Post on 08-Jun-2020
ConvergenceInformatics
Chapter 1 & 2 (Week 1)Course overview & introduction
DCCS326 Korea University 2019 Fall
Asst. Prof. Minseok Seo
mins@korea.ac.kr
01Course OverviewConvergence (Multidisciplinary) Informatics
Contents
Definition of Informatics
Introduction to Informatics2.
Brief introduction of professor & course
Course Overview1. Object & Aim of the course
Assignments & Quiz
Evaluation
Application fields of the Informatics
Core technology of Informatics
4 / 20copyrightⓒ 2018 All rights reserved by Korea University
Course OverviewCourse information
Convergence (Multidisciplinary) Informatics, DCCS326, Fall 2019.
Lecture time: Mon. (2,3) and Thu (9)
Location: 7-324
Completion division: Major elective subject
Level: Junior / Senior
Informatics is actually very difficult, but this course would not be difficult !
5 / 20copyrightⓒ 2018 All rights reserved by Korea University
Course OverviewBrief introduction of professor, Definition of the “Convergence (Multidisciplinary)”
B.Sc. 2006.02 – 2010.02
Dept. of Computer Science
Ph.D. 2012.06 – 2016.02
Dept. of Statistics & Animal/Plant Science
Dept. of Microbiology & Population Genetics
Interdisciplinary Program in Bioinformatics
Seoul National University
M.Sc. 2010.02 – 2012.02
Dept. of Medical Science
PostDoc. 2017.04 – 2019.08
Dept. of Medicine
Harvard Medical School
Brigham & Women’s Hospital
Why did you study different fields?
Key question could be…
Convergence (Multidisciplinary) era
6 / 20copyrightⓒ 2018 All rights reserved by Korea University
Course OverviewBrief introduction of professor, Definition of the “Convergence (Multidisciplinary)”
Asst.Prof. 2019.09 – present
Dept. of Computer Convergence Software
Korea University
Married… & Have two children, Ryan & Logan
This is first class in this department
I’d like to convey at least a sense of convergence (Multidisciplinary)
field to you to help your next career
7 / 20copyrightⓒ 2018 All rights reserved by Korea University
Course OverviewDefinition of Informatics
8 / 20copyrightⓒ 2018 All rights reserved by Korea University
Course OverviewDefinition of Informatics
Etymology
‘Informatik’ (Steinbuch, K. 1957), German
‘Informatik’ == Computer Science (in English)
‘Informatique’ (Philippe, 1692), French
‘Informatics’ (Walter, 1967)
Every day we are touched/influenced by informatics
E-mail Google Youtube Facebook Kakao
Actually, Informatics is applied in most disciplines and industries.
Pharmacology Medicine Biology Smart
manufacturing
Network
9 / 20copyrightⓒ 2018 All rights reserved by Korea University
Course OverviewObject & Aim of the course
Students who have taken this course expect to be able to learn:
Convergence
Informatics
Concept of Data Science
Application of Informatics
Computational technologies
for Informatics
Statistical skill for Informatics
R programming
Bioinformatics &
Computational Biology
10 / 20copyrightⓒ 2018 All rights reserved by Korea University
Course OverviewCourse schedule (Before Mid-term exam)
Week Period Study Contents
1 09.02 - 09.08Introduction to Informatics applied in various fields I(Applications in Medicine, Pharmacology, Biology, Agricultural science, Smart farm and
etc.)
2 09.09 - 09.15Introduction to Informatics applied in various fields II(Applications in Social science, Network science, Smart manufacturing, Meteorology,
Autonomous vehicles, and etc.)
3 09.16 - 09.22R programming & Data analysis I(Installation, Data input/output, Data visualization, Fundamental grammar such as
conditional statement and loop, and etc.)
4 09.23 - 09.29R programming & Data analysis II(Statistical estimation and prediction)
5 09.30 - 10.06Clustering analysis (Unsupervised learning methods)(Illustrate examples of clustering analytics in various fields)
6 10.07 - 10.13 Algorithms of Dimensionality Reduction
7 10.14 - 10.20Classification analysis (Supervised learning methods)(Illustrate examples of classification/prediction issue in various fields)
8 10.21 - 10.27 Mid-term Exam
11 / 20copyrightⓒ 2018 All rights reserved by Korea University
Course OverviewThe second half of this course
It is impossible to cover all fields because the applications of Informatics are
actually endless.
So, we will study at bio-medical science field, where the concept of
Informatics is best established in the second half of this course.
12 / 20copyrightⓒ 2018 All rights reserved by Korea University
Course OverviewBioinformatics
R language will be used in this class.
