(switch on tape-recorder). 2 Plädoyer für die angewandte Ontologie Barry Smith

(switch on tape-recorder)

2

Plädoyer für die angewandte Ontologie

Barry Smith

http://ifomis.de

3

Plädoyer für eine angewandte (realistische) Ontologie

Barry Smith

http://ifomis.de

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IFOMIS

Institute for Formal Ontology and Medical Information Science

Faculty of Medicine

University of Leipzig

http://ifomis.de

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The Idea

Computational medical research

will transform the discipline of medicine

… but only if communication problems can be solved

6

Medicine

desperately needs to find a way

to enable the huge amounts of data

resulting from trials by different groups

to be (f)used together

7

How resolve incompatibilities?

Ganze Industrie von ‘Ontologien’ in der heutigen Informationswissenschaft

“ONTOLOGY” = the solution of first resort (compare: kicking a television set)

But what does ‘ontology’ mean?Current most popular answer: a hierarchy of concepts (a thesaurus, a list of terms)

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Aristotle

First ontologist

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First ontology

(from Porphyry’s Commentary on Aristotle’s Categories)

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Linnaean Ontology

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Medical Diagnostic Ontology

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Problems with this solution

13

Example 1: UMLS

Universal Medical Language System

Very large taxonomy maintained by National Library of Medicine in Washington DC

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Example 1: UMLS

134 semantic types800,000 concepts10 million interconcept relationships UMLS is the product of fusion of several

source vocabularies(built out of concept trees)

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Example 2: SNOMED-RT

Systematized Nomenclature of Medicine

A Reference Terminology with Legal Force

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Example 2: SNOMED-RT

121,000 concepts,

340,000 relationships

“common reference point for comparison and aggregation of data throughout the entire healthcare process”

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Problems with UMLS and SNOMED

Each is a ‘fusion’ of several source vocabularies, some of dubious quality

They were fused without an ontological system being established first

They contain circularities, taxonomic gaps, and unnatural ad hoc determinations

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Representation of Blood in UMLS

Blood

Tissue

EntityPhysical Object

Anatomical StructureFully Formed Anatomical Structure

Body SubstanceBody Fluid Soft Tissue

Blood as tissue

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Representation of Blood in SNOMED

Blood

Liquid Substance

Substance categorized by physical state

Body fluid

Body Substance

Substance

Blood as Fluid

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UMLS: blood is a tissue

SNOMED: blood is a fluid

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Example: The Gene Ontology (GO)

hormone ; GO:0005179

%digestive hormone ; GO:0046659 %peptide hormone ; GO:0005180 %adrenocorticotropin ; GO:0017043 %glycopeptide hormone ; GO:0005181 %follicle-stimulating hormone ; GO:0016913

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as tree

hormone

digestive hormone peptide hormone

adrenocorticotropin glycopeptide hormone

follicle-stimulating hormone

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Eine Ontologie von medizinischen Diagnosen

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Problem: There exist multiple databases

genomic cellular

structural phenotypic

… and even for each specific type of information, e.g. DNA sequence data, there exist several databases of different scope and organisation

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What is a gene?GDB: a gene is a DNA fragment that can

be transcribed and translated into a protein

Genbank: a gene is a DNA region of biological interest with a name and that carries a genetic trait or phenotype

GO does not tell us which of these is correct, or indeed whether either is correct, and it does not tell us how to integrate data from the corresponding sources

26

Example: The Semantic Web

Vast amount of heterogeneous data sourcesNeed dramatically better support to yield the ability to query and integrate across different conceptual systemsThe currently preferred answer is The Semantic Web, based on tagging websites in terms of conceptual hierarchiesWill not work: How tag blood? how tag gene?

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Concept hierarchies

cannot solve the problems of database integration

There can be no mechanical solution to the problems of data integration

in a domain like medicine or genetics

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The problem in every case

is one of finding an overarching framework for good definitions,

definitions which will be adequate to the nuances of the domain under investigation

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Concept hierarchy ontology:

Ontologies are inside the computer

thus subject to severe constraints on expressive power

(effectively the expressive power of description logic)

30

Concept hierarchy ontology cannot solve the data-integration

problem

because of its roots in knowledge representation/knowledge mining

31

different conceptual systems

32

need not interconnect at all

33

we cannot make incompatible concept-systems interconnect

just by looking at concepts, or knowledge – we need some tertium quid

34

Concept hierarchy ontology

has its philosophical roots also in Quine’s doctrine of ontological commitment and in the ‘internal metaphysics’ of Carnap/Putnam Roughly, for an concept hierarchy ontology the world and the semantic model are one and the sameWhat exists = what the system says exists

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Quineanism:

ontology is the study of the ontological commitments or presuppositions embodied in scientific theories (or in the beliefs of experts)

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Quineanism, too, faces the integration problem

If an ontology is the set of ontological commitments of a theory, how can we cope with questions pertaining to the relations between the objects to which different theories are committed?

