Simulation of Cognitive Processes P41 RRO0785-08
II.A.2.6 Simulation of Cognitive Processes

Simulation of Cognitive Processes

James G. Greeno
Alan M. Lesgold
Learning Research and Development Center
University of Pittsburgh

I. SUMMARY OF RESEARCH PROGRAM
A. Project Rationale

Our goal is to improve understanding of the basic cognitive processes
involved in the use and acquisition of cognitive skills. Concern is spread
between basic competence in reading, mathematics and general problem
solving on the one hand and complex expertise in domains such as radiology
on the other. A basic form for our theorizing is computer simulation of
human performance. Such simulation modeling allows richer understanding in
the course of theory building and stronger empirical validation of theory
than would otherwise be possible in domains where several separate
cognitive systems or components interact during skilled performance.

B. Medical Relevance

Increased understanding of basic cognitive processes is relevant to
medical needs in two ways. One form of relevance involves performance of
professional medical tasks. Lesgold has been working with other local
colleagues to understand the nature of the skill of reading and diagnosing
chest radiographs. The work is leading toward both insights into |
techniques for improving the training of radiologists and improved
understanding of the aspects of radiology that seem to be learned only with
many years of experience. This latter improved specification of what is
hard to learn and why this is the case will hopefully inform decision
making on automatic diagnostic facilities and diagnostic "prostheses" whose
cost-effectiveness is otherwise difficult to establish. The second form of
relevance of basic research in cognition to medical needs is in development
of understanding of the cognitive requirements of elementary skills such as
reading and arithmetic computation, in which cognitive deficits can
constitute severe disability. Improved understanding of these basic skills
should provide principles useful in developing a more valid approach to
diagnosis and remediation of learning disabilities.

C. Highlights of Research Progress
1. Accomplishments This Past Year
In the study of the acquisition of reading processes, firm data began
to emerge documenting the causal role of slow and nonfacile word

recognition in hampering progress in the acquisition of higher-order
reading skills (Lesgold, Resnick, Roth, & Hammond, 1981; Lesgold & Curtis,

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in press; Resnick, Lesgold & Roth, in preparation). Recent results of
longitudinal research in our laboratory have shown curriculum differences
in the primary grades that significantly affect the specific patterns of
learning word recognition that different children exhibit. In addition,
there has been an improved understanding of the nature of component process
interactions in reading that will drive a simulation of the specific
problems in learning comprehension skills that come from inadequately
practiced word recognition.

The work on radiological skill has been progressing (Lesgold,
Feltovich, Glaser, and Wang, 1981). After extensive review of protocol
data from both expert radiologists and residents, we have a good sense of
the ways in which radiology skill is a blend of opportunistic problem
solving skills from medical diagnosis and more specific spatial
representation skills for human anatomy. Modeling work is beginning in
earnest, now. We will be experimenting with both the sorts of blackboard
approaches subsumed under the AGE system and with parallel activation
models of the sort being used in perception work (e.g., CAPS).

A modeling effort that was carried out in its initial phase with the
SUMEX facility, enabling use of Anderson's ACT system, involved study of
the use of spatial information in solving problems in elementary
probability theory. In this project we are simulating the processing of
information in Venn diagrams in the calculation of probabilities of
composite events. The study extends earlier analyses of spatial
information in probtem solving in the domain of geometry proof exercises,
which also included collaboration with Anderson and use of SUMEX in early
phases of simulation programming (Anderson, Greeno, Kline, & Neves, in
press).

We have developed a simulation of learning by children who have
defective procedures for arithmetic calculation. This work has depended on
concepts and techniques with which we became familiar initially in
collaborative work with Anderson's group. The model simulates learning
from special instruction designed to communicate understanding of concepts
of place value as well as a correct computational procedure, and thus
provides a preliminary hypothesis about the nature of learning in which
conceptual understanding and procedural knowledge interact meaningfully.

2. Research in Progress

Research is continuing on all these topics. In each case, we are
building, through porting of code from other centers and through some
efforts of our own, an appropriate simulation environment on our own VAX-
11-780 system. We are clearly building on what we've learned within the
SUMEX community in doing this.

The work in reading and radiology has many aspects in common, and we
hope to exploit this commonality in simulation modeling. However, the
emphases will be slightly different. The radiology effort will concentrate
on a highly refined level of skill, even in the learner, while the reading
effort deals with the earliest stages of skill acquisition and is
particularly concerned with coordinations in time (in active memory) of
representations for concepts that are interrelated in a text.

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Studies of mathematical cognition are continuing, with increasing
emphasis on individual differences and on learning. We are pursuing
empirical and theoretical studies of individuals' differences in the use of
composite forms in Venn diagrams THAT correspond to composite events that
are involved in problems. We are extending the work on learning in
arithmetic, relating our model of acquiring understanding to some general
principles of heuristic procedure modification, and we will apply these
results to analysis of other learning phenomena in the early arithmetic
domain, such as those studied by Riley, Greeno, and Heller (forthcoming).

D. List of Relevant Publications

Anderson, J.R., Greeno, J.G., Kline, P.J., & Neves, D.M. Acquisition of
problem-solving skill. In J.R. Anderson (Ed.), Cognitive skills and
their acquisition. Hillsdale, NJ: Lawrence Erlbaum Associates, in
press.

 

Lesgold, A.M., Resnick, L.B., Roth, S.F., & Hammond, K.L. Patterns of
learning to read. Paper presented a the biennial meeting of the
Society for Research in Child Development, 1981. Lesgold, A.M.,
Feltovich, P., Glaser, R., & Wang, Y. Radiological expertise.
Symposium presentation at the annual meeting of the American
Educational Research Association, 1981.

Lesgold, A.M., & Curtis, M.E. Learning to read words efficiently. To
appear in A.M. Lesgold & C.A. Perfetti (Eds.)}, Interactive processes in
reading, Hillsdale, NJ: Erlbaum, in press.

 

Lesgold, A.M., & Perfetti, C.A. Interactive processes in reading: Where do
we stand? In A.M. Lesgold & C.A. Perfetti (Eds.), Interactive
processes in reading, Hillsdale, NJ: Erlbaum, in press.