It is not required any prior knowledge of the R language because I plan to provide
example code for student's practice.
It also does not require prior knowledge of biology and medicine.
The minimum knowledge of biology and medicine required to proceed course will
be learned in the theory class.
https://cran.r-project.org/
Monday2hrs
Thu. Day1hr
Lecture for Theory Hands-on lectureWith R-code
Homework
Practice R-codewith real data
Course flow to fully understand bioinformatics
13 / 20copyrightⓒ 2018 All rights reserved by Korea University
Course OverviewCourse schedule (After Mid-term exam)
Week Period Study Contents
9 10.28 - 11.03Introduction to Bioinformatics & Computational Biology(Accompanying knowledge of the basic level of Biology and Medicine)
10 11.04 - 11.10Algorithm for DNA / RNA / Protein sequencing data analysis(This content technically belongs to the text mining category)
11 11.11 - 11.17 Statistics in Bioinformatics & other multidisciplinary fields
12 11.18 - 11.24
Discovery of significant biomarkers for personalized medicine or
specific biological phenomena(This content technically belongs to the feature selection/extraction category)
13 11.25 - 12.01Gene expression profiling using clustering/network approach(This content technically belongs to the clustering category)
14 11.02 - 12.08Machine learning approaches for disease/prognosis prediction(This content technically belongs to the classification category)
15 12.09 - 12.15 Role of software scientists for interdisciplinary work
16 12.16 - 12.22 Final Exam
14 / 20copyrightⓒ 2018 All rights reserved by Korea University
Course OverviewMid-term and final exams
You can earn 100 points if you follow the course faithfully.
This means that I will not ask questions that are quite difficult in the exam.
About 70% of questions will be taken on the slides of theoretical lecture, and the
rest will be derived from hand-on assignment.
15 / 20copyrightⓒ 2018 All rights reserved by Korea University
Course OverviewQuiz & Assignment (Homework)
There will be two simple quizzes in class to check the student's learning
progress of the course.
Depending on the situation, it may be replaced by a homework instead of a
quiz. In that case, assignment will be 6 times and 30 percent of the total score.
Quiz
Homework
There will be 4-6 times assignments based on the R-programming.
It’s not difficult & just application of theoretical knowledge into real data.
16 / 20copyrightⓒ 2018 All rights reserved by Korea University
Course OverviewTextbook
No Textbook
This course will be proceed based on the presentation slide
I will upload presentation slide in Blackboard & my homepage
Homepage: https://scholar.harvard.edu/msseo
Teaching >> Multidisciplinary Informatics >> Related Materials
Reference 1
Introduction to Data Science by Rafael A. Irizarry, 2019.
(online textbook and free)
https://rafalab.github.io/dsbook/
Reference 2
R for Data Science by Garrett Grolemund.
(online textbook and free)
https://r4ds.had.co.nz/
Reference 3
Modern Statistics for Biology by Wolfgang Huber.
(online textbook and free)
https://www.huber.embl.de/msmb/index.html
17 / 20copyrightⓒ 2018 All rights reserved by Korea University
Course OverviewEvaluation plan
Absolute grading system
Score ≥ 95, you will get A+
Score ≥ 90, you will get A
Score ≥ 85, you will get B+
and...
30%
30%
10%
20%
10%
Midterm Final Quiz Assignment Attendance
18 / 20copyrightⓒ 2018 All rights reserved by Korea University
Course OverviewFor successful class
Welcome questions related to any type of course.
One of the good academic habit is Googling.
Before asking anyone, do a Googling and ask questions that you still don't
understand.
Other knowledge gained from googling will accumulate and revisit.
In order to maximize learning outcomes, students should actively participate in
discussions.
19 / 20copyrightⓒ 2018 All rights reserved by Korea University
Course OverviewContact information
Prof. Minseok Seo
Location: 7-203
Tel: TBA
Email: mins@korea.ac.kr
TA. Sungwon Moon
Location: 7-308
Email: mmsw0324@naver.com
If you have any questions about the course please email me and I will reply as
soon as I see it.
If you need to meet in person, please make an appointment by email first.
I will be available at Mon: 12:00 - 17:00 | Wed: 10:00 - 13:00 | Thu: 10:00 - 13:00.
End of Orientation
Contents
Definition of Informatics
Introduction to Informatics2.
