ppxscal/embedding_network huggingface dataset:
IT solutions for imaging biomarkers in biopharmaceutical research and development
Authors: Michael Hehenberger, Avijit Chatterjee, Usha Reddy, Joyce Hernandez, Jörg Sprengel
Venue: IBM Systems Journal (2007)

Biomarkers are indicators of normal biological processes, pathogenic processes, or pharmacological responses to a therapeutic intervention. The biopharmaceutical industry is building significant molecular-imaging capabilities and in this context is incorporating biomarker concepts throughout its research. In this paper, we discuss and propose information technology (IT) standards and architectures that support incorporation of imaging biomarkers into the drug discovery and clinical development process. In particular, we cover various uses of emerging imaging technologies in biopharmaceutical research and development, examples of imaging biomarkers in therapeutic areas, IT requirements related to the use of imaging technologies, challenges related to the integration of imaging biomarker data with clinical and genotypic data, and the need to integrate external public data sources. We discuss IT standards and architectures associated with the inclusion of biomarker-related data in the submission of new drug applications, with emphasis on imaging technologies. We suggest extensions to the Study Data Tabulation Model of the Clinical Data Interchange Standards Consortium and the JANUS Data Model of the Food and Drug Administration with data elements based on imaging biomarkers.
Switching Serial-Number Coding Scheme and Its Application in FFS Scheduling Problem with Inter-stage Constraints
Authors: Yimin Shen, Yushun Fan, Sen Zeng
Venue: Proceedings of the Third International Conference on Natural Computation - Volume 04 (2007)

Flexible Flow Shop (FFS) has multiple machines in each stage, and usually not all the machines of a stage, but a subset of them can be assigned to a job because of various constraints. Recent studies have considered the inner-stage constraints, and this paper addresses the inter-stage constraints between two successive working centers. Traditional Genetic Algorithm (GA) is not applicable because its chromosome becomes too long when the problem size increases. This paper proposes Serial-number Coding Scheme (SCS) firstly, which can shorten chromosome length substantially. Then Switching SCS (SSCS) is developed further to reduce hamming distance between neighboring solutions. SSCS Based Genetic Algorithm (SSGA) shows better computability and performance than traditional genetic algorithm.
Modular neural-visual servoing with image compression input
Authors: Kevin Stanley, Q. M. Jonathan Wu, Clarence W. de Silva, William A. Gruver
Venue: Journal of Intelligent Fuzzy Systems: Applications in Engineering and Technology (2001)

One of the essential problems of feature-based visual servoing is calculating the inverse Jacobian, which relates changes in features to changes in robot position. Neural networks can approximate the inverse feature Jacobian. Neural networks also allow other forms of vision input to be easily used to position the robot. The vision system is primarily responsible for reducing the dimensionality of the input to reduce the size and therefore computational load on the system. In this paper we develop a system which uses neural networks to both encode the image and generate control signals. In our system, the image dimensionality can be reduced in four ways: feature extraction, averaging compression, vector quantization, and principal component expansion. We demonstrate that it is possible to use neural networks for both image analysis and control of a vision guided robot, with little loss of accuracy when compared to feature based extraction.
Photometric clustering of regenerated plants of gladiolus by neural networks and its biological validation
Authors: V. S. S. Prasad, S. Dutta Gupta
Venue: Computers and Electronics in Agriculture (2008)

