Portail HAL des publications du LIRMM
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How fast are viruses spreading in the wild?
No full textInternational audienceGenomic data collected from viral outbreaks can be exploited to reconstruct the dispersal history of viral lineages in a two-dimensional space using continuous phylogeographic inference. These spatially explicit reconstructions can subsequently be used to estimate dispersal metrics allowing to unveil the dispersal dynamics and evaluate the capacity to spread among hosts. Heterogeneous sampling intensity of genomic sequences can however impact the accuracy of dispersal insights gained through phylogeographic inference. In our study, we implement a simulation framework to evaluate the robustness of three dispersal metrics — a lineage dispersal velocity, a diffusion coefficient, and an isolation-by-distance signal metric — to the sampling effort. Our results reveal that both the diffusion coefficient and isolation-by-distance signal metrics appear to be robust to the number of samples considered for the phylogeographic reconstruction. We then use these two dispersal metrics to compare the dispersal pattern and capacity of various viruses spreading in animal populations. Our comparative analysis reveals a broad range of isolation-by-distance patterns and diffusion coefficients mostly reflecting the dispersal capacity of the main infected host species but also, in some cases, the likely signature of rapid and/or long-distance dispersal events driven by human-mediated movements through animal trade. Overall, our study provides key recommendations for the lineage dispersal metrics to consider in future studies and illustrates their application to compare the spread of viruses in various settings
A Proof-Theoretical Approach to Some Extensions of First Order Quantification
No full textWorkshop associated with IJCAR 2024International audienceGeneralised quantifiers, which include Henkin's branching quantifiers, have been introduced by Mostowski and Lindström and developed as a substantial topic application of logic, especially model theory, to linguistics with work by Barwise, Cooper, Keenan.In this paper, we mainly study the proof theory of some non-standard quantifiers as second order formulae. Our first example is the usual pair of first order quantifiers (for all / there exists) when individuals are viewed as individual concepts handled by second order deductive rules. Our second example is the study of a second order translation of the simplest branching quantifier: "A member of each team and a member of each board of directors know each other", for which we propose a second order treatment.</p
Overview of LifeCLEF 2024: Challenges on Species Distribution Prediction and Identification
No full textInternational audienceBiodiversity monitoring using machine learning and AI-based approaches is becoming increasingly popular. It allows for providing detailed information on species distribution and ecosystem health at a large scale and contributes to informed decision-making on environmental protection. Species identification based on images and sounds, in particular, is invaluable for facilitating biodiversity monitoring efforts and enabling prompt conservation actions to protect threatened and endangered species. The multiplicity of methods developed, however, makes it important to evaluate their performance on realistic datasets and using standardized evaluation protocols. The LifeCLEF lab has been setting up such evaluations since 2011, encouraging machine learning researchers to work on this topic and promoting the adoption of the technologies developed by stakeholders. The 2024 edition proposes five data-oriented challenges related to the identification and prediction of biodiversity: (i) BirdCLEF: bird call identification in soundscapes, (ii) FungiCLEF: revisiting fungi species recognition beyond 0-1 cost, (iii) GeoLifeCLEF: remote sensing based prediction of species, (iv) PlantCLEF: Multi-species identification in vegetation plot images, and (v) SnakeCLEF: revisiting snake species identification in medically important scenarios. This paper overviews the motivation, methodology, and main outcomes of those five challenges
Digital Generation of RF Phase-Modulated Test Stimuli: Application to BPSK Modulation Scheme
No full textInternational audienceThis paper presents an original strategy for low-cost generation of Radio-Frequency (RF) phase-modulated test stimuli using a standard digital Automated Test Equipment (ATE). The main idea is to generate a modulated digital signal at relatively low-frequency and exploit one of its harmonic replicas to get a signal at higher frequency. Given the specificity of a digital ATE, which manipulates data in the discrete-time domain, one of the cornerstones of the technique is to identify favorable sampling conditions that preserve the spectral content of the generated signal around the targeted harmonic replica. To this end, a corruption estimator is defined based on an analytical expression of a sampled-and-held digital carrier. The approach is illustrated in this paper using the Binary Phase Shift Keying (BPSK) modulation scheme with the objective of generating a 2.4GHz signal, assuming a maximum ATE sampling rate of 1.6Gbps. Simulation results and hardware measurements are presented, validating the proposed solution
Classifier Chains pour le codage LOINC
