Anastasia Analyti

Foundation for Research and Technology - Hellas | forth · Institute of Computer Science

We present a P2P framework based on asynchronous messaging for collaborative reasoning over modular disjunctive knowledge bases with weak negation, strong negation, and constraints. In particular, we present algorithms running upon receival from a knowledge base of a corresponding $Ask\_pred$, $Tell\_pred$, $Ask\_\KB$, or $Tell\_\KB$ message, which...

Parkinson’s disease (PD) is a progressive neurodegenerative movement disorder where motor dysfunction gradually increases. PD-specific dopaminergic drugs can ameliorate symptoms, but neurologists also strongly recommend physiotherapy combined with regular exercise. As there is no known cure for PD, traditional rehabilitation programs eventually tir...

Our Kinect-based physiotherapy platform tailored to Parkinson’s disease (PD) patients employs a Kinect sensor to extract 3D skeletal data in real-time from an exercising patient. The initial collection of five exercises served by the platform has now been enriched with an additional five exercises which are also based on traditional PD-specific phy...

In the linked open data cloud, the biggest open data graph that currently exists, a remarkable percentage of data are unnamed resources, also called blank nodes. Several fundamental tasks, such as graph isomorphism checking and RDF data versioning, require computing a map between the sets of blank nodes of two graphs. This map aims at minimizing th...

Public and private organisations increasingly release their data. The use of these open data can be supported and stimulated by providing considerable metadata, including discovery, contextual and other detailed metadata. This paper argues that faceted indexing of the RDF ontologies, published as linked open data (LOD), is an important part of thei...

We report on a Kinect-based, augmented reality, real-time physiotherapy platform tailored to Parkinson’s disease (PD) patients. The platform employs a Kinect sensor to extract real-time 3D skeletal data (joint information) from a patient facing the sensor (at 30 frames per second). In addition, a small collection of exercises practiced in tradition...

Recently, (Viegas Damásio et al. 2013) introduced a way to construct propositional formulae encoding provenance information for logic programs. From these formulae, justifications for a given interpretation can be extracted. However, explaining why such interpretation is not an answer-set (debugging) was not attained. Resorting to a meta-programmin...

ERDF stable model semantics is a recently proposed semantics for ERDF ontologies and a faithful extension of RDFS semantics on RDF graphs. In this paper, we elaborate on the computability and complexity issues of the ERDF stable model semantics. Based on the undecidability result of ERDF stable model semantics, decidability under this semantics can...

The notion of context is important since it can capture many of the interesting aspects of the way we understand the world such as relativity, locality, partiality, and context-dependence. In this work, we define the contextual RDFS model theory, called c-RDFS model theory for short, where a context is a triple of a name, a c-RDF graph, and a set o...

Generators for synthetic RDF datasets are very important for testing and benchmarking various semantic data management tasks (e.g. querying, storage, update, compare, integrate). However, the current generators do not support sufficiently (or totally ignore) blank node connectivity issues. Blank nodes are used for various purposes (e.g. for describ...

The provenance (i.e., origins) of derived information on the Web is crucial in many applications to allow information quality assessment, trust judgments, accountability, as well as understanding the temporal and spatial status of the information. On the other hand, the inclusion of negative information in knowledge representation both in the form...

Semantic web ontologies are not static but evolve as the understanding of the domain (or the domain itself) grows or evolves. This evolution is usually independent of the ontological instance descriptions which are stored in knowledge bases (KBs). Therefore, the effects of an ontology update on instance descriptions which are migrated to a new onto...

Understanding why and how a given answer to a query is generated from a deductive or relational database is fundamental to obtain justifications, assess trust, and detect dependencies on contradictions. Propagating provenance information is a major technique that evolved in the database literature to address the problem, using annotated relations w...

Semantic Web Ontologies are not static, but evolve, however, this evolution usually happens independently of the ontological instance descriptions (usually referred as “metadata”) which are stored in the various Metadata Repositories or Knowledge Bases. Nevertheless, it is a common practice for a MR/KB to periodically update its ontologies to their...

The success of the Semantic Web is impossible without any form of modularity, encapsulation, and access control. In an earlier paper, we extended RDF graphs with weak and strong negation, as well as derivation rules. The ERDF #n-stable model semantics of the extended RDF framework (ERDF) is defined, extending RDF(S) semantics. In this paper, we pro...

