RESEARCH PLAN

II. RESEARCH PLAN ~ BOOK I

This is an application for renewal of a grant supporting the Stanford
University Medical Experimental computer (SUMEX) research resource for
applications of Artificial Intelligence in Medicine (AIM). The research plan has
been divided into several logical parts:

1) Book L - Resource research objectives and rationale, progress report, and
detailed research plans.

2) Book Il - Biographical sketches, collaborating project reports and plans,
and supporting appendixes.

3) Budget - First year budget detail, five-year budget summary, and budget
explanation and justification,

1 BACKGROUND AND PROPOSED WORK

1.1 OVERVIEW OF OBJECTIVES AND RATIONALE

The SUMEX-AIM project is a national computer resource with a dual mission:
1) the promotion of applications of artificial intelligence (AI) computer science
research to biological and medical problems and 2) the demonstration of computer
resource sharing within a national community of health research projects.

In the body of this proposal, we offer definitions and explanations of
these efforts at several levels of detail to meet the needs of reviewers from
various perspectives. For this overview, we give only a brief summary of our
recent accomplishments, present status and expectations for the requested term of
the renewal, the five years beginning August 1,1978.

Definitive funding of the SUMEX-AIM resource was initiated in December
1973. The principal hardware was delivered and accepted in April 1974, and the
system became operational for users during the summer of 1974. The present
renewal is therefore written from a perspective of just short of three years of
experience in attempting to develop and serve the user community for the
resource.

The original SUMEX proposal was an outgrowth of two lines of endeavor at
Stanford that had been supported by the Biotechnology Resources Program. The
ACHE project (Advanced Computer for MEdical Research), 1965-72, had introduced
the innovation of interactive time-shared computing to the medical research
community at the Stanford Medical Center. Based on an IBM 360/50 with mass core
storage, this system was notaole for the ease with which physicians and
scientists, previously inexperienced with computers, were able to learn a variety
of applications with minimal help from professional programmers. With the further
development of the technology, and the rationalization of computer support
functions at Stanford, this system was eventually integrated with the university-

Privileged Communication 1 J. Lederberg
Section 1.1 OVERVIEW OF OBJECTIVES AND RATIONALE

wide time-sharing service. While ACME had some shortcomings as a production
(contra development) tool many of our colleagues at the medical school still look
back regretfully at having lost it as a medical-school-dedicated system tuned to
their special needs. The second line, the DENDRAL project, is a resource-related
project connected with applications of artificial intelligence to problems of
molecular characterization by analytical instruments like mass-spectrometry, gas-
ecnromatography, nuclear magnetic resonance, and so on.

In 1972 we applied to NIH for the establishment at Stanford of a next
generation computer resource to supplant ACME for applications for which the
university-wide facility was inadequate. The DENDRAL project was the central
source of this initiative; several others entailing real-time instrumentation as
much as AI needs were also specified. During the subsequent 18 months, we
entered a phase of protracted review and negotiations with BRP and its advisory
groups, from which emerged the policy determination that resources of this scope
were best justified if they could be functionally specialized, but geographically .
generalized. The emerging technology of computer networking opened an
opportunity to demonstrate this model in a way that could serve both local and
national needs. With all of this in mind, we were happy to undertake the
responsibility of such a demonstration, which seemed important as a step in
community-building as well as in providing the computing resources so urgently
needed for our own and others” research efforts. In many respects it would have
been far more convenient to focus on our own requirements, but the satisfaction
of these seemed both infeasible and too limited an aspiration in the face of the
suggested opportunity.

Three years is hardly long enough for a conclusive determination of the
success of such a model, though we ean fairly take pride in the diligence and
technical competence with which we nave responded to the community
responsibilities mandated by the terms of the award. An important element in
satisfying those responsibilities was the establishment of a mutually
satisfactory management structure, on which we report in further detail below.
Good will and common purpose are of course the indispensable ingredients, and we
are grateful to have been able to offer this service in a congenial framework,
and at the same time to be able to support our local computing research needs.

Our technical task has been achieved: to collect and implement an effective
set of hardware and software tools supporting the development of large and
complex AI programs and to facilitate communications and interactions between
user groups. In effect, users throughout the country can turn on their own
teletype or CRT-display terminals, dial a local number, and logon to SUMEX-AIM
with the same ease as if it were located on their own campus -- and have access
to a specialized resource unlikely to be matched nearby. From the community
viewpoint, we have substantially increased the roster of user projects (from an
initial 5) to 11 current major projects plus a group of pilot efforts. Many of
these projects are built around the communications network facilities we have
assembled; bringing together medical and computer science collaborators from
remote institutions and making their research programs available to still other
remote users. As discussed in the sections describing the individual projects, a
number of the computer programs under development by these groups are maturing
into tools increasingly useful to the raspective research communities. The
demand for production-level use of these programs has surpassed the capacity of
the present SUMEX facility and has raised the general issues of how such software
systems can be optimized for production environments, exported, and maintained.

J. Lederberg 2 Privileged Communication
OVERVIEW OF OBJECTIVES AND RATIONALE Section 1.1

The principal thrust of this renewal proposal is to sustain the momentum of
SUMEX-~AIM, both as a facility and as a community, during a period of rapid change
in the technology and economics of computers. For reasons that will be justified
in more detail, we do not plan further major expansion of centralized hardware at
SUMEX, believing that growing community needs should now be met as justified at
distributed nodes. It is difficult to make firm predictions of the technological
changes that will present themselves during the period of the grant, but it may
be that some conversion of the system will be necessary if only to keep pace with
the software exchanged with cognate communities.

More concretely, our objectives for this next grant term include:

1) Maintaining the vitality of the ATM community of projects. This will entail
scrutiny of old and new projects in what is approaching a steady-state of
maximum capacity, and improving the efficiency with which developmental
programs can be furnished to medical research groups.