No full textNational audiencePurpose : This article presents a study on the coding of real data from French laboratories into the LOINC terminology. Methods : We present a comparison of three approaches for LOINC coding. These approaches include both a state- of-the-art language model approach and a classifier chains approach. Results : Our study demonstrates that we successfully improve the performance of the baseline using the classifier chains approach and compete effectively with state-of-the-art language models. Conclusions : Our approach proves to be efficient and cost-effective despite re- producibility challenges with perspectives for future optimizations and dataset testing.Objectif : Cet article présente une étude sur le codage de données réelles issues de laboratoires français vers la terminologie LOINC. Méthodes : Nous présentons une comparaison de trois approches pour le codage LOINC. Ces approches incluent à la fois une approche de modèle linguistique de l'état de l'art ainsi qu'un classifier chains. Résultats : Notre étude démontre que nous améliorons avec succès la performance de labaseline en utilisant le classifier chains et que nous nous comparons efficacement aux modèles linguistiques de l'état de l'art. Conclusions : Bien que notre approche rencontre des défis de reproductibilité et présente des perspectives d'optimisations et de tests futurs sur des ensembles de données, elle s'avère néanmoins efficace et économique
Degree-Constrained Minimum Spanning Hierarchies in Graphs
No full textInternational audienceThe minimum spanning tree problem in graphs under budget-type degree constraints (DCMST) is a well-known NP-hard problem. Spanning trees do not always exist, and the optimum can not be approximated within a constant factor. Recently, solutions have been proposed to solve degree-constrained spanning problems in the case of limited momentary capacities of the nodes. For a given node, the constraint represents a limited degree of the node for each visit. Finding the solution with minimum cost is NP-hard and the related algorithms are not trivial. This paper focuses on this new spanning problem with heterogeneous capacity-like degree bounds. The minimum cost solution corresponds to a graph-related structure, i.e., a hierarchy. We study the conditions of its existence, and we propose its exact computation, a heuristic algorithm, and its approximation
Hybrid Cable Thruster Actuated Remotely Operated Underwater Vehicle
No full textInternational audienceThis paper introduces a novel Hybrid Cable Thruster Actuated Remotely Operated Underwater Vehicle (HCT-ROV), merging the strengths of ROVs and Cable-Driven Parallel Robots for enhanced underwater capabilities. It presents the world's first HCT-ROV prototype, together with a control law using Quadratic Programming (QP) for efficient operation. Extensive MATLAB simulations and prototype tests demonstrate superior performance in tasks like object transportation. This research work paves the way for advanced underwater exploration and operations, emphasizing the need for further optimization in real-world applications
Pour un renouvellement durable des processeurs de calcul
No full textInternational audienceLa révolution numérique a apporté d'innombrables avantages à la société moderne, mais elle s'accompagne également d'un impact environnemental croissant, souvent difficile à appréhender. Pour mettre en place une stratégie de renouvellement durable des processeurs, il est crucial d'effectuer une analyse en profondeur des répercussions environnementales. Nous proposons un modèle de raisonnement simple, basé sur une approche analytique s'inscrivant dans les contraintes planétaires, tout en préservant les acquis sociaux et économiques. A travers une étude de cas portant sur les processeurs Intel et en exploitant les données de l'analyse de cycle de vie (ACV) issues d'une base de données d'analyse de cycle de vie du numérique, nous illustrons la pertinence du modèle de raisonnement, tout en mettant en évidence la complexité inhérente au choix de stratégies de renouvellement des processeurs judicieuses
Euclidean Bottleneck Steiner Tree is Fixed-Parameter Tractable
No full textInternational audienceIn the Euclidean Bottleneck Steiner Tree problem, the input consists of a set of points in called terminals and a parameter , and the goal is to compute a Steiner tree that spans all the terminals and contains at most points of as Steiner points such that the maximum edge-length of the Steiner tree is minimized, where the length of a tree edge is the Euclidean distance between its two endpoints. The problem is well-studied and is known to be NP-hard. In this paper, we give a -time algorithm for Euclidean Bottleneck Steiner Tree, which implies that the problem is fixed-parameter tractable (FPT). This settles an open question explicitly asked by Bae et al. [Algorithmica, 2011], who showed that the and variants of the problem are FPT. Our approach can be generalized to the problem with metric for any rational , or even other metrics on
Conditional normality and finite-state dimensions revisited
No full textThe notion of a normal bit sequence was introduced by Borel in 1909; it was the first definition of an individual random object. Normality is a weak notion of randomness requiring only that all 2 n factors (substrings) of arbitrary length n appear with the same limit frequency 2 -n . Later many stronger definitions of randomness were introduced, and in this context normality found its place as "randomness against a finite-memory adversary". A quantitative measure of finite-state compressibility was also introduced (the finite-state dimension) and normality means that the finite state dimension is maximal (equals 1).Recently Nandakumar, Pulari and S (2023) introduced the notion of relative finite-state dimension for a binary sequence with respect to some other binary sequence (treated as an oracle), and the corresponding notion of conditional (relative) normality. (Different notions of conditional randomness were considered before, but not for the finite memory case.) They establish equivalence between the block frequency and the gambling approaches to conditional normality and finite-state dimensions.In this note we revisit their definitions and explain how this equivalence can be obtained easily by generalizing known characterizations of (unconditional) normality and dimension in terms of compressibility (finite-state complexity), superadditive complexity measures and gambling (finite-state gales), thus also answering some questions left open in the above-mentioned paper.</p