ppxscal/embedding_network huggingface dataset:
Optimizing static thermodynamic models of transcriptional regulation
Authors: Denis C. Bauer, Timothy L. Bailey
Venue: Bioinformatics (2009)

Motivation: Modeling transcriptional regulation using thermo-dynamic modeling approaches has become increasingly relevant as a way to gain a detailed understanding of transcriptional regulation. Thermodynamic models are able to model the interactions between transcription factors (TFs) and DNA that lead to a specific transcriptional output of the target gene. Such models can be ‘trained’ by fitting their free parameters to data on the transcription rate of a gene and the concentrations of its regulating factors. However, the parameter fitting process is computationally very expensive and this limits the number of alternative types of model that can be explored. Results: In this study, we evaluate the ‘optimization landscape’ of a class of static, quantitative models of regulation and explore the efficiency of a range of optimization methods. We evaluate eight optimization methods: two variants of simulated annealing (SA), four variants of gradient descent (GD), a hybrid SA/GD algorithm and a genetic algorithm. We show that the optimization landscape has numerous local optima, resulting in poor performance for the GD methods. SA with a simple geometric cooling schedule performs best among all tested methods. In particular, we see no advantage to using the more sophisticated ‘LAM’ cooling schedule. Overall, a good approximate solution is achievable in minutes using SA with a simple cooling schedule. Contact:d.bauer@uq.edu.au; t.bailey@imb.uq.edu.au Supplementary information: Supplementary data are available at Bioinformatics online.
Anti-synchronization of stochastic perturbed delayed chaotic neural networks
Authors: Fengli Ren, Jinde Cao
Venue: Neural Computing and Applications (2009)

This paper studies the anti-synchronization of a class of stochastic perturbed chaotic delayed neural networks. By employing the Lyapunov functional method combined with the stochastic analysis as well as the feedback control technique, several sufficient conditions are established that guarantee the mean square exponential anti-synchronization of two identical delayed networks with stochastic disturbances. These sufficient conditions, which are expressed in terms of linear matrix inequalities (LMIs), can be solved efficiently by the LMI toolbox in Matlab. Two numerical examples are exploited to demonstrate the feasibility and applicability of the proposed synchronization approaches.
Keyboarding Course, 17th edition
Authors: Susie H. VanHuss, Connie M. Forde, Donna L. Woo, Linda Hefferin
Venue:  (2008)

Introduce students to the keyboarding with COLLEGE KEYBOARDING 17E: KEYBOARDING COURSE, LESSONS 1-25. This brief text emphasizes new-key learning and skill building while teaching the alphabetic keys, numeric keys, symbols, as well as the numeric keypad. Combined with the fun and engaging Keyboarding Pro 5, this package builds a strong keyboarding foundation.
A theory-based alternative for the design of instruction: functional design
Authors: Andrew S. Gibbons
Venue: Proceedings of the 4th International Conference on Design Science Research in Information Systems and Technology (2009)

An approach to instructional design is described which avoids some of the problems traditionally associated with process design models, sometimes referred to as waterfall models. The new approach is based on the functional decomposition of a generic instructional artifact and the use of the functions as entry points to the design. A theory of design architecture is described that relates artifact functions to the "layers" of a design, similar to Sch&ouml;n's architectural domains. By viewing the instructional artifact functionally, the designer takes advantage of the correspondence of instructional design layers and their associated theories. Thus, instructional theory can be applied more directly to designs. A design order that is adaptive to the individual design project is obtained as the process order restraints of the waterfall model are traded for ordering on the basis of a set of decision priority rules.
A Blueprint for a Calculator of Intensions
Authors: Alik Pelman
Venue: Proceeding of the 2006 conference on Formal Ontology in Information Systems: Proceedings of the Fourth International Conference (FOIS 2006) (2006)