(Recall the Vienna Circle program of the Unity of Science)

37

What is needed

is some sort of wider common framework

sufficiently rich and nuanced to allow concept systems deriving from different theoretical/data sources to be hand-callibrated

38

What is needed

is not a Concept Hierarchy Ontology

but

a Reference Ontology

(something like old-fashioned,

realist,

metaphysics)

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Reference Ontology

An ontology is a theory of a domain of entities in the world

Ontology is outside the computer

seeks maximal expressiveness and adequacy to reality

and sacrifices computational tractability for the sake of representational adequacy

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Belnap

“it is a good thing logicians were around before computer scientists;

“if computer scientists had got there first, then we wouldn’t have numbers

because arithmetic is undecidable”

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It is a good thing

Aristotelian metaphysics was around before description logic, because otherwise

we would have only hierarchies of

concepts/universals/classes and no individual instances …

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Reference Ontology

a theory of the tertium quid

– called reality –

needed to hand-callibrate database/terminology systems

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Methodology

Get ontology right first

(realism; descriptive adequacy; rather powerful logic);

solve tractability problems later

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The Reference Ontology Community

IFOMIS (Leipzig) Laboratories for Applied Ontology

(Trento/Rome, Turin)Foundational Ontology Project (Leeds)Ontology Works (Baltimore)BORO Program (London)Ontek Corporation (Buffalo/Leeds)LandC (Belgium/Philadelphia)

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Domains of Current Work

IFOMIS Leipzig: Medicine

Laboratories for Applied Ontology

Trento/Rome: Ontology of Cognition/Language

Turin: Law

Foundational Ontology Project: Space, Physics

Ontology Works: Genetics, Molecular Biology

BORO Program: Core Enterprise Ontology

Ontek Corporation: Biological Systematics

LandC: NLP

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Recall:

GDB: a gene is a DNA fragment that can be transcribed and translated into a protein

Genbank: a gene is a DNA region of biological interest with a name and that carries a genetic trait or phenotype

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Ontology

Note that terms like ‘fragment’, ‘region’, ‘name’, ‘carry’, ‘trait’, ‘type’

… along with terms like ‘part’, ‘whole’, ‘function’, ‘substance’, ‘inhere’ …

are ontological terms in the sense of traditional (philosophical) ontology

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Was ist Gesundheit? WHO, 1948: Gesundheit = Zustand des

psychischen und physischen Wohlbefindens eines Menschen

Zustand als ontologische Kategorie

Psychisch–Physisch als ontologische Dichotomie

… sonst Zirkulär (‘Wohlbefinden’ = ‘Gesundheit’)

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Gesundheit also statistische Norm:

Gesund = was auf die Mehrzahl der Menschen zutrifft

Krankheit = ein Zustand, der vom normalen Zustand des Patienten abweicht

… Kranksein abhängig von generellem Zustand der Gesellschaft

Norm als ontologische Kategorie

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Gesundheit als Abwesenheit von Krankheit

Abwesenheit?

als ontologische Kategorie?

… sonst zirkulär

Gesundheit/Krankheit gegenseitig voneinander abhängig

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Krankheit als Defekt

Körper = Maschine

Behandlungsziel = Defekt beheben

Krankenhaus als Werkstatt

Was ist die eigentliche Funktion (telos) dieser Maschine?

