pinecone/core-2020-05-10-deduplication huggingface dataset:
An efficiently computable graph-based metric for the classification of small molecules

In machine learning, there has been an increased interest in metrics on structured data. The application we focus on is drug discovery. Although graphs have become very popular for the representation of molecules, a lot of operations on graphs are NP-complete. Representing the molecules as outerplanar graphs, a subclass within general graphs, and using the block-and-bridge preserving subgraph isomorphism, we define a metric and we present an algorithm for computing it in polynomial time. We evaluate this metric and more generally also the block-and-bridge preserving matching operator on a large dataset of molecules, obtaining favorable results.status: publishe
Empirical asymmetric selective transfer in multi-objective decision trees

We consider learning tasks where multiple target variables
need to be predicted. Two approaches have been used in this setting:
(a) build a separate single-target model for each target variable, and (b)
build a multi-target model that predicts all targets simultaneously; the
latter may exploit potential dependencies among the targets. For a given
target, either (a) or (b) can yield the most accurate model. This shows
that exploiting information available in other targets may be beneficial
as well as detrimental to accuracy. This raises the question whether it is
possible to find, for a given target (we call this the main target), the best
subset of the other targets (the support targets) that, when combined
with the main target in a multi-target model, results in the most accurate
model for the main target. We propose Empirical Asymmetric Selective
Transfer (EAST), a generally applicable algorithm that approximates
such a subset. Applied to decision trees, EAST outperforms single-target
decision trees, multi-target decision trees, and multi-target decision trees
with target clustering.status: publishe
DFS Based Partial Pathways in GA for Protein Structure Prediction

Nondeterministic conformational search techniques, such as Genetic Algorithms (GAs) are promising for solving protein structure prediction (PSP) problem. The crossover operator of a GA can underpin the formation of potential conformations by exchanging and sharing potential sub-conformations, which is promising for solving PSP. However, the usual nature of an optimum PSP conformation being compact can produce many invalid conformations (by having non-self-avoiding-walk) using crossover. While a crossover-based converging conformation suffers from limited pathways, combining it with depth-first search (DFS) can partially reveal potential pathways. DFS generates random conformations increasingly quickly with increasing length of the protein sequences compared to random-move-only-based conformation generation. Random conformations are frequently applied for maintaining diversity as well as for initialization in many GA variations.Griffith Sciences, School of Information and Communication TechnologyFull Tex
On the Integration of a TSP Heuristic into an EA for the Bi-objective Ring Star Problem

International audienceThis paper discusses a new hybrid solution method for a bi-objective routing problem, namely the bi-objective ring star problem. The bi-objective ring star problem is a generalization of the ring star problem in which the assignment cost has been dissociated from the cost of visiting a subset of nodes. Here, we investigate the possible contribution of incorporating specialized TSP heuristics into a multiobjective evolutionary algorithm. Experiments show that the use of this hybridization scheme allows a strict improvement of the generated sets of non-dominated solutions
Spatially-Variant Directional Mathematical Morphology Operators Based on a Diffused Average Squared Gradient Field

International audienceThis paper proposes an approach for mathematical morphology operators whose structuring element can locally adapt its orientation across the pixels of the image. The orientation at each pixel is extracted by means of a diffusion process of the average squared gradient field. The resulting vector field, the average squared gradient vector flow, extends the orientation information from the edges of the objects to the homogeneous areas of the image. The provided orientation field is then used to perform a spatially variant filtering with a linear structuring element. Results of erosion, dilation, opening and closing spatially-variant on binary images prove the validity of this theoretical sound and novel approach
A Use-Case Driven Approach to Formal Service-Oriented Modelling.

This is the author's final draft of the paper published as Communications in Computer and Information Science, 2008, 17 (6), pp. 155-169.  The final version is available from http://www.springerlink.com/content/p7188017hp7k0081/.  Doi: 10.1007/978-3-540-88479-8_12We put forward a use-case based approach for SRML – a formal framework that is being defined by the SENSORIA consortium for service-oriented modelling. We expand on the way SRML contributes to the engineering\ud
of software systems and we propose a number of extensions to the UML for supporting that approach. We use a mortgage brokerage scenario for illustrating our approach
SENSORIA Patterns: Augmenting Service Engineering with Formal Analysis, Transformation and Dynamicity