We are on Mars again --the favourite laboratory for philosophical experiments. Our host colleagues introduce us to some Martian stuff referred to as “T”, and ask us to help them to identify T on other possible worlds. Or, technically speaking, we are asked to determine the intension of “T”, i.e., what the term designates with respect to different possible worlds. Following a short series of experiments on the planet, we conclude that the intension of “T” depends upon three factors: (1) The semantic rule linked with the term, i.e., the way in which the term is designed to pick out its referent with respect to different possible worlds (e.g., as a definite description, or as a proper name, or as an actualised description etc.); (2) The properties of the referent of “T” in the actual world; and, (3) What we shall call 'the metaphysical background of the universe', i.e., what counts as a thing vs. what counts as a property of things (e.g., whether the universe is such that it contains material objects that merely happen to have their manifest properties, or whether the universe primarily contains manifest objects that merely happen to have their material constitution). As our experiments show, changing the values of any of these variables will result in a change in the reference of the term with respect to different possible worlds, viz., it will result in a change in the intension of the term. We then demonstrate how the three variables are interrelated, and specify how exactly they combine to produce a particular intension of a term. We conclude with a general “formula” that determines what will deserve to be called “T” relative to the different values of the above variables, i.e., we come up with a calculator of intensions. Finally, we also draw some morals about rigidity.
FCMAC Based Guidance Law for Lifting Reentry Vehicles
Authors: Hao Wu, Chuanfeng Li, Yongji Wang
Venue: Proceedings of the 6th International Symposium on Neural Networks: Advances in Neural Networks - Part III (2009)

An improved nominal trajectory based guidance law for lifting reentry vehicle is proposed. In longitudinal guidance, an integrated controller comprised of LQR and FCMAC is utilized. LQR method is adopted to design state feedback controller according to the linearized models. FCMAC are introduced to correct the value of angle of attack and bank angle adaptively, by which the tracking performance of radial distance and range-to-go along the nominal trajectory is enhanced. In lateral guidance, a crossrange corridor is established to determine bank reversals according to dynamic adjusting criterion. 3DOF simulations for a lifting reentry vehicle model demonstrated the validity of this improved method.
Applying adaptation design patterns
Authors: Andres J. Ramirez, Betty H.C. Cheng
Venue: Proceedings of the 6th international conference on Autonomic computing (2009)

Dynamic adaptation may be used to prevent software downtime while new requirements and responses to environmental conditions are incorporated into the system. Previously, we studied over thirty adaptation-related projects to develop twelve adaptation-oriented design patterns that can be leveraged from one adaptive system to another. This paper presents a case study in which we apply our adaptation patterns in the design of a dynamically adaptive news web server. This pattern-based design separates the functional logic from the adaptive logic, resulting in a system that supports dynamic adaptation and is easier to maintain and analyze. Furthermore, to address assurance concerns, we applied automated formal verification techniques to ensure instantiated pattern models satisfy invariant properties specified in each adaptation pattern.
Multiobjective Evolutionary Algorithm for DS-CDMA Pseudonoise Sequence Design in a Multiresolutive Acquisition
Authors: Rosa Maria Alsina Pagès, Lluís Formiga Fanals, Joan Claudi Socoró Carrié, Ester Bernadó Mansilla
Venue: Proceeding of the 2007 conference on Artificial Intelligence Research and Development (2007)

In DS-CDMA communications, pseudonoise sequence sets must fulfil crosscorrelation and autocorrelation minimization properties in order to minimize multiuser interference and improve the probability of acquisition. When a multiresolutive acquisition scheme is to be used [3] the pseudonoise sequences (PN) have to satisfy more strict constraints for achieving proper acquisition performance. In this paper we present a multiobjective evolutionary algorithm to design a set of pseudonoise sequences meeting all the constraints that the receiver of DS-CDMA communication system demands. The new pseudonoise sequence set accomplishes not only the basic pseudorandom waveform properties but also the new crosscorrelation and autocorrelation features required by the multiresolutive structure, obtaining better results in terms of crosscorrelation and stability. This way a better trade off between mean acquisition time and computational requirements can be achieved regarding traditional adquisition schemes.
Multi-rate multicasting with network coding
Authors: Subhash Lakshminarayana, Atilla Eryilmaz
Venue: Proceedings of the 4th Annual International Conference on Wireless Internet (2008)

