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Medical Informatics:. Computers, Decisions, and Communications. Vlad Olchanski, PhD o Moscow Institute of Physics and Technology o Institute of Control Sciences o International Institute for Applied Systems Analysis o World Health Organization o Medical College of Virginia. Download

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medical informatics

Medical Informatics:

Computers, Decisions, and Communications

Vlad Olchanski, PhD

o Moscow Institute of Physics and Technology

o Institute of Control Sciences

o International Institute for Applied Systems Analysis

o World Health Organization

o Medical College of Virginia


content as



MCV Course for 4th year medical students

Dr. Olchanski Home Page

November 14, 2001

medical informatics2
Medical Informatics

Outline of Course

Philosophy of Governing Life


Component 2

Decision Support and Theory

Medical Records

Diagnostic Support

Pharmaceutical Prescriptions

Health System Modeling

Data Mining

Component 1

Information Technology




medical informatics3
Medical Informatics



content as



why learn medical informatics
Why Learn Medical Informatics?

Cutting Edge Technologies:

1930s 1990s

Radio communications

Computers, Internet

why learn medical informatics5
Why Learn Medical Informatics?
  • In the 1920-1930s the Radio was very cool.
  • In those days, the Radio was not a black box with buttons you have in your car.
  • To get a good reception, you had to know a little bit about electronics and things...
why learn medical informatics6
Why Learn Medical Informatics?
  • Computers are cool today.
  • If you don’t know a little bit about what "coils” are inside -
  • you will get frustrated and will bother other people.
  • And yet we want computers and IT now!
why learn medical informatics7
Why Learn Medical Informatics?

21st Century the Age of Informatics

Major Tool of Informatics -- INTERNET

  • IT is not as simple today as is Radio.
  • Internet will turn into a black box with buttons.
  • But not today.
  • And not tomorrow.
why learn medical informatics8
Why Learn Medical Informatics?
  • Therefore, to behave as a conscious Medical Professional, a Physician of today has to know the basics of Information Technologyas well as the basics of Physiology and Pharmacology.
  • Yet the Information Technology alone cannot help you without the intellectual component of Medical Informatics: the Decision Theory.
phi beta kappa philosophia biou kybernetes philosophy governs life
Phi Beta Kappa- philosophia biou kybernetes Philosophy Governs Life
  • Philosophy
  • Mathematics
  • Natural Philosophy
  • Physics
  • Engineering
  • General Theory of Systems
  • Cybernetics
  • Informatics



general theory of systems
General Theory of Systems

Bertalanffy (Austria-Hungary), Bogdanov (Russia) - 1908

Crash of empires after the Great War

The Second World War: FLAK, Enigma

Norbert Wiener (MIT):

Cybernetics: Control and Communication in the

Animal and the Machine - 1948

Theory of Information, Finite Mathematics, Probabilities

John von Neumann (Princeton)

Alan Turing (Bletchley Park)

Claud Shannon (MIT)

Andrey Kolmogorov (Moscow State)

first computers
First Computers

This weaponry could not protect England:

  • Theory of InformationCommunicationsCodingAlgorithmsProbabilities and Stochastic Processes
  • Theory of ControlOperations ResearchOptimizationManagement Science
  • Systems Analysis
  • Live, bio-systems
  • Engineering, machines, robots
  • Organizational systems
  • Computer Science
  • Systems AnalysisDecision Support, Artificial Intelligence
whence informatics
Whence Informatics?
  • Concept of Cybernetics too broad
  • Word Cybernetics tarnished, devalued by Sci-Fi and Pop culture
  • Pragmatic reduction to Computer Sciencein USA
  • CS translated into INFORMATIQUE in France
  • Backward translation of CS as INFORMATICS expanding the scope
handbook of medical informatics
Handbook of Medical Informatics

This excellent book unfortunately

has very little coverage of the

Internet applications.