2) Continued computational support for the AIM community based initially on our
existing KI-10 facility. We expect the computing hardware technology to
change substantially in the next few years with the availability of both more
powerful and smaller and cheaper machines. Additional large-machine
resources may still be necessary to meet the growing needs of the community
during this period. As already stated, this kind of growth should be
implemented at sites other than Stanford, but can be embraced by the same
management structure as governs SUMEX-AIM. We plan to study these new
technological alternatives affecting our central facility and to attempt to
maintain software compatibility for our dual KI-10 system. Only should this
prove untenable or grossly inefficient will we consider a hardware conversion
to a more directly compatible implementation.

3) Continued work to improve system software and communication facilities for
community interactions and tne dissemination of programs. This will include
advantageous connections to emerging communications networks and
administrative efforts to exploit community expertise and sharing in software
development.

4) Core research work to explore ways of exporting complex AI programs including
new language support (MAINSAIL), specialized satellite computer systems, the
use of networks for software dissemination and maintenance, and examinations
of more operationally efficient implementations of AI programs. We will
continue to work closely with the XEROX-PARC group, which remains primarily
responsible for maintaining INTERLISP.

 

5) Core research work to attempt to generalize and document AI tools that have
been developed in the context of a number of individual application projects.
This will include work to organize the present state-of-the-art in AI
techniques and tools through the AI-Handbook effort and the development of
generalized software packages for the acquisition, representation, and
utilization of knowledge in AI programs. These packages will facilitate the
exploration of new areas of application of these tools.

Privileged Communication 3 J. Lederberg
Section 1.2 SIGNIFICANCE

1.2 SIGNIFICANCE

Viewed in the narrowest definition of a biotechnology resource, SUMEX-AIM
is justified by the technical capabilities it offers for the pursuit of research
using advanced computer applications relevant to the NIH mission. The progress
reports of the various user projects speak for themselves in the diversity and
pertinence of the work accomplished. We do not underestimate (and share as a
grave responsibility) the overall investment charged to the resource; but this is
quite reasonable when apportioned over the whole range of projects. The shared
resource is plainly far more economical than any alternative method of providing
comparable facilities to such a range of users distributed over the country.

Similar considerations apply to a variety of other kinds of research
hardware. Unique to the computer is the extent to which shared hardware
contributes to methodological cooperation; wnat in this context we call software
compatibility. This follows from the unparalleled complexity of computer
programs as process-specifications. What other techniques are or can be
formulated as recipes of 190,000 or more instructions, each of which must be
faithfully executed or the whole system will collapse? Yet we know that a sreat
deal of our knowledge, e.g., in medical diagnosis, may prove to be of similar
couplexity when explicitly and formally expressed. We infer that many fields of
scientific inquiry will have to use similar methods of exchange of critical
commentary; that the electronic communications of computer programs is a
prototype for the maintenance of other knowledge bases essential for the fabric
of a. complex and demanding society. The conputer is at one time the node of a
knowledge-sharing network, and the device for verifying the consistency and
pertinence of the updates and criticisms that the users remit. Thus we can view
our resource as exemplifying a technology that induces a new social organization
of seientific effort (we would not be the first to recall Gutenberg; and to view
ourselves as analogs of some of the early experiments with the use of the print
medium for journals and academies.) From this perspective, it is quite fittins
that the initial grant that established SUMEX-AIM was attended by so much
preoccupation with managerial design, not ordinarily the favorite occupation of
scientific types.

several concrete illustrations of the encouragement of dynamic criticism
that enhances the robustness of shared knowledge can be elicited from current
projects (see Section 6 on page 41 in Book II), apart from the most familiar
instances of sharing of software over the computer networks. The MYCIN rule
bases, and the text of the AIHANDBOOX are continuously updated by critical users
and reviewers. In fact, the text of various parts of this proposal went through
dozens of iterative revisions, with comments fron many interested groups, within
the several weeks that were dedicated to its preparation. Another, and one of
the most interesting examples, was the experimental use of the CONGEN program
(See the DENDRAL progress report on page 42 in Book II) in a graduate class in
advanced organic chemistry taught by Professor Djerassi. Each of 25 students
scanned tne recent literature for claims of new structures whose proofs were
deemed to be interesting or dubious or both. Five exanples were selected for
exhaustive reexamination by the students. In each case, the published proof was
found to be defective when it was checked by CONGEN -- alternative structures
Naving been overlooked by the authors that still gave good fits to the given
data. These and several comparable examples of asserted scientific fact are
being more carefully reexamined in the autnors’” laboratories in response to the

Jd. Lederberg 4 Privileged Communication
SIGNIFICANCE a Section 1.2

program’s refutations. In due course, we believe this kind of mechanized
checking of "proofs" of chemical structures will be a routine part of the peer
review critical function of the editorial staff of the journals. These advances
are facilitated by the tight internal cohesion of argument in structural organic
chemistry, compared to other scientific fields -~ precisely why this scientific
domain was the one chosen for our initial work on applied AI.

The technical and sociological implications of our program are in fact
elaborated throughout this proposal. By contrast, this may be the place to
digress with some more personal observations (in the voice of the principal
investigator) about the need for scientists to attend more self-consciously to
the process of science itself, and to the political questions of social choice

that are part of the accountability of science, to offer due return for value
received.

