New Perspectives on the Evaluation of Link Prediction Algorithms for Dynamic Graphs

There is a fast-growing body of research on predicting future links in dynamic networks, with many new algorithms. Some benchmark data exists, and performance evaluations commonly rely on comparing the scores of observed network events (positives) with those of randomly generated ones (negatives). These evaluation measures depend on both the predictive ability of the model and, crucially, the type of negative samples used. Besides, as generally the case with temporal data, prediction quality may vary over time. This creates a complex evaluation space. In this work, we catalog the possibilities for negative sampling and introduce novel visualization methods that can yield insight into prediction performance and the dynamics of temporal networks. We leverage these visualization tools to investigate the effect of negative sampling on the predictive performance, at the node and edge level. We validate empirically, on datasets extracted from recent benchmarks that the error is typically not evenly distributed across different data segments. Finally, we argue that such visualization tools can serve as powerful guides to evaluate dynamic link prediction methods at different levels

Physical validation of simulators in Computer Graphics: A new framework dedicated to slender elastic structures and frictional contact

International audienceWe introduce a selected set of protocols inspired from the Soft Matter Physics community in order to validate Computer Graphics simulators of slender elastic structures possibly subject to dry frictional contact. Although these simulators were primarily intended for feature film animation and visual effects, they are more and more used as virtual design tools for predicting the shape and deformation of real objects; hence the need for a careful, quantitative validation. Our tests, experimentally verified, are designed to evaluate carefully the predictability of these simulators on various aspects, such as bending elasticity, bend-twist coupling, and frictional contact. We have passed a number of popular codes of Computer Graphics through our benchmarks by defining a rigorous, consistent, and as fair as possible methodology. Our results show that while some popular simulators for plates/shells and frictional contact fail even on the simplest scenarios, more recent ones, as well as well-known codes for rods, generally perform well and sometimes even better than some reference commercial tools of Mechanical Engineering. To make our validation protocols easily applicable to any simulator, we provide an extensive description of our methodology, and we shall distribute all the necessary model data to be compared against

Test et validation de codes de simulation d'informatique graphique pour les structures élastiques minces et le contact frottant

National audienceNous présentons un jeu de quatre protocoles de test, inspirés de problèmes classiques en calcul de structures, dans le but de valider des codes de simulation d’informatique graphique pour les poutres et plaques élastiques, ainsi que le contact frottant. Ces codes d’informatique graphique ont été conçus initialement pour simuler des effets visuels complexes dans le cinéma, application pour laquelle la crédibilité au service de la narration prime sur le réalisme physique. Cela explique que de tels simulateurs ont été finalement peu confrontés au réel de façon quantitative, contrairement aux simulateurs développés en mécanique. Pourtant, ces simulateurs graphiques, grâce à leur robustesse et leur efficacité, sont de plus en plus détournés du secteur du film pour être utilisés dans la conception de systèmes réels, avec de vrais attendus en terme de prédiction. Ce nouvel usage appelle une validation quantitative rigoureuse et complète, non seulement pour pouvoir certifier la gamme de validité de tels simulateurs, mais également pour pouvoir les comparer à des outils numériques standard employés en mécanique. Les protocoles de test que nous proposons sont validés expériementalement et sont conçus pour vérifier le traitement de la flexion, de l’interaction flexion-torsion, et du contact frottant solide

Ghrelin treatment induces rapid and delayed increments of food intake : A heuristic model to explain ghrelin's orexigenic effects

Ghrelin is a stomach-derived peptide hormone with salient roles in the regulation of energy balance and metabolism. Notably, ghrelin is recognized as the most powerful known circulating orexigenic hormone. Here, we systematically investigated the effects of ghrelin on energy homeostasis and found that ghrelin primarily induces a biphasic effect on food intake that has indirect consequences on energy expenditure and nutrient partitioning. We also found that ghrelin-induced biphasic effect on food intake requires the integrity of Agouti-related peptide/neuropeptide Y-producing neurons of the hypothalamic arcuate nucleus, which seem to display a long-lasting activation after a single systemic injection of ghrelin. Finally, we found that different autonomic, hormonal and metabolic satiation signals transiently counteract ghrelin-induced food intake. Based on our observations, we propose a heuristic model to describe how the orexigenic effect of ghrelin and the anorectic food intake-induced rebound sculpt a timely constrain feeding response to ghrelin.Instituto Multidisciplinario de Biología Celula

