From: KDD-96 Proceedings. Copyright © 1996, AAAI (www.aaai.org). All rights reserved.
Undiscovered Public Knowledge: a Ten-Year Update
Don R. Swanson* and Neil R. Smalheiserf
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numaruues,
wnrversitt of Chicago,
1010E. 59th St.,Chicago,IL 60637;swanson@kiwi.uchicago.edu
tDepartmentof Pediatrics,Universityof Chicago,
5841 S. Maryland Ave., Chicago,IL 68637;sma2@midway.uchicago.edu
Abstract
Two literatures or setsof articles are complementaryif,
consideredtogether, they can reveal useful information of
scientik interest not apparentin either of the two setsalone.
Of particular interest are complementaryliteratures that are also
mutually isolated and noninteractive (they do not cite each other
and are not co-cited). In that case,the intriguing possibility
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During the past decade,we have identified seven examplesof
complementary noninteractive structuresin the biomedical
literature. Each structure led to a novel, plausible, and
testablehypothesis that, in severalcases,was subsequently
corroboratedby medical researchersthrough clinical or
laboratory investigation. We have also developed,tested,and
described a systematic,computer-sided approachto iinding
and identifying complementary noninteractive literatures.
Specialization, Fragmentation,
and a Connection Explosion
By someobscurespontaneous
processscientistshave
respondedto the growth of scienceby organizingtheir
work into soecialties,
-r- -~ thus permittingeachindividualto
focuson a smallpart of the total literature. Specialties
that grow too large tend to divide into subspecialties
that
havetheir own literatureswhich, by a processof repeated
splitting,maintainmore or lessfixed and manageablesize.
As the total literaturegrows,the numberof specialties,but
not in generalthe sizeof each,increases(Kochen,1963;
Swanson,199Oc).
But the unintendedconsequence
of specializationis
fragmentation.By dividing up the pie, the potential
relationshipsamongits piecestendto be neglected.
Althoughscientificliteraturecannot,in the long run, grow
disproportionatelyto the growth of the communitiesand
resourcesthat produceit, combinationsof implicitlyrelatedsegmentsof literaturecan grow much fasterthan
the literatureitself and can readily exceedthe capacityof
the communityto identify and assimilatesuchrelatedness
(Swanson,1993). The signilicanceof the “information
explosion”thusmay lie not in an explosionof quantityper
se,but in an incalculablygreatercombinatorialexplosion
of unnoticedand unintendedlogical connections.
The Significance of Complementary
Noninteractive Literatures
If two literatureseachof substantialsize are linked by
argumentsthat they respectivelyput forward -- that is, are
“logically”related,or complementary-- one would expect
to gain usefuiinformationby combiningthem. For
example,supposethat one (biomedical)literature
establishesthat someenvironmentalfactor A influences
certaininternalphysiologicalconditionsand a second
literatureestablishesthat thesesamephysiological
changesinfluencethe courseof diseaseC. Presumably,
then,anyonewho readsboth literaturescould conclude
that factor A might influencediseaseC. Under such
--->!L--- -f -----l-----ry-?r-.
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two literaturesto refer to eachother. If, however,the two
literatureswere developedindependentlyof one another,
the logical linkageillustratedmay be both unintendedand
unnoticed.To detectsuchmutualisolation,we examine
the citation pattern. If two literaturesare “noninteractive”
=
that
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together,and if neithercites the other,- then it is
possiblethat scientistshavenot previouslyconsidered
both iiteraturestogether,and so it is possiblethat no one is
awareof the implicit A-C connection.The two
conditions,complementarilyand noninteraction,describe
a model structurethat showshow useful informationcan
remainundiscoveredeventhoughits componentsconsist
of public knowledge(Swanson,1987,199l).
Public Knowledge / Private Knowledge
Thereis, of course,no way to know in any particularcase
whetherthe possibilityof an AC relationshipin the above
modelhasor hasnot occurredto someone,or whetheror
not anyonehasactuallyconsideredthe two literatureson
A andC together,a private matterthat necessarily
remainsconjectural.However,our argumentis based
only on determiningwhetherthereis any printed evidence
to the contrary. We are concernedwith public ratherthan
Data Mining: Integration Q Application
295
private knowledge
-- with the state of the recordproduced
rather than the state of mindof the producers(Swanson,
1990d).Thepoint of bringing together the ABand BC
literatures, in anyevent, is not to "prove"an AClinkage,
(by consideringonlytransitive relationships)but rather
call attention to an apparentlyunnoticedassociationthat
maybe worthinvestigating. In principle anychain of
scientific, includinganalogic,reasoningin whichdifferent
links appearin noninteractiveliteratures maylead to the
discoveryof newinteresting connections.
