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  • Neuroinformatics
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Thomas Arbogast; Abdel-Mouttalib Ouagazzal; Claire Chevalier; Maksym V. Kopanitsa; +7 Authors

    The 16p11.2 600 kb BP4-BP5 deletion and duplication syndromes have been associated with developmental delay; autism spectrum disorders; and reciprocal effects on the body mass index, head circumference and brain volumes. Here, we explored these relationships using novel engineered mouse models carrying a deletion (Del/+) or a duplication (Dup/+) of the Sult1a1-Spn region homologous to the human 16p11.2 BP4-BP5 locus. On a C57BL/6N inbred genetic background, Del/+ mice exhibited reduced weight and impaired adipogenesis, hyperactivity, repetitive behaviors, and recognition memory deficits. In contrast, Dup/+ mice showed largely opposite phenotypes. On a F1 C57BL/6N × C3B hybrid genetic background, we also observed alterations in social interaction in the Del/+ and the Dup/+ animals, with other robust phenotypes affecting recognition memory and weight. To explore the dosage effect of the 16p11.2 genes on metabolism, Del/+ and Dup/+ models were challenged with high fat and high sugar diet, which revealed opposite energy imbalance. Transcriptomic analysis revealed that the majority of the genes located in the Sult1a1-Spn region were sensitive to dosage with a major effect on several pathways associated with neurocognitive and metabolic phenotypes. Whereas the behavioral consequence of the 16p11 region genetic dosage was similar in mice and humans with activity and memory alterations, the metabolic defects were opposite: adult Del/+ mice are lean in comparison to the human obese phenotype and the Dup/+ mice are overweight in comparison to the human underweight phenotype. Together, these data indicate that the dosage imbalance at the 16p11.2 locus perturbs the expression of modifiers outside the CNV that can modulate the penetrance, expressivity and direction of effects in both humans and mice. Author Summary The 16p11.2 BP4-BP5 deletion and duplication syndromes are frequent copy number variants in humans, and are associated with developmental delay and autism spectrum disorders, with a reciprocal effect on head circumference and body mass index. Here we explored gene dosage effect in mouse models and found that the deletion and duplication induced opposite behavioral phenotypes. Notably, we observed that some behavioral phenotypes, such as social interaction, were sensitive to the genetic background. For the metabolism, the energy imbalance and adipocyte phenotypes were mirrored in the deletion and duplication carriers but opposite to the human phenotypes, the deletion mouse carriers were lean whereas the individuals with the deletion were obese. The main cause of the phenotypic features is the copy number variation of the 16p11.2 region with many genetic pathways altered in the striatum and the liver. Thus the final consequences of the rearrangement are likely governed by the interplay between many cellular pathways in both human cases and mouse models.

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    Europe PubMed Central
    Article . 2016
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    Other literature type . 2016
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    PLoS Genetics
    Article . 2016 . Peer-reviewed
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    PLoS Genetics
    Article . 2016
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    PLoS Genetics
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      Europe PubMed Central
      Article . 2016
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      Other literature type . 2016
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      PLoS Genetics
      Article . 2016 . Peer-reviewed
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    Authors: Lim, Soon Hoe; Wan, Yijun; Şimşekli, Umut;

    Recent studies have shown that gradient descent (GD) can achieve improved generalization when its dynamics exhibits a chaotic behavior. However, to obtain the desired effect, the step-size should be chosen sufficiently large, a task which is problem dependent and can be difficult in practice. In this study, we incorporate a chaotic component to GD in a controlled manner, and introduce multiscale perturbed GD (MPGD), a novel optimization framework where the GD recursion is augmented with chaotic perturbations that evolve via an independent dynamical system. We analyze MPGD from three different angles: (i) By building up on recent advances in rough paths theory, we show that, under appropriate assumptions, as the step-size decreases, the MPGD recursion converges weakly to a stochastic differential equation (SDE) driven by a heavy-tailed L\'evy-stable process. (ii) By making connections to recently developed generalization bounds for heavy-tailed processes, we derive a generalization bound for the limiting SDE and relate the worst-case generalization error over the trajectories of the process to the parameters of MPGD. (iii) We analyze the implicit regularization effect brought by the dynamical regularization and show that, in the weak perturbation regime, MPGD introduces terms that penalize the Hessian of the loss function. Empirical results are provided to demonstrate the advantages of MPGD. Comment: 24 pages, accepted at NeurIPS 2022