 

lesgold, A.M., & Perfetti, C.A. (Eds.). Interactive processes in reading,
Hillsdate, Nj: Erlbaum, in press.

 

Resnick, L.B., & Lesgold, A.M. A longitudinal study of difficulties in
learning to read. To appear in J.P. Das, R. Mulcahy, & A.E. Wall
(Eds.), Theory and Research in Learning Disability, forthcoming.

Riley, M.S., Greeno, J.G., & Heller, J.I. Development of children’s
problem-solving ability in arithmetic. In H.P. Ginsburg (Ed.),
Development of mathematical thinking. New York: Academic Press, in
press.

Lesgold, A.M. Cognitive simulation modeling on the VAX-11. Behavior
Research Methods and Instrumentation, in press.

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P41 RROO785-08 Simulation of Cognitive Processes

IT.

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Funding Support

1) National Institute of Education

. Title: Research on learning and schooling.

Principal Investigators: Robert Glaser, University Professor

and Co-Director, Learning Research and Development Center (LRDC),
University of Pittsburgh; and Lauren Resnick, University Professor
of Psychology and Co-Director, LRDC.

 

. Funding Agency: National Institute of Education

. Grant Number: NIE-G-80-0014

. Total Award: 1 December 79 to 30 November 82, $7,880,729.

. Current Period: 1 December 80 to 30 November 81, $2,627,067.

2) Office of Naval Research

. Title: Cognitive and instructional factors in the acquisition

and maintenance of skill.

Principal Investigators: Robert Glaser, University Professor
and Co-Director, LRDC; James Greeno, University Professor;
Alan Lesgold, Research Associate Professor of Psychology;
Michelene Chi, Research Assistant Professor of Psychology.

. Funding Agency: Office of Naval Research

. Contract Number: N0Q0014-79-C-0215

. Total Award: 1 January 79 to 30 September 83, $1,676,950.
. Current Period: 1 October 80 to 30 September 81, $247,053.

3) National Science Foundation/National Institute of Education

. Title: Invention and understanding in the acquisition of

computation.

Principal Investigators: Lauren B. Resnick, Professor of
Psychology and Co-Director, LRDC; and James Greeno, University
Professor of Psychology.

 

. Funding Agency: National Science Foundation and National

Institute of Education (Joint Program)

. Grant Number: SED78-22289
. Total Award: $149,967.
. Current Period: 1 December 78 to 31 August 81

INTERACTIONS WITH THE SUMEX-AIM RESOURCE

A.

Medical Collaborations and Program Distribution via SUMEX

The work on development of radiology skills is being done in
collaboration with Dr. Yen Wang, Clinical Professor of Medicine, University
of Pittsburgh.

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B. Sharing and Interaction with Other SUMEX-AIM Projects

We have shared software from the ACT and AGE projects via SUMEX. In
addition, the ties to the ACT project have led to interactions and joint
software and programming environment development with psychologists at
Carnegie-Mellon University. We expect to maintain a common simulation
development environment for psychologists in both institutions, largely
because SUMEX proved the value of such standardization. Similarly,
especially if the COGNET proposal for a cognitive Science Network is
funded, we expect to support a standard demo and guest interface in both
places.

C. Critique of Resource Management
None.
D. Future Involvement

This is a final report for this project. Because of the successful
acquisition of on-site facilities for artificial intelligence work, we are
moving from national project to associate status within the SUMEX-AIM
community. We are particularly grateful for the many opportunities SUMEX
involvement provided when we most needed them. We have learned from them
in building our own resource and expect to continue to share in the
community-building aspects of AIM in the future.

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I1.A.2.7 SECS - Simulation and Evaluation of Chemical Synthesis

SECS - Simulation and Evaluation of Chemical Synthesis

PI: W. Todd Wipke
Board of Studies in Chemistry
University of California
Santa Cruz, California 95064

Coworkers:

D. Dolata (Grad student)

I. Kim (Grad student)

D. Rogers (Grad Student)

J. Chou (Postdoctoral)

P., Condran (Postdoctoral)

T. Moock (Postdoctoral)

H. Kuehmstedt (Visiting Professor,

Univ. of Greifswald, East Germany)

I, SUMMARY OF RESEARCH PROGRAM

 

A. Technical Goals. The long range goal of this project is to develop
the logical principles of molecular construction and to use these in
developing practical computer programs to assist investigators in designing
stereospecific syntheses of complex bio-organic molecules. Our specific
goals this past year included adding a starting material library, initial
exploration of strategies based on starting materials, developing the
representation for a reasoning modute, and completion of the user-defined
transform capabilities. The objectives for the XENO project were to
establish extensive collaborations with metabolism experimentalists to test
XENO predictions and to begin development on methods for assessing the
potential biological activity of each metabolite. The world-wide SECS
User’s Group for sharing chemical transforms was initiated.

B. Medical Relevance and Collaboration

The development of new drugs and the study of how drug structure is
related to biological activity depends upon the chemist's ability to
Synthesize new molecules as well as his ability to modify existing
structures, @.g., incorporating isotopic labels or other substituents into
biomolecular substrates. The Simulation and Evaluation of Chemical
Synthesis (SECS) project aims at assisting the synthetic chemist in
designing stereospecific syntheses of biologically important molecules.
The advantages of this computer approach over normal manual approaches are
many: 1) greater speed in designing a synthesis; 2) freedom from bias of
past experience and past solutions; 3) thorough consideration of all
possible syntheses using a more extensive library of chemical reactions
than any individual person can remember; 4) greater capability of the
computer to deal with the many structures which result; and 5) capability

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of computer to see molecules in graph theoretical sense, free from bias of
2-D projection.

The objective of using XENO (a spinoff of SECS) in metabolism is to
predict the plausible metabolites of a given xenobiotic in order that they
may be analyzed for possible carcinogenicity. Metabolism research may also
find this useful in the identification of metabolites in that it suggests
what to look for. Finally, it seems there may even be application of this
technique in problem domains where one wishes to alter molecules so certain
types of metabolism will be blocked.

