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  <front>
    <journal-meta />
    <article-meta>
      <title-group>
        <article-title>Modeling issues and choices in the Data Mining OPtimization Ontology</article-title>
      </title-group>
      <contrib-group>
        <contrib contrib-type="author">
          <string-name>C. Maria Keet</string-name>
          <email>keet@ukzn.ac.za</email>
          <xref ref-type="aff" rid="aff3">3</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Agnieszka Ławrynowicz</string-name>
          <email>agnieszka.lawrynowicz@cs.put.poznan.pl</email>
          <xref ref-type="aff" rid="aff2">2</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Claudia d'Amato</string-name>
          <email>claudia.damato@uniba.it</email>
          <xref ref-type="aff" rid="aff1">1</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Melanie Hilario</string-name>
          <email>melanie.hilario@unige.ch</email>
          <xref ref-type="aff" rid="aff0">0</xref>
        </contrib>
        <aff id="aff0">
          <label>0</label>
          <institution>Artificial Intelligence Laboratory, University of Geneva</institution>
          ,
          <country country="CH">Switzerland</country>
        </aff>
        <aff id="aff1">
          <label>1</label>
          <institution>Dipartimento di Informatica, Universita degli Studi di Bari</institution>
          ,
          <country country="IT">Italy</country>
        </aff>
        <aff id="aff2">
          <label>2</label>
          <institution>Institute of Computing Science, Poznan University of Technology</institution>
          ,
          <country country="PL">Poland</country>
        </aff>
        <aff id="aff3">
          <label>3</label>
          <institution>School of Mathematics</institution>
          ,
          <addr-line>Statistics, and Computer Science</addr-line>
          ,
          <institution>University of KwaZulu-Natal, and UKZN/CSIR-Meraka Centre for Artificial Intelligence Research</institution>
          ,
          <country country="ZA">South Africa</country>
        </aff>
      </contrib-group>
      <abstract>
        <p>We describe the Data Mining OPtimization Ontology (DMOP), which was developed to support informed decision-making at various choice points of the knowledge discovery (KD) process. It can be used as a reference by data miners, but its primary purpose is to automate algorithm and model selection through semantic meta-mining, i.e., ontology-based meta-analysis of complete data mining processes in view of extracting patterns associated with mining performance. DMOP contains in-depth descriptions of DM tasks (e.g., learning, feature selection), data, algorithms, hypotheses (mined models or patterns), and workflows. Its development raised a number of non-trivial modeling problems, the solution to which demanded maximal exploitation of OWL 2 representational potential. We discuss a number of modeling issues encountered and the choices made that led to version 5.3 of the DMOP ontology.</p>
      </abstract>
    </article-meta>
  </front>
  <body>
    <sec id="sec-1">
      <title>-</title>
      <p>
        Meta-learning, or learning to learn, is defined in computer science as the application of
machine learning techniques to meta-data about past machine learning experiments; the
goal is to modify some aspect of the learning process in order to improve the
performance of the resulting model. Traditional meta-learning focused on the learning phase
of the data mining (or KD) process, and regarded learning algorithms as black boxes,
correlating the observed performance of their output (learned model) with
characteristics of their input (data). Though learning is the central phase of the KD process, the
quality of the mined model depends strongly also on other phases (e.g. data cleaning
or feature selection). Knowledge on how the different components of the data
mining process interact opens up a way for optimizing KD processes. However, besides
the existence of CRISP-DM [
        <xref ref-type="bibr" rid="ref1">1</xref>
        ], a high-level standard process model for developing
knowledge discovery projects, this is far from being understood.
      </p>
      <p>
        The primary goal of the Data Mining OPtimization Ontology (DMOP, pronounced
dee-mope; http://www.dmo-foundry.org/) is to support all decision-making steps
that determine the outcome of the data mining process. It focuses specifically on DM
tasks that require non-trivial search in the space of alternative methods. While DMOP
can be used by data mining practitioners to inform manual algorithm selection and
model (or parameter) selection, it has been designed to automate these two operations
through semantic meta-mining [
        <xref ref-type="bibr" rid="ref2">2</xref>
        ]. Semantic meta-mining is distinguished from
traditional meta-learning by the following properties: i) it extends the meta-learning
approach to the full knowledge discovery process taking into account the
interdependencies and interactions between the different process operations; ii) it opens up the black
box by explicitly analysing DM algorithms along various dimensions to correlate
observed performance of learned hypotheses with both data and algorithm characteristics;
iii) it represents expertise on the DM process and its components in the DM ontology
and knowledge base.
