Laboratoire Lorrain de Recherche en Informatique et ses Applications

This article presents a multiple-precision binary floating-point library, written in the ISO C language, and based on the GNU MP library. Its particularity is to extend to arbitrary-precision, ideas from the IEEE 754 standard, by providing correct rounding and exceptions . We demonstrate how these strong semantics are achieved---with no significant slowdown with respect to other arbitrary-precision tools---and discuss a few applications where such a library can be useful.

The topic of this review is geometric registration in robotics. Registration algorithms associate sets of data into a common coordinate system. They have been used extensively in object reconstruction, inspection, medical application, and localization of mobile robotics. We focus on mobile robotics applications in which point clouds are to be registered. While the underlying principle of those algorithms is simple, many variations have been proposed for many different applications. In this review, we give a historical perspective of the registration problem and show that the plethora of solutions can be organized and differentiated according to a few elements. Accordingly, we present a formalization of geometric registration and cast algorithms proposed in the literature into this framework. Finally, we review a few applications of this framework in mobile robotics that cover different kinds of platforms, environments, and tasks. These examples allow us to study the specific requirements of each use case and the necessary configuration choices leading to the registration implementation. Ultimately, the objective of this review is to provide guidelines for the choice of geometric registration configuration.

HexServer (http://hexserver.loria.fr/) is the first Fourier transform (FFT)-based protein docking server to be powered by graphics processors. Using two graphics processors simultaneously, a typical 6D docking run takes approximately 15 s, which is up to two orders of magnitude faster than conventional FFT-based docking approaches using comparable resolution and scoring functions. The server requires two protein structures in PDB format to be uploaded, and it produces a ranked list of up to 1000 docking predictions. Knowledge of one or both protein binding sites may be used to focus and shorten the calculation when such information is available. The first 20 predictions may be accessed individually, and a single file of all predicted orientations may be downloaded as a compressed multi-model PDB file. The server is publicly available and does not require any registration or identification by the user.

In this paper, we propose a novel polygonal remeshing technique that exploits a key aspect of surfaces: the intrinsic anisotropy of natural or man-made geometry. In particular, we use curvature directions to drive the remeshing process, mimicking the lines that artists themselves would use when creating 3D models from scratch. After extracting and smoothing the curvature tensor field of an input genus-0 surface patch, lines of minimum and maximum curvatures are used to determine appropriate edges for the remeshed version in anisotropic regions, while spherical regions are simply point sampled since there is no natural direction of symmetry locally. As a result our technique generates polygon meshes mainly composed of quads in anisotropic regions, and of triangles in spherical regions. Our approach provides the flexibility to produce meshes ranging from isotropic to anisotropic, from coarse to dense, and from uniform to curvature adapted.

The use of networks for communications between the electronic control units (ECU) of a vehicle in production cars dates from the beginning of the 1990s. The specific requirements of the different car domains have led to the development of a large number of automotive networks such as Local Interconnect Network, J1850, CAN, TTP/C, FlexRay, media-oriented system transport, IDB1394, etc. This paper first introduces the context of in-vehicle embedded systems and, in particular, the requirements imposed on the communication systems. Then, a comprehensive review of the most widely used automotive networks, as well as the emerging ones, is given. Next, the current efforts of the automotive industry on middleware technologies, which may be of great help in mastering the heterogeneity, are reviewed. Finally, we highlight future trends in the development of automotive communication systems.

BACKGROUND: The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. RESULTS: Here, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory. CONCLUSION: We conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens.

This paper presents a comprehensive introduction to the ELAN rule-based programming language. We describe the main features of the language, the ELAN environment, and introduce bibliographic references to various papers addressing foundations, implementation and applications of ELAN.