C. Highlights of Research Progress
1. Progress and Accomplishments

RESEARCH ENVIRONMENT: At the University of California, Santa Cruz, we
have a GT40 and a GT46 graphics terminal connected to the SUMEX-AIM
resource by 1200 and 2400 baud leased lines (one leased line supported by
SUMEX). We also have a T1725, T1745, CDI-1030, DIABLO 1620, and an ADM-3A
terminal used over 300 baud leased lines to SUMEX, UCSC has only a small
IBM 370/145, a PDP-11/45, 11/70 and a VAX 11/780, (the 11's are restricted
to running small jobs for student time-sharing) all of which are unsuitable
for this research. .The SECS laboratory is located in a newly renovated
room with raised floor in 125 Thimann Laboratories, adjacent to the
synthetic organic laboratories at Santa Cruz so the environment is
excellent.

2. SECS Program Developments

The Simulation and Evaluation of Chemical Synthesis (SECS) program
has undergone many additions to improve its capabilities and usefulness to
synthetic chemists.

The ALCHEM language has been made extensible to facilitate addition
of new groups. New functional groups and ring systems can be defined and
referred to by name within a transform and individual atoms and bonds
within the named entity can also be referenced. Thus, a transform may now
inquire if an indole ring system exists elsewhere in the molecule, and may
then inquire about substituents at various positions on that ring system.
Such a query was previously impossible. This kind of query arises
frequently in heterocyclic chemistry.

The User Defined Transform module (UDT) allows the chemist to define
a chemical transform on-line in the middle of a synthetic analysis. We
have now enabled the program to "learn" the transform, i.e., remember it
and be able to apply it again where applicable. This is the first work in
machine learning of chemical reactions. A graphical front-end to the UDT
module was added and the whole module incorporated into the production SECS
version,

A META-SECS top-level plan generator is being implemented to reason

using synthetic principles and conclude plans which will then be used to
guide the existing SECS program in synthetic analysis. The First Order

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Predicate Calculus is being used to represent the synthetic strategies -and
principles. The statement parser and data structure manipulation routines
have been implemented, the inference engine is in progress at this time.
This explicit reasoning in synthetic strategies should prove very
interesting as a way to control development of the synthesis tree.

Synthesis tree output is now possible on the PRINTRONIX printer/
plotter using a new software vector to raster conversion program developed
by our group. The resulting raster file is compressed, transmitted from
SUMEX to Santa Cruz, then expanded and fed to the printer. This approach
avoids our previous problems resulting from the long transmission time
required to plot the big trees over a slow communication Vine and the
mechanical problems associated with pen plotters.

The Aldrich catalog of commercially available chemicals has been
converted from Wisswesser line notation to connection table and to the SEMA
unique representation. This allows SECS to determine if a precursor is
commercially available. Initial studies of using this library to develop
Synthetic strategies has begun. Several algorithms have been developed to
identify potential starting materials for a target molecule The
effectiveness of these algorithms is being evaluated against literature
syntheses,

3. XENO - A Program to Predict Plausible Metabolites

The XENO program was developed to assist metabolism researchers in
predicting plausible metabolites of compounds foreign to an organism, and
in evaluating the potential biological activity of the resulting
metabolites. The knowledge base of XENO has been revised completely and
now includes 110 types of metabolic processes. We have specialized on rat
and mouse systems to date. The XENO program takes graphical input of a
compound to be metabolized and stepwise generates a tree of metabolite
structures which might result.

The second phase of XENO which evaluates potential biological
activity is underway. We are developing a series of rules for each class
of compounds to relate structure to biological activity. Work to date has
concentrated on aromatic amines and polycyclic aromatic hydrocarbons.

Collaborations with metabolism experimentalists have begun in order
that XENO can make predictions for compounds actively being studied in the
laboratory. Initial feedback from ICI Pharmaceuticals on one particular
drug indicates that the major metabolites were correctly generated and that
XENO proposed structures that may explain some polar compounds that ICI has
not yet been able to identify. XENO generated several possible pathways to
explain an unusual metabolite. ICI is seeking to differentiate between the
pathways. We are similarly collaborating with Mead Johnson. Initial
results there indicated several transforms were missing from the XENO
library or were improperly represented. Those have been corrected and new
analyses sent for evaluation. Other collaborations are in progress with
investigators at NIH and at the Australian National University.

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We are also comparing XENO analyses to results reported in the
literature for compounds such as cyclophosphamide. This work is sponsored
by the National Cancer Institute.

D. List of Current Project Publications

M.L. Spann, K.C. Chu, W.T. Wipke, and G. Ouchi, "Use of Computerized
Methods to Predict Metabolic Pathways and Metabolites," J. of Env.
Pathology and Toxicology, 2, 123 (1978); also reprinted in "Hazards
from Toxic Chemicals," ed. M.A. Mehiman, R.E. Shapiro, M.F. Cranmer and
M.J. Norvell, Pathotox Publishers, Inc., Park Forest South, I11., 1978,
pp. 123-121.

P. Gund, E.J.J. Grabowski, D.R. Hoff, G.H. Smith, J.D. Andose, J.B.
Rhodes, and W.T. Wipke, "Computer-Assisted Synthetic Analysis at
Merck," J. Chem. Info. and Comput. Sci., 20, 288 (1980).

S.A. Godleski, P.v.R. Schleyer, E. Osawa, and W. T. Wipke, “The Systematic
Prediction of the Most Stable Neutral Hydrocarbon Isomer," Progress in
Physical Organic Chemistry, Vol. 13, 1981, pp. 63-118.

R.E. Carter and W.T. Wipke, "SECS--EH Hjalpmedel Vid Organisk
Syntesplanering,” Kemisk Tidskrift, in press.

W.T. Wipke, G. Ouchi, and J. Chou, "Computer-Assisted Prediction of
Metabolites,” Proceedings of Conference Structure Activity Relations,
Research Triangle Park, N.C., Feb., 1980.

E. Funding Status

1) Resource-Related Research: Biomolecular Synthesis
PI: W. Todd Wipke, Associate Professor, UCSC
Agency: NIH, Research Resources
No: RRO1059-035S1
7/1/80-12/31/81 $ 36,949 TDC

2) Computer-Aided Prediction of Metabolites for Carcinogenicity Studies
PI: W. Todd Wipke
Agency: NIH, National Cancer Institute
No: NO1-CP-75816
1/1/80-7/31/81 $74,394 TDC

Il. INTERACTIONS WITH SUMEX-AIM RESOURCE

A. Medical Collaborations and Program Dissemination via SUMEX, SECS
is available in the GUEST area of SUMEX for casual users, and in the SECS
DEMO area for serious collaborators who plan to use a significant amount of
time and need to save the synthesis tree generated. Much of the access by
others has been through the terminal equipment at Santa Cruz because
graphic terminals make it so much more convenient for structure input and
output.