Single-rate multicasting may yield low utilization of the network resources when a subset of the receivers creates a bottleneck for the whole multicast group. Thus, practical multi-rate multicasting strategies are required to allow users with better channels to achieve maximum performance. While earlier studies have investigated such mechanisms using routing strategies over fixed trees, in this work we consider the possibility of using network coding without a given subgraph. Our scheme identifies the optimal routes and provides the utility maximizing rate allocation and coding solution. We also propose and investigate a nested multicasting method to reduce the complexity of the original scheme for practical implementation.
Advances in Open Domain Question Answering, 1st edition
Authors: Tomek Strzalkowski, Sanda Harabagiu
Venue: Text, Speech And Language Technology (2007)

Automated question answering - the ability of a machine to answer questions, simple or complex, posed in ordinary human language - is one of todays most exciting technological developments. It has all the markings of a disruptive technology, one that is poised to displace the existing search methods and establish new standards for user-centered access to information. This book gives a comprehensive and detailed look at the current approaches to automated question answering. The level of presentation is suitable for newcomers to the field as well as for professionals wishing to study this area and/or to build practical QA systems. The book can serve as a "how-to" handbook for IT practitioners and system developers. It can also be used to teach advanced graduate courses in Computer Science, Information Science and related disciplines. The readers will acquire in-depth practical knowledge of this critical new technology.
Period sensitivity analysis and D-P domain feasibility region in dynamic priority systems
Authors: Patricia Balbastre, Ismael Ripoll, Alfons Crespo
Venue: Journal of Systems and Software (2009)

In the design of a real-time application it is fundamental to know how a change in the task parameters would affect the feasibility of the system. Relaxing the classical assumptions on static task sets with fixed periods and deadlines can give higher resource utilisation and better performance. But the changes on task parameters have to be done always maintaining feasibility. In practice, period and deadline modifications are only necessary on single tasks. Our work focuses on finding the feasibility region of deadlines and periods (called D-P feasibility region) for a single task in the context of dynamic, uniprocessor scheduling of hard real-time systems. This way, designers can choose the optimal deadline and period pairs that best fit application requirements. We provide an exact and an approximated algorithm to calculate this region. We will show that the approximated solution is very close to the exact one and it takes considerably less time.
Acquiring Marketing Knowledge from Internet Bulletin Boards
Authors: Hiroshi Uehara, Kenichi Yoshida
Venue: Knowledge Acquisition: Approaches, Algorithms and Applications: Pacific Rim Knowledge Acquisition Workshop, PKAW 2008, Hanoi, Vietnam, December 15-16, 2008, Revised Selected Papers (2009)

This paper proposes a method to acquire marketing knowledge from Internet bulletin boards. It aims to clarify how viewers' interest in TV advertisements are reflected on their perceived images on the promoted products. By analyzing viewers' interests, we can acquire various knowledge which we can use to promote products. Two kinds of time series data are generated based on the proposed method. The first one represents the time series fluctuation of the interest in the TV advertisements. The other one represents the time series fluctuation of the image perception on the products. By analysing the correlations between these two time series data, we will try to clarify the implicit relationship between the viewer's interest in the TV advertisement and their perceived image of the promoted products. By applying the proposed method to an Internet bulletin board that deals with certain cosmetic brands, we will show how we can acquire marketing knowledge from Internet bulletin boards.
E-Mail Marketing For Dummies
Authors: John Arnold
Venue:  (2007)