Although SUMEX-AIM is rooted in the sub-discipline of "Artificial
Intelligence" we understand and share the discomfort that many bystanders have in
trying to give it a precise definition. It might have been preferable to think
of "knowledge-engineering" as the thread that links almost all of our projects.
This has connotations that might recall "data-base-management"; and we should not
disparage the role that efficient systems for retrieving complex data will have
in our effort. But our task is not usually to maintain a telephone-directory
witn yellow pages, but instead to gather, test and validate a hierarchy of
generalized rules that operate both on each other, and on data of the kind that
are the province of the information-retrieval subdiscipline. The development of
the computer programs to perform these operations is the software-science part of
our effort. Benind it is necessarily a new level of focussed inquiry into the
rules of scientific inference in detail. that could only be cross-—checked by
interaction with the machine.

We are traversing a time when the very justification for basic research is
under critical, often even hostile scrutiny. Many quarters are asking such
questions as "How much of the health progress of the past 30 years can be
attributed to advances in knowledge connected with NIH-supported research?" Are
our institutional arrangements and patterns of funding really the most
appropriate for the most efficient “transfer of technology” from the basic
laboratory “to the bedside’?" Less often raised by external critics is, "To what
extent does the present system support the most fundamental innovations within
science itself; or does it inevitably focus overwhelming support on the most
obvious, transparent questions and discourage more revolutionary kinds of
inquiry?"

Within the NIH directorate, it has been stipulated that "Currently, within
the research community, formal processes are lacking to assure systematic
identification and evaluation of clinically relevant research information, and
its effective transfer to the health care community...."

It is not always popular to insist that these questions must be faced up to
-~ that basic science cannot indefinitely subsist on unconfirmed faith as to its
promise. Furthermore, it is easy to show that many short-term advances have
arisen from the most pragmatic kinds of investigation: empirical screening for
antibiotics or antidiuretics has undoubtedly generated more life-saving
therapeutic products than the most sophisticated molecular biology, up to the

Privileged Communication 5 J. Lederberg
Section 1.2 SIGNIFICANCE

present moment. Indeed, salt-water, intelligently administered, has been one of
the great life-savers of the recent era! On the other hand, I hold that it would
be tragic to undermine the enormous long range potential of basic insight without
a deeper analysis of the process by which knowledge and insight move from basic
science into clinical problems; and we just might find some ways to improve the
system without wrecking it!

These remarks should be taken as exposing a philosophical preoccupation
ratner than as the design of a research program. Tney do relate to efforts like
the MOLGEN project, which include a great deal of focussed introspection on the
intellectual substance of scientific inquiry. It would be premature to clain
that computer programs per se will soon be delegated the major responsibility for
"systematic identification of relevant knowledge", although they can already play
a very helpful role in assisting human intelligence to correlate bibliographic
data, and in other ways. However, the very process of implementing an "applied
philosophy of science", which is the principal forework of developing a domain
for the application of knowledge-based AI, is exactly the kind of formal
systematization called for in these renewed efforts to facilitate technology
transfer to health care. Longer range success in our AI research will be as
important in helping us understand what we are doing as scientists and
diagnosticians as in providing mechanical assistance to these ends.

Aithough our substantive efforts are mostly concerned with the "micro.
problems" of scientific or clinical inference, there may be more important
treasures in a macro-perspective on the integration of knowledge in medicine. My
own most important laboratory accomplishments have all concerned the discovery of
new problems, and the bringing together of previously disparate disciplines,
rather than the solution of extant puzzles -- the discovery of sex in bacteria,
better viewed as the marriage of genetics and bacteriology is perhaps the least
controversial instance. I believe that it is reasonable to expect that the
systematization of biomedical knowledge, to which computer AI will make an
indispensable contribution, is an important side effect of these investigations
in knowledge-engineering; and that this will lead in turn to the recognition of
holes in the overall fabric tnat badly need patching.

We have too little theory of the practice of science to offer more than
case studies at this time -- I have been spending some time in collaboration with
a historian and sociologist in trying to achieve a better understanding of the
dynamics of discovery of bacterial recombination, and found there is more to the
context of that story than my own ingenuity. But it is also very difficult to
reconstruct such events without critical recordings of the incidents as they
occur -- recordings we are learning how to make in the MOLGEN work. [** Copies
of a working paper illustrating this are available on request. **]

To turn to a more clinically urgent arena, it is somewhat dismaying to
recall that it took 35 years from Beadle and Tatum’s discovery of nutritional
mutants in Neurospora to tne beginnings of the biochemical genetics of such
important situations in man as atherosclerosis. I do intend to initiate some
inquiry as to the inevitability of delays of that kind, which seem
retrospectively absurd. We will not get analytically versuasive or policywise
sound determinations of such questions without more attention to the underlying
process of scientific inquiry tnan unselfconscious scientists are customarily
wont to indulge in.

J. Lederberg 6 Privileged Communication
SIGNIFICANCE Section 1.2

This kind of speculation can also be translated into conerete research
programs, which in turn may evoke some new principles. Kidney-stones are an
unlikely arena of concern for someone of my particular scientific background: but
a number of issues have emerged in consultations with some of my colleagues in
tne Stanford Division of Urology. There has been substantial evidence for some
time of a significant genetic factor in chronic recurrence of stones. This does
not seem to be correlated with overall rates of calcium oxalate excretion; indeed
one must focus on the stone as a pathological form of crystal aggregation -~- much
larger quantities of calcium oxalate are passed as microcrystals by normal
individuals. Several workers nave identified mucopolysaccharides in the matrix
of these stones, and some have speculated about their possible role as initiators
or cements in stone formation. On the other hand, geneticists have long known
that blood-group substances, (mucopolysaccharides!) appear in the secretions,
including the urine, of the Se/se and Se/Se [Secretor] genotypes; although saliva
is the preferred sample for diagnosis. Still another worker, a pathologist, has
remarked on the occurrence of mucopolysaccharide concretions in the tubules near
the renal papillae of Se/se subjects. To the best of my knowledge, these
disciplinary nuggets have been privately and separately held, and there has been
no effort to study their possible interconnection. A survey is now underway at
Stanford to test a possible statistical association of Secretor and blood group
type with stone recurrence.