In this paper, we consider provenance and temporally annotated logic rules (pt-logic rules, for short), which are definite logic programming rules associated with the name of the source that they originate and the temporal interval during which they are valid. A collection of pt-logic rules form a provenance and temporally annotated logic program P...

Extended logic programs (ELPs) are a set of logic rules with strong negation  allowed in the bodies or head of the rules and weak negation ~ allowed in the bodies of the rules. ELPs enable for various forms of reasoning that cannot be achieved by definite logic programs. Answer Set Programming provides a widely acceptable semantics for ELPs. Howev...

The main digital preservation strategies are based on metadata and in many cases Semantic Web languages, like RDF/S, are used for expressing them. However RDF/S schemas or ontologies are not static, but evolve. This evolution usually happens independently of the “metadata” (ontological instance descriptions) which are stored in the various Metadata...

Determining trust of data available in the Semantic Web is fundamental for applications and users, in particular for linked open data obtained from SPARQL endpoints. There exist several proposals in the literature to annotate SPARQL query results with values from abstract models, adapting the seminal works on provenance for annotated relational dat...

In this paper, we provide a survey on the models and query languages for temporally annotated RDF. In most of the works, a temporally annotated RDF ontology is essentially a set of RDF triples associated with temporal constraints, where, in the simplest case, a temporal constraint is a validity temporal interval. However, a temporally annotated RDF...

Ontologies and automated reasoning are the building blocks of the Semantic Web initiative. Derivation rules can be included in an ontology to define derived concepts, based on base concepts. For example, rules allow to define the extension of a class or property, based on a complex relation between the extensions of the same or other classes and pr...

We address the problem of answering queries over a distributed information system, storing objects indexed by terms organized in a taxonomy. The taxonomy consists of subsumption relationships between negation-free DNF formulas on terms and negation-free conjunctions of terms. In the first part of the paper, we consider the centralized case, derivin...

The adoption of standards by the knowledge representation and logic programming communities is essential for their visibility and impact. The Rule Interchange Format is a fundamental effort in this direction that should be supported by users, developers and theoreticians. For this reason, it is essential to the community to discuss the recommendati...

We present a principled framework for modular Web rule bases, called MWeb. According to this framework, each predicate defined in a rule base is characterized by its defining reasoning mode, scope, and exporting rule base list. Each predicate used in a rule base is characterized by its requesting reasoning mode and importing rule base list. For leg...

The Extended Resource Description Framework has been proposed to equip RDF graphs with weak and strong negation, as well as derivation rules, increasing the expressiveness of ordinary RDF graphs. In parallel, the Modular Web framework enables collaborative and controlled reasoning in the Semantic Web. In this paper we exploit the use of the Modular...

The Extended Resource Description Framework has been proposed to equip RDF graphs with weak and strong negation, as well as derivation rules, increasing the expressiveness of ordinary RDF graphs. In parallel, the Modular Web framework enables collaborative and controlled reasoning in the Semantic Web. In this paper we show how to use the Modular We...

In previous work, we proposed an algebra whose operators allow to specify the valid compound terms of a faceted taxonomy, in a flexible manner (by combining positive and negative statements). In this paper, we treat the same problem but in a more general setting, where the facet taxonomies are not independent but are (possibly) interrelated through...

The success of the Semantic Web is impossible without any form of modularity, encapsulation, and access control. In an earlier paper, we extended RDF graphs with weak and strong negation, as well as derivation rules. The ERDF #n-stable model semantics of the extended RDF framework (ERDF) is defined, extending RDF(S) semantics. In this paper, we pro...

ERDF stable model semantics is a recently proposed semantics for ERDF ontologies and a faithful extension of RDFS semantics on RDF graphs. In this paper, we elaborate on the computability and complexity issues of the ERDF stable model semantics. We show that decidability under this semantics cannot be achieved, unless ERDF ontologies of restricted...

The aim of this study is to identify a gene expression signature which is characteristic of ER status in breast cancer patients. To our knowledge, this is the first microarray study in Greece involving clinical samples. We identified 97 genes that are characteristic for ER status and can well distinguish the ER+ from the ER- samples. We shrank our...

We present a principled framework for modular web rule bases, called MWeb. According to this framework, each pred- icate defined in a rule base is characterized by its defining reasoning mode, scope, and exporting rule base list. Each predicate used in a rule base is characterized by its requesting reasoning mode and importing rule base list. For v...

