Ontology and the AustrianTraditionBarry Smith
Brentano and his studentsBrentanob. Marienberg am Rhein1838Meinongb. Lemberg1853Ehrenfelsb. Rodaun1859Husserlb. Proβnitz18...
Brentano revolutionizes psychologyBrentanopublished Psychologyfrom an EmpiricalStandpoint, 1874Meinong Ehrenfelsfounder of...
Brentanists revolutionize ontologyBrentanoMeinongOn the TheoryofObjects, 1904EhrenfelsHusserlfirst formalmereology, 1902__...
Brentanists revolutionize our understandingof the relations between psychology andontologyIn 1874 Brentano (re-)introduces...
7the arrow of intentionality
Brentanists introduce the problem ofunderstanding the relation betweenintentionality and languageBrentanoMeinong Ehrenfels...
The Logicians: Leśniewski, Tarski, Łukasiewicz, TwardowskiMain Library of the University of Warsaw
“From Intentionality to Formal Semantics”BrentanoHusserl TwardowskiLeśniewskiformalmereologyTarskiformalsemanticsJoseph Wo...
11the arrow of intentionality
The varieties of aboutnessBrentanoMeinong EhrenfelsHusserlsimpleperceptually filledveridicalrelationalmediated by language...
± simplemental process content (putative) targetpresenting actcontent of presentation“apple”object of presentationjudging ...
mental process content targetyou see an apple “apple” an apple• you are in physical contact with target― cf. Russell’s kno...
mental process content (putative) targetpresenting actsensory content object of presentationobjectexistsobject doesnot exi...
mental process content (putative) targetpresenting actsensory content object of presentationobjectexistsobject doesnot exi...
mental process content (putative) targetpresenting act content of presentation“apple” + sensationoriginating causally atta...
mental process content (putative) targetpresenting act content of presentation“apple” + sensationoriginating causally atta...
mental process content (putative) targetpresenting act content of presentation“apple”object of presentationobjectexistsobj...
mental process content (putative) targetpresenting act content of presentation“apple”object of presentationobject existsob...
content match“apple”
content match“food”
mental process content (putative) targetpresenting act content of presentation“apple”object of presentationobject existsob...
content mismatch“poison”
content mismatch“apple”content here not just a matte of language
mental process content targetyou see an apple “apple” an apple± linguistically mediatedA cat can see a king
28the primacy of language (Sellars …)mental experiences are about objects becausewords have meaningword / meaning
29the primacy of the intentional(Brentano, Husserl, …):linguistic expressions have meanings because thereare („animating‟)...
dimension of content / belief prior todimension of language
language comes later than mentalaboutness31
to create a general theoryof aboutness not markedby the prejudice in favorof veridical intentionalitynon-veridical intenti...
Investigations onthe Theory ofObjects andPsychology
“From Intentionality to Formal Ontology”BrentanoHusserl TwardowskiLeśniewskiformalmereologyTarskiformalsemanticsJoseph Woo...
“From Intentionality to Formal Ontology”BrentanoHusserl TwardowskiLeśniewskiformalmereologyTarskiformalsemanticsJoseph Woo...
38Google hits Jan. 2004ontology + Heidegger 58Kontology + Aristotle 77Kontology + philosophy 327K
39Google hits Jan. 2004ontology + Heidegger 58Kontology + Aristotle 77Kontology + philosophy 327Kontology + software 468Ko...
40Comparison 2004/2012ontology + Heidegger 58K 0.99Montology + Aristotle 77K 1.35Montology + philosophy 327K 4.84Montology...
Investigations onthe Theory ofObjects andPsychologywith support fromthe Imperial-RoyalMinister of Cultureand Education inV...
Examples of Ontology Projects fundedby National Institutes of HealthNIH / NHGRI* GO: Gene OntologyNIH / NIGMS PRO: Protein...
43http://bioontology.orgNIH National Center for Biomedical ComputingUS Consortium Partners:Stanford University School of M...
Distributed Common Ground System–Army (DCGS-A)SemanticEnhancement ofthe Dataspaceon the CloudIntelligence and Information ...
Old biology data45/
MKVSDRRKFEKANFDEFESALNNKNDLVHCPSITLFESIPTEVRSFYEDEKSGLIKVVKFRTGAMDRKRSFEKVVISVMVGKNVKKFLTFVEDEPDFQGGPISKYLIPKKINLMVYTLFQVH...
next generation genomics47
How to do biology across the genome?MKVSDRRKFEKANFDEFESALNNKNDLVHCPSITLFESIPTEVRSFYEDEKSGLIKVVKFRTGAMDRKRSFEKVVISVMVGKNVKK...
how to link the kinds of phenomenarepresented here49
or here50
MKVSDRRKFEKANFDEFESALNNKNDLVHCPSITLFESIPTEVRSFYEDEKSGLIKVVKFRTGAMDRKRSFEKVVISVMVGKNVKKFLTFVEDEPDFQGGPIPSKYLIPKKINLMVYTLFQV...
52or this?
MouseEcotope GlyProtDiabetInGeneGluChemsphingolipidtransporteractivityannotation using common ontologies allowsnavigation ...
this allows integration of databasesMouseEcotope GlyProtDiabetInGeneGluChemHolliday junctionhelicase complex54
How annotate this55
or this?56
or this?57
Mental Functioning Ontology (Draft)
Mental Functioning Ontology (Draft)with thanks to Janna Hastings and Kevin MulliganSwiss Center for Affective Sciences)
Basic Formal Ontology60BFO:EntityBFO:Continuant BFO:OccurrentBFO:ProcessBFO:IndependentContinuantBFOBFO:DependentContinuan...
Basic Formal Ontologyand Mental Functioning Ontology (MFO)61BFO:EntityBFO:Continuant BFO:OccurrentBFO:ProcessOrganismBFO:I...
Functions vs. FunctioningsContinuants vs. Occurrents6262BFO:EntityBFO:Continuant BFO:OccurrentBFO:ProcessOrganismBFO:Indep...
Aboutness (‘Intentionality’)63BFO:EntityBFO:Continuant BFO:OccurrentBFO:ProcessOrganismBFO:IndependentContinuantBFOMFOBFO:...