      </p>
      <p>DMOP was developed within the EU FP7 e-LICO project (http://www.e-lico.
eu) where it provided DM expertise to the Intelligent Discovery Assistant (IDA),
comprised of an AI planner and semantic meta-miner. The planner produces a set of
candidate workflows that are correct but not necessarily optimal with respect to a given cost
function. To help the planner to select the best workflows from a massive set of
workflow candidates, an ontology-based meta-learner mines past data mining experiments
in order to learn models for recommending best combinations of DM algorithms to be
used in a KD process to achieve the best performance for a given problem, data set and
evaluation function.</p>
      <p>To support semantic meta-mining, DMOP models a detailed taxonomy of
algorithms used in KD processes, each described in terms of its underlying assumptions, the
cost functions and optimization strategies it uses, the classes of hypotheses—models or
pattern sets—it generates, and other properties. This allows meta-learners using DMOP
to generalize over algorithms and their properties, including those algorithms that did
not appear in the training set, provided they are annotated in DMOP. DMOP is
complemented by the DM knowledge base that uses terms from DMOP to model existing
data mining algorithms and their implementations (operators) in popular DM software
(such as RapidMiner or Weka). Meta-data recorded during data mining experiments are
described using terms from DMOP and its associated KB and stored in data mining
experiment repositories, providing training and testing data for the meta-miner.</p>
      <p>DMOP provides a unified conceptual framework for analyzing DM tasks,
algorithms, models, datasets, workflows and performance metrics, and their relationships,
which is described in Section 3. To fulfill requirements of this in-depth analysis, we
have encountered a number of non-trivial modeling issues in DMOP development, of
which the main ones are discussed in Section 4. DMOP’s goals and required coverage
resulted in using almost all OWL 2 features.
2</p>
    </sec>
    <sec id="sec-2">
      <title>Related work</title>
      <p>
        An overview of early approaches to methodical descriptions of DM processes may be
found in [
        <xref ref-type="bibr" rid="ref2">2</xref>
        ]. The majority of work concerning formal representation of data mining in
ontology languages is aimed at the construction of workflows for knowledge discovery.
One line of this research deals with the development of distributed KD applications on
the Grid [
        <xref ref-type="bibr" rid="ref3 ref4">3, 4</xref>
        ]. The pre-OWL DAMON ontology provides a characterization of
available data mining software in order to allow the user the semantic search for appropriate
DM resources and tools [
        <xref ref-type="bibr" rid="ref3">3</xref>
        ]. The ontology of GridMiner Assistant (GMA) [
        <xref ref-type="bibr" rid="ref4">4</xref>
        ] aims to
support dynamic, interactive construction of data mining workflows in Grid-enabled
data mining systems. Other ontologies developed for DM workflow construction are
KDDONTO [
        <xref ref-type="bibr" rid="ref5">5</xref>
        ], KD ontology [
        <xref ref-type="bibr" rid="ref6">6</xref>
        ] and DMWF [
        <xref ref-type="bibr" rid="ref7">7</xref>
        ], all of them using OWL as a
major representation language. These ontologies are focused on modeling algorithms’
inputs/outputs to enable generation of valid compositions of them. For instance, a
Hierarchical Task Network (HTN) based planner eProPlan [
        <xref ref-type="bibr" rid="ref7">7</xref>
        ], uses DMWF to plan a set
of valid workflows based on operator (algorithm implementation) preconditions and
effects modeled in DMWF by means of SWRL rules.
      </p>
      <p>
        Very few existing DM ontologies go beyond supporting workflow construction.
OntoDM [
        <xref ref-type="bibr" rid="ref8">8</xref>
        ] aims to provide a unified framework for data mining, contains definitions of
the basic data mining concepts, but lacks a particular use case. Expose´ [
        <xref ref-type="bibr" rid="ref9">9</xref>
        ] aims to
provide a formal domain model for a database of data mining experiments. It uses OntoDM
together with the data mining algorithms from DMOP, and a description of experiments
(algorithm setup, execution, evaluation) to provide the basis of an Experiment Markup
Language. The primary use of OntoDM and Expose´ may thus be viewed as providing
controlled vocabulary for DM investigations.