Mobile communication networks connect much of the world's population. The security of users' calls, SMSs, and mobile data depends on the guarantees provided by the Authenticated Key Exchange protocols used. For the next-generation network (5G), the 3GPP group has standardized the 5G AKA protocol for this purpose. We provide the first comprehensive formal model of a protocol from the AKA family: 5G AKA. We also extract precise requirements from the 3GPP standards defining 5G and we identify missing security goals. Using the security protocol verification tool Tamarin, we conduct a full, systematic, security evaluation of the model with respect to the 5G security goals. Our automated analysis identifies the minimal security assumptions required for each security goal and we find that some critical security goals are not met, except under additional assumptions missing from the standard. Finally, we make explicit recommendations with provably secure fixes for the attacks and weaknesses we found.

Distributed computing is a very broad and active research area comprising fields such as cluster computing, computational grids, desktop grids and peer-to-peer (P2P) systems. Unfortunately, it is often impossible to obtain theoretical or analytical results to compare the performance of algorithms targeting such systems. One possibility is to conduct large numbers of back-to-back experiments on real platforms. While this is possible on tightly-coupled platforms, it is infeasible on modern distributed platforms as experiments are labor-intensive and results typically not reproducible. Consequently, one must resort to simulations, which enable reproducible results and also make it possible to explore wide ranges of platform and application scenarios. In this paper we describe the SimGrid framework, a simulation-based framework for evaluating cluster, grid and P2P algorithms and heuristics. This paper focuses on SimGrid v3, which greatly improves on previous versions thanks to a novel and validated modular simulation engine that achieves higher simulation speed without hindering simulation accuracy. Also, two new user interfaces were added to broaden the targeted research community. After surveying existing tools and methodologies we describe the key features and benefits of SimGrid.

YASS is a DNA local alignment tool based on an efficient and sensitive filtering algorithm. It applies transition-constrained seeds to specify the most probable conserved motifs between homologous sequences, combined with a flexible hit criterion used to identify groups of seeds that are likely to exhibit significant alignments. A web interface (http://www.loria.fr/projects/YASS/) is available to upload input sequences in fasta format, query the program and visualize the results obtained in several forms (dot-plot, tabular output and others). A standalone version is available for download from the web page.

In this paper, we propose a novel polygonal remeshing technique that exploits a key aspect of surfaces: the intrinsic anisotropy of natural or man-made geometry. In particular, we use curvature directions to drive the remeshing process, mimicking the lines that artists themselves would use when creating 3D models from scratch. After extracting and smoothing the curvature tensor field of an input genus-0 surface patch, lines of minimum and maximum curvatures are used to determine appropriate edges for the remeshed version in anisotropic regions, while spherical regions are simply point sampled since there is no natural direction of symmetry locally. As a result our technique generates polygon meshes mainly composed of quads in anisotropic regions, and of triangles in spherical regions. Our approach provides the flexibility to produce meshes ranging from isotropic to anisotropic, from coarse to dense, and from uniform to curvature adapted.

In this paper, we present a novel framework for semi-automatically creating linguistically challenging microplanning data-to-text corpora from existing Knowledge Bases. Because our method pairs data of varying size and shape with texts ranging from simple clauses to short texts, a dataset created using this framework provides a challenging benchmark for microplanning. Another feature of this framework is that it can be applied to any large scale knowledge base and can therefore be used to train and learn KB verbalisers. We apply our framework to DBpedia data and compare the resulting dataset with Wen et al. (2016)'s. We show that while Wen et al.'s dataset is more than twice larger than ours, it is less diverse both in terms of input and in terms of text. We thus propose our corpus generation framework as a novel method for creating challenging data sets from which NLG models can be learned which are capable of handling the complex interactions occurring during in micro-planning between lexicalisation, aggregation, surface realisation, referring expression generation and sentence segmentation. To encourage researchers to take up this challenge, we recently made available a dataset created using this framework in the context of the WEBNLG shared task.

