Motivation: This paper extends Röhl & Jansen's (2011) model of dispositions by introducing a ... more Motivation: This paper extends Röhl & Jansen's (2011) model of dispositions by introducing a relation of parthood between dispositions to formalize multi-track dispositions. Results: We suggest axioms for parthood relations between dispositions and discuss possible applications to life sciences.
Frontiers in Artificial Intelligence and Applications
Belief, desire, and intention are central notions in mentality and agency. We provide conceptual ... more Belief, desire, and intention are central notions in mentality and agency. We provide conceptual and formal foundations for an ontology of those mental entities. In this framework, beliefs and desires have a dual face: dispositional and occurrent. As distinct from beliefs and desires, intentions are dispositions to actions that emerge from a decision process in which occurrent beliefs and occurrent desires interact. We also discuss how our theory can be extended to some major philosophical accounts of desires, and cognitive biases such as wishful thinking.
Le risque est une entité omniprésente dans le domaine biomédical. Une caractérisation ontologique... more Le risque est une entité omniprésente dans le domaine biomédical. Une caractérisation ontologique cohérente du risque est donc nécessaire pour faciliter l'échange et le rassemblement des données informatiques du domaine biomédical à des fins cliniques et des fins de recherche à l'aide d'outils nommés « ontologies appliquées ». Nous analysons certaines définitions du risque et en tirons deux traits généraux que le risque partage avec les dispositions. Nous proposons par conséquent une définition du risque comme une disposition dont la réalisation est indésirable pour un agent. Cette définition permet de concilier la dimension objective et la dimension subjective du risque : un risque existe indépendamment de notre connaissance de celui-ci, mais le statut de risque d'une disposition pour un agent dépend des préférences de cet agent.
The medical world is replete with documents that ontologies can help to analyze and disambiguate.... more The medical world is replete with documents that ontologies can help to analyze and disambiguate. This paper provides a mereological analysis of such documents as structured by informational slots and fillers, completing recent work by our teams inspired by Bennett. It introduces the notion of adequate filling of a document’s slot, and the representation of the layered structure of a document. An application is provided on the Prescription of drugs ontology (PDRO).
Informational entities, such as words, can be used not only to make statements about the world, b... more Informational entities, such as words, can be used not only to make statements about the world, but also to direct actions. This happens when they describe actions, and those actions are then performed by some agents on the basis of this description. This paper investigates the characteristics of the relation of directedness and compliance and distinguishes between attempted, successful and maximal direction. It discusses the case when directive entities are synonymous or specialize one another.
Background The advent of learning healthcare systems (LHSs) raises an important implementation ch... more Background The advent of learning healthcare systems (LHSs) raises an important implementation challenge concerning how to request and manage consent to support secondary use of data in learning cycles, particularly research activities. Current consent models in Quebec were not established with the context of LHSs in mind and do not support the agility and transparency required to obtain consent from all involved, especially the citizens. Therefore, a new approach to consent is needed. Previous work identified the meta-consent model as a promising alternative to fulfill the requirements of LHSs, particularly large-scale deployments. We elicited the public’s attitude toward the meta-consent model to evaluate if the model could be understood by the citizens and would be deemed acceptable to prepare for its possible implementation in Quebec. Methods Eight focus groups, with a total of 63 members of the general public from various backgrounds were conducted in Quebec, Canada, in 2019. E...
Affordances and image schemas are two building blocks of cognitive and behavioral modeling. In th... more Affordances and image schemas are two building blocks of cognitive and behavioral modeling. In this paper, we present initial steps towards an extension of our dispositional view of affordances and effectivities to image schemas. In particular, we consider image schemas as mental patterns that are, in most cases, about classes of affordances and effectivities.
QUESTO is an ontology formalizing questionnaires and related entities, such as the processes of a... more QUESTO is an ontology formalizing questionnaires and related entities, such as the processes of administering the questionnaire or capturing the answers. It is built according to the OBO Foundry methodology and is a component of an ontological model that aims to enable interoperability between various clinical data sources in the context of a Learning Health System. This article presents the main entities of QUESTO and provides an example of its application: a relational data model is generated from the ontology and used to retrieve data from public health questionnaires stored in a REDCap database.