SQL, Prolog, RDF and OWL are among the most promi-nent and most widely used computational logic languages. However, SQL, Prolog and RDF do not allow the representation of negative in-formation, only OWL does so. RDF does not even include any negation concept. While SQL and Prolog only support reasoning with closed pred-icates based on negation-as-f...

With the completion of the human genome and the entrance into the post-genomic era, translational research rises as a major need. In this paper, we present a knowledge discovery workflow (KDw) and its utilization in the context of clinico-genomic trials. KDw aims towards the discovery of 'evidential' correlations between patients' genomic and clini...

In this study, we address the problem of answering queries over a peer-to-peer system of taxonomy-based sources. A taxonomy states subsumption relationships between negation-free DNF formulas on terms and negation-free conjunctions of terms. To the end of laying the foundations of our study, we first consider the centralized case, deriving the comp...

Faceted indexing and searching are being increasingly studied in the literature and used for real-life applications, e.g., for publishing heterogeneous museum collections on the Web. In this paper, we discuss in brief several aspects of managing (faceted) taxonomy-based information sources. Specifically, we discuss (i) the semantic description of f...

The exponential growth of the web and the extended use of database management systems in widely distributed information systems has brought to the fore the need for seamless interconnection of diverse and large numbers of information sources. Our contribution is a system that provides a flexible ap- proach for integrating and transparently querying...

A faceted taxonomy is a set of taxonomies, each describing a given knowledge domain from a different aspect. The indexing of the domain objects is done using compound terms, i.e. conjunctive combinations of terms from the taxonomies. A faceted taxonomy has several advantages over a single taxonomy, including conceptual clarity, compactness, and sca...

The notion of context appears in computer science, as well as in several other disciplines, in various forms. In this paper, we present a general framework for representing the notion of context in information modeling. First, we define a context as a set of objects, within which each object has a set of names and possibly a reference: the referenc...

The ultimate goal of the biomedical informatics project PrognoChip is the identification of classification and prognosis molecular markers for breast cancer. This requires not only an understanding of the genetic basis of the disease, based on the patient's tumor gene expression profiles but also the correlation of this data with knowledge normally...

The Compound Term Composition Algebra(CTCA) is an algebra with four algebraic op- erators, which can be used to generate the valid (meaningful) compound terms of a given faceted taxonomy, in an efficient and flexible manner. The positive operations allow the derivation of valid compound terms through the declaration of a small set of valid compound...

In this paper general mechanisms and syntactic restrictions are explored in order to specify and merge rule bases in the Semantic Web. Rule bases are expressed by extended logic programs having two forms of negation, namely strong (or explicit) and weak (also known as default negation or negation-as-failure). The proposed mechanisms are deflned by...

A materialized faceted taxonomy is an information source where the objects of interest are indexed according to a faceted taxonomy. This paper shows how from a materialized faceted taxonomy, we can mine an expression of the Compound Term Composition Algebra that specifies exactly those com- pound terms (conjunctions of terms) that have non-empty in...

This paper presents the needs and requirements that led to the formation of the ACGT (Advancing Clinico Genomic Trials) integrated project, its vision and methodological approaches of the project. The ultimate objective of the ACGT project is the development of a European biomedical grid for cancer research, based on the principles of open access a...

This paper presents the needs and requirements that led to the formation of the ACGT (Advancing Clinico Genomic Trials on Cancer) integrated project, its vision and methodological approaches. The ultimate objective of the ACGT project is the development of a European biomedical grid for cancer research, based on the principles of open access and op...

Ontologies and automated reasoning are the building blocks of the Semantic Web initiative. Derivation rules can be included in an ontology to define derived concepts based on base concepts. For exam- ple, rules allow to define the extension of a class or property based on a complex relation between the extensions of the same or other classes and pr...

A materialized faceted taxonomy is an information source where the objects of interest are indexed according to a faceted taxon- omy. This paper shows how from a materialized faceted taxonomy, we can mine an expression of the Compound Term Composition Algebra that specifies exactly those compound terms that have non-empty interpre- tation. The mine...

A faceted ontology consists of a set of facets, where each facet consists of a predefined set of terms structured by a subsumption relation. We propose two extensions of faceted ontologies, which allow inferring conjunctions of terms that are valid in the underlying domain. We give a model-theoretic interpretation to these extended faceted ontologi...

