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Vlad Olchanski, PhDo Moscow Institute of Physics and Technologyo Institute of Control Scienceso International Institute for Applied Systems Analysiso World Health Organizationo Medical College of Virginia
November 14, 2001
MCV Course for 4th year medical studentsDr. Olchanski Home Page
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Medical Informatics:Computers, Decisions, and Communications
Medical Informatics
Outline of Course
Philosophy of Governing LifeInformatics
Component 1Information TechnologyComputersCommunicationsInternet
Component 2Decision Support and TheoryMedical RecordsDiagnostic SupportPharmaceutical PrescriptionsHealth System ModelingData Mining
Medical Informatics
INTRODUCTION
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Why Learn Medical Informatics?
Cutting Edge Technologies:
1930s 1990s
Radio communications Computers, Internet
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 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 Informatics?
IT is not as simple today as is Radio.Internet will turn into a black box
with buttons.But not today. And not tomorrow.
21st Century the Age of InformaticsMajor Tool of Informatics -- INTERNET
Why Learn Medical Informatics?
Therefore, to behave as a conscious Medical Professional, a Physician of today has to know the basics of Information Technology as 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
PhilosophyMathematicsNatural PhilosophyPhysicsEngineeringGeneral Theory of Systems CyberneticsInformatics
KybernetesGovernsCybernetics
General Theory of Systems
Bertalanffy (Austria-Hungary), Bogdanov (Russia) - 1908 Crash of empires after the Great War The Second World War: FLAK, EnigmaNorbert Wiener (MIT):
Cybernetics: Control and Communication in theAnimal and the Machine - 1948
Theory of Information, Finite Mathematics, ProbabilitiesJohn von Neumann (Princeton)Alan Turing (Bletchley Park)Claud Shannon (MIT)Andrey Kolmogorov (Moscow State)
Cybernetics
Theory of InformationCommunicationsCodingAlgorithmsProbabilities and Stochastic Processes
Theory of ControlOperations ResearchOptimizationManagement Science
Systems Analysis
Applications
Live, bio-systemsEngineering, machines, robotsOrganizational systemsComputer Science Systems Analysis
Decision Support, Artificial Intelligence
Whence Informatics?
Concept of Cybernetics too broadWord Cybernetics tarnished, devalued
by Sci-Fi and Pop culturePragmatic reduction to Computer Science
in USACS translated into INFORMATIQUE in
FranceBackward translation of CS as
INFORMATICS expanding the scope
Handbook of Medical Informatics
http://www.mieur.nl/mihandbook http://www.mihandbook.stanford.edu/
This excellent book unfortunatelyhas very little coverage of theInternet applications.
Otherwise, this is the #1 Resource!
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 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
medical computer sciencemedical information sciencecomputer application(s) in medicinehealth informatics,
and more specialized terms such as nursing informaticsdental informaticsand so on.
Informatics - What?
Information Technology and TheoryComputers, Communications, Data Processing, Algorithms
Decision Theory and ApplicationsBayesian Approach, Expert Systems, Artificial Intelligence, Knowledge-based Systems, Algorithms
Computers: Evolution
Von Neuman and the first MAINFRAME at IAS (1948)
Vacuum tubes, punch cards or tapeBatch mode of operationLow reliability - maintenance team of electronics engineers
Transistors - Bill Shockley, 1956 NP
MINICOMPUTERSInteractive mode of operationHigher reliability due to Transistors
MICROCOMPUTERSInteractive mode of operationReduced size and enhancedreliability due to Integrated Circuits
PERSONAL COMPUTERSRenamed from minicomputers to show due respect
SUPERMINISWORKSTATIONS
SUPERCOMPUTERS
Computers: Operating Systems
Mainframe OS -- oriented to batch processingMinicomputers -- more interactive, usually designed by
hardware manufacturer, like RSX, VMS for lateDEC machines
Unix - an attempt to standardizePersonal computers -- CP/M, MS DOS, IBM OS/2,
Mac OS, Windows, Unix
Internet developed mainly on Unix machines
Programming Mainframe
Booting your computer --giving it a kick?
No!It is short from bootstrapping.
