, S9, S10
P4 => S1, S2, S3, S4, S5, S6, S7, S8, S9, S10
P5 => S1, S2, S3, S4, S5, S6, S7, S8, S9, S10
P6 => S1, S2, S3, S4, S5, S6, S7, S8, S9, S10
…
…
…
P99 => S1, S2, S3, S4, S5, S6, S7, S8, S9, S10
P100=> S1, S2, S3, S4, S5, S6, S7, S8, S9, S10
Detect Abnormal
(發現異常)
=>產品(半成品)完成時

逐一檢查產銷過程?
• P3 => S1, S2, S3, S4, S5, S6, S7, S8, S9, S10
• P99 => S1, S2, S3, S4, S5, S6, S7, S8, S9, S10
Figure: www.yuhing.edu.tw

P1 => S1, S2, S3, S4, S5, S6, S7, S8, S9, S10
P2 => S1, S2, S3, S4, S5, S6, S7, S8, S9, S10
P3 => S1, S2, S3, S4, S5, S6, S7, S8, S9, S10
P4 => S1, S2, S3, S4, S5, S6, S7, S8, S9, S10
P5 => S1, S2, S3, S4, S5, S6, S7, S8, S9, S10
P6 => S1, S2, S3, S4, S5, S6, S7, S8, S9, S10
…
…
…
P99 => S1, S2, S3, S4, S5, S6, S7, S8, S9, S10
P100=> S1, S2, S3, S4, S5, S6, S7, S8, S9, S10

P3 => S1, S2, S3, S4, S5, S6, S7, S8, S9, S10
P99 => S1, S2, S3, S4, S5, S6, S7, S8, S9, S10
P2 => S1, S2, S3, S4, S5, S6, S7, S8, S9, S10
P4 => S1, S2, S3, S4, S5, S6, S7, S8, S9, S10
P6 => S1, S2, S3, S4, S5, S6, S7, S8, S9, S10
P1 => S1, S2, S3, S4, S5, S6, S7, S8, S9, S10
P4 => S1, S2, S3, S4, S5, S6, S7, S8, S9, S10
P5 => S1, S2, S3, S4, S5, S6, S7, S8, S9, S10
…
…
P100=> S1, S2, S3, S4, S5, S6, S7, S8, S9, S10

S5, S6, S7
S1, S2, S3, S4
S1, S2, S3
S8, S9, S10
S1, S2, S3, S4, S5, S6, S7, S8, S9, S10
S9, S10

Ma_1
Ma_2
Mb_1
Mb_2
Ma_3
Mc_1
Mc_2
…-[S3,Ma_1]-[S4,Mb_2]-[S5,Mc_1]-…

[Step,Machine]
P1 =>[S1,M]-[S2,M]-[S3,M]-…-[S9,M] -[S10,M]
P2 =>[S1,M]-[S2,M]-[S3,M]-…-[S9,M] -[S10,M]
P3 =>[S1,M]-[S2,M]-[S3,M]-…-[S9,M] -[S10,M]
P4 =>[S1,M]-[S2,M]-[S3,M]-…-[S9,M] -[S10,M]
P5 =>[S1,M]-[S2,M]-[S3,M]-…-[S9,M] -[S10,M]
P6 =>[S1,M]-[S2,M]-[S3,M]-…-[S9,M] -[S10,Mj]
…
…
…
P99 =>[S1,M]-[S2,M]-[S3,M]-…-[S9,M] -[S10,M]
P100 =>[S1,M]-[S2,M]-[S3,M]-…-[S9,M] -[S10,M]
10 Steps(步驟)
100
Products
(產品)

…-[S3,Ma_2]-[S4,Mb_1]-[S5,Mc_2]-…
…-[S3,Ma_1]-[S4,Mb_2]-[S5,Mc_1]-…
…-[S3,Ma_1]-[S4,Mb_3]-[S5,Mc_1]-…
…-[S3,Ma_2]-[S4,Mb_3]-[S5,Mc_1]-…
…-[S3,Ma_2]-[S4,Mb_2]-[S5,Mc_2]-…
…-[S3,Ma_1]-[S4,Mb_2]-[S5,Mc_2]-…
…-[S3,Ma_2]-[S4,Mb_1]-[S5,Mc_2]-…
…-[S3,Ma_2]-[S4,Mb_2]-[S5,Mc_1]-…