These suggestions were arrived at through interpersonal discourse, experts
from different disciplines being able to furnish provocative data points when
prodded by a more general inquiry. Could one imagine a more general problem.
generator that could arrive at similar conclusions? Pernaps so -- one could
parse through the medical subspecialties, or through significant diseases, to ask
more systematically if they had been scrutinized from the perspective of, say,
biochemical genetics. And this raises many other nypothetical inputs to a
combinatorial-generator of potential, new interdisciplines. One hastens to add,
that most of the rotely drawn intersections will be meaningless or empty --
enough perhaps that the whole game may end up looking quite silly. However, the
problematics of the game have not been explored, and to that extent, there is a
pilot project here that I intend to pursue. Its practical feasibility will
depend in part on the briskness with which relevant data can be fetched from the
literature and from other experts, and I will be exploring possibilities of on-
line access to bibliographic databases 1) to help support this effort, and 2) to
suggest further research efforts in the use of AI techniques for bibliographic
inquiry in ways that may be pertinent to macro-policy of research management.

Privileged Communication 7 J. Lederberg
Section 1.3 BACKGROUND AND PROGRESS
1.3 BACKGROUND AND PROGRESS

1.3.1 PROGRESS SUMMARY

This progress summary covers the period from December 1973, when the SUMEX-
AIM resource was initially funded, through April 1977. During this period we
have met all of the defined goals of the resource:

i) We have established an effective computing facility to support a nation-
wide community of medical AI research projeets including connections to
two computer communication networks to provide wide geographical access to
the facility and research programs.

ii) We have actively recruited a growing community of user projects and
collaborations. The initial complement of collaborators included five
projects. This roster nas grown to eleven fully authorized projects
currently plus a group of approximately six pilot efforts in various
stages of formulation. Recruiting efforts have included a public
dedication and announcement of the resource, NIH referrals from computer-
based project reviews, direct contacts by resource personnel and on-going
projects as well as contacts through the AIM workshop series coordinated
by the Rutgers Computers in Biomedicine resource under Dr. Saul Amarel.

iii) We have established an AIM community management structure based on an
overseeing Executive Committee and an Advisory Group to assist in
recruiting and assessing new project applications and in guiding the
priorities for SUMEX-AIM developments and resource allocations. These
committees also provide a formal mechanism for user projects. to request
adjustments in their allocated share of facility resources and to make
known their desires for resource developments and priorities.

iv) SUMEX user projects have made good progress in developing more effective
consultative computer programs for medical research; one of the major
goals toward which our AI applications are aimed. These performance
programs provide expertise in analytical biochemical analyses and
syntheses, medical diagnoses, and various kinds of cognitive and affective
psychological modeling.

v) We have worked hard to build system facilities to enable the inter- and
intra-~ group communications and collaborations upon whicn SUMEX is based.
We have a number of examples in which user projects combine medical and
computer science expertise from geozrapnically remote institutions and
numerous examples of users from all over the United States and
occasionally from Europe experimenting with the developing AT programs.
The SUMEX staff itself nas had good success in establishing such sharing
relationships on a system level with otner research groups and has many
examples of complementary development and maintenance agreements for
system programs.

vi) We have made numerous improvements to the computing resource to extend its
capacity, to improve its efficiency, to enhance its human interfaces, to

improve its documentation, and to enhance tne range of software facilities
available to user projects.

J. Lederberg 8 Privileged Communication
PROGRESS SUMMARY Section 1.3.1

vii) We have begun a core research effort to investigate alternatives and
programming tools to facilitate the exportability of user and system
software. This is just now producing a "machine-independent"
implementation of the ALGOL-like SAIL languaze which will run ona range

of large and small machines and provide a language base for transferring
programs,

viii) We have supported community efforts in the more systematic documentation
of AI concepts and techniques and in buildings more general software tools
for the design and implementation of AI application programs. These have
included a Stanford AI Handbook project comprising a compendium of short
articles about the projects, ideas, problems, and techniques that make up
the field of ATI.

Privileged Communication 9 J. Lederb
J. Le erg
Section 1.3.2 DETAILED PROGRESS REPORT

1.3.2 DETAILED PROGRESS REPORT

The following material covers in greater detail the SUMEX-AIM resource
activities over the past 3.5 years. These sections attempt to define in more
detail the technical objectives of our research community and include progress in
the context of the resource staff and the resource management. Details of the
progress and plans for our external collaborator projects are presented in
Seetion 6 on page 41 (in Book II).

1.3.2.1 DEFINITION OF TERMS AND OBJECTIVES

Artificial Intelligence is a branch of computer science which attempts to
discern the underlying principles involved in the acquisition and utilization of
knowledge in reasoning, deduction, and problem-solving activities (1). Currently
authorized projects in the SUMEX community are concerned in some way with the
application of these principles to biomedical research. The tangible objective
of this approach is the development of computer programs which, using formal and
informal knowledge bases together with mechanized hypothesis formation and
problem solving procedures, will be more general and effective consultative tools
for the clinician and medical scientist. The exhaustive search potential of
computerized hypothesis formation and knowledge base utilization, constrained
where appropriate by heuristic rules or interactions with the user, has already
produced promising results in areas such as chemical structure elucidation and
synthesis, diagnostic consultation, and mental function modeling. Needless to
Say, much is yet to be learned in the process of fashioning a coherent scientific
discipline out of the assemblage of personal intuitions, mathematical procedures,
and emerging theoretical structure of the "analysis of analysis" and of problem
solving. State-of-the-art programs are far more narrowly specialized and
inflexible than the corresponding aspects of human intelligence they emulate;
however, in special domains they may be of comparable or greater power, e.g., in
the solution of formal problems in organic chemistry or in the integral calculus.

