ppxscal/embedding_network huggingface dataset:
Modular Ontology Design Using Canonical Building Blocks in the Biochemistry Domain
Authors: Christopher J. Thomas, Amit P. Sheth, William S. York
Venue: Proceeding of the 2006 conference on Formal Ontology in Information Systems: Proceedings of the Fourth International Conference (FOIS 2006) (2006)

The field of BioInformatics has become a major venue for the development and application of computational ontologies. Ranging from controlled vocabularies to annotation of experimental data to reasoning tasks, BioOntologies are advancing to form a comprehensive knowledge foundation in this field. With the Glycomics Ontology (GlycO), we are aiming at providing both a sufficiently large knowledge base and a schema that allows classification of and reasoning about the concepts we expect to encounter in the glycoproteomics field. The schema exploits the expressiveness of OWL-DL to place restrictions on relationships, thus making it suitable to be used as a means to classify new instance data. On the instance level, the knowledge is modularized to address granularity issues regularly found in ontology design. Larger structures are semantically composed from smaller canonical building blocks. The information needed to populate the knowledge base is automatically extracted from several partially overlapping sources. In order to avoid multiple entries, transformation and disambiguation techniques are applied. An intelligent search is then used to identify the individual building blocks that model the larger chemical structures. To ensure ontological soundness, GlycO has been annotated with OntoClean properties and evaluated with respect to those. In order to facilitate its use in conjunction with other biomedical Ontologies, GlycO has been checked for NCBO compliance and has been submitted to the OBO website.
Synchrony, modality and semantics: explorations of predicate detection in a formal framework
Authors: Monica Brockmeyer
Venue:  (2008)

Predicate detection is the challenge to monitor the behavior of distributed systems and track their internal states. It is essential to achieve the benefits promised by distributed systems, such as increased reliability, availability and computational performance. After identifying the major challenges to predicate detection that remain unsolved, this dissertation addresses predicate detection both theoretically and practically. It introduces computation observability and proposes a layered model for predicate detection. The relationship of synchrony, predicate modality and detection semantics is investigated, which leads to a formal framework of predicate detection. Within this framework, this research formally studies the impact of partial synchrony on predicate detection and practically develops efficient detection approaches in realistic partially synchronous models. It also applies symbolic model checking and partial computation to online predicate detection in asynchronous systems.
Normalized queueing delay: congestion control jointly utilizing delay and marking
Authors: Mingyu Chen, Xingzhe Fan, Manohar N. Murthi, T. Dilusha Wickramarathna, Kamal Premaratne
Venue: IEEE/ACM Transactions on Networking (TON) (2009)

Depending upon the type of feedback that is primarily used as a congestion measure, congestion control methods can be generally classified into two categories: marking/loss-based or delay-based. While both marking and queueing delay provide information about the congestion state of a network, they have been largely treated with separate control strategies. In this paper, we propose the notion of the normalized queueing delay, which serves as a congestion measure by combining both delay and marking information. Utilizing normalized queueing delay (NQD), we propose an approach to congestion control that allows a source to scale its rate dynamically to prevailing network conditions through the use of a time-variant set-point. In ns-2 simulation studies, an NQD-enabled FAST TCP demonstrates a significant link utilization improvement over FAST TCP under certain conditions. In addition, we propose another NQD-based controller D + M TCP (Delay+Marking TCP) that achieves quick convergence to fair and stable rates with nearly full link utilization. Therefore, NQD is a suitable candidate as a congestion measure for practical congestion control.
An EM approach to mineral analysis using natural gamma rays
Authors: Bill Moran, Du Q. Huynh, Xuezhi Wang, Michael Edwards, Andrew Harris, Barbara F. La Scala
Venue: Digital Signal Processing (2009)

We describe here a method for the analysis of materials on a conveyor belt using the natural gamma spectra collected with a BGO (Bismuth Germanate) gamma ray detector. This detector collects gamma ray emissions from the Potassium (K), Uranium (U), and Thorium (Th) atoms in the materials. Based on these data, and using a Poisson model for the data generation, a statistical model is proposed and an approximate maximum likelihood (ML) technique based on the expectation-maximization (EM) algorithm is then used to estimate the amount of each of the three elements in the material. The statistical model is further refined to incorporate parameters of drift in the detector and an estimation technique for this is developed and tested against real data. The Cramer-Rao lower bounds for the estimators are calculated.
Rational choice and AGM belief revision
Authors: Giacomo Bonanno
Venue: Artificial Intelligence (2009)