…-[S3,Ma_2]-[S4,Mb_2]-[S5,Mc_1]-…
…-[S3,Ma_2]-[S4,Mb_2]-[S5,Mc_2]-…
…-[S3,Ma_1]-[S4,Mb_2]-[S5,Mc_2]-…
…-[S3,Ma_2]-[S4,Mb_1]-[S5,Mc_2]-…
…-[S3,Ma_1]-[S4,Mb_3]-[S5,Mc_1]-…
…-[S3,Ma_2]-[S4,Mb_3]-[S5,Mc_1]-…
…-[S3,Ma_1]-[S4,Mb_2]-[S5,Mc_1]-…
…-[S3,Ma_2]-[S4,Mb_1]-[S5,Mc_2]-…

…-[S3,Ma_1]
[S4,Mb_2]-…
[S4,Mb_2]-…
…-[S3,Ma_2]-[S4,Mb_1]-[S5,Mc_2]-…
-[S5,Mc_1]-…

[Step,Machine,Time]
P1 =>[S1,Ma,T1]-[S2,Mb,T2]-[S3,Mc,T3]-…-[S9,Mi,T9] -[S10,Mj,T10]
…
…
…

[Step,Machine,Time]
…
…
…

逆向思考
• 實驗中找出為何{ 好}的原因?
frank727.pixnet.net

城市獵人沙漠之鷹
(萬中選一)
detail.chiebukuro.yahoo.co.jp
www.aigouboke.com

85
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專家意見

電容-生產履歷(Traceability)
Tags + Sequential Data
• 序列資料 (Sequential Data)
– 生產過程中-自動化數據收集
• (材料批號、機台、時間等)。
• 專家意見(Tags)
– (出廠前)電容品質
• (標籤: ok, 缺失A, 缺失B, 缺失C,… )
– (出廠後) 電容保固期間損壞
• (標籤: ok, 缺失D, 缺失E, 缺失F,… )

研華股份有限公司(研華)
Advantech Co.,Ltd.
From: http://www.advantech.com.tw/

打造企業的資料湖泊（ ETU ）
From:http://etusolution.com/index.php/tw/solution-tw/etu-datalake
生產履歷
分析
(jdwang: Maximal
Repeat Extraction)

工業4.0 製造業
產銷履歷分析
製造業工廠
(Factory)
嵌入式系統業
(Embedded
System)
雲端計算服務
平台 (Cloud
Computing
Platform)
產銷履歷-分析
(Maximal
Repeat
Extraction)
品管部門
(Quality
Department )
管理決策
(Decision
Management)

http://d1zlh37f1ep3tj.cloudfront.net/wp/wblob/54592E651337D2/33A8/5D7B11/lCIOuvczuB3
U81XGqm9nag/903_1438243768yq2L.jpg

我懂【半導體產業】嗎?
http://technews.tw/2016/04/11/tsmc-and-largan/
http://image.slidesharecdn.com/random-09062
phpapp02/95/-9-728.jpg?cb=1245484455
http://www.slideshare.net/5045033/ss-1002323

It will be a hard work!
http://previews.123rf.com/images/dirkercken/dirkercken1208/dirkercken120800053/14852048-
hard-work-ahead-tough-job-be-ambitious-even-if-you-have-a-difficult-challenging-task-with-
impact-to--Stock-Photo.jpg

New Direction & Thinking!
http://switchandshift.com/11-trademarks-of-rebellious-leadership

94
晶片-生產履歷
****************************************
www.iconarchive.comhttp://technews.tw/2016/04/11/tsmc-and-largan/
http://www.slideshare.net/5045033/ss-1002323

台積電再度與清大合辦
「第2屆半導體大數據分析競賽」
http://www.appledaily.com.tw/realtimenews/article/new/20150713/647073/

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專家意見
(Tags)
時間、機台、原料(廠牌)、溫度、壓力、操作人員等
Sequential Data (序列化資料)

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Products
(產品)
Sequential Data (序列化資料)
專家意見(Tags)
Tags +Sequential Data

98
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專家意見

Obstacles
• Numerical Values => Symbols
• Expert Opinions
– (Class or Tag)
• Interactive Interfaces
• Computing Environment
• Chip- Traceability
http://sponsorshipgreen.com/wp-content/uploads/2015/05/overcoming-obstacles-web-
1200x725.jpg

推動產學合作狀況!
• 廠商、公司:有機會，再研究!?
https://includedbygrace.files.wordpress.com/2014/01/upset-character.jpg

Make a wish or hope!?
http://ncmissionofhope.org/updates/wp-content/uploads/2016/03/Hope.jpg

回到原點!
http://books.cw.com.tw/sites/default/files/blog/images/%E6%88%9
1%E7%9A%84%E5%8F%B0%E6%9D%B1%E5%A4%A2.jpg

From: http://image.slidesharecdn.com/a-systematic-approach-to-genotypephenotype-
correlations-1203626174948644-4/95/a-systematic-approach-to-genotypephenotype-
correlations-4-728.jpg?cb=1203597376
From: Nucleic Acids Res. 2007 Aug; 35(16): 5625–5633.