Extending the MFO• to linguistic competence and performance64
Linguistic Functioning Ontology(1. Speech and hearing)6565BFO:EntityBFO:Continuant BFO:OccurrentBFO:ProcessBFO:Independent...
Linguistic Functioning Ontology(2. Reading and writing)6666BFO:EntityBFO:Continuant BFO:OccurrentBFO:ProcessBFO:Independen...
Linguistic Functioning Ontology(the whole thing)6767BFO:EntityBFO:Continuant BFO:OccurrentBFO:ProcessBFO:IndependentContin...
Extending the MFO to mental disease68
69
70
Mental Functioning Ontology (MF)71brainendocrinegland
http://bioportal.bioontology.org/ontologies/49078/72Extending MFO toEmotions
need link to a physiology ontology 73‘physiological response to emotion’
74‘emotionprocess’
Using the Emotion Ontologyfor self-report of emotional experiencesObjectives:• Capture emotional experiences in astandardi...
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Studies of the biochemical basis ofemotionEmotions are effected in part byneurotransmitters such as dopamine, tryptophanTh...
Ontological traffic rule:to build an ontology of the types ofentities in a complex domain, focus firston the canonical ins...
Canonical pain & variantsPCT: pain with concordant tissue damage: pain ofthe evolutionarily most basic sort = pain inrespo...
85
Pain-related phenomena without painPBWP: pain behavior without pain: there is acry or report of pain, but no pain is being...
Pain Ontology (PN) branch of MF-EMLyingabout pain87
Canonical pain89canonicalpainpainEMOTION COMPONENT CHARACTERISTIC FOR PAINAction tendency WithdrawalSubjective emotional f...
Canonical fear91canonicalfearfearEMOTION COMPONENT CHARACTERISTIC FOR FEARAction tendency Fight-or-flightSubjective emotio...
Canonical and non-canonical fearCanonical fear gives rise to action tendenciesthat are conformant to a perceived dangerPho...
mental process content (putative) targetpresenting act content of presentation“apple”object of presentationobjectexistsobj...
mental process content there is no targetpresenting act content of presentation“apple”underlying false beliefnon-veridical...
mental process content (putative) targetpresenting act content of presentation“apple”objectpresentobjectabsentnon-veridica...
mental process content (putative) targetpresenting act content of presentation“apple”objectpresentobjectabsentnon-veridica...
in the Macbeth case we are dealing withthe sort of thing that happens when, toquote Witters, “language goes onholiday”97
Brentano revolutionizes psychologyBrentanopublished Psychologyfrom an EmpiricalStandpoint, 1874Meinongfounded first labora...
Brentano revolutionizes psychologyBrentanopublished Psychologyfrom an EmpiricalStandpoint, 1874Meinongfounded first labora...
Mental Functioning is Neural Functioning:Towards a Unified Ontology ofMind, Brain, and BehaviorGwen A. FrishkoffDepartment...
Outline of Talk• What is a mental process?– A view from cognitive psychology– The Mind–Brain problem and three proposedsol...
What is a Mental Process?A view from cognitive psychologyShort-term memoryCognitive controlMotor control,ActionSensation,P...
How do we know any of this?That is, where did the components of thestandard model come from?
• Mental processes cannot be observed.*• They must be inferred based on what we can observe.What can we observe?...*We can...
• Physical processes in body  Behavior(response type, accuracy, reaction time)• Physiological processes in brain Neural ...
“A mental process is a neural process.”• Avoids Mind-Body dualism• More precise than other twosolutions• Gives ready frame...
Mental Functioning Ontology (MF)110braininendocrinegland
Aboutness111brain retinaENVIRONMENT
Levels of brain, levels of mindMesulam, 1990113Representation, monitoring andcontrol of internal environment(“self”)Repres...
Levels of brain, levels of mindMesulam, 1990114Representation, monitoring andcontrol of internal environment(“self”)Repres...
Mental representations: What are they “about”?Peripheral (sensory-motor) parts of the bodyare “mapped” to (represented by)...
116Perception ofinternal(bodily)environment(“self”)Perception ofexternalenvironment/sensory input(“real world”)
117Shimon Edelman‟sRiddle of Representationtwo humans, a monkey, and a robotare looking at a piece of cheese;what is commo...
118Answer:The cheese, of course
119The real cheese
or objects or processesinside the body
or objects or processesinside the bodyobjects and processes inside andoutside the body play a role here too
external targetsinternal and external features causallyrelevant to perception, nociception, etc.allofthesetogetherformthee...
externaltargetsinternal and external features causallyrelevant to perception, nociception, etc.the arrow of aboutness
What is a Mental Process?A view from cognitive psychologyShort-term memoryCognitive controlMotor control,ActionSensation,P...
What does a temperature chartrepresent?147
148606570758085Time 1 Time 2 Time 3What does a chart representing your pulse rate represent?
Cardiac Cycle, Left Ventricle149
150606570758085Time 1 Time 2 Time 3What does a chart of changes in your pulse raterepresent?
151139113921393139413951396139713981399What does a chart of changes in the DowJones industrial average represent?time
152activity during thistime interval
153
15413911392139313941395139613971398time
15513911392139313941395139613971398timeWhat this represents is real, and not just “real”
coronary heartdiseaseJohn’s coronary heart diseasedisease duringphase ofasymptomatic(‘silent’)infarctiondisease duringphas...
What did your temperature do over the lastmonth, Jim?Jim’s temperature process profile, thetarget of a certain sort of cog...
The graph picks out just one dimension ofqualitative change within a much largerconglomerate of processes within JimHence ...
Compare perception of polyphonicmusic• Cognitive selection of the cello part when youlisten to a string quartet• Picking o...
Compare perception of polyphonicmusic• Cognitive selection of the cello part when youlisten to a string quartet• Picking o...
time-series graph of acousticsignal, spectrogram, formants, jawdisplacement and other speech parameters161
adding phonetic, phonemic and syllable levels162
g u t e n163
add brain164
speech is a process profilethe speech process is to the totality of acousticsignal, spectrogram, formants, jawdisplacement...
Breakthrough: First sound recordings based on readinghuman auditory cortex (PLoS Biology, January 2012)166
Top: spectrogram of words presented to subject.Middle and bottom: reconstructions of speech based onreadings from electrod...