An analysis based on referent tracking systems shows that a classical medical application of bite... more An analysis based on referent tracking systems shows that a classical medical application of bitemporalized relational database that uses classes as attribute values is ambiguous in several respects. This suggests that to avoid such ambiguities, bitemporalized relational databases could be structured on the basis of ontological representations that give adequate attention to particulars.
LABO is an ontology formalizing laboratory test prescriptions and reporting documents. It is buil... more LABO is an ontology formalizing laboratory test prescriptions and reporting documents. It is built according to the OBO Foundry methodology, and is a component of a core ontological model that aims to enable interoperability between various clinical data sources in the context of a Learning Health System. This article presents LABO, distinguishing between directive entities and data items, and using the relations directs and is about to represent their connections with the relevant laboratory test processes.
A property particular is a particular that characterizes the satisfaction of a property by an obj... more A property particular is a particular that characterizes the satisfaction of a property by an object, for example the ‘redness’ of a specific rose. We consider three theories of identity for property particulars, illustrating them on a common example. We discuss their strengths and weaknesses, and whether they can be interpreted in an epistemic or realist perspective. We introduce some first steps of a theory of reification of property types and discuss the benefits that it could bring.
Clear criteria for the identity of dispositions are still lacking, and this has been presented as... more Clear criteria for the identity of dispositions are still lacking, and this has been presented as one of the main challenge raised by such entities. It is of prime importance to identify or distinguish dispositions such as diseases or risks. This article first introduces conventional ways to refer to a disposition (such as “fragility”) and canonical ways (such as “disposition to break in case of a strong shock”). This raises the issue of how should exactly be defined a “disposition d to R when TR”, where R is a realization specification and TR a trigger specification. Two ontological frameworks are distinguished. The first framework, which has been largely used so far in the literature on dispositions, interprets d as a disposition which can only be triggered by instances of TR, and can only be realized by instances of R. The second, new framework introduces the notion of “minimal trigger” and “maximal realization”, and interprets TR as a parent class of a class of processes that ha...
We present a formalization of indicators of diagnostic performance (sensitivity, specificity, pos... more We present a formalization of indicators of diagnostic performance (sensitivity, specificity, positive predictive value and negative predic-‐ tive value) in the context of a realist ontology. We dissociate the indica-‐ tors of diagnostic performance from their estimations and argue that the former should be represented in a first place in biomedical ontolo-‐ gies. Our formalization does not require to introduce any possible, non-‐actual entities -‐ like the result a person would get if a medical test would be performed on her -‐ and is therefore acceptable in an ontology built in a realist spirit. We formalize an indicator of diagnostic perfor-‐ mance as a data item that is about a disposition borne by a group; the diagnostic value of this indicator is given by the objective probability value assigned to this disposition.
We investigate how probabilities can be assigned to dispositions in ontologies, building on Poppe... more We investigate how probabilities can be assigned to dispositions in ontologies, building on Popper's propensity approach. We show that if D is a disposition universal associated with a trigger T and a realization R, and d is an instance of D, then one can assign a probability to the triplets (d,T,R) and (D,T,R). These probabilities measure the causal power of dispositions, which can be defined as limits of relative frequencies of possible instances of T triggering an instance of R over a hypothetical infinite random sequence of possible instances of T satisfying certain conditions. Adopting a fallibilist methodology, these probability values can be estimated by relative frequencies in actual finite sequences.
We propose a taxonomy of mereological relations between dispositions, as well as a series of axio... more We propose a taxonomy of mereological relations between dispositions, as well as a series of axioms relating the bearers, triggers or realizations of disposition-complexes and disposition-parts. We apply them on a use case to show how basic dispositions can be combined to express elaborate dispositions. We consider whether those relations of partial ordering satisfy axioms of composition and decomposition.
Belief, desire, and intention are central notions in mentality and agency. We provide conceptual ... more Belief, desire, and intention are central notions in mentality and agency. We provide conceptual and formal foundations for an ontology of those mental entities. In this framework, beliefs and desires have a dual face: dispositional and occurrent. As distinct from beliefs and desires, intentions are dispositions to actions that emerge from a decision process in which occurrent beliefs and occurrent desires interact. We also discuss how our theory can be extended to some major philosophical accounts of desires, and cognitive biases such as wishful thinking.