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    https://doi.org/10.48550/arxiv...
    Article . 2022
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    Other literature type . 2022
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    Authors: Bosc, Romain; Tijou, Antoine; Rosi, Giuseppe; Nguyen, Vu-Hieu; +4 Authors

    International audience; Background: The acetabular cup (AC) implant primary stability is an important determinant for the success of cementless hip surgery but it remains difficult to assess the AC implant fixation in the clinic. A method based on the analysis of the impact produced by an instrumented hammer on the ancillary has been developed by our group (Michel et al., 2016a). However, the soft tissue thickness present around the acetabulum may affect the impact response, which may hamper the robustness of the method. The aim of this study is to evaluate the influence of the soft tissue thickness (STT) on the acetabular cup implant primary fixation evaluation using impact analyses.Methods: To do so, different AC implants were inserted in five bovine bone samples. For each sample, different stability conditions were obtained by changing the cavity diameter. For each configuration, the AC implant was impacted 25 times with 10 and 30 mm of soft tissues positioned underneath the sample. The averaged indicator Im was determined based on the amplitude of the signal for each configuration and each STT and the pull-out force was measured.Findings: The results show that the resonance frequency of the system increases when the value of the soft tissue thickness decreases. Moreover, an ANOVA analysis shows that there was no significant effect of the value of soft tissue thickness on the values of the indicator Im (F = 2.33; p-value = 0.13).Interpretation: This study shows that soft tissue thickness does not appear to alter the prediction of the acetabular cup implant primary fixation obtained using the impact analysis approach, opening the path towards future clinical trials.

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    Other literature type . 2018
    HAL - UPEC / UPEM
    Article . 2018
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    Authors: Pousse, Alexandre; Niederman, Laurent; Robutel, Philippe;

    Popular science article associated with the work `On the co-orbital motion in the three-body problem: existence of quasi-periodic horseshoe-shaped orbits" (arXiv:1806.07262) from the same authors. Janus and Epimetheus are two moons of Saturn which exhibit a really peculiar dynamics. As they orbit on circular trajectories whose radii are only 50 km apart (less than their respective diameters), every four (terrestrial) years the bodies are getting closer and their mutual gravitational influence leads to a swapping of the orbits: the outer moon becoming the inner one and vice-versa. In this article, we describe how, from this specific astronomical problem to the KAM theory, we came to prove the existence of perpetually stable trajectories associated with the Janus and Epimetheus orbits. Comment: 16 pages, 7 figures, article de vulgarisation scientifique

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    Authors: Simonnot, Josephine;

    La plateforme web en ligne pour les archives sonores du CNRS-Musée de l’Homme permet d’accéder à des enregistrements musicaux du monde entier, publiés (disques) et inédit, collectés depuis les années 1900 jusqu’à nos jours. Nous présentons d’abord ces archives sonores gérées par le Centre de recherche en ethnomusicologie. Nous expliquons ensuite leur entrée dans le nouvel écosystème du Web ainsi que leur ouverture à un large public grâce à des outils d’analyse et de visualisation du son. Enfin, nous étudions comment une base de données d’archives sonores peut devenir un outil de collaboration pour produire et la diffuser des connaissances. The online web-based platform for the French CNRS-Musée de l'Homme sound archives offers access to published and unpublished recordings of music from all over the world, collected from the 1900's through the present day. We first introduce these sound archives managed by the Research Centre for Ethnomusicology. We then explain their entry in the new web ecosystem as well as their availability to a broad audience through a suite of tools for analysis and visualization. Finally, we study how a sound archive database can become a collaborative tool for the production and dissemination of knowledge.

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    Authors: Elena Longo; Elena Longo; Lucie Sancey; Alessia Cedola; +14 Authors

    Characterizing nanoparticles (NPs) distribution in multiple and complex metastases is of fundamental relevance for the development of radiological protocols based on NPs administration. In the literature, there have been advances in monitoring NPs in tissues. However, the lack of 3D information is still an issue. X-ray phase-contrast tomography (XPCT) is a 3D label-free, non-invasive and multi-scale approach allowing imaging anatomical details with high spatial and contrast resolutions. Here an XPCT qualitative study on NPs distribution in a mouse brain model of melanoma metastases injected with gadolinium-based NPs for theranostics is presented. For the first time, XPCT images show the NPs uptake at micrometer resolution over the full brain. Our results revealed a heterogeneous distribution of the NPs inside the melanoma metastases, bridging the gap in spatial resolution between magnetic resonance imaging and histology. Our findings demonstrated that XPCT is a reliable technique for NPs detection and can be considered as an emerging method for the study of NPs distribution in organs.