Funktion als ontologische Kategorie

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Gesundheit/Krankheit = soziale Konstruktionen

x ist krank =def.

die Gesellschaft sagt, x ist krank

oder:

Der Zunft der Ärzte sagt, x ist krank

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Reference Ontology =

Formal Ontology (IFOMIS)

+

Material/Regional Ontologies

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Edmund Husserl

55

Formal Ontology

term coined by Husserl

= the theory of those ontological structures

such as part-whole, universal-particular

which apply to all domains whatsoever

Formal ontology = theory of things

Formal logic = theory of truths

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Husserl outlines a new methodof constituent ontology

to study a domain ontologically

is to establish the parts of the domain

and the interrelations between them

especially the dependence relations

(assembly structures, modules)

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Ontological Dependence

a color is dependent on an extension

a charge is dependent on a conductor

a speech act is dependent on a speaker

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Logical Investigations¸1900/01

Aristotelian theory of universals and particulars

theory of part and whole

theory of ontological dependence

the theory of boundaries and fusion

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Formal Ontology

contrasted with material or regional ontologies

(compare relation between pure and applied mathematics)

Husserl’s idea:

If we can build a good formal ontology, this should save time and effort in building reference ontologies for each successive domain

60

Roman Ingarden

Material Ontology

Theory of Causality

Theory of Relatively Isolated Systems

61

Organisms

order to be able to sustain themselves effectively as identical through time, must be at least in some respects “bounded off from the surrounding world and partially isolated or shielded from it.”

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Each multi-cellular organism

is a system of relatively isolated causal systems organized in modular fashion in such a way as to contain within itself further relatively isolated causal systems on successively lower levels.

The systems within this modular hierarchy are both partially interconnected (they collaborate in their functioning)

and also partially segregated via coverings or membranes

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Bodily systems

are not absolutely closed off from each other: they are partially open and partially shielded. There are paths between them along which a certain restricted spectrum of causal influences and substances may flow. Each sense organ is a partially open system which is “attuned to a special selection of outside processes and at the same time also shielded in other respects.”

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Basic Formal Ontology

BFO

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Basic Formal Ontology

Aristotelian theory of universals and instances

theory of part and whole

theory of ontological dependence

theory of boundary, continuity and contact/fusion

theory of states, powers, qualities, roles, functions, systems

dual ontology of endurants and perdurants

theory of environments/niches/contexts and spatial and spatio-temporal regions

theory of normativity (health, sickness, malfunction)

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SNAP: Ontology of entities enduring through time

Concrete Entity[Exists in Space and Time]


Entity in 3-D Ontology[Endure. No Temporal Parts]


Entity in 4-D Ontology[Perdure. Unfold in Time]Entity in 4-D Ontology

[Perdure. Unfold in Time]

Processual EntityProcessual EntitySpatio-Temporal Region

Dim = T, T+0, T+1, T+2, T+3Spatio-Temporal Region

Dim = T, T+0, T+1, T+2, T+3

Spatial regions of dimension0,1,2,3

Spatial regions of dimension0,1,2,3 Dependent EntityDependent Entity

Independent EntityIndependent Entity

Quality (Your Redness, My Tallness)[Form Quality Regions/Scales]


Role, Function, PowerHave realizations (called: Processes)


Substance[maximally connected causal unity]


Boundary of Substance *Fiat or Bona Fide or MixedBoundary of Substance *

Fiat or Bona Fide or Mixed

Aggregate of Substances * (includes masses of stuff? liquids?)


Fiat Part of Substance * Nose, Ear, Mountain


Process [Has Unity]Clinical trial; exercise of role


Fiat Part of Process*Fiat Part of Process*

Aggregate of Processes*Aggregate of Processes*

Instantaneous Temporal Boundary of Process (= Ingarden’s 'Event’)*


Quasi-ProcessJohn’s Youth. John’s Life


Quasi-Quality Prices, Values, Obligations


Quasi-SubstanceChurch, College, Corporation


Quasi-Role/Function/PowerThe Functions of the PresidentQuasi-Role/Function/Power

The Functions of the President

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SPAN: Ontology of entities extended in time

SPANEntity extended in time

Portion of Spacetime

Fiat part of process *First phase of a clinical trial

Spacetime worm of 3 + Tdimensions

occupied by life of organism

Temporal interval *projection of organism’s life

onto temporal dimension

Aggregate of processes *Clinical trial

Process[±Relational]

Circulation of blood,secretion of hormones,course of disease, life

Processual Entity[Exists in space and time, unfolds

in time phase by phase]

Temporal boundary ofprocess *

onset of disease, death

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BFOnot just a system of categories

but a formal theory

with definitions, axioms, theorems

designed to provide the resources for reference ontologies for specific domains

the latter should be of sufficient richness that terminological incompatibilities can be resolves intelligently rather than by brute force

