sexta-feira, 19 de julho de 2024

FOIS'24 - Ontology Engineering Session

A Textual Syntax and Toolset for Well-Founded Ontologies
Matheus L. Coutinho, João Paulo Almeida, Tiago Prince Sales and Giancarlo Guizzardi

Idea behind Tonto:
- Easier to read syntax, like programming language
- Text-based specification to cope with git-like mechanisms
- Dual-channel processing theory Textual+Visual= Enhanced comprehension

- Better version control - Easier modularization Tonto Editor:
- java-like syntax
- you can declare concepts, properties and relations
- you can change the text specification and have a visual (diagramatic) view of the changes in the ontology
- they use colors for the different types of elements (stereotypes), both in the text and in the diagram
- you can use some validators: e.g., a semantic-motivator syntatic validator
- they created a package manager to support modularization

Integration with OntoUML server and ontouml-js
- JSON generation cmpliant to OntoUML Schema
- importing JSON to Visual Paradigm
- Importing JSON to Tonto
- Model validation
- Transformation to UFO-based OWL.

Keynote@FOIS'24 - Stop Data Sharing - Barend Mons

Big data:
Volume - Variety - Velocity
Volume: 10^14 assertions of the type S-P-O

Sensitive data - Privacy
E.g., Data about tigers in China would lead tigers to extinction

He is working with Giancarlo, Luiz Olavo and others to constrain LLMs to avoid and explain hallucinations.

Genome project - Researchers working on the genome of humanity needs very sensitive data. So people in Africa tell him: "You want our data? Come visit us!".
- If you use LLM here, you will get the knowledge that is already out there, so that's not what you need.
FAIR (and the FAIR Train Architecture) supports the inauguration of the data visiting paradigm. The data stays where it belongs (with its owner/controller) and the algorithms travel and process the data according to specific protocols and permissions.
How to approach Data Governance:
How Knowlets can help srinking the volume of big data:
The concept of qua individual helps us solve the problem of near-seameness.
The importance of near-sameness provided by Knowlets:
There are many applications for machines in which we would never be able to calculate or find information alone. So machine readable data can allow us to do researchers in Biology that we would never be able to do before, due to its processing capacity. It is cognitively impossible for us to gather, find and process so much information, and machines do that in a few seconds.
He has rescently started an institute part of the Univ. of Leiden (and having Univ. of Twente as co-founder) to do research in this topic.
Here is how research is made:
FAIR Library of Instructions:
How FAIR works:
There are many countries interested in creating institutes such as LIFES and work together with he in this initiative (some of these contacts come from initiative in which he participates)
Making ethical and legal constraints machine-readable. This way, machines (even not understanding what ethics means) know where to stop. Then you can add in the data station a list of ethical constraints and before the algorithm enters the station, the station needs to make sure that these constraints are met.

Ontological precision is very, very important. But it does not need to be perfect, since the world is vague and we like it that way. So let's work on ontologies, but forget about going the last extra miles.

quinta-feira, 18 de julho de 2024

Keynote@FOIS'24 - Where to locate the explainability of explainable machine learning? By Mieke Boon

New title: Exploring AI/MLR Epistemology
Epistemology 16th-17th century
- Rationalism - Rene Descartes
- Empiricism - Francis Bacon

Thinking about Empiricism (which resembles ML processes), there were criticism:

Hume (1748) An enquiry concerning Human Understanding
Threre are fundamental problems:
- induction: the principle of induction is logically invalid;
- causality: causal connection, e.g., the power, cannot be observed.

Practical example of (lack of) causality:
Further developments in Empiricism:
Problems with ML empiricism:
Problem 1 - If you look for patterns in the data, you will find them (even if there is no causation)
Problem 2 - Need for explanations

How does (Logical) empriicism solve the problem of explanation? - without causes or mechanism (anti-metaphysics)

The way it is looked at today in ML, explanations are similar to what we do in the lab: this variable has a lot of effect in the result, while this one does not. Problem 3 - It denies the epistemic and pragmatic value of (causal)-mechanistics explanation: explanations of regularities.
Philosophers of science criticize empiricist epistemology and aim at solutions
- Alternative epistemology should answer: what is a real law? How do we know that a mathematical structure or statically relevant correlation found in the data is a real law? Response: iff there is a mechanism that explains the law.
- the mechanism thus makes the law intelligibel - i.e., it explains the law
- human reasoning in science: rather than identifying laws, researchers explain by constructing a model of the underlying mechanism.