      </p>
      <p>Concluding related work, none of the related ontologies was developed with as goal
the optimization of the performance of KD processes. They do not provide sufficient
level of details needed to support semantic meta-mining. In particular, the ontologies
focused on workflow construction do not model internal characteristics of algorithms
but just their inputs and outputs. Hence they aid in answering the question how to build
a valid workflow, but not necessarily how to build an optimal workflow.
3</p>
    </sec>
    <sec id="sec-3">
      <title>Overview of DMOP</title>
      <p>The primary goal of DMOP is to support all decision-making steps that determine the
outcome of the data mining process. A set of competency questions were formulated at
the start of the project, some of which are: “Given a data mining task/data set, which of
the valid or applicable workflows/algorithms will yield optimal results (or at least better
results than the others)?”, “Given a set of candidate workflows/algorithms for a given
task/data set, which workflow/algorithm characteristics should be taken into account
in order to select the most appropriate one?”, and even more detailed ones, such as
“Which learning algorithms perform best on microarray or mass spectrometry data?”.
Due to space limitations, this overview of DMOP will not discuss the answers to these
competency questions explicitly.</p>
      <p>The core concepts of DMOP (Fig. 1) are the different ingredients that go into the
data mining process (DM-Process). The input is composed of a task specification
(DMTask) and training/test data (DM-Data) provided by the user; its output is a hypothesis
(DM-Hypothesis), which can take the form of a global model (DM-Model) or a set of
local patterns (DM-PatternSet). Tasks and algorithms as defined in DMOP are not
processes that directly manipulate data or models, rather they are specifications of such
processes. A DM-Task specifies a DM process (or any part thereof) in terms of the input
it requires and the output it is expected to produce. A DM-Algorithm is the
specification of a procedure that addresses a given Task, while a DM-Operator is a program
that implements a given DM-Algorithm. Instances of DM-Task and DM-Algorithm do no
DM‐Task
addresses</p>
      <p>DM‐Algorithm
specifiesInputClass
specifiesOutputClass</p>
      <p>achieves
implements
realizes
DM-Operator
hasSubworkflow
DM‐Workflow</p>
      <p>DM‐Data
DM‐Hypothesis
executes
executes</p>
      <p>DM‐Opera on
hasSubprocess</p>
      <p>DM‐Process
hasInput
hasOutput
DM‐Model</p>
      <p>DM‐Pa ernSet
more than specify their input/output types; only processes called DM-Operations have
actual inputs and outputs. A process that executes a DM-Operator also realizes the
DMAlgorithm implemented by the operator and achieves the DM-Task addressed by the
algorithm. Finally, a DM-Workflow is a complex structure composed of DM operators, a
DM-Experiment is a complex process composed of operations (or operator executions).
An experiment is described by all the objects that participate in the process: a workflow,
data sets used and produced by the different data processing phases, the resulting
models, and meta-data quantifying their performance. In the following, the basic elements
of DMOP are detailed.</p>
      <p>DM Tasks: The top-level DM tasks are defined by their inputs and outputs. A
DataProcessingTask receives and outputs data. Its three subclasses produce new data
by cleansing (DataCleaningTask), reducing (DataReductionTask), or otherwise
transforming the input data (DataTransformationTask). These classes are further articulated
in subclasses representing more fine-grained tasks for each category. An
InductionTask consumes data and produces hypotheses. It can be either a ModelingTask or a
PatternDiscoveryTask, based on whether it generates hypotheses in the form of global
models or local pattern sets. Modeling tasks can be predictive (e.g. classification) or
descriptive (e.g., clustering), while pattern discovery tasks are further subdivided into
classes based on the nature of the extracted patterns: associations, dissociations,
deviations, or subgroups. A HypothesisProcessingTask consumes hypotheses and transforms
(e.g., rewrites or prunes) them to produce enhanced—less complex or more readable—
versions of the input hypotheses.</p>
      <p>Data: As the primary resource that feeds the knowledge discovery process, data
have been a natural research focus for data miners. Over the past decades meta-learning
researchers have actively investigated data characteristics that might explain
generalization success or failure. Fig. 2 shows the characteristics associated with the different Data
subclasses (shaded boxes). Most of these are statistical measures, such as the number of</p>
      <p>ProportionOf.M..issingValues
DataTable
hasFeature</p>
      <p>Feature
hasFValue</p>
      <p>FeatureValue</p>
      <p>Instance</p>
      <p>ContFValue
CategoricalFeature
AvgMutualInformation
Entropy
NumDistinctValues</p>
      <p>
        CategFValue
AbsoluteFreq
ClassAbsFreq
RelativeFreq
ClassRelFreq
instances or the number of features of a data set, or the absolute or relative frequency of
a categorical feature value. Others are information-theoretic measures (italicized in the
figure). Characteristics in bold font, like the maximum value of Fisher’s Discriminant
Ratio, which measures the highest discriminatory power of any single feature in the data
set, are geometric indicators of data set complexity (see [
        <xref ref-type="bibr" rid="ref10">10</xref>
        ] for detailed definitions).