Ancient Plasmodium genomes shed light on the history of human malaria

Malaria-causing protozoa of the genus Plasmodium have exerted one of the strongest selective pressures on the human genome, and resistance alleles provide biomolecular footprints that outline the historical reach of these species1. Nevertheless, debate persists over when and how malaria parasites emerged as human pathogens and spread around the globe1,2. To address these questions, we generated high-coverage ancient mitochondrial and nuclear genome-wide data from P. falciparum, P. vivax and P. malariae from 16 countries spanning around 5,500 years of human history. We identified P. vivax and P. falciparum across geographically disparate regions of Eurasia from as early as the fourth and first millennia bce, respectively; for P. vivax, this evidence pre-dates textual references by several millennia3. Genomic analysis supports distinct disease histories for P. falciparum and P. vivax in the Americas: similarities between now-eliminated European and peri-contact South American strains indicate that European colonizers were the source of American P. vivax, whereas the trans-Atlantic slave trade probably introduced P. falciparum into the Americas. Our data underscore the role of cross-cultural contacts in the dissemination of malaria, laying the biomolecular foundation for future palaeo-epidemiological research into the impact of Plasmodium parasites on human history. Finally, our unexpected discovery of P. falciparum in the high-altitude Himalayas provides a rare case study in which individual mobility can be inferred from infection status, adding to our knowledge of cross-cultural connectivity in the region nearly three millennia ago.This project was funded by the National Science Foundation, grants BCS-2141896 and BCS-1528698; the European Research Council (ERC) under the European Union’s Horizon 2020 programme, grants 851511-MICROSCOPE (to S. Schiffels), 771234-PALEoRIDER (to W.H.) and starting grant 805268-CoDisEASe (to K.I.B.); and the ERC starting grant Waves ERC758967 (supporting K. Nägele and S.C.). We thank the Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean for supporting M. Michel, E. Skourtanioti, A.M., R.A.B., L.C.B., G.U.N., N.S., V.V.-M., M. McCormick, P.W.S., C.W. and J.K.; the Kone Foundation for supporting E.K.G. and A.S.; and the Faculty of Medicine and the Faculty of Biological and Environmental Sciences at the University of Helsinki for grants to E.K.G. A.S. thanks the Magnus Ehrnrooth Foundation, the Sigrid Jusélius Foundation, the Finnish Cultural Foundation, the Academy of Finland, the Life and Health Medical Foundation and the Finnish Society of Sciences and Letters. M.C.B. acknowledges funding from: research project PID2020-116196GB-I00 funded by MCIN/AEI/10.13039/501100011033; the Spanish Ministry of Culture; the Chiang Ching Kuo Foundation; Fundación Palarq; the EU FP7 Marie Curie Zukunftskolleg Incoming Fellowship Programme, University of Konstanz (grant 291784); STAR2-Santander Universidades and Ministry of Education, Culture and Sports; and CEI 2015 project Cantabria Campus Internacional. M.E. received support from the Czech Academy of Sciences award Praemium Academiae and project RVO 67985912 of the Institute of Archaeology of the Czech Academy of Sciences, Prague. This work has been funded within project PID2020-115956GB-I00 ‘Origen y conformación del Bronce Valenciano’, granted by the Ministry of Science and Innovation of the Government of Spain, and grants from the Canadian Institutes for Health Research (MZI187236), Research Nova Scotia (RNS 2023-2565) and The Center for Health Research in Developing Countries. D.K. is the Canada research chair in translational vaccinology and inflammation. R.L.K. acknowledges support from a 2019 University of Otago research grant (Human health and adaptation along Silk Roads, a bioarchaeological investigation of a medieval Uzbek cemetery). P.O. thanks the Jane and Aatos Erkko Foundation, the Finnish Cultural Foundation and the Academy of Finland. S. Peltola received support from the Emil Aaltonen Foundation and the Ella and Georg Ehrnrooth Foundation. D.C.S.-G. thanks the Generalitat Valenciana (CIDEGENT/2019/061). E.W.K. acknowledges support from the DEEPDEAD project, HERA-UP, CRP (15.055) and the Horizon 2020 programme (grant 649307). M. Spyrou thanks the Elite program for postdocs of the Baden-Württemberg Stiftung. Open access funding provided by Max Planck Society

Decoding the historical tale: COVID-19 impact on haematological malignancy patients-EPICOVIDEHA insights from 2020 to 2022

The COVID-19 pandemic heightened risks for individuals with hematological malignancies due to compromised immune systems, leading to more severe outcomes and increased mortality. While interventions like vaccines, targeted antivirals, and monoclonal antibodies have been effective for the general population, their benefits for these patients may not be as pronounced.Peer reviewe

Modélisation numérique de rubans en éléments de haut degré

National audienceNous proposons un modèle numérique robuste et efficace pour calculer les états d'équilibre stables d'un ruban naturellement plat ou courbé. Notre discrétisation spatiale se base sur des éléments à courbure normale linéaire et torsion géodésique quadratique en l'abscisse curviligne, qui permettent une grande richesse de représentation cinématique tout en garantissant l'inextensibilité parfaite du ruban. Les équilibres stables sont calculés par minimisation des énergies de gravité et d'élasticité du ruban, sous contrainte de développabilité

Exploring the Performance of Continuous-Time Dynamic Link Prediction Algorithms

Dynamic Link Prediction (DLP) addresses the prediction of future links in evolving networks. However, accurately portraying the performance of DLP algorithms poses challenges that might impede progress in the field. Importantly, common evaluation pipelines usually calculate ranking or binary classification metrics, where the scores of observed interactions (positives) are compared with those of randomly generated ones (negatives). However, a single metric is not sufficient to fully capture the differences between DLP algorithms, and is prone to overly optimistic performance evaluation. Instead, an in-depth evaluation should reflect performance variations across different nodes, edges, and time segments. In this work, we contribute tools to perform such a comprehensive evaluation. (1) We propose Birth–Death diagrams, a simple but powerful visualization technique that illustrates the effect of time-based train–test splitting on the difficulty of DLP on a given dataset. (2) We describe an exhaustive taxonomy of negative sampling methods that can be used at evaluation time. (3) We carry out an empirical study of the effect of the different negative sampling strategies. Our comparison between heuristics and state-of-the-art memory-based methods on various real-world datasets confirms a strong effect of using different negative sampling strategies on the test area under the curve (AUC). Moreover, we conduct a visual exploration of the prediction, with additional insights on which different types of errors are prominent over time

Numerical modeling of inextensible elastic ribbons with curvature-based elements

International audienc