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Utilisation conjointe de FlowCAM / ZooPhytoImage et de la cytométrie en flux. Premiers résultats et perspectives. Action 9. FlowCam ZooPhytoImage. Livrable n° 4. Rapport final, 23 septembre 2014 ArchiMer
Ali, Nour; Wacquet, Guillaume; Didry, Morgane; Hamad, Denis; Artigas, Luis Felipe; Grosjean, Philippe.
The goal of this study is to investigate about the possibility of coupling measurements made by image analysis from the FlowCAM with Zoo/PhytoImage with data obtained with a flux cytometer (pulse-shape-recording Scanning Flow Cytometry) on the same samples gathered in current monitoring networks in the eastern Channel and southern North Sea. In this preliminary study, we collected a series of samples off Boulogne-sur-Mer (SRN-REPHY monitoring system run by IFREMER) and along a transect in the Baie St-Jean (Wimereux-Slack) run by LOG. All these samples were digitized with a FlowCAM and measured with a scanning flow cytometer (CytoSense). The complete analysis with the FlowCAM and Zoo/PhytoImage is detailed in the present report. In order to get a better...
Tipo: Text Palavras-chave: Manche – Mer du Nord; Phytoplancton; Analyse d'image; Classification supervisée; Cytométrie en flux; Eastern English Channel and southern North Sea; Phytoplankton; Image analysis; Machine learning; Scanning Flow Cytometry.
Ano: 2014 URL: http://archimer.ifremer.fr/doc/00363/47442/47470.pdf
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Heuristic methods applied in reference evapotranspiration modeling Ciência e Agrotecnologia
Althoff,Daniel; Bazame,Helizani Couto; Filgueiras,Roberto; Dias,Santos Henrique Brant.
ABSTRACT The importance of the precise estimation of evapotranspiration is directly related to sustainable water usage. Since agriculture represents 70% of Brazil’s water consumption, adequate and efficient application of water may reduce the conflicts over the use of water among the multiple users. Considering the importance of accurate estimation of evapotranspiration, the objective of the present study was to model and compare the reference evapotranspiration from different heuristic methodologies. The standard Penman-Monteith method was used as reference for evapotranspiration, however, to evaluate the heuristic methodologies with scarce data, two widely known methods had their performances assessed in relation to Penman-Monteith. The methods used to...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Machine learning; Model comparison; Water management.
Ano: 2018 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1413-70542018000300314
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Breast Cancer Prediction Using Dominance-based Feature Filtering Approach: A Comparative Investigation in Machine Learning Archetype BABT
Atrey,Kushangi; Sharma,Yogesh; Bodhey,Narendra K.; Singh,Bikesh Kumar.
Abstract Breast cancer is the most commonly witnessed cancer amongst women around the world. Computer aided diagnosis (CAD) have been playing a significant role in early detection of breast tumors hence to curb the overall mortality rate. This work presents an enhanced empirical study of impact of dominance-based filtering approach on performances of various state-of-the-art classifiers. The feature dominance level is proportional to the difference in means of benign and malignant tumors. The experiments were done on original Wisconsin Breast Cancer Dataset (WBCD) with total nine features. It is found that the classifiers’ performances for top 4 and top 5 dominant-based features are almost equivalent to performances for all nine features. Artificial neural...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Breast cancer; Computer aided diagnosis; Dominance-based filtering; Machine learning.
Ano: 2019 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-89132019000100611
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An Alternative to Static Climatologies: Robust Estimation of Open Ocean CO2 Variables and Nutrient Concentrations From T, S, and O-2 Data Using Bayesian Neural Networks ArchiMer
Bittig, Henry C.; Steinhoff, Tobias; Claustre, Harve; Fiedler, Bjoern; Williams, Nancy L.; Sauzede, Raphaelle; Koertzinger, Arne; Gattuso, Jean-pierre.
This work presents two new methods to estimate oceanic alkalinity (A(T)), dissolved inorganic carbon (C-T), pH, and pCO(2) from temperature, salinity, oxygen, and geolocation data. "CANYON-B" is a Bayesian neural network mapping that accurately reproduces GLODAPv2 bottle data and the biogeochemical relations contained therein. "CONTENT" combines and refines the four carbonate system variables to be consistent with carbonate chemistry. Both methods come with a robust uncertainty estimate that incorporates information from the local conditions. They are validated against independent GO-SHIP bottle and sensor data, and compare favorably to other state-of-the-art mapping methods. As "dynamic climatologies" they show comparable performance to classical...