An equally important function of the SUMEX-AIM resource is an exploration
of the use of computer communications as a means for interactions and sharing
between geographically remote research groups in the context of medical computer
science research. This facet of scientific interaction is becoming increasingly
important with the explosion of complex information sources and the regional
specialization of grouns and facilities that might be shared by remote
researchers. Qur community building role is based upon the current state of
computer communications technology. While far from perfected, these new
capabilities offer nighly desirable latitude for collaborative linkages, both
within a given research project and among them. Several of the active projects
on SUMEX are based upon the collaboration of computer and medical scientists at

me me en ee ee ee ee ce ee ee ee ee ar eae ne a ae ne ee a ee ee ene eee ee ee ee ee re ee ee ee ee ee ee ee

(1) For recent reviews to give some perspective on the current state of AI,
see: (i) Winston, P.H., “Artificial Intelligence", Addison-Wesley Publishing Co.,
1977; (ii) Nilsson, N.J-., "Artificial Intelligence", Information Processing 74,
North-Holland Pub. Co. (1975); and (iii) a summary by Feigenbaum, E. A., attached
as Appendix I, page 202 (see Book II). An additional overview of research
areas in AI is provided by the outline for an "Artificial Intelligence Handbook"
being prepared under Professor Feigenbaum by computer science students at
Stanford (see Appendix II on page 225 in Book II).

J. Lederberg 10 Privileged Communication
DeTAILED PROGRESS REPORT Section 1.3.2.1

geographically separate institutions; separate both from each other and from the
computer resource. The network experiment also enables diverse projects to
interact more directly and to facilitate selective demonstrations of available
programs to physicians and medical students. Even in their current developing
State, we have been able to demonstrate that such communication facilities allow
access to the rather specialized SUMEX computing environment and programs from a
great many areas of the United States (even to a limited extent from Europe) for
potential new research projects and for research product dissemination and
demonstration. In a similar way, the network connections have made possible

close collaborations in the development and maintenance of system software with
other facilities.

1.3.2.2 FACTLITY HARDWARE

Based on the AI mission of SUMEX-AIM, we selected a Digital Equipment
Corporation (DEC) model KI-10 computer system for our facility. This selection
was based on 1) hardware architectural and performance features, 2) available
software support relevant to AI applications, 3) price versus performance data
for the system, and 4) the scope of the user community from which we might expect

to draw collaborators and share software. This choice has proved highly
effective.

The current system hardware configuration is diagrammed in Figure 1 on
page 14. It is the result of a number of augmentations over the past 3 years to
meet the capacity needs of the growing SUMEX-AIM project community. Our initial
configuration consisted of a KI-10 processor, core memory (192K 36-bit words @ 1
microsecond), swapping storage (1.7M words 9 8 msec average rotational latency
and 2 microsecond/word transfer rate), file storage (40M words), magnetic tapes,
DEC tapes, terminal line scanner, and line printer. Our network connections are
discussed in Section 1.3.2.4 on page 20.

This system reached prime-time saturation by fall of 1974. Since many of
our medical and other professional collaborators cannot adjust their schedules to
maten light computer loading during the night-time hours, the prime-time
responsiveness is crucial to being able to support medical experimentation with
developing programs and to allow community growth. We have taken active steps to
transfer as much prime-time loading as feasible to evening and night hours
including shifting personnel schedules (particularly for Stanford-—based
projects), controlling the allocations of CPU resources between various user
communities and projects, and encouraging jobs not requiring intimate user
interaction to run during off hours by developing bateh job facilities. Despite
tnese efforts, prime-time loading has remained quite high, particularly with the
growth of the number of user projects.

A similar congestion has persisted in the on-line file space we have been
able to allocate to user projects. Again we have implemented controls to try to
assure effective use of available space and to encourage use of external file
Storage facilities such as the ARPANET Data Computer and other computer sites.
Nevertneless, the interactive character of SUHMEX use, the large AI program files,
and the extensive use of SUMEX for collaborator communications have continuously
raised file space demands beyond those we could meet.

Privileged Communication 11 J. Lederberg
Section 1.3.2.2 DETATLED PROGRESS REPORT |

We have proposed a number of hardware configuration augmentation steps to
the Executive Committee to cost-effectively provide additional capacity. These
were based on analyses of predominant system bottlenecks and enhancement steps
feasible within available budgets. The enhancements approved by the committee
and implemented include:

1) Add 64K words of core memory and 20ri words of file storage (11/74)
2) Add second KI-10 CPU for dual processor operation (5/75)

3) Add 256K words of core memory and upgrade file system to higher volume,
lower cost technology (recently approved by NIH and the AIM Executive
Committee with implementation in progress)

A plot of effective CPU capacity as a function of continuing investment is
shown in Figure 2 on page 15 and displays the cost-effectiveness of our
sequential augmentations. At the present time our hardware configuration has
grown about as much as is cost-effective. Additional growth would entail
Significant redesigns of the system including upgrades of existing hardware.
Contemplating such future expansion also raises the issues of compatibility with
newer hardware technologies being announced. These provide advantages in speed,
cost, size, and maintainability. Such a complete upgrade is not envisioned in
the immediate future as a number of interesting new product announcements are
expected over the next 1 or 2? years that could substantially affect such an
upgrade strategy. Our plans in this direction are discussed in more detail under
the proposed resource plans for the continuation period (see Section 3.1 on
page 62).