      </p>
      <p>
        DM Algorithms: The top levels of the Algorithm hierarchy reflect those of the Task
hierarchy, since each algorithm class is defined by the task it addresses. However, the
Algorithm hierarchy is much deeper than the Task hierarchy: for each leaf class of the task
hierarchy, there is an often dense subhierarchy of algorithms that specify diverse ways
of addressing each task. For instance, the leaf concept ClassificationModelingTask in the
DM-Task hierarchy maps directly onto the ClassificationModelingAlgorithm class, which
has three subclasses [
        <xref ref-type="bibr" rid="ref11">11</xref>
        ]. Generative methods compute the class-conditional densities
p(xjCk) and the priors p(Ck) for each class Ck. Examples of generative methods are
normal (linear or quadratic) discriminant analysis and Naive Bayes. Discriminative
methods such as logistic regression compute posterior probabilities p(Ckjx) directly
to determine class membership. Discriminant functions build a direct mapping f (x)
from input x onto a class label; neural networks and support vector classifiers (SVCs)
are examples of discriminant function methods. These three Algorithm families spawn
multiple levels of descendant classes that are distinguished by the type and structure of
the models they generate.
      </p>
      <p>One innovative feature of DMOP is the modeling and exploitation of algorithm
properties in meta-mining. All previous research in meta-learning has focused
exclusively on data characteristics and treated algorithms as black boxes. DMOP-based
metamining brings to bear in-depth knowledge of algorithms as expressed in their elaborate
network of object properties. One of these is the object property has-quality, which
relates a DM-Algorithm to an AlgorithmCharacteristic (Fig. 3). A few characteristics
are common to all DM algorithms; examples are characteristics that specify whether
an algorithm makes use of a random component, or handles categorical or
continuous features. Most other characteristics are subclass-specific. For instance,
charachasQuality</p>
      <p>AlgorithmCharacteris c
DataProcessing
AlgoCharacteris c</p>
      <p>RandomComponent
HandlingOfCategoricalFeatures</p>
      <p>HandlingOfCon nuousFeatures
FeatureWeigh ng
AlgoCharacteris c
FeatureEvalua onTarget
FeatureEvalua onContext</p>
      <p>Predic veModeling
AlgoCharacteris c</p>
      <p>...</p>
      <p>BiasVarianceProfile</p>
      <p>Classifica on</p>
      <p>AlgoCharacteris c
Classifica onProblemType
HandlingOfClassifica onCosts</p>
      <p>ToleranceToClassImbalance
Classifica onRuleInduc on Classifica onTreeInduc on</p>
      <p>AlgoCharacteris c AlgoCharacteris c
RuleInduc onStrategy TreeBranchingFactor
SampleHandlingForInduc on
teristics such as LearningPolicy (Eager/Lazy) are common to induction algorithms in
general, whereas ToleranceToClassImbalance and HandlingOfClassificationCosts make
sense only for classification algorithms.</p>
      <p>Note that has-quality is only one among the many object properties that are used to
model DM algorithms. An induction algorithm, for instance, requires other properties
to fully model its inductive bias. For instance, the property assumes expresses its
underlying assumptions concerning the training data. SpecifiesOutputType links to the class
of models generated by the algorithm, making explicit its hypothesis language or
representational bias. Finally, hasOptimizationProblem identifies its optimization problem
and the strategies followed to solve it, thus defining its preference or search bias.
