SUMEX

STANFORD UNIVERSITY
MEDICAL EXPERIMENTAL COMPUTER RESOURCE
RR-00785

 

ANNUAL REPORT - YEAR 16

Submitted to

BIOMEDICAL RESEARCH TECHNOLOGY PROGRAM
NATIONAL INSTITUTES OF HEALTH

June 1, 1989

STANFORD UNIVERSITY SCHOOL OF MEDICINE

Edward H. Shortliffe, Principal Investigator
Edward A. Feigenbaum, Co-Principal Investigator
DEPARTMENT OF HEALTH AND HUMAN SERVICES
PUBLIC HEALTH SERVICE
NATIONAL INSTITUTES OF HEALTH

DIVISION OF RESEARCH RESOURCES
BIOMEDICAL RESEARCH TECHNOLOGY PROGRAM

ANNUAL PROGRESS REPORT
PART L., TITLE PAGE

. PHS GRANT NUMBER:

. TITLE OF GRANT:

. NAME OF RECIPIENT INSTITUTION:

. HEALTH PROFESSIONAL SCHOOL:

. REPORTING PERIOD:

5a. FROM:
5b. TO:

. PRINCIPAL INVESTIGATOR:

6a. NAME:
6b. TITLE:

5 P41 RROO785-16

SUMEX — Stanford University
Medical Experimental Computer
Resource

Stanford University

School of Medicine

08-01-88
07-31-89

Edward H. Shortliffe, M.D., Ph.D.

Associate Professor of Medicine
and Computer Science

6c. SIGNATURE: — Ebua eal kL. Lelie.

. DATE SIGNED:

. TELEPHONE:

June 1, 1989

415-723-6979
5 P41 RROO785-16 Table of Contents
Table of Contents:
J. Title Page wo... .iecccssscccccssssscccesssessecesssssceeesessenceeeseeseessensessesseeseesensecaseuasaaseesoes 1
II. Description of Program Activities ........:.ccccsssssscnesccseesseersssseeecesesssesessesaeans 3
TILA. Scientific Subproject ............ccccsscsccccsssssnscccececesesccseesssceacccessnsesccaeeeness 3
TI.B. Books, Papers, and Abstracts ............c:::sccceressesesssssssesneceeseonessseeeeecesecs 3
ILC. Resource Summary Table ............:cccccsssssensecccesceeceseesscacceeneeeesssseeeasees 3
TIL. Narrative Description. ...............cesceseseeeeeeceeeeeeeeeseeseeeeecesseeeensosseessasnesssenseees 5
TIT.A. Summary of Research Progress ..........ssssccssesesssscsssesencceeceessosssneseeesees 5
THL.A.1 Resource Overview .........s:::cccsssssecscessecessssensscseceeeseessscreasoesooenees 5
TH.A.1.1 SUMEX-AIM as a ReSOurce ..0........eeecesesseereeeeseeesseseneeeees 5
T1.A.1.2 Significance and Impact in Biomedicine .............eseeeeeeee 11
TII.A.1.8 Summary of Current Resource Goals ............ccsccceesseereeees 12
TT.A.2 Details of Technical Progress............sscscccsccceseessscseeeesscsecssssseeees 16
TILA.2.1 Key Areas of Progress ...........:ccccssssssessscsecceeecseseenceneeeeeeeeees 16
TIT.A.2.3. Core ONCOCIN Research .......sessssssssecsescsstecseessseeseeesseeens 26
(1) Overview of the ONCOCIN Therapy Planning System......... 26
(2) Implementation of the ONCOCIN Workstation in the
Stanford Clinic .0.......cessssssessssscnscsenssessessnsnssssncecesecseeeaereee 27
(3) E-ONCOCIN: Domain Independent Therapy Planning ....... 28
(4) OPAL: Graphical Knowledge Acquisition Interface............. 29
(5) Generalized Knowledge Acquisition through PROTEGE... 31
(6) Speech Input to Expert Systems ..........ccccsssseccessteerseseereeeeeee 31
(6.1) Prototype Speech Hardware/Software System ............. 31
(6.2) Speech Experiment ..........c:cccccsessseesneccceserseseensceeteeeeeess 33
(7) Object Language Support for ONCOCIN Project.................. 34
(8) Personnel ..0............cccccescesecececeescetssesseseeeseeeseesesseseesessessenteeesess 34
THA.2.2. Core AI Research ...........cccsscscsssscssccenccenseccecaeeeeeseeeeeesereners 36
(1) Ratiomale.........cccccccessseneenscsecceccecceseeeccceceeeseeeceseesstcereeteeseetes 36
(2) Highlights of Progress..........:sccccccscsssesssenseseeecessesesceeeeeeeseteeees 37
(2.1) Large Multi-use Knowledge Bases for Science and
EXMGIne ering ............:::cscsesseeceececcecenaaeececsnceccesccecneececseserees 37
(2.2) Adaptive Intelligent Systems ................c::ssccceceesesseneeeeee 40
(2.8) Advanced Architectures...........:ccccccccccesssscesceeereeeseseneseees 41
(2.4) Knowledge Acquisition and Machine Learning............ 45
(2.5) Symbolic Simulation... ccccssecccencnnececceeceeeeeeesoeeees 45
TI.A.2.4. Core System Research and Development................000006 47
(1) Introduction and Overview .........csccsccccssssscnsscncnscseceesceteceeesos AT