We establish a correspondence between the rationalizability of choice studied in the revealed preference literature and the notion of minimal belief revision captured by the AGM postulates. A choice frame consists of a set of alternatives @W, a collection E of subsets of @W (representing possible choice sets) and a function f:E->2^@W (representing choices made). A choice frame is rationalizable if there exists a total pre-order R on @W such that, for every E@?E, f(E) coincides with the best elements of E relative to R. We re-interpret choice structures in terms of belief revision. An interpretation is obtained by adding a valuation V that assigns to every atom p the subset of @W at which p is true. Associated with an interpretation is an initial belief set and a partial belief revision function. A choice frame is AGM-consistent if, for every interpretation of it, the associated partial belief revision function can be extended to a full-domain belief revision function that satisfies the AGM postulates. It is shown that a finite choice frame is AGM-consistent if and only if it is rationalizable.
Ranking Approximate Answers to Semantic Web Queries
Authors: Carlos A. Hurtado, Alexandra Poulovassilis, Peter T. Wood
Venue: Proceedings of the 6th European Semantic Web Conference on The Semantic Web: Research and Applications (2009)

We consider the problem of a user querying semistructured data such as RDF without knowing its structure. In these circumstances, it is helpful if the querying system can perform an approximate matching of the user's query to the data and can rank the answers in terms of how closely they match the original query. Our approximate matching framework allows us to incorporate standard notions of approximation such as edit distance as well as certain RDFS inference rules, thereby capturing semantic as well as syntactic approximations. The query language we adopt comprises conjunctions of regular path queries, thus including extensions proposed for SPARQL to allow for querying paths using regular expressions. We provide an incremental query evaluation algorithm which runs in polynomial time and returns answers to the user in ranked order.
Runtime efficiency of adaptive mobile software agents in pervasive computing environments
Authors: Kutila Gunasekera, Shonali Krishnaswamy, Seng Wai Loke, Arkady Zaslavsky
Venue: Proceedings of the 2009 international conference on Pervasive services (2009)

Developing software that can support heterogeneous hardware platforms, adapt to dynamic highly variable environments and meet rapidly changing requirements is a challenge of pervasive computing. Dynamic adaptive software agents are a promising approach to develop software for such environments. We previously proposed an agent architecture which brings together features such as runtime adaptivity, agent mobility, platform-independence, context-awareness and lightweightness which are desirable in pervasive environments. In this paper, we propose and analyse a cost model of network load for our runtime adaptive mobile software agents. We compare our adaptive agents against standard non-adaptive mobile agents using this cost model. Subsequent experimental results demonstrate that our agents outperform non-adaptive mobile agents. We also propose and discuss further features which make our adaptive agent based software solution more suitable for pervasive computing environments.
Constraint Reasoning for Differential Models
Authors: Jorge Cruz
Venue: Proceeding of the 2005 conference on Constraint Reasoning for Differential Models (2005)

The basic motivation of this work was the integration of biophysical models within the interval constraints framework for decision support. Comparing the major features of biophysical models with the expressive power of the existing interval constraints framework, it was clear that the most important inadequacy was related with the representation of differential equations. System dynamics is often modelled through differential equations but there was no way of expressing a differential equation as a constraint and integrate it within the constraints framework. Consequently, the goal of this work is focussed on the integration of ordinary differential equations within the interval constraints framework, which for this purpose is extended with the new formalism of Constraint Satisfaction Differential Problems. Such framework allows the specification of ordinary differential equations, together with related information, by means of constraints, and provides efficient propagation techniques for pruning the domains of their variables. This enabled the integration of all such information in a single constraint whose variables may subsequently be used in other constraints of the model. The specific method used for pruning its variable domains can then be combined with the pruning methods associated with the other constraints in an overall propagation algorithm for reducing the bounds of all model variables. The application of the constraint propagation algorithm for pruning the variable domains, that is, the enforcement of local-consistency, turned out to be insufficient to support decision in practical problems that include differential equations. The domain pruning achieved is not, in general, sufficient to allow safe decisions and the main reason derives from the non-linearity of the differential equations. Consequently, a complementary goal of this work proposes a new strong consistency criterion, Global Hull-consistency, particularly suited to decision support with differential models, by presenting an adequate trade-of between domain pruning and computational effort. Several alternative algorithms are proposed for enforcing Global Hull-consistency and, due to their complexity, an effort was made to provide implementations able to supply any-time pruning results. Since the consistency criterion is dependent on the existence of canonical solutions, it is proposed a local search approach that can be integrated with constraint propagation in continuous domains and, in particular, with the enforcing algorithms for anticipating the finding of canonical solutions. The last goal of this work is the validation of the approach as an important contribution for the integration of biophysical models within decision support. Consequently, a prototype application that integrated all the proposed extensions to the interval constraints framework is developed and used for solving problems in different biophysical domains.
Neurocomputing Research Developments
Authors: Edgar Korner, Rudiger Kupper, M. K. M. Rahman, Yuri Shkuro, Marc-Oliver Gewaltig, James A. Reggia, Carter Wendelken, Lokendra Shastri, Ursula Korner, Marc de Kamps, Andreas Knoblauch, Alfredo Vellido, Alexander Grushin, Tommy W. S. Chow, Hugo A. Svensson
Venue:  (2007)