PathwaydiagramPathwayReactionMolecularcollectiveIndividualmoleculeBFO:ProcessBFO:IndependentContinuantBFO:DispositionInfor...
mental processes, too, are process profiles169
177177BFO:EntityBFO:Continuant BFO:OccurrentBFO:ProcessBFO:IndependentContinuantBFOMFOBFO:DependentContinuantBehaviourindu...
• Examples of dispositions that are constantlybeing realized:– stock exchange– heart beat– brain activity– social order– l...
Investigations onthe Theory ofObjects andPsychologywith support fromthe Imperial-RoyalMinister of Cultureand Education inV...
Horizontal Integration of WarfighterIntelligence Data180
Horizontal Integration• “Horizontally integrating warfighterintelligence data … requires access (includingdiscovery, searc...
Horizontal integration=def. multiple heterogeneous data resourcesbecome aligned in such a way that search andanalysis proc...
UnclassifiedUnclassifiedCommand and Control OntologyArmy Fires PlanArmy Maneuver PlanNaval Fires PlanDefinition: An inform...
UnclassifiedUnclassifiedCommand and Control OntologySituationalAwarenessSituationalUnderstandingCommander‟s Intent…184
Horizontal integration=def. multiple heterogeneous data resourcesbecome aligned through association withcommon ontology te...
=def. multiple heterogeneous data resourcesbecome aligned through association withcommon ontology terms in such a way that...
Ontology and the Austrian tradition
Ontology and the Austrian tradition
Ontology and the Austrian tradition
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Ontology and the Austrian tradition

  1. 1. Ontology and the AustrianTraditionBarry Smith
  2. 2. Brentano and his studentsBrentanob. Marienberg am Rhein1838Meinongb. Lemberg1853Ehrenfelsb. Rodaun1859Husserlb. Proβnitz1859Twardowskib. Vienna1866
  3. 3. Brentano revolutionizes psychologyBrentanopublished Psychologyfrom an EmpiricalStandpoint, 1874Meinong Ehrenfelsfounder of Gestaltpsychology, 1890Husserl Twardowski
  4. 4. Brentanists revolutionize ontologyBrentanoMeinongOn the TheoryofObjects, 1904EhrenfelsHusserlfirst formalmereology, 1902______first use of‘formal ontology’~1905;TwardowskiLeśniewskilogicalformalizationofmereology, 1916
  5. 5. Brentanists revolutionize our understandingof the relations between psychology andontologyIn 1874 Brentano (re-)introduces intophilosophy the idea of intentionaldirectedness (aboutness)Meinong Ehrenfels Husserl Twardowskihow can we think about what does not exist?
  6. 6. 7the arrow of intentionality
  7. 7. Brentanists introduce the problem ofunderstanding the relation betweenintentionality and languageBrentanoMeinong Ehrenfels Husserlcategorialgrammar, 1901TwardowskiLeśniewskifounder offormalmereologyTarski inventsformalsemantics
  8. 8. The Logicians: Leśniewski, Tarski, Łukasiewicz, TwardowskiMain Library of the University of Warsaw
  9. 9. “From Intentionality to Formal Semantics”BrentanoHusserl TwardowskiLeśniewskiformalmereologyTarskiformalsemanticsJoseph WoodgerAxiomatic Method inBiology
  10. 10. 11the arrow of intentionality
  11. 11. The varieties of aboutnessBrentanoMeinong EhrenfelsHusserlsimpleperceptually filledveridicalrelationalmediated by languageTwardowski
  12. 12. ± simplemental process content (putative) targetpresenting actcontent of presentation“apple”object of presentationjudging actjudgment-content“the apple over there isripe”state of affairs(Objektive)evaluating actemotional actappraisal…“it is good that the appleover there is ripe”?
  13. 13. mental process content targetyou see an apple “apple” an apple• you are in physical contact with target― cf. Russell’s knowledge by acquaintance;J. J. Gibson’s ecological theory of perception± relational intentionality
  14. 14. mental process content (putative) targetpresenting actsensory content object of presentationobjectexistsobject doesnot existobjectpresentobjectabsent± perceptually filledordinary perception
  15. 15. mental process content (putative) targetpresenting actsensory content object of presentationobjectexistsobject doesnot existobjectpresentobjectabsentperceptually filled does not implyveridicalhallucination
  16. 16. mental process content (putative) targetpresenting act content of presentation“apple” + sensationoriginating causally attargetobject of presentationobjectexistsobject doesnot existobjectpresentobjectabsentthe evolutionarily most basic caseordinary perception
