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Training a supermodel with noisy and sparse observations: a case study with CPT and the synch rule on SPEEDO – v.1
Full text linkAs an alternative to using the standard multi-model ensemble (MME) approach to combine the output of different models to improve prediction skill, models can also be combined dynamically to form a so-called supermodel. The supermodel approach enables a quicker correction of the model errors. In this study we connect different versions of SPEEDO, a global atmosphere-ocean-land model of intermediate complexity, into a supermodel. We focus on a weighted supermodel, in which the supermodel state is a weighted superposition of different imperfect model states. The estimation, “the training”, of the optimal weights of this combination is a critical aspect in the construction of a supermodel. In our previous works two algorithms were developed: (i) cross pollination in time (CPT)-based technique and (ii) a synchronization-based learning rule (synch rule). Those algorithms have so far been applied under the assumption of complete and noise-free observations. Here we go beyond and consider the more realistic case of noisy data that do not cover the full system's state and are not taken at each model's computational time step. We revise the training methods to cope with this observational scenario, while still being able to estimate accurate weights. In the synch rule an additional term is introduced to maintain physical balances, while in CPT nudging terms are added to let the models stay closer to the observations during training. Furthermore, we propose a novel formulation of the CPT method allowing the weights to be negative. This makes it possible for CPT to deal with cases in which the individual model biases have the same sign, a situation that hampers constructing a skillfully weighted supermodel based on positive weights. With these developments, both CPT and the synch rule have been made suitable to train a supermodel consisting of state of the art weather and climate models
Exploring the influence of spatio-temporal scale differences in coupled data assimilation
Full text linkIdentifying the optimal strategy for initializing coupled climate prediction systems is challenging due to the spatio-temporal scale separation and disparities in the observational network. We aim to clarify when strongly coupled data assimilation (SCDA) is preferable to weakly coupled data assimilation (WCDA). We use a two-components coupled Lorenz-63 system, mimicking the atmosphere and the ocean, and the Ensemble Kalman Filter (EnKF) to compare WCDA and SCDA for diverse spatio-temporal scale separations and observational networks - only in the atmosphere, the ocean, or both components. In the fully observed scenario, SCDA and WCDA yield similar performances. However, little differences are present, and we conjecture these are due to the SCDA being more sensitive to the approximations at the basis of the EnKF present in the cross-update - linear analysis update and sampling error, and how they impact the cross-update between ocean and atmosphere. This sensitivity increases as the temporal scale separation increases and is stronger on the slow and large-scale components. When observations are only in one of the components, the spatio-temporal scale separation influences SCDA's performance. In this scenario, the largest improvements are found when the observed component has a smaller spatial scale. The fast-to-slow update has a larger benefit with a larger temporal scale separation. Meanwhile, with the slow-to-fast update, the improvement is limited to instances when the temporal scale separation is less than one-half. This suggests that SCDA of fast atmospheric observations can potentially improve the large and slow ocean component. Conversely, observations of the fine ocean can improve the large atmosphere at a comparable temporal scale. However, when both components are highly chaotic, and the observed component's spatial scale is the largest, SCDA does not improve over WCDA. In such a case, the cross-updates may become too sensitive to data assimilation approximations. We further validated that WCDA systematically outperforms uncoupled data assimilation (UCDA) in both components, legitimizing the transition toward WCDA
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Bayesian inference of chaotic dynamics by merging data assimilation, machine learning and expectation-maximization
Full text linkThe reconstruction from observations of high-dimensional chaotic dynamics such as geophysical flows is hampered by (ⅰ) the partial and noisy observations that can realistically be obtained, (ⅱ) the need to learn from long time series of data, and (ⅲ) the unstable nature of the dynamics. To achieve such inference from the observations over long time series, it has been suggested to combine data assimilation and machine learning in several ways. We show how to unify these approaches from a Bayesian perspective using expectation-maximization and coordinate descents. In doing so, the model, the state trajectory and model error statistics are estimated all together. Implementations and approximations of these methods are discussed. Finally, we numerically and successfully test the approach on two relevant low-order chaotic models with distinct identifiability
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Investigating ecosystem connections in the shelf sea environment using complex networks
Full text linkWe use complex network theory to better represent and understand the ecosystem connectivity in a shelf sea
environment. The baseline data used for the analysis are obtained from a state-of-the-art coupled marine physics–biogeochemistry model simulating the North West European Shelf (NWES). The complex network built on model outputs is used to identify the functional groups of variables behind the biogeochemistry dynamics, suggesting how to simplify our understanding of the complex web of interactions within the shelf sea ecosystem. We demonstrate that complex networks can also be used to understand spatial ecosystem connectivity, identifying both the (geographically varying) connectivity length-scales and the clusters of spatial locations that are connected. We show that the biogeochemical length-scales vary significantly between variables and are not directly transferable. We also find that the spatial pattern of length-scales is similar across each variable, as long as a specific scaling factor for each variable is taken into account. The clusters indicate geographical regions within which there is a large exchange of information within the ecosystem, while information exchange across the boundaries between these regions is limited. The results of this study describe how information is expected to propagate through the shelf sea ecosystem, and how it can be used in multiple future applications such as stochastic noise modelling, data assimilation, or machine learning