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    Article . 2021
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    Authors: J. B. Vielfaure; S. D. Vergani; J. Japelj; Johan P. U. Fynbo; +22 Authors

    Context. The identification of the sources that reionized the Universe and their specific contribution to this process are key missing pieces of our knowledge of the early Universe. Faint star-forming galaxies may be the main contributors to the ionizing photon budget during the epoch of reionization, but their escaping photons cannot be detected directly due to inter-galactic medium opacity. Hence, it is essential to characterize the properties of faint galaxies with significant Lyman continuum (LyC) photon leakage up to z ∼ 4 to define indirect indicators allowing analogs to be found at the highest redshift. Aims. Long gamma-ray bursts (LGRBs) typically explode in star-forming regions of faint, star-forming galaxies. Through LGRB afterglow spectroscopy it is possible to detect directly LyC photons. Our aim is to use LGRBs as tools to study LyC leakage from faint, star-forming galaxies at high redshift. Methods. Here we present the observations of LyC emission in the afterglow spectra of GRB 191004B at z = 3.5055, together with those of the other two previously known LyC-leaking LGRB host galaxies (GRB 050908 at z = 3.3467, and GRB 060607A at z = 3.0749), to determine their LyC escape fraction and compare their properties. Results. From the afterglow spectrum of GRB 191004B we determine a neutral hydrogen column density at the LGRB redshift of log(NH I/cm−2) = 17.2 ± 0.15, and negligible extinction (AV = 0.03 ± 0.02 mag). The only metal absorption lines detected are C IV and Si IV. In contrast to GRB 050908 and GRB 060607A, the host galaxy of GRB 191004B displays significant Lyman-alpha (Lyα) emission. From its Lyα emission and the non-detection of Balmer emission lines we constrain its star-formation rate (SFR) to 1 ≤ SFR ≤ 4.7 M⊙ yr−1. We fit the Lyα emission with a shell model and find parameters values consistent with the observed ones. The absolute (relative) LyC escape fractions we find for GRB 191004B, GRB 050908 and GRB 060607A are of 0.35−0.11+0.10 (0.43−0.13+0.12), 0.08−0.04+0.05 (0.08−0.04+0.05) and 0.20−0.05+0.05 (0.45−0.15+0.15), respectively. We compare the LyC escape fraction of LGRBs to the values of other LyC emitters found from the literature, showing that LGRB afterglows can be powerful tools to study LyC escape for faint high-redshift star-forming galaxies. Indeed we could push LyC leakage studies to much higher absolute magnitudes. The host galaxies of the three LGRBs presented here have all M1600 > −19.5 mag, with the GRB 060607A host at M1600 > −16 mag. LGRB hosts may therefore be particularly suitable for exploring the ionizing escape fraction in galaxies that are too faint or distant for conventional techniques. Furthermore, the time involved is minimal compared to galaxy studies. © J.-B. Vielfaure et al. 2020 This work is part of the BEaPro project (PI: S.D. Vergani) funded by the French Agence Nationale de la Recherche (ANR-16-CE31-0003). We thank Giancarlo Ghirlanda for providing useful information. JBV and SDV thank Anne Verhamme for useful discussions. SDV acknowledges financial support from the French Space Agency (CNES). MG was supported by NASA through the NASA Hubble Fellowship grant HST-HF2-51409 and acknowledges support from HST grants HST-GO-15643.017-A, HST-AR-15039.003-A, and XSEDE grant TG-AST180036. The Cosmic DAWN center is funded by the DNRF. JPUF thanks the Carlsberg foundation for support. DBM acknowledges support from VILLUM FONDEN research grant 19054. NRT acknowledges support from STFC via grant ST/N000757/1. DAK acknowledges support from Spanish research project RTI2018-098104-J-I00 (GRBPhot). The PanSTARRS1 Surveys (PS1) and the PS1 public science archive have been made possible through contributions by the Institute for Astronomy, the University of Hawaii, the Pan-STARRS Project O ffice, the Max-Planck Society and its participating institutes, the Max Planck Institute for Astronomy, Heidelberg and the Max Planck Institute for Extraterrestrial Physics, Garching, The Johns Hopkins University, Durham University, the University of Edinburgh, the Queen's University Belfast, the Harvard-Smithsonian Center for Astrophysics, the Las Cumbres Observatory Global Telescope Network Incorporated, the National Central University of Taiwan, the Space Telescope Science Institute, the National Aeronautics and Space Administration under Grant No. NNX08AR22G issued through the Planetary Science Division of the NASA Science Mission Directorate, the National Science Foundation Grant No. AST-1238877, the University of Maryland, Eotvos Lorand University (ELTE), the Los Alamos National Laboratory, and the Gordon and Betty Moore Foundation. This work has made use of data from the European Space Agency (ESA) mission Gaia (https://www.cosmos.esa.int/gaia), processed by the Gaia Data Processing and Analysis Consortium (DPAC, https://www.cosmos.esa.int/web/gaia/dpac/consortium).Funding for the DPAC has been provided by national institutions, in particular the institutions participating in the Gaia Multilateral Agreement. The NumPy (van der Walt et al. 2011), SciPy (Virtanen et al. 2020) and matplotlib (Hunter 2007) packages have been extensively used for the preparation and presentation of this work. Open Access article, published by EDP Sciences, under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Peer reviewed

