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Article ; Online: SMOTE-CD: SMOTE for compositional data.

Nguyen, Teo / Mengersen, Kerrie / Sous, Damien / Liquet, Benoit

2023 Volume 18, Issue 6, Page(s) e0287705

Abstract: Compositional data are a special kind of data, represented as a proportion carrying relative information. Although this type of data is widely spread, no solution exists to deal with the cases where the classes are not well balanced. After describing ... ...

Abstract	Compositional data are a special kind of data, represented as a proportion carrying relative information. Although this type of data is widely spread, no solution exists to deal with the cases where the classes are not well balanced. After describing compositional data imbalance, this paper proposes an adaptation of the original Synthetic Minority Oversampling TEchnique (SMOTE) to deal with compositional data imbalance. The new approach, called SMOTE for Compositional Data (SMOTE-CD), generates synthetic examples by computing a linear combination of selected existing data points, using compositional data operations. The performance of the SMOTE-CD is tested with three different regressors (Gradient Boosting tree, Neural Networks, Dirichlet regressor) applied to two real datasets and to synthetic generated data, and the performance is evaluated using accuracy, cross-entropy, F1-score, R2 score and RMSE. The results show improvements across all metrics, but the impact of oversampling on performance varies depending on the model and the data. In some cases, oversampling may lead to a decrease in performance for the majority class. However, for the real data, the best performance across all models is achieved when oversampling is used. Notably, the F1-score is consistently increased with oversampling. Unlike the original technique, the performance is not improved when combining oversampling of the minority classes and undersampling of the majority class. The Python package smote-cd implements the method and is available online.
MeSH term(s)	Acclimatization ; Benchmarking ; Entropy ; Minority Groups ; Neural Networks, Computer
Language	English
Publishing date	2023-06-29
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0287705
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: A Richards’ equation-based model for wave-resolving simulation of variably-saturated beach groundwater flow dynamics

Clément, Jean-Baptiste / Sous, Damien / Bouchette, Frédéric / Golay, Frédéric / Ersoy, Mehmet

Journal of Hydrology. 2023 Apr., v. 619 p.129344-

2023

Abstract: This study introduces a model based on Richards’ equation to describe variably-saturated beach groundwater flow. The surface wave propagation is computed by the phase-resolving non-hydrostatic SWASH code. The SWASH data are used to make a suitable ... ...

Abstract	This study introduces a model based on Richards’ equation to describe variably-saturated beach groundwater flow. The surface wave propagation is computed by the phase-resolving non-hydrostatic SWASH code. The SWASH data are used to make a suitable dynamic boundary condition at the beach face to force Richards’ equation. The latter is solved by a weighted discontinuous Galerkin method together with adaptive mesh refinement. The model is validated by comparison with a laboratory experiment of a transient water table recharge problem. Then, the BARDEX II prototype-scale experiment is considered to assess the model abilities for beach groundwater dynamics. The barrier beach is studied for three cases with different lagoon levels. Steady-state results with no-wave conditions show excellent agreement. Transient waves simulations are evaluated in terms of pressure heads, saturations, water table position and groundwater velocities for time-averaged, swash-resolving and spectral analysis. Results bring interesting insights about beach groundwater modelling by comparison with the experimental data as well as a Darcy’s equation-based model. A first investigation is carried out to assess the groundwater effect on the bed sediment dynamics through the modification of sediment relative weight.
Keywords	beaches ; equations ; groundwater ; groundwater flow ; hydrodynamics ; laboratory experimentation ; models ; sediments ; spectral analysis ; water table ; Swash zone ; Barrier beach ; Numerical modelling ; Unsaturated porous media ; Seepage ; Adaptive discontinuous Galerkin method
Language	English
Dates of publication	2023-04
Publishing place	Elsevier B.V.
Document type	Article ; Online
Note	Pre-press version
ZDB-ID	1473173-3
ISSN	1879-2707 ; 0022-1694
ISSN (online)	1879-2707
ISSN	0022-1694
DOI	10.1016/j.jhydrol.2023.129344
Database	NAL-Catalogue (AGRICOLA)

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Article: Mapping of Coral Reefs with Multispectral Satellites: A Review of Recent Papers

Nguyen, Teo / Liquet, Benoît / Mengersen, Kerrie / Sous, Damien

Remote Sensing. 2021 Nov. 07, v. 13, no. 21

2021

Abstract: Coral reefs are an essential source of marine biodiversity, but they are declining at an alarming rate under the combined effects of global change and human pressure. A precise mapping of coral reef habitat with high spatial and time resolutions has ... ...

