Evaluation of machine learning algorithms for classification of primary biological aerosol using a new UV-LIF spectrometer

Abstract. Characterisation of bioaerosols has important implications within environment and public health sectors. Recent developments in ultraviolet light-induced fluorescence (UV-LIF) detectors such as the Wideband Integrated Bioaerosol Spectrometer (WIBS) and the newly introduced Multiparameter Bioaerosol Spectrometer (MBS) have allowed for the real-time collection of fluorescence, size and morphology measurements for the purpose of discriminating between bacteria, fungal spores and pollen.This new generation of instruments has enabled ever larger data sets to be compiled with the aim of studying more complex environments. In real world data sets, particularly those from an urban environment, the population may be dominated by non-biological fluorescent interferents, bringing into question the accuracy of measurements of quantities such as concentrations. It is therefore imperative that we validate the performance of different algorithms which can be used for the task of classification.For unsupervised learning we tested hierarchical agglomerative clustering with various different linkages. For supervised learning, 11 methods were tested, including decision trees, ensemble methods (random forests, gradient boosting and AdaBoost), two implementations for support vector machines (libsvm and liblinear) and Gaussian methods (Gaussian naïve Bayesian, quadratic and linear discriminant analysis, the k-nearest neighbours algorithm and artificial neural networks).The methods were applied to two different data sets produced using the new MBS, which provides multichannel UV-LIF fluorescence signatures for single airborne biological particles. The first data set contained mixed PSLs and the second contained a variety of laboratory-generated aerosol.Clustering in general performs slightly worse than the supervised learning methods, correctly classifying, at best, only 67. 6 and 91. 1 % for the two data sets respectively. For supervised learning the gradient boosting algorithm was found to be the most effective, on average correctly classifying 82. 8 and 98. 27 % of the testing data, respectively, across the two data sets.A possible alternative to gradient boosting is neural networks. We do however note that this method requires much more user input than the other methods, and we suggest that further research should be conducted using this method, especially using parallelised hardware such as the GPU, which would allow for larger networks to be trained, which could possibly yield better results.We also saw that some methods, such as clustering, failed to utilise the additional shape information provided by the instrument, whilst for others, such as the decision trees, ensemble methods and neural networks, improved performance could be attained with the inclusion of such information.

Download Full-text

Evaluation of Machine Learning Algorithms for Classification of Primary Biological Aerosol using a new UV-LIF spectrometer

10.5194/amt-2016-214 ◽

2016 ◽

Cited By ~ 1

Author(s):

Simon Ruske ◽

David O. Topping ◽

Virginia E. Foot ◽

Paul H. Kaye ◽

Warren R. Stanley ◽

...

Keyword(s):

Supervised Learning ◽

Fungal Spores ◽

Machine Learning Algorithms ◽

Gradient Boosting ◽

Support Vector ◽

Data Sets ◽

Agglomerative Clustering ◽

Real World Data ◽

Linear Discriminant ◽

Accuracy Of Measurements

Abstract. Characterisation of bio-aerosols has important implications within Environment and Public Health sectors. Recent developments in Ultra-Violet Light Induced Fluorescence (UV-LIF) detectors such as the Wideband Integrated bio-aerosol Spectrometer (WIBS) and the newly introduced Multiparameter bio-aerosol Spectrometer (MBS) has allowed for the real time collection of fluorescence, size and morphology measurements for the purpose of discriminating between bacteria, fungal Spores and pollen. This new generation of instruments has enabled ever larger data sets to be compiled with the aim of studying more complex environments. In real world data sets, particularly those from an urban environment, the population may be dominated by non-biological fluorescent interferents bringing into question the accuracy of measurements of quantities such as concentrations. It is therefore imperative that we validate the performance of different algorithms which can be used for the task of classification. For unsupervised learning we test Hierarchical Agglomerative Clustering with various different linkages. For supervised learning, ten methods were tested; including decision trees, ensemble methods: Random Forests, Gradient Boosting and AdaBoost; two implementations for support vector machines: libsvm and liblinear; Gaussian methods: Gaussian naïve Bayesian, quadratic and linear discriminant analysis and finally the k-nearest neighbours algorithm. The methods were applied to two different data sets measured using a new Multiparameter bio-aerosol Spectrometer which provides multichannel UV-LIF fluorescence signatures for single airborne biological particles. Clustering, in general performs slightly worse than the supervised learning methods correctly classifying, at best, only 72.7 and 91.1 percent for the two data sets respectively. For supervised learning the gradient boosting algorithm was found to be the most effective, on average correctly classifying 88.1 and 97.8 percent of the testing data respectively across the two data sets.