i E. H. Shortliffe
Table of Contents 5 P41 RROO0785-16

(2) The Phase-Out of the DECSystem-20.........e ee eesseeeeoeseneeeees 49
(3) The New SUN-Based SUMEX-AIM Resource..................000 51
(3.1) File Access and Management.............csccccssssssceereesereers 52
(3.2) The SUMEX Perpetual Archive System..............::000: 53
(3.3) Printing Services.............:ccccccsssssessscssssrcecesnseeceseesssseeseees 55
(4) Electromic Mail ............ccccccsssssccssccesssssctercessneccsssecceseeesnessaaenenses 56
(4.1) Macintosh client - MacM............ccsssssscessesseesressseeseees 58
(4.2) Mail Reader User-Interface.............c:ccessscecesessseeceeeseeees 58
(4.3) The Mail Composition User Interface ...............::::ee00 60
(4.4) Texas Instruments Explorer Client.............eccceeeseeees 60
(4.5) DEC-20 IMAP2 Server ..............scccccessscsesereeceessseesseeeeeees 60
(4.6) UNIX IMAP2 Server..........ccccccssessessessssesceseensenecsseeseeseees 61
(4.7) Transition Strategy and Plan............cccccccccssececceseeeeeees 62
(5) Lisp Systems..............ccscsccseccessscessesseceesceeeescceeseeetensceeeerenseeeaes 62
(5.1) Stamdards ......ccecccccccccscccssesscceseecsccessecneeseeesseesseceseeeaes 62
(5.2) Lisp System Performance...............:ccescccseccceseeeeeeceesseeeees 63
(5.3) Lisp Programming Environments ...............:::esseceee w. «65
(6) Workstation System Environments ............:cccccccccceseeeeesseeees 66
(6.1) Macintosh IT Workstations. ...............:ccssenceseseeseeseeneeeees 66
(6.2) Texas Instruments Explorer6............ccccccccsssecececetereeeees 68
(6.3) SUN Workstations ..............cccccssssssssecsscscceseseneceneceeeseeeees 72
(6.4) NeXT Workstations ..........cccccsessscssessecssscsssessesessrsenseess 73
(6.5) Xerox D-Machines............ccccsscsscsecccscssssreneeceesseeseeeeeseneeeees 75
(6.6) Symbolics Lisp Machines ...............cccccscssecceesssnceeceneereees 79
(6.7) HP 9836 Workstations...............cccsscsseseccessnssceceeesseesesees 80
(7) Remote Workstation Access, Virtual Graphics, and
WIndWS ......cccccsssseccsssccessstcessescecsnenseeseseecessceeseeceseesanecsecenseees 80
(7.1) Remote AcceSS..........:cccccccssssssecccsessencceseneccecsssnsceeeeeceeseees 80
(7.2) Virtual Graphics and Window... ...........:cccccesssseessesssseeees 80
(7.3) Remote Graphics Applications..............ccccccesssecceeesseeees 81
(8) Network Services ..........::ccssesccscsssceeceseecesssecsnesesscesenscseeseseess 84
(8.1) National and Wide-Area Networks...............ccccccceeeseeee 84
(8.2) Local Area Networks - LAN'S..........ccsscceccsssneereceteceseees 86
(9) Distributed Information Resources and Access .............cc0008 88
(10) Distributed system operation and management................ 90
TiT.A.2.5. Relevant Core Research Publications ............cceccceeeeees 91
THI.A.2.6. Resource Equipment. .w.........ccccccccessesssstcecsseteeeeeeeneeseeseeees 98
(1) Purchases This Past Year..........ccccccccccccsssssssecceeeeceeeeeeeeseeeeeees 98
(2) Current Subsystem Configurations ..........:::.::ccceessceceereeteeeees 100

E. H. Shortliffe i
5 P41 RROO785-16 Table of Contents

THI.A.2.7. Training Activities ............ccccsssccccssseeecccesstecesessssssencessesecs 105
TII.A.2.8. Resource Operations and Usage ...........ssessescssssereesseseeenes 108

(1) Operations and Support...........ceeseesseeecseeeeseesceenaeenseneueeeeeess 108

(2) Resource Usage Details .0............cseccccessreceecsseeeeeseeeeeeceeeeseesooses 108