Abstract	Coral reefs are an essential source of marine biodiversity, but they are declining at an alarming rate under the combined effects of global change and human pressure. A precise mapping of coral reef habitat with high spatial and time resolutions has become a necessary step for monitoring their health and evolution. This mapping can be achieved remotely thanks to satellite imagery coupled with machine-learning algorithms. In this paper, we review the different satellites used in recent literature, as well as the most common and efficient machine-learning methods. To account for the recent explosion of published research on coral reel mapping, we especially focus on the papers published between 2018 and 2020. Our review study indicates that object-based methods provide more accurate results than pixel-based ones, and that the most accurate methods are Support Vector Machine and Random Forest. We emphasize that the satellites with the highest spatial resolution provide the best images for benthic habitat mapping. We also highlight that preprocessing steps (water column correction, sunglint removal, etc.) and additional inputs (bathymetry data, aerial photographs, etc.) can significantly improve the mapping accuracy.
Keywords	benthic ecosystems ; biodiversity ; coral reefs ; corals ; evolution ; global change ; humans ; remote sensing ; support vector machines
Language	English
Dates of publication	2021-1107
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2513863-7
ISSN	2072-4292
ISSN	2072-4292
DOI	10.3390/rs13214470
Database	NAL-Catalogue (AGRICOLA)

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Article: Effects of Biofilms and Particle Physical Properties on the Rising and Settling Velocities of Microplastic Fibers and Sheets

Jalón-Rojas, Isabel / Romero-Ramírez, Alicia / Fauquembergue, Kelly / Rossignol, Linda / Cachot, Jérôme / Sous, Damien / Morin, Bénédicte

Environmental science & technology. 2022 May 20, v. 56, no. 12

2022

Abstract: Vertical dynamics of microplastics (MPs) in the water column are complex and not fully understood due to the diversity of environmental MPs and the impact of weathering and biofouling on their dynamical properties. In this study, we investigate the ... ...

Abstract	Vertical dynamics of microplastics (MPs) in the water column are complex and not fully understood due to the diversity of environmental MPs and the impact of weathering and biofouling on their dynamical properties. In this study, we investigate the effects of the particle properties and biofilm on the vertical (settling or rising) velocity of microplastic sheets and fibers under laboratory conditions. The experiments focus on three types of MPs (polyester PES fibers, polyethylene terephthalate PET sheets, and polypropylene PP sheets) of nine sizes and two degrees of biological colonization. Even though pristine PES fibers and PET sheets had a similar density, the sinking velocity of fibers was much smaller and independent of their length. The settling or rising velocity of sheets increased with the particle size up to a threshold and then decreased in the wake of horizontal oscillations in large particles. Biofilms had unexpected effects on vertical velocities. Irregular biofilm distributions can trigger motion instabilities that decrease settling velocities of sheets despite the increase in density. Biofilms can also modify the orientation of fibers, which may increase their settling velocity. Finally, we selected the most performant theoretical formulation for each type of particle and proposed modifications to consider the effect of biofilm distribution.
Keywords	biofilm ; biofouling ; microplastics ; particle size ; polypropylenes ; technology
Language	English
Dates of publication	2022-0520
Size	p. 8114-8123.
Publishing place	American Chemical Society
Document type	Article
ISSN	1520-5851
DOI	10.1021/acs.est.2c01302
Database	NAL-Catalogue (AGRICOLA)

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Article: Detecting the effects of inter-annual and seasonal changes in environmental factors on the striped red mullet population in the Bay of Biscay

Kermorvant, Claire / Caill-Milly, Nathalie / Sous, Damien / Paradinas, Iosu / Lissardy, Muriel / Liquet, Benoit

Journal of sea research. 2021 Mar., v. 169

2021

Abstract: Climate fluctuations affect a wide range of environmental factors that may impact fish populations with various response mechanisms. For a major part of world fisheries stocks, only abundance time-series are available. Relations between abundance of ... ...