Kant's epistemology (18th centruy) : concepts + power of jusdgement Kant reconciled and transcended the rationalist and empiricist epistemologies. by providing an alterrnative to the traditional questions of: what is the baseis of true knowelge? how can we be certain?
Kant's questions: How is it possible that we have knoweldge of the world? What are the conditions for the possibility of having knowelvge anyway?

Kant claims:
- Man himself creates all his respresnetations and concepts. - Concepts as conditions for the posbiiility of having anc crating knowlefge about reality. withouth these concepts, we would not be albe to make any staetemnt about reality on the bases of mere observations.
- Perceptions without concepts are empty; concepts without perceptions are blind.
- Kant considers the crucial and intellegcuatl role of human in creating concepts.
Kantian Epistemology => Conceptual Modeling

She presents a High school level in which conceptual modeling precedes mathematical modeling:
Kant:
Concepts (verstand) + power of judgement (urteilskraft) - meaning, values appreciation / emotion.

How do we make sure the model is a good representation of the world?
- Picture of the pope is a good model of the Pope.
- ... But not of Trump
However, Trump is also seating in a chair in the same position as the pope! So, in the world, a model can be similar to the world in many different ways.

In summary...

FOIS'24 Session on Domain and Core Ontologies

OnNER: An Ontology for Semantic Representation of Named Entities in Scholarly Publications
Umayer Reza, Xuelian Zhang and Torsten Hahmann

What Named Entity Recognition is:
Competency Questions guiding this work:
The proposed graph:
How to query the graph:


The Common Core Ontologies
Mark Jensen, Giacomo De Colle, Sean Kindya, Cameron More, Alex Cox and John Beverley

Origins:
- Created at CUBRC and UB as part of the IARPA Knowldge, Discovery and Dissemination Program (2010-2015)
- CCO was open sourced in 2017

What is CCO?
- CCO is comprised of 11 ontologies that jointly provide a mid-level architecture for resue and extension.
- CCO refers to a suite
- CCO is a referecne for representing common things to all domains
- It is appication agnostic.

What kind of concept is in CCO?
In 2023, they created a governance committee to take care of CCO. Their responsibility is to engage key stakeholders, improve logistics, improve visibility, transparency, access, supporting the creation of IEEE SA Open Standard for mid-level ontologies.
There is a UB NCOR CCO working group - johnbeve@buffalo.edu. Representing Energy in the Midlevel Energy Ontology (MENO)
Mirjam Stappel and Fabian Neuhaus

Bearers of energy
In MENO, energies are qualities. Material entities can be bearers of quality

What is energy?
MENO Ontology:
Interesting take aways:

FOIS'24 Session: Ontological Analysis

Ontological Analysis of Money
Riichiro Mizoguchi, Stefano Borgo and Yoshinobu Kitamura

Using three basic theories obtained int he FOIS community: Representation, Physical objects and Roles
Agreed thesis - money is something possessing:
- unit of economic value,
- exchangeability with commodities and
- storability.

He tries to respond the U. Maki's 12 core questions about money inthis work

Take John Searle's thesis: Money is an institutional status that is imposed on physical objects.
There is a serios criticism about this view: it doesnt apply to digital numbers ian a bank account. They seem to be non-physical and mre records to cash.
FOIS theory 01:
FOIS theory 02:
FOIS theory 03:
Definitions
Monetary role: solial role in the context of an economic systems and it is characterized by : unit, exchangeability relation, storability quality and trust of a community.
Legitimate representing thing: medium enriched with form, a content and an encoding method.
Monetary ojbect (Currency)
Money is a (non-intrinsic) property of the owner of monetary objects

His model is composed of three layers: 1) representation layer, 2) role layer and 3) property layer

Money as quantity: use value vs. exchange value.