The IST-FET Integrated Project Sensoria is developing a novel comprehensive approach to the engineering of service-oriented software systems where foundational theories, techniques and methods are fully integrated into pragmatic software engineering processes. The techniques and tools of Sensoria encompass the whole software development cycle, from business and architectural design, to quantitative and qualitative analysis of system properties, and to transformation and code generation. The Sensoria approach takes also into account reconfiguration of service-oriented architectures (SOAs) and re-engineering of legacy systems.\ud
In this paper we give first a short overview of Sensoria and then present a pattern language for augmenting service engineering with formal analysis, transformation and dynamicity. The patterns are designed to help software developers choose appropriate tools and techniques to develop service-oriented systems with support from formal methods. They support the whole development process, from the modelling stage to deployment activities and give an overview of many of the research areas pursued in the Sensoria project.\u
Measurement-Based Timing Analysis

In this paper we present a measurement-based worst-case execution time (WCET) analysis method. Exhaustive end-to-end execution-time measurements are computationally intractable in most cases. Therefore, we propose to measure execution times of subparts of the application code and then compose these times into it safe WCET bound. This raises a number of challenges to be solved. First. there is the question of how to define and Subsequently calculate adequate subparts. Second, a huge amount of test data is required enforcing the execution of selected paths to perform the desired runtime measurements. The presented method provides solutions to both problems. In a number of experiments we show the usefulness of the theoretical concepts and the practical feasibility by using current state-of-the-art industrial case studies from project partners
The subductability of continental lithosphere: the before and after story

The temporal evolution of internal forces in a collision environment controls first-order characteristics such as convergence rate, slab dip, subduction stall, and slab breakoff, amongst others. Foremost among these forces are the positive buoyancy provided by the subduction of felsic continental material and the negative buoyancy associated with the slab. In this work we use fully dynamic thermomechanical models coupled with thermodynamic/petrological formalisms to study the evolution of these forces during a continent–arc/microcontinent collision and their influence on the large-scale dynamics of the system. Two distinctive features of our models that allow a self-consistent assessment of collision dynamics are: (1) the use of a new thermodynamic database valid up to ~25–30 GPa that includes most of the major phases relevant to continental subduction, and (2) a fully dynamic approach in which no velocities are imposed to either force or stop subduction. The former allows realistic computations of the buoyancy forces driving the system as a function of P-T-composition. The latter assures that computed velocities emerge self-consistently in our simulations in response to the balance between internal forces in our numerical domain. The main results from our experiments can be summarized as follows. (1) The delamination of the lithospheric mantle after a short episode of continental subduction is a viable scenario to end continental subduction; the associated evolution of convergence is comparable to those proposed for real collision setting. (2) We corroborate previous results showing that the main control on the dynamics and final configuration (type of slab breakoff) of the collision is the rheology and composition of the continental crust; strong mafic crusts favor deep subduction and recycling of significant volumes of continental material, while soft felsic crusts preclude them. (3) Subducted continental crust remains buoyant with respect to the surrounding mantle down to depths of ~250–300 km, thus allowing exhumation of deeply subducted crust as long as a detachment from the slab occurs. (4) Realistic compositional stratifications in the continental lithospheric mantle exert only a modest influence on the overall evolution of the collision system. (5) Subducted continental crust to depths >250–300 km becomes significantly denser than the surrounding mantle due to the appearance in the solid assemblage of high-density phases such as hollandite and stishovite; this provides extra negative buoyancy to the slab and precludes the exhumation of crustal components. This supports the idea of the existence of a “depth of no return” for continental material at around 250 km depth.Peer ReviewedPostprint (author's final draft
Enhancing semantic web services with inheritance

Currently proposed Semantic Web Services technologies allow the creation of ontology-based semantic annotations of Web services so that software agents are able to discover, invoke, compose and monitor these services with a high degree of automation. The OWL Services (OWL-S) ontology is an upper ontology in OWL language, providing essential vocabularies to semantically describe Web services. Currently OWL-S services can only be developed independently; if one service is unavailable then finding a suitable alternative would require an expensive and difficult global search/match. It is desirable to have a new OWL-S construct that can systematically support substitution tracing as well as incremental development and reuse of services. Introducing inheritance relationship (IR) into OWL-S is a natural solution. However, OWL-S, as well as most of the other currently discussed formalisms for SemanticWeb Services such as WSMO or SAWSDL, has yet to define a concrete and self-contained mechanism of establishing inheritance relationships among services, which we believe is very important for the automated annotation and discovery of Web services as well as human organization of services into a taxonomy-like structure. In this paper, we extend OWL-S with the ability to define and maintain inheritance relationships between services. Through the definition of an additional “inheritance profile”, inheritance relationships can be stated and reasoned about. Two types of IRs are allowed to grant service developers the choice to respect the “contract” between services or not. The proposed inheritance framework has also been implemented and the prototype will be briefly evaluated as well
Semantic modelling of user interests based on cross-folksonomy analysis