“Bootstrap” was the name ofa short length of the punchedtape that was fed to acomputer to initiate loading ofthe Operating System.
Computers: Objects
Files: Windows Commander: “http://www.ghisler.com”
Name long name, DOS name avoid spaces in names!Type extension, internal header, MIME typeSize actual / on diskTime creation / modification / accessAttrib hidden / systemOwner sysadmin/owner / group / world/other
Directories (folders):
c:\ root..\ parent
Computers: Startup Files
config.sysautoexec.batsystem.iniwin.ini
in Unix:.cshrc
Registry
System.datUser.dat SAM
Text editors: Notepad.exe UltraEdit.exe
Computers: Commands
dircddeletecopymkdirrmdirattribxcopydiskcopyformattree
date, timepathsetsortmore /p - by pagehelp
/? -? /h -h
Computer Architecture
Data storage on disksFile Allocation TableSecurity issuesare discussed in classafter Information Codingpresentation
Some Utilities
Calculator (scientific mode)Character Map (Symbols to
Computer Code)Notepad (Text editor)
Communication Protocol Layers
the physical layer is a stream of bits
ISO Open System Interface
Internet
the application level is what we use: Email, FTP, Telnet, HTTP, etc.
Internet Protocols
FTP (file transfer protocol) serves to exchange data with a remote computer
Telnet allows to run programs on a remote computer
Terms:
Upload - send TO a remote recipientDownload - receive FROM a remote sender
Remote Computing - II
Wilma at CUNY has data, needs report!
Fred sends Wilmathe usernameand the password
Never by EMAIL !!!
Remote Computing - IV
Wilma manipulates her data on Fred’scomputer with Telnet
Fred at UBC hasreport software...
Telnet
Remote Computing - VI
Wilma prints the report in her officeand sends her kisses to Fred by email
Fred at UBC hasreport software...
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 - 3
You send an email thru a SMTP server
You may use any one you find in the Internet
access controlledaccess controlled
access controlled
access controlled
access controlled access controlled
open for all
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 mailboxor 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 mayhave as many as you may wish.
POP3 server receives email
Using Email - 6To 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 - 7POP server delivers all messages to your computer --
good when you are on a fast connection
IMAP server delivers only message headers and messageson 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
You read and send email with Email Client
There are so many different Email Client programs --make your own choice
BUT
some of Email Clientsand some of Email USERS
go outside of Internet Standards
- incompatibility of messages- errors in transmission and reception
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 virusesHow to avoid binary attachments in Email, see“http://www.intmed.vcu.edu/inm/advice.html”
The Most Intimate Secret
Like Wine dichotomy in Russia
- White wine: Moonshine, Vodka, Brandy
- Red wine:all the rest
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 SecretSymbols -- Bytes -- Octets
Bits
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 11100111Now you see that the French have a reason to callthe “byte” not “septet” but “octet”!
If you strip the 8th bit then corruption occurs:
É -> 49 == I and ç -> 67 == g
The Most Intimate SecretThe Revelation
Only text files may be sent through InternetBinary files will come corrupted
To send a binary, it must be converted toa text file (encoded) and on the receiving endthe encoded file must be decoded.
In FTP protocol, the type must be told explicitlyIn Email, binary files go as attachments.
There are different encode/decode procedureswhich may lead to confusion and errors
Security: Cryptography
Sherlock Holmes: The Dancing men
ELSIE .RE . ARE . O EET . HY . O .
elsie PrePare To Meet Thy GoD
come here at once
Security: Cryptography
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*-
Edgar Allan Poe: Gold-bug
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: CryptographyEncryption with a keyword
“this is plaintext” , the key is “key”+ (add codes)
“keykeykeykeykeyke”Encrypted text:
“dxkfpsnputmsodjss”
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)
“keykeykeykeykeyke”Decrypted text:
“this is plaintext”
Plain book, a simplebut efficient tool
One-timepad
Security: Cryptography
My key ring of public keys of my correspondents
My secret private key
My public keystored on mywebsite and inpublic depositories
Fred’spublickey
PGP:Pretty GoodProtection
Security: CryptographyI send message to Fred Fred reads my message
I read Fred’s answer
Dear Fred, bla-bla... Dear Fred, bla-bla...]hk@s#2kdMs0fHquja...
