ppxscal/embedding_network huggingface dataset:
Predicting the similarity search performance of fingerprints and their combination with molecular property descriptors using probabilistic and information theoretic modeling
Authors: Martin Vogt, Britta Nisius, Jürgen Bajorath
Venue: Statistical Analysis and Data Mining (2009)

Similarity searching is currently one of the most widely applied approaches to computationally screen large databases for novel active compounds, and molecular fingerprints are among the most popular search tools. Fingerprint searching has recently also been applied in chemical biology to identify compounds that are selective for a target within a group of related ones. In general, fingerprints are bit string representations of molecular structure and properties but their design, size, and complexity often vary substantially. Like essentially all similarity search tools, fingerprints display a strong compound class dependence in their ability to identify active molecules and distinguish them from other database compounds. In practical applications, this limitation makes it very difficult to select or prioritize fingerprints that are most suitable for a given search problem. We have previously (i) devised a Bayesian-scoring scheme to combine fingerprints and molecular property descriptors for similarity searching and (ii) developed an information-theoretic approach to predict active compound recall rates for fingerprint searching. Herein, we combine these methods and present an approach for the prediction of compound recall in search calculations using Bayesian screening with molecular property descriptors, fingerprints and their combination. For practical similarity search applications, this analysis is highly relevant because it makes it possible to identify search methods that are most likely to be successful for a given compound activity class and screening database. Copyright &copy; 2009 Wiley Periodicals, Inc. Statistical Analysis and Data Mining 2: 123-134, 2009
Managing Trusted Keys in Internet-Scale Systems
Authors: Eric Osterweil, Dan Massey, Lixia Zhang
Venue: Proceedings of the 2009 Ninth Annual International Symposium on Applications and the Internet (2009)

In this paper we examine open issues in deploying cryptographic protections for Internet scale systems, and explore a new direction dubbed Public Space to address the challenge of distributing and maintaining trusted keys.
Attractive Visualization Influences the Perceived Quality of the Living Environment
Authors: Joske M. Houtkamp, Stefan Colijn, Arno Bouwman
Venue: Proceedings of the 2009 Second International Conference in Visualisation (2009)

An experiment was conducted with a Google Earth application which presents current and future land use in the Netherlands. Three visualization techniques representing future land use were compared: abstract colored surfaces, icons, and 3D-objects. None of the visualizations show a significant improvement of the accuracy of the information transfer or of the speed of the task performance in this experiment. The version with 3D-objects was appreciated most, and elicited more positive judgments on qualitative aspects of the perceived environment, although the visualization contained the same information as the other two conditions. This demonstrates the influence of the representation on the content, which should be considered in the design of visualizations for strategic government policy, as well as other purposes.
A Vision for Next Generation Query Processors and an Associated Research Agenda
Authors: Anastasios Gounaris
Venue: Proceedings of the 2nd International Conference on Data Management in Grid and Peer-to-Peer Systems (2009)

Query processing is one of the most important mechanisms for data management, and there exist mature techniques for effective query optimization and efficient query execution. The vast majority of these techniques assume workloads of rather small transactional tasks with strong requirements for ACID properties. However, the emergence of new computing paradigms, such as grid and cloud computing, the increasingly large volumes of data commonly processed, the need to support data driven research, intensive data analysis and new scenarios, such as processing data streams on the fly or querying web services, the fact that the metadata fed to optimizers are often missing at compile time, and the growing interest in novel optimization criteria, such as monetary cost or energy consumption, create a unique set of new requirements for query processing systems. These requirements cannot be met by modern techniques in their entirety, although interesting solutions and efficient tools have already been developed for some of them in isolation. Next generation query processors are expected to combine features addressing all of these issues, and, consequently, lie at the confluence of several research initiatives. This paper aims to present a vision for such processors, to explain their functionality requirements, and to discuss the open issues, along with their challenges.
Scene direction based reference in drama scenes
Authors: Hiroshi Nakagawa, Yoshitomo Yaginuma, Masao Sakauchi
Venue: Referring Phenomena in a Multimedia Context and their Computational Treatment (1997)

Out research target is reference relations between descriptions of script and an actor/actress who actually plays in the drama scene that correspond to the scene direction which is a part of the script. In this paper, first we analyze sentences used as the scene directions, and classify them. Then we propose the rules to extract subjects and predicates from those sentences. With the extracted subjects and predicates, we build the existence/action map that explains the situations happening on each scene. The existence/action map we build describes scenes very correctly as for whether each player appears in each scene or not. Our experiment shows that the recall is around 80% and the precision is over 90%. This means that our system of inferring reference relations works well for scene directions. Then we develop the scene retrieval system in which this map is used to retrieve scenes from the drama video database according to the input query. We also show some experimental results of our retrieval system.
An Affine Optical Flow Model for Dynamic Surface Reconstruction
Authors: Tobias Schuchert, Hanno Scharr
Venue: Statistical and Geometrical Approaches to Visual Motion Analysis: International Dagstuhl Seminar, Dagstuhl Castle, Germany, July 13-18, 2008. Revised Papers (2009)