The final publication is available at Springer via http://dx.doi.org/10.1007/978-3-540-88564-1_40Proceedings of 7th International Semantic Web Conference, ISWC 2008, Karlsruhe, Germany, October 26-30, 2008.The continued increase in Web usage, in particular participation in folksonomies, reveals a trend towards a more dynamic and interactive Web where individuals can organise and share resources. Tagging has emerged as the de-facto standard for the organisation of such resources, providing a versatile and reactive knowledge management mechanism that users find easy to use and understand. It is common nowadays for users to have multiple profiles in various folksonomies, thus distributing their tagging activities. In this paper, we present a method for the automatic consolidation of user profiles across two popular social networking sites, and subsequent semantic modelling of their interests utilising Wikipedia as a multi-domain model. We evaluate how much can be learned from such sites, and in which domains the knowledge acquired is focussed. Results show that far richer interest profiles can be generated for users when multiple tag-clouds are combined.This research has been supported by the TAGora project funded by the Future and
Emerging Technologies program (IST-FET) of the European Commission under the
contract IST-34721. The information provided is the sole responsibility of the authors
and does not reflect the Commission’s opinion. The Commission is not responsible for
any use that may be made of data appearing in this publicatio
A fuzzy approach to skin color detection

Skin detection is a useful tool for many subsequent image processing tasks, such as face detection, face tracking or human-computer interfaces. In many cases, using a skin color detection scheme is related to a proper representation of the color space chosen to interpret image information. In this work, we propose a fuzzy system for detecting skin in the RGB color space, so that each color plane is modeled using fuzzy sets. As a consequence, the development of the membership functions, the inference system and the defuzzifying process are described throughout this paper. The experiments have been performed with the XM2VTS and VALID face databases and the results show that our system has high detection rates and low false positive rates compared to other similar skin color detectors
Cooperation strategies for pursuit games: from a greedy to an evolutive approach

Developing coodination among groups of agents is a big challenge in multi-agent systems. An appropriate enviroment to test new solutions is the prey-predator pursuit problem. As it is stated many times in literature, algorithms and conclusions obtained in this environment can be extended and applied to many particular problems. The first solutions for this problem proposed greedy algorithms that seemed to do the job. However, when concurrency is added to the environment it is clear that inter-agent communication and coordination is essential to achieve good results. This paper proposes two new ways to achieve agent coodination. It starts extending a well-known greedy strategy to get the best of a greedy approach. Next, a simple coodination protocol for prey-sight notice is developed. Finally, under the need of better coordination, a Neuroevolution approach is used to improve the solution. With these solutions developed, experiments are carried out and performance measures are compared. Results show that each new step represents an improvement with respect to the previous one. In conclusion, we consider this approach to be a very promising one, with still room for discussion and more improvements
Structural Sensitivity of Neural and Genetic Networks

International audienceThis paper aims at giving new results on the structural sensitivity of biological networks represented by threshold Boolean networks and ruled by Hopfield-like evolution laws classically used in the context of neural and genetic networks. Indeed, the objective is to present how certain changes and/or perturbations in such networks can modify signicantly their asymptotic behaviour. More precisely, this work has been focused on three diferent kinds of what we think to be relevant in the biological area of robustness (in both theoretical and applied frameworks): the boundary sensitivity (external fields, hormone flows, ...), the state sensitivity (axonal or somatic modulations, microRNAs actions, ...) and the updating sensitivity
Transforming data by calculation

Thispaperaddressesthefoundationsofdata-modeltransformation.A catalog of data mappings is presented which includes abstraction and representa- tion relations and associated constraints. These are justified in an algebraic style via the pointfree-transform, a technique whereby predicates are lifted to binary relation terms (of the algebra of programming) in a two-level style encompassing both data and operations. This approach to data calculation, which also includes transformation of recursive data models into “flat” database schemes, is offered as alternative to standard database design from abstract models. The calculus is also used to establish a link between the proposed transformational style and bidi- rectional lenses developed in the context of the classical view-update problem.Fundação para a Ciência e a Tecnologia (FCT
A Language for Specifying Informational Graphics from First Principles