  17. 17. mental process content (putative) targetpresenting act content of presentation“apple” + sensationoriginating causally attargetobject of presentationobjectexistsobject doesnot existobjectpresentobjectabsentrelational implies veridicalordinary perception
  18. 18. mental process content (putative) targetpresenting act content of presentation“apple”object of presentationobjectexistsobject doesnot existobjectpresentobjectabsentveridical does not imply relationalveridical thinking about
  19. 19. mental process content (putative) targetpresenting act content of presentation“apple”object of presentationobject existsobjectpresentobjectabsent± content match
  20. 20. content match“apple”
  21. 21. content match“food”
  22. 22. mental process content (putative) targetpresenting act content of presentation“apple”object of presentationobject existsobjectpresentobjectabsentveridical does not imply content match
  23. 23. content mismatch“poison”
  24. 24. content mismatch“apple”content here not just a matte of language
  25. 25. mental process content targetyou see an apple “apple” an apple± linguistically mediatedA cat can see a king
  26. 26. 28the primacy of language (Sellars …)mental experiences are about objects becausewords have meaningword / meaning
  27. 27. 29the primacy of the intentional(Brentano, Husserl, …):linguistic expressions have meanings because thereare („animating‟) mental experiences which haveaboutness
  28. 28. dimension of content / belief prior todimension of language
  29. 29. language comes later than mentalaboutness31
  30. 30. to create a general theoryof aboutness not markedby the prejudice in favorof veridical intentionalitynon-veridical intentionality
  31. 31. Investigations onthe Theory ofObjects andPsychology
  32. 32. “From Intentionality to Formal Ontology”BrentanoHusserl TwardowskiLeśniewskiformalmereologyTarskiformalsemanticsJoseph WoodgerThe Axiomatic Method inBiology (1937)with Appendix by Tarski
  33. 33. “From Intentionality to Formal Ontology”BrentanoHusserl TwardowskiLeśniewskiformalmereologyTarskiformalsemanticsJoseph Woodger AxiomaticMethod in BiologyPatrick Hayes“Ontology of Liquids” (1985)…formal ontologies ininformation systems
  34. 34. 38Google hits Jan. 2004ontology + Heidegger 58Kontology + Aristotle 77Kontology + philosophy 327K
  35. 35. 39Google hits Jan. 2004ontology + Heidegger 58Kontology + Aristotle 77Kontology + philosophy 327Kontology + software 468Kontology + database 594Kontology + information systems 702K
  36. 36. 40Comparison 2004/2012ontology + Heidegger 58K 0.99Montology + Aristotle 77K 1.35Montology + philosophy 327K 4.84Montology + software 468K 7.68Montology + database 594K 8.15Montology +information systems 702K 5.99M
  37. 37. Investigations onthe Theory ofObjects andPsychologywith support fromthe Imperial-RoyalMinister of Cultureand Education inVienna, 1904
  38. 38. Examples of Ontology Projects fundedby National Institutes of HealthNIH / NHGRI* GO: Gene OntologyNIH / NIGMS PRO: Protein OntologyNIH / NIAID IDO: Infectious Disease OntologyNIH / NIAID Major Histocompatilibity Complex(MHC) OntologyNIH / NHGRI SO: Sequence OntologyNIH / NLM FMA: Foundational Model ofAnatomyNIH / NHGRI CL: Cell Ontology*National Human Genome Research Institute42
  39. 39. 43http://bioontology.orgNIH National Center for Biomedical ComputingUS Consortium Partners:Stanford University School of MedicineThe Mayo ClinicUniversity at Buffalo Department of Philosophy
  40. 40. Distributed Common Ground System–Army (DCGS-A)SemanticEnhancement ofthe Dataspaceon the CloudIntelligence and Information WarfareDirectorateResearch, Development and Engineering Command
  41. 41. Old biology data45/
  42. 42. MKVSDRRKFEKANFDEFESALNNKNDLVHCPSITLFESIPTEVRSFYEDEKSGLIKVVKFRTGAMDRKRSFEKVVISVMVGKNVKKFLTFVEDEPDFQGGPISKYLIPKKINLMVYTLFQVHTLKFNRKDYDTLSLFYLNRGYYNELSFRVLERCHEIASARPNDSSTMRTFTDFVSGAPIVRSLQKSTIRKYGYNLAPYMFLLLHVDELSIFSAYQASLPGEKKVDTERLKRDLCPRKPIEIKYFSQICNDMMNKKDRLGDILHIILRACALNFGAGPRGGAGDEEDRSITNEEPIIPSVDEHGLKVCKLRSPNTPRRLRKTLDAVKALLVSSCACTARDLDIFDDNNGVAMWKWIKILYHEVAQETTLKDSYRITLVPSSDGISLLAFAGPQRNVYVDDTTRRIQLYTDYNKNGSSEPRLKTLDGLTSDYVFYFVTVLRQMQICALGNSYDAFNHDPWMDVVGFEDPNQVTNRDISRIVLYSYMFLNTAKGCLVEYATFRQYMRELPKNAPQKLNFREMRQGLIALGRHCVGSRFETDLYESATSELMANHSVQTGRNIYGVDFSLTSVSGTTATLLQERASERWIQWLGLESDYHCSFSSTRNAEDVDISRIVLYSYMFLNTAKGCLVEYATFRQYMRELPKNAPQKLNFREMRQGLIALGRHCVGSRFETDLYESATSELMANHSVQTGRNIYGVDFSLTSVSGTTATLLQERASERWINew biology data46