In this paper we develop a differential model for simultaneous estimation of geometry and dynamics of a surface patch. To do so we combine a surface patch model in local 3D coordinates, a pinhole camera grid model and a brightness change model analogous to the brightness constancy constraint equation for optical flow. It turns out to be an extension of the well known affine optical flow model to higher dimensional data sets. Each of the translational and affine components of the optical flow is a term consisting of a mixture of surface patch parameters like its depth, slope, velocities etc. We evaluate the model by comparing estimation results using a simple local estimation scheme to available ground-truth. This simple estimation scheme already allows to get results in the same accuracy range one can achieve using range flow, i.e. a model for the estimation of 3D velocities of a surface point given a measured surface geometry. Consequently the new model allows direct estimation of additional surface parameters range flow is not capable of, without loss of accuracy in other parameters. What is more, it allows to design estimators coupling shape and motion estimation which may yield increased accuracy and/or robustness in the future.
Comparing Pre-filtering and Post-filtering Approach in a Collaborative Contextual Recommender System: An Application to E-Commerce
Authors: Umberto Panniello, Michele Gorgoglione, Cosimo Palmisano
Venue: Proceedings of the 10th International Conference on E-Commerce and Web Technologies (2009)

Recent literature predicts that including context in a recommender system may improve its performance. The context-based recommendation approaches are classified as pre-filtering, post-filtering and contextual modeling. Little research has been done on studying whether including context in a recommender system improves the recommendation performance and no research has compared yet the different approaches to contextual RS. The research contribution of this work lies in studying the effect of the context on the recommendation performance and comparing a pre-filtering approach to a post-filtering using a collaborative filtering recommender system.
The Inverse Taylor Expansion Problem in Linear Logic
Authors: Michele Pagani, Christine Tasson
Venue: Proceedings of the 2009 24th Annual IEEE Symposium on Logic In Computer Science (2009)

Linear Logic is based on the analogy between algebraic linearity (i.e. commutation with sums and with products with scalars) and the computer science linearity (i.e. calling inputs only once). Keeping on this analogy, Ehrhard and Regnier introduced Differential Linear Logic(DiLL) --- an extension of Multiplicative Exponential Linear Logic with differential constructions. In this setting, promotion (the logical exponentiation) can be approximated by a sum of promotion-free proofs f DiLL via Taylor expansion. We present a constructive way to revert Taylor expansion. Precisely, we define merging reduction --- a rewriting system which merges a finite sum of DiLL proofs into a proof with promotion whenever the sum is an approximation of the Taylor expansion of this proof. We prove that this algorithm is sound, complete and can be run in non-deterministic polynomial time.
From XQuery to relational logics
Authors: Michael Benedikt, Christoph Koch
Venue: ACM Transactions on Database Systems (TODS) (2009)

Predicate logic has long been seen as a good foundation for querying relational data. This is embodied in the correspondence between relational calculus and first-order logic, and can also be seen in mappings from fragments of the standard relational query language SQL to extensions of first-order logic (e.g. with counting). A key question is what is the analog to this correspondence for querying tree-structured data, as seen, for example, in XML documents. We formalize this as the question of the appropriate logical query language for defining transformations on tree-structured data. The predominant practitioner paradigm for defining such transformations is top-down tree building. This is embodied by the XQuery query language, which builds the output tree in parallel starting at the root, based on variable bindings and nodeset queries in the XPath language. The goal of this article is to compare the expressiveness of top-down tree-building languages based on a benchmark of predicate logic. We start by giving a formalized XQuery XQ that can serve as a representative of the top-down approach. We show that all queries in XQ with only atomic equality are equivalent to first-order interpretations, an analog to first-order logic (FO) in the setting of transformations of tree-structured data. We then consider fragments of atomic XQ. We identify a fragment that maps efficiently into first-order, a fragment that maps into existential first-order logic, and a fragment that maps into the navigationally two-variable fragment of first-order logic&mdash;an analog of two-variable logic in the setting where data values are unbounded. When XQ is considered with deep equality, we find that queries can be translated into FO with counting (FO(Cnt)). Translations from XQ to logical languages on relations have a number of consequences. We use them to derive complexity bounds for XQ fragments, and to bound the Boolean expressiveness of XQ fragments.
Analyzing Cryptographic Protocols Using AI Planning Technology
Authors: Yadi Wang, Zhiyong Zhou, Yu Zhao, Jihong Han
Venue: Proceedings of the 2009 Second International Symposium on Electronic Commerce and Security - Volume 01 (2009)