70

Three types of reference ontology

1. formal ontology = framework for definition of the highly general concepts – such as object, event, part – employed in every domain

2. domain ontology, a top-level theory with a few highly general concepts from a particular domain, such as genetics or medicine

3. terminology-based ontology, a very large theory embracing many concepts and inter-concept relations

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MedO: medical domain ontology

universals and instances and normativitytheory of part and whole and absencetheory of ontological dependencetheory of boundaries/membranestheory of states, powers, qualities, roles,

(mal)functions, bodily systemsdual ontology of endurants and perdurants:

anatomy and physiologytheory of environments: inside and outside

the organism

72

MedO

including sub-ontologies:

cell ontology

drug ontology

protein ontology

gene ontology

73

and sub-ontologies:anatomical ontology

epidemiological ontology

disease ontology

therapy ontology

pathology ontology

the whole designed to give structure to the medical domain

(currently medical education comparable to stamp-collecting)

74

If sub-domains like these

cell ontology

drug ontology

protein ontology

gene ontology

are to be knitted together within a single theory,

then we need also a theory of granularity

75

Testing the BFO/MedO approach

within a software environment for NLP of unstructured patient records

collaborating with

Language and Computing nv (www.landc.be)

76

L&C

LinKBase®: world’s largest terminology-based ontology

incorporating UMLS, SNOMED, etc.

+ LinKFactory®: suite for developing and managing large terminology-based ontologies

77

L&C’s long-term goal

Transform the mass of unstructured patient records into a gigantic medical experiment

78

LinKBase

LinKBase still close to being a flat list

BFO and MedO designed to add depth, and so also reasoning capacity

79

Problem

Wie findet man Subjekte für klinische Studien?

Wie stellt man automatisch die Zuläßigkeit von Patienten auf dem Basis von unstrukturierten Patientenberichten?

80

www.LandC.be

Language and Communication nv

bietet Informationssysteme für die Gewinnung digitaler Inhalte aus unstrukturieren medizinischen Texten

81

Clinical history description

Mr. Kovács is an 83-year-old man with a past medical history of hypertension, congestive heart failure, atrial fibrillation, hypercholesterolemia, and a history of CVA, who presented himself to the Budapest Emergency Room on April 25 with primary complaint of right-sided chest pain since April 24. The patient was in his usual state of health until April 24 when he experienced right-sided chest pain after 10 minutes of bicycling exercise at the YMCA. He described the chest pain as a dull ache in the right side of his chest radiating posteriorly to the right scapular area. …

82

Zuläßigkeitskriteria für die Studie

1. Male or female

2. Age 50 to no upper limit

3. a) Hypertension documented as according to the 6th report of the Joint National Committee on Detection and Evaluation of the treatment of high BP (JNC VI) , b) and the need for drug therapy (previously documented hypertension in patients currently taking antihypertensive agents is acceptable)

4. Documented CAD (e.g., classic angina pectoris; stable angina pectoris; Heberden angina pectoris), myocardial infarction three or more months ago, abnormal coronary angiography, or concordant abnormalities on two different types of stress tests

5. Willingness to sign informed consent

83

Passen sie zusammen?

• Mr. Kovács is … an 83-year-old man with past medical history of hypertension, congestive heart failure, atrial fibrillation, hypercholesterolemia, history of CVA who presented to Budapest Emergency Room on April 25 with chief complaint of right-sided chest pain since April 24. The patient was in his usual state of health until April 24 when he experienced right-sided chest pain after 10 minutes of bicycling exercise at YMCA. He described the chest pain as a dull ache in the right side of his chest radiating posteriorly to the right scapular area. He rated the intensity as 7 out of 10. The chest pain lasted about 3 minutes and resolved with rest. That same night, the patient once again experienced right-sided chest pain while lying in bed right before he went to sleep. He describes the pain as right-sided chest pain with same radiation to posterior at an intensity of 6-7 out of 10. The chest pain lasted about 10 minutes and resolved spontaneously.

• 1. Male or female • 2. Age 50 to no upper limit

• 3. Hypertension documented according to the 6th report of the Joint National Committee on Detection and Evaluation of the treatment of high BP (JNC VI) and the need for drug therapy (previously documented hypertension in patients currently taking antihypertensive agents is acceptable)

• 4. Documented CAD (e.g., classic angina pectoris (stable angina pectoris; Heberden angina pectoris), myocardial infarction three or more months ago, abnormal coronary angiography, or concordant abnormalities on two different types of stress tests)

• 5. Willingness to sign informed consent

84

Der Rechner wird diese Schlussfolgerung machen können ...