Download Full-text

Popular Ensemble Methods: An Empirical Study

Journal of Artificial Intelligence Research ◽

10.1613/jair.614 ◽

1999 ◽

Vol 11 ◽

pp. 169-198 ◽

Cited By ~ 1161

Author(s):

D. Opitz ◽

R. Maclin

Keyword(s):

Neural Networks ◽

Empirical Study ◽

Decision Trees ◽

Noisy Data ◽

Ensemble Methods ◽

Classification Algorithm ◽

The Other ◽

Data Sets ◽

Data Set ◽

Networks Analysis

An ensemble consists of a set of individually trained classifiers (such as neural networks or decision trees) whose predictions are combined when classifying novel instances. Previous research has shown that an ensemble is often more accurate than any of the single classifiers in the ensemble. Bagging (Breiman, 1996c) and Boosting (Freund & Shapire, 1996; Shapire, 1990) are two relatively new but popular methods for producing ensembles. In this paper we evaluate these methods on 23 data sets using both neural networks and decision trees as our classification algorithm. Our results clearly indicate a number of conclusions. First, while Bagging is almost always more accurate than a single classifier, it is sometimes much less accurate than Boosting. On the other hand, Boosting can create ensembles that are less accurate than a single classifier -- especially when using neural networks. Analysis indicates that the performance of the Boosting methods is dependent on the characteristics of the data set being examined. In fact, further results show that Boosting ensembles may overfit noisy data sets, thus decreasing its performance. Finally, consistent with previous studies, our work suggests that most of the gain in an ensemble's performance comes in the first few classifiers combined; however, relatively large gains can be seen up to 25 classifiers when Boosting decision trees.

Download Full-text

Comparison of the Validity and Generalizability of Machine Learning Algorithms for the Prediction of Energy Expenditure: Validation Study

JMIR mhealth and uhealth ◽

10.2196/23938 ◽

2021 ◽

Vol 9 (8) ◽

pp. e23938

Author(s):

Ruairi O'Driscoll ◽

Jake Turicchi ◽

Mark Hopkins ◽

Cristiana Duarte ◽

Graham W Horgan ◽

...

Keyword(s):