E-mail seems like a terrific marketing tool until you think about all that spam clogging up your own inbox. But of course YOUR message isnt spam. So how do you use e-mail to market without becoming a spammer? Done properly, e-mail marketing is highly effective. E-Mail Marketing For Dummies can help you send your message to the inboxes of the world while observing professional standards, improving your deliverability, and executing your e-mail marketing strategy in line with current laws. You'll discover the secrets to creating professional and inviting e-mail messages, locating receptive respondents, tracking the results, and finding out whether your program is working. Youll be able to: Combine e-mail with other marketing media Develop a winning strategy, build a quality e-mail list, and find success Comply with anti-spam laws Set reasonable objectives Decide whether to use an e-mail service provider Brand your e-mails Build relationships with your customers Increase your open rate and find out whos actually opening your e-mails Use e-mail to improve search engine optimization And if youre not a bona fide, pocket-protector-carrying geek, this book is perfect. Its written for business people who need to get return on their time as well as their marketing efforts. Whether you read it straight through or dive right into the part you need most, E-Mail Marketing For Dummies is all about using e-mail to help your business prosper.
A Multiple Correspondence Analysis to Organize Data Cubes
Authors: Riadh Ben Messaoud, Omar Boussaid, Sabine Loudcher Rabaséda
Venue: Proceeding of the 2007 conference on Databases and Information Systems IV: Selected Papers from the Seventh International Baltic Conference DB&IS'2006 (2007)

On Line Analytical Processing (OLAP) is a technology basically created to provide users with tools in order to explore and navigate into data cubes. Unfortunately, in huge and sparse data, exploration becomes a tedious task and the simple user's intuition or experience does not lead to efficient results. In this paper, we propose to exploit the results of the Multiple Correspondence Analysis (MCA) in order to enhance data cube representations and make them more suitable for visualization and thus, easier to analyze. Our approach addresses the issues of organizing data in an interesting way and detects relevant facts. Our purpose is to help the interpretation of multidimensional data by efficient and simple visual effects. To validate our approach, we compute its efficiency by measuring the quality of resulting multidimensional data representations. In order to do so, we propose an homogeneity criterion to measure the visual relevance of data representations. This criterion is based on the concept of geometric neighborhood and similarity between cells. Experimental results on real data have shown the interest of using our approach on sparse data cubes.
Extracting Modules from Ontologies: A Logic-Based Approach
Authors: Bernardo Cuenca Grau, Ian Horrocks, Yevgeny Kazakov, Ulrike Sattler
Venue: Modular Ontologies: Concepts, Theories and Techniques for Knowledge Modularization (2009)

The ability to extract meaningful fragments from an ontology is essential for ontology reuse. We propose a definition of a module that guarantees to completely capture the meaning of a given set of terms, i.e., to include all axioms relevant to the meaning of these terms. We show that the problem of determining whether a subset of an ontology is a module for a given vocabulary is undecidable even for OWL DL. Given these negative results, we propose sufficient conditions for a for a fragment of an ontology to be a module. We propose an algorithm for computing modules based on those conditions and present our experimental results on a set of real-world ontologies of varying size and complexity.
Low-complexity high-speed decoder design for quasi-cyclic LDPC codes
Authors: Zhongfeng Wang, Zhiqiang Cui
Venue: IEEE Transactions on Very Large Scale Integration (VLSI) Systems (2007)

This paper studies low-complexity high-speed decoder architectures for quasi-cyclic low density parity check (QC-LDPC) codes. Algorithmic transformation and architectural level optimization are incorporated to reduce the critical path. Enhanced partially parallel decoding architectures are proposed to linearly increase the throughput of conventional partially parallel decoders through introducing a small percentage of extra hardware. Based on the proposed architectures, a (8176, 7154) Euclidian geometry-based QC-LDPC code decoder is implemented on Xilinx field programmable gate array (FPGA) Virtex-II 6000, where an efficient nonuniform quantization scheme is employed to reduce the size of memories storing soft messages. FPGA implementation results show that the proposed decoder can achieve a maximum (source data) decoding throughput of 172 Mb/s at 15 iterations.
Compositional performance prediction exemplified using generic object finalization analysis
Authors: Nighat Yasmin, Murali Sitaraman
Venue: Proceedings of the 47th Annual Southeast Regional Conference (2009)