In [TASC03], we proposed an algebra with four algebraic operators, whose composition can be used to generate valid compound terms in a given faceted taxonomy in an e#cient and flexible manner.

Indexing and retrieval in Web catalogs can benefit from using faceted taxonomies. A faceted taxonomy consists of a set of facets, where each facet consists of a predefined set of terms structured by a subsumption relation. We propose two extensions of faceted taxonomies, which allow inferring conjunctions of terms that are valid in the underlying d...

One way of designing a taxonomy is by identifying a number of different aspects, or facets of the domain and then designing one taxonomy per facet. In such a faceted taxonomy, the indexing of objects is done by combining terms from di#erent facets. A faceted taxonomy has several advantages by comparison to a single hierarchical taxonomy, such as co...

A materialized faceted taxonomy is an information source where the objects of interest are indexed according to a faceted taxonomy.

Breast cancer is the most common malignancy affecting women, the life time risk being approximately 10%. Breast cancer is both genetically and histopathologically heterogeneous, and the underling development mechanisms remain largely unknown. Global expression analysis using microarrays offers unprecedented opportunities to obtain molecular signatu...

The concept of negation plays a special role in non-classical logics and also in knowledge represen-tation formalisms where negative information has to be taken into account on par with positive information. In the tradition of mathematical logic, there is a general preference to consider positive information as basic and treat negative information...

We present a new semantics for extended logic programs with rule prioritization (EPP). The semantics, called reliable semantics (RS), generalizes the well-founded semantics which is defined for normal programs. It also generalizes the extended well-founded semantics which is defined for non-contradictory extended programs. Because of the classical...

In [11], we proposed an algebra with four algebraic operators, whose composition can be used to generate valid compound terms in a given faceted taxonomy in an efficient and flexible manner. The positive operations allow the derivation of valid compound terms through the declaration of a small set of valid compound terms. The negative operations al...

Extended programs are normal programs extended with classical negation. Because of the classical negation in the head of the rules, an extended logic program can be contradictory. Human reasoning is often based on conflicting evidence and on assumptions which are not always valid. Our goal is to derive useful conclusions from programs that may be c...

A complex reasoning system can be designed as an interaction between reasoning modules. A module consists of a declaration of exported/imported predicates and a set of rules containing both negation by default and classical negation. A prioritized modular logic program (PMP) consists of a set of modules and a partial order < on the predicate defini...

Multimedia Database Systems (MMDS) support rich data types, such as text, images, video, and sound. Queries in MMDSs may refer to the content of the stored multimedia objects. This is called content-based querying. However, manual entry of content descriptions is very difficult and subjective.

A faceted taxonomy is a set of taxonomies, each describing a given domain from a different aspect, or facet. The indexing of domain objects is done through conjunctive combinations of terms from the facets, called compound terms. A faceted taxonomy has several advantages over a single hierarchy of terms, including conceptual clarity, compactness an...

Indexing and retrieval in Web catalogs can benefit from using faceted taxonomies. A faceted taxonomy consists of a set of facets, where each facet consists of a predefined set of terms structured by a subsumption relation. We propose two extensions of faceted taxonomies, which allow inferring conjunctions of terms that are valid in the underlying d...

Although semantic data models provide expressive conceptual modeling mechanisms, they do not support context, i.e. providing controlled partial information on conceptual entities by viewing them from different viewpoints or in different situations. In this paper, we present a model for representing contexts in information bases along with a set of...

In semantic and object-oriented data models, each class has one or more typing properties that associate it to other classes, and carry type information about all instances of the class. Weintroduce a new kind of property that wecallinstance-typing property. An instance-typing property associates an instance of a class to another class, and carries...

Covering is a well-known relationship in semantic and object-oriented data models. Covering holds when a class is the union of a collection of subclasses. However, covering has been studied only for entity classes. In this paper, we investigate covering for properties, as well. We introduce a new relationship among properties, called property cover...

Traditional database systems have been successful in handling large amounts of data but lack mechanisms for schema derivations and schema verification. In this paper, we propose (i) structures that carry expressive and useful information on the database schema, (ii) a set of inference rules for schema derivations, and (iii) a mechanism for discover...

The notion of context appears in several disciplines, including computer science, in various forms. In this paper, we are concerned with a notion of context in the area of information bases. First, we present a general definition whereby a context is seen as a set of objects, within which each object has a set of names and possibly a reference: the...