Physical Activity ◽

Machine Learning ◽

Neural Networks ◽

Random Forest ◽

Energy Expenditure ◽

Superior Performance ◽

Gradient Boosting ◽

Support Vector ◽

Data Sets ◽

Out Of Sample

Background Accurate solutions for the estimation of physical activity and energy expenditure at scale are needed for a range of medical and health research fields. Machine learning techniques show promise in research-grade accelerometers, and some evidence indicates that these techniques can be applied to more scalable commercial devices. Objective This study aims to test the validity and out-of-sample generalizability of algorithms for the prediction of energy expenditure in several wearables (ie, Fitbit Charge 2, ActiGraph GT3-x, SenseWear Armband Mini, and Polar H7) using two laboratory data sets comprising different activities. Methods Two laboratory studies (study 1: n=59, age 44.4 years, weight 75.7 kg; study 2: n=30, age=31.9 years, weight=70.6 kg), in which adult participants performed a sequential lab-based activity protocol consisting of resting, household, ambulatory, and nonambulatory tasks, were combined in this study. In both studies, accelerometer and physiological data were collected from the wearables alongside energy expenditure using indirect calorimetry. Three regression algorithms were used to predict metabolic equivalents (METs; ie, random forest, gradient boosting, and neural networks), and five classification algorithms (ie, k-nearest neighbor, support vector machine, random forest, gradient boosting, and neural networks) were used for physical activity intensity classification as sedentary, light, or moderate to vigorous. Algorithms were evaluated using leave-one-subject-out cross-validations and out-of-sample validations. Results The root mean square error (RMSE) was lowest for gradient boosting applied to SenseWear and Polar H7 data (0.91 METs), and in the classification task, gradient boost applied to SenseWear and Polar H7 was the most accurate (85.5%). Fitbit models achieved an RMSE of 1.36 METs and 78.2% accuracy for classification. Errors tended to increase in out-of-sample validations with the SenseWear neural network achieving RMSE values of 1.22 METs in the regression tasks and the SenseWear gradient boost and random forest achieving an accuracy of 80% in classification tasks. Conclusions Algorithms trained on combined data sets demonstrated high predictive accuracy, with a tendency for superior performance of random forests and gradient boosting for most but not all wearable devices. Predictions were poorer in the between-study validations, which creates uncertainty regarding the generalizability of the tested algorithms.

Download Full-text

Effect of normalization methods on the performance of supervised learning algorithms applied to HTSeq-FPKM-UQ data sets: 7SK RNA expression as a predictor of survival in patients with colon adenocarcinoma

Briefings in Bioinformatics ◽

10.1093/bib/bbx153 ◽

2017 ◽

Vol 20 (3) ◽

pp. 985-994 ◽

Cited By ~ 15

Author(s):

Leili Shahriyari

Keyword(s):

Supervised Learning ◽

Unit Length ◽

Learning Algorithms ◽

Colon Adenocarcinoma ◽

Support Vector ◽

Data Sets ◽

Data Set ◽

Maximum Accuracy ◽

Normalization Methods ◽

Supervised Learning Algorithms

Abstract Motivation: One of the main challenges in machine learning (ML) is choosing an appropriate normalization method. Here, we examine the effect of various normalization methods on analyzing FPKM upper quartile (FPKM-UQ) RNA sequencing data sets. We collect the HTSeq-FPKM-UQ files of patients with colon adenocarcinoma from TCGA-COAD project. We compare three most common normalization methods: scaling, standardizing using z-score and vector normalization by visualizing the normalized data set and evaluating the performance of 12 supervised learning algorithms on the normalized data set. Additionally, for each of these normalization methods, we use two different normalization strategies: normalizing samples (files) or normalizing features (genes). Results: Regardless of normalization methods, a support vector machine (SVM) model with the radial basis function kernel had the maximum accuracy (78%) in predicting the vital status of the patients. However, the fitting time of SVM depended on the normalization methods, and it reached its minimum fitting time when files were normalized to the unit length. Furthermore, among all 12 learning algorithms and 6 different normalization techniques, the Bernoulli naive Bayes model after standardizing files had the best performance in terms of maximizing the accuracy as well as minimizing the fitting time. We also investigated the effect of dimensionality reduction methods on the performance of the supervised ML algorithms. Reducing the dimension of the data set did not increase the maximum accuracy of 78%. However, it leaded to discovery of the 7SK RNA gene expression as a predictor of survival in patients with colon adenocarcinoma with accuracy of 78%.

Download Full-text

Comparison of the Validity and Generalizability of Machine Learning Algorithms for the Prediction of Energy Expenditure: Validation Study (Preprint)

10.2196/preprints.23938 ◽

2020 ◽

Author(s):

Ruairi O'Driscoll ◽

Jake Turicchi ◽

Mark Hopkins ◽

Cristiana Duarte ◽

Graham W Horgan ◽

...