J. Lederberg 12 Privileged Communication
Section 1.3.2.2

DETAILED PROGRESS REPORT

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

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13

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DETAILED PROGRESS REPORT Section 1.3.2.2

Figure 2. Cost-effectiveness of SUMEX Augmentations

Estimated Capacity in
Useful KI-10 Equivalents
(Net of overhead)

 

 

24
- Add 256K memory and upgrade
file/tape system [estimated
improvement - upgrade in progress]
\
Add second KI-10, 5/76
1 +
- Add 64K memory, 11/74
\
Initial purchase, 3/74
KI-10 with 192K memory
0 1 2

Cumulative System Investment ($M)

This plot illustrates the incremental increases in computing capacity
achieved as a function of cumulative investment in the SUMEX-AIM facility. The
higher slope of the curve after the initial investment illustrates both the
substantial investment in peripheral devices (file system, tapes, communications,
ete.) and the trend toward lower memory prices. The largest impact in terms of
PDP-10 memory price reductions occurred around the time of adding the 64x
increment in November 1974. Since then processor prices have stayed relatively
stable and memory prices have dropped less dramatically. It should be noted that
semi-conductor memories have not yet made a big in-road in the PDP-10 market;
this technology is where the more recent memory price reductions have occurred.

The original purchase of 1 KI-10 with 192K of memory for about $800K
performed with about 60% efficiency under peak load. Adding the 64K of memory
for $75K brought the efficiency up to about 85%. Then adding the second
processor for $200K increased throughput to about 1.3-1.4 KI-10 equivalents.

This step represents about a 59% increase in throughput for a 20% increased
investment. A proposal has been approved recently by the AIM Executive Committee
and NIH to augment core memory by 256K words. This augmentation would increase
throughput to about 1.7 KI-10 equivalents for another $100K; this would be a 26%

Privileged Communication 15 J. Lederberg
Section 1.3.2.2 DETAILED PROGRESS REPORT

throughput increase for 8% additional investment. As part of the proposed memory
augmentation we plan to upgrade the file and tape systems as well to relieve file
Space congestion and increase system operations efficiency. Including the net
cost of the file/tape upgrade in these figures (purchase price less resale of
existing equipment) raises the proposed additional investment to $160K and the
fractional increase from 8% to 13%. Of course, the disk upgrade affects CPU
throughput only indirectly in that the increased speed reduces contention,
particularly when moving head swapping is necessary. It contributes primarily to
supporting the growing on-line file needs of the projects.

J. Lederberg 16 Privileged Communication
DETAILED PROGRESS REPORT Section 1.3.2.2

Figure 3. Capacity and Loading Increase with Dual Processor Augmentation

1-PROC OP’N 2-PROC TRNS‘N 2-PROC OP’N 2-PROC OPN

1/76 - 4/76 5/76 ~ 8/76 9/76 - 12/76 W/TT - 3/77
Peak Ld Ave 4.8 5.6 6.0 6.6
Peak Jobs 30.2 33.3 34.7 38.1
% Overhead/ 18.1 31.1 33.2 31.9
processor
Total CPu 304 4 384.9 534.0 520.1
Hrs/Mo

'Tnis table presents system usage data averaged over several months
preceding, during, and after installation of the SUMEX-AIM dual processor system
in order to show real changes in peak loading capacity and computing resources
delivered. The first three rows of data are derived from monthly diurnal loading
data and reflect average prime-time peak loading conditions (daily peak usage
figures are often considerably higher, but those shown better represent gross

trends). The last row gives average total monthly CPU hours delivered during the
various periods.

With the common criterion that users have pushed both the single and dual
processor systems to the limits of useful work in terms of prime time
responsiveness, it is clear that the second processor has substantially increased
throughput ("tolerable" peak load average up 38%, number of jobs up 26%, and
delivered CPU hours up 71%). At the same time the overhead burden per machine
has risen from 18 to 32%, principally in the category of I/0 wait (total
scheduler time and time waiting for a runnable job to be loaded in core). An
additional factor, not explicitly shown in these data (because we only have a J
msec clock), is the added time spent at interrupt level servicing drum swapping.
This adds another 10-15% estimated overhead.

We feel these increased overhead fisures can be reduced roughly to the
single processor levels by adding more memory, thereby effectively recovering
about 40-50% of the capacity of a KI-10 processor. A proposal is now pending
witn the AIM Executive Committee for this augmentation and we expect it to be
implemented within the funding ceiling of the current grant.

Privileged Communication 17 J. Lederberg
Section 1.3.2.3 DETAILED PROGRESS REPORT

1.3.2.3 SsYvsTten SOFTWARE

In parallel with the choice of DEC PDP-10 hardware for the SUMEX-AIM
facility, we selected the TENEX operating system developed by Bolt, Baranek, and
Newman (BBN) as the most effective for our medical AI applications work. TENEX
was the only available demand-paged system to support simultaneous large address
space users, offered the INTERLISP language for LISP-oriented program
development, and was well integrated with the ARPANET facilities which provide an
excellent base for our community sharing efforts. This choice has proven a very

effective one in that the productivity of the TENEX community in AI research has
been highly advantageous to us (2).

The original BBN TENEX was written for a hardware-modified KA-10 system.
This version of the system required a substantial amount of work to accommodate
the relatively limited paging facilities of the KI-10 to run effectively. These
early phases also included substantial monitor work to incorporate the TYMNET
memory-sharing interface which connects us to the TYMNET and to integrate the
high speed swapping storage. We have made numerous enhancements to the monitor
calls and corrections of bugs to develop a hizhly reliable and effective
operating system for our community work.

We continue to work to improve the efficiency of the system and its
effectiveness in allocating valuable resources. For example we have modified the
handling of user page tables so that the expensive procedure of clearing page
tables and setting them up to run time-shared users could be minimized. This
involved creating a pool of page tables which could be allocated to currently
running users and could be kept available without setup overhead. we also
implemented a system for migrating dormant pages from our fast swapping storage
to moving head disk. This preserves the use of this limited resource for the
currently active jobs.