Photometric clustering of regenerated plants of gladiolus was described using fuzzy adaptive resonance theory (ART) and the resultant grouping pattern was compared with ART 2, and self-organizing map (SOM) neural network modules. Classical clustering techniques such as hierarchical (HC) and k-means clustering (KM) were also applied to analyze the same data set to evaluate the performance of the artificial neural network (ANN)-based clustering. Regenerated plants were clustered into two groups in varying numbers by ART 2, SOM, HC and KM. With ART 2, 19 of 55 plants were sorted into group '0' and the remaining 36 plants were placed in group '1', whereas; SOM distributed the regenerated plants in the ratio of 28:27. The clustering ratios of HC and KM were 34:21 and 26:29, respectively. However, a refined clustering of regenerated plants into seven groups was observed with Fuzzy ART. There was a similarity in the number of generated clusters between the training and validation data sets indicating the network efficiency. Biological validation of photometric clustering of regenerated plants was also assessed by indexing the corm induction potential of the sorted groups. A significant difference in corm induction potential between the groups was noted only with ART 2. Fuzzy ART-assisted grouping patterns are not conducive to segregate the potential corm producing shoots. ART 2-aided clustering of the regenerated plants appeared to be more promising for selecting group of plants capable of corm development than did other clustering approaches.
Letters: Neural modelling of hand grip formation during reach to grasp
Authors: J. Molina-Vilaplana, J. López-Coronado
Venue: Neurocomputing (2007)

We investigate the spatio-temporal dynamics of hand preshaping during prehension through a biologically plausible neural model. The hand grip formation is generated through neural modulation of basic motor programs that can be rescaled to accommodate different task demands. The model assumes a timing role to propioceptive reafferent information generated by the reaching component of the movement, avoiding the need of a preorganized functional temporal structure for the timing of prehension as some previous models have proposed. Predictions of the model in both Normal and Altered initial hand aperture conditions match key kinematic features present in human data.
Edge Tracking of subjective contours in Biomedical Imaging
Authors: Giovanni Garibotto, Valentina Garibotto
Venue: Proceedings of the 14th International Conference on Image Analysis and Processing (2007)

The paper describes a method for computer-assisted edge tracking and following by local profile matching. It is used primarily to integrate and support manual selection when complex contours have to be found and identified. Such a requirement is quite common in biomedical applications, including a wide spectrum of image modalities, from histological samples to MRI images. The referred example takes part in the analysis of in vitro receptor auto-radiographic data, for the architectonic characterization of transmitter receptors within a defined cortical region. The practical validation we provide of the proposed tracking model reveals that it is a very promising approach, enabling accurate and fast processing of multiple images.
A neural network approach to prediction of glass transition temperature of polymers: Research Articles
Authors: Xi Chen, Les Sztandera, Hugh M. Cartwright
Venue: International Journal of Intelligent Systems (2008)

Polymeric materials are finding increasing application in commercial optical communication systems. Taking advantage of techniques from the field of artificial intelligence, the goal of our research is to construct systems that can computationally design polymer formulations, including polymer optical fibers, with specified desirable consumer characteristics. Through the use of an extensive structure&mdash;property correlation database, properties of polymers can be predicted by an artificial network and the structure of novel polymers with desired properties can be optimized by a genetic algorithm. In this paper, we are focusing on one of the parameters, glass transition temperature (Tg) that influences a desired outcome in polymer optical fibers. Performance of such fibers can be optimized by engineering a polymer to exhibit a lower refractive index and Tg. This paper compares and discusses a neural network model and a linear model that have been developed to correlate Tg and repeating units of polymers. A neural network and multiple linear regression analysis were used in the study. A set of descriptors, chosen based on previous studies on the relations between Tg and polymer structure, were used to describe the structure of repeating units, individual bond energies, and intermolecular forces, especially hydrogen bonding, which is the strongest intermolecular force and exerts the greatest influence on Tg compared with other intermolecular interactions. A comprehensive neural network model with 28 descriptors was developed to predict Tg values of 6 randomly selected polymers from a database containing 71 polymers. The network was trained with the remaining 65 polymers and had a typical training root mean square error of 17 K (R2 = 0.95) and prediction average error of 17 K (R2 = 0.85). A linear regression model developed for comparison had an average error of 30 K (R2 = 0.88). &copy; 2007 Wiley Periodicals, Inc.
Grid Workflow Optimization Regarding Dynamically Changing Resources and Conditions
Authors: Helmut Wanek, Erich Schikuta, Irfan Ul Haq
Venue: Proceedings of the Sixth International Conference on Grid and Cooperative Computing (2007)