Otherwise, this is the #1 Resource!

medical informatics definitions
Medical InformaticsDefinitions
  • Medical Information Science is the science of using system-analytic tools . . . to develop procedures (algorithms) for management, process control, decision making and scientific analysis of medical knowledge - Ted Shortliffe
  • Medical Informatics comprises the theoretical and practical aspects of information processing and communication, based on knowledge and experience derived from processes in medicine and health care - Jan van Bemmel
whence informatics17
Whence Informatics?
  • Computer Science and Informatics are practically synonyms: the difference in emphasizing the application aspect
  • Informatics is frequently understood as broadly as Cybernetics --Information Processing including Decision Making and Systems Analysis
names used for medical informatics
Names used for Medical Informatics
  • medical computer science
  • medical information science
  • computer application(s) in medicine
  • health informatics, and more specialized terms such as
  • nursing informatics
  • dental informatics
  • and so on.
informatics what
Informatics - What?
  • Information Technology and TheoryComputers, Communications, Data Processing, Algorithms
  • Decision Theory and ApplicationsBayesian Approach, Expert Systems, Artificial Intelligence, Knowledge-based Systems, Algorithms
a good intro to informatics
A Good INTRO to Informatics

But should we go all the way together?

medical informatics21
Medical Informatics




content as



computers evolution
Computers: Evolution

Von Neuman and the first MAINFRAME at IAS (1948)

Vacuum tubes, punch cards or tape

Batch mode of operation

Low reliability - maintenance team of electronics engineers

Transistors- Bill Shockley, 1956 NP


Interactive mode of operation

Reduced size and enhanced

reliability due to Integrated Circuits


Interactive mode of operation

Higher reliability due to Transistors




Renamed from minicomputers to show due respect


computers operating systems
Computers: Operating Systems

Mainframe OS -- oriented to batch processing

Minicomputers -- more interactive, usually designed by

hardware manufacturer, like RSX, VMS for late

DEC machines

Unix - an attempt to standardize

Personal computers -- CP/M, MS DOS, IBM OS/2,

Mac OS, Windows, Unix

Internet developed mainly on Unix machines

computers operating systems24
Computers: Operating Systems

Windows should not be used for critical applications

programming mainframe
Programming Mainframe

A punch card and the editing tool


Page 104 of a program listing

programming mainframe26
Programming Mainframe

Booting your computer -- giving it a kick?

programming mainframe27
Programming Mainframe

Booting your computer --

giving it a kick?


It is short from bootstrapping.

“Bootstrap” was the name of

a short length of the punched

tape that was fed to a

computer to initiate loading of

the Operating System.

computer architecture
Computer Architecture

CPU, RAM, Bus, etc.

are discussed in class

computers objects
Computers: Objects

Files:Windows Commander: “”

Name long name, DOS name avoid spaces in names!

Type extension, internal header, MIME type

Size actual / on disk

Time creation / modification / access

Attrib hidden / system

Owner sysadmin/owner / group / world/other

Directories (folders):

c:\ root

..\ parent

computers startup files
Computers: Startup Files





in Unix:






Text editors: Notepad.exe UltraEdit.exe

computers commands
Computers: Commands












date, time




more /p - by page


/? -? /h -h

computer architecture32
Computer Architecture

Data storage on disks

File Allocation Table

Security issues

are discussed in class

after Information Coding


some utilities
Some Utilities
  • Calculator (scientific mode)
  • Character Map (Symbols to Computer Code)
  • Notepad (Text editor)
medical informatics34
Medical Informatics




content as



communication protocol layers
Communication Protocol Layers

ISO Open System Interface


the application level is what we use: Email, FTP, Telnet, HTTP, etc.

the physical layer is a stream of bits

internet protocols
Internet Protocols
  • FTP (file transfer protocol) serves to exchange data with a remote computer
  • Telnet allows to run programs on a remote computer


Upload - send TO a remote recipient

Download - receive FROM a remote sender

remote computing i
Remote Computing - I

Fred at UBC hasreport software...

Wilma at CUNY has data, needs report!


Remote Computing - II

Fred sends Wilma

the username

and the password

Never by EMAIL !!!

Wilma at CUNY has data, needs report!


Remote Computing - III

Fred at UBC hasreport software...


Wilma uploads her data with FTP


Remote Computing - IV

Fred at UBC hasreport software...


Wilma manipulates her data on Fred’s

computer with Telnet


Remote Computing - V

Fred at UBC hasreport software...


Wilma downloads the report with FTP


Remote Computing - VI

Fred at UBC hasreport software...