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Prof. H. Kuehmstedt of the University of Greifswald, E. Germany used
SECS to generate some interesting and novel synthetic routes to
progesterone. Demonstrations and sample synthetic analyses were generated
for Ors. Terry Brunck and Steve Roman of Shell Development, John Harper of
Amoco Chemicals, Prof. Fujiwara, University of Tsukuba, Japan, Dr. Peder
Berntsson, Hassle, Sweden. Other visitors included Dr. M. Onozuka, A.
Tomonaga and H. Itoh, Kureha Chemical Co., Tokyo, Japan, Dr. Rhyner,
Director of Research, Ciba-Geigy, Basel, Switzerland. Demonstrations of
SECS in Sweden were performed by Dr. Carter at many universities and
companies. Ned Phillips of the College of Pharmacy, Univ. of Florida is
accessing SECS via SUMEX GUEST access. A synthesis of vellerolactone,.a
substance found to be toxic and teratogenic was generated for Prof. R. E.
Carter, Univ. Lund, Sweden.

Dr. Wipke has also used several SUMEX programs such as CONGEN in his
course on Computers and Information Processing in Chemistry. Communication
between SECS collaborators is facilitated by using SUMEX message drops,
especially since the time difference between the U.S. and Europe and
Australia makes normal telephone communication practically impossible.
Testing and collaboration on the XENO project with researchers at the NCI
depend on having access through SUMEX and TYMNET.

B. Examples of Sharing, Contacts and Cross-Fertilization with Other
SUMEX-AIM Projects. This year the SECS and XENO project have made use of
the teletype plot program which Ray Carhart of the CONGEN project wrote at
Stanford. We modified the program to fit the needs of our projects. This
was facilitated by being able to transfer the programs within areas on the
same computer system at SUMEX. We continue to have intellectual
interactions with the DENDRAL and MOLGEN project in areas where we have
common interests and have had people from those projects speak at our group
seminars. SUMEX also is used for discussions with others in the area of
artificial intelligence on the ARPANET.

We developed a local print capability through SUMEX with the help of
the SUMEX staff which has facilitated our work greatly. We have also
communicated with SUMEX staff regarding selection of terminals and other
computer equipment.

C. Critique of Resource Services. We find the SUMEX-AIM network very
well human engineered and the staff very friendly and helpful. The SECS
project is probably one of the few on the AIM network which must depend
exclusively on remote computers, and we have been able to work rather
effectively via SUMEX. Basically we have found that SUMEX-AIM provides a
productive and scientifically stimulating environment and we are thankful
that we are able to access the resource and participate in its activities.

SUMEX-AIM gives us at UCSC, a small university, the advantages of a
larger group of colleagues, and interaction with people all over the
country. We especially thank SUMEX for support of the leased line for our
GT40, and for helping develop our remote print capability.

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SUMEX however has fallen short of our goals and desires: the load
average on SUMEX has increased and reduced my group's efficiency greatly--
the system is too overloaded. We are installing SECS on the 2020 to begin
to make use of that additional capability. We also have not been able to
utilize the 4800 baud high speed line we purchased because SUMEX
limitations forced running at 2400 baud. We had hoped to be able to write
tapes locally with the 4800 baud line, but at 2400 baud it is too slow to
be practical. We would like to see some of their local lines slowed down
so those remote people doing graphics can run at a higher speed. We have
found that when a FORTRAN program is overlayed, the symbol table is lost,
making symbolic debugging with DDT impossible, we wish that could be
corrected.

D. Collaborations and Medical Use of Programs via Computers other
than SUMEX. SECS 2.9 now resides on the CompuServe computer networks so
anyone can access it without having to convert code for their machine.
This has proved very useful as a method of getting people to try this new
technology. Dr. George Purvis of Battelle is accessing SECS via
CompuServe, as are Gene Dougherty of Rohm and Haas and many others. SECS
also resides on the Medicindat machine at the University of Gothenborg,
Sweden, and is available all over that country by phone. Similarly in
Australia, SECS resides at the University of Western Australia and is
available throughout the country over CSIRONET. Plans are underway for a
similar situation in Japan.

 

III. RESEARCH PLANS (6/81-6/82)

A. Long Range Project Goals and Plans. The SECS project now consists
of two major efforts, computer synthesis and metabolism, the latter being a
very young project. Our plans for SECS for-the next year include
completing the high level reasoning module for proposing strategies and
goals, and providing control which continues over several steps. This
reasoning module also will be able to trace the derivation of goals and
thus explain some of its reasoning. We also plan to focus on bringing the
transform library up in sophistication to improve the performance and
capabilities of SECS. In particular we plan to allow a transform to have
access to the precursors generated as well as to the product, this will
allow much greater control and more natural transform writing, but it
requires extensive changes in the SECS control structure to permit this.

We will continue to explore starting material oriented strategies
based on the Aldrich Chemical file we now have implemented. We especially
are interested in chirality based strategies which we feel are very strong.

We plan to explore running SECS on a virtual memory 32-bit computer
like a VAX-11/780 or a PRIME since many chemistry departments now have
these machines available and thus could run SECS.

The XENO metabolism project will be expanding the data base to cover
more metabolic transforms, including species differences, sequences of
transforms, and stereochemical specificities of enzymatic systems.
Development of the second phase which assesses the biological activity of

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the metabolites will continue as will efforts to simulate excretion and
incorporation, the endpoints of metabolism. Finally, application of the
current program to the molecules actively being investigated by metabolism
researchers will occur concurrently to test and verify the work done to
date on XENO and provide examples for publication.

In the next five years we foresee the SECS and XENO projects reaching
a stage of maturity where they will find much application in other research
groups. Our research will continue in these areas, but turn to some new
programs that approach the probtems from different viewpoints and allow us
an opportunity to begin fresh taking advantage of what we have learned from
the building of SECS and XENO.