• Mr. Kovács is … an

83-year-old man with past medical history of hypertension, congestive heart failure, atrial fibrillation, hypercholesterolemia, history of CVA who presented to Budapest Emergency Room on April 25 with chief complaint of right-sided chest pain since April 24. The patient was in his usual state of health until April 24 when he experienced right-sided chest pain after 10 minutes of bicycling exercise at YMCA. He described the chest pain as a dull ache in the right side of his chest radiating posteriorly to the right scapular area. He rated the intensity as 7 out of 10. The chest pain lasted about 3 minutes and resolved with rest. That same night, the patient once again experienced right-sided chest pain while lying in bed right before he went to sleep. He describes the pain as right-sided chest pain with same radiation to posterior at an intensity of 6-7 out of 10. The chest pain lasted about 10 minutes and resolved spontaneously.

• 1. Male or female • 2. Age 50 to no upper limit • 3. Hypertension documented according to

the 6th report of the Joint National Committee on Detection and Evaluation of the treatment of high BP (JNC VI) and the need for drug therapy (previously documented hypertension in patients currently taking antihypertensive agents is acceptable)

• 4. Documented CAD (e.g., classic angina pectoris (stable angina pectoris; Heberden angina pectoris), myocardial infarction three or more months ago, abnormal coronary angiography, or concordant abnormalities on two different types of stress tests)

• 5. Willingness to sign informed consent

... nur wenn er versteht.

85

Example: joint anatomyjoint HAS-HOLE joint spacejoint capsule IS-OUTER-LAYER-OF jointmeniscus

IS-INCOMPLETE-FILLER-OF joint spaceIS-TOPO-INSIDE joint capsuleIS-NON-TANGENTIAL-MATERIAL-PART-OF

joint

joint IS-CONNECTOR-OF bone XIS-CONNECTOR-OF bone Y

synoviaIS-INCOMPLETE-FILLER-OF joint space

synovial membrane IS-BONAFIDE-BOUNDARY-OF joint space

86

LandC-Ontologie

Having a healthcare phenomenon

Generalised PossessionHealthcare phenomenonHuman

IS-A

Has-possessor Has-

possessed

PatientIs-possessor-of

Cancer patient

IS-A

Has-Healthcare-phenomenon

Malignant neoplasm

IS-A

11

1

2

2

IS-A

3

3lung carcinoma

IS-A

Mr. Kovács has a pulmonary carcinoma

87

LinKBase

LinKBase still close to being a flat list

BFO and MedO designed to add depth, and so also reasoning capacity

88

So what is the ontology of blood?

89

We cannot solve this problem just by looking at concepts (by engaging in further acts of

knowledge mining)

90

concept systems may be simply incommensurable

91

the problem can only be solved

by taking the world itself into account

92

A reference ontology

is a theory of reality

But how is this possible?

How can we get beyond our concepts?

answer: ontology must be maximally opportunistic

93

“Maximally opportunistic”

means:

draw on 2 millennia of philosophical research

pertaining to realism, scepticism, error, theory change, and the language/concept/world relation

cognitive science (theories of error, bias)

but also pertaining to the structure of reality itself and to the relations between different scientific disciplines

94

Maximally opportunistic

means:

don’t just look at beliefs

look at the objects themselves

from every possible direction,

formal and informal

scientific and non-scientific …

95

It means further:

looking at concepts and beliefs critically

and always in the context of a wider view which includes independent ways to access the objects at issue at different levels of granularity

including physical ways (involving the use of physical measuring instruments, real physical contact with objects/bodies/organs)

96

And also:

taking account of tacit knowledge of those features of reality of which the domain experts are not consciously aware

look not at concepts, representations, of a passive observer

but rather at agents, at organisms acting in the world

97


means:

look not at what the expert says

but at what the expert does

Experts have expertise = knowing how

Ontologists skilled in extracting knowledge that from knowing how

The experts don’t know what the ontologist knows

98

Topography

as unifying factor in generating practical knowledge in the medical sphere

(missing from computers;

missing from most medical education)

99


means:look at the same objects at different levels of granularity:

100

We then recognize

that the same object can be apprehended at different levels of granularity:

at the perceptual level blood is a liquid

at the cellular level blood is a tissue

101

select out the good conceptualizations

those which have a reasonable chance of being integrated together into a single ontological system because they are

• based on tested principles• robust• conform to natural science

102

Partitions should be cuts through reality

a good medical ontology should NOT be compatible with a conceptualization of disease as caused by evil spirits

103

How to test a philosophical theory empirically

104

The Tests

Uniform top-level formal ontology

Domain ontology for medicine applicable at distinct granularities

Show that this medical domain ontology can increase efficiency and scope of existing industrial-strength software systems applied to processing of unstructured patient records

105

Can our ontological system

help to convert the huge existing mass of unstructured patient records into a unified, structured database

which can be used as a new type of gigantic object for medical research

106

The GoalsUniform top-level ontology for testing in medical

domainONE YEARApplicable at distinct granularities (e.g. gene

ontology)TWO YEARSTesting in processing of unstructured patient

records (www.landc.be)THREE YEARS

107

Measures of SuccessUniform top-level ontology for medicine

NO COMPETITORapplicable at distinct granularities

NO COMPETITORProcessing of unstructured patient records MANY COMPETITORS (INCLUDING DUMB

STATISTICAL PATTERN-RECOGNITION)BUT GOOD MEASURES OF EFFECTIVENESS

108

109

Brooks’ Engineering Approach to Robotics

takes its inspiration from evolutionary biology

lends very little weight to the role of representations or models

AI should use the world in all its complexity in producing systems that react directly to the world

110

Engineering Approach

An intelligent system embodies a number of distinct layers of activity (compare: faculties of the mind, plus sensor-motoric faculties)

These layers operate independently and connect directly to the environment outside the system

Each layer operates as a complete system that copes in real time with a changing environment

Layers evolve through interaction with the environment (artificial insects/vehicles …)

111

Brooks: An intelligent system

must be situated

it is situatedness which gives the processes within each layer meaning

Most importantly:

the world serves to unify the different layers together and to make them compatible/mutually adjusting

112

Organisms, especially humans,

fix their beliefs not only in their heads but in their worlds, as they attune themselves differently to different parts of the world as a result of their experience. And they pull the same trick with their memories, not only by rearranging their parsing of the world (their understanding of what they see), but by marking it. They place traces out there which changes what they will be confronted with the next time it comes around. Thus they don't have to carry their memories with them.

“Intelligence without Representation”

113

J. J. Gibson The Ecological Approach to Visual Perception

we are like (multi-layered) tuning forks – tuned to the environment which surrounds us(we have evolved in such a way as to be attuned to our environment;we are all experts in common sense;our perceptual beliefs are almost always true)

114

Organisms are tuning forks

They have evolved to resonate automatically and directly to those quality regions in their niche which are relevant for survival

-- perception is a form of automatic resonation-- cognitive beings resonate to speech acts and

to linguistic records-- cognitive beings resonate deontically

115

The Ecological Approach

To understand cognition we should study the moving, acting organism as it exists in its real-world environment

and for human organisms this is a social environment which includes records and traces of prior actions in the form of communication systems (languages), storage systems (libraries), transport systems (roads), legal systems

116

Gibson: Environment as Array of Affordances

“The affordances of the environment are what it offers the animal, what it provides or furnishes, either for good or evil.”

James J. Gibson, The Ecological Approach to Visual Perception

The environment of a commercial organism includes affordances such as prices.

117

Gibson’s theory of surface layout

Niches = systems of barriers, openings, pathways to which organisms are specifically attuned,

Include: temperature gradients, patterns of movement of air or water molecules, electro-chemical signals guiding the movements of micro-organisms

But also: traffic signs, instructions posted on notice boards or displayed on the computer screen

118

Application of the niche concept

in biology, ecology

in medicine (embryology …)

in anthropology

in economics

in the ontology of artifacts

in law

in politics

119

Roger G. Barker’s Eco-Behavioral Science

Gibson: Ecological Psychology of Perception

Barker: Ecological Psychology of Social Action

P. Schoggen, Behavior Settings: A Review and Extension of Roger G. Barker’s Ecological

Psychology. Stanford, CA: Stanford University Press, 1989.

120

Roger Barker: Niche as Behavioral SettingNiches are recurrent settings which serve as the environments for our everyday activities:

a newspaper kiosk in the morning rush-hour,

your table in the cafeteria,

the 5pm train to Long Island.