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    Authors: Branco, Mário J. J.; Pin, Jean-Éric;

    International audience; Let a be a letter of an alphabet A. Given a lattice of languages L, we describe the set of ultrafilter inequalities satisfied by the lattice La generated by the languages of the form L or LaA * , where L is a language of L. We also describe the ultrafilter inequalities satisfied by the lattice L1 generated by the lattices La, for a ∈ A. When L is a lattice of regular languages, we first describe the profinite inequalities satisfied by La and L1 and then provide a small basis of inequalities defining L1 when L is a Boolean algebra of regular languages closed under quotient.

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    Authors: Sophie Bouton; Valérian Chambon; Rémi Tyrand; Adrian G. Guggisberg; +4 Authors

    Percepts and words can be decoded from distributed neural activity measures. However, the existence of widespread representations might conflict with the more classical notions of hierarchical processing and efficient coding, which are especially relevant in speech processing. Using fMRI and magnetoencephalography during syllable identification, we show that sensory and decisional activity colocalize to a restricted part of the posterior superior temporal gyrus (pSTG). Next, using intracortical recordings, we demonstrate that early and focal neural activity in this region distinguishes correct from incorrect decisions and can be machine-decoded to classify syllables. Crucially, significant machine decoding was possible from neuronal activity sampled across different regions of the temporal and frontal lobes, despite weak or absent sensory or decision-related responses. These findings show that speech-sound categorization relies on an efficient readout of focal pSTG neural activity, while more distributed activity patterns, although classifiable by machine learning, instead reflect collateral processes of sensory perception and decision. Significance When listening to speech, phonemes are represented in a distributed fashion in our temporal and prefrontal cortices. How these representations are selected in a phonemic decision context, and in particular whether distributed or focal neural information is required for explicit phoneme recognition, is unclear. We hypothesized that focal and early neural encoding of acoustic signals is sufficiently informative to access speech sound representations and permit phoneme recognition. We tested this hypothesis by combining a simple speech-phoneme categorization task with univariate and multivariate analyses of fMRI, magnetoencephalography, intracortical, and clinical data. We show that neural information available focally in the temporal cortex prior to decision-related neural activity is specific enough to account for human phonemic identification.

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      Proceedings of the National Academy of Sciences
      Article . 2018 . Peer-reviewed
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      Proceedings of the National Academy of Sciences
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      Hal-Diderot
      Article . 2017
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    Authors: Kirchev, Angel; Guillet, Nicolas; Brun-Buisson, David; Gau, Vincent;

    International audience; The normal operation of a 18650 Lithium-ion cells has been monitored using rectangular rosette strain gauge and a pair of piezoelectric transducers. The sensors for mechanical measurements provide information about the cell deformation mechanism and electrodes structure during the cycling. The strain gauge signal revealed three type of mechanical processes. The predominant deformation pattern during galvanostatic discharge process is an isotropic cylindrical shrinkage relevant to the extraction of lithium ions from the graphite negative electrode. In the case of low-rate discharge in cyclic voltammetry mode, the deformation pattern changes to spherical growth when the state of charge falls below 40. In contrast, the thermal shrinkage and growth of the cell corresponds to simple decrease of the cell diameter with much smaller hysteresis effect. The ultrasound interrogation is able to detect repeatable progressive change of the acoustic waveform transferred across the cell in direction of the jellyroll diameter, which depends on the state of charge and does not undergo any significant changes at different cycling rates. The impact of the state of health under 2h rated charge/discharge cycling at 25°C reveals slow progressive drift of the strain and acoustic signals corresponding to the growth of the cell size.