  43. 43. next generation genomics47
  44. 44. How to do biology across the genome?MKVSDRRKFEKANFDEFESALNNKNDLVHCPSITLFESIPTEVRSFYEDEKSGLIKVVKFRTGAMDRKRSFEKVVISVMVGKNVKKFLTFVEDEPDFQGGPISKYLIPKKINLMVYTLFQVHTLKFNRKDYDTLSLFYLNRGYYNELSFRVLERCHEIASARPNDSSTMRTFTDFVSGAPIVRSLQKSTIRKYGYNLAPYMFLLLHVDELSIFSAYQASLPGEKKVDTERLKRDLCPRKPIEIKYFSQICNDMMNKKDRLGDILHIILRACALNFGAGPRGGAGDEEDRSITNEEPIIPSVDEHGLKVCKLRSPNTPRRLRKTLDAVKALLVSSCACTARDLDIFDDNNGVAMWKWIKILYHEVAQETTLKDSYRITLVPSSDGISLLAFAGPQRNVYVDDTTRRIQLYTDYNKNGSSEPRLKTLDGLTSDYVFYFVTVLRQMQICALGNSYDAFNHDPWMDVVGFEDPNQVTNRDISRIVLYSYMFLNTAKGCLVEYATFRQYMRELPKNAPQKLNFREMRQGLIALGRHCVGSRFETDLYESATSELMANHSVQTGRNIYGVDFSLTSVSGTTATLLQERASERWIQWLGLESDYHCSFSSTRNAEDVMKVSDRRKFEKANFDEFESALNNKNDLVHCPSITLFESIPTEVRSFYEDEKSGLIKVVKFRTGAMDRKRSFEKVVISVMVGKNVKKFLTFVEDEPDFQGGPISKYLIPKKINLMVYTLFQVHTLKFNRKDYDTLSLFYLNRGYYNELSFRVLERCHEIASARPNDSSTMRTFTDFVSGAPIVRSLQKSTIRKYGYNLAPYMFLLLHVDELSIFSAYQASLPGEKKVDTERLKRDLCPRKPIEIKYFSQICNDMMNKKDRLGDILHIILRACALNFGAGPRGGAGDEEDRSITNEEPIIPSVDEHGLKVCKLRSPNTPRRLRKTLDAVKALLVSSCACTARDLDIFDDNNGVAMWKWIKILYHEVAQETTLKDSYRITLVPSSDGISLLAFAGPQRNVYVDDTTRRIQLYTDYNKNGSSEPRLKTLDGLTSDYVFYFVTVLRQMQICALGNSYDAFNHDPWMDVVGFEDPNQVTNRDISRIVLYSYMFLNTAKGCLVEYATFRQYMRELPKNAPQKLNFREMRQGLIALGRHCVGSRFETDLYESATSELMANHSVQTGRNIYGVDFSLTSVSGTTATLLQERASERWIQWLGLESDYHCSFSSTRNAEDVMKVSDRRKFEKANFDEFESALNNKNDLVHCPSITLFESIPTEVRSFYEDEKSGLIKVVKFRTGAMDRKRSFEKVVISVMVGKNVKKFLTFVEDEPDFQGGPISKYLIPKKINLMVYTLFQVHTLKFNRKDYDTLSLFYLNRGYYNELSFRVLERCHEIASARPNDSSTMRTFTDFVSGAPIVRSLQKSTIRKYGYNLAPYMFLLLHVDELSIFSAYQASLPGEKKVDTERLKRDLCPRKPIEIKYFSQICNDMMNKKDRLGDILHIILRACALNFGAGPRGGAGDEEDRSITNEEPIIPSVDEHGLKVCKLRSPNTPRRLRKTLDAVKALLVSSCACTARDLDIFDDNNGVAMWKWIKILYHEVAQETTLKDSYRITLVPSSDGISLLAFAGPQRNVYVDDTTRRIQLYTDYNKNGSSEPRLKTLDGLTSDYVFYFVTVLRQMQICALGNSYDAFNHDPWMDVVGFEDPNQVTNRDISRIVLYSYMFLNTAKGCLVEYATFRQYMRELPKNAPQKLNFREMRQGLIALGRHCVGSRFETDLYESATSELMANHSVQTGRNIYGVDFSLTSVSGTTATLLQERASERWIQWLGLESDYHCSFSSTRNAEDVMKVSDRRKFEKANFDEFESALNNKNDLVHCPSITLFESIPTEVRSFYEDEKSGLIKVVKFRTGAMDRKRSFEKVVISVMVGKNVKKFLTFVEDEPDFQGGPISKYLIPKKINLMVYTLFQVHTLKFNRKDYDTLSLFYLNRGYYNELSFRVLERCHEIASARPNDSSTMRTFTDFVSGAPIVRSLQKSTIRKYGYNLAPYMFLLLHVDELSIFSAYQASLPGEKKVDTERLKR48
  45. 45. how to link the kinds of phenomenarepresented here49
  46. 46. or here50
  47. 47. MKVSDRRKFEKANFDEFESALNNKNDLVHCPSITLFESIPTEVRSFYEDEKSGLIKVVKFRTGAMDRKRSFEKVVISVMVGKNVKKFLTFVEDEPDFQGGPIPSKYLIPKKINLMVYTLFQVHTLKFNRKDYDTLSLFYLNRGYYNELSFRVLERCHEIASARPNDSSTMRTFTDFVSGAPIVRSLQKSTIRKYGYNLAPYMFLLLHVDELSIFSAYQASLPGEKKVDTERLKRDLCPRKPIEIKYFSQICNDMMNKKDRLGDILHIILRACALNFGAGPRGGAGDEEDRSITNEEPIIPSVDEHGLKVCKLRSPNTPRRLRKTLDAVKALLVSSCACTARDLDIFDDNNGVAMWKWIKILYHEVAQETTLKDSYRITLVPSSDGISLLAFAGPQRNVYVDDTTRRIQLYTDYNKNGSSEPRLKTLDGLTSDYVFYFVTVLRQMQICALGNSYDAFNHDPWMDVVGFEDPNQVTNRDISRIVLYSYMFLNTAKGCLVEYATFRQYMRELPKNAPQKLNFREMRQGLIALGRHCVGSRFETDLYESATSELMANHSVQTGRNIYGVDSFSLTSVSGTTATLLQERASERWIQWLGLESDYHCSFSSTRNAEDVVAGEAASSNHHQKISRVTRKRPREPKSTNDILVAGQKLFGSSFEFRDLHQLRLCYEIYMADTPSVAVQAPPGYGKTELFHLPLIALASKGDVEYVSFLFVPYTVLLANCMIRLGRRGCLNVAPVRNFIEEGYDGVTDLYVGIYDDLASTNFTDRIAAWENIVECTFRTNNVKLGYLIVDEFHNFETEVYRQSQFGGITNLDFDAFEKAIFLSGTAPEAVADAALQRIGLTGLAKKSMDINELKRSEDLSRGLSSYPTRMFNLIKEKSEVPLGHVHKIRKKVESQPEEALKLLLALFESEPESKAIVVASTTNEVEELACSWRKYFRVVWIHGKLGAAEKVSRTKEFVTDGSMQVLIGTKLVTEGIDIKQLMMVIMLDNRLNIIELIQGVGRLRDGGLCYLLSRKNSWAARNRKGELPPKEGCITEQVREFYGLESKKGKKGQHVGCCGSRTDLSADTVELIERMDRLAEKQATASMSIVALPSSFQESNSSDRYRKYCSSDEDSNTCIHGSANASTNASTNAITTASTNVRTNATTNASTNATTNASTNASTNATTNASTNATTNSSTNATTTASTNVRTSATTTASINVRTSATTTESTNSSTNATTTESTNSSTNATTTESTNSNTSATTTASINVRTSATTTESTNSSTSATTTASINVRTSATTTKSINSSTNATTTESTNSNTNATTTESTNSSTNATTTESTNSSTNATTTESTNSNTSAATTESTNSNTSATTTESTNASAKEDANKDGNAEDNRFHPVTDINKESYKRKGSQMVLLERKKLKAQFPNTSENMNVLQFLGFRSDEIKHLFLYGIDIYFCPEGVFTQYGLCKGCQKMFELCVCWAGQKVSYRRIAWEALAVERMLRNDEEYKEYLEDIEPYHGDPVGYLKYFSVKRREIYSQIQRNYAWYLAITRRRETISVLDSTRGKQGSQVFRMSGRQIKELYFKVWSNLRESKTEVLQYFLNWDEKKCQEEWEAKDDTVVVEALEKGGVFQRLRSMTSAGLQGPQYVKLQFSRHHRQLRSRYELSLGMHLRDQIALGVTPSKVPHWTAFLSMLIGLFYNKTFRQKLEYLLEQISEVWLLPHWLDLANVEVLAADDTRVPLYMLMVAVHKELDSDDVPDGRFDILLCRDSSREVGELIGLFYNKTFRQKLEYLLEQISEVWLLPHWLDLANVEVLAADDTRVPLYMLMVAVHKELDSDDVPDGRFDILLCRDSSREVGELIGLFYNKTFRQKLEYLLEQISEVWLLPHWLDLANVEVLAADDTRVPLYMLMVAVHKELDSDDVPDG51to this?