B. Justification and Requirements for Continued Use of SUMEX. The
SECS and XENO projects require a large interactive time-sharing capability
with high level languages and support programs. I am on the campus
computing advisory committee and am the campus representative to the UC
systemwide computing advisory committee and know that the UCSC campus is
not likely in the future to be able to provide this kind of resource.
Further there does not appear to be in the offing anywhere in the UC system
a computer which would be able to offer the capabilities we need. Thus
from a practical standpoint, the SECS and XENO projects still need access
to SUMEX for survival.

Scientifically, interaction with the SUMEX community is still
extremely important to my research, and will continue to be so because of
the direction and orientation of our projects. Collaborations on the
metabolism project and the synthesis project need the networking capability
of SUMEX-AIM, for we are and will continue to be interacting with synthetic
chemists at distant sites and metabolism experts at the National Cancer
Institute. Our requirements are for good support of FORTRAN.

Our needs for SUMEX include fixing the overlay loader so that an
overlaid program can retain its symbol 1 table and permit symbolic use of
DDT. This is a serious problem we hope can be fixed by SUMEX staff because
without symbols, debugging is very difficult and time-consuming, since we
must run SECS and XENO overlaid.

C. Needs beyond SUMEX-AIM. We do plan to acquire a virtual memory
minicomputer like a VAX or PRIME in the future to offload some of our
processing from SUMEX. Such a machine would enable us to do some
production and development work locally and would explore the feasibility
of those types of machines as hosts for SECS and XENO. A local machine
would also free us from the problems we have experienced in the winter when
the telephone lines to Stanford get wet. and are too noisy to use. Even if
we had such a machine we still need to use SUMEX because we plan to
continue to develop and maintain the PDP-10 version of SECS and we need
SUMEX for its networking capabilities. In the future if we had a mini at
UCSC, we would lighten our load on SUMEX, but currently we see our load
increasing as our group grows and as we start new projects yet mus
maintain existing large programs.

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We especially need the local capabilities to read and write magnetic
tape because we receive and send many tapes between our collaborators,
Driving to SUMEX to write a tape is not efficient for our personnel and
hinders communication with collaborators via tape. The problem will worsen
because the SECS Users Group will be sending UCSC tapes of chemical
transforms on a regular basis.

D. Recommendations for Community and Resource Development. The AIM
Workshops have been excellent in the past and should be continued. We feel
the SUMEX resource is too heavily utilized at times to get any productive
work done. SUMEX staff could tighten the load on the machine by reducing
the speed of text terminals at Stanford from 2400 baud and above down to
1200 baud which is plenty fast for humans to read, and giving remote users
faster capabilities, say 4800 baud. We feel the community would benefit if
remote users such as we had a virtual minicomputer so the load could be
distributed more and not have everything go through Stanford which is
highly congested and quite expensive for multiple leased lines. SUMEX can
not currently handle an increase in the outside community using SECS or
XENO for testing. The response time guests and outside collaborators see
is not a good reflection on the actual efficiency of the programs.

E. A. Feigenbaum 238
P41 RROO785-08 SOLVER Project

TI.A.2.8 SOLVER Project

SOLVER: Problem Solving Expertise

Dr. P. E. Johnson
Center For Research In Human Learning
University of Minnesota

Dr. W. B. Thompson
Department of Computer Science
University of Minnesota

I. SUMMARY OF RESEARCH PROGRAM
A. Project Rationale

This project focuses upon the development of strategies for
discovering and documenting the knowledge and skill of expert problem
solvers. In the last fifteen years, great progress has been made in
synthesizing the expertise required for solving extremely complex problems.
Computer programs exist with competency comparable to human experts in
diverse areas ranging from the analysis of mass spectrograms and nuclear
magnetic resonance [DENDRAL] to the diagnosis of certain infectious
diseases [MYCIN].

Design of an expert system for a particular task domain usually
involves the interaction of two distinct groups of individuals, "knowledge
engineers," who are primarily concerned with the specification and
implementation of formal problem solving techniques, and "experts" (in the
relevant problem area) who provide factual and heuristic information of use
for the problem solving task under consideration. Typically, the knowledge
engineer, after consulting with one or more experts, decided on a
particular Knowledge representational structure and inference strategy.
Next, "units" of factual information are specified. That is, properties of
the problem domain are decomposed into a set of manageable elements
suitable for processing by the inference operations. Once this
organization has been established, major efforts are required to refine
representations and acquire factual knowledge organized in an appropriate
form. Major research problems exist in developing more effective
representations, improving the inference process, and in finding better
means of acquiring information from either experts or the problem area
itself.

Programs currently exist for empirical investigation of some of these
questions for a particular problem domain [AGE, UNITS, RLL]. These tools
allow the investigation of alternate organizations, inference strategies,
and rules bases in an efficient manner. What is stil] lacking, however, is
a theoretical framework capable of reducing dependence on the expert's
intuition or on near exhaustive testing of possible organizations. Despite
their successes, there seems to be a consensus that expert systems could be

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better than they are. Most expert systems embody only the limited amount
of expertise that individuals are able to report in a particular,
constrained language (e.g. production rules). If current systems are
approximately as good as human experts, given that they represent only a
portion of what individual human experts know, then improvement in the
"knowledge capturing” process should lead to systems with considerably
better performance.

B. Medical Relevance and Collaboration

Collaboration with Dr. James Moller, Department of Pediatrics, and
Dr. Donald Connelly in the Department of Laboratory Medicine and
Pathology, both at the University of Minnesota Medical School.

C. Highlights of Research Progress

Accomplishments of this past year. Prior research at Minnesota on
expertise in diagnosis of congenital heart disease has resulted in a theory
of diagnosis and an embodiment of that theory in the form of a computer
simulation model which diagnoses cases of congenital heart disease.