Wilma prints the report in her office

and sends her kisses to Fred by email

using email 1
Using Email - 1

Email is very much like Regular Mail:sending mail and receiving are done quite differently!

To send mail, you may to drop it in any mail drop box in the street.

To send email, you may connect and use any SMTP serverin the world. It is for public convenience.

SMTP server sends email

using email 2
Using Email - 2

You send a letter thru a Mail Drop Box

You may use any one you find in the street

using email 3
Using Email - 3

You send an email thru a SMTP server

access controlled

access controlled

access controlled

access controlled

access controlled

access controlled

open for all

You may use any one you find in the Internet

using email 4
Using Email - 4

Email is very much like Regular Mail:sending mail and receiving are done quite differently!

To receive mail, you must have either your own mailbox

or rent a box at any Post Office.

To receive email, you must have an account with any

POP3 server. It will be your private possession. You may

have as many as you may wish.

POP3 server receives email

using email 5
Using Email - 5

To receive a letter, you must have a homeor a number in a US Post Office

using email 6
Using Email - 6

To receive an email, you must have an accountat a POP or IMAP mail server

you may have as many of these as you like

using email 7
Using Email - 7

POP server delivers all messages to your computer --good when you are on a fast connection

IMAP server delivers only message headers and messages on demand -- good when you are on a dial-upYet you will not have all messages on your computer

T’bird, Eudora, TheBat! support multiple email accounts

Webmail allows to use email with your browser --good when you are on the go

Hotmail, Yahoo, etc. may be used for simple purposes --but it is not a true email

using email 8
Using Email - 8

You read and send email with Email Client

There are so many different Email Client programs --

make your own choice


some of Email Clients

and some of Email USERS

go outside of Internet Standards

- incompatibility of messages

- errors in transmission and reception

using email 9
Using Email - 9



An operative

set of POP3 boxes

using email 10 basic rules of nice conduct
Using Email - 10 Basic Rules of Nice Conduct

1. Never consider email as confidential

2. Email should best be a simple message

3. Do not send messages formatted with HTML --

not all email clients can deal with them,

confirms a hit for spammers

(impossible in AOL email program )

4. Avoid sending binary attachments

these may come corrupted and can carry


How to avoid binary attachments in Email, see


the most intimate secret
The Most Intimate Secret

Like Wine dichotomy in Russia

- White wine: Moonshine, Vodka, Brandy

- Red wine: all the rest

the most intimate secret55
The Most Intimate Secret

Data dichotomy in Internet

- Text files: Plain English text: A-Z, a-z, 0-9

- Binary files: all the rest

the most intimate secret56
The Most Intimate Secret

Symbols -- Bytes -- Octets

Secret == 53 65 63 72 65 74


1010011 1100101 1100011 1110010 1100101 1110100

Sept “bits” fassent un “octet”! This is the ASCII Standard.

Yet --

Éç == C9 E7 == 11001001 11100111

Now you see that the French have a reason to call

the “byte” not “septet” but “octet”!

If you strip the 8th bit then corruption occurs:

É -> 49 == I and ç -> 67 == g

the most intimate secret57
The Most Intimate Secret
  • The 7-bit data trasmission was set into the infrastructure
the most intimate secret58
The Most Intimate Secret

The Revelation

Only text files may be sent through Internet

Binary files will come corrupted

To send a binary, it must be converted to

a text file (encoded) and on the receiving end

the encoded file must be decoded.

In FTP protocol, the type must be told explicitly

In Email, binary files go as attachments.

There are different encode/decode procedures

which may lead to confusion and errors

security cryptography
Security: Cryptography

Sherlock Holmes: The Dancing men


elsie PrePare To Meet Thy GoD

come here at once

security cryptography60
Security: Cryptography

Edgar Allan Poe: Gold-bug

53++!305))6*;4826)4+.)4+);806*;48!8`60))85;]8*:+*8!83(88)5*!; 46(;88*96*?;8)*+(;485);5*!2:*+(;4956*2(5*-

4)8`8*; 4069285);)6!8)4++;1(+9;48081;8:8+1;48!85;4)485!528806*81(+9;48;(88;4(+?3 4;48)4+;161;:188;+?;

8 there are 33.

; " 26.

4 " 19.

+ ) " 16.

* " 13.

