ppxscal/embedding_network huggingface dataset:
Pharmaceutical Informatics and the Pathway to Personalized Medicines
Authors: Sangtae Kim, Venkat Venkatasubramanian
Venue: Proceedings of the 7th international conference on Computational Science, Part I: ICCS 2007 (2007)

The present computational era has witnessed the evolution of the field of computational biology into two somewhat disjoint communities: one group focused on the "wriggling of molecules" (e.g. molecular dynamics) and another focused on pattern matching and informatics (e.g. sequence alignment). The separation starts relatively early in the training of the community, as is evident from the relative weighting of calculus vs. computer science courses in the curriculum of undergraduate majors in the various disciplines of computational biology. But at the dawn of the petascale era in computational science, exciting advances in healthcare can be envisioned at a new niche in the computational biology ecosystem - a niche formed by the reunion of the separated branches of computational biology. We consider some illustrative examples from pharmaceutical informatics of data-intensive informatics approaches applied to "objects" that are not simply numbers or static molecular structures but instead are (CPU-intensive) molecular simulations. These results suggest a promising pathway for applying petascale informatics to shift the paradigm in pharmaceutical and biotechnology R D to a future world of personalized medicines. The early examples from pharmaceutical informatics also indicate that the foundational framework will be based on the concept of Dynamic Data Driven Application Systems (DDDAS).
IBGP Confederation Provisioning
Authors: M. Nassar, R. State, O. Festor
Venue: Proceedings of the 1st international conference on Autonomous Infrastructure, Management and Security: Inter-Domain Management (2007)

This paper proposes an optimization method for the design of large scale confederation based BGP networks. We propose a graph based model and an associated metric to evaluate the reliability of large scale autonomous systems. We propose and validate an effective methodology to find the optimal design for a given physical topology. According to our experiments, we consider that replacing the traditional IBGP topology by an appropriate confederation design could increase at the same time the scalability and the reliability into the domain. Our work might be a step further towards a large scale confederation deployment.
A Service-Oriented Infrastructure for Early Citation Management
Authors: José H. Canós, Manuel Llavador, Eduardo Mena, Marcos R. Borges
Venue: Proceedings of the 12th European conference on Research and Advanced Technology for Digital Libraries (2008)

Citation analysis needs an in-depth transformation. Current systems have been long criticized due to defects such as lack of coverage and low accuracy of the citation data. Surprisingly, incorrect or incomplete data are used to make important decisions about researchers' careers. We argue that a new approach based on the collection of citation data when they are actually generated (that is, during the edition of papers) can overcome current limitations, and propose a new framework in which the research community as a whole is the owner as well as beneficiary of a Global Citation Registry characterized by high quality citation data. The registry will be accessible for all the interested parties and will be the source over which the different impact models can be applied.
Fusion of Vibrotactile Signals Used in a Tactile Display in Computer Aided Surgery
Authors: Melina Brell, Dirk Roßkamp, Andreas Hein
Venue: Proceedings of the 6th international conference on Haptics: Perception, Devices and Scenarios (2008)

In this paper the humans' hand movement as response to a vibration signal is presented. The signal thereby is composed of single vibration stimuli. The results of this study are used for signal generation of a tactile display for computer aided surgery. Each of the display's tactors represents one movement direction of the hand. To present directions between single movement axes it is necessary to combine single vibration signals. Therefore an experiment is presented to examine the fusion of single tactile signals. The experiment is divided into three parts to compare three different ways of merging vibration signals. Best results were achieved with a modulation of the pulse duty factor.
Design, implementation and evaluation of interfaces to haptic and locomotor spaces in robot-assisted shopping for the visually impaired
Authors: Vladimir A. Kulyukin
Venue:  (2008)

