Gene expression changes in phosphorus deficient potato (Solanum tuberosum L.) leaves and the potential for diagnostic gene expression markers

Background: There are compelling economic and environmental reasons to reduce our reliance on inorganic phosphate (Pi) fertilisers. Better management of Pi fertiliser applications is one option to improve the efficiency of Pi fertiliser use, whilst maintaining crop yields. Application rates of Pi fertilisers are traditionally determined from analyses of soil or plant tissues. Alternatively, diagnostic genes with altered expression under Pi limiting conditions that suggest a physiological requirement for Pi fertilisation, could be used to manage Pifertiliser applications, and might be more precise than indirect measurements of soil or tissue samples. Results: We grew potato (Solanum tuberosum L.) plants hydroponically, under glasshouse conditions, to control their nutrient status accurately. Samples of total leaf RNA taken periodically after Pi was removed from the nutrient solution were labelled and hybridised to potato oligonucleotide arrays. A total of 1,659 genes were significantly differentially expressed following Pi withdrawal. These included genes that encode proteins involved in lipid, protein, and carbohydrate metabolism, characteristic of Pi deficient leaves and included potential novel roles for genes encoding patatin like proteins in potatoes. The array data were analysed using a support vector machine algorithm to identify groups of genes that could predict the Pi status of the crop. These groups of diagnostic genes were tested using field grown potatoes that had either been fertilised or unfertilised. A group of 200 genes could correctly predict the Pi status of field grown potatoes. Conclusions: This paper provides a proof-of-concept demonstration for using microarrays and class prediction tools to predict the Pi status of a field grown potato crop. There is potential to develop this technology for other biotic and abiotic stresses in field grown crops. Ultimately, a better understanding of crop stresses may improve our management of the crop, improving the sustainability of agriculture.

Nonlinear identification using orthogonal forward regression with nested optimal regularization

An efficient data based-modeling algorithm for nonlinear system identification is introduced for radial basis function (RBF) neural networks with the aim of maximizing generalization capability based on the concept of leave-one-out (LOO) cross validation. Each of the RBF kernels has its own kernel width parameter and the basic idea is to optimize the multiple pairs of regularization parameters and kernel widths, each of which is associated with a kernel, one at a time within the orthogonal forward regression (OFR) procedure. Thus, each OFR step consists of one model term selection based on the LOO mean square error (LOOMSE), followed by the optimization of the associated kernel width and regularization parameter, also based on the LOOMSE. Since like our previous state-of-the-art local regularization assisted orthogonal least squares (LROLS) algorithm, the same LOOMSE is adopted for model selection, our proposed new OFR algorithm is also capable of producing a very sparse RBF model with excellent generalization performance. Unlike our previous LROLS algorithm which requires an additional iterative loop to optimize the regularization parameters as well as an additional procedure to optimize the kernel width, the proposed new OFR algorithm optimizes both the kernel widths and regularization parameters within the single OFR procedure, and consequently the required computational complexity is dramatically reduced. Nonlinear system identification examples are included to demonstrate the effectiveness of this new approach in comparison to the well-known approaches of support vector machine and least absolute shrinkage and selection operator as well as the LROLS algorithm.

An LDA and probability-based classifier for the diagnosis of Alzheimer's Disease from structural MRI

In this paper a custom classification algorithm based on linear discriminant analysis and probability-based weights is implemented and applied to the hippocampus measurements of structural magnetic resonance images from healthy subjects and Alzheimer’s Disease sufferers; and then attempts to diagnose them as accurately as possible. The classifier works by classifying each measurement of a hippocampal volume as healthy controlsized or Alzheimer’s Disease-sized, these new features are then weighted and used to classify the subject as a healthy control or suffering from Alzheimer’s Disease. The preliminary results obtained reach an accuracy of 85.8% and this is a similar accuracy to state-of-the-art methods such as a Naive Bayes classifier and a Support Vector Machine. An advantage of the method proposed in this paper over the aforementioned state of the art classifiers is the descriptive ability of the classifications it produces. The descriptive model can be of great help to aid a doctor in the diagnosis of Alzheimer’s Disease, or even further the understand of how Alzheimer’s Disease affects the hippocampus.