We have implemented a form of "soft" CPU allocation control in the monitor,
assisted by a program which adjusts user percentages for the scheduler based on
the dynamic loading of the system. The allocation control structure works based
on the scheduler queue system and takes account of the a priori allocation of CPU
time and that actually consumed. Our TENEX uses a hierarchy of five queues for
jobs ranging from highly interactive jobs requiring only small amounts of CPU
time between waits to more CPU intensive jobs which can run for long periods
without user interaction. These interactive queues (text editting, ete.) are
scheduled at highest priority without consideration of allocation percentages.

If nothing is runnable from the high priority queues, the CPpU-bound queues are
scanned and jobs are selected for running Sased on how much of their allocated
time has been received during a given allocation cycle time (currently 100
seconds). If no such jobs are runnable, then those that have received their
allocation of CPU time already are scheduled based on how much they are over

(2) It should be noted that DEC has recently adopted a form of TENEX (TOPS-—
20) as their choice for future system marketing. They have made improvements in
a number of areas of the monitor and subsystem software but have also shown an
increasing tendency to make changes to the TOPS-20 system that impair
compatibility with older TENEX systems. The long-term impact of this trend
toward incompatibilities with the coming DeC "standard" is discussed in more
detail on page 62.

J. Lederberg 13 Privileged Communication
DETAILED PROGRESS REPORT Section 1.3.2.3

allocation and how long they have waited to be run again. This system is not a
reservation system in that it does not guarantee a given user some percentage of
the system. It allocates cycles preferentially, trading off a priori allocations
with actual demand but does not waste cycles. This allocation control system is
Still in an experimental state and we are attempting to evolve the "best"
policies with the AIM Executive Committee for dividing the system fairly and
effectively among the various communities of users.

During the spring of 1976 we implemented a dual processor version of TENEX
as the most cost-effective way to increase our processing capacity. In order to
upgrade to the new KL-"n" technology, we would have had to replace most of the
equipment that had been purchased initially. For the cost of an additional
processor and 8 man-months of intensive software development we were able to
increase our CPU capacity by 75%. We have an additional 40% equivalent of a KI-
10 processor which can be made available by increasing memory to reduce our
swapping contention. The dual processor system that has evolved is running quite
reliably. It treats the two machines in an almost symnetric manner. The only
difference is that one of the machines has all of the I/O equipment attached to
it. They both schedule jobs independently and share the rest of the non-I/0-
device monitor code. The areas of the monitor involving the management of
resources and jobs which cannot be manipulated by both machines simultaneously
are protected by a system of locks. We have made some measurements indicating
that overhead for lock waits is less than 10%. The overall increase in capacity
provided by the processor upgrade is illustrated in Figure 3 on page 17 which
measures key loading parameters in the periods before and after tne dual
processor installation. Observing the delivery of DEC’s high-performance KL-
TENEX systems8 over the past 6 months, it seems clear that for the investment, we
made the best choice for the community by implementing the dual processor
upgrade. We hope to augment the memory soon to finisn exploiting the capacity
this extra machine provides and to remove some non-linearities remaining in
system swapping performance.

Now that the dual processor system has stabilized, we are undertaking
another assessment of system performance to be sure we have removed residual and
correctable inefficiencies. This study is on-going now.

Finally, over the past year we made several substantial improvements in the
"GTJFN" monitor call which interactively acquires handles on file names specified
by the user. These extensions allow for more general "wild card" specifications
and interactive help in deciding between and searching for existing file name
alternatives. They also give the user much more flexibility in designating
groups of files and therefore in structuring his data.

With a working dual processor systen, the current implementation of
allocation controls in our system, the diverging path of tne DEC TOPS-20 system,
the termination of active BBN TENEX development, and the unique complications of
the KI-10 paging system, we have not made any concerted effort to upgrade our
TENEX system to the latest BBN release (1.34). The advantages of such an upgrade
are not overwhelming in face of the complicated conversion (XI paging, dual
processor, special swapping device handler, TYMNET service routines, local
JSYS’s, ete.) and resulting system unreliability for some period.

Privileged Communication 19 Jd. Lederberg
Section 1.3.2.3 DETAILED PROGRESS REPORT

Anotner area of software development is in the EXECutive program which is
the basic user interface to manipulate files, directories, and devices; control
joo and terminal parameter settings; observe job and system status; and execute
public and private programs. This work improves system accommodation to users
and provides more convenient and useful information about system and job status.
Through such features as login default files, directed file search path commands,
mail notification, help facilities, better file archival and retrieval commands,
and flexible status information, we have tried to make it easier for users to
work on the SUMEX-AIM machine.

1.3.2.4 NETWORK COMMUNICATION FACILITIES

A highly important aspect of the SUMEX system is effective communication
with remote users. In addition to the economic arguments for terminal access,
networking offers other advantages for shared computing such as uniform user
access to multiple machines and special purpose resources, convenient file
transfers for software sharing and multiple machine use, more effective backup,
co-processing between remote machines, and improved inter-user communications.
Over the past year we have been substantially aided in exporting the MAINSAIL
system through our network connections. Because of the developmental nature of
the language at present, it is important that we have close interactions with the
user community and that we be able to effectively perform bug fixes and upgrades.
Since MAINSAIL by its nature involves operations on a variety of machines and
Since our access to example systems cannot be entirely local, the network
connections to Rutgers, the Stanford AI Lab, and Stanford Research Institute have
been invaluable. It would be considerably more difficult to export MAINSAIL and
communicate with users via tapes and mail.