Fred’s publickey
Fred’s private key
Dear Vlad, bla-bla... Dear Vlad, bla-bla...Msios$[\iqN7dkoZnu...
My private keyMy public key
Fred answers my message
Internet Protocols
Usenet, News, Forums -- NNTP Protocol
A small ISP carries ~45,000 groups.
Different ISPs give different groups,have different scopes
Medical and HealthRelated Groups listed:www.mipt.vcu.edu/ng.html
Internet Protocols
World Wide Web == HTTP protocolUser client -- browser Netscape, Internet Explorer, Opera, Firefox
WWW is only a small part of Internet !!!
AOL and MSN are not Internet at all !!!
InternetAOL MSN
gateway gatewayarchive.salon.com/tech/feature/2001/06/26/locking_up_the_web/index3.html
Internet Services Providers give you full Internet
Internet Connectivity
Internet AddressesDSN:views.vcu.edu
Host fileDomain Name Server
IP:128.172.65.8
TelephonesName:Vlad Olchanski
Personal notebookPhone Directory
Number:804.828.5384
look uplook up
dialconnect
PING and TRACERT accessible through START/RUN
Internet Connectivity
A decent ISP must give a client:o SMTP address to send emailo POP3 address to access the mailboxo NNTP address to get Newsgroups
Additionally:o Space to host website at ISP’s IP addresso FTP access to update website
Optionally:o Static IP address for hosting own website
Information TechnologyViruses
Viruses, Trojans, Worms, Bots, Denial of ServiceVirus Shields, Firewalls
are discussed in class.
Read also Steve Gibson’s saga about a virus attack:
http://grc.com/dos/intro.htm
Information Technology: Secure Use of Internet
Now let us see a presentation on how to practice Internet connectivity safely.
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 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
Sender and ReceiverNoise and DistortionCodes Detecting ErrorsCodes Correcting ErrorsChecksumsData Packets
are discussed in class
Information Theory
Data Compressionzip, arj, rar, tar, gz, binhex, 7u, etc.
Image CompressionImage 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
webpagesthatsuck.com
review the Daily Sucker site daily!
A web design project is doneby students.Collection here
The Fundamental Principle of Decision Theory
THE BAYES THOREM[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
Function: 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 Supportto mention a few
Clinical SystemsFinancialMedical RecordsComprehensive
Diagnostic SystemsQMR, Iliad, DXPlain, etc.
Pharmaceutical Prescriptions
ResearchData Mining
Health System Modeling
Medical Decision SupportClinical Systems
Computerized Medical Record systems are discussed in class:TMR -- CMR from Duke Medical CenterMedicaLogica
Pharmaceutical System for Multiple DrugTherapy in ICU, Pharm-X is discussed in class
Comprehensive system for VCU HealthSystemis discussed in class.
Medical Decision SupportDiagnostic Systems
Knowledge Engineering, Expert Systems, AIare discussed in class
observationsknowledge base
decision mechanism diagnoses
explanations
feedback to adjust observations
Medical Decision SupportMeasurement and Statistics
Use only reasonable precision, round up numbers to convey your purpose
Handbook of Medical Informatics
http://www.mieur.nl/mihandbook http://www.mihandbook.stanford.edu/
MCV Course for 4th year medical students
Handbook of Medical Informatics
I. Data and Information
1 Introduction and Overview
2 Information and Communication
Handbook of Medical Informatics
II. Data in Computers
3 Data Processing 4 Database Management 5 Telecommunication, Networking and
Integration
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 Informatics
IV. Patient-Centered Information Systems
11 Primary Care
12 Clinical Departmental Systems
13 Clinical Support Systems
14 Nursing Information Systems
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 Informatics
VI. Institutional Information Systems
19 Modeling of Health Care for Information SystemsDevelopment
20 Hospital Information Systems: Clinical Use
21 Hospital Information Systems; Technical Choices
22 Health Information Resources
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 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 Informatics
IX. Medical Informatics as a Profession
36 Education and Training in Medical Informatics
37 International Developments in Medical Informatics