5 " 12.

6 " 11.

! 1 " 8.

0 " 6.

9 2 " 5.

: 3 " 4.

? " 3.

` " 2.

- . " 1.

5 represents a

! " d

8 " e

3 " g

4 " h

6 " i

* " n

+ " o

( " r

; " t

In English, the letter which most frequently occurs is e. Afterwards, the succession runs thus: a o i d h n r s t u y c f g l m w b k p q x z

A good glass in the bishop's hostel in the devil's seat twenty-one degrees and thirteen minutes northeast and by north main branch seventh limb east side shoot from the left eye of the death's-head a bee line from the tree through the shot fifty feet out.

security criptography
Security: Criptography

Enigma, German Coding Machine

security cryptography62
Security: Cryptography

Encryption with a keyword

“this is plaintext” , the key is “key”

+ (add codes)


Encrypted text:


Decryption with a keyword -- the key must be sent to the recipient this is the weakest point

Encrypted text:

“dxkfpsnputmsodjss” , the key is “key”

- (subtract codes)


Decrypted text:

“this is plaintext”

Plain book, a simple

but efficient tool



security cryptography63
Security: Cryptography

My secret

private key


Pretty Good





My public key

stored on my

website and in

public depositories

My key ring of public keys of

my correspondents

security cryptography64
Security: Cryptography

Fred reads my message

I send message to Fred

Dear Fred, bla-bla...


Dear Fred, bla-bla...

Fred’s public


Fred’s private key

Fred answers my message

I read Fred’s answer

My public key

My private key

Dear Vlad, bla-bla...


Dear Vlad, bla-bla...

communications security
Communications. Security

80% trash, 5% pearls

internet protocols67
Internet Protocols

Usenet, News, Forums -- NNTP Protocol

A small ISP carries

~45,000 groups.

Different ISPs

give different groups,

have different scopes

Medical and Health

Related Groups listed:

internet protocols68
Internet Protocols

World Wide Web == HTTP protocol

User client -- browser

Netscape, Internet Explorer, Opera, Firefox

WWW is only a small part of Internet !!!

AOL and MSN are not Internet at all !!!





gateway Services Providers give you full Internet

internet connectivity
Internet Connectivity

Internet Addresses


Host file

Domain Name Server




Vlad Olchanski

Personal notebook

Phone Directory



look up

look up



PING and TRACERT accessible through START/RUN

internet connectivity70
Internet Connectivity

A decent ISP must give a client:

o SMTP address to send email

o POP3 address to access the mailbox

o NNTP address to get Newsgroups


o Space to host website at ISP’s IP address

o FTP access to update website


o Static IP address for hosting own website

information technology viruses
Information TechnologyViruses

Viruses, Trojans, Worms, Bots, Denial of Service

Virus Shields, Firewalls

are discussed in class.

Read also Steve Gibson’s saga about a virus attack:

information technology secure use of internet
Information Technology: Secure Use of Internet

Now let us see a presentation on how to practice Internet connectivity safely.

information technology basics of security 1
Information TechnologyBasics of Security - 1
  • make sure workstation is physically safe and secure
  • never send passwords by email
  • never paste passwords beside the workstation
  • install and regularly (weekly) update virus protection
  • avoid sending attachments
  • never open unsolicited attachments, always check and double-check the attachment’s file extension
information technology basics of security 2
Information TechnologyBasics of Security -2
  • never open unexpected file with extensions EXE COM DOC DLL PIF LNK VBS (Windows does not show LNK and PIF extensions)
  • Never click on a link – hover the link with mouse and look at the status bar where the link leads when clicked
  • firewall may protect both yourself and the world but may also cheat you)
information theory
Information Theory

Sender and Receiver

Noise and Distortion

Codes Detecting Errors

Codes Correcting Errors


Data Packets

are discussed in class

information theory76
Information Theory

Data Compression

zip, arj, rar, tar, gz, binhex, 7u, etc.

Image Compression

Image Formats

bmp, tiff, gif, jpg, png, etc.

are discussed in class.

Image compression immediately leads to


web design
Web Design

What is a good website?

-- presentable for all users: WIN, Mac, Unix, etc.

-- acceptable for all browsers: Opera, Netscape,

Firefox, MSIE, Safari, etc.