This dissertation addresses the problem of large-scale assisted shopping for the visually impaired. The task of grocery shopping is composed of two main sub-tasks: navigating to a product, and retrieving the product from the shelf. To be able to do grocery shopping independently, a visually impaired shopper should be able to perform both the sub-tasks. This dissertation forwards and defends two claims. Claim 1: To guarantee independence, any assistive shopping device for the visually impaired must necessarily address navigation and product retrieval tasks and provide the shopper with effective interfaces to the locomotor and haptic spaces in supermarkets. Claim 2: Robots can act as effective interfaces to the haptic and locomotor spaces of the supermarket, and thus enable visually impaired shoppers to do large-scale grocery shopping independently. Most existing assisted-shopping devices fail to provide the visually impaired shopper either the interface to the locomotor space or the interface to the haptic space. This dissertation presents RoboCart, a robotic shopping-assistant for the visually impaired, which realizes interfaces to both haptic and locomotor spaces. The locomotor module, which realizes the interface to the locomotor space, implements Monte Carlo Markov localization in combination with radio frequence identification (RFID)-based recalibration. The interface to the haptic space in the supermarket cues the shopper to the prominent haptic cues in the vicinity of the product, and thus helps the shopper retrieve the desired product from the shelf. The results of a longitudnal series of experiments with ten visually impaired shoppers in a real supermarket are presented. It was observed that the shoppers' performance with RoboCart improved when the shopper repeatedly shopped for the same product with RoboCart. Another problem addressed in the dissertation is that of communicating user intent in robot-assisted shopping for the blind. Searching and browsing-based interfaces with three interaction modalities (browsing, typing and speech) are presented and evaluated over a publicly available database of 11,947 household products, with five blind and five sighted-blindfolded participants. Administration of the NASA Task Load Index questionnaire revealed that the browsing modality imposed a maximum workload. Also, though typing imposed a higher workload than speech, participants prefered typing over speech due to a higher frustration caused by speech misrecognitions.
Coefficient Structure of Kernel Perceptrons and Support Vector Reduction
Authors: Daniel García, Ana González, José R. Dorronsoro
Venue: Proceedings of the 2nd international work-conference on The Interplay Between Natural and Artificial Computation, Part I: Bio-inspired Modeling of Cognitive Tasks (2007)

Support Vector Machines (SVMs) with few support vectors are quite desirable, as they have a fast application to new, unseen patterns. In this work we shall study the coefficient structure of the dual representation of SVMs constructed for nonlinearly separable problems through kernel perceptron training. We shall relate them with the margin of their support vectors (SVs) and also with the number of iterations in which these SVs take part. These considerations will lead to a remove---and---retrain procedure for building SVMs with a small number of SVs where both suitably small and large coefficient SVs will be taken out from the training sample. Besides providing a significant SV reduction, our method's computational cost is comparable to that of a single SVM training.
Dynamics of learning near singularities in radial basis function networks
Authors: Haikun Wei, Shun-ichi Amari
Venue: Neural Networks (2008)

The radial basis function (RBF) networks are one of the most widely used models for function approximation in the regression problem. In the learning paradigm, the best approximation is recursively or iteratively searched for based on observed data (teacher signals). One encounters difficulties in such a process when two component basis functions become identical, or when the magnitude of one component becomes null. In this case, the number of the components reduces by one, and then the reduced component recovers as the learning process proceeds further, provided such a component is necessary for the best approximation. Strange behaviors, especially the plateau phenomena, have been observed in dynamics of learning when such reduction occurs. There exist singularities in the space of parameters, and the above reduction takes place at the singular regions. This paper focuses on a detailed analysis of the dynamical behaviors of learning near the overlap and elimination singularities in RBF networks, based on the averaged learning equation that is applicable to both on-line and batch mode learning. We analyze the stability on the overlap singularity by solving the eigenvalues of the Hessian explicitly. Based on the stability analysis, we plot the analytical dynamic vector fields near the singularity, which are then compared to those real trajectories obtained by a numeric method. We also confirm the existence of the plateaus in both batch and on-line learning by simulation.
Ubiquitous Interactive Video Editing Via Multimodal Annotations
Authors: Maria Graça C. Pimentel, Rudinei Goularte, Renan G. Cattelan, Felipe S. Santos, Cesar Teixeira
Venue: Proceedings of the 6th European conference on Changing Television Environments (2008)