  48. 48. 52or this?
  49. 49. MouseEcotope GlyProtDiabetInGeneGluChemsphingolipidtransporteractivityannotation using common ontologies allowsnavigation between databases53
  50. 50. this allows integration of databasesMouseEcotope GlyProtDiabetInGeneGluChemHolliday junctionhelicase complex54
  51. 51. How annotate this55
  52. 52. or this?56
  53. 53. or this?57
  54. 54. Mental Functioning Ontology (Draft)
  55. 55. Mental Functioning Ontology (Draft)with thanks to Janna Hastings and Kevin MulliganSwiss Center for Affective Sciences)
  56. 56. Basic Formal Ontology60BFO:EntityBFO:Continuant BFO:OccurrentBFO:ProcessBFO:IndependentContinuantBFOBFO:DependentContinuantBFO:Disposition
  57. 57. Basic Formal Ontologyand Mental Functioning Ontology (MFO)61BFO:EntityBFO:Continuant BFO:OccurrentBFO:ProcessOrganismBFO:IndependentContinuantBFOMFOBFO:DependentContinuantBehaviourinducing stateMental FunctioningRelated AnatomicalStructureCognitiveRepresentationBFO:QualityAffectiveRepresentationMental ProcessBodily ProcessBFO:Disposition
  58. 58. Functions vs. FunctioningsContinuants vs. Occurrents6262BFO:EntityBFO:Continuant BFO:OccurrentBFO:ProcessOrganismBFO:IndependentContinuantBFOMFOBFO:DependentContinuantMentalFunctionCognitiveRepresentationBFO:QualityMental ProcessBodily ProcessBFO:DispositionMentalFunctioning
  59. 59. Aboutness (‘Intentionality’)63BFO:EntityBFO:Continuant BFO:OccurrentBFO:ProcessOrganismBFO:IndependentContinuantBFOMFOBFO:DependentContinuantMentalFunctionCognitiveRepresentationBFO:QualityMental ProcessBodily ProcessBFO:DispositionMentalFunctioningdoes all mental functioning involve cognitiverepresentation (aboutness)?what is aboutness?
  60. 60. Extending the MFO• to linguistic competence and performance64
  61. 61. Linguistic Functioning Ontology(1. Speech and hearing)6565BFO:EntityBFO:Continuant BFO:OccurrentBFO:ProcessBFO:IndependentContinuantBFOMFOBFO:DependentContinuantBehaviourinducing stateCognitiveRepresentationBFO:QualitySpeech-mediatedcognitiverepresentationSpeechprocessBodily ProcessBFO:DispositionLinguisticcompetenceSpeech competence of apopulation= a [spoken] languageSpeech competence ofan individualHearing(registering)process
  62. 62. Linguistic Functioning Ontology(2. Reading and writing)6666BFO:EntityBFO:Continuant BFO:OccurrentBFO:ProcessBFO:IndependentContinuantBFOMFOBFO:DependentContinuantBehaviourinducing stateCognitiveRepresentationBFO:QualityWritten-language-mediatedcognitiverepresentationWritingprocessBodily ProcessBFO:DispositionLinguisticcompetenceWritten linguisticcompetence of apopulation= a [written] languageWritten linguisticcompetence of anindividualReading(registering)process
  63. 63. Linguistic Functioning Ontology(the whole thing)6767BFO:EntityBFO:Continuant BFO:OccurrentBFO:ProcessBFO:IndependentContinuantBFOMFOBFO:DependentContinuantBehaviourinducing stateCognitiveRepresentationBFO:QualityLanguage-mediatedcognitiverepresentationWritingBodily ProcessBFO:DispositionLinguisticcompetenceLinguistic competenceof a population= a language Linguistic competenceof an individualReadingSpeaking
  64. 64. Extending the MFO to mental disease68
  65. 65. 69
  66. 66. 70
  67. 67. Mental Functioning Ontology (MF)71brainendocrinegland
  68. 68. http://bioportal.bioontology.org/ontologies/49078/72Extending MFO toEmotions
  69. 69. need link to a physiology ontology 73‘physiological response to emotion’
  70. 70. 74‘emotionprocess’
  71. 71. Using the Emotion Ontologyfor self-report of emotional experiencesObjectives:• Capture emotional experiences in astandardised fashion using the underlyingvocabulary of the Emotion Ontology1. prediction of suicide via aggregation of textmessages2. evaluation of scientific conferences
  72. 72. View all presentations for conference
  73. 73. Select a presentation
  74. 74. Tag options available in tool
  75. 75. Studies of the biochemical basis ofemotionEmotions are effected in part byneurotransmitters such as dopamine, tryptophanThursday, May 02, 2013 82dopamine(CHEBI:25375)molecular entity(CHEBI:25375)biological role(CHEBI:24432)neurotransmitter(CHEBI:25512)has roleneurotransmitterreceptor activity(GO:0030594)Molecular function(GO:0003674)realized inhappiness(MFOEM:42)part ofemotion(MFOEM:1)subtype
  76. 76. Ontological traffic rule:to build an ontology of the types ofentities in a complex domain, focus firston the canonical instances83
  77. 77. Canonical pain & variantsPCT: pain with concordant tissue damage: pain ofthe evolutionarily most basic sort = pain inresponse to concordant tissue damageVariant painPNT: pain with peripheral trauma but discordant(elevated) relative to tissue damage: there isperipheral trauma, but the patient is experiencingpain of much too high an intensityNN: neuropathic nociception: no peripheraltrauma, but the patient is experiencing pain inresult of a neuropathic disorder in the nociceptivesystem.84
  78. 78. 85
  79. 79. Pain-related phenomena without painPBWP: pain behavior without pain: there is acry or report of pain, but no pain is beingexperienced (a fact which may or may not bedetectable by an external observer)TWP: Tissue-damage without pain: tissuedamage normally of the sort to cause pain doesnot activate the pain system.86
  80. 80. Pain Ontology (PN) branch of MF-EMLyingabout pain87
  81. 81. Canonical pain89canonicalpainpainEMOTION COMPONENT CHARACTERISTIC FOR PAINAction tendency WithdrawalSubjective emotional feeling Negative, tense, powerlessBehavioural response Characteristic painful facialexpressionCharacteristic appraisal Something is dangerous to me