Motivation: This paper extends Röhl & Jansen's (2011) model of dispositions by introducing a ... more Motivation: This paper extends Röhl & Jansen's (2011) model of dispositions by introducing a relation of parthood between dispositions to formalize multi-track dispositions. Results: We suggest axioms for parthood relations between dispositions and discuss possible applications to life sciences.
Frontiers in Artificial Intelligence and Applications
Belief, desire, and intention are central notions in mentality and agency. We provide conceptual ... more Belief, desire, and intention are central notions in mentality and agency. We provide conceptual and formal foundations for an ontology of those mental entities. In this framework, beliefs and desires have a dual face: dispositional and occurrent. As distinct from beliefs and desires, intentions are dispositions to actions that emerge from a decision process in which occurrent beliefs and occurrent desires interact. We also discuss how our theory can be extended to some major philosophical accounts of desires, and cognitive biases such as wishful thinking.
Le risque est une entité omniprésente dans le domaine biomédical. Une caractérisation ontologique... more Le risque est une entité omniprésente dans le domaine biomédical. Une caractérisation ontologique cohérente du risque est donc nécessaire pour faciliter l'échange et le rassemblement des données informatiques du domaine biomédical à des fins cliniques et des fins de recherche à l'aide d'outils nommés « ontologies appliquées ». Nous analysons certaines définitions du risque et en tirons deux traits généraux que le risque partage avec les dispositions. Nous proposons par conséquent une définition du risque comme une disposition dont la réalisation est indésirable pour un agent. Cette définition permet de concilier la dimension objective et la dimension subjective du risque : un risque existe indépendamment de notre connaissance de celui-ci, mais le statut de risque d'une disposition pour un agent dépend des préférences de cet agent.
The medical world is replete with documents that ontologies can help to analyze and disambiguate.... more The medical world is replete with documents that ontologies can help to analyze and disambiguate. This paper provides a mereological analysis of such documents as structured by informational slots and fillers, completing recent work by our teams inspired by Bennett. It introduces the notion of adequate filling of a document’s slot, and the representation of the layered structure of a document. An application is provided on the Prescription of drugs ontology (PDRO).
Informational entities, such as words, can be used not only to make statements about the world, b... more Informational entities, such as words, can be used not only to make statements about the world, but also to direct actions. This happens when they describe actions, and those actions are then performed by some agents on the basis of this description. This paper investigates the characteristics of the relation of directedness and compliance and distinguishes between attempted, successful and maximal direction. It discusses the case when directive entities are synonymous or specialize one another.
Background The advent of learning healthcare systems (LHSs) raises an important implementation ch... more Background The advent of learning healthcare systems (LHSs) raises an important implementation challenge concerning how to request and manage consent to support secondary use of data in learning cycles, particularly research activities. Current consent models in Quebec were not established with the context of LHSs in mind and do not support the agility and transparency required to obtain consent from all involved, especially the citizens. Therefore, a new approach to consent is needed. Previous work identified the meta-consent model as a promising alternative to fulfill the requirements of LHSs, particularly large-scale deployments. We elicited the public’s attitude toward the meta-consent model to evaluate if the model could be understood by the citizens and would be deemed acceptable to prepare for its possible implementation in Quebec. Methods Eight focus groups, with a total of 63 members of the general public from various backgrounds were conducted in Quebec, Canada, in 2019. E...
Affordances and image schemas are two building blocks of cognitive and behavioral modeling. In th... more Affordances and image schemas are two building blocks of cognitive and behavioral modeling. In this paper, we present initial steps towards an extension of our dispositional view of affordances and effectivities to image schemas. In particular, we consider image schemas as mental patterns that are, in most cases, about classes of affordances and effectivities.
QUESTO is an ontology formalizing questionnaires and related entities, such as the processes of a... more QUESTO is an ontology formalizing questionnaires and related entities, such as the processes of administering the questionnaire or capturing the answers. It is built according to the OBO Foundry methodology and is a component of an ontological model that aims to enable interoperability between various clinical data sources in the context of a Learning Health System. This article presents the main entities of QUESTO and provides an example of its application: a relational data model is generated from the ontology and used to retrieve data from public health questionnaires stored in a REDCap database.