MOTIVATION: Modelling protein-protein interactions (PPIs) is an increasingly important aspect of structural bioinformatics. However, predicting PPIs using in silico docking techniques is computationally very expensive. Developing very fast protein docking tools will be useful for studying large-scale PPI networks, and could contribute to the rational design of new drugs. RESULTS: The Hex spherical polar Fourier protein docking algorithm has been implemented on Nvidia graphics processor units (GPUs). On a GTX 285 GPU, an exhaustive and densely sampled 6D docking search can be calculated in just 15 s using multiple 1D fast Fourier transforms (FFTs). This represents a 45-fold speed-up over the corresponding calculation on a single CPU, being at least two orders of magnitude times faster than a similar CPU calculation using ZDOCK 3.0.1, and estimated to be at least three orders of magnitude faster than the GPU-accelerated version of PIPER on comparable hardware. Hence, for the first time, exhaustive FFT-based protein docking calculations may now be performed in a matter of seconds on a contemporary GPU. Three-dimensional Hex FFT correlations are also accelerated by the GPU, but the speed-up factor of only 2.5 is much less than that obtained with 1D FFTs. Thus, the Hex algorithm appears to be especially well suited to exploit GPUs compared to conventional 3D FFT docking approaches. AVAILABILITY: http://hex.loria.fr/ and http://hexserver.loria.fr/.

Network Functions Virtualization (NFV) is incrementally deployed by Internet Service Providers (ISPs) in their carrier networks, by means of Virtual Network Function (VNF) chains, to address customers' demands. The motivation is the increasing manageability, reliability and performance of NFV systems, the gains in energy and space granted by virtualization, at a cost that becomes competitive with respect to legacy physical network function nodes. From a network optimization perspective, the routing of VNF chains across a carrier network implies key novelties making the VNF chain routing problem unique with respect to the state of the art: the bitrate of each demand flow can change along a VNF chain, the VNF processing latency and computing load can be a function of the demands traffic, VNFs can be shared among demands, etc. In this paper, we provide an NFV network model suitable for ISP operations. We define the generic VNF chain routing optimization problem and devise a mixed integer linear programming formulation. By extensive simulation on realistic ISP topologies, we draw conclusions on the trade-offs achievable between legacy Traffic Engineering (TE) ISP goals and novel combined TE-NFV goals.

The WebNLG challenge consists in mapping sets of RDF triples to text. It provides a common benchmark on which to train, evaluate and compare "microplanners", i.e. generation systems that verbalise a given content by making a range of complex interacting choices including referring expression generation, aggregation, lexicalisation, surface realisation and sentence segmentation. In this paper, we introduce the microplanning task, describe data preparation, introduce our evaluation methodology, analyse participant results and provide a brief description of the participating systems.

Conformal parameterization of mesh models has numerous applications in geometry processing. Conformality is desirable for remeshing, surface reconstruction, and many other mesh processing applications. Subject to the conformality requirement, these applications typically benefit from parameterizations with smaller stretch. The Angle Based Flattening (ABF) method, presented a few years ago, generates provably valid conformal parameterizations with low stretch. However, it is quite time-consuming and becomes error prone for large meshes due to numerical error accumulation. This work presents ABF++, a highly efficient extension of the ABF method, that overcomes these drawbacks while maintaining all the advantages of ABF. ABF++ robustly parameterizes meshes of hundreds of thousands and millions of triangles within minutes. It is based on three main components: (1) a new numerical solution technique that dramatically reduces the dimension of the linear systems solved at each iteration, speeding up the solution; (2) a new robust scheme for reconstructing the 2D coordinates from the angle space solution that avoids the numerical instabilities which hindered the ABF reconstruction scheme; and (3) an efficient hierarchical solution technique. The speedup with (1) does not come at the expense of greater distortion. The hierarchical technique (3) enables parameterization of models with millions of faces in seconds at the expense of a minor increase in parametric distortion. The parameterization computed by ABF++ are provably valid, that is they contain no flipped triangles. As a result of these extensions, the ABF++ method is extremely suitable for robustly and efficiently parameterizing models for geometry-processing applications.