Neurocomputing is at the center of multidisciplinary research ,which involves computations by biological neural networks and those by artificial neural networks. Topics include vision, signal and pattern processing, learning, neurodynamics, associative memory, hardware and so on in the networks.This new and important book presents new research in the field.
Aspect Oriented Approach for Capturing and Verifying Distributed Properties
Authors: Tzilla Elrad
Venue: Languages: From Formal to Natural: Essays Dedicated to Nissim Francez on the Occasion of His 65th Birthday (2009)

Given an initial decomposition of a distributed program into processes we are faced with two classes of properties that are tightly bounded. One is the class of intra- process properties; these are relationships and requirements over a local state of a process. The second class is inter- processes properties; these are relationships and requirements over different processes local states that depict the consistencies and cooperation among a collection of cooperative processes that might be tightly bounded to achieve a certain collective goal. Both classes of system properties are crucial for system development and verification. The intra-process properties are relatively easier to define and carry on through system development life cycle. This paper concentrates on the challenges of expressing and imposing inter-processes properties during a distributed execution.The approach taken here is based on two completely independent areas of research The first is the CCL - Communication Closed Layers; a formal system for developing, maintaining, and verifying distributed programs [EF82] and the second is the aspect oriented software development [AOSD, CACM] that enables simplification and automation of CCL implementations. Aspect-oriented approach provides a natural framework to address inter-processes cooperation. The essence of aspect oriented software developments is the localization of crosscutting concerns. Under CCL constrains cooperative global properties can be considered as a special case of crosscutting concerns. (Note that this is not true in general; layers closeness, as defined in the following, is a necessary condition for the validity of cooperative global virtual assertions).Both CCL and AOSD are software development methodologies; their synergy for distributed systems development and runtime verification of system virtual global assertions is a promising match to handle the complexities of global system cooperation and consistencies. Both are centered on the notion of crosscutting concerns; CCL captures the semantics whereas AOSD provides the expressive tools. Together, it enables a design-by-contract discipline [M93] to be applicable to a wider range of distributed programs.There is still ongoing research to use the WEAVR , an aspect oriented model driven engineering [tool developed by Motorola, to automate code generation from precise behavioral models to express layers and global assertions. [CE1, CE2, CVE1, CVE2, CVE3].
Learning with Virtual Peers
Authors: Justine Cassell
Venue: Proceeding of the 2005 conference on Artificial Intelligence in Education: Supporting Learning through Intelligent and Socially Informed Technology (2005)

Schools aren't the only places people learn, and in the field of educational technology, informal learning is receiving increasing attention. In informal learning peers are of primary importance. But, how do you discover what works in peer learning? If you want to discover what peers do for one other so that you can then set up situations and technologies that maximize peer learning, where do you get your data from? You can study groups of children and hope that informal learning will happen and hope that you have a large enough sample to witness examples of each kind of peer teaching that you hope to study. Or you can make a peer Unfortunately, the biological approach takes years, care and feeding is expensive, diary studies are out of fashion, and in any case the human subjects review board frowns on the kind of mind control that would allow one to manipulate the peer so as to provoke different learning reactions. And so, in my own research, I chose to make a bionic peer. In this talk I describe the results from a series of studies where we manipulate a bionic peer to see the effects of various kinds of peer behavior on learning. The peer is sometimes older and sometimes younger than the learners, sometimes the same race and sometimes a different race, sometimes speaking at the same developmental level --and in the same dialect --and the learners, and sometimes differently. In each case we are struck by how much learning occurs when peers play, how learning appears to be potentiated by the rapport between the real and virtual child, and how many lessons we learn about the more general nature of informal learning mediated by technology.
The Lecture Contents with the Captions by Using Meaningful Reception Learning
Authors: Rihito Yaegashi, Kazuhiro Uenosono, Hedezi Enokizu, Seiichi Komiya
Venue: Proceeding of the 2008 conference on Knowledge-Based Software Engineering: Proceedings of the Eighth Joint Conference on Knowledge-Based Software Engineering (2008)