Automatic construction of workflows on the Grid currently is a hot research topic. The problems that have to be solved are manifold: How can existing ser- vices be integrated into a workflow, that is able to ac- complish a specific task? How can an optimal workflow be constructed in respect to changing resource charac- teristics during the optimization process? How to cope with dynamically changing or incomplete knowledge of the goal function of the optimization process? - and fi nally: How to react to service failures during workflow execution? In this paper we propose a method to optimize a workflow based on a heuristic A* approach that allows to react to dynamics in the environment, as changes in the Grid infrastructure and in the users requirements during the optimization process and failing resources during execution.
An efficient unification-based multimodal language processor in multimodal input fusion
Authors: Yong Sun, Yu Shi, Fang Chen, Vera Chung
Venue: Proceedings of the 19th Australasian conference on Computer-Human Interaction: Entertaining User Interfaces (2007)

A Multimodal User Interface (MMUI) allows a user to interact with a computer in a way similar to human-to-human communication, for example, through speech and gesture. Being an essential component in MMUIs, Multimodal Input Fusion should be able to find the semantic interpretation of a user's intention from recognized multimodal symbols which are semantically complementary. We enhanced our efficient unification-based multimodal parsing processor, which has the potential to achieve low polynomial computational complexity while parsing versatile multimodal inputs within a speech and gesture based MMUI, to handle multimodal inputs from more than two modalities. Its ability to disambiguate speech recognition results with gesture recognition results was verified with an experiment. The analysis of experiment results demonstrates that the improvement is significant after applying this technique.
From the Editor in Chief: All Systems Go
Authors: Fred Douglis
Venue: IEEE Internet Computing (2007)

Collective Wisdom: A Modest Proposal to Improve Peer Review, Part 2. Neutral agents can serve many functions on the Internet. EIC Fred Douglis continues his discussion of peer review by focusing on reviewer integrity and discussing how neutral agents play a part in the process.
Nondeterministic Testing with Linear Model-Checker Counterexamples
Authors: Gordon Fraser, Franz Wotawa
Venue: Proceedings of the Seventh International Conference on Quality Software (2007)

In model-based testing, software test-cases are derived from a formal specification. A popular technique is to use traces created by a model-checker as test-cases. This ap- proach is fully automated and flexible with regard to the structure and type of test-cases. Nondeterministic models, however, pose a problem to testing with model-checkers. Even though a model-checker is able to cope with nonde- terminism, the traces it returns make commitments at non- deterministic transitions. If a resulting test-case is executed on an implementation that takes a different, valid transition at such a nondeterministic choice, then the test-case would erroneously detect a fault. This paper discusses the exten- sion of available model-checker based test-case generation methods so that the problem of nondeterminism can be over- come.
Traveling Light, the Lua Way
Authors: Ashwin Hirschi
Venue: IEEE Software (2007)

Dynamically typed languages are in vogue. And for good reason. But, what about your C/C++ systems? Can you combine the advantages of statically typed software with the flexibility of dynamically typed systems? Lua was all this and more for the authors and helped them become more productive in the process. This article is part of a special issue on dynamically typed languages.
Three-valued logic in bounded model checking
Authors: T. Schuele, K. Schneider
Venue: Proceedings of the 2nd ACM/IEEE International Conference on Formal Methods and Models for Co-Design (2005)

In principle, bounded model checking (BMC) leads to semi-decision procedures that can be used to verify liveness properties and to falsify safety properties. If the procedures fail, there is usually no information about the validity of the considered specification. In this paper, we present a new approach to BMC based on three-valued logic that allows us in many cases to falsify liveness properties and to verify safety properties. Moreover, we employ both global and local model checking to take advantage of the different types of specifications that can be handled by these techniques.
Early face processing specificity: It's in the eyes!
Authors: Roxane J. Itier, Claude Alain, Katherine Sedore, Anthony R. McIntosh
Venue: Journal of Cognitive Neuroscience (2007)