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    Authors: Thomas Arbogast; Abdel-Mouttalib Ouagazzal; Claire Chevalier; Maksym V. Kopanitsa; +7 Authors

    The 16p11.2 600 kb BP4-BP5 deletion and duplication syndromes have been associated with developmental delay; autism spectrum disorders; and reciprocal effects on the body mass index, head circumference and brain volumes. Here, we explored these relationships using novel engineered mouse models carrying a deletion (Del/+) or a duplication (Dup/+) of the Sult1a1-Spn region homologous to the human 16p11.2 BP4-BP5 locus. On a C57BL/6N inbred genetic background, Del/+ mice exhibited reduced weight and impaired adipogenesis, hyperactivity, repetitive behaviors, and recognition memory deficits. In contrast, Dup/+ mice showed largely opposite phenotypes. On a F1 C57BL/6N × C3B hybrid genetic background, we also observed alterations in social interaction in the Del/+ and the Dup/+ animals, with other robust phenotypes affecting recognition memory and weight. To explore the dosage effect of the 16p11.2 genes on metabolism, Del/+ and Dup/+ models were challenged with high fat and high sugar diet, which revealed opposite energy imbalance. Transcriptomic analysis revealed that the majority of the genes located in the Sult1a1-Spn region were sensitive to dosage with a major effect on several pathways associated with neurocognitive and metabolic phenotypes. Whereas the behavioral consequence of the 16p11 region genetic dosage was similar in mice and humans with activity and memory alterations, the metabolic defects were opposite: adult Del/+ mice are lean in comparison to the human obese phenotype and the Dup/+ mice are overweight in comparison to the human underweight phenotype. Together, these data indicate that the dosage imbalance at the 16p11.2 locus perturbs the expression of modifiers outside the CNV that can modulate the penetrance, expressivity and direction of effects in both humans and mice. Author Summary The 16p11.2 BP4-BP5 deletion and duplication syndromes are frequent copy number variants in humans, and are associated with developmental delay and autism spectrum disorders, with a reciprocal effect on head circumference and body mass index. Here we explored gene dosage effect in mouse models and found that the deletion and duplication induced opposite behavioral phenotypes. Notably, we observed that some behavioral phenotypes, such as social interaction, were sensitive to the genetic background. For the metabolism, the energy imbalance and adipocyte phenotypes were mirrored in the deletion and duplication carriers but opposite to the human phenotypes, the deletion mouse carriers were lean whereas the individuals with the deletion were obese. The main cause of the phenotypic features is the copy number variation of the 16p11.2 region with many genetic pathways altered in the striatum and the liver. Thus the final consequences of the rearrangement are likely governed by the interplay between many cellular pathways in both human cases and mouse models.

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    Europe PubMed Central
    Article . 2016
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    Other literature type . 2016
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    PLoS Genetics
    Article . 2016 . Peer-reviewed
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    PLoS Genetics
    Article . 2016
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    PLoS Genetics
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      PLoS Genetics
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      PLoS Genetics
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    Authors: Lim, Soon Hoe; Wan, Yijun; Şimşekli, Umut;

    Recent studies have shown that gradient descent (GD) can achieve improved generalization when its dynamics exhibits a chaotic behavior. However, to obtain the desired effect, the step-size should be chosen sufficiently large, a task which is problem dependent and can be difficult in practice. In this study, we incorporate a chaotic component to GD in a controlled manner, and introduce multiscale perturbed GD (MPGD), a novel optimization framework where the GD recursion is augmented with chaotic perturbations that evolve via an independent dynamical system. We analyze MPGD from three different angles: (i) By building up on recent advances in rough paths theory, we show that, under appropriate assumptions, as the step-size decreases, the MPGD recursion converges weakly to a stochastic differential equation (SDE) driven by a heavy-tailed L\'evy-stable process. (ii) By making connections to recently developed generalization bounds for heavy-tailed processes, we derive a generalization bound for the limiting SDE and relate the worst-case generalization error over the trajectories of the process to the parameters of MPGD. (iii) We analyze the implicit regularization effect brought by the dynamical regularization and show that, in the weak perturbation regime, MPGD introduces terms that penalize the Hessian of the loss function. Empirical results are provided to demonstrate the advantages of MPGD. Comment: 24 pages, accepted at NeurIPS 2022

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    https://doi.org/10.48550/arxiv...
    Article . 2022
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