Informational visualization tools, such as commercial charting packages, provide a standard set of visualizations for tabular data, including bar charts, scatter plots, pie charts, and the like. For some combinations of data and task, these are suitable visualizations. For others, however, novel visualizations over multiple variables would be preferred but are unavailable in the fixed list of standard options. To allow for these cases, we introduce a declarative language for specifying visualizations on the basis of the first principles on which (a subset of) informational graphics are built. The functionality we aim to provide with this language is presented by way of example, from simple scatter plots to versions of two quite famous visualizations: Minard’s depiction of troop strength during Napoleon’s march on Moscow and a map of the early ARPAnet from the ancient history of the Internet. Benefits of our approach include flexibility and expressiveness for specifying a range of visualizations that cannot be rendered with standard commercial systems.Engineering and Applied Science
A Simple Language for Novel Visualizations of Information

While information visualization tools support the representation of abstract data, their ability to enhance one’s understanding of complex relationships can be hindered by a limited set of predefined charts. To enable novel visualization over multiple variables, we propose a declarative language for specifying informational graphics from first principles. The language maps properties of generic objects to graphical representations based on scaled interpretations of data values. An iterative approach to constraint solving that involves user advice enables the optimization of graphic layouts. The flexibility and expressiveness of a powerful but relatively easy to use grammar supports the expression of visualizations ranging from the simple to the complex.Engineering and Applied Science
Recovering light directions and camera poses from a single sphere

LNCS v. 5302 is the conference proceedings of ECCV 2008This paper introduces a novel method for recovering both the light directions and camera poses from a single sphere. Traditional methods for estimating light directions using spheres either assume both the radius and center of the sphere being known precisely, or they depend on multiple calibrated views to recover these parameters. It will be shown in this paper that the light directions can be uniquely determined from the specular highlights observed in a single view of a sphere without knowing or recovering the exact radius and center of the sphere. Besides, if the sphere is being observed by multiple cameras, its images will uniquely define the translation vector of each camera from a common world origin centered at the sphere center. It will be shown that the relative rotations between the cameras can be recovered using two or more light directions estimated from each view. Closed form solutions for recovering the light directions and camera poses are presented, and experimental results on both synthetic and real data show the practicality of the proposed method. © 2008 Springer Berlin Heidelberg.postprintThe 10th European Conference on Computer Vision (ECCV 2008), Marseille, France, 12-18 October 2008. In Lecture Notes in Computer Science, 2008, v. 5302, pt. 1, p. 631-64
Local Statistic Based Region Segmentation with Automatic Scale Selection

International audienceRecently, new segmentation models based on local information have emerged. They combine local statistics of the regions along the contour (inside and outside) to drive the segmentation procedure. Since they are based on local decisions, these models are more robust to local variations of the regions of interest (contrast, noise, blur, . . . ). They nonetheless also introduce some new difficulties which are inherent to the fact of basing a global property (the segmentation) on pure local decisions. This papers explores some of those difficulties and proposes some possible corrections. Results on both 2D and 3D data are compared to those obtained without these corrections
An extended phase field higher-order active contour model for networks and its application to road network extraction from VHR satellite images.

This paper addresses the segmentation from an image of entities that have the form of a 'network', i.e. the region in the image corresponding to the entity is composed of branches joining together at junctions, e.g. road or vascular networks. We present a new phase field higher-order active contour (HOAC) prior model for network regions, and apply it to the segmentation of road networks from very high resolution satellite images. This is a hard problem for two reasons. First, the images are complex, with much 'noise' in the road region due to cars, road markings, etc., while the background is very varied, containing many features that are locally similar to roads. Second, network regions are complex to model, because they may have arbitrary topology. In particular, we address a severe limitation of a previous model in which network branch width was constrained to be similar to maximum network branch radius of curvature, thereby providing a poor model of networks with straight narrow branches or highly Curved, wide branches. To solve this problem, we propose a new HOAC prior energy term, and reformulate it as a nonlocal phase field energy. We analyse the stability of the new model, and find that in addition to solving the above problem by separating the interactions between points on the same and opposite sides of a network branch, the new model permits the modelling of two widths simultaneously. The analysis also fixes some of the model parameters in terms of network width(s). After adding a likelihood energy, we use the model to extract the road network quasi-automatically from pieces of a QuickBird image, and compare the results to other models in the literature. The results demonstrate the superiority of the new model, the importance of strong prior knowledge in general, and of the new term in particular