A Genetic Algorithm for the selection of structural MRI features for classification of Mild Cognitive Impairment and Alzheimer's Disease

This work investigates the problem of feature selection in neuroimaging features from structural MRI brain images for the classification of subjects as healthy controls, suffering from Mild Cognitive Impairment or Alzheimer’s Disease. A Genetic Algorithm wrapper method for feature selection is adopted in conjunction with a Support Vector Machine classifier. In very large feature sets, feature selection is found to be redundant as the accuracy is often worsened when compared to an Support Vector Machine with no feature selection. However, when just the hippocampal subfields are used, feature selection shows a significant improvement of the classification accuracy. Three-class Support Vector Machines and two-class Support Vector Machines combined with weighted voting are also compared with the former and found more useful. The highest accuracy achieved at classifying the test data was 65.5% using a genetic algorithm for feature selection with a three-class Support Vector Machine classifier.

An investigation into feature construction to assist word sense disambiguation

Identifying the correct sense of a word in context is crucial for many tasks in natural language processing (machine translation is an example). State-of-the art methods for Word Sense Disambiguation (WSD) build models using hand-crafted features that usually capturing shallow linguistic information. Complex background knowledge, such as semantic relationships, are typically either not used, or used in specialised manner, due to the limitations of the feature-based modelling techniques used. On the other hand, empirical results from the use of Inductive Logic Programming (ILP) systems have repeatedly shown that they can use diverse sources of background knowledge when constructing models. In this paper, we investigate whether this ability of ILP systems could be used to improve the predictive accuracy of models for WSD. Specifically, we examine the use of a general-purpose ILP system as a method to construct a set of features using semantic, syntactic and lexical information. This feature-set is then used by a common modelling technique in the field (a support vector machine) to construct a classifier for predicting the sense of a word. In our investigation we examine one-shot and incremental approaches to feature-set construction applied to monolingual and bilingual WSD tasks. The monolingual tasks use 32 verbs and 85 verbs and nouns (in English) from the SENSEVAL-3 and SemEval-2007 benchmarks; while the bilingual WSD task consists of 7 highly ambiguous verbs in translating from English to Portuguese. The results are encouraging: the ILP-assisted models show substantial improvements over those that simply use shallow features. In addition, incremental feature-set construction appears to identify smaller and better sets of features. Taken together, the results suggest that the use of ILP with diverse sources of background knowledge provide a way for making substantial progress in the field of WSD.

Aplicação de técnicas de aprendizado de máquina no reconhecimento de classes estruturais de proteínas

Nowadays, classifying proteins in structural classes, which concerns the inference of patterns in their 3D conformation, is one of the most important open problems in Molecular Biology. The main reason for this is that the function of a protein is intrinsically related to its spatial conformation. However, such conformations are very difficult to be obtained experimentally in laboratory. Thus, this problem has drawn the attention of many researchers in Bioinformatics. Considering the great difference between the number of protein sequences already known and the number of three-dimensional structures determined experimentally, the demand of automated techniques for structural classification of proteins is very high. In this context, computational tools, especially Machine Learning (ML) techniques, have become essential to deal with this problem. In this work, ML techniques are used in the recognition of protein structural classes: Decision Trees, k-Nearest Neighbor, Naive Bayes, Support Vector Machine and Neural Networks. These methods have been chosen because they represent different paradigms of learning and have been widely used in the Bioinfornmatics literature. Aiming to obtain an improvment in the performance of these techniques (individual classifiers), homogeneous (Bagging and Boosting) and heterogeneous (Voting, Stacking and StackingC) multiclassification systems are used. Moreover, since the protein database used in this work presents the problem of imbalanced classes, artificial techniques for class balance (Undersampling Random, Tomek Links, CNN, NCL and OSS) are used to minimize such a problem. In order to evaluate the ML methods, a cross-validation procedure is applied, where the accuracy of the classifiers is measured using the mean of classification error rate, on independent test sets. These means are compared, two by two, by the hypothesis test aiming to evaluate if there is, statistically, a significant difference between them. With respect to the results obtained with the individual classifiers, Support Vector Machine presented the best accuracy. In terms of the multi-classification systems (homogeneous and heterogeneous), they showed, in general, a superior or similar performance when compared to the one achieved by the individual classifiers used - especially Boosting with Decision Tree and the StackingC with Linear Regression as meta classifier. The Voting method, despite of its simplicity, has shown to be adequate for solving the problem presented in this work. The techniques for class balance, on the other hand, have not produced a significant improvement in the global classification error. Nevertheless, the use of such techniques did improve the classification error for the minority class. In this context, the NCL technique has shown to be more appropriated