Keyword(s):

Physical Activity ◽

Machine Learning ◽

Neural Networks ◽

Random Forest ◽

Energy Expenditure ◽

Superior Performance ◽

Gradient Boosting ◽

Support Vector ◽

Data Sets ◽

Out Of Sample

BACKGROUND Accurate solutions for the estimation of physical activity and energy expenditure at scale are needed for a range of medical and health research fields. Machine learning techniques show promise in research-grade accelerometers, and some evidence indicates that these techniques can be applied to more scalable commercial devices. OBJECTIVE This study aims to test the validity and out-of-sample generalizability of algorithms for the prediction of energy expenditure in several wearables (ie, Fitbit Charge 2, ActiGraph GT3-x, SenseWear Armband Mini, and Polar H7) using two laboratory data sets comprising different activities. METHODS Two laboratory studies (study 1: n=59, age 44.4 years, weight 75.7 kg; study 2: n=30, age=31.9 years, weight=70.6 kg), in which adult participants performed a sequential lab-based activity protocol consisting of resting, household, ambulatory, and nonambulatory tasks, were combined in this study. In both studies, accelerometer and physiological data were collected from the wearables alongside energy expenditure using indirect calorimetry. Three regression algorithms were used to predict metabolic equivalents (METs; ie, random forest, gradient boosting, and neural networks), and five classification algorithms (ie, k-nearest neighbor, support vector machine, random forest, gradient boosting, and neural networks) were used for physical activity intensity classification as sedentary, light, or moderate to vigorous. Algorithms were evaluated using leave-one-subject-out cross-validations and out-of-sample validations. RESULTS The root mean square error (RMSE) was lowest for gradient boosting applied to SenseWear and Polar H7 data (0.91 METs), and in the classification task, gradient boost applied to SenseWear and Polar H7 was the most accurate (85.5%). Fitbit models achieved an RMSE of 1.36 METs and 78.2% accuracy for classification. Errors tended to increase in out-of-sample validations with the SenseWear neural network achieving RMSE values of 1.22 METs in the regression tasks and the SenseWear gradient boost and random forest achieving an accuracy of 80% in classification tasks. CONCLUSIONS Algorithms trained on combined data sets demonstrated high predictive accuracy, with a tendency for superior performance of random forests and gradient boosting for most but not all wearable devices. Predictions were poorer in the between-study validations, which creates uncertainty regarding the generalizability of the tested algorithms. CLINICALTRIAL

Download Full-text

Hyperspectral and LiDAR Fusion Using Deep Three-Stream Convolutional Neural Networks

Remote Sensing ◽

10.3390/rs10101649 ◽

2018 ◽

Vol 10 (10) ◽

pp. 1649 ◽

Cited By ~ 15

Author(s):

Hao Li ◽

Pedram Ghamisi ◽

Uwe Soergel ◽

Xiao Zhu

Keyword(s):

Neural Networks ◽

Convolutional Neural Networks ◽

Rural Areas ◽

Remote Sensing Data ◽

Classification Performance ◽

Sensor Data ◽

Support Vector ◽

Data Sets ◽

Data Set ◽

Multi Sensor Data Fusion

Recently, convolutional neural networks (CNN) have been intensively investigated for the classification of remote sensing data by extracting invariant and abstract features suitable for classification. In this paper, a novel framework is proposed for the fusion of hyperspectral images and LiDAR-derived elevation data based on CNN and composite kernels. First, extinction profiles are applied to both data sources in order to extract spatial and elevation features from hyperspectral and LiDAR-derived data, respectively. Second, a three-stream CNN is designed to extract informative spectral, spatial, and elevation features individually from both available sources. The combination of extinction profiles and CNN features enables us to jointly benefit from low-level and high-level features to improve classification performance. To fuse the heterogeneous spectral, spatial, and elevation features extracted by CNN, instead of a simple stacking strategy, a multi-sensor composite kernels (MCK) scheme is designed. This scheme helps us to achieve higher spectral, spatial, and elevation separability of the extracted features and effectively perform multi-sensor data fusion in kernel space. In this context, a support vector machine and extreme learning machine with their composite kernels version are employed to produce the final classification result. The proposed framework is carried out on two widely used data sets with different characteristics: an urban data set captured over Houston, USA, and a rural data set captured over Trento, Italy. The proposed framework yields the highest OA of 92 . 57 % and 97 . 91 % for Houston and Trento data sets. Experimental results confirm that the proposed fusion framework can produce competitive results in both urban and rural areas in terms of classification accuracy, and significantly mitigate the salt and pepper noise in classification maps.