121

Behavior Settings

Each behavior setting is associated with certain standing patterns of behavior.

122

Settings, for Barker,

are natural units in no way imposed by an investigator.

To laymen they are as objective as rivers and forests

— they are parts of the objective environment that are experienced as directly as rain and sandy beaches are experienced. (Barker 1968, p. 11)

123

Unity of Behaviour and Ecological Setting

A physical-behavioural unit is a unit: its parts are unified together, but not through any similarity or community of substance.

Transcategorial complexity of behavior and setting

124

Barker on Unity of Social Reality

“The conceptual incommensurability of phenomena which is such an obstacle to the unification of the sciences does not appear to trouble nature’s units.

Within the larger units, things and events from conceptually more and more alien sciences are incorporated and regulated.”

125

Barker on Unity of Social Reality

“As far as our behaviour is concerned, … even the most radical diversity of kinds and categories need not prevent integration”

126

The Systematic Mutual Fittingness of Behaviour and Setting

The behaviour and the physical objects … are intertwined in such a way as to form a pattern that is by no means random: there is a relation of harmonious fit between the standard patterns of behaviour occurring within the unit and the pattern of its physical components.

127

The Systematic Mutual Fittingness of Behaviour and Setting

The seats in the lecture hall face the speaker. The speaker addresses his remarks out towards the audience.

The boundary of the football field is … the boundary of the game.

Non-transposability

128

Non-transposability

This mutual fittingness of behaviour and physical environment extends to the fine, interior structure of behaviour in a way which will imply a radical nontransposability of standing patterns of behaviour from one environment to another.

(Can’t play football in a lecture theater)

129

Power and Authority

… forces which help to sustain this mutual fittingness and thus to constitute the unity of the physical-behavioural unit through time. These include physical constraints exercised by hedges, walls or corridors or by persons with sticksalso social forces manifested in threats, promises, warnings, admonitions

130

Settings shape Persons

Each person has many strengths, many intelligences, many social maturities, many speeds, many degrees of liberality and conservativeness, and many moralities, depending in large part on the particular contexts of the person’s behavior.

131

Aurel Kolnai

a human society

… comprehends the same individual over and over again in line with his various social affiliations …

What an agent is, depends on the agent’s environment

132

Daily life

= passage through a succession of physical-behavioural units The latter are as much a part of the furniture of reality as are garden-variety continuants and occurrents

133

Environments may be nested may have actual parts which are also environmental settings(hierarchical nesting)

Theory of the organization of organizations:

the roles you take on as inhabitant of the niche called IBMthe roles you take on as inhabitant of the niche called US-Division 4B/661 of IBM (YOU ARE

THE BOSS)the roles you take on as inhabitant of the niche called your local office (YOU ISSUE

COMMANDS)

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Marks of (bodily) substance

i. Rounded-offness

ii. Occupies space

iii. Complete boundary

iv. May have substantial parts (nesting)

v. May be included in larger substances

vi. Has a life (manifests contrary accidents at different times)

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Corresponding Marks of Niches (3-Dimensional Environments)

(i) A niche enjoys a certain natural completeness or rounded-offness,

being neither too small nor too large

—in contrast to the arbitrary undetached parts of environmental settings and to arbitrary heaps or aggregates of environmental settings.

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(ii) A niche takes up space,

it occupies a physical-temporal locale,

and is such as to have spatial parts.

Within this physical-temporal locale is a privileged locus—a hole—

into which the tenant or occupant of the setting fits exactly.

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(iii) A niche

has an outer boundary:

there are objects which fall clearly within it,

and other objects which fall clearly outside it.

(The boundary itself need not be crisp.)

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(iv) A niche

may have actual parts which are also environmental settings

Barker: Many settings occur in assemblies. A unit in the middle range of a nesting structure is simultaneously both … whole and part, both entity and environment.

Compare the hierarchical organization of the human body into organs, cells, …

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(v) A niche

may be a proper part of larger, circumcluding niche.