4</p>
    </sec>
    <sec id="sec-4">
      <title>Modeling choices and their discussion</title>
      <p>In this section we present the main modeling choices, issues arisen, and solutions
adopted, therewith providing some background as to why certain aspects from the
overview in the preceding section are modeled the way they are.
4.1</p>
      <sec id="sec-4-1">
        <title>Meta-modeling in DMOP</title>
        <p>
          Right from the start of DMOP development, one of the most important modeling
issues concerning DM algorithms was to decide whether to model them as classes or
individuals. Though DM algorithms may have different implementations, the common
view is to see particular algorithms as single instances, and not collections of instances.
However, the modeling problem arises when we want to express the types of inputs
and outputs associated with a particular algorithm. Recall that in fact only processes
(executions of workflows) and operations (executions of operators) consume inputs and
produce outputs. DM algorithms (as well as operators and workflows) can, in turn, only
specify the type of input or output. Inputs and outputs (DM-Dataset and DM-Hypothesis
class hierarchy, respectively) are modeled as subclasses of IO-Object class. Then
expressing a sentence like “the algorithm C4.5 specifiesInputClass
CategoricalLabeledDataSet” became problematic. It would mean that a particular algorithm (C4.5, an
instance of DM-Algorithm class) specifies a particular type of input
(CategoricalLabeledDataSet, a subclass of DM-Hypothesis class), but classes cannot be assigned as property
values to individuals in OWL. To tackle this problem, we initially created one artificial
class per each single algorithm with a single instance corresponding to this
particular algorithm, as recommended in [
          <xref ref-type="bibr" rid="ref12">12</xref>
          ] (e.g. C4.5Algorithm class with single instance
C4.5). However, in our case, such modeling led to technical problems. Since each of
the four properties—hasInput, hasOutput, specifiesInputClass, specifiesOutputClass—
were assigned a common range—IO-Object—it opened a way for making semantically
problematic ABox assertions like C4.5 specifiesInputClass Iris, where Iris is a concrete
dataset. Clearly, any DM algorithm is not designed to handle only a particular dataset.
        </p>
        <p>
          We noticed that CategoricalLabeledDataSet could be perceived as an instance of
a meta-class—the class of all classes of input and output objects, named IO-Class in
DMOP. In this way, the sentence C4.5 specifiesInputClass CategoricalLabeledDataSet
delivers the intended semantics. However, we also wanted to express sentences like
DM-Process hasInput some CategoricalLabeledDataSet. The use of the same IO object
(like CategoricalLabeledDataSet) once as a class (subclass of IO-Object) and at other
times as an instance required some form of meta-modeling. In order to implement it, we
investigated some available options. This included an approach based on an
axiomatisation of class reification proposed in [
          <xref ref-type="bibr" rid="ref13">13</xref>
          ], where in a metamodeling-enabled version
Ometa of a given ontology O, class-level expressions from O are transformed into
individual asssertions such that each model of Ometa has two kinds of individuals, those
representing classes and those representing proper individuals, and meta-level rules are
encoded in class level. We resigned from it due to its possible efficiency issues raised
in the paper.
        </p>
        <p>To this end, we decided to use the weak form of punning available in OWL 2.
Punning is applied only to leaf-level classes of IO-Object; non-leaf classes are not punned
but represented by associated meta-classes, e.g., the IO-Object subclass DataSet maps
to the IO-Class subclass DataSetClass. Similarly, the instances of DM-Hypothesis class
represent individual hypotheses generated by running an algorithm on the particular
dataset, while the class DM-HypothesisClass is the meta-class whose instances are the
leaf-level descendant classes of DM-Hypothesis. Except for the leaf-level classes, the
IO-Class hierarchy structure mimics that of the IO-Object hierarchy.