An analysis based on referent tracking systems shows that a classical medical application of bite... more An analysis based on referent tracking systems shows that a classical medical application of bitemporalized relational database that uses classes as attribute values is ambiguous in several respects. This suggests that to avoid such ambiguities, bitemporalized relational databases could be structured on the basis of ontological representations that give adequate attention to particulars.
LABO is an ontology formalizing laboratory test prescriptions and reporting documents. It is buil... more LABO is an ontology formalizing laboratory test prescriptions and reporting documents. It is built according to the OBO Foundry methodology, and is a component of a core ontological model that aims to enable interoperability between various clinical data sources in the context of a Learning Health System. This article presents LABO, distinguishing between directive entities and data items, and using the relations directs and is about to represent their connections with the relevant laboratory test processes.
A property particular is a particular that characterizes the satisfaction of a property by an obj... more A property particular is a particular that characterizes the satisfaction of a property by an object, for example the ‘redness’ of a specific rose. We consider three theories of identity for property particulars, illustrating them on a common example. We discuss their strengths and weaknesses, and whether they can be interpreted in an epistemic or realist perspective. We introduce some first steps of a theory of reification of property types and discuss the benefits that it could bring.
Clear criteria for the identity of dispositions are still lacking, and this has been presented as... more Clear criteria for the identity of dispositions are still lacking, and this has been presented as one of the main challenge raised by such entities. It is of prime importance to identify or distinguish dispositions such as diseases or risks. This article first introduces conventional ways to refer to a disposition (such as “fragility”) and canonical ways (such as “disposition to break in case of a strong shock”). This raises the issue of how should exactly be defined a “disposition d to R when TR”, where R is a realization specification and TR a trigger specification. Two ontological frameworks are distinguished. The first framework, which has been largely used so far in the literature on dispositions, interprets d as a disposition which can only be triggered by instances of TR, and can only be realized by instances of R. The second, new framework introduces the notion of “minimal trigger” and “maximal realization”, and interprets TR as a parent class of a class of processes that ha...
We present a formalization of indicators of diagnostic performance (sensitivity, specificity, pos... more We present a formalization of indicators of diagnostic performance (sensitivity, specificity, positive predictive value and negative predic-‐ tive value) in the context of a realist ontology. We dissociate the indica-‐ tors of diagnostic performance from their estimations and argue that the former should be represented in a first place in biomedical ontolo-‐ gies. Our formalization does not require to introduce any possible, non-‐actual entities -‐ like the result a person would get if a medical test would be performed on her -‐ and is therefore acceptable in an ontology built in a realist spirit. We formalize an indicator of diagnostic perfor-‐ mance as a data item that is about a disposition borne by a group; the diagnostic value of this indicator is given by the objective probability value assigned to this disposition.
We investigate how probabilities can be assigned to dispositions in ontologies, building on Poppe... more We investigate how probabilities can be assigned to dispositions in ontologies, building on Popper's propensity approach. We show that if D is a disposition universal associated with a trigger T and a realization R, and d is an instance of D, then one can assign a probability to the triplets (d,T,R) and (D,T,R). These probabilities measure the causal power of dispositions, which can be defined as limits of relative frequencies of possible instances of T triggering an instance of R over a hypothetical infinite random sequence of possible instances of T satisfying certain conditions. Adopting a fallibilist methodology, these probability values can be estimated by relative frequencies in actual finite sequences.
We propose a taxonomy of mereological relations between dispositions, as well as a series of axio... more We propose a taxonomy of mereological relations between dispositions, as well as a series of axioms relating the bearers, triggers or realizations of disposition-complexes and disposition-parts. We apply them on a use case to show how basic dispositions can be combined to express elaborate dispositions. We consider whether those relations of partial ordering satisfy axioms of composition and decomposition.
Belief, desire, and intention are central notions in mentality and agency. We provide conceptual ... more Belief, desire, and intention are central notions in mentality and agency. We provide conceptual and formal foundations for an ontology of those mental entities. In this framework, beliefs and desires have a dual face: dispositional and occurrent. As distinct from beliefs and desires, intentions are dispositions to actions that emerge from a decision process in which occurrent beliefs and occurrent desires interact. We also discuss how our theory can be extended to some major philosophical accounts of desires, and cognitive biases such as wishful thinking.
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Papers by Adrien Barton