Brief introduction of professor & course
Course Overview1. Object & Aim of the course
Assignments & Quiz
Evaluation
Application fields of the Informatics
Core technology of Informatics
22 / 20copyrightⓒ 2018 All rights reserved by Korea University
Definition of InformaticsWhat is Data Science & Informatics
Data Science == Informatics =~ Machine Learning
An area that manages, manipulates, extracts, and interprets knowledge from
tremendous amount of data (automatically or computationally)
Data science and Informatics are multidisciplinary field of study with goal to
address the challenges
Data science principles apply to all data – big and small
Theories and techniques from many fields and disciplines are used to investigate
and analyze a large amount of data to help decision makers in many industries
such as science, engineering, economics, politics, finance, and education
23 / 20copyrightⓒ 2018 All rights reserved by Korea University
Future prospects of InformaticsImportance of Informatics field
Informatics (Data science) is very important in the past, now, and in the future!
24 / 20copyrightⓒ 2018 All rights reserved by Korea University
Definition of InformaticsKey elements of Informatics
Many fields need to interact with each other to achieve their goals.
25 / 20copyrightⓒ 2018 All rights reserved by Korea University
Data scientistsSexiest job
Data Scientists (==Informatician)
The Sexiest Job of the 21st Century
You can get love calls in all fields!
26 / 20copyrightⓒ 2018 All rights reserved by Korea University
Data scientistsSexiest job (Why!?)
Data scientists are the key to realizing the opportunities presented by big data.
They bring structure to it, find compelling patterns in it, and advise executives on
the implications for products, processes, and decisions.
In short, it is a position that can be involved in everything except the president like
a Superman!
27 / 20copyrightⓒ 2018 All rights reserved by Korea University
Concentration in Data ScienceDisadvantage?
Mathematics and Applied Mathematics
Statistics and Applied Statistics
Solid Programming Skills (C/C++, JAVA, R, Python, Julia, SQL, Java Script)
Data Mining
Data Base Storage and Management
Machine Learning and discovery
It’s hard to become good Informatician because you have to learn too much
But, all disciplines is interacted each other
28 / 20copyrightⓒ 2018 All rights reserved by Korea University
Concentration in Data ScienceDisadvantage?
Mathematics and Applied Mathematics
Statistics and Applied Statistics
Solid Programming Skills (C/C++, JAVA, R, Python, Julia, SQL, Java Script)
Data Mining
Data Base Storage and Management
Machine Learning and discovery
It’s hard to become good Informatician because you have to learn too much
But, all disciplines is interacted each other
A journey of a thousand miles begins with a single step.
29 / 20copyrightⓒ 2018 All rights reserved by Korea University
30 / 20copyrightⓒ 2018 All rights reserved by Korea University
National health databank
National health code
National health card
ApplicationMedical Informatics
Medical informatics is the application of computers, communications and
information technology and systems to all fields of medicine-medical care,
medical education and medical research.
DatabasesSearch enginesValue added Pub.EB Pub.POEM collections
Decision-Support Systems
Diagnosis / Interpretation
Therapy / Management
Automated reminders and alert systems
Electronic prescription and order entry
Drug IS and Automated dispensing
Telemedicine
Care Providers
Patients
Data
Dx/TxData acquisition
Data storage
Vocabularies
Organization of data
Machine interfaces
Data retrieval
Electronic medical records
Laboratory IS
Digital imaging and
Radiological IS
Patient monitoring systems
Clinical Judgment
Diagnostic ReasoningTherapeutic Planning
31 / 20copyrightⓒ 2018 All rights reserved by Korea University
ApplicationMedical Informatics
Medical Informatics is Multidisciplinary field itself
Medicine/ Biology
Mathematics
Information Systems
Computer Science
Statistics
Decision Analysis
Economics/Health Care Policy
Psychology
32 / 20copyrightⓒ 2018 All rights reserved by Korea University
Medical Informatics
Electronic medical record (EMR)
• Access, Availability, transfer and retrieval
• Legibility, Abstraction, reporting
• Saves time: find data 4 times faster
• Reduced data entry (reuse data)
• Better organization by imposing structure
• Storage space
• Allow multiple views including aggregation
• Automated checks on data entry (spelling checks)
• Data quality and standards
• Automated decision support
• Statistics and research
Application
33 / 20copyrightⓒ 2018 All rights reserved by Korea University
Medical Informatics
Decision Support for Diagnosing Disease
Application
34 / 20copyrightⓒ 2018 All rights reserved by Korea University
ApplicationMedical Informatics
Virtual reality (Computational simulation)
The da Vinci Surgical System
(Intuitive Surgical, California, USA)
The surgeon sits at a control console with 3D visualization of the surgical
field and the robotic surgical instruments.