  82. 82. Canonical fear91canonicalfearfearEMOTION COMPONENT CHARACTERISTIC FOR FEARAction tendency Fight-or-flightSubjective emotional feeling Negative, tense, powerlessBehavioural response Characteristic fearful facialexpressionCharacteristic appraisal Something (some real thing) inmy environment is dangerousto mesubtype
  83. 83. Canonical and non-canonical fearCanonical fear gives rise to action tendenciesthat are conformant to a perceived dangerPhobias = dispositions giving rise to non-canonical fear, e.g. laridaphobiaAnother case involving non-canonical fear:people taking pleasure in watching horror films92
  84. 84. mental process content (putative) targetpresenting act content of presentation“apple”object of presentationobjectexistsobject doesnot existobjectpresentobjectabsentMeinong’s treatment of non-veridicalintentionality goes wrong because ittreats it as canonicalthe presenting act is targeted on anobject of a special kind (namely: thenon-existent kind)
  85. 85. mental process content there is no targetpresenting act content of presentation“apple”underlying false beliefnon-veridical intentionality is a untidycollection of non-canonical casesthe presenting act is dependent on anunderlying belief or attitude of one orother deviant types
  86. 86. mental process content (putative) targetpresenting act content of presentation“apple”objectpresentobjectabsentnon-veridical intentionalitytype 1. ontological errorhallucination, deception, …the presenting act is dependent on afalse underlying belief
  87. 87. mental process content (putative) targetpresenting act content of presentation“apple”objectpresentobjectabsentnon-veridical intentionalitytype 2. fictionthinking-about-Macbeth = thepresenting act is not dependent onan underlying false belief“The Substitution Theory of Art”, Grazer Philosophische Studien, 25/26 (1986)
  88. 88. in the Macbeth case we are dealing withthe sort of thing that happens when, toquote Witters, “language goes onholiday”97
  89. 89. Brentano revolutionizes psychologyBrentanopublished Psychologyfrom an EmpiricalStandpoint, 1874Meinongfounded first laboratoryof experimentalpsychology in Austria-Hungary in 1897Ehrenfels Husserl Twardowskifounded firstlaboratory of experimentalpsychologyin Poland in 1907
  90. 90. Brentano revolutionizes psychologyBrentanopublished Psychologyfrom an EmpiricalStandpoint, 1874Meinongfounded first laboratoryof experimentalpsychology in Austria-Hungary in 1897Ehrenfels Husserl Twardowskifounded firstlaboratory of experimentalpsychologyin Poland in 1907Wundtfirst laboratory ofexperimental psychology,1879
  91. 91. Mental Functioning is Neural Functioning:Towards a Unified Ontology ofMind, Brain, and BehaviorGwen A. FrishkoffDepartment of Psychology NeuroInformatics CenterGeorgia State University University of Oregon
  92. 92. Outline of Talk• What is a mental process?– A view from cognitive psychology– The Mind–Brain problem and three proposedsolutions (ontology views)• A neurophsysiological framework forunderstanding mental processes– Levels of brain, levels of mind– What are mental representations “about”?(Proposed solution to problems of subjectivity, aboutness)
  93. 93. What is a Mental Process?A view from cognitive psychologyShort-term memoryCognitive controlMotor control,ActionSensation,PerceptionLong-term MemoryHabits & Skills
  94. 94. How do we know any of this?That is, where did the components of thestandard model come from?
  95. 95. • Mental processes cannot be observed.*• They must be inferred based on what we can observe.What can we observe?...*We can revise this assumption later (if Mind = Brain)The mind as a black boxX
  96. 96. • Physical processes in body  Behavior(response type, accuracy, reaction time)• Physiological processes in brain Neural activity and correlates of neuralactivity (blood flow to brain regions)What we can observe… and HowA schematic of Helmholtz’s apparatusfor measuring the time course ofmuscle contraction and thepropagation velocity of the nerveimpulse. Source: Bennett, 1999.A 256-channel electrode “net” that is usedto measure brain electrical activity (EEG)CogPO!
  97. 97. “A mental process is a neural process.”• Avoids Mind-Body dualism• More precise than other twosolutions• Gives ready framework forcomparative neurophysiology &comparative cognition• Knowledge of brain structure &function informs understandingof mental function (anddysfunction)ARGUMENTS IN FAVOR
  98. 98. Mental Functioning Ontology (MF)110braininendocrinegland
  99. 99. Aboutness111brain retinaENVIRONMENT
  100. 100. Levels of brain, levels of mindMesulam, 1990113Representation, monitoring andcontrol of internal environment(“self”)Representation, monitoring andcontrol of bodily interface toexternal environment(“real world”)
  101. 101. Levels of brain, levels of mindMesulam, 1990114Representation, monitoring andcontrol of internal environment(“self”)Representation, monitoring andcontrol of bodily interface toexternal environment(“real world”)Note use of “sneer” quotesaround “real world” and “self”
  102. 102. Mental representations: What are they “about”?Peripheral (sensory-motor) parts of the bodyare “mapped” to (represented by) an orderlyset of discrete regions within sensory andmotor cortex.Sensory-motor maps in thebrainThe Hypothalamic-Pituitary-Adrenal (HPA) Axismonitors and controls internal bodily functions, suchas blood circulation, breathing, digestion, stress, andarousal.Maps of the internal milieux
  103. 103. 116Perception ofinternal(bodily)environment(“self”)Perception ofexternalenvironment/sensory input(“real world”)
  104. 104. 117Shimon Edelman‟sRiddle of Representationtwo humans, a monkey, and a robotare looking at a piece of cheese;what is common to the representationalprocesses in their visual systems?
