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• 1
Article
Language: English
In: Stochastic Environmental Research and Risk Assessment, 2016, Vol.30(7), pp.1981-2008
Description: The percent model affinity ( PMA ) index is used to measure the similarity of two probability profiles representing, for example, an ideal profile (i.e. reference condition) and a monitored profile (i.e. possibly impacted condition). The goal of this work is to study the effects of sample size, evenness, true value of the index and number of classes on the statistical properties of the estimator of the PMA index. We derive and extend previous formulas of the expectation and variance of the estimator for estimated monitored profile and fixed reference profile. Using the obtained extension, we find that the estimator is asymptotically unbiased, converging faster when the profiles differ. When both profiles are estimated, we calculate the expectation using transformation rules for expectation and in addition derive the formula for the estimator’s variance. Since the computation of the probabilities in the variance formula is slow, we study the behavior of the variance with simulation experiments and assess whether it could be approximated with the variance for the fixed reference profile. Finally, we provide a set of recommendations for the users of the PMA index to avoid the most common caveats of the index.
Keywords: Percent model affinity index ; Similarity measure ; Statistical properties ; Decision making ; Biomonitoring
ISSN: 1436-3240
E-ISSN: 1436-3259
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• 2
Article
Description: The assessment of diversity and similarity is relevant in monitoring the status of ecosystems. The respective indicators are based on the taxonomic composition of biological communities of interest, currently estimated through the proportions computed from sampling multivariate counts. In this work we present a novel method able to work with only one sample to estimate the taxonomic composition when the data are affected by overdispersion. The presence of overdispersion in taxonomic counts may be the result of significant environmental factors which are often unobservable but influence communities. Following the empirical Bayes approach, we combine a Bayesian model with the marginal likelihood method to jointly estimate the taxonomic proportions and the level of overdispersion from one sample of multivariate counts. Our proposal is compared to the classical maximum likelihood method in an extensive simulation study with different realistic scenarios. An application to real data from aquatic biomonitoring is also presented. In both the simulation study and the real data application, we consider communities characterized by a large number of taxonomic categories, such as aquatic macroinvertebrates or bacteria which are often overdispersed. The applicative results demonstrate an overall superiority of the empirical Bayes method in almost all examined cases, for both assessments of diversity and similarity. We would recommend practitioners in biomonitoring to use the proposed approach in addition to the traditional procedures. The empirical Bayes estimation allows to better control the error propagation due to the presence of overdispersion in biological data, with a more efficient managerial decision making. Comment: 40 pages, 10 figures, 5 tables, 2 appendices
Keywords: Statistics - Applications
Source: Cornell University
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• 3
Article
Language: English
In: Image and Vision Computing, October 2018, Vol.78, pp.73-83
Description: Managing the water quality of freshwaters is a crucial task worldwide. One of the most used methods to biomonitor water quality is to sample benthic macroinvertebrate communities, in particular to examine the presence and proportion of certain species. This paper presents a benchmark database for automatic visual classification methods to evaluate their ability for distinguishing visually similar categories of aquatic macroinvertebrate taxa. We make publicly available a new database, containing 64 types of freshwater macroinvertebrates, ranging in number of images per category from 7 to 577. The database is divided into three datasets, varying in number of categories (64, 29, and 9 categories). Furthermore, in order to accomplish a baseline evaluation performance, we present the classification results of Convolutional Neural Networks (CNNs) that are widely used for deep learning tasks in large databases. Besides CNNs, we experimented with several other well-known classification methods using deep features extracted from the data.