Unlike most other objects that are processed analytically, faces are processed configurally. This configural processing is reflected early in visual processing following face inversion and contrast reversal, as an increase in the N170 amplitude, a scalp-recorded event-related potential. Here, we show that these face-specific effects are mediated by the eye region. That is, they occurred only when the eyes were present, but not when eyes were removed from the face. The N170 recorded to inverted and negative faces likely reflects the processing of the eyes. We propose a neural model of face processing in which face-and eye-selective neurons situated in the superior temporal sulcus region of the human brain respond differently to the face configuration and to the eyes depending on the face context. This dynamic response modulation accounts for the N170 variations reported in the literature. The eyes may be central to what makes faces so special.
Suggestions for stream based parallel systems in Ada
Authors: M. Ward, N. C. Audsley
Venue: Proceedings of the 13th international workshop on Real-time Ada (2007)

Ada provides good support for the implementation of dependable, real-time, control systems. However, its support for other styles of systems is not as good. This paper explores the support available for implementing parallel, stream based systems. The paper presents an implementation of an image manipulation system which highlights deficiencies in the support for such systems in the Ada language. Two additional semantics are proposed for addition to the Ada language which will provide for the needs of these systems. The broadcast semantic allows the same data to be written to several POs simultaneously. The guarded protected function semantic permits several readers to wait on an entry and simultaneously read data from the PO.
Belnap's logic and conditional composition
Authors: Alban Ponse, Mark B. van der Zwaag
Venue: Theoretical Computer Science (2007)

We study two alternative bases for Belnap's four-valued logic and provide complete equational axiomatizations for them. One is called conditional composition logic. It has a single, ternary if-then-else connective with a sequential, operational reading, and four constants for the truth values. The other logic is called guard logic. The main motivation for this logic lies in its technical properties. It admits a useful type of canonical form (term representation), and a relatively simple strategy for equational reasoning.
On k-detour subgraphs of hypercubes
Authors: Nana Arizumi, Peter Hamburger, Alexandr Kostochka
Venue: Journal of Graph Theory (2008)

A spanning subgraph G of a graph H is a k-detour subgraph of H if for each pair of vertices $x,y \in V(H)$, the distance, ${\rm dist}_G(x,y)$, between x and y in G exceeds that in H by at most k. Such subgraphs sometimes also are called additive spanners. In this article, we study k-detour subgraphs of the n-dimensional cube, $Q^n$, with few edges or with moderate maximum degree. Let $\Delta(k,n)$ denote the minimum possible maximum degree of a k-detour subgraph of $Q^n$. The main result is that for every $k\geq 2$ and $n \geq 21$ $$e^{-2k} {{n} \over {\ln n}} \le \Delta(k,n) \le 20 {n{\ln {\ln n}} \over {\ln n}}.$$ On the other hand, for each fixed even $k \geq 4$ and large n, there exists a k-detour subgraph of $Q^n$ with average degree at most $2 + 2^{4-k/2}+o(1)$. &copy; 2007 Wiley Periodicals, Inc. J Graph Theory 57: 55&ndash;64, 2008
Analysis of selection algorithms: A markov chain approach
Authors: Uday Kumar Chakraborty, Kalyanmoy Deb, Mandira Chakraborty
Venue: Evolutionary Computation (1996)