(2.1) Overall Resource Loading Data ...........cccceseeseeeeeeeteeeeene 109

(2.2) Individual Project and Community Usage ..............06 110

TH.B. Research Highlights .0..........cccccsescccesessseseeeesssceesesssneneesssstaeeusorsesensees 117
— TIB.1. INTERNIST-U/QMR .......:.ccccssscseesssecsseseesacessecceessercesesseeoesensaee 118
THI.B.2. Path Finder.............cc:sscssscssssssccsercccsaccccessesaccceesesesesneuneesseeneneusaes 119
III.B.3. The Distributed SUMEX-AIM Community ..........cccessssssereerees 120
THI.B.4. ONCOCIN .........cccccccccsssscccesssecesssnsersssecesceeeceeseeceececeesceeeseeseeeeses 121
TIL.C. Administrative Changes...........ccssccccssssessesseeeceeeseessccsseeecessosseenensoenes 123
III.D. Resource Management and Allocation ............:.c:cssscesesenenceeeeseeseoeees 124
TII.D.1. Overall Management Plan................eceeeeeesceceeessneconeenereeseeeeensens 124
TTI.D.2. Cost Cemrter........cccccccssssssesccscssssscesessssssssccsssssccenenseseeseessssssueoeeens 124
II.E. Dissemination of Resource Information ...............ccssscsccesseeereeceeseeees 127
THL.E.1. Software Distribution...............ccccssssscccssscreecseeceeesssserceeeeeeeesssees 127
ITL.E.2. AIM Community Systems Support..............ccssscsceessessencceeeeeeees 128
TH.E.3. Video Tapes and Films... cesesceceesnceceseeeeceeensessesseseeeaes 128
TIT.B.4. Special Seminar ..........sccesssscsssssssesesseressssscensecteseneeeseesessessetens 128
TILF. Suggestions and Comments ..............:ssscccsssssecessssnerceesceaeeeeneeessssseceaens 129
TH.F.1. Resource Organization ..............cccscccecesseteceeeseeceeetessesereessessssaanars 129
TILF.2. Electronic Communications ............cccccccssssccesseserctesssneeeeeeessoesees 129
IV. Description of Scientific Subprojects...............c:cscccsssceccesseeeeessssseeeeeeeesesesees 130
IV.A, Stamford Projects............ccccccssssssseccsssssnsnesecsssceesesenceceseesneneeeeessessennneees 131
IV.A.1. Guardian Project............cccscccccssssccesssscessnseesesecsseneeeeneneeteceeneeeeoees 132
TV.A.2. MOLGEN Project........ccccccccssccscescescssssnsssaceececsssessecscesenceteeeeeseoees 137
TV.A.3. ONCOCIN Project....cccccccccscccccccssseeseecssseesecessaceseesesenseeeeeeeeseses 143
TV.A.4. PENGUIN Project..........ccccessssesssssssccccceccssssncenenerssestseceaaaaeesooes 157
TV.A.5. PROTEAN Project .........ccccsssssssccccccccccssssenscneccesssssssenccesecnneceseetee 166
IV.A.6. Reasoning Under Uncertainty .............:cccccsscsseeeceeceeeeeeeceeeeeteeeees 174
IV.A.7. VentPlan Project ..........ccccsssssssssccccesccccssssnsncneeseesssnnsessensenaessonooes 183
IV.B. National AIM Projects ..............cccccccecececcececeececcesceceenscneeeseseereeoesoaaaaaas 190
IV.B.1. INTERNIST-/QMR, Project .............csssssesseecceeesssereneeneenseeeeeesenens 191
IV.B.2. MENTOR Project........cccccccccceseseesesssseeeseccessssusenneeceteeseeeeeseseeneetes 197

lii E. H. Shortliffe
Table of Contents 5 P41 RROO785-16

IV.C. Pilot Stanford Projects............ccccccssssssesscseenes uessssreasuasonsevacraessiseesesese 202
IV.C.1. REFEREE Project...............:ccscssessesseseesecseeseeseeesesessseseneeesesseeeenees 203
TV.D. Pilot AIM Projects...........cccccsscscsssesseccesesssseecersessseueeseescecesessaaeesesesaeees 210
IV.D.1. The Pathfinder Project...............ccccccccsecesseecesesssceesceececenssnsnnncecess 211
Appendix A: Knowledge Systems Laboratory Brochure............. passesseneceeesssnees 219
Appendix B: Lisp Performance Studies .0..............sscsssssssssccecetessessescenersesssesenees 229
Appendix C: AIM Management Committee Membership.................::ceeeeeee 261
List of Figures:
Figure 1. NSFNet Configuration as of January 1989 ............sseecsseeesesseeeeeees 85
Figure 2. SUMEX-AIM DEC 2060 Configuration ..............ccsececeeeseeesteeeeeneeeees 100
Figure 3. SUMEX-AIM SUN-4 Configuration. ............ccssscccccccsssssessercensesssseenes 101
Figure 4. SUMEX-AIM SUN-83 File Server Configuration .............s:cscccssseeees 101
Figure 5. SUMEX-AIM Xerox File Server Configuration..............c:sccccssesees 102
Figure 6. SUMEX-AIM VAX File Server Configuration..............cccccssseereeeesees 103
Figure 7. SUMEX-AIM Develcon X.25/TCP-IP Gateway Configuration ...... 103
Figure 8. SUMEX-AIM Ethernet Configuration ............::cccssscccsesioressossereeeeees 104
Figure 9. Total CPU Hours Consumed by Month ..........ccccccceesececceneseesseneees 110
Figure 10. CPU Usage Histogram by Project and Community ................:06 111
Figure 11. Table of Resource Use by Project .............ccccccssessensecceseessrnseeeceseees 112

E. H. Shortliffe iv