A real-time phenotyping framework using machine learning for plant stress severity rating in soybean

Background: Phenotyping is a critical component of plant research. Accurate and precise trait collection, when integrated with genetic tools, can greatly accelerate the rate of genetic gain in crop improvement. However, efficient and automatic phenotyping of traits across large populations is a challenge; which is further exacerbated by the necessity of sampling multiple environments and growing replicated trials. A promising approach is to leverage current advances in imaging technology, data analytics and machine learning to enable automated and fast phenotyping and subsequent decision support. In this context, the workflow for phenotyping (image capture → data storage and curation → trait extraction → machine learning/classification → models/apps for decision support) has to be carefully designed and efficiently executed to minimize resource usage and maximize utility. We illustrate such an end-to-end phenotyping workflow for the case of plant stress severity phenotyping in soybean, with a specific focus on the rapid and automatic assessment of iron deficiency chlorosis (IDC) severity on thousands of field plots. We showcase this analytics framework by extracting IDC features from a set of ~4500 unique canopies representing a diverse germplasm base that have different levels of IDC, and subsequently training a variety of classification models to predict plant stress severity. The best classifier is then deployed as a smartphone app for rapid and real time severity rating in the field. Results: We investigated 10 different classification approaches, with the best classifier being a hierarchical classifier with a mean per-class accuracy of ~96%. We construct a phenotypically meaningful ‘population canopy graph’, connecting the automatically extracted canopy trait features with plant stress severity rating. We incorporated this image capture → image processing → classification workflow into a smartphone app that enables automated real-time evaluation of IDC scores using digital images of the canopy. Conclusion: We expect this high-throughput framework to help increase the rate of genetic gain by providing a robust extendable framework for other abiotic and biotic stresses. We further envision this workflow embedded onto a high throughput phenotyping ground vehicle and unmanned aerial system that will allow real-time, automated stress trait detection and quantification for plant research, breeding and stress scouting applications

Dynamic adversarial mining - effectively applying machine learning in adversarial non-stationary environments.

While understanding of machine learning and data mining is still in its budding stages, the engineering applications of the same has found immense acceptance and success. Cybersecurity applications such as intrusion detection systems, spam filtering, and CAPTCHA authentication, have all begun adopting machine learning as a viable technique to deal with large scale adversarial activity. However, the naive usage of machine learning in an adversarial setting is prone to reverse engineering and evasion attacks, as most of these techniques were designed primarily for a static setting. The security domain is a dynamic landscape, with an ongoing never ending arms race between the system designer and the attackers. Any solution designed for such a domain needs to take into account an active adversary and needs to evolve over time, in the face of emerging threats. We term this as the ‘Dynamic Adversarial Mining’ problem, and the presented work provides the foundation for this new interdisciplinary area of research, at the crossroads of Machine Learning, Cybersecurity, and Streaming Data Mining. We start with a white hat analysis of the vulnerabilities of classification systems to exploratory attack. The proposed ‘Seed-Explore-Exploit’ framework provides characterization and modeling of attacks, ranging from simple random evasion attacks to sophisticated reverse engineering. It is observed that, even systems having prediction accuracy close to 100%, can be easily evaded with more than 90% precision. This evasion can be performed without any information about the underlying classifier, training dataset, or the domain of application. Attacks on machine learning systems cause the data to exhibit non stationarity (i.e., the training and the testing data have different distributions). It is necessary to detect these changes in distribution, called concept drift, as they could cause the prediction performance of the model to degrade over time. However, the detection cannot overly rely on labeled data to compute performance explicitly and monitor a drop, as labeling is expensive and time consuming, and at times may not be a possibility altogether. As such, we propose the ‘Margin Density Drift Detection (MD3)’ algorithm, which can reliably detect concept drift from unlabeled data only. MD3 provides high detection accuracy with a low false alarm rate, making it suitable for cybersecurity applications; where excessive false alarms are expensive and can lead to loss of trust in the warning system. Additionally, MD3 is designed as a classifier independent and streaming algorithm for usage in a variety of continuous never-ending learning systems. We then propose a ‘Dynamic Adversarial Mining’ based learning framework, for learning in non-stationary and adversarial environments, which provides ‘security by design’. The proposed ‘Predict-Detect’ classifier framework, aims to provide: robustness against attacks, ease of attack detection using unlabeled data, and swift recovery from attacks. Ideas of feature hiding and obfuscation of feature importance are proposed as strategies to enhance the learning framework\u27s security. Metrics for evaluating the dynamic security of a system and recover-ability after an attack are introduced to provide a practical way of measuring efficacy of dynamic security strategies. The framework is developed as a streaming data methodology, capable of continually functioning with limited supervision and effectively responding to adversarial dynamics. The developed ideas, methodology, algorithms, and experimental analysis, aim to provide a foundation for future work in the area of ‘Dynamic Adversarial Mining’, wherein a holistic approach to machine learning based security is motivated

Computer vision based classification of fruits and vegetables for self-checkout at supermarkets

The field of machine learning, and, in particular, methods to improve the capability of machines to perform a wider variety of generalised tasks are among the most rapidly growing research areas in today’s world. The current applications of machine learning and artificial intelligence can be divided into many significant fields namely computer vision, data sciences, real time analytics and Natural Language Processing (NLP). All these applications are being used to help computer based systems to operate more usefully in everyday contexts. Computer vision research is currently active in a wide range of areas such as the development of autonomous vehicles, object recognition, Content Based Image Retrieval (CBIR), image segmentation and terrestrial analysis from space (i.e. crop estimation). Despite significant prior research, the area of object recognition still has many topics to be explored. This PhD thesis focuses on using advanced machine learning approaches to enable the automated recognition of fresh produce (i.e. fruits and vegetables) at supermarket self-checkouts. This type of complex classification task is one of the most recently emerging applications