Considering that, when users watch a video with someone else, they are used to make comments regarding its contents --- such as a comment with respect to someone appearing in the video --- in previous work we exploited ubiquitous computing concepts to propose the watching-and-commenting authoring paradigm in which a user's comments are automatically captured so as to automatically generate a corresponding annotated interactive video. In this paper we revisit and extend our previous work and detail our prototype that supports the watching-and-editing paradigm, discussing how a ubiquitous computing platform may explore digital ink and associated gestures to support the authoring of multimedia content while enhancing the social aspects of video watching.
The Dinosaur and the Butterfly: A Tale of Computer Ethics
Authors: John Lenarcic
Venue: IEEE Security and Privacy (2003)

Humans aspire to be rational beings, but our feelings often drive us more than logic does. Emotional intelligence-or the lack of it-often plays a key role in our daily decisions. Some philosophers would argue, though, that every time we make a choice, ethics are at play. In the immortal words of television's favorite psychiatrist, Frasier's Frasier Crane, "Ethics are what you do when no one is looking."
An analysis on the global exponential stability and the existence of periodic solutions for non-autonomous hybrid BAM neural networks with distributed delays and impulses
Authors: Yao-tang Li, Jiyu Wang
Venue: Computers Mathematics with Applications (2008)

In this paper, by utilizing the Lyapunov functional method, applying M-matrix, Young inequality technique and other analysis techniques, we analyze the exponential stability and the existence of periodic solutions for non-autonomous hybrid BAM neural networks with distributed delays and impulses. Sufficient conditions are obtained for the global exponential stability and the existence of periodic solutions for non-autonomous hybrid bidirectional associative memory (BAM) neural networks with Lipschitzian activation functions without assuming their boundedness, monotonicity or differentiability and subjected to impulsive state displacements at fixed instants of time. Finally, two examples are also provided to demonstrate the effectiveness of the results obtained.
A Collaborative Method for Reuse Potential Assessment in Reengineering-Based Product Line Adoption
Authors: Muhammad Asim Noor, Paul Grünbacher, Christopher Hoyer
Venue: Balancing Agility and Formalism in Software Engineering: Second IFIP TC 2 Central and East European Conference on Software Engineering Techniques, CEE-SET 2007, Poznan, Poland, October 10-12, 2007, Revised Selected Papers (2008)

Software product lines are rarely developed from scratch. Instead the development of a product line by reengineering existing systems is a more common scenario, which relies on the collaboration of diverse stakeholders to lay its foundations. The paper describes a collaborative scoping approach for organizations migrating existing products to a product line. The approach uses established practices from the field of reengineering and architectural recovery and synthesizes them in a collaborative process. The proposed approach employs best practices and tools from the area of collaboration engineering to achieve effective collaboration. The paper presents a case study as initial validation of the proposed approach.
Relational Sequence Alignments and Logos
Authors: Andreas Karwath, Kristian Kersting
Venue: Inductive Logic Programming: 16th International Conference, ILP 2006, Santiago de Compostela, Spain, August 24-27, 2006, Revised Selected Papers (2007)

The need to measure sequence similarity arises in many applicitation domains and often coincides with sequence alignment: the more similar two sequences are, the better they can be aligned. Aligning sequences not only shows how similar sequences are, it also shows where there are differences and correspondences between the sequences.Traditionally, the alignment has been considered for sequences of flat symbols only. Many real world sequences such as natural language sentences and protein secondary structures, however, exhibit rich internal structures. This is akin to the problem of dealing with structured examples studied in the field of inductive logic programming (ILP). In this paper, we introduce Real, which is a powerful, yet simple approach to align sequence of structured symbols using well-established ILP distance measures within traditional alignment methods. Although straight-forward, experiments on protein data and Medline abstracts show that this approach works well in practice, that the resulting alignments can indeed provide more information than flat ones, and that they are meaningful to experts when represented graphically.
Finding Corrupted Computers Using Imperfect Intrusion Prevention System Event Data
Authors: Danielle Chrun, Michel Cukier, Gerry Sneeringer
Venue: Proceedings of the 27th international conference on Computer Safety, Reliability, and Security (2008)