Answers to Maki's core questions:

Ontological Analysis of Malfunctions: Some Formal Considerations
Francesco Compagno and Stefano Borgo
Malfunction: if you have a theory of causation, it makes it much easier to define malfunction.
Literature (Rasmussen and Jensen 1974)
Ontological view (Del Frate 2012):
- Function-based failure
- Specification-based failure
- Material-based failure

According to Del Frate:
- faults are often said to be state (events) that are caused by a faiure (bring about a fault);
- failure modes are often describe either as specific parts of a causal chain (consequence of a cause and cause of an effect) at a specific granularity level, or as symptoms immediately perceivable of a malfunction;
- causes are either immediate causes, when they are superficial/apparent, or root causes, when they are deep/definitive/true.

This work is based on the Toyoshima's causal otnology (Toyoshima, Mizoguchi, ,and Ikeda 2019). to buiild a formal taxonomy of malgfucntion-related happenings.
Important to consider:
Taxonomy:
Key points of this talk:
Unpacking the Semantics of Risk in Climate Change Discourses
Greta Adamo, Anna Sperotto, Mattia Fumagalli, Alessandro Mosca, Tiago Prince Sales and Giancarlo Guizzardi

Motivation: Climate change is happening now. This impact human safety and health, besides the ecosystem. There is lack of knowledge in this area, specifically related to climate-related changes and extreme events.
There is a lot of impact of climate change and the extreme events affect the world in an uneven way. The scenario is very complex

Intergovernmental Panel on Climate Change (IPCC)
Problems in the IPCC glossary (definitions of riks and related concepts, such as hazard, explosure and vulnerability):
- common sense form
- unclear semantics and ambiguous communication
- chanigng through years
- innefective for operational purpose (too theory-based)
Objective of the work: ontological clarification.
For that, this work adopts COVER - Common Ontology of Value and Risk.
She explained the main concepts in COVER. Definition
Ontological unpacking:
- hazard (i.e., a threat event) is a natural anthropogenic event that is likely to cause a loss event.
- exposure is a situation in which objects at risk valuable to agents might be negatively affected by the occruene of hazards
- vulnerability is a disposition whose manifestation constitutes a threat event or loss event. It may inhere in objects at risk or risk enablers.
Ontological unpacking (cont.):
- She defined impact according to COVER/UFO (read definition in the paper).

- Value in IPCC is both a (UFO) belief and a (COVER) value.
Ontological unpacking (cont.2):
Conclusions and Future Work:
- extending the analysis, for example by considering dynamic interactions of hazard, exposure, and vulnerability under a risk progpagation lens.
- sharpening shcallenging notions, such as vulnerabiltiy and value;
- considering and comparing related notions, as resilience
- extension of cover for limate change risk
- modeling climaget change risk with stakeholders.

quarta-feira, 17 de julho de 2024

FOIS'24 Showcase

Extending the Common Greenhouse Ontology with Incident Reporting from Autonomous Systems
Tim Eichhorn, Ghusen Chalan, Simon van Roozendaal, Jens Reil, Tim van Ee, João Moreira and Tiago Prince Sales

Context of this research: TNO Farming Project Objectives
Main problem: Lack of uniformity in the terms regarding greenhouse production.
They decided to extend the Greenhouse Ontology to solve this problem.

There are two robots used in production that they use in this research (these systems need to collaborate):
Honest Agtest System
Ridder CoRanger

Problem Statement
Lack of semantics for robot instructions and actions
limited localization and nvaigation capability
inneficient communication and coordination
limited interoperability and collaboration between the greenshoues
need for an estension and or a software tool

Objectives of their research: Semantic Explanation and Navigation System

He briefly showed the content of the data sets of both robot systems, referring to their positions (althogh the CoRanger is less precise), and obstacles in the greenhouse map.

He showed the ontology they created by extending the Greenhouse Ontology.
TNO uses the Unified Robot Description Format (URDF) and so the authors decided to adopt this format as well, so that it may facilitate a CGO-Robot extension, including other robots of interest of TNO in the future.

They only did a preliminary validation with data, but not really putting it to work in the robots. So they need to do further validations in the near future. Moreover, their research agenda also includes the CGO Robot extension.