4.2</p>
      </sec>
      <sec id="sec-4-2">
        <title>Property chains in DMOP</title>
        <p>
          DMOP has 11 property chains, which have been investigated in detail in [
          <xref ref-type="bibr" rid="ref14">14</xref>
          ]. The
principal issues in declaring safe property chains, i.e., that are guaranteed not to cause
unsatisfiable classes or other undesirable deductions, are declaring and choosing properties,
and their domain and range axioms. To illustrate one of the issues declaring property
chains, we use hasMainTable hasFeature v hasFeature: chaining requires compatible
domains and ranges at the chaining ‘points’, such as the range of hasMainTable and
domain of hasFeature, and with the domain and range of the property on the
righthand side. In this case, hasFeature’s domain is DataTable that is a sister-class of
hasMainTable’s domain DataSet, but the chain forces that each participating entity in
hasFeature has to be a subclass of its declared domain class, hence DataSet v DataTable is
derived to keep the ontology consistent. Ontologically, this is clearly wrong, and
hasFeature’s domain is now set to DataSet or DataTable. Each chain has been analysed in
a similar fashion and adjusted where deemed necessary (see [
          <xref ref-type="bibr" rid="ref14">14</xref>
          ] for the generic set of
tests and how to correct any flaws for any property chain).
        </p>
        <p>DMOP typically contains more elaborate property chains than the aforementioned
one. For instance, realizes addresses v achieves, so that if a DM-Operation realises a
DM-Algorithm that addresses a DM-Task, then the DM-Operation achieves that DM-Task,
and with the chain implements specifiesInputClass v specifiesInputClass, we obtain
that when a DM-Operator or OperatorParameter implements an AlgorithmParameter or
DM-Algorithm and that specifies the input class IO-Class, then the DM-Operator or
OperatorParameter specifies the input class IO-Class.
4.3</p>
      </sec>
      <sec id="sec-4-3">
        <title>Alignment of DMOP with the DOLCE foundational ontology</title>
        <p>
          It may seem that the choice whether, and if so how, to map one’s domain ontology
to a foundational ontology is unrelated to interesting modeling features of the OWL
language. This is far from the case, although the modeling arguments (summarised and
evaluated in [
          <xref ref-type="bibr" rid="ref15">15</xref>
          ]) still do hold. The principal issues from a language viewpoint are:
1) to import or to extend, 2) if import, whether that should be done in whole or just
the relevant module extracted from the foundational ontology, 3) how to handle the
differences in expressiveness that may exist—and possibly be required—between the
foundational ontology and the domain ontology, 4) how to rhyme different modeling
‘philosophies’ between what comes from Ontology, what is represented in foundational
ontologies, and what is permitted in OWL (i.e., features that are objectionable from an
ontological viewpoint, such as class-as-instance, nominals, and data properties). Due to
space limitations, we only summarise how DMOP was mapped to DOLCE [
          <xref ref-type="bibr" rid="ref16">16</xref>
          ].
        </p>
        <p>The two main reasons to align DMOP with a foundational ontology were the
considerations about attributes and data properties, where extant non-foundational ontology
solutions were partial re-inventions of how they are treated in a foundational
ontology (see next section), and reuse of the ontology’s object properties. DOLCE, GFO,
and YAMATO are available in OWL and have extensive entities on ‘attributes’ and
many reusable object properties. At the time when the need for a mapping arose,
YAMATO documentation was limited and GFO less well-known by the authors, which led
to the case of mapping DMOP to DOLCE-lite (it now can be swapped for GFO and
BFORO anyway, thanks to the foundational ontology library ROMULUS [http://
www.thezfiles.co.za/ROMULUS/]. The only addition to DOLCE’s perdurant branch
is that dolce:process has as subclasses DM-Experiment and DM-Operation. Most DM
classes, such as algorithm, software, strategy, task, and optimization problem, are
subclasses of dolce:non-physical-endurant. Characteristics and parameters of such entities
have been made subclasses of dolce:abstract-quality, and for identifying discrete
values, classes were added as subclasses of dolce:abstract-region. That is, each of the four
DOLCE main branches have been used. Regarding object properties, DMOP reuses
mainly DOLCE’s parthood, quality, and quale relations. Choosing the suitable DOLCE
category for alignment and carrying out the actual mapping has been done manually;
some automation to suggest mappings would be a welcome addition. Mapping DMOP
into DOLCE had the most effect regarding representing DM characteristics and
parameters (‘attributes’), which is the topic of the next section.