  105. 105. 118Answer:The cheese, of course
  106. 106. 119The real cheese
  107. 107. or objects or processesinside the body
  108. 108. or objects or processesinside the bodyobjects and processes inside andoutside the body play a role here too
  109. 109. external targetsinternal and external features causallyrelevant to perception, nociception, etc.allofthesetogetherformtheenvironment
  110. 110. externaltargetsinternal and external features causallyrelevant to perception, nociception, etc.the arrow of aboutness
  111. 111. What is a Mental Process?A view from cognitive psychologyShort-term memoryCognitive controlMotor control,ActionSensation,PerceptionLong-term MemoryHabits & SkillsAll of this is present before there is language
  112. 112. What does a temperature chartrepresent?147
  113. 113. 148606570758085Time 1 Time 2 Time 3What does a chart representing your pulse rate represent?
  114. 114. Cardiac Cycle, Left Ventricle149
  115. 115. 150606570758085Time 1 Time 2 Time 3What does a chart of changes in your pulse raterepresent?
  116. 116. 151139113921393139413951396139713981399What does a chart of changes in the DowJones industrial average represent?time
  117. 117. 152activity during thistime interval
  118. 118. 153
  119. 119. 15413911392139313941395139613971398time
  120. 120. 15513911392139313941395139613971398timeWhat this represents is real, and not just “real”
  121. 121. coronary heartdiseaseJohn’s coronary heart diseasedisease duringphase ofasymptomatic(‘silent’)infarctiondisease duringphase of earlylesions andsmall fibrousplaquesstableanginadisease duringphase ofsurfacedisruption ofplaqueunstableanginainstantiatesat t1instantiatesat t2instantiatesat t3instantiatesat t4instantiatesat t5time 156What this represents is real, and not just “real”
  122. 122. What did your temperature do over the lastmonth, Jim?Jim’s temperature process profile, thetarget of a certain sort of cognitiveselection, or cognitive profiling 157
  123. 123. The graph picks out just one dimension ofqualitative change within a much largerconglomerate of processes within JimHence ‘process profile’ 158
  124. 124. Compare perception of polyphonicmusic• Cognitive selection of the cello part when youlisten to a string quartet• Picking out a certain sonic partial processwithin a larger body of vibrations• Ignoring sneezes, coughs, …• (or sometimes focusing on sneezes andcoughs for diagnostic purposes)159
  125. 125. Compare perception of polyphonicmusic• Cognitive selection of the cello part when youlisten to a string quartet• Picking out a certain sonic partial processwithin a larger body of vibrations• Ignoring sneezes, coughs, …• (or sometimes focusing on sneezes andcoughs for diagnostic purposes)160
  126. 126. time-series graph of acousticsignal, spectrogram, formants, jawdisplacement and other speech parameters161
  127. 127. adding phonetic, phonemic and syllable levels162
  128. 128. g u t e n163
  129. 129. add brain164
  130. 130. speech is a process profilethe speech process is to the totality of acousticsignal, spectrogram, formants, jawdisplacement, mental and neurologicalprocessesasthe pulse rate process is to the totality ofaortic, ventricular and atrialpressure, ventricular volume, electricalactivity, arterial flow, and other processes in theheart165
  131. 131. Breakthrough: First sound recordings based on readinghuman auditory cortex (PLoS Biology, January 2012)166
  132. 132. Top: spectrogram of words presented to subject.Middle and bottom: reconstructions of speech based onreadings from electrodes attached to patients brain.167
  133. 133. PathwaydiagramPathwayReactionMolecularcollectiveIndividualmoleculeBFO:ProcessBFO:IndependentContinuantBFO:DispositionInformationContent Entityinheres inexplicitlyrepresentsimplicitlyrepresentshas participantBULKMOLECULARhas grainBFO: GDCbiological pathways are process profiles
  134. 134. mental processes, too, are process profiles169
  135. 135. 177177BFO:EntityBFO:Continuant BFO:OccurrentBFO:ProcessBFO:IndependentContinuantBFOMFOBFO:DependentContinuantBehaviourinducing stateCognitiveRepresentationBFO:QualityLanguage-mediatedcognitiverepresentationWritingBodily ProcessBFO:DispositionLinguisticcompetenceLinguistic competenceof a population= a language Linguistic competenceof an individualReadingSpeakingwhat is a language?something analogous to a biologicalspecies (a population of competences)
  136. 136. • Examples of dispositions that are constantlybeing realized:– stock exchange– heart beat– brain activity– social order– language (social)178
  137. 137. Investigations onthe Theory ofObjects andPsychologywith support fromthe Imperial-RoyalMinister of Cultureand Education inVienna, 1904
  138. 138. Horizontal Integration of WarfighterIntelligence Data180
  139. 139. Horizontal Integration• “Horizontally integrating warfighterintelligence data … requires access (includingdiscovery, search, retrieval, and display) tointelligence data among the warfighters andother producers and consumers viastandardized services and architectures.”Chairman of the Joint Chiefs of StaffInstruction J2 CJCSI 3340.02A1 August 2011
  140. 140. Horizontal integration=def. multiple heterogeneous data resourcesbecome aligned in such a way that search andanalysis procedures can be applied to theircombined content as if they formed a singleresource
  141. 141. UnclassifiedUnclassifiedCommand and Control OntologyArmy Fires PlanArmy Maneuver PlanNaval Fires PlanDefinition: An informationcontent entity that is aspecification of events that areto occur in order to obtain someobjective.183
  142. 142. UnclassifiedUnclassifiedCommand and Control OntologySituationalAwarenessSituationalUnderstandingCommander‟s Intent…184
  143. 143. Horizontal integration=def. multiple heterogeneous data resourcesbecome aligned through association withcommon ontology terms in such a way thatsearch and analysis procedures can be appliedto their combined content as if they formed asingle resource
  144. 144. =def. multiple heterogeneous data resourcesbecome aligned through association withcommon ontology terms in such a way thatsearch and analysis procedures can be appliedto their combined content as if they formed asingle resourceSemantic Technology in Intelligence, Defense and Security, 2012

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