In this paper, protocol insecurity problem is described, and AI planning system is used to solve the problem. Based on running characteristics and laws of cryptographic protocols, a planning-based formal model for cryptographic protocol analysis is presented, after its first-order syntax, formal definition and operational semantics are given, formalization for protocol honest agents, the intruder and protocol insecurity goals are presented, and a SAT-based solving algorithm for attack planning is proposed.
A Network-Integrated Feature-Driven Engineering Environment: Information Modeling and Process Management
Authors: Guo-xian Wang, Wen-zu Zhang, Andrew Yeh-Ching Nee
Venue: Proceedings of the 2009 International Conference on Measuring Technology and Mechatronics Automation - Volume 03 (2009)

Conventional data-centric integration approaches assume that the end-users are fully responsible for work-flow control, data consistency and integrity maintenance and inter-process coordination, generally without computer augmentation. The objective of this study is to develop a network-integrated engineering environment with an expanding set of system capabilities that can off-load engineers from some of these responsibilities and complexity, based on an integration approach which is both data- and process-centric. The envisioned system is configured on top of a generic CAX framework with a process management module encapsulated for assisting engineers to carry out a set of tightly-interrelated engineering activities in a product development cycle following a feature-driven process pattern. Sheet metal products using progressive dies were selected as the demonstration case to show two main aspects of the approach: information modeling and implementation of the process management module.
Issues in Dynamic Generation of Sign Language Utterances for a Web 2.0 Virtual Signer
Authors: Annelies Braffort, Jean-Paul Sansonnet, Cyril Verrecchia
Venue: Proceedings of the 9th International Conference on Intelligent Virtual Agents (2009)

In this paper, we present our current study on the design of a virtual agent able to express sentences in Sign Language (SL), so-called `Virtual Signer', in the context of interactive web-based applications.Up now, little work has been carried out on web-based virtual signers. As for current research on virtual signers in standalone applications, it relies on two main approaches: Pre-synthesized animations based on motion capture [1] or rotoscoping [2], and generated animations [3], with very little interactivity. Our aim is to provide the virtual signer with richer interacting capabilities with the data contained in the web page.
A Proposal of Awareness Services for the Construction of Quality Community Knowledge Supported by the Knowledge Management System KnowCat
Authors: Ruth Cobos, Ivan Dario Claros Gómez, Jaime Moreno-Llorena
Venue: Proceedings of the Symposium on Human Interface 2009 on ConferenceUniversal Access in Human-Computer Interaction. Part I: Held as Part of HCI International 2009 (2009)

It is well known that members of work groups need awareness about one another, about shared elements, and about the group process. We present a generic framework of awareness services for groupware systems. The proposed approach has been tested through the implementation of a prototype composed by several awareness services for the Knowledge Management system called KnowCat. KnowCat is a groupware that supports the collaborative construction of quality community knowledge. We carried out a research study with a group of students enrolled in a graduate course at Universidad Autónoma de Madrid (Spain) to test our approach. The study outcomes corroborated that providing to the KnowCat users the most useful information about how the classmates have interacted with the system through the awareness services, can help them to know how they should solve their own work in the system and to be aware that they are working in a collaborative way.
The Lessons Learned in Developing Multi-user Attentive Quiz Agents
Authors: Hung-Hsuan Huang, Takuya Furukawa, Hiroki Ohashi, Aleksandra Cerekovic, Yuji Yamaoka, Igor S. Pandzic, Yukiko Nakano, Toyoaki Nishida
Venue: Proceedings of the 9th International Conference on Intelligent Virtual Agents (2009)

This paper presents two attempts in integrating attentiveness into a virtual quiz agent in the situation when multiple game participants present. One of them features an utterance strategy to determine when and whom to talk to among the participants. The other one features a SVM (support vector machine) triggered transition state model of the agent's attitude toward the participants in expressing observable behaviors. Both of them are driven by timings determined on video and audio information of the participants' activity while they are trying to solve the quizzes. To evaluate these two prototype systems, we applied GNAT (Go/No-go Task) method in addition to questionnaires. From the joint results of the subject experiments, the direction in finding appropriate action timings of the agent is proved to be able to improve user impressions.
Using the ENF Criterion for Determining the Time of Recording of Short Digital Audio Recordings
Authors: Maarten Huijbregtse, Zeno Geradts
Venue: Proceedings of the 3rd International Workshop on Computational Forensics (2009)