4.4</p>
      </sec>
      <sec id="sec-4-4">
        <title>Qualities and attributes</title>
        <p>A seemingly straightforward but actually rather intricate, and essentially unresolved,
issue is how to handle ‘attributes’ in OWL ontologies, and, in a broader context,
measurements. For instance, each FeatureExtractionAlgorithm has as an ‘attribute’ a
transformation function that is either linear or non-linear. One might be tempted to take the easy
way out and simply reuse the “UML approach” where an attribute is a binary functional
relation between a class and a datatype; e.g., with a simplified non-DMOP intuitive
generic example, given a data property hasWeight with as XML data type integer,
one can declare Elephant v =1 hasWeight.integer. And perhaps a
hasWeightPrecise with as data type real may be needed elsewhere. And then it appears later on
that the former two were assumed to have been measured in kg, but someone else
using the ontology wants to have it in lbs, so we would need another hasWeightImperial,
and so on. Essentially, with this approach, we end up with exactly the same issues as
in database integration, precisely what ontologies were supposed to solve. Instead of
building into one’s ontology application decisions about how to store the data in the
information system (and in which unit it is), one can generalize the (binary) attribute
into a class, reuse the very notion of Weight that is the same in all cases, and then have
different relations to both value regions and units of measurement. This means to
unfold the notion of an object’s property, like its weight, from one attribute/OWL data
property into at least two properties: one OWL object property from the object to the
‘reified attribute’—a so-called “quality property”, represented as an OWL class—and
then another property to the value(s). The latter, more elaborate, approach is favoured in
foundational ontologies, especially in DOLCE, GFO and YAMATO. DOLCE uses the
combination Endurant that has a qt relation to Quality (disjoint branches) that, in turn,
has a ql relation to a Region (a subclass of the yet again disjoint Abstract branch). While
this solves the problem of non-reusability of the ‘attribute’ and prevents duplication of
data properties, neither ontology has any solution to representing the actual values and
units of measurements. But they are needed for DMOP too, as well as complex data
types, such as an ordered tree and a multivariate series.</p>
        <p>
          We considered in more detail related work on qualities, measurements and similar
proposals from foundational ontologies, to general ontologies, to domain ontologies for
the experimental sciences [
          <xref ref-type="bibr" rid="ref16 ref17 ref18 ref19 ref20">16–20</xref>
          ]. This revealed that the measurements for DMOP are
not measurements in the sense of recording the actual measurements, their instruments,
and systems of units of measurements, but more alike values for parameters, e.g., that
the TreeDepth has a certain value and a LearningPolicy is eager or lazy, and that some
proposals, such as OBOE [
          <xref ref-type="bibr" rid="ref18">18</xref>
          ], are versions of DOLCE’s approaches1. This being the
case, we opted for the somewhat elaborate representation of DOLCE, and added a minor
1 DOLCE materials differ slightly, with quale as relation in [
          <xref ref-type="bibr" rid="ref16">16</xref>
          ] and as unary in [
          <xref ref-type="bibr" rid="ref17">17</xref>
          ] and in
the DOLCE-lite.owl, and Region is a combination of a (data) value + measurement unit
dolce:non-physical-endurant
dolce:quality
        </p>
        <p>dolce:abstract
dolce:has-quality</p>
        <p>dolce:q-location
DM-Data
DataTable
dolce:abstract-quality</p>
        <p>dolce:has-quale
has-quality</p>
        <p>Characteristic Parameter</p>
        <p>hasDataType
extension to that for our OWL ontology in two ways (see Fig. 4): i) DM-Data is
associated with a primitive or structured DataType (which is a class in the TBox) through the
object property hasDataType, and ii), the data property hasDataValue relates DOLCE’s
Region with any data type permitted by OWL, i.e., anyType. In this way, one obtains a
‘chain’ from the endurant/perdurant through the dolce:has-quality property to the
quality, that goes on through the dolce:q-location/dolce:has-quale property to region and
on with the hasDataValue data property to the built-in data type (instead of one single
data property between the endurant and the data type). For instance, we have
ModelingAlgorithm v =1 has-quality.LearningPolicy, where LearningPolicy is a dolce:quality,
and then LearningPolicy v =1 has-quale.Eager-Lazy, where Eager-Lazy is a subclass
of dolce:abstract-region (that is a subclass of dolce:region), and, finally, Eager-Lazy v
1 hasDataValue.anyType, so that one can record the value of the learning policy
of a modeling algorithm. In this way, the ontology can be linked to many different
applications, who even may use different data types, yet still agree on the meaning of
the characteristics and parameters (‘attributes’) of the algorithms, tasks, and other DM
endurants.</p>
        <p>A substantial amount of classes have been represented in this way: dolce:region’s
subclass dolce:abstract-region has 43 DMOP subclasses, which represent ways of
carving out discrete value regions for the characteristics and parameters of the endurants
DM-Data, DM-Algorithm, and DM-Hypothesis. Characteristic and Parameter are direct
subclasses of dolce:abstract-quality, which have 94 and 42 subclasses, respectively.
