convergence informatics - harvard university · medical informatics medical informatics is the...

ConvergenceInformatics

Chapter 1 & 2 (Week 1)Course overview & introduction

DCCS326 Korea University 2019 Fall

Asst. Prof. Minseok Seo

[email protected]

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 !


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


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


Course OverviewDefinition of Informatics


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


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


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


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.


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


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


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.


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.


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.


https://r4ds.had.co.nz/

Reference 3

Modern Statistics for Biology by Wolfgang Huber.


https://www.huber.embl.de/msmb/index.html


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


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.


Course OverviewContact information

Prof. Minseok Seo

Location: 7-203

Tel: TBA

Email: [email protected]

TA. Sungwon Moon

Location: 7-308

Email: [email protected]

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


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


Future prospects of InformaticsImportance of Informatics field

Informatics (Data science) is very important in the past, now, and in the future!


Definition of InformaticsKey elements of Informatics

Many fields need to interact with each other to achieve their goals.


Data scientistsSexiest job

Data Scientists (==Informatician)

The Sexiest Job of the 21st Century

You can get love calls in all fields!


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!


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


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.


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



Medical Informatics is Multidisciplinary field itself

Medicine/ Biology

Mathematics

Information Systems

Computer Science

Statistics

Decision Analysis

Economics/Health Care Policy

Psychology


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


Medical Informatics

Decision Support for Diagnosing Disease

Application



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.

http://bmj.com/content/vol323/issue7318/images/large/mccr4060.f3.jpeg

http://bmj.com/content/vol323/issue7318/images/large/mccr4060.f3.jpeg

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