Download Full-text

In silico Prediction of Inhibitory Constant of Thrombin Inhibitors Using Machine Learning

Combinatorial Chemistry & High Throughput Screening ◽

10.2174/1386207322666181220130232 ◽

2019 ◽

Vol 21 (9) ◽

pp. 662-669 ◽

Cited By ~ 1

Author(s):

Junnan Zhao ◽

Lu Zhu ◽

Weineng Zhou ◽

Lingfeng Yin ◽

Yuchen Wang ◽

...

Keyword(s):

Machine Learning ◽

Prediction Models ◽

Regression Tree ◽

Large Data ◽

Thrombin Inhibitors ◽

Coagulation Cascade ◽

Gradient Boosting ◽

Support Vector ◽

Data Set ◽

Descriptor Selection

Background: Thrombin is the central protease of the vertebrate blood coagulation cascade, which is closely related to cardiovascular diseases. The inhibitory constant Ki is the most significant property of thrombin inhibitors. Method: This study was carried out to predict Ki values of thrombin inhibitors based on a large data set by using machine learning methods. Taking advantage of finding non-intuitive regularities on high-dimensional datasets, machine learning can be used to build effective predictive models. A total of 6554 descriptors for each compound were collected and an efficient descriptor selection method was chosen to find the appropriate descriptors. Four different methods including multiple linear regression (MLR), K Nearest Neighbors (KNN), Gradient Boosting Regression Tree (GBRT) and Support Vector Machine (SVM) were implemented to build prediction models with these selected descriptors. Results: The SVM model was the best one among these methods with R2=0.84, MSE=0.55 for the training set and R2=0.83, MSE=0.56 for the test set. Several validation methods such as yrandomization test and applicability domain evaluation, were adopted to assess the robustness and generalization ability of the model. The final model shows excellent stability and predictive ability and can be employed for rapid estimation of the inhibitory constant, which is full of help for designing novel thrombin inhibitors.

Download Full-text

Comparison of Ensemble Machine Learning Methods for Soil Erosion Pin Measurements

ISPRS International Journal of Geo-Information ◽

10.3390/ijgi10010042 ◽

2021 ◽

Vol 10 (1) ◽

pp. 42

Author(s):

Kieu Anh Nguyen ◽

Walter Chen ◽

Bor-Shiun Lin ◽

Uma Seeboonruang

Keyword(s):