A Domain Reference Ontology for Design Sicence Research Knowledge Bases
Jean Paul Sebastian Piest, Victor Benoiston, Jales de Oliveira, Patrício de Alencar Silva and Manoel Ricardo da Cunha Junior

Sebastian's Thesis Title: A Design Science Research Knowlege Base for Intelligence Amplification

Related Works: - (Gergor and Hevner) DSR KB Framework is an important related work for him.
Limitation: DSR KBs need to integrate different positions and perspective regarding ontology and epistemology.

- Gass et al. SLR on DSR KBS Contents

Limitation: No consensus regarding...
- Vom Brocke et al. 6 Modes for using Design Knowledge in DSR
Limitation: Most DSR projects focus on fitness for use and not on fitness for evolution.
Motivation: faciliate cumulative developmenf o design knowledge through a domain reference ontology on DSR KBs. A goal is to enable reuse.

They apply the SABIO Ont.Engineering Methodology for the development of the ontology. The ontology reuqirements specification document is included in the paper.

Coneptual models he created:
- Agent taxonomy and DSR projects: The Agent taxonomy and DSR is the basic model, composed of the core concepts on DSR.
- Types of Knoweldge: For the Types of Knowledge model, he used Gass's taxonomy. This model is important for enabling reuse of knowledge.
- Design theorizing: Gregory and Jones' work was used as basis for the Design theorizing model.
- Cases and applications: The last model is the simplest model but it is extandable.

He implemented and populated the ontology. Then, he tested if he was able to respond to the competency questions.

He has everything available on GitHub so it is all open for access.

He is now working on the validation of the developed conceptual models. Some validation studies have been completed and others are underway. He is also implementing an interactive KB to respond to queries about DSR. For future work, he wants also to target an interface to suport this.

Keynote@FOIS'24 - Ontologies for Machine Learning - Frank van Harmelen

Intro
AI seems to be a tale of two towers: the Statistical AI tower vs. the Symbolic AI tower
It seems more like a religion, "you don't want to read the other's books because they are wrong anyway".

But he wants to put these two towers together.

It is important to note that ML work is extremely unaware of ontology work. They are now learning about simple things we already know (e.g., about types)

In this talk, he is going to give examples from the literature where ontologies are solving problems in ML contexts.

Hard problems in ML
ML is not:
- Explainable
- Generalisable: Generalisation is good only for the data similar to the one for which they train
And ML is:
-Data Hungry: Data sparcity - data acquisition bottleneck
- Black box
- (they have a) Performance Cliff

He uses a graphical notation to talk about ML systems

Synmbol or data

Conditions to be a synbol according to What the -0.70, 1.17, 0.99, 1.07- is a Symbol?, Istvan Berkeley, Minds and Machines, 2008
1. A symbol must designate an object, a class or a relation in the world (= the interpretation of a symbol)
2. symbol can either be atomic or complex (=composed of other symbols according to compositional rules)
3. there must be a system of operations that, when applied to a symbol, generates another sybol that again could have a designation.

Examples

Example 1:
He gives an example to explain how ontology can help solve the problem of semantic loss-function. How can a ML understand the difference between a flower and a cushion with flowers in it. The system should see that if this is attached to a chair and that cushions may have flowers in it, the probability that the object is a cushion is higher than a flower. And if the ontology shows the relation between cushion and chair and the ML recognizes the chair, then they know that the object is a cushion.

Example 2:
Informed ML using KR. An ontology can give the background knowledge you need to guide the final neural network (NN) layer. Example of the photo of Queen Elizabeth in which the system gave a 99% answer saying the object in her head was a showercap. But if they know what queens usually wear in public, then the NN would know that the object is a crown. The ontology helps to provide justification/explanation for the response.
In this case, the ontology is not involved in the prediction, but afterwards in the justification.
There is a mistake now on how the ML communicty looks for explanations (by undesrstanding how the NN arrived at the result), because people will not be interested in understanding how the NN arrived at the result, but they require a plausible explanation for why that result is correct.

Example 3:
Learning intermediate abstract for learning. He shows an example in wich the authors proposes an architecture composed of two agents: a Neural Back End and a Symbolic Backend. Comparing the performance of the two, the symbolic agent did much better because by the time the neural agent learned about the world, then the world had already changed.