Abstract	Climate fluctuations affect a wide range of environmental factors that may impact fish populations with various response mechanisms. For a major part of world fisheries stocks, only abundance time-series are available. Relations between abundance of these species and ocean variables, including long term trends and patterns of seasonal change, remain sparsely documented. The main aim of our work is to determine to what extent effects of inter-annual and seasonal changes in environmental factors can be identified and quantified on a selected time-series of abundance data-set: the striped red mullet population within the Bay of Biscay. 8 Landings per unit of effort (LPUE) for striped red mullet data are compared with environmental covariates extracted from the Copernicus web database. Our strategy is to decompose the patterns of change in fish populations into long-term and seasonal components and to analyse the possible dependency of both components on environmental factors. The overall tendencies are a decrease of the long-term component and a modification of the seasonality, with additional spatial variability. The observed tendencies and seasonal changes are discussed against the spatio-temporal patterns of change in environmental factors. High spatial heterogeneity within the Bay of Biscay was found, both for striped red mullet long-term trends and seasonal changes. Most inter-annual and seasonal changes in striped red mullet abundance can be related to environmental factors. In addition to the well-known annual fluctuation, most coastal sites revealed a bi-annual seasonality possibly related to the recruitment process.
Keywords	Mullus surmuletus ; climate ; data collection ; databases ; fish ; research ; seasonal variation ; spatial variation ; time series analysis ; Bay of Biscay
Language	English
Dates of publication	2021-03
Publishing place	Elsevier B.V.
Document type	Article
Note	NAL-AP-2-clean
ISSN	1385-1101
DOI	10.1016/j.seares.2021.102008
Database	NAL-Catalogue (AGRICOLA)

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Article: An adaptive strategy for discontinuous Galerkin simulations of Richards’ equation: Application to multi-materials dam wetting

Clément, Jean-Baptiste / Golay, Frédéric / Ersoy, Mehmet / Sous, Damien

Advances in water resources. 2021 May, v. 151

2021

Abstract: Numerical solution of Richards’ equation remains challenging to get robust, accurate and cost-effective results, particularly for moving sharp wetting fronts. An adaptive strategy for both space and time is proposed to deal with 2D sharp wetting fronts ... ...

Abstract	Numerical solution of Richards’ equation remains challenging to get robust, accurate and cost-effective results, particularly for moving sharp wetting fronts. An adaptive strategy for both space and time is proposed to deal with 2D sharp wetting fronts associated with varying and possibly vanishing diffusivity caused by nonlinearity, heterogeneity and anisotropy. Adaptive time stepping makes nonlinear convergence reliable and backward difference formula provides high-order time scheme. Adaptive mesh refinement tracks wetting fronts with an a posteriori error indicator. The novelty of this paper consists in using this technique in combination with a weighted discontinuous Galerkin framework to better approximate steep wetting fronts by a discontinuity. The potential of the overall approach is shown through various examples including analytical and laboratory benchmarks and simulation of full-scale multi-materials dam wetting experiment.
Keywords	anisotropy ; cost effectiveness ; diffusivity ; space and time ; water
Language	English
Dates of publication	2021-05
Publishing place	Elsevier Ltd
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	2023320-6
ISSN	1872-9657 ; 0309-1708
ISSN (online)	1872-9657
ISSN	0309-1708
DOI	10.1016/j.advwatres.2021.103897
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Behaviour of plastic litter in nearshore waters: First insights from wind and wave laboratory experiments.

Forsberg, Pernille Louise / Sous, Damien / Stocchino, Alessandro / Chemin, Remi

Marine pollution bulletin

2020 Volume 153, Page(s) 111023

Abstract: Plastic litter in nearshore waters is an environmental pollutant with increasing impact on coastal environments. At present, knowledge on basic plastic particle dynamics and the interaction with complex hydrodynamics is lacking. The present laboratory ... ...

Abstract	Plastic litter in nearshore waters is an environmental pollutant with increasing impact on coastal environments. At present, knowledge on basic plastic particle dynamics and the interaction with complex hydrodynamics is lacking. The present laboratory study, performed under controlled wave and wind conditions, demonstrates the dispersion of plastics in shallow waters. The study presents a simple case looking solely at cross-shore particle transport. The results show that both wind and waves as well as plastic properties (shape and density) govern the behaviour of plastic litter in the nearshore zone. Heavy particles behave like natural sand with accumulation in the wave breaking zone. Light particles have varying accumulation along the coastal profile depending on the wind, waves and particle shapes. More extensive characterization remains to be done in future studies.
MeSH term(s)	Environmental Monitoring ; Hydrodynamics ; Laboratories ; Plastics ; Water Pollutants/analysis ; Wind
Chemical Substances	Plastics ; Water Pollutants
Language	English
Publishing date	2020-03-25
Publishing country	England
Document type	Journal Article
ZDB-ID	2001296-2
ISSN	1879-3363 ; 0025-326X
ISSN (online)	1879-3363
ISSN	0025-326X
DOI	10.1016/j.marpolbul.2020.111023
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Effects of Biofilms and Particle Physical Properties on the Rising and Settling Velocities of Microplastic Fibers and Sheets.