"Whatpeople know"is a common
understandingof
whatis meantby "knowledge".
If takenin this subjective
sense, the idea of "knowledge
discovery"could mean
merelythat someonediscoveredsomethingthey hadn’t
knownbefore. Ourfocus in the present paper is on a
secondsense of the word"knowledge",a meaning
associatedwith the productsof human
intellectual
activity, as encoded
in the public record,rather than with
the contents of the humanmind.This abstract worldof
human-created"objective" knowledgeis opento
explorationanddiscovery,for it cancontainterritory that
is subjectively unknown
to anyone(Popper, 1972). Our
workis directedtowardthe discoveryof scientificallyuseful informationimplicit in the public record,but not
previously madeexplicit. Theproblemweaddress
concernsstructureswithinthe scientific literature, not
withinthe mind.
The Process of Finding
Complementary Noninteractive Literatures
Duringthe past ten years, wehavepursuedthree goals: i)
to showin principle hownewknowledgemightbe gained
by synthesizinglogically- related noninteractive
literatures; ii) to demonstrate
that suchstructuresdo exist,
at least withinthe biomedical
literature; andiii) to develop
a systematicprocessfor findingthem.
In pursuit of goal iii, wehavecreatedinteractive
softwareanddatabasesearchstrategies that can facilitate
the discoveryof complementary
structures in the
publishedliterature of science. Theuniverseor searchspace underconsiderationis limited only by the coverage
of the majorscientific databases,thoughwehavefocused
primarily on the biomedicalfield and the MEDLINE
database(8 millionrecords). In 1991,a systematic
approachto finding complementary
structures was
outlined andbecamea point of departurefor software
development(Swanson,1991). The systemthat has now
taken shapeis basedon a 3-wayinteraction between
computersoftware, bibliographic databases, and a human
operator. Taeinteraction generatesinformationstructtues
that are usedheuristicallyto guidethe searchfor
promisingcomplementary
literatures.
Theuser of the systembeginsby choosinga question
296
Technology
Spotlight
or problem
area of scientific interest that can be associated
with a literature, C. Elsewherewedescribe andevaluate
experimentalcomputersoftware, whichwecall
ARROWSMITH
(Swanson& Smalheiser, 1997), that
performstwo separate functionsthat can be used
independently.Thefirst functionproducesa list of
candidatesfor a secondliterature, A, complementary
to C,
fromwhichthe user can select one candidate(at a time)
an input, alongwith C, to the secondfunction.This first
function can be consideredas a computer-assistedprocess
of problem-discovery,
an issue identified in the AI
literature (Langley,et al., 1987;p304-307).
Alternatively,
the user maywishto identify a secondliterature, A, as a
conjectureor hypothesisgeneratedindependentlyof the
computer-produced
list of candidates.
Ourapproachhas beenbasedon the use of article titles
as a guideto identifying complementary
literatures. As
indicatedabove,our point of departurefor the second
functionis a tentative scientific hypothesisassociatedwith
twoliteralxtres, AandC. Atitle-word searchof
MEDLINE
is usedto create twolocal computertitle-files
associatedwith A andC, respectively.Thesefiles are
used as input to the ARROWSMITH
software, which then
producesa list of all wordscommon
to the two sets of
titles, exceptfor wordsexcludedby an extensivestoplist
(presently about5000words).Theresulting list of words
providesthe basis for identifyingtitle-wordpathways
that
mightprovide clues to the presenceof complementary
argumentswithinthe literatures corresponding
to Aand
C. Theoutputof this procedureis a structuredtitledisplay(plusjournalcitation), that servesas a heuristic
aid to identifyingword-linked
titles andservesalso as an
organizedguideto the literature.