With the increase of attacks on the Internet, a primary concern for organizations is how to protect their network. The objectives of a security team are 1) to prevent external attackers from launching successful attacks against organization computers that could become compromised, 2) to ensure that organization computers are not vulnerable (e.g., fully patched) so that in either case the organization computers do not start launching attacks. The security team can monitor and block malicious activity by using devices such as intrusion prevention systems. However, in large organizations, such monitoring devices could record a high number of events. The contributions of this paper are 1) to introduce a method that ranks potentially corrupted computers based on imperfect intrusion prevention system event data, and 2) to evaluate the method based on empirical data collected at a large organization of about 40,000 computers. The evaluation is based on the judgment of a security expert of which computers were indeed corrupted. On the one hand, we studied how many computers classified as of high concern or of concern were indeed corrupted (i.e., true positives). On the other hand, we analyzed how many computers classified as of lower concern were in fact corrupted (i.e., false negatives).
Mobility Versus Density Metric for OLSR Enhancement
Authors: Cholatip Yawut, Beatrice Paillassa, Riadh Dhaou
Venue: Proceedings of the 3rd Asian conference on Internet Engineering: Sustainable Internet (2007)

In order to improve network performance, adaptive protocol would adapt to different aspects of the network dynamic exhibited by the wireless systems and more particularly by the ad hoc networks. In this paper we consider the adaptation to the ad hoc network dynamic through two parameters: mobility and density. We study the impact part of the density metric and of the mobility metric. Considering the Optimized Link State Routing protocol (OLSR), our work focus on the Multipoint Relays (MPR) selection. A new approach to select a MPR by using a simple modification and no additional packet header is proposed. It introduces the idea of Link Duration criterion as mobility metric for MPR selection. From simulation results it appears that the protocol performance can be enhanced by mobility adaptation after the density one. The proposed scheme outperforms the standard protocol for large number of nodes.
On the current environments for e-Government development in the enlarged European Union
Authors: Cene Bavec
Venue: Information Polity (2006)

The paper provides an empirical insight into the global conditions in which e-Government projects are developing in EU countries. We were looking for differences in national environments, identifying forces that defy or stimulate e-Government projects, examining dissimilarities between old and new EU member states, and seeking an overall assessment of the Central European countries. Research confirms that e-Government readiness correlates to national competitiveness (0.77) and particularly innovativeness (0.90). On the other hand, there is surprisingly low correlation between e-Government readiness and overall Government efficiency (0.54). Use confidence expressed terms of Composite Trust correlates with e-Government readiness (0.79), but confidence has a low impact on user preference for new services (0.55). Slightly higher is the correlation between national innovativeness and user preference for innovative services (0.62). Central European countries show the same development patterns as the old European Union member states, but the environment in the former is generally less favorable for e-Government development in all the studied aspects. Research also suggests that a more holistic view of e-Government projects would reveal a complex interplay of new Government services, economy, national innovativeness, and social structures.
Cellular Automata-Based Development of Combinational and Polymorphic Circuits: A Comparative Study
Authors: Michal Bidlo, Zdeněk Vašíček
Venue: Proceedings of the 8th international conference on Evolvable Systems: From Biology to Hardware (2008)

Cellular automata-based evolutionary development is presented for the design of single-function and polymorphic (two-function) combinational circuits. The impact of evolution of the cellular automaton initial state on the success rate of the evolved solutions is investigated. The experiments show that it is more suitable to fix a proper initial state in order to increase the successfulness and speed of evolution. The proposed developmental model is capable to design a wide range of both single-function and polymorphic circuits.
Estimation of the precision matrix of a singular Wishart distribution and its application in high-dimensional data
Authors: Tatsuya Kubokawa, Muni S. Srivastava
Venue: Journal of Multivariate Analysis (2008)