Jalón-Rojas, Isabel / Romero-Ramírez, Alicia / Fauquembergue, Kelly / Rossignol, Linda / Cachot, Jérôme / Sous, Damien / Morin, Bénédicte

Environmental science & technology

2022 Volume 56, Issue 12, Page(s) 8114–8123

Abstract	Vertical dynamics of microplastics (MPs) in the water column are complex and not fully understood due to the diversity of environmental MPs and the impact of weathering and biofouling on their dynamical properties. In this study, we investigate the effects of the particle properties and biofilm on the vertical (settling or rising) velocity of microplastic sheets and fibers under laboratory conditions. The experiments focus on three types of MPs (polyester PES fibers, polyethylene terephthalate PET sheets, and polypropylene PP sheets) of nine sizes and two degrees of biological colonization. Even though pristine PES fibers and PET sheets had a similar density, the sinking velocity of fibers was much smaller and independent of their length. The settling or rising velocity of sheets increased with the particle size up to a threshold and then decreased in the wake of horizontal oscillations in large particles. Biofilms had unexpected effects on vertical velocities. Irregular biofilm distributions can trigger motion instabilities that decrease settling velocities of sheets despite the increase in density. Biofilms can also modify the orientation of fibers, which may increase their settling velocity. Finally, we selected the most performant theoretical formulation for each type of particle and proposed modifications to consider the effect of biofilm distribution.
MeSH term(s)	Biofilms ; Biofouling ; Environmental Monitoring ; Microplastics ; Plastics ; Water Pollutants, Chemical/analysis
Chemical Substances	Microplastics ; Plastics ; Water Pollutants, Chemical
Language	English
Publishing date	2022-05-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1520-5851
ISSN (online)	1520-5851
DOI	10.1021/acs.est.2c01302
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Microplastics in a salt-wedge estuary: Vertical structure and tidal dynamics

Defontaine, Sophie / Sous, Damien / Tesan, Javier / Monperrus, Mathilde / Lenoble, Véronique / Lanceleur, Laurent

Marine pollution bulletin. 2020 Nov., v. 160

2020

Abstract: The abundance and distribution of microplastics in estuaries have been barely documented, and generally without accounting for the vertical structure in the water column. This study presents the very first data on the occurrence and distribution of ... ...

Abstract	The abundance and distribution of microplastics in estuaries have been barely documented, and generally without accounting for the vertical structure in the water column. This study presents the very first data on the occurrence and distribution of microplastics in the Adour Estuary, SW France. The experimental data set was complemented by numerical simulations to gain understanding of the behaviour of suspended microplastics. Microplastics were found throughout the water column with a mean abundance of 1.13 part/m³. Films and fragments were the most abundant types of particles collected. Numerical simulations demonstrated that vertical distribution of microplastics in the water column is highly dependent on particle characteristics and on the local hydrodynamics. The main trend is that neutrally-buoyant microplastics are easily flushed out while heavier microplastics are prone to entrapment in the estuary, in particular under low discharge conditions. The present study suggest that estuaries could be a sink of microplastics.
Keywords	data collection ; estuaries ; hydrodynamics ; marine pollution ; microplastics ; spatial distribution ; France
Language	English
Dates of publication	2020-11
Publishing place	Elsevier Ltd
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	2001296-2
ISSN	1879-3363 ; 0025-326X
ISSN (online)	1879-3363
ISSN	0025-326X
DOI	10.1016/j.marpolbul.2020.111688
Database	NAL-Catalogue (AGRICOLA)

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Article: Behaviour of plastic litter in nearshore waters: First insights from wind and wave laboratory experiments

Forsberg, Pernille Louise / Sous, Damien / Stocchino, Alessandro / Chemin, Remi

Marine pollution bulletin. 2020 Apr., v. 153

2020

Abstract	Plastic litter in nearshore waters is an environmental pollutant with increasing impact on coastal environments. At present, knowledge on basic plastic particle dynamics and the interaction with complex hydrodynamics is lacking. The present laboratory study, performed under controlled wave and wind conditions, demonstrates the dispersion of plastics in shallow waters. The study presents a simple case looking solely at cross-shore particle transport. The results show that both wind and waves as well as plastic properties (shape and density) govern the behaviour of plastic litter in the nearshore zone. Heavy particles behave like natural sand with accumulation in the wave breaking zone. Light particles have varying accumulation along the coastal profile depending on the wind, waves and particle shapes. More extensive characterization remains to be done in future studies.
Keywords	hydrodynamics ; marine pollution ; pollutants ; sand ; wind
Language	English
Dates of publication	2020-04
Publishing place	Elsevier Ltd
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	2001296-2
ISSN	1879-3363 ; 0025-326X
ISSN (online)	1879-3363
ISSN	0025-326X
DOI	10.1016/j.marpolbul.2020.111023
Database	NAL-Catalogue (AGRICOLA)

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