A repetition in a word w is a subword with the period of at most half of the subword length. We study maximal repetitions occurring in w, that is those for which any extended subword of w has a bigger period. The set of such repetitions represents in a compact way all repetitions in w. We first prove a combinatorial result asserting that the sum of exponents of all maximal repetitions of a word of length n is bounded by a linear function in n. This implies, in particular that there is only a linear number of maximal repetitions in a word. This allows us to construct a linear-time algorithm for finding all maximal repetitions. Some consequences and applications of these results are discussed, as well as related works.

We introduce the first large-scale corpus for long-form question answering, a task requiring elaborate and in-depth answers to openended questions. The dataset comprises 270K threads from the Reddit forum "Explain Like I'm Five" (ELI5) where an online community provides answers to questions which are comprehensible by five year olds. Compared to existing datasets, ELI5 comprises diverse questions requiring multi-sentence answers. We provide a large set of web documents to help answer the question. Automatic and human evaluations show that an abstractive model trained with a multi-task objective outperforms conventional Seq2Seq, language modeling, as well as a strong extractive baseline. However, our best model is still far from human performance since raters prefer gold responses in over 86% of cases, leaving ample opportunity for future improvement.

article Free Access Share on Mining frequent patterns with counting inference Authors: Yves Bastide LIMOS, université Blaise Pascal, complexe scientifique des, C6zeanx, 24 av. des Landais, 63177 Aubière Cedex, France LIMOS, université Blaise Pascal, complexe scientifique des, C6zeanx, 24 av. des Landais, 63177 Aubière Cedex, FranceView Profile , Rafik Taouil INRIA Lorraine, 54506 Vandoeuvre-lès-Nancy Cedex, France INRIA Lorraine, 54506 Vandoeuvre-lès-Nancy Cedex, FranceView Profile , Nicolas Pasquier I3S (CNRS UPRESA 6070) - uuiversité de Nice, 06903, Sophia Antipolis, France I3S (CNRS UPRESA 6070) - uuiversité de Nice, 06903, Sophia Antipolis, FranceView Profile , Gerd Stumme Institut für Angewandte Informatik und Formale Beschreibungsverfahren, Universität Karlsruhe (TH), D-76128 Karlsruhe, Germany Institut für Angewandte Informatik und Formale Beschreibungsverfahren, Universität Karlsruhe (TH), D-76128 Karlsruhe, GermanyView Profile , Lotfi Lakhal LIM (CNRS FRE 2246) - université de la Méditerranée, 13288 Marseille Cedex 09, France LIM (CNRS FRE 2246) - université de la Méditerranée, 13288 Marseille Cedex 09, FranceView Profile Authors Info & Claims ACM SIGKDD Explorations NewsletterVolume 2Issue 2Dec. 2000 pp 66–75https://doi.org/10.1145/380995.381017Published:01 December 2000Publication History 205citation795DownloadsMetricsTotal Citations205Total Downloads795Last 12 Months63Last 6 weeks6 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF

This article addresses the problem of multichannel audio source separation. We propose a framework where deep neural networks (DNNs) are used to model the source spectra and combined with the classical multichannel Gaussian model to exploit the spatial information. The parameters are estimated in an iterative expectation-maximization (EM) fashion and used to derive a multichannel Wiener filter. We present an extensive experimental study to show the impact of different design choices on the performance of the proposed technique. We consider different cost functions for the training of DNNs, namely the probabilistically motivated Itakura-Saito divergence, and also Kullback-Leibler, Cauchy, mean squared error, and phase-sensitive cost functions. We also study the number of EM iterations and the use of multiple DNNs, where each DNN aims to improve the spectra estimated by the preceding EM iteration. Finally, we present its application to a speech enhancement problem. The experimental results show the benefit of the proposed multichannel approach over a single-channel DNN-based approach and the conventional multichannel nonnegative matrix factorization-based iterative EM algorithm.