Tipo: Text Palavras-chave: Carbon cycle; GLODAP; Marine carbonate system; Surface pCO(2) climatology; Revelle buffer factor increase; Machine learning; Nutrient estimation.
Ano: 2018 URL: https://archimer.ifremer.fr/doc/00675/78681/80879.pdf
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Comparative analysis of decision tree algorithms on quality of water contaminated with soil Ciência Rural
Dota,Mara Andrea; Cugnasca,Carlos Eduardo; Barbosa,Domingos Sávio.
Agriculture, roads, animal farms and other land uses may modify the water quality from rivers, dams and other surface freshwaters. In the control of the ecological process and for environmental management, it is necessary to quickly and accurately identify surface water contamination (in areas such as rivers and dams) with contaminated runoff waters coming, for example, from cultivation and urban areas. This paper presents a comparative analysis of different classification algorithms applied to the data collected from a sample of soil-contaminated water aiming to identify if the water quality classification proposed in this research agrees with reality. The sample was part of a laboratory experiment, which began with a sample of treated water added with...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Environmentalcontrol; Runoff; Wireless sensor networks; Machine learning; Data mining.
Ano: 2015 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0103-84782015000200267
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Evaluation of gene selection metrics for tumor cell classification Genet. Mol. Biol.
Faceli,Katti; Carvalho,André C.P.L.F. de; Silva Jr,Wilson A..
Gene expression profiles contain the expression level of thousands of genes. Depending on the issue under investigation, this large amount of data makes analysis impractical. Thus, it is important to select subsets of relevant genes to work with. This paper investigates different metrics for gene selection. The metrics are evaluated based on their ability in selecting genes whose expression profile provides information to distinguish between tumor and normal tissues. This evaluation is made by constructing classifiers using the genes selected by each metric and then comparing the performance of these classifiers. The performance of the classifiers is evaluated using the error rate in the classification of new tissues. As the dataset has few tissue samples,...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Gene selection; Machine learning; Gene expression; Sage.
Ano: 2004 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572004000400029
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Guide méthodologique. Version actualisée de ZooPhytoImage avec refonte de l’interface graphique. Action 9. FlowCam ZooPhytoImage. Livrable n°1. Rapport final ArchiMer
Grosjean, Philippe.
Zoo/PhytoImage 4 is an « open source » software based on R and ImageJ. It processes numerical images of plankton particles digitized using a FlowCAM, a flat-bed scanner, microor macrophotos, etc. The general concept consists in the individual outlining of particles on the pictures, followed by their measurements (so-called « attributes ») such the size, the shape, transparency, textures, etc. These attributes are then used by a classification tool to automatically predict the taxonomic group the particles belong to. The classifier is obtained after a learning stage using a machine learning algorithm and a training set of pre-identified particles. The algorithm learns to recognize the taxonomic group from the set of attributes measured on the picture. The...
Tipo: Text Palavras-chave: Océanographie biologique; Plancton; Surveillance côtière; Analyse automatisée; Analyse d'image; Classification supervisée; Biological oceanography; Plankton; Costal survey; Automated analysis; Image analysis; Machine learning.
Ano: 2014 URL: http://archimer.ifremer.fr/doc/00363/47436/47461.pdf
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Optimisation de l’identification et du dénombrement du microphytoplancton avec le système couplé de numérisation et d’analyse d’images FlowCAM – Zoo/PhytoImage (système innovant) ArchiMer
Grosjean, Philippe; Wacquet, Guillaume.
This report details the work accomplished to enhance the Zoo/PhytoImage software to optimize its use for the analysis of phytoplankton samples in general, but more particularly, in the framework of an operational survey of coastal seawater (REPHY, IFREMER). Zoo/PhytoImage allows to analyze “numerically recorded” plankton samples, that is, by using digital images gathered with specialized devices such as the FlowCAM, or the FastCAM (see report 3). A machine learning approach allows to automatically classify the digitized particles into various taxonomic groups. Once this is done, global statistics are calculated on each sample, including the number of particles, the biomass, and the size spectrum per taxonomic group. Two major changes are introduced in the...
Tipo: Text Palavras-chave: Phytoplancton; REPHY; Analyse d'image; Classification supervisée; Dénombrement de cellules; Apprentissage actif; Manche; Atlantique.; Phytoplankton; REPHY; Image analysis; Machine learning; Cells enumeration; Active learning; The Channel; Atlantic Ocean.
Ano: 2016 URL: http://archimer.ifremer.fr/doc/00389/49990/50578.pdf
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A machine learning algorithm for high throughput identification of FTIR spectra: Application on microplastics collected in the Mediterranean Sea ArchiMer
Kedzierski, Mikaël; Falcou-préfol, Mathilde; Kerros, Marie Emmanuelle; Henry, Maryvonne; Pedrotti, Maria Luiza; Bruzaud, Stéphane.
The development of methods to automatically determine the chemical nature of microplastics by FTIR-ATR spectra is an important challenge. A machine learning method, named k-nearest neighbors classification, has been applied on spectra of microplastics collected during Tara Expedition in the Mediterranean Sea (2014). To realize these tests, a learning database composed of 969 microplastic spectra has been created. Results show that the machine learning process is very efficient to identify spectra of classical polymers such as poly(ethylene), but also that the learning database must be enhanced with less common microplastic spectra. Finally, this method has been applied on more than 4000 spectra of unidentified microplastics. The verification protocol...
Tipo: Text Palavras-chave: Microplastic; Tara mediterranean campaign; FTIR spectra; Machine learning; K-nearest neighbor classification.
Ano: 2019 URL: https://archimer.ifremer.fr/doc/00501/61247/64825.pdf
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Global patterns and predictors of trophic position, body size and jaw size in fishes ArchiMer
Kopf, R. Keller; Yen, Jian D. L.; Nimmo, Dale G.; Brosse, Sébastien; Villeger, Sébastien; Tittensor, Derek.
Aim The aim of this study was test whether maximum body mass and jaw length are reliable predictors of trophic position (TP) in fishes, and to compare linear and nonlinear machine‐learning (ML) models incorporating biogeography, habitat and other morphological traits. Location Global. Time period Modern. Major taxa studied Fishes. Methods We compiled a global database of TP (2.0–4.5), maximum body mass, jaw length, order, ecoregion, habitat and other morphological traits of freshwater, estuarine and diadromous fishes (n = 1,991). We used Bayesian linear mixed effects and ML, with r2 analogues and 10‐fold cross‐validation, to explain and predict TP. Results Random forest models outperformed Bayesian models in all comparisons. Jaw length was the most...
Tipo: Text Palavras-chave: Allometric trophic network models; Allometry; Body mass; Gape limitation; Machine learning; Predator– Prey; Random forest; Trophic network theory.
Ano: 2021 URL: https://archimer.ifremer.fr/doc/00661/77349/78823.pdf
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Evaluation of noise reduction techniques in the splice junction recognition problem Genet. Mol. Biol.
Lorena,Ana C.; Carvalho,André C. P. L. F. de.
The Human Genome Project has generated a large amount of sequence data. A number of works are currently concerned with analyzing these data. One of the analyses carried out is the identification of genes' structures on the sequences obtained. As such, one can search for particular signals associated with gene expression. Splice junctions represent a type of signal present on eukaryote genes. Many studies have applied Machine Learning techniques in the recognition of such regions. However, most of the genetic databases are characterized by the presence of noisy data, which can affect the performance of the learning techniques. This paper evaluates the effectiveness of five data pre-processing algorithms in the elimination of noisy instances from two splice...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Pre-processing; Machine learning; Splice junction recognition.
Ano: 2004 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572004000400031
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Reconstructing Global Chlorophyll-a Variations Using a Non-linear Statistical Approach ArchiMer
Martinez, Elodie; Gorgues, Thomas; Lengaigne, Matthieu; Fontana, Clement; Sauzède, Raphaëlle; Menkes, Christophe; Uitz, Julia; Di Lorenzo, Emanuele; Fablet, Ronan.
Monitoring the spatio-temporal variations of surface chlorophyll-a concentration (Chl, a proxy of phytoplankton biomass) greatly benefited from the availability of continuous and global ocean color satellite measurements from 1997 onward. These two decades of satellite observations are however still too short to provide a comprehensive description of Chl variations at decadal to multi-decadal timescales. This paper investigates the ability of a machine learning approach (a non-linear statistical approach based on Support Vector Regression, hereafter SVR) to reconstruct global spatio-temporal Chl variations from selected surface oceanic and atmospheric physical parameters. With a limited training period (13 years), we first demonstrate that Chl variability...
Tipo: Text Palavras-chave: Machine learning; Phytoplankton variability; Satellite ocean color; Decadel variability; Global scale.
Ano: 2020 URL: https://archimer.ifremer.fr/doc/00641/75314/75810.pdf
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Digital Soil Mapping Using Machine Learning Algorithms in a Tropical Mountainous Area Rev. Bras. Ciênc. Solo
Meier,Martin; Souza,Eliana de; Francelino,Marcio Rocha; Fernandes Filho,Elpídio Inácio; Schaefer,Carlos Ernesto Gonçalves Reynaud.
ABSTRACT: Increasingly, applications of machine learning techniques for digital soil mapping (DSM) are being used for different soil mapping purposes. Considering the variety of models available, it is important to know their performance in relation to soil data and environmental variables involved in soil mapping. This paper investigated the performance of eight machine learning algorithms for soil mapping in a tropical mountainous area of an official rural settlement in the Zona da Mata region in Brazil. Morphometric maps generated from a digital elevation model, together with Landsat-8 satellite imagery, and climatic maps, were among the set of covariates to be selected by the Recursive Feature Elimination algorithm to predict soil types using machine...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Soil classification; Machine learning; Pedometrics; Land use planning; Agrarian reform.
Ano: 2018 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-06832018000100313
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THE USE OF ARTIFICIAL INTELLIGENCE FOR ESTIMATING SOIL RESISTANCE TO PENETRATION REA
Pereira,Tonismar dos S.; Robaina,Adroaldo D.; Peiter,Marcia X.; Torres,Rogerio R.; Bruning,Jhosefe.
ABSTRACT The aim of this study was to present and to evaluate methodologies for the estimation of soil resistance to penetration (RP) using artificial intelligence prediction techniques. In order to do so, a data base with values of physical-water characteristics of the soils available in the literature was used, and the performances of Artificial Neural Networks (ANN) and Support Vector Machines (SVM) were evaluated. The models generated from the ANNs were implemented through the multilayer perceptron with backpropagation algorithm of Matlab software, varying the number of neurons in the input and intermediate layers. For the procedure from SVM, the RapidMiner software was used, varying input variables, the kernel function and the coefficients of these...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Soil compaction; Machine learning; Support vector machines; Artificial neural networks.
Ano: 2018 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-69162018000100142
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Exploring Machine Learning to Correct Satellite-Derived Sea Surface Temperatures ArchiMer
Picart, Stephane Saux; Tandeo, Pierre; Autret, Emmanuelle; Gausset, Blandine.
Machine learning techniques are attractive tools to establish statistical models with a high degree of non linearity. They require a large amount of data to be trained and are therefore particularly suited to analysing remote sensing data. This work is an attempt at using advanced statistical methods of machine learning to predict the bias between Sea Surface Temperature (SST) derived from infrared remote sensing and ground “truth” from drifting buoy measurements. A large dataset of collocation between satellite SST and in situ SST is explored. Four regression models are used: Simple multi-linear regression, Least Square Shrinkage and Selection Operator (LASSO), Generalised Additive Model (GAM) and random forest. In the case of geostationary satellites for...
Tipo: Text Palavras-chave: Machine learning; Systematic error; Sea surface temperature; Random forest.
Ano: 2018 URL: https://archimer.ifremer.fr/doc/00426/53797/54721.pdf
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TEXT CATEGORIZATION USING ONLY FRAGMENTS OF DOCUMENTS AgEcon
Pilaszy, Istvan; Dobrowiecki, Tadeusz.
In this paper we presented a lot of experiments that examine how the particular parts of the documents do contribute to the performance of a classifier. We evaluated text classifiers on two very different text corpora. We conclude that some parts of the text are more important from the point of text classification performance. Giving higher weights to more important parts can increase the performance of the classifier. The question, that which parts are more or less important depends on the nature of the documents in the corpora. Some tasks that remains to be done: − More text corpora should be investigated. − In section 6.4 we optimized the number of features to be kept independent from the section. However, it could be optimized for each section. −...
Tipo: Journal Article Palavras-chave: Machine learning; Text categorization; Classifier ensembles; Research and Development/Tech Change/Emerging Technologies.
Ano: 2007 URL: http://purl.umn.edu/58927
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Construction of Multi-Year Time-Series Profiles of Suspended Particulate Inorganic Matter Concentrations Using Machine Learning Approach ArchiMer
Renosh, Pannimpullath R.; Jourdin, Frederic; Charantonis, Anastase A.; Yala, Khalil; Rivier, Aurelie; Badran, Fouad; Thiria, Sylvie; Guillou, Nicolas; Leckler, Fabien; Gohin, Francis; Garlan, Thierry.
Hydro-sedimentary numerical models have been widely employed to derive suspended particulate matter (SPM) concentrations in coastal and estuarine waters. These hydro-sedimentary models are computationally and technically expensive in nature. Here we have used a computationally less-expensive, well-established methodology of self-organizing maps (SOMs) along with a hidden Markov model (HMM) to derive profiles of suspended particulate inorganic matter (SPIM). The concept of the proposed work is to benefit from all available data sets through the use of fusion methods and machine learning approaches that are able to process a growing amount of available data. This approach is applied to two different data sets entitled “Hidden” and “Observable”. The hidden...
Tipo: Text Palavras-chave: Suspended particulate inorganic matter; Self-organizing maps; Hidden Markov Model; Machine learning; English Channel; ROMS.
Ano: 2017 URL: http://archimer.ifremer.fr/doc/00415/52653/53511.pdf
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Water Mass and Biogeochemical Variability in the Kerguelen Sector of the Southern Ocean: A Machine Learning Approach for a Mixing Hotspot ArchiMer
Rosso, Isabella; Mazloff, Matthew R.; Talley, Lynne D.; Purkey, Sarah G.; Freeman, Natalie M.; Maze, Guillaume.
The Southern Ocean (SO) is one of the most energetic regions in the world, where strong air‐sea fluxes, oceanic instabilities, and flow‐topography interactions yield complex dynamics. The Kerguelen Plateau (KP) region in the Indian sector of the SO is a hotspot for these energetic dynamics, which result in large spatio‐temporal variability of physical and biogeochemical (BGC) properties throughout the water column. Data from Argo floats (including biogeochemical) are used to investigate the spatial variability of intermediate and deep water physical and BGC properties. An unsupervised machine learning classification approach is used to organize the float profiles into five SO frontal zones based on their temperature and salinity structure between 300 and...
Tipo: Text Palavras-chave: Southern Ocean; Kerguelen Plateau; Argo; Unsupervised clustering; Machine learning.
Ano: 2020 URL: https://archimer.ifremer.fr/doc/00613/72471/71438.pdf
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Evaluation of imputed genomic data in discrete traits using Random forest and Bayesian threshold methodsb Animal Sciences
Sadeghi, Saadat; Rafat, Seyed Abbas; Alijani, Sadegh.
The objectives of this study were (1) to quantify imputation accuracy and to assess the factors affecting it; and (2) to evaluate the accuracy of threshold BayesA (TBA), Bayesian threshold LASSO (BTL) and random forest (RF) algorithms to analyze discrete traits. Genomic data were simulated to reflect variations in heritability (h2 = 0.30 and 0.10), number of QTL (QTL = 81 and 810), number of SNP (10 K and 50 K) and linkage disequilibrium (LD=low and high) for 27 chromosomes. For real condition simulating, we randomly masked markers with 90% missing rate for each scenario; afterwards, hidden markers were imputed using FImpute software. In imputed genotypes, a wide range of accuracy was observed for RF (0.164-0.512) compared to TBA (0.283-0.469) and BTL...
Tipo: Info:eu-repo/semantics/article Palavras-chave: PhD candidate of animal breeding accuracy; Genomic architecture; Linkage disequilibrium; Machine learning; Masked genotypes..
Ano: 2018 URL: http://periodicos.uem.br/ojs/index.php/ActaSciAnimSci/article/view/39007
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Metodologia para processamento de imagens digitais do sistema radicular de milho e sorgo utilizando a plataforma Digital Imaging of Root Traits (DIRT). Infoteca-e
SANTOS, T. T.; SOUSA, S. M. de; CAMPOLINO, M. L.; LANA, U. G. de P.; COELHO, A. M..
Neste trabalho, apresentamos uma nova metodologia para segmentação e identificação de itens em imagens, baseada em aprendizado de máquina, que é mais robusta que a metodologia de pré-processamento de imagens originalmente proposta para o DIRT.
Tipo: Boletim de Pesquisa e Desenvolvimento (INFOTECA-E) Palavras-chave: Metodologia; Processamento de imagem digital; Digital Imaging of Root Traits; Raiz de planta; Aprendizado de máquina; Shovelomics; Árvore de decisão; Image processing; Machine learning; Decision tree; Fósforo; Digital images; Phosphorus; Roots; Image analysis..
Ano: 2019 URL: http://www.infoteca.cnptia.embrapa.br/infoteca/handle/doc/1117049
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