異中求同（不同物種間的比對）

同中求異(同物種間的比對)

Human 23 Chromsome
https://zh.wikipedia.org/wiki/%E4%BA%BA%E9%A1%9E%E5%9F%BA%E5%9B%A0%E7%B5%
84#/media/File:Karyotype.png

Coding Genes
https://zh.wikipedia.org/wiki/%E4%BA%BA%E9%A1%9E%E5%9F%BA%E5%9B%A0%E7%B5%84#
/media/File:Human_genome_to_genes_zh.png

49267 Human Genes
(upstream 5000 bp)
Class Types # of Genes Percent
Coding Genes 38,645 78%
NonCoding Genes 10,622 22%

https://en.wikipedia.org/wiki/Gene#/media/File:DNA_to_protein_or_ncRNA.svg

Upstream & Downstream
********************************
********************************
********************************
********************************
********************************
********************************
********************************
********************************
********************************
********************************
********************************
***
***
***
***
***
***
***
***
***
***
***
5000 bp 500 bp
Coding
Genes
NonCoding
Genes
Classes

Finding Possibility
http://engage.riggspartners.com/r-blog/3business/finding-possibility

OncoGene&TumorSuppressor
Genes
ClassID Class Types # of Genes Percent
Coding Genes
C1 Non-Cancer Gene 37,914 76.96%
C2 OncoGene 345 0.70%
C3
TumorSuppressor
Gene
386 0.78%
NonCoding
Genes
C4 NonCoding Gene 10,622 21.56%

37,914
345
386 10,622
Human Genes
(49,267 )
Non-Cancer Gene OncoGene TumorSuppressor Gene NonCoding Gene

Experiments
1: Existence.
0: Non-
Existence
Condition
C1 C2 C3 C4
DF
(≧)
Length
(≧)
# of
Maxiaml
Repeats
C1C2C3C4 1 1 1 1 1000 36 143
C2C3C4 0 1 1 1 10 10 1
C2C3 0 1 1 0 2 10 1788
C2C4 0 1 0 1 10 10 35
C3C4 0 0 1 1 10 10 53

Acknowledgements
• 張建國教授
– 中國醫藥大學
• 詹雯玲助理教授
– (亞洲大學)
• 王昭能助理教授
– (亞洲大學)
100 萬

次世代定序
(Next Generation Sequencing , NGS)
http://www.slideshare.net/ueb52/introduction-to-next-generation-sequencing-v2

美國總統向癌症宣戰! 全力推動抗癌
登月計畫(Cancer Moonshot)
http://i2.wp.com/geneonline.news/wp-
content/uploads/2016/01/Obama_precision_medicine_0130151-
e1453785268417.jpg?fit=1292%2C665

千兆基因組定序完成
癌症研究重大里程碑
• 「加拿大卑詩癌症中心完成定序 1,000 兆位
元組（Terabyte，TB）的基因序列，相當於
一個拍位元組（Petabyte，PB），遠比國際
性的人類基因體計畫所定序的 DNA 超出
33,000 倍；科學家更找出全球第四大致死
癌症——胃癌的變異基因。」
http://geneonline.news/index.php/2016/05/30/canada-bioinformatics/

Maximal Repeats appearing in
all of 24 human chromosomes.
• Length |Maximal Repeats| <= 500 bp
– Ok!
• Length |Maximal Repeats| <= 1000 bp
– Disk Space Full!

Acknowledgements
• 王耀聰 (Jazz Wang)

國際半導體展
(2016.9.9,台北南港展覽館)

Future Works
• Hadoop (OffLine) => Spark (OnLine)
• Next Generation Sequence (次世代基因定序)
• Product Traceability (產品履歷)
• 立隆電子-亞洲大學 (產學合作案)
• Web Logs Analysis (駭客行為?)
• User Behavior Analysis (使用者行為分析)

亞洲大學-產學合作機會
• 測試生產履歷(Traceability) 儲存空間
• 巨量資料計算平台

Thanks for your listening!
感謝聆聽! 請多指教!
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