At a macroscopic level, the simulation model contains four categories
of knowledge used by the expert physician (pediatric cardiologist) in
diagnosis. First, the model has clinical knowledge of disease. This
knowledge is hierarchically structured, including categories of disease,
specific diseases, and variants of the same disease that differ in
presentation. From each element in the hierarchy, there is knowledge of
the associated anatomy and physiology and the expected clinical
manifestations. Second, the model has deductive knowledge of disease -
knowledge of principles of cardiovascular pathophysiology and the clinical
manifestations useful in detecting underlying pathology. The causal
knowledge deductively relates cardiovascular defects to hemodynamics and to
expected patient data. This category of knowledge is not typically used in
diagnosis, since the expert physician can simply recall expected clinical
manifestations through clinical knowledge of disease, rather than deduce
them. Third, the model has heuristic knowledge of disease and of clinical
findings useful in its diagnosis. One aspect of this knowledge provides
indices from clinical manifestations to diseases and from disease to
disease, useful in choosing diagnostic hypotheses to consider. Another
aspect of heuristic knowledge is related to evaluation of diagnostic
alternatives -- rules of thumb for ruling in and ruling out alternatives as
correct or incorrect. Another form of heuristic knowledge screens abnormal
from normal clinical findings and identifies subsets of findings which are
likely to have the same underlying cause. All heuristics are aimed at
basically the same end -- reducing the cognitive demands of diagnosis
without loss of diagnostic accuracy. The fourth and last category is
knowledge of data acquisition techniques: interviewing methods, physical
exam maneuvers, special procedures, and laboratory utilization.

Diagnosis is characterized as a heuristic search process, with four
sources of knowledge involved. Clinical knowledge of disease is the
hierarchical structure to be searched. Deductive knowledge of disease is
useful in construction of missing pieces of that hierarchy and in

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justifying the clinical information it contains. Heuristic knowledge aids
in limiting the section of clinical knowledge to be searched and in
providing simple evaluation functions for use in search. Data acquisition
for knowledge is essential in obtaining patient information to be used in
the search process.

The simulation model is currently programmed in UT Lisp on the
University of Minnesota CDC Cyber 74; it contains just over one million
characters, One of the first goals of our project is to transfer this
program over to‘the Sumex-AIM system - see Project goals and Plans (below).

Research in progress. The methodology of our research derives from
the discipline of cognitive science, and from our study of expert problem
solvers. This methodology consists of: (1) extensive use of verbal
thinking aloud protocois as well as other experimental data as a source of
information from which to make inferences about underlying cognitive
structures and processes; (2) development of computer models as a means of
testing the adequacy of inferences derived from the protocol studies; (3)
testing and refinement of the cognitive models based upon the study of
human and model performance in experimental settings.

This past year we have been investigating expertise in solving
certain classes of physics problems. We have chosen this area because
reasonable data on human competency is available from past work at
Minnesota and elsewhere, some work on formal modeling has already been
done, and both the problems and required knowledge are well specified.
Effort will be concentrated on investigating control structures and search
heuristics. Those portions of the system unique to physics will be
isolated so that generality can be easily studied by extending the program
to other domains.

Once a computational model has been implemented, three classes of
experiments will provide useful information. First, a series of validation
tests will be used to estimate the effectiveness of the model. A series of
problems will be given to the model and a solution trace produced. The
degree to which the program's behavior corresponded to the ways in which
the humans solved the same problems will be determined. In addition, the
effectiveness of the heuristics in producing efficiencies relative to
alternative approaches to the problems will be estimated. In the second
set of experiments, the model will be optimized for different types of
problems within the same domain to determine which heuristics are likely to
be problem specific. We are particularly interested in the degree to which
the problems are well specified and the effects of problem space topology.

Expert/novice differences will be investigated by operating the model
with different levels of sophistication in its knowledge base. The last
set of experiments will investigate errors in problem solving. Classes of
problems likely to produce an incorrect answer will be identified. The
degree to which these errors are a necessary consequence of the search
heuristics will be investigated. Finaltty, the model will be extended so
that when garden path errors are recognized, a generalization process is
invoked so that similar situations can be avoided in the future.

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D. List of Relevant Publications

Connelly, D., & Johnson, P.E. The medical problem solving process. Human
Pathology, 1980, 11, 412-419

Elstein, A., Gorry, A., Johnson, P., & Kassirer, J. New research
direction. In Clinical Decision Making and Laboratory Use. D.C.
Connelly, E. Benson, & D. Burke (Eds.)}, University of Minnesota Press
(in press).

Feltovich, P.d., Kngwledge based components of expertise in medical

diagnosis. Unpublished doctoral dissertation, University of Minnesota,
1981,

 

Johnson, P.E. Cognitive models of medical problem solvers. In D.C.
Connelly, E. Benson, & D. Burke (Eds.) Clinical Decision Making and
Laboratory Use. University of Minnesota Press (in press).

 

Johnson, P.E., Severance, D.G., & Feltovich, P.J. Design of decision
support systems in medicine: Rationale and principles from the analysis
of physician expertise. Proceedings of the Twelfth Hawaii
International Conference on System Sciences, Western Periodicals Co.,
1979, 3, 105-118.

Johnson, P.E., Barreto, A., Hassebrock, F., Moller, J., & Prietula, M.

Expertise and error in diagnostic reasoning. Cognitive Science (in
press).

Johnson, P.E., & Thompson, W.B. Strolling down the garden path: Detection
and recovery from error in expert problem solving. Proceedings of the
seventh International Joint Conference on Artificial Intelligence,
Vancouver, B.C., August 1981.

Moller, J.H., Bass, G.M., Jr., & Johnson, P.E. New techniques in the
construction of patient management problems. Medical Education (in
press).

Swanson, D.B., Computer simulation of expert problem solving in medical
‘ diagnosis. Unpublished doctoral dissertation, University of Minnesota,
1978.

Swanson, D.B., Feltovich, P.J., & Johnson, P.£. Analysis of physician
expertise: Implications for the design of decision support systems. In
D.B. Shires & H. Wold (Eds.), Medinfo77. Amsterdam: North-Holland
Publishing Co., 1977.

E. Funding and Support

Work being done in scientific reasoning is sponsored under a current
NSF (SE079-13036) grant to Paul Johnson. The work in law has been
supported by by the Minnesota Center for Research in Human Learning and is
described in a proposal which is currently under review by the NSF Law and
Social Science Program. The work in medicine has been supported by NICHD

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(T736-HD-17151 and HD-01136) and NSF (NSF/BNS-77-22075) grants to the
Minnesota Center for Research in Human Learning of which Paul Johnson is a
principal investigator. Additional support is being sought from the
National Library of Medicine and the Information Sciences Program at NSF.