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Ensemble Kalman filter in latent space using a variational autoencoder pair
No full textPopular (ensemble) Kalman filter data assimilation (DA) approaches assume that the errors in both the a priori estimate of the state and those in the observations are Gaussian. For constrained variables, e.g. sea ice concentration or stress, such an assumption does not hold. The variational autoencoder (VAE) is a machine learning (ML) technique that allows to map an arbitrary distribution to/from a latent space in which the distribution is supposedly closer to a Gaussian. We propose a novel hybrid DA-ML approach in which VAEs are incorporated in the DA procedure. Specifically, we introduce a variant of the popular ensemble transform Kalman filter (ETKF) in which the analysis is applied in the latent space of a single VAE or a pair of VAEs. In twin experiments with a simple circular model, whereby the circle represents an underlying submanifold to be respected, we find that the use of a VAE ensures that a posteriori ensemble members lie close to the manifold containing the truth. Furthermore, online updating of the VAE is necessary and achievable when this manifold varies in time, i.e. when it is non-stationary. We demonstrate that introducing an additional second latent space for the observational innovations improves robustness against detrimental effects of non-Gaussianity and bias in the observational errors but it slightly lessens the performance if observational errors are strictly Gaussian
Dataset and neural network weights to the paper: "Generative diffusion for regional surrogate models from sea-ice simulations"
No full text<p>All the needed code and data to reproduce the results from the paper: "Generative diffusion for regional surrogate models from sea-ice simulations".<br>While most of the code is a frozen clone of the original <a href="https://github.com/cerea-daml/diffusion-nextsim-regional">Repository</a>, this capsule also includes the dataset and neural network weights to train and apply the surrogate models.</p>
<p>The <strong>dataset</strong> for training and evaluation can be found at <em>data/nextsim</em>, which includes three different Zarr folders for training/validation/testing. The dataset is based on neXtSIM simulation data and ERA5 forcing data and extracted from the <a href="https://ige-meom-opendap.univ-grenoble-alpes.fr/thredds/catalog/meomopendap/extract/catalog.html">SASIP shared data OpenDAP server</a>:</p>
<ul>
<li>The neXtSIM simulations were performed by Gauillaume Boutin and published in the paper "<a href="https://doi.org/10.5194/tc-17-617-2023">Arctic sea ice mass balance in a new coupled ice–ocean model using a brittle rheology framework</a>" (Boutin et al., 2023) and available as Zenodo <a href="../records/7277523">dataset</a> (Boutin et al., 2022).</li>
<li>The forcing data is based on the ERA5 reanalysis dataset published in the paper: "<a href="https://doi.org/10.1002/qj.3803">The ERA5 global reanalysis</a>" (Hersbach et al., 2020) and available as dataset from the Copernicus Climate Change Service (C3S, Copernicus Climate Change Service, 2023). The here used forcing data is based on the <a href="https://cds.climate.copernicus.eu/cdsapp#!/dataset/reanalysis-era5-single-levels">hourly reanalysis data on single levels</a> and interpolated with nearest neighbors to the curvilinear grid as used in the output from the neXtSIM simulations. <strong>Disclaimer:</strong> The results contain modified Copernicus Climate Change Service information, 2023. Neither the European Commission nor ECMWF is responsible for any use that may be made of the Copernicus information or data it contains.</li>
</ul>
<p>The <strong>neural network weights</strong> are included under <em>data/models </em>and split into weights for the deterministic models and the diffusion models.<br>These neural network weights have been used to generate the results presented in the paper.</p>
<p>In this capsule, the <em>notebooks</em> folder includes also the figures used within the paper and additional trajectory data used in the qualitative analysis of the paper.</p>
<p>Generally, we recommend to just download the <em>data.tar.gz </em>file and use otherwise the original <a href="https://github.com/cerea-daml/diffusion-nextsim-regional">Repository</a>, since the here included code can be outdated. We further refer to the repository for additional information.</p>
<p> </p>
<p>Contained in this capsule:</p>
<ul>
<li>configs.tar.gz: The configuration files for the experiments.</li>
<li>data.tar.gz: The dataset and neural network weights.</li>
<li>diffusion_nextsim.tar.gz: The main code for the neural network etc.</li>
<li>environment.yaml: The anaconda environment file, can be used to install the needed packages.</li>
<li>notebooks.tar.gz: The notebooks that were used to create the figures in the paper. The figures from the paper and the data from the qualitative analysis are included as well.</li>
<li>readme.md: The readme file from the repository.</li>
<li>scripts.tar.gz: The scripts used for the experiments.</li>
<li>setup.py: the file to install the <em>diffusion_nextsim</em> package in a python environment.</li>
</ul>
<p>References:</p>
<p>Guillaume Boutin, Heather Regan, Einar Ólason, Laurent Brodeau, Claude Talandier, Camille Lique, & Pierre Rampal. (2022). Data accompanying the article "Arctic sea ice mass balance in a new coupled ice-ocean model using a brittle rheology framework" (1.0) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.7277523</p>
<p>Boutin, G., Ólason, E., Rampal, P., Regan, H., Lique, C., Talandier, C., Brodeau, L., and Ricker, R.: Arctic sea ice mass balance in a new coupled ice–ocean model using a brittle rheology framework, The Cryosphere, 17, 617–638, https://doi.org/10.5194/tc-17-617-2023, 2023.</p>
<p>Copernicus Climate Change Service (2023): ERA5 hourly data on single levels from 1940 to present. Copernicus Climate Change Service (C3S) Climate Data Store (CDS), DOI: <a href="https://doi.org/10.24381/cds.adbb2d47">10.24381/cds.adbb2d47</a>.</p>
<p>Hersbach H, Bell B, Berrisford P, et al. The ERA5 global reanalysis. <em>Q J R Meteorol Soc</em>. 2020; 146: 1999–2049. <a href="https://doi.org/10.1002/qj.3803">https://doi.org/10.1002/qj.3803</a></p>
<p> </p><p>This research has received financial support from the project SASIP (grant no. 353) funded by Schmidt Science – a philanthropic initiative that seeks to improve societal outcomes through the development of emerging science and technologies.</p>
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
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