Covering is a well-known relationship in semantic and objectoriented models that holds when a class is the union of a collection of subclasses. Covering has been studied in the past only for entity classes.

A faceted taxonomy is a set of taxonomies, each describing a given do- main from a different aspect, or facet. The indexing of domain objects is done through conjunctive combinations of terms from the facets, called compound terms. A faceted taxonomy has several advantages over a single hierarchy of terms, including concep- tual clarity, compactnes...

Abstract The notion of context appears in several disciplines, including com - puter science, under various forms In this paper, we are concerned with a notion of context in the area of conceptual modeling First, we present a simple defini - tion whereby a context is seen as a set of objects, within which each object has a set of names and possibly...

We elaborate on the semantics of an enhanced object-oriented semantic network, where multiple instantiation, multiple specialization, and meta-classes are supported for both kinds of objects: entities and properties. By semantics of a semantic network, we mean the information (both explicit and derived) that the semantic network carries. Several da...

Although semantic data models provide expressive conceptual modeling mechanisms, they do not support context, i.e. providing controlled partial information on conceptual entities by viewing them from different viewpoints or in different situations. The authors present a model for representing contexts in information bases along with a set of operat...

In semantic and object-oriented data models, each class has one or more typing properties that associate it to other classes, and carry type information about all instances of the class. We introduce a new kind of property that we call instance-typing property. An instance-typing property associates an instance of a class to another class, and carr...

Specialization and inheritance are well-known concepts in the area of object-oriented modelling and knowledge representation. However, certain aspects of these concepts lack formal foundations. In particular, when properties of different classes are semantically related, several different semantics are possible for the inherited properties, and a c...

Traditional database systems have been successful in handling large amounts of data but lack mechanisms for schema derivations and schema verification. In this paper, we propose (i) structures that carry expressive and useful information on the database schema, (ii) a set of inference rules for schema derivations, and (iii) a mechanism for discover...

Covering is a well-known relationship in semantic and object-oriented data models. Covering holds when a class is the union of a collection of subclasses. However, covering has been studied only for entity classes. In this paper, we investigate covering for properties. We introduce a new relationship among properties, called property covering. Prop...

We elaborate on the semantics of an enhanced object-oriented semantic network, where multiple instantiation, multiple specialization, and meta-classes are supported for both kinds of objects: entities and properties. By semantics of a semantic network, we mean the information (both explicit and derived) that the semantic network carries. Several da...

A Multimedia Database System MMDS deals with the storage, manipulation, and retrieval of all types of digitally-representable information objects such as text, still images, video, and sound [Gro94], [CK95]. Providing mechanisms that allow the user to retrieve desired multimedia information is an important issue in MMDSs. Information about the cont...

A complex reasoning system can be designed as an interaction between reasoning modules. A module consists of a declaration of exported/imported predicates and a set of rules containing both negation by default and classical negation. A prioritized modular logic program (PMP) consists of a set of modules and a partial order <def on the predicate def...

Optimal search in main memory databases requires at most one key comparisonto locate a record. Extendible hashing becomes impractical when it is adapted to yield optimal search in main memory databases because of its large directory size. Multi-directory hashing techniques can provide significantly improved directory utilization over extendible has...

We present a new dynamic hashing scheme for disk-based databases, called Multi-Directory Hashing (MDH). MDH uses multiple hash directories to access a file. The size of each hash directory grows dynamically with the file size. The advantages of MDH are enhanced concurrency, improved bucket utilization and smaller total directory size than single-di...

The objective of this paper is to develop and analyze high performance hash based search methods for main memory databases. We define optimal search in main memory databases as the search that requires at most one key comparison to locate a record. Existing hashing techniques become impractical when they are adapted to yield optimal search in main...

The objective of this paper is to develop and analyze high performance hash based search methods for main memory databases. We define optimal search in main memory databases as the search that requires at most one key comparison to locate a record. Existing hashing techniques become impractical when they are adapted to yield optimal search in main...

In this paper 1 general mechanisms and syntactic restrictions are explored in or-der to specify and merge rule bases in the Semantic Web. Rule bases are expressed by extended logic programs having two forms of negation, namely strong (or explicit) and weak (also known as default negation or "nega-tion as failure"). The proposed mech-anisms are defi...