Machine Learning ◽

Soil Erosion ◽

Ensemble Methods ◽

Machine Learning Algorithms ◽

Multivariate Adaptive Regression Splines ◽

Gradient Boosting ◽

Support Vector ◽

Ensemble Machine Learning ◽

Boosting Method ◽

Bagging Method

Although machine learning has been extensively used in various fields, it has only recently been applied to soil erosion pin modeling. To improve upon previous methods of quantifying soil erosion based on erosion pin measurements, this study explored the possible application of ensemble machine learning algorithms to the Shihmen Reservoir watershed in northern Taiwan. Three categories of ensemble methods were considered in this study: (a) Bagging, (b) boosting, and (c) stacking. The bagging method in this study refers to bagged multivariate adaptive regression splines (bagged MARS) and random forest (RF), and the boosting method includes Cubist and gradient boosting machine (GBM). Finally, the stacking method is an ensemble method that uses a meta-model to combine the predictions of base models. This study used RF and GBM as the meta-models, decision tree, linear regression, artificial neural network, and support vector machine as the base models. The dataset used in this study was sampled using stratified random sampling to achieve a 70/30 split for the training and test data, and the process was repeated three times. The performance of six ensemble methods in three categories was analyzed based on the average of three attempts. It was found that GBM performed the best among the ensemble models with the lowest root-mean-square error (RMSE = 1.72 mm/year), the highest Nash-Sutcliffe efficiency (NSE = 0.54), and the highest index of agreement (d = 0.81). This result was confirmed by the spatial comparison of the absolute differences (errors) between model predictions and observations using GBM and RF in the study area. In summary, the results show that as a group, the bagging method and the boosting method performed equally well, and the stacking method was third for the erosion pin dataset considered in this study.

Download Full-text

Generation of geometric interpolations of building types with deep variational autoencoders

Design Science ◽

10.1017/dsj.2020.31 ◽

2020 ◽

Vol 6 ◽

Author(s):

Jaime de Miguel Rodríguez ◽

Maria Eugenia Villafañe ◽

Luka Piškorec ◽

Fernando Sancho Caparrini

Keyword(s):

Machine Learning ◽

Neural Networks ◽

Large Data ◽

Learning Model ◽

Large Data Sets ◽

Data Sets ◽

Connectivity Map ◽

Data Set ◽

3D Objects ◽

Machine Learning Model

Abstract This work presents a methodology for the generation of novel 3D objects resembling wireframes of building types. These result from the reconstruction of interpolated locations within the learnt distribution of variational autoencoders (VAEs), a deep generative machine learning model based on neural networks. The data set used features a scheme for geometry representation based on a ‘connectivity map’ that is especially suited to express the wireframe objects that compose it. Additionally, the input samples are generated through ‘parametric augmentation’, a strategy proposed in this study that creates coherent variations among data by enabling a set of parameters to alter representative features on a given building type. In the experiments that are described in this paper, more than 150 k input samples belonging to two building types have been processed during the training of a VAE model. The main contribution of this paper has been to explore parametric augmentation for the generation of large data sets of 3D geometries, showcasing its problems and limitations in the context of neural networks and VAEs. Results show that the generation of interpolated hybrid geometries is a challenging task. Despite the difficulty of the endeavour, promising advances are presented.

Download Full-text

Uncertainty-Aware Deep Classifiers Using Generative Models

Proceedings of the AAAI Conference on Artificial Intelligence ◽

10.1609/aaai.v34i04.6015 ◽

2020 ◽

Vol 34 (04) ◽

pp. 5620-5627 ◽

Cited By ~ 1

Author(s):

Murat Sensoy ◽

Lance Kaplan ◽

Federico Cerutti ◽

Maryam Saleki

Keyword(s):

Neural Networks ◽

Epistemic Uncertainty ◽

Feature Space ◽

Generative Models ◽

Detection Methods ◽

Generative Adversarial Networks ◽

Data Sets ◽

Bayesian Approaches ◽

Data Set ◽

Auxiliary Data

Deep neural networks are often ignorant about what they do not know and overconfident when they make uninformed predictions. Some recent approaches quantify classification uncertainty directly by training the model to output high uncertainty for the data samples close to class boundaries or from the outside of the training distribution. These approaches use an auxiliary data set during training to represent out-of-distribution samples. However, selection or creation of such an auxiliary data set is non-trivial, especially for high dimensional data such as images. In this work we develop a novel neural network model that is able to express both aleatoric and epistemic uncertainty to distinguish decision boundary and out-of-distribution regions of the feature space. To this end, variational autoencoders and generative adversarial networks are incorporated to automatically generate out-of-distribution exemplars for training. Through extensive analysis, we demonstrate that the proposed approach provides better estimates of uncertainty for in- and out-of-distribution samples, and adversarial examples on well-known data sets against state-of-the-art approaches including recent Bayesian approaches for neural networks and anomaly detection methods.

Download Full-text