Classification of Urinary Calculi using Feed-Forward Neural Networks

Recent studies have shown that more than 80% of the analysed samples of urinary calculi in our  laboratory were mainly composed of four types of calculi, consisting of the following substances: (1) whewellite and weddellite, (2) whewellite, weddellite and uric acid, (3) whewellite, weddellite and struvite and (4) whewellite, weddellite and carbonate apatite. In this work the results of classification of these types of calculi (using their infrared spectra in the region 1450–450 cm–1) by feed-forward neural networks are presented. Genetic algorithms were used for optimization of neural networks and for selection of the spectral regions most suitable for classification purposes. The generalization abilities of the neural networks were controlled by an early stopping procedure. The best network architecture and the most suitable spectral regions were chosen using twentyfold cross-validation. The cross-validation error for the real samples varies from 5.3% to 5.9% misclassifications, which makes the proposed method a promising tool for the identification of these types of calculi.KEY WORDS:Urinary calculi, infrared spectroscopy, classification, neural networks, variable selection, genetic algorithms

Neural networks in petroleum geology as interpretation tools

Abstract Three examples of the use of neural networks in analyses of geologic data from hydrocarbon reservoirs are presented. All networks are trained with data originating from clastic reservoirs of Neogene age located in the Croatian part of the Pannonian Basin. Training always included similar reservoir variables, i.e. electric logs (resistivity, spontaneous potential) and lithology determined from cores or logs and described as sandstone or marl, with categorical values in intervals. Selected variables also include hydrocarbon saturation, also represented by a categorical variable, average reservoir porosity calculated from interpreted well logs, and seismic attributes. In all three neural models some of the mentioned inputs were used for analyzing data collected from three different oil fields in the Croatian part of the Pannonian Basin. It is shown that selection of geologically and physically linked variables play a key role in the process of network training, validating and processing. The aim of this study was to establish relationships between log-derived data, core data, and seismic attributes. Three case studies are described in this paper to illustrate the use of neural network prediction of sandstone-marl facies (Case Study # 1, Okoli Field), prediction of carbonate breccia porosity (Case Study # 2, Beničanci Field), and prediction of lithology and saturation (Case Study # 3, Kloštar Field). The results of these studies indicate that this method is capable of providing better understanding of some clastic Neogene reservoirs in the Croatian part of the Pannonian Basin

Machine Learning and Integrative Analysis of Biomedical Big Data.

Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues

Bayesian Deep Net GLM and GLMM

Deep feedforward neural networks (DFNNs) are a powerful tool for functional approximation. We describe flexible versions of generalized linear and generalized linear mixed models incorporating basis functions formed by a DFNN. The consideration of neural networks with random effects is not widely used in the literature, perhaps because of the computational challenges of incorporating subject specific parameters into already complex models. Efficient computational methods for high-dimensional Bayesian inference are developed using Gaussian variational approximation, with a parsimonious but flexible factor parametrization of the covariance matrix. We implement natural gradient methods for the optimization, exploiting the factor structure of the variational covariance matrix in computation of the natural gradient. Our flexible DFNN models and Bayesian inference approach lead to a regression and classification method that has a high prediction accuracy, and is able to quantify the prediction uncertainty in a principled and convenient way. We also describe how to perform variable selection in our deep learning method. The proposed methods are illustrated in a wide range of simulated and real-data examples, and the results compare favourably to a state of the art flexible regression and classification method in the statistical literature, the Bayesian additive regression trees (BART) method. User-friendly software packages in Matlab, R and Python implementing the proposed methods are available at https://github.com/VBayesLabComment: 35 pages, 7 figure, 10 table

Wavelet Neural Networks: A Practical Guide

Wavelet networks (WNs) are a new class of networks which have been used with great success in a wide range of application. However a general accepted framework for applying WNs is missing from the literature. In this study, we present a complete statistical model identification framework in order to apply WNs in various applications. The following subjects were thorough examined: the structure of a WN, training methods, initialization algorithms, variable significance and variable selection algorithms, model selection methods and finally methods to construct confidence and prediction intervals. In addition the complexity of each algorithm is discussed. Our proposed framework was tested in two simulated cases, in one chaotic time series described by the Mackey-Glass equation and in three real datasets described by daily temperatures in Berlin, daily wind speeds in New York and breast cancer classification. Our results have shown that the proposed algorithms produce stable and robust results indicating that our proposed framework can be applied in various applications

Crop Yield Prediction Using Deep Neural Networks

Crop yield is a highly complex trait determined by multiple factors such as genotype, environment, and their interactions. Accurate yield prediction requires fundamental understanding of the functional relationship between yield and these interactive factors, and to reveal such relationship requires both comprehensive datasets and powerful algorithms. In the 2018 Syngenta Crop Challenge, Syngenta released several large datasets that recorded the genotype and yield performances of 2,267 maize hybrids planted in 2,247 locations between 2008 and 2016 and asked participants to predict the yield performance in 2017. As one of the winning teams, we designed a deep neural network (DNN) approach that took advantage of state-of-the-art modeling and solution techniques. Our model was found to have a superior prediction accuracy, with a root-mean-square-error (RMSE) being 12% of the average yield and 50% of the standard deviation for the validation dataset using predicted weather data. With perfect weather data, the RMSE would be reduced to 11% of the average yield and 46% of the standard deviation. We also performed feature selection based on the trained DNN model, which successfully decreased the dimension of the input space without significant drop in the prediction accuracy. Our computational results suggested that this model significantly outperformed other popular methods such as Lasso, shallow neural networks (SNN), and regression tree (RT). The results also revealed that environmental factors had a greater effect on the crop yield than genotype.Comment: 9 pages, Presented at 2018 INFORMS Conference on Business Analytics and Operations Research (Baltimore, MD, USA). One of the winning solutions to the 2018 Syngenta Crop Challeng

Development of Neurofuzzy Architectures for Electricity Price Forecasting

In 20th century, many countries have liberalized their electricity market. This power markets liberalization has directed generation companies as well as wholesale buyers to undertake a greater intense risk exposure compared to the old centralized framework. In this framework, electricity price prediction has become crucial for any market player in their decision‐making process as well as strategic planning. In this study, a prototype asymmetric‐based neuro‐fuzzy network (AGFINN) architecture has been implemented for short‐term electricity prices forecasting for ISO New England market. AGFINN framework has been designed through two different defuzzification schemes. Fuzzy clustering has been explored as an initial step for defining the fuzzy rules while an asymmetric Gaussian membership function has been utilized in the fuzzification part of the model. Results related to the minimum and maximum electricity prices for ISO New England, emphasize the superiority of the proposed model over well‐established learning‐based models