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(vi) A niche has a lifeNiches are endurants/continuants

is now warm, now cold

now at peace, now at war ….

now expanding, now contracting

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Marks of (bodily) substance

i. Rounded-offness

ii. Occupies space

iii. Complete boundary

iv. May have substantial parts (nesting)

v. May be included in larger substances

vi. Has a life; is now warm, now cold (Substances are endurants/continuants)

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On being in a niche

Niches are in some ways like the interiors of substances

Two concepts of car:

John is in his car

John saw his car from a distance

The embryo is in the uterus

The doctor examined the uterus

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Two concepts of London

John is in London

John saw London from the air

London London

IBM IBM

A is part of B vs. A is in the interior of B as a tenant is in its niche

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3-dimensional environments

EnglandThe Nile DeltaThe interior of your carA stagnant pond

+ ecologists’ habitat

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4-dimensional environments

Lobsters have evolved into environments marked by cyclical patterns of temperature change

Tudor EnglandThe Afghan winterThe window of opportunity for an invasion of Iraq

+ Barker’s behavior settings

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Where are Niches?Concrete Entity

[Exists in Space and Time]Concrete Entity

[Exists in Space and Time]







Dim = T, T+0, T+1, T+2, T+3

Spatial Regionof Dimension 0,1,2,3

Spatial Regionof Dimension 0,1,2,3 Dependent EntityDependent Entity




























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SNAP: Ontology of entities enduring through time









Dim = T, T+0, T+1, T+2, T+3

Spatial regions of dimension0,1,2,3

Spatial regions of dimension0,1,2,3 Dependent EntityDependent Entity




























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Where are Places?Concrete Entity

[Exists in Space and Time]Concrete Entity

[Exists in Space and Time]







Dim = T, T+0, T+1, T+2, T+3

Spatial Regionof Dimension

0,1,2,3

Spatial Regionof Dimension

0,1,2,3

Dependent EntityDependent Entity


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Where are behavior-settings?















spatio-temporal volumes

150

SPAN: Ontology of entities extended in time















spatio-temporal volumes

standardizedpatterns of

behavior

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Three Main Ingredients to the SNAP/SPAN Framework

Independent SNAP entities: Substances

Dependent SNAP entities: powers, qualities, roles, functions

SPAN entities: Processes

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Gene Ontology

Cellular Component Ontology: subcellular structures, locations, and macromolecular complexes;examples: nucleus, telomere

Molecular Function Ontology: tasks performed by individual gene products; examples: transcription factor, DNA helicase

Biological Process Ontology: broad biological goals accomplished by ordered assemblies of molecular functions; examples: mitosis, purine metabolism

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Three Main Ingredients to the SNAP/SPAN Framework

Independent SNAP entities: Molecular Components

Dependent SNAP entities: Functions

SPAN entities: Processes

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Conclusions

Two sorts of ontology:

Domain ontology (ontology within an agent/information system)

Reference ontology (including both agents/systems and environment within a single theory)

Communication between agents/systems can be achieved only via hand-callibration of their communication protocols via reference ontology

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Conclusions for a Theory of Agents

Agents are in the world, they have to achieve their goals in relation to a particular environment, and adapt to this environment

Therefore if we want to have a good theory of agent-based computing, we need to have a good theory of (worldly) environments

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Humans, Machines, and the Structure of Knowledge

Harry M. CollinsSEHR, 4: 2 (1995)

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Knowledge-down-a-wireImagine a 5-stone weakling having his brain loaded with the knowledge of a champion tennis player.

He goes to serve in his first match

-- Wham! –

his arm falls off.

He just doesn't have the bone structure or muscular development to serve that hard.

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Types of knowledge/ability/skill

1. those that can be transferred simply by passing signals from one brain/computer to another.

2. those that can’t:

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Sometimes it is the body (the hardware) which knows

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and sometimes it is the world outside which knows

161

Types of knowledge/ability/skill

1. those that can be transferred simply by passing signals from one brain/computer to another.

2. those that can’t: -- here the "hardware" is important;abilities/skills contained (a) in the body(b) in the world

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From

The Methodological Solipsist Approach to Information Processing

ToThe Ecological Approach to Information

Processing

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Fodorian Psychology

To understand human cognition we should study the mind/brain in abstraction from its real-world environment

(as if it were a hermetically sealed Cartesian ego)

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I know where the book is= I know how to find it

I know what the square root of 2489 is= I know how to calculate it

I know how to recognize the presence of a tiger

= by smell, noise … (in real-world context)

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How to solve this problem

Compare the way in which the physical properties of ROADS help people to obey the traffic laws when driving

Deal with obligations, norms not via deontic logic but via the comparison

with roads?

Documents

(switch on tape-recorder). 2 Plädoyer für die angewandte Ontologie Barry Smith