Il. INTERACTIONS WITH THE SUMEX-AIM RESOURCE
A. Medical Collaborations and Program Dissemination via SUMEX

Collaboration with Tufts University - New England Medical Center
(See III.A.)

B. Sharing and Interactions with Other SUMEX-AIM Projects

Our work is complementary to many of the current projects supported
on Sumex-AIM. We will be investigating certain aspects of expert problem
solving in order to develop better organizational and knowledge acquisition
strategies. Such work requires that we be able to build upon the extensive
experience in knowledge engineering within the Sumex-AIM communities.
Specifically, we first need to investigate the number of existing programs
in order to determine the degree to which they satisfy the design goals
which we will be establishing. We then hope to use the program
construction tools that are available in order to build prototype systems
to illustrate our ideas.

C. Critique of Resource Management

(None)

I1I. RESEARCH PLANS
A. Project Goals and Plans

Near term. The research for which we wish to use the Sumex-AIM
resource has two subcomponents, one directed at selective reimplementation
of the diagnosis program (described above) and the other directed at
extensions of the research more broadly. Reimplementation of the diagnosis
program will be carried out first, using AGE and UNITS knowledge
engineering tools, and Interlisp. The present program is a blend of a
semantic network representation (for clinical knowledge of disease) in a
production system/blackboard control structure (heuristic activation of
portions of clinica? knowledge). This structure is nicely congruent with
the facilities provided through UNITS and AGE linked togethcr. This
relatively well specified reimplementation task will provide an appropriate
environment for learning about Sumex-AIM and the resources it provides. It
will also provide an interesting comparison of performance of similar
diagnosis programs implemented in different ways. The second subcomponent
of the proposed research will focus upon data collection and patient
management skills of the expert physician. Work thus far has focused
largely on diagnosis because of our lack of familiarity with the medical
domain and because of the paramount importance of methodological

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development, as discussed in the next section on knowledge capturing. In
pediatric cardiology, we now have the substantive knowledge and
methodological tools required to approach medical problem solving more
broadly, including knowledge and procedures retated to both collection of
patient data for diagnostic purposes and patient management. In
collaboration with experimental psychologists and physicians at Minnesota,
and computer scientists and physicians at Tufts University in Boston we
propose to investigate the stimulus information utilized by physicians in
various patient data sources (X-ray, EKG, and heart sounds).

Long range. We propose to investigate the "knowledge capturing"
process that occurs in the early stages of the development of expert
systems when problem decomposition and solution strategies are being
specified. Several related questions will be addressed: What are the
performance consequences of different organization approaches, how can
these consequences be evaluated, and what tools can assist in making the
best choice? How can organizations be determined which not only perform
well, but are structured so as to facilitate knowledge acquisition from
human experts?

B. Justification and Requirements for Continued SUMEX Use

We are currently using a CDC Cyber 74 and Cyber 172 for most of our
work in problem solving. The Cyber computers are not well suited for
interactive computing and have serious limitations with respect to address
Space and available support software.

C. Needs and Plans for Other Computing Resources beyond SUMEX-AIM

We expect delivery on a VAX-11/780 in June 1981 at the University of
Minnesota. Hopefully, much of our work will eventually be implementable on
the VAX. However, this depends both on our ability to acquire additional
peripheral hardware and on increased availability of AI software for the
VAX. Until that time, access to a TENEX facility is extremely desirable.

D. Recommendations for Future Community and Resource Development

(None)

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P4t RROO785-08 Pilot Stanford Projects

I1.A.3 Pilot Stanford Projects

 

The following are descriptions of the informal pilot projects
currently using the Stanford portion of the SUMEX-AIM resource pending
funding, and full review and authorization.

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II.A.3.1 Protein Secondary Structure Project

 

Protein Secondary Structure Project

Robert M. Abarbanel, M.D.
University of California Medical Center
University of California at San Francisco

I. SUMMARY OF RESEARCH
A. Project Rationale

Development of a protein structure knowledge base and tools for
manipulation of that knowledge to aid in the investigation of new
structures. System to include cooperating knowledge sources that work
under the guidance of other system drivers to find solutions to protein
secondary structure problems. Evaluations of structure predictions using
known proteins and other user feedbacks available to aid user in developing
new methods of prediction.

B. Medical Relevance and Collaboration

Many important proteins have been sequenced but have not, as yet, had
their secondary or tertiary structures revealed. The systems developed
here would aid medical scientists in the search for particular
configurations, for example, around the active sites in enzymes.
Predictions of secondary structure will aid in the determination of the
full "natural" configuration of important biological materials.

Development of systems such as these will contribute to our knowledge of
medical scientific data representation and retrieval.

C. Highlights of Research Progress

This is a relatively new project at SUMEX. During the last year, a
representation of protein sequences and rules for their manipulation have
been built using the UNITS system developed at SUMEX. At this time,
various existing structure prediction algorithms are being implemented to
explore the needs for tools in a fully developed system where a scientist
may describe a new prediction scheme in nearly natural language, and see it
run on protein sequences with aids to discovery of errors and problems in
the new methods developed.

D. List of Relevant Publications

None.

E. Funding Support

New Investigator Award proposal pending with NLM.

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Il. INTERACTIONS WITH SUMEX-AIM RESOURCE
A. Medical Collaborations
None.
B. Sharing and Interactions with SUMEX Projects

This project is closely allied with the MOLGEN group, both in
computer and scientific interests. Some pattern matching methodology
created for the protein data base has been adopted and used in the various
DNA knowledge bases. The principal persons in the MOLGEN group have
contributed to this project's use and understanding of knowledge base
software and resources.

C. Critique of Resource Management

System load has been a significant problem. Except during late night
or early morning hours, use of complex packages like the UNITS editor or
other system available text editors is a major burden. Often the schedule
manager has moved the active processes to background. This is a problem
shared with many others in the community using knowledge base tools. It is
a common practice to transfer files to other computing resources for
interaction during daylight hours. Communications via MSG have aided this
project in establishing connections with other researchers and groups with
parallel interests.