Example 4: he gave an example of early cancer diagnosis. In this example, ontology provides intermediate abstraction. Try to learn early symptoms of CRC from GP data (symbol, life style, diagnosis, drugs)

1. Raw data: no meaningful signal
2. Raw data + snomed = abstracted data: significant results.
Predictive modeling of colorectal cancer using a dedicated pre-processing pipeline on routine electronic medical records, R. Kop et al.

About LLMs...
LMMs Modulo
LLMs can't calculate, but they can learn when to call a calculator.
LLMs can't do formal ontological derivations, but they can learn when to call an reasoner.

The Vienna Study: looked in 300+ semantic web systems to understand the role of the ontology in these studies
- Clean the data
- Abstract the data
- Explain the results
- Guide the search
- etc.

Open Questions
We know that domain ontology can help ML, how about foundational ontologies?
- invariance to time, space, roles
- improve out-of-distribution generalization

What ontological representation languages are suitable to interfact with ML
- differentiate vs. discrete?
- classes vs. prototypes

Can ontologies help to resolve some of the inherent weakness of LLMs?
- halluncinamtion
- lack of planning, inference.

We have early empirical evidence that ontology knowledge can help ML, but no theory which types of ML will/won't benefit, for which functionalities?

In the discussion, Nicola makes a point that theory may be started by looking for principles to construct such theory. For example, perhaps understanding the difference between justification and explanation.
Someone in the audience made a point that even wrong ontology may help, but then I said that little ontology may help, but the wrong ontology may hurt. Frank said these are claims that we must experiment.
Data will always underrepresent the world. We deal by this by common sense reaoning. However, we have made little progress in that, because we've been obsessing about the symbol when we should actually be worried about the concepts. Analogical reasoning can play a role here to apply structures in similar contexts. Frank says that ML can do a lot for Common sense reasoning, because they are trained in huge corpora and they can lead to the extraction of common sense knowledge. He says that he would love to see analogical reasoning come back to being fashionable.

terça-feira, 16 de julho de 2024

FAUST@FOIS - 8th Workshop on Foundational Ontology

Taking a constructional turn to radically enrich a top ontology’s foundation: a case history
(Chris Partridge, Andrew Mitchell, Sergio de Cesare, Andreas Cola, Mesbah Khan, Justin Price and Alexander Hierl)

Talk by Chris Partidge

Research Questions: What does it mean to have a constructional ontology in practice?
what are the practical advantages of adopting such an approach?

Constructionalism: Shifting the way an ontology is defined.



BORO
-includes a foundational (or upper) ontology and closely intertwined methodology for IS re-engeneering.
- was originally conceived in the late 1980s in a real world project.

Using BORO as a constructionalist ontology
There is something named Ontology Sandbox that he uses to build ontologies.

Practical advantages and Issues to Overcome
- categorical transparency, dependency, reduction and consistency, as well as simplicity and explanatory
- however, these qualities are for the most part, broad theoretical advantages whose immediate practicality ius less obvious.
- cannot easily piggy-back on top ontology's semantic interoperability claim because the constructional turn did not change the base form of the top ontology.

This is according to him the best attempt to explain the proposed approach (more detail in the paper):
The Mereology of Concepts: Preliminary Explorations Guendalina Righetti Different theories on concepts: for example Features vs. Concepts. While the first is an exemplar theory, the latter is a prototypical one.
Do concepts have parts in the constructional perspective?

Rigid vs Variable Embodiments
Time absolute parthoold - sandwich example
rigid embodiment: a certain form R (principle of rigit embodiment) is embodied in some fixed matter)
slice1, slice2, ham/R

Time variable embodiment - river example (The variation of the amount of water in a river).
Variable environment of F: the object selecte dby ausuitable function F or principle (from times to things)

Another way of seeing this:
Variable embodiment is not a new notion. The idea of this paper is to verify if this may also be used to conceive concepts. Example:
When everything in a car is changed, is it still the same concept?

Semi-vriable embodiments - some parts can change but others are essential. E.g. "Nick Cave and The Bad Seeds" - Nick Cave is the essential part; In a concert, a band would be an essential part while the participants could vary.