There are some programs which give the Malaysian students the pre-education for studying in Japan such as JAD program (Japan Associate Degree Program) in Malaysia. In these programs, it is impossible for the lecturers who are dispatched from Japan to cover all the majors. Therefore, they often give some lessons by the distance learning from Japan, but they have not got the sufficient educational effect yet. Distance learning are the real-time lecture which Japanese lectures give to Japanese students, or the lecture contents which just record these lectures. It is very difficult for the students at JAD programs who are not Japanese natives to understand all the contents of these distance learning. From these background, JAD Program makes the lecture contents with the captions for all the sentences, and conducts the distance learning. This paper discusses the method to relate with the background information by using the Advanced organizer which D.P.Ausubel proposed. Also, this paper describes the interface technology which uses the visual effect of the captions to express the relationship of Advanced organizer. The authors are conducting the distance learning, using these lecture contents which are based on these methods. The authors aim to inspect the effect of these lecture contents.
A weakest precondition approach to active attacks analysis
Authors: Musard Balliu, Isabella Mastroeni
Venue: Proceedings of the ACM SIGPLAN Fourth Workshop on Programming Languages and Analysis for Security (2009)

Information flow controls can be used to protect both data confidentiality and data integrity. The certification of the security degree of a program that runs in untrusted environments still remains an open problem in language-based security. The notion of robustness asserts that an active attacker, who can modify program code in some fixed points (holes), is not able to disclose more private information than a passive attacker, who merely observes public data. In this paper, we extend a method recently proposed for checking declassified non-interference in presence of passive attackers only, in order to check robustness by means of the weakest precondition semantics. In particular, this semantics simulates the kind of analysis that can be performed by an attacker, i.e., from the public output towards the private input. The choice of the semantics lets us distinguish between different attacks models. In this paper, we also introduce relative robustness that is a relaxed notion of robustness for restricted classes of attacks.
Collaborative robotic instruction: A graph teaching experience
Authors: Rubén Mitnik, Matías Recabarren, Miguel Nussbaum, Alvaro Soto
Venue: Computers Education (2009)

Graphing is a key skill in the study of Physics. Drawing and interpreting graphs play a key role in the understanding of science, while the lack of these has proved to be a handicap and a limiting factor in the learning of scientific concepts. It has been observed that despite the amount of previous graph-working experience, students of all ages experience a series of difficulties when trying to comprehend graphs or when trying to relate them with physical concepts such as position, velocity and acceleration. Several computational tools have risen to improve the students' understanding of kinematical graphs; however, these approaches fail to develop graph construction skills. On the other hand, Robots have opened new opportunities in learning. Nevertheless, most of their educational applications focus on Robotics related subjects, such as robot programming, robot construction, and artificial intelligence. This paper describes a robotic activity based on face-to-face computer supported collaborative learning. By means of a set of handhelds and a robot wirelessly interconnected, the aim of the activity is to develop graph construction and graph interpretation skills while also reinforcing kinematics concepts. Results show that students using the robotic activity achieve a significant increase in their graph interpreting skills. Moreover, when compared with a similar computer-simulated activity, it proved to be almost twice as effective. Finally, the robotic application proved to be a highly motivating activity for the students, fostering collaboration among them.
Starting Out With Visual Basic 2008 Update, 4th edition
Authors: Tony Gaddis, Kip Irvine
Venue:  (2009)

KEY BENEFIT: This step-by-step approach helps readers understand the logic behind developing quality programs while introducing the Visual Basic 2008 language. KEY TOPICS: Introduction to Programming and Visual Basic 2008; Creating Applications with Visual Basic; Input, Variables, Exceptions, and Calculations; Making Decisions and Working with Strings; Lists, Loops, Validation, and More; Sub Procedures and Functions; Multiple Forms, Standard Modules, and Menus; Arrays, Timers, and More; Files, Printing, and Structures; Working with Databases; Developing Web Applications; Classes, Exceptions, Collections, and Scrollable Controls. MARKET: Ideal for beginners to programming and the Visual Basic language.