TIT. RESEARCH PLANS
A. Project Goals and Plans

Near-Term: Design of rules modules in UNITS editor that will allow an
inexperienced user to express algorithms for structure prediction in near-
natural language. These prediction schemata will then be translated into
appropriate combinations of invocations of knowledge sources, editors, and
feedback tools to aid the user in further refinement of his algorithms,

Long-Term: Systems to be developed for the discovery of rules and/or
algorithms that can transform a protein sequence into a secondary
siructure, possibly with implications about tertiary structure. This will
involve an effort along the lines of the meta-DENDRAL project.

B. Need for Resources
1. SUMEX Resources

Environment of knowledge base tools and people is the primary motive
for doing this work using SUMEX. Access to both established and developing
systems aids this project in setting down standards of excellence, forward
thinking about computing tools and methodologies, and active exchange of
techniques and ideas. The close collaboration with the MOLGEN researchers
is particularly useful in this regard.

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2. Other Computing Resources

A soon to be established network connection with the Computer
Graphics Laboratory at UCSF will provide access to .1) the latest in protein
structural information, and 2) color line drawing graphics facilities for
evaluation and display of this projects product. A real time display using
color graphics will become a possibility.

Connections with the HPP Unix system may also prove useful for
program sharing.

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II.A.3.2 Ultrasonic Imaqing Project

ULTRASONIC IMAGING PROJECT

James F. Brinkley, M.D.
W.D. McCallum, M.D.
Depts. of Computer Science,
Obstetrics and Gynecology
Stanford University

I. SUMMARY OF RESEARCH PROGRAM
A. Project Rationale

The long range goal of this project is the development of an
ultrasonic imaging and display system for three-dimensional modeling of
body organs. The models will be used for non-invasive study of anatomic
structure and shape as well as for calculation of accurate organ volumes
for use in clinical diagnosis. Initially, the system will be used to
determine fetal volume as an indicator of fetal weight; later it will be
adapted to measure left ventricular volume, or liver and kidney volume.

The general method we are using is the reconstruction of an organ
from a series of ultrasonic cross-sections taken in an arbitrary fashion. A
real-time ultrasonic scanner is coupled to a three-dimensional acoustic
position locating system so that the three-dimensional orientation of the
scan plane is known at all times. During the patient exam a dedicated
microcomputer based data acquisition system is used to record a series of
scans over the organ being modelled. The scans are recorded on a video tape
recorder before being transferred to a video disk. 3D position information
is stored on a floppy disk file. In the proposed system the microprocessor
will then be connected to SUMEX where it will become a slave to an AI
program running on SUMEX. The SUMEX program will use a model appropriate
for the organ which will form the basis of an initial hypothesis about the
shape of the organ. This hypothesis will be refined at first by asking the
user relevant clinical questions such as (for the fetus) the gestational
age, the lie of the fetus in the abdomen and complicating medical factors.
This kind of information is the same as that used by the clinician before
li@ even places the scan head on the patient. The model will then be used to
request those scans from the video disk which have the best chance of
giving useful information. Heuristics based on the protocols used by
clinicians during an exam will be incorporated since clinicians tend to
collect scans in a manner which gives the most information about the organ.
For each requested scan a prototype outline derived from the model will be
sent to the microcomputer. The requested scan will be retrieved from the
video disk, digitized into a frame buffer, and the prototype used to direct
a border recognition process that will determine the organ outline on the
scan, The resulting outline will be sent to SUMEX where it will be used to
update the model. The scan requesting process will be continued until it is
judged that enough information has been collected. The final model will
then be used to determine volume and other quantitative parameters, and
will be displayed in three dimensions.

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We believe that this hypothesize verify method is similar to that
used by clinicians when they perform an ultrasound exam. An initial model,
based on clinical evidence and past experience, is present in the
clinician's mind even before he begins the exam. During the exam this model
is updated by collecting scans in a very specific manner which is known to
provide the maximum amount of information. By building an ultrasound
imaging system which closely resembles the way a physician thinks we hope
to not only provide a useful diagnostic tool but also to explore very
fundamental questions about the way people see.

We are developing this system in phases, starting with an earlier
version developed at the University of Washington. During the first phase
the previous system has been adapted and extended to run in the SUMEX
environment. Clinical studies have been initiated to determine its
effectiveness in predicting fetal weight and left ventricular volume. At
the same time computer vision techniques are being studied in order to
devetop the system further in the direction of increased applicability and
ease of use. We thus hope to develop a limited system in order to
demonstrate the feasibility of the technique, and then to gradually extend
it with more complex computer processing techniques, to the point where it
becomes a useful clinical tool.

B. Medical Relevance

This project is being developed in collaboration with the Ultrasound
Division of the Department of Obstetrics at Stanford, of which W.D.
McCallum is the head.

Fetal weight is known to be a strong indicator of fetal well-being:
small babies generally do more poorly than larger ones. In addition, the
rate of growth is an important indicator: fetuses which are “small-for-
dates" tend to have higher morbidity and mortality. It is thought that
these small-for-dates fetuses may be suffering from placental
insufficiency, so that if the diagnosis could be made soon enough early
delivery might prevent some of the complications. In addition such growth
curves would aid in understanding the normal physiology of the fetus.
Several attempts have been made to use ultrasound for predicting fetal
weight since ultrasound is painless, noninvasive, and apparently risk-free.
These techniques generally use one or two measurements such as abdominal
circumference or biparietal diameter in a multiple regression against
weight. We recently studied several of these methods and concluded that the
most accurate were about +/-200 gms/kg, which is not accurate enough for
adequate growth curves (the fetus grows about 200 gms/week). The method we
are proposing is based on the assumption that fetal weight is directly
related to volume since the density of fetal tissue is nearly constant. We
are hoping that by utilizing three dimensional information more accurate
volumes and hence weights can be obtained.

In addition to fetal weight, the current implementation of this
system is now being evaluated for its ability to determine other organ
volumes. In collaboration with Dr. Richard Popp of the Stanford Division of
Cardiology we have started to evaluate the system on in vitro hearts. Left
ventricular volumes are routinely obtained by means of cardiac

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