A Markov chain framework is developed for analyzing a wide variety of selection techniques used in genetic algorithms (GAs) and evolution strategies (ESs). Specifically, we consider linear ranking selection, probabilistic binary tournament selection, deterministic s-ary (s = 3,4,...) tournament selection, fitness-proportionate selection, selection in Whitley's GENITOR, selection in (μ, λ)-ES, selection in (μ + λ)-ES, (μ, λ)-linear ranking selection in GAs, (μ + λ)-linear ranking selection in GAs, and selection in Eshelman's CHC algorithm. The analysis enables us to compare and contrast the various selection algorithms with respect to several performance measures based on the probability of takeover. Our analysis is exact---we do not make any assumptions or approximations. Finite population sizes are considered. Our approach is perfectly general, and following the methods of this paper, it is possible to analyze any selection strategy in evolutionary algorithms.
Application of an adaptive neural fuzzy inference system to thermal comfort and group technology problems
Authors: G. Naadimuthu, D. M. Liu, E. S. Lee
Venue: Computers Mathematics with Applications (2007)

The Adaptive Neural Fuzzy Inference System (ANFIS) is used to design two vague systems, namely thermal comfort and group technologies in production and operations management. Results show that both systems can be modeled successfully by the combined use of a fuzzy approach and neural network learning.
Utilizing a geometry of context for enhanced implicit feedback
Authors: Massimo Melucci, Ryen W. White
Venue: Proceedings of the sixteenth ACM conference on Conference on information and knowledge management (2007)

Implicit feedback algorithms utilize interaction between searchers and search systems to learn more about users' needs and interests than expressed in query statements alone. This additional information can be used to formulate improved queries or directly improve retrieval performance. In this paper we present a geometric framework that utilizes multiple sources of evidence present in this interaction context (e.g., display time, document retention) to develop enhanced implicit feedback models personalized for each user and tailored for each search task. We use rich interaction logs (and associated metadata such as relevance judgments), gathered during a longitudinal user study, as relevance stimuli to compare an implicit feedback algorithm developed using the framework with alternative algorithms. Our findings demonstrate both the effectiveness of our proposed algorithm and the potential value of incorporating multiple sources of interaction evidence when developing implicit feedback algorithms.
Service-oriented computing
Authors: Fabio Casati
Venue: ACM SIGWEB Newsletter (2007)

Workflow management and service composition technologies have been around for over twenty years now (or more, depending on who you ask and how you define them). The objective of these technologies is to automate process execution across people and systems. These technologies generated an incredible hype both in the academia and in the industry, at least in the software development industry. Hundreds of process and service composition models have been defined, thousands of papers have been written on the topic, and dozens of commercial workflow/service composition systems have been developed. With all this large effort, one would imagine that such technology is in widespread use and that, if not, the key problems have been identified and that is what generates so much effort from the research community. I believe that this is not the case.
Optimal Design of PID Controller Using Modified Ant Colony System Algorithm
Authors: Qingdong Zeng, Guanzheng Tan
Venue: Proceedings of the Third International Conference on Natural Computation - Volume 05 (2007)

A novel intelligent design method for PID controller with optimal self-tuning parameters is proposed based on the modified Ant Colony System (ACS) algorithm. By testing four different control systems with the typical characteristic such as high order, time delays, and nonlinearity, the proposed ACS-PID algorithm has been demonstrated to have an adaptive property and robust stability in searching for the optimal PID controller parameters. By comparing with the PID controllers designed by use of the differential evolution (DE), the real-coded genetic algorithm (GA), and the simulated annealing (SA), the proposed ACS-PID controller has been demonstrated to be better than or equivalent to these PID controllers in control performance.
A Role-Based Secure Workflow Model
Authors: Chunyan, Jianliang Xu, Shenhua Li, Mingqiang Wang
Venue: Proceedings of the Sixth International Conference on Grid and Cooperative Computing (2007)

Workflow Management System is used for supporting many day-to-day workflows in large organizations. But heterogeneous and distributed computing systems make security management of WFMS decentralized, thus its security must be noticed. In this paper, we propose a role-based secure workflow model which realizes the principle of separation of duties (SoD), the principle of least privilege, integrity, authorization and availability. We also portray the whole model as a multi-layered architecture with a multilayered state graph for expressing and analyzing the flow of authorization. The layers are, respectively, role layer, task layer, control layer and data layer.