We have based our remote communication services on two networks — TYMNET
and ARPANET. These were the only networks existing at the start of the project
which allowed foreign host access. Since then, other commercial network systems
(notably TELENET) have come into existence and are growing in coverage and
services. The two networks to which we are currently connected complement each
other; the TYMNET providing primarily terminal service with very broad
geographical coverage and unrestricted user access, and the ARPANET having more
limited access but providing a broader range of communication services.

Togetner, these networks give a good view of the current strengths and weaknesses
of this approach.

Users asked to accept a remote computer as if it were next door will use a
local telephone call to the computer as a standard of comparison. Current
network terminal facilities do not quite accomplish the illusion of a local eall.
Data loss is not a problem in network communications - in fact with the more
extensive error checking schemes, data integrity is much higher than for a long
distance phone link. On the other hand, networking relies upon shared community
use of telephone lines to procure widespread geographical coverage at
Substantially reduced cost. However, unless enough total line capacity is
provided to meet peak loads, substantial queueing and traffic jans result in the
loss of terminal responsiveness.

J. Lederberg 20 Privileged Communication
DETAILED PROGRESS REPORT Section 1.3.2.4

TYMNET:

Networks such as TYMNET are a complex interconnection of nodes and lines
spanning the country (see Figure 4 on page 24). The primary cause of delay in
passing a message through the network is the time to transfer a message from node
to node and the scheduling of this traffic over multiplexed lines. This latter
effect only becomes important in heavily loaded situations; the former is always
present. Clearly from the user viewpoint, the best situation is to have as few
nodes as possible between him and the host ~ this means many interconnecting
lines through the network and correspondingly higher costs for the network
manager. TENEX in some ways emphasizes this conflict more than other time-—
Ssnaring systems because of the highly interactive nature of terminal handling
(e.g., command and file name recognition and non-printing program commands as in
text editors or INTERLISP). In such instances, individual characters must be
seen by the host machine to determine the proper echo response in contrast to
other systems where only "line at a time™ commands are allowed. We have
connected SUMEX to the TYMNET in two places as shown in Figure 4 so as to allow
more direct access from different parts of the country. Based on delay time
statistics collected during the previous year from our TYMSTAT program, the
response times are scarcely acceptable. When delay times exceed 200-300
milliseconds, the character printing lag problems become noticable with a full
duplex, 30 char/sec terminal. In the past these times have been particularly bad
in New York with peak delays approaching 3 seconds one way! Other nodes have
shown uniformly high readings as well. These data were reflected in the
subjective, but strongly articulated, comments of many of our user groups.

We have had numerous meetings with TYMNET personnel to try to ease these
problems and have instituted reroutings of the lines connecting SUMEX-AIM to the
network. Also local lines to more strategic terminal nodes have been considered
for users in areas poorly served by the existing line layout. TYMNET has also
made some upgrades in the internal connectivity and speeds with which data is
switched within their node clusters. These changes seem to have had some

beneficial effects in that delay. times have improved and user complaints have
subsided.

We will continue to pursue improvements in TYMNET response but user
terminal interactions such as used in TENEX programs are not realized in the
time-sharing systems offered by most other TYMNET users and hence are not
supported well by TYMNET. TYMNET has implemented 1200 baud service in 7 major
cities over the past year. Unfortunately many of our users are not in these
cities so we have only limited experience with the 1200 baud support.

ARPANET:

The ARPANET, while designed for aore general information transfer than
purely terminal nandling, has similar bottleneck problems in its topology (see
the current geographical and logical maps of the ARPANET in Figure 5 and Figure
6 on page 25). These are reduced by the use of relatively higher speed
interconnection lines (50 K baud instead of 2400 - 9500 baud lines as in TYMNET)
but response delays through many nodes become objectionable eventually as well.

Privileged Communication 21 J. Lederberg
section 1.3.2.4 DETAILED PROGRESS REPORT

Consistent with the agreements with ARPA when we were granted network
access initially, we are enforcing a policy to restrict the use of the ARPANET to
users who have affiliations with ARPA-supported contractors and system/software
interchange with cooperating TENEX sites. The administration of the network
passed from the ARPA Information Processing Techniques Office to the Defense
Communications Agency as of July 1975. At that time policies were announced
restricting access to DoD-affiliated users. We have restricted the facilities
for calling from SUMEX out to other sites on the ARPANET to authorized users.
This also protects the SUMEX-AIM machine from acting as an expensive terminal
handler for other machines - this function is better fulfilled by dedicated
terminal handling machines (TIPS). In general, we have developed excellent
working relationships with other sites on the ARPANET for system backup and
software interchange ~ such day-to-day working interactions with remote
facilities would not be possible without the integrated file transfer,
communication, and terminal handling capabilities unique to the ARPANET.

We take very seriously the responsibility to provide effective
communication capabilities to SUMEX-AIM users and are continuously looking for
ways to improve our existing facilities as well as investigate alternatives
becoming available. We have done preliminary investigations of the TELENET
facilities that have been rapidly expanding this past year. BB&N has hooked one
of their TENEX systems up to TELENET and whereas we did not have the same
quantitative tools we have for measuring response on the TYMNET, we observed
TELENET delays at least as long as those encountered on TYMNET. We did the
reverse experiment by using long distance telephone to connect from the TELENET
node in Washington, D.C. to the SUMEX macnine in California and observed the
same sort of delays reaching several seconds per character. The TELENET has many
attractive feature in terms of a symmetry analogous to that of the ARPANET for
terminal traffic and file transfers and being commercial would not have the
access restrictions of the ARPANET. However, until the network throughput
improves we would not get substantial benefits from connecting to it.

J. Lederberg

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Privileged Communication
Section 1.3.2.4

DETAILED PROGRESS REPORT

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