-- loads fast: byte size < 50 kB

-- does not use Cutting Edge technologies

Learn the culture of Web Design at

review the Daily Sucker site daily!

A web design

project is done

by students.

Collection here

medical informatics78
Medical Informatics



content as



the fundamental principle of decision theory
The Fundamental Principle of Decision Theory


[New Knowledge] = [Experimentation] x [Old Knowledge]

Application: Making Diagnosis

[Old Knowledge] - we know disease D prevalence, p(D)

[New Knowledge] - we need to know if the patient has

disease D if he has symptom S, p(D|S)

[Experimentation] - Bayes Theorem builds the Likelihood


L(D|S) = p(S|D) / {p(S|D) p(D) + p(S|’D) p(‘D)}

Now this Likelihood Function modifies the Old Knowledge:

p(D|S) = L(D|S) p(D)

medical decision support
Medical Decision Support

to mention a few

Clinical Systems


Medical Records


Diagnostic Systems

QMR, Iliad, DXPlain, etc.

Pharmaceutical Prescriptions

Health System Modeling


Data Mining

medical decision support clinical systems
Medical Decision SupportClinical Systems

Computerized Medical Record systems

are discussed in class:

TMR -- CMR from Duke Medical Center


Pharmaceutical System for Multiple Drug

Therapy in ICU, Pharm-X is discussed in class

Comprehensive system for VCU HealthSystem

is discussed in class.

medical decision support diagnostic systems
Medical Decision SupportDiagnostic Systems

knowledge base

decision mechanism




feedback to adjust observations

Knowledge Engineering, Expert Systems, AI

are discussed in class

medical decision support measurement and statistics
Medical Decision SupportMeasurement and Statistics

Use only reasonable precision,

round up numbers to convey your purpose

medical informatics87
Medical Informatics




content as



handbook of medical informatics88
Handbook of Medical Informatics

MCV Course for

4th year medical students

handbook of medical informatics89
Handbook of Medical Informatics

I. Data and Information

1 Introduction and Overview

2 Information and Communication

handbook of medical informatics90
Handbook of Medical Informatics

II. Data in Computers

3 Data Processing     

4 Database Management     

5 Telecommunication, Networking and Integration

handbook of medical informatics91
Handbook of Medical Informatics

III. Data from Patients

6 Coding and Classification

7 The Patient Record

8 Biosignal Analysis

9 Medical Imaging

10 Image Processing and Analysis

handbook of medical informatics92
Handbook of Medical Informatics

IV. Patient-Centered Information Systems

11 Primary Care

12 Clinical Departmental Systems

13 Clinical Support Systems

14 Nursing Information Systems

handbook of medical informatics93
Handbook of Medical Informatics

V. Medical Knowledge and Decision Support

15 Methods for Decision Support

16 Clinical Decision-Support Systems

17 Strategies for Medical Knowledge Acquisition

18 Predictive Tools for Clinical Decision Support

handbook of medical informatics94
Handbook of Medical Informatics

VI. Institutional Information Systems

19 Modeling of Health Care for Information Systems


20 Hospital Information Systems: Clinical Use

21 Hospital Information Systems; Technical Choices

22 Health Information Resources

handbook of medical informatics95
Handbook of Medical Informatics

VII. Methodology for Information Processing

23 Logical Operations     

24 Biostatistical Methods     

25 Biosignal Processing Methods     

26 Advances in Image Processing     

27 Pattern Recognition     

28 Modeling for Decision Support     

29 Structuring the Computer-based Patient Record     

30 Evaluation of Clinical Information Systems

handbook of medical informatics96
Handbook of Medical Informatics

VIII. Methodology for Information Systems

31 Human-Computer Interaction in Health Care

32 Costs and Benefits of Information Systems

33 Security in Medical Information Systems

34 Standards in Health-care Informatics and Telematics

in Europe

35 Project Management

handbook of medical informatics97
Handbook of Medical Informatics

IX. Medical Informatics as a Profession

36 Education and Training in Medical Informatics

37 International Developments in Medical Informatics

handbook of medical informatics98
Handbook of Medical Informatics

Unfortunately lacks the details on the Internet

medical informatics100
Medical Informatics




content as



MCV Course for 4th year medical students