Seven Examples of
Literature.Based Knowledge Synthesis
Theconcept of "undiscoveredpublic knowledge"based
on complementary
noninteractiveliteratures was
introduced,developed,andexemplifiedin (Swanson,
1986a, 1986b).Since 1986, wehave described six more
examples,each representinga synthesis of two
complementary
literatures in whichbiomedical
relationshipsnot previouslynotedin print werebroughtto
light. Wedescribe also the hypothesesto whichthey have
led, andthe strategies wehavefollowedin findingand
identifying these structures (Swanson
1988,1989a,1989b,
1990a; Smalheiser& Swanson1994, 1996). Weidentify
these exampleshere in terms of A, B, andC, wherein
associationsbetweenAand B are foundin oneliterature
andassociationsbetweenB andC in anotherliterature,
leadingus to drawcertain inferencesabouta previously
mreportedassociation betweenAand C. In most cases
weanalyzedmultiple B-termsfor a given Aand C. In the
fo l l o w i dn eg s c ri p tiw oeind e n tiofyn i yA a n dC , a n da fe w
o f th em o rei m p o rtaBn-ct o n n e c tiao l nosnw, gi thth em a i n
c o n c l u soi roh ny p o th etos wi sh i c wh ew e rel e d O
. th e r
a u th ohrsa v re
e v i e w e dx ,te n d oe rda ,s s e s th
s ei sdw o rk
(C h e n1 ,9 9 D
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9 ;a rfi e l1d 9, 9 4G ;o rd o&n
L i n d s a1 y9, 9 L6 e, s k1, 9 9 1S p; a s si enpr, re s s ).
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R a y n a u dD’si s e a s(C
e)
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fi s ho i l s(e s pe .i c o s a p e n taa ec ni dol e)i ca to
d
c e rta bi nl o oadn dv a s c u cl ah ra n g( eBjsth a at res e p a ra te i y
k n o w ton b eb e n e fi ctoi ap la ti e nwtsi thR a y n a uddi ’s
sease.
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e i c o s a p e n taa ec ni cdoai ncd e c re ab sl oe ovdi s c o s (B);
i ty
a b n o rm ah li lgybh l o o vdi s c o s hi tya bs e eren p o rtei nd
p a ti e nwtsi thR a y n a uddi ’s
s e a s( Se w. a n s o1 n9 ,8 6 a ,
1 9 8 6 1b 9, 8 7T).h ei n fe re nthc ea fit s ho i l sm a yb e n e fi t
R a y n a pu ad ti e nmtsa yb ere g a rd ae sda s u c c e s s fu l
p re d i c ti tw
o no;y e a rs
a fte pr u b l i c a oti of thn ea b o v e
a n a l y sthi sefi, rs ct l i n i ctria al dl e m o n s tras tiu nc gah
b e n e fi cei ffe
a l cot f fi s ho i lw a sre p o rteb dy m e d i c a l
re s e a rc h(cei rs
te ad n d i s c u s isneSdw a n s o1 n9 ,9 3 ).
E x a m p l2e,1 9 8 8 M: a g n e s i uDme B c i e n c( Ay ) a n d
M i g ra i n (C
e ).
B c o n s i os ts
fe l e v ei nnd i reccot n n e c ti wo hn isc, lhe dto a
p re d i c titho an m
t a g n e s di ue mfi c i e nmci yg hb tei m p l i c a te d
i nm i g ra i hn ee a d a c (T
h ew. os u c lhi n k a gaeres fo, r
e x a m p ml ea: g n e s ci ua m
ni n h i bsi pt re a d idnegp re s s ii no n
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i oanyb ei m p l i c ai te
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u s e ad sa m o d eo lfe p i l e p as yn ,de p i l e phs ay bs e e n
a s s o c i awtei thdm i g ra i n( Se w) a n s o1 n9 ,8 8 ,1 9 8 9S bi n).c e
p u b l i c a oti of thn a at n a l y smi so ,reth a n1 2d i ffe re gn ro
t ups
o f m e d i crea sl e a rc hh ea rs
v re
e p o rtea ds y s te moi rcl o c a l
m a g n e s di ue m
fi c i e ni ncmy i g ra i on rea fa v o ra brel es p o n s e
o fm i g ra i pn ae ti e ntotsd i e ta sryu p p l e m e n wtai th
ti o n
m a g n e s (c
i ui m
te ad n dd i s c u s isneS dw a n s o1 n9 ,9 3 ).
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(C j .