Static analysis methods for performance prediction of component-based software must be compositional in order to be scalable. In this paper, we explain the problem and our solution approach by analyzing the time to finalize or destroy generic objects, in the presence of data abstraction. Unlike initialization of objects to pre-specified values, finalization has to contend with objects with arbitrary values. In the process, we explain necessary trade-offs between precision and complexity and the need to strengthen specifications of operations and internal assertions, such as loop invariants for performance analysis.
Simple optimization techniques for A*-based search
Authors: Xiaoxun Sun, William Yeoh, Po-An Chen, Sven Koenig
Venue: Proceedings of The 8th International Conference on Autonomous Agents and Multiagent Systems - Volume 2 (2009)

In this paper, we present two simple optimizations that can reduce the number of priority queue operations for A* and its extensions. Basically, when the optimized search algorithms expand a state, they check whether they will expand a successor of the state next. If so, they do not first insert it into the priority queue and then immediately remove it again. These changes might appear to be trivial but are well suited for Generalized Adaptive A*, an extension of A*. Our experimental results indeed show that they speed up Generalized Adaptive A* by up to 30 percent if its priority queue is implemented as a binary heap.
Clustering sequences by overlap
Authors: Dietmar H. Dorr, Anne M. Denton
Venue: International Journal of Data Mining and Bioinformatics (2009)

A clustering algorithm is introduced that combines the strengths of clustering and motif finding techniques. Clusters are identified based on unambiguously defined sequence sections as in motif finding algorithms. The definition of similarity within clusters allows transitive matches and, thereby, enables the discovery of remote homologies that cannot be found through motif-finding algorithms. Directed Acyclic Graph (DAG) structures are constructed that link short clusters to the longer ones. We compare the clustering results to the corresponding domains in the InterPro database. A second comparison shows that annotations based on our domains are inherently more consistent than those based on InterPro domains.
Projective cone scheduling (PCS) algorithms for packet switches of maximal throughput
Authors: Kevin Ross, Nicholas Bambos
Venue: IEEE/ACM Transactions on Networking (TON) (2009)

We study the (generalized) packet switch scheduling problem, where service configurations are dynamically chosen in response to queue backlogs, so as to maximize the throughput without any knowledge of the long term traffic load. Service configurations and traffic traces are arbitrary. First, we identify a rich class of throughput-optimal linear controls, which choose the service configuration S maximizing the projection 〈S,BX〉 when the backlog is X. The matrix B is arbitrarily fixed in the class of positive-definite, symmetric matrices with negative or zero off-diagonal elements. In contrast, positive off-diagonal elements may drive the system unstable, even for subcritical loads. The associated rich Euclidian geometry of projective cones is explored (hence the name projective cone scheduling PCS). The maximum-weight-matching (MWM) rule is seen to be a special case, where B is the identity matrix. Second, we extend the class of throughput maximizing controls by identifying a tracking condition which allows applying PCS with any bounded time-lag without compromising throughput. It enables asynchronous or delayed PCS implementations and various examples are discussed.
On understanding transient interdomain routing failures
Authors: Feng Wang, Jian Qiu, Lixin Gao, Jia Wang
Venue: IEEE/ACM Transactions on Networking (TON) (2009)

The convergence time of the interdomain routing protocol, BGP, can last as long as 30 minutes. Yet, routing behavior during BGP route convergence is poorly understood. During route convergence, an end-to-end Internet path can experience a transient loss of reachability. We refer to this loss of reachability as transient routing failure. Transient routing failures can lead to packet losses, and prolonged packet loss bursts can make the performance of applications such as Voice-over-IP and interactive games unacceptable. In this paper, we study how routing failures can occur in the Internet. With the aid of a formal model that captures transient failures of the interdomain routing protocol, we derive the sufficient conditions that transient routing failures could occur. We further study transient routing failures in typical BGP systems where commonly used routing policies are applied. Network administrators can apply our analysis to improve their network performance and stability.