Classificação de padrões através de um comitê de máquinas aprimorado por aprendizagem por reforço

Reinforcement learning is a machine learning technique that, although finding a large number of applications, maybe is yet to reach its full potential. One of the inadequately tested possibilities is the use of reinforcement learning in combination with other methods for the solution of pattern classification problems. It is well documented in the literature the problems that support vector machine ensembles face in terms of generalization capacity. Algorithms such as Adaboost do not deal appropriately with the imbalances that arise in those situations. Several alternatives have been proposed, with varying degrees of success. This dissertation presents a new approach to building committees of support vector machines. The presented algorithm combines Adaboost algorithm with a layer of reinforcement learning to adjust committee parameters in order to avoid that imbalances on the committee components affect the generalization performance of the final hypothesis. Comparisons were made with ensembles using and not using the reinforcement learning layer, testing benchmark data sets widely known in area of pattern classification

Sistema inteligente para detecção de manchas de óleo na superfície marinha através de imagens de SAR

Oil spill on the sea, accidental or not, generates enormous negative consequences for the affected area. The damages are ambient and economic, mainly with the proximity of these spots of preservation areas and/or coastal zones. The development of automatic techniques for identification of oil spots on the sea surface, captured through Radar images, assist in a complete monitoring of the oceans and seas. However spots of different origins can be visualized in this type of imaging, which is a very difficult task. The system proposed in this work, based on techniques of digital image processing and artificial neural network, has the objective to identify the analyzed spot and to discern between oil and other generating phenomena of spot. Tests in functional blocks that compose the proposed system allow the implementation of different algorithms, as well as its detailed and prompt analysis. The algorithms of digital image processing (speckle filtering and gradient), as well as classifier algorithms (Multilayer Perceptron, Radial Basis Function, Support Vector Machine and Committe Machine) are presented and commented.The final performance of the system, with different kind of classifiers, is presented by ROC curve. The true positive rates are considered agreed with the literature about oil slick detection through SAR images presents

An Intelligent System for Petroleum Well Drilling Cutting Analysis

Cutting analysis is a important and crucial task task to detect and prevent problems during the petroleum well drilling process. Several studies have been developed for drilling inspection, but none of them takes care about analysing the generated cutting at the vibrating shale shakers. Here we proposed a system to analyse the cutting's concentration at the vibrating shale shakers, which can indicate problems during the petroleum well drilling process, such that the collapse of the well borehole walls. Cutting's images are acquired and sent to the data analysis module, which has as the main goal to extract features and to classify frames according to one of three previously classes of cutting's volume. A collection of supervised classifiers were applied in order to allow comparisons about their accuracy and efficiency. We used the Optimum-Path Forest (OPF), Artificial Neural Network using Multi layer Perceptrons (ANN-MLP), Support Vector Machines (SVM) and a Bayesian Classifier (BC) for this task. The first one outperformed all the remaining classifiers. Recall that we are also the first to introduce the OPF classifier in this field of knowledge. Very good results show the robustness of the proposed system, which can be also integrated with other commonly system (Mud-Logging) in order to improve the last one's efficiency.

Artificial immune systems for classification of petroleum well drilling operations

This paper presents two approaches of Artificial Immune System for Pattern Recognition (CLONALG and Parallel AIRS2) to classify automatically the well drilling operation stages. The classification is carried out through the analysis of some mud-logging parameters. In order to validate the performance of AIS techniques, the results were compared with others classification methods: neural network, support vector machine and lazy learning.