B c o n s i os ts
ffi v ep h y s i o l oa gs isco c i a til eo an ds i to
n gth e
i n fe re nthc ae ot ra l lay d m i n i s tea re
rg di n i m
n ea yi n c re a s e
b l o ol de v e ol sf s o m a to m eC d(thi nel a ttebr e i nkgn o wton
h a v aen u m b oe frb e n e fi cei ffe
a l c ts F). o er x a m p l e ,
i n fu s ea drg i n i sn tiem u l a thte esre l e a os feg ro w th
h o rm o na en ,dth el a tte i rntu rni sk n o w ton i n c re absl eo o d
l e v e ol sf s o m a to m eC d( Si nw a n s o1 n9 ,9 O aO ).u r
i n fe re n cl ee dsto a p ro p o sb aym
l e d i crea sl e a rc htoe rs
c o n d uacc tl i n i ctria al l(d i s c u s fus erthd ei rn ( S w a n s o n ,
1 9 9 3 )).
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N e u ro l o g Di ci s e a s(C
e j.
E n d o g e nmo au gs n e s ii ou nmps l a ay k e yro l ei nre g u l a ti n g
e x c i to to x i mc ietyd i a bteydth eN M D Are c e p to
(B).
r
E x c i to to x i icni tu
ty rni sth o u g toh th a v ae ni m p o rtaron lt e
i n v a ri o un se u ro l odgi isce a sWe ses. u g g e sthteadth
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m a g n e s oi unbmra i fu
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i n v e s ti g a( tiS m
o na l h e i&s Sc wr a n s o1 n9 ,9 4 ).
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a resn e i th de ir s j o i n t
n o nr o n i n te ra c In
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( S m a l h e i&s Se wr a n s o1 n9 ,% ).
E x a m p l6e ,1 9 9 5 E: s tro g e n( A ) a n dA l z h e i m e r’s
D i s e a s(C
e)
A s i ne x a m p5l ,th
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e s tro g re
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w i tha i o w ei rn c i d e no cf Ael z h e i m ed r’s
i s e a bs ue th
t, e
m e c h a n oi sf smu c ah ne ffe ci tsu n k n o wWn .ere p o rte d
s e v e ra
p rel v i o u s l y -u n i n v eB s-re
ti gl aa titeodn s h i p s ,
p a rti c u l ao rln yei n v o l v ianngti o x i daacntit v i tyth ,a t
a p p e a to
remd e rii tn v e s ti g aatispo on s s i be lxep l a n a tio of n s
th i si n tri g u ire
n gl a ti o n s( hS m
i pa l h e idszSe wr a n s oi nn ,
p re s s ).
E x a m p l 7e ,1 9 9 6 P: h o s p h o l i p a (sAe) as n dS l e e (C
p )
T h eA a n dC l i te ra tu re
a resd i s j o iannt dn o n i n te ra c ti v e ,
b u it m p i i c ire
tl yl a tethd ro u ga hs e ot f s u b s ta n(nc eo sta b i y
i n te rl e u lk=i nD F tu, m onr e c ro sfai cs toar n d
e n d o to x i n /l i p o p o l y s wa ch ci chahareriwdeel kl) n o wbn o th
to p ro m o stel e eapn dto s ti m u l ao te
n eo rm o re
p h o s p h o l i pTahs iess stu. d iyd e n ti fiael di s ot f a g e n ts
w h o seeffe c ts
o ns l e eapx e s p e c i al i lkl ey ltoy i n v o l v e
p h o s p h o l i pa an sdseusg; g e sstee vd e ra
s tra
l i g h tfo rw a rd
e x p e ri m eten statsol f o u hr y p o th eths ai spt h o s p h o l i p a s e s
m a yb ei n v o l v iende n d o g e np oa uthsw athy sa re
t g u l a te
s l e e( Sp m a l h e i&s Se wr a n s oi nnp, re p a ra ti o n ).
D a ta M i n i n g :In te g ra ti o n6 r A p p l i c a ti o n
297
Comment
The objectsof studyin the work summarizedhereare
complementarystructureswithin the scientificliterature.
The recognitionof meaningfulassociationsandultimately
that of complementarityrequirea high level of subject
expertise.The unruly problemsof meaningwithin the
naturallanguageof titles and abstractspresentserious
obstaclesto more fully automatingthis processof
knowledgediscovery. Our computeraidsare therefore
designedto enhanceand stimulatehumanability to see
connectionsandrelationships.Theseaidsnecessarily
derivefrom the immensedatabasesthat providethe routes
of intellectualaccessto the literature. Our goal thusfar
hasbeento producea working practicalsystemthat yields
immediateresultsin furtheringthe aims of biomedical
re-w&.
and which
ueneratfs &&
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atd
problemsthat contributeto understandingliterature-based
scientiticdiscovery.
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