In this article, the Stein-Haff identity is established for a singular Wishart distribution with a positive definite mean matrix but with the dimension larger than the degrees of freedom. This identity is then used to obtain estimators of the precision matrix improving on the estimator based on the Moore-Penrose inverse of the Wishart matrix under the Efron-Morris loss function and its variants. Ridge-type empirical Bayes estimators of the precision matrix are also given and their dominance properties over the usual one are shown using this identity. Finally, these precision estimators are used in a quadratic discriminant rule, and it is shown through simulation that discriminant methods based on the ridge-type empirical Bayes estimators provide higher correct classification rates.
POD Analysis of Near-wake Structures of an Elliptic Cylinder Adjacent to a Free Surface
Authors: Daichin, Sang Joon Lee
Venue: Journal of Visualization (2004)

The POD (Proper Orthogonal Decomposition) method was used to investigate the near-wake behind an elliptic cylinder located under a free surface. For two different depths of cylinder submergence, the first four eigenmodes of the flow field were calculated and their structures were analyzed. The first four eigenmodes reveal the details about the global mean flow structure, with the large-scale structure being mainly related to the most energetic flow motion. The convergence of accumulated eigenvalues shows a slight dependence on the number of instantaneous velocity fields used in POD analysis.
Toward Human Arm Attention and Recognition
Authors: Takeharu Yoshizuka, Masaki Shimizu, Hiroyuki Miyamoto
Venue: Neural Information Processing: 14th International Conference, ICONIP 2007, Kitakyushu, Japan, November 13-16, 2007, Revised Selected Papers, Part I (2007)

We aim to develop a vision system that focuses on the human arm and recognizes the arm posture in complex scenes. In this paper, we introduce a computer-vision-based approach and a neocognitron-type neural network. In our computer-vision-based approach, we propose a method for arm posture estimation using an arm model with three kinds of small areas in the complex background and clothes patterns. In our neocognitron-based approach, we investigate the functional similarity between the neocognitron and the ventral visual pathway. We examine to the expand neocognitron base on stereo.
Intelligent Software Agents' Influence on Media-Based Systems
Authors: Helen D. Karatza
Venue: IEEE Distributed Systems Online (2004)

A review of Intelligent Agents for Mobile and Virtual Media, edited by Rae Earnshaw and John Vince.
A decision support system for suggesting ventilator settings: Retrospective evaluation in cardiac surgery patients ventilated in the ICU
Authors: Charlotte Allerød, Stephen E. Rees, Bodil S. Rasmussen, Dan S. Karbing, Søren Kjírgaard, Per Thorgaard, Steen Andreassen
Venue: Computer Methods and Programs in Biomedicine (2008)

Selecting appropriate ventilator settings decreases the risk of ventilator-induced lung injury. A decision support system (DSS) has been developed based on physiological models, which can advise on setting of tidal volume (Vt), respiratory frequency (f) and fraction of inspired oxygen (FiO"2). The aim of this study is to assess the feasibility of the DSS by comparing its advice with the values used in clinical practice. Data from 20 patients following uncomplicated coronary artery bypass grafting (CABG) with cardiopulmonary bypass was used to test the DSS. Ventilator settings suggested by the DSS were compared to the settings selected by the clinician. When compared to the clinician the DSS suggested: lowering FiO"2 (by median 7%, range 2-17%) at high SpO"2 and increasing FiO"2 (by median 2%, range 1-5%) at low SpO"2; lowering ventilation volume (by median 0.57lmin^-^1, range 0.2-1.1lmin^-^1) at high pHa and increasing ventilation volume (by median 0.4lmin^-^1, range 0.1-0.9lmin^-^1) at low pHa. Suggested changes in ventilation volume were such that simulated values of PIP were @?22.9cmH"2O and respiratory frequency @?18breathsmin^-^1. In all cases, computer suggested values of FiO"2, Vt or f were consistent with maintaining sufficient oxygenation, normalising pH and obtaining low values of PIP.