Estimativa de ocorrência de precipitação em áreas agrícolas utilizando floresta de caminhos ótimos

As condições meteorológicas são determinantes para a produção agrícola; a precipitação, em particular, pode ser citada como a mais influente por sua relação direta com o balanço hídrico. Neste sentido, modelos agrometeorológicos, os quais se baseiam nas respostas das culturas às condições meteorológicas, vêm sendo cada vez mais utilizados para a estimativa de rendimentos agrícolas. Devido às dificuldades de obtenção de dados para abastecer tais modelos, métodos de estimativa de precipitação utilizando imagens dos canais espectrais dos satélites meteorológicos têm sido empregados para esta finalidade. O presente trabalho tem por objetivo utilizar o classificador de padrões floresta de caminhos ótimos para correlacionar informações disponíveis no canal espectral infravermelho do satélite meteorológico GOES-12 com a refletividade obtida pelo radar do IPMET/UNESP localizado no município de Bauru, visando o desenvolvimento de um modelo para a detecção de ocorrência de precipitação. Nos experimentos foram comparados quatro algoritmos de classificação: redes neurais artificiais (ANN), k-vizinhos mais próximos (k-NN), máquinas de vetores de suporte (SVM) e floresta de caminhos ótimos (OPF). Este último obteve melhor resultado, tanto em eficiência quanto em precisão.

Fast automatic microstructural segmentation of ferrous alloy samples using optimum-path forest

In this work we propose a novel automatic cast iron segmentation approach based on the Optimum-Path Forest classifier (OPF). Microscopic images from nodular, gray and malleable cast irons are segmented using OPF, and Support Vector Machines (SVM) with Radial Basis Function and SVM without kernel mapping. Results show accurate and fast segmented images, in which OPF outperformed SVMs. Our work is the first into applying OPF for automatic cast iron segmentation. © 2010 Springer-Verlag.

An intelligent system to detect drilling problems through drilled cuttings return analysis

Cuttings return analysis is an important tool to detect and prevent problems during the petroleum well drilling process. Several measurements and tools have been developed for drilling problems detection, including mud logging, PWD and downhole torque information. Cuttings flow meters were developed in the past to provide information regarding cuttings return at the shale shakers. Their use, however, significantly impact the operation including rig space issues, interferences in geological analysis besides, additional personel required. This article proposes a non intrusive system to analyze the cuttings concentration at the shale shakers, which can indicate problems during drilling process, such as landslide, the collapse of the well borehole walls. Cuttings images are acquired by a high definition camera installed above the shakers and sent to a computer coupled with a data analysis system which aims the quantification and closure of a cuttings material balance in the well surface system domain. No additional people at the rigsite are required to operate the system. Modern Artificial intelligence techniques are used for pattern recognition and data analysis. Techniques include the Optimum-Path Forest (OPF), Artificial Neural Network using Multilayer Perceptrons (ANN-MLP), Support Vector Machines (SVM) and a Bayesian Classifier (BC). Field test results conducted on offshore floating vessels are presented. Results show the robustness of the proposed system, which can be also integrated with other data to improve the efficiency of drilling problems detection. Copyright 2010, IADC/SPE Drilling Conference and Exhibition.

Fast petroleum well drilling monitoring through optimum-path forest

Automatic inspection of petroleum well drilling has became paramount in the last years, mainly because of the crucial importance of saving time and operations during the drilling process in order to avoid some problems, such as the collapse of the well borehole walls. In this paper, we extended another work by proposing a fast petroleum well drilling monitoring through a modified version of the Optimum-Path Forest classifier. Given that the cutting's volume at the vibrating shale shaker can provide several information about drilling, we used computer vision techniques to extract texture informations from cutting images acquired by a digital camera. A collection of supervised classifiers were applied in order to allow comparisons about their accuracy and effciency. We used the Optimum-Path Forest (OPF), EOPF (Efficient OPF), Artificial Neural Network using Multilayer Perceptrons (ANN-MLP) Support Vector Machines (SVM), and a Bayesian Classifier (BC) to assess the robustness of our proposed schema for petroleum well drilling monitoring through cutting image analysis.