The Electric Network Frequency (ENF) Criterion is a recently developed forensic technique for determining the time of recording of digital audio recordings, by matching the ENF pattern from a questioned recording with an ENF pattern database. In this paper we discuss its inherent limitations in the case of short --- i.e., less than 10 minutes in duration --- digital audio recordings. We also present a matching procedure based on the correlation coefficient, as a more robust alternative to squared error matching.
Narcissus: Group and Individual Models to Support Small Group Work
Authors: Kimberley Upton, Judy Kay
Venue: Proceedings of the 17th International Conference on User Modeling, Adaptation, and Personalization: formerly UM and AH (2009)

Long term group work by small teams is a central part of many learning and workplace activities. Widespread group support tools such as wikis, version control systems and issue tracking systems are an invaluable aid for groups. They also have the potential to provide evidence for valuable models of the group activity. This paper describes Narcissus, designed as a new way to improve group-work by exploiting evidence from use of such group-work tools, to create a visual presentation of a group model. The Narcissus models and interfaces were designed to help groups function more effectively. It helps individuals see how well they are contributing to the group. It enables groups to assess contributions relative to plans. And it helps facilitators identify problems. The Narcissus interface supports scrutability and control over its models. We report a four part evaluation of Narcissus: individual level with 23 students; group level by 5 groups; facilitator level with 5 facilitators; and fine grained study with 8 students. Results indicate that all these groups were able to understand and use Narcissus and that they considered it effective in modelling the group activity in useful ways. They particularly valued the support for scrutability. Key contributions of this work are the creation of a scrutable and user controlled group model to support group work and to provide a new form of navigation interface for a complex groupware site.
Another Reason Why Conceptual Graphs Need Actors
Authors: B. J. Smith, Harry Delugach
Venue: Proceedings of the 17th International Conference on Conceptual Structures: Conceptual Structures: Leveraging Semantic Technologies (2009)

Conceptual graphs (CGs) are a knowledge representation formalism that models monotonic first-order logic. However, in the case of an active knowledge base and in other cases, it is necessary to modify a CG dynamically, rendering the preceding static first-order CG possibly inconsistent and in need of further analysis. In order to extend monotonic first-order logic to non-monotonic second-order computation, and therefore achieve all of the power of a modern computer, CGs need to use atomic actors to represent change. To illustrate the power of actors, we represent the well-defined Turing machine; this has the added effect of showing that CGs can represent any of the power of a modern computer. This addition to the CG theory will have other similar practical effects.
Testing with model checkers: a survey
Authors: Gordon Fraser, Franz Wotawa, Paul E. Ammann
Venue: Software Testing, Verification Reliability (2009)

About a decade after the initial proposal to use model checkers for the generation of test cases we take a look at the results in this field of research. Model checkers are formal verification tools, capable of providing counterexamples to violated properties. Normally, these counterexamples are meant to guide an analyst when searching for the root cause of a property violation. They are, however, also very useful as test cases. Many different approaches have been presented, many problems have been solved, yet many issues remain. This survey paper reviews the state of the art in testing with model checkers. Copyright &copy; 2008 John Wiley & Sons, Ltd.
Class Prediction from Disparate Biological Data Sources Using an Iterative Multi-Kernel Algorithm
Authors: Yiming Ying, Colin Campbell, Theodoros Damoulas, Mark Girolami
Venue: Proceedings of the 4th IAPR International Conference on Pattern Recognition in Bioinformatics (2009)

For many biomedical modelling tasks a number of different types of data may influence predictions made by the model. An established approach to pursuing supervised learning with multiple types of data is to encode these different types of data into separate kernels and use multiple kernel learning. In this paper we propose a simple iterative approach to multiple kernel learning (MKL), focusing on multi-class classification. This approach uses a block L 1-regularization term leading to a jointly convex formulation. It solves a standard multi-class classification problem for a single kernel, and then updates the kernel combinatorial coefficients based on mixed RKHS norms. As opposed to other MKL approaches, our iterative approach delivers a largely ignored message that MKL does not require sophisticated optimization methods while keeping competitive training times and accuracy across a variety of problems. We show that the proposed method outperforms state-of-the-art results on an important protein fold prediction dataset and gives competitive performance on a protein subcellular localization task.
Software Chip Design Method and Its Application
Authors: Deng Chunjian, Zhuo Hong
Venue: Proceedings of the 2009 Asia-Pacific Conference on Information Processing - Volume 01 (2009)

Software chip is designed to present a study software platform without support of hardware entity by simulating hardware chip operating function. The paper introduces the concept of software chip, and presents software chip design methods. When designing a software chip, specific and related things or controls are chosen to substitute for the abstract functions of the chip, and signal flow trend and corresponding output, following operating principle of the chip, will be designed in the style that functions of the chip are visually displayed on the action of virtual input controls. Two different types of examples are presented to explain the design methods, and the mechanisms, functions and intuitive demonstration means of the example hardware chips are analyzed and all these by software simulation are realized.