4.5</p>
      </sec>
      <sec id="sec-4-5">
        <title>Other modeling considerations</title>
        <p>
          There are several other OWL 2 features that are or were used in DMOP to model the
subject domain. One that was used in some cases was the ObjectInverseOf, so
that for some object property hasX in an OWL 2 ontology, one does not have to
extend the vocabulary with an Xof property and declare it as the inverse of hasX with
condensed into one (e.g. “80 kg”) in [
          <xref ref-type="bibr" rid="ref16">16</xref>
          ] to deal with attribute values/qualia (there were no
examples in [
          <xref ref-type="bibr" rid="ref17">17</xref>
          ] and the DOLCE-lite.owl)
InverseObjectProperties, but one can use the meaning of Xof with the
axiom ObjectInverseOf(hasX) instead. Both approaches were used initially and
eventually inverses were added explicitly where needed, for readability of the class
expressions.
        </p>
        <p>The so-called “object property characteristics” have been used sparingly, and only
the basic ‘functional’ characteristic is asserted. Local reflexivity was investigated on
a subsumes property for instances in DMOP v5.2, but eventually modeled differently
with classes and metamodeling/punning to achieve the desired effect. DOLCE’s
parthood is transitive, hence it should be transitive in DMOP as well, but it was discovered
after the release of v5.3 that the object property copy function in Prote´ge´ does not
copy any property characteristics. This will be corrected in the next version. In general,
though, if one extracts the properties from an ontology, it ought to take with it at least
the characteristics of those properties (and, though arguable, also any domain and range
axioms declared for the selected properties).</p>
        <p>The desire to specify the order of subprocesses remains, and a satisfactory solution
has yet to be found. Likewise, there are object properties in the current DMOP
version that merit closer investigation whether they are indeed more specific versions of
parthood; e.g., a DecisionCriterion is part of DecisionRule, but it merits further
investigation whether, e.g., hasDecisionTarget with as domain DecisionStrategy and range
DecisionTarget is indeed a subproperty of has-part.
5</p>
      </sec>
    </sec>
    <sec id="sec-5">
      <title>Conclusions</title>
      <p>In this paper, the DMOP ontology has been presented. It provides a unified conceptual
framework for analyzing DM tasks, algorithms, models, datasets, workflows and
performance metrics, and their relationships. While modeling data mining knowledge in
DMOP, almost all OWL 2 features were used to solve a number of non-trivial modeling
issues that had been encountered. These include: i) the hurdle of relating instances to
classes and using classes as instances (and vv.), which has been solved by exploiting the
weak form of metamodeling with OWL’s punning available in OWL 2; ii) finding and
resolving in a systematic way the undesirable deductions caused by property chains;
iii) representation of ‘attributes’, where its solution is ontology-driven yet merged with
OWL’s data property and built-in data types to foster their reuse across applications; iv)
linking to a foundational ontology; and v) the considerations on adoption of the OWL
2 ObjectInverseOf to avoid extending the vocabulary with new properties to be
declared as the inverse of existing properties, but where human readability prevailed.</p>
      <p>
        Current and future work includes investigating aspects such as DMOP object
properties, the effects of ObjectInverseOf vs. InverseObjectProperties, and
the deductions with respect to the DM algorithms branch and metamodeling. DMOP
(version 5.2) has already been applied successfully to the meta-mining task [
        <xref ref-type="bibr" rid="ref2">2</xref>
        ]. Further
meta-mining experiments will be performed with the goal of validating the modelling
choices introduced in version 5.3.
      </p>
      <p>Acknowledgements. This work was supported by the European Community 7th
framework ICT-2007.4.4 (No 231519) ”e-LICO: An e-Laboratory for Interdisciplinary
Collaborative Research in Data Mining and Data-Intensive Science”. We thank all our</p>
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