Keywords: Biomonitoring ; Fine-Grained Classification ; Benthic Macroinvertebrates ; Deep Learning ; Convolutional Neural Networks ; Engineering ; Applied Sciences
ISSN: 0262-8856
E-ISSN: 1872-8138
Source: ScienceDirect Journals (Elsevier)
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• 4
Article
Language: English
In: Computers in Biology and Medicine, 2011, Vol.41(7), pp.463-472
Description: Aquatic ecosystems are continuously threatened by a growing number of human induced changes. Macroinvertebrate biomonitoring is particularly efficient in pinpointing the cause–effect structure between slow and subtle changes and their detrimental consequences in aquatic ecosystems. The greatest obstacle to implementing efficient biomonitoring is currently the cost-intensive human expert taxonomic identification of samples. While there is evidence that automated recognition techniques can match human taxa identification accuracy at greatly reduced costs, so far the development of automated identification techniques for aquatic organisms has been minimal. In this paper, we focus on advancing classification and data retrieval that are instrumental when processing large macroinvertebrate image datasets. To accomplish this for routine biomonitoring, in this paper we shall investigate the feasibility of automated river macroinvertebrate classification and retrieval with high precision. Besides the state-of-the-art classifiers such as Support Vector Machines (SVMs) and Bayesian Classifiers (BCs), the focus is particularly drawn on feed-forward artificial neural networks (ANNs), namely multilayer perceptrons (MLPs) and radial basis function networks (RBFNs). Since both ANN types have been proclaimed superior by different investigations even for the same benchmark problems, we shall first show that the main reason for this ambiguity lies in the static and rather poor comparison methodologies applied in most earlier works. Especially the most common drawback occurs due to the limited evaluation of the ANN performances over just one or few network architecture(s). Therefore, in this study, an extensive evaluation of each classifier performance over an ANN architecture space is performed. The best classifier among all, which is trained over a dataset of river macroinvertebrate specimens, is then used in the MUVIS framework for the efficient search and retrieval of particular macroinvertebrate peculiars. Classification and retrieval results present high accuracy and can match an experts' ability for taxonomic identification.
Keywords: Biomonitoring ; Classification ; Radial Basis Function Networks ; Multilayer Perceptrons ; Bayesian Networks ; Support Vector Machines ; Benthic Macroinvertebrate ; Medicine
ISSN: 0010-4825
E-ISSN: 1879-0534
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• 5
Article
Language: English
In: Ecological Informatics, March 2014, Vol.20, pp.1-12
Description: Macroinvertebrates form an important functional component of aquatic ecosystems. Their ability to indicate various types of anthropogenic stressors is widely recognized which has made them an integral component of freshwater biomonitoring. The use of macroinvertebrates in biomonitoring is dependent on manual taxa identification which is currently a time-consuming and cost-intensive process conducted by highly trained taxonomical experts. Automated taxa identification of macroinvertebrates is a relatively recent research development. Previous studies have displayed great potential for solutions to this demanding data mining application. In this research we have a collection of 1350 images from eight different macroinvertebrate taxa and the aim is to examine the suitability of artificial neural networks (ANNs) for automated taxa identification of macroinvertebrates. More specifically, the focus is drawn on different training algorithms of Multi-Layer Perceptron (MLP), probabilistic neural network (PNN) and Radial Basis Function network (RBFN). We performed thorough experimental tests and we tested altogether 13 training algorithms for MLPs. The best classification accuracy of MLPs, 95.3%, was obtained by two conjugate gradient backpropagation variations and scaled conjugate gradient backpropagation. For PNN 92.8% and for RBFN 95.7% accuracies were achieved. The results show how important a proper choice of ANN is in order to obtain high accuracy in the automated taxa identification of macroinvertebrates and the obtained model can outperform the level of identification which is made by a taxonomist.
Keywords: Benthic Macroinvertebrates ; Artificial Neural Networks ; Multi-Layer Perceptron ; Radial Basis Function Network ; Probabilistic Neural Network ; Classification ; Ecology
ISSN: 1574-9541
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• 6
Article
Language: English
In: Expert Systems With Applications, 15 April 2017, Vol.72, pp.108-120
Description: In benthic macroinvertebrate biomonitoring systems, the target is to determine the status of ecosystems based on several biological indices. To increase cost-efficiency, computer-based taxa identification for image data has recently been developed. Taxa identification errors can, however, have strong effects on the indices and thus on the determination of the ecological status. In order to shift the biomonitoring process towards automated expert systems, we need a clear understanding on the bias caused by automation. In this paper, we examine eleven classification methods in the case of macroinvertebrate image data and show how their classification errors propagate into different biological indices. We evaluate 14 richness, diversity, dominance and similarity indices commonly used in biomonitoring. Besides the error rate of the classification method, we discuss the potential effect of different types of identification errors. Finally, we provide recommendations on indices that are least affected by the automatic identification errors and could be used in automated biomonitoring.
Keywords: Biomonitoring ; Classification Error ; Diversity: Error Propagation ; Identification ; Similarity ; Computer Science
ISSN: 0957-4174
E-ISSN: 1873-6793
Source: ScienceDirect Journals (Elsevier)
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• 7
Article
Description: The step of expert taxa recognition currently slows down the response time of many bioassessments. Shifting to quicker and cheaper state-of-the-art machine learning approaches is still met with expert scepticism towards the ability and logic of machines. In our study, we investigate both the differences in accuracy and in the identification logic of taxonomic experts and machines. We propose a systematic approach utilizing deep Convolutional Neural Nets with the transfer learning paradigm and extensively evaluate it over a multi-pose taxonomic dataset with hierarchical labels specifically created for this comparison. We also study the prediction accuracy on different ranks of taxonomic hierarchy in detail. Our results revealed that human experts using actual specimens yield the lowest classification error ($\overline{CE}=6.1\%$). However, a much faster, automated approach using deep Convolutional Neural Nets comes close to human accuracy ($\overline{CE}=11.4\%$). Contrary to previous findings in the literature, we find that for machines following a typical flat classification approach commonly used in machine learning performs better than forcing machines to adopt a hierarchical, local per parent node approach used by human taxonomic experts. Finally, we publicly share our unique dataset to serve as a public benchmark dataset in this field.
Keywords: Statistics - Machine Learning ; Computer Science - Machine Learning ; Quantitative Biology - Quantitative Methods
Source: Cornell University
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• 8
Conference Proceeding
Language: English
In: 2010 IEEE International Workshop on Machine Learning for Signal Processing, August 2010, pp.373-378
Description: We apply and compare a random Bayes forest classifier and three traditional classification methods to a dataset of complex benthic macroinvertebrate images of known taxonomical identity. Since in biomonitoring changes in benthic macroinvertebrate taxa proportions correspond to changes in water quality, their correct estimation is pivotal. As classification errors are passed on to the allocated proportions, we explore a correction method known as a confusion matrix correction. Classification methods were compared using the misclassification error and the χ〈sup〉2〈/sup〉 distance measures of the true proportions to the allocated and to the corrected proportions. Using low misclassification error and smallest χ〈sup〉2〈/sup〉 distance measures as performance criteria the classical Bayes classifier performed best followed closely by the random Bayes forest.
Keywords: Decision Trees ; Training Data ; Feature Extraction ; Radio Frequency ; Training ; Entropy ; Estimation ; Computer Science
ISBN: 9781424478750
ISBN: 1424478758
ISSN: 15512541
E-ISSN: 15512541
Source: IEEE Conference Publications
Source: IEEE Xplore
Source: IEEE Journals & Magazines
Source: IEEE eBooks
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• 9
Article
Language: English
In: Ecological Indicators
Description: The assessment of diversity and similarity is relevant in monitoring the status of ecosystems. The respective indicators are based on the taxonomic composition of biological communities of interest, currently estimated through the proportions computed from sampling multivariate counts. In this work we present a novel method to estimate the taxonomic composition able to work even with a single sample and no covariates, when data are affected by overdispersion. The presence of overdispersion in taxonomic counts may be the result of significant environmental factors which are often unobservable but influence communities. Following the empirical Bayes approach, we combine a Bayesian model with the marginal likelihood method to jointly estimate the taxonomic proportions and the level of overdispersion from one set of multivariate counts. We also present an extension of the methodological framework to the case of more than one sampling collection. Our proposal is compared to the classical maximum likelihood method in an extensive simulation study with different realistic scenarios. As an exemplary case, a comparison with real data from aquatic biomonitoring is also presented. In both the simulation study and the comparison with real data, we consider communities characterized by a large number of taxonomic categories, such as aquatic macroinvertebrates or bacteria which are often observed in overdispersed data. The applicative results demonstrate an overall superiority of the empirical Bayes method in almost all examined cases, for both assessments of diversity and similarity. We would recommend practitioners in biomonitoring to use the proposed approach in addition to the traditional procedures. The empirical Bayes estimation allows to better control the error propagation due to the presence of overdispersion in biological data, with a more efficient managerial decision making.
Keywords: Biodiversity Assessment ; Dirichlet-Multinomial Model ; Empirical Bayesian Estimation ; Environmental Monitoring ; Taxonomic Composition ; Environmental Sciences
ISSN: 1470-160X
E-ISSN: 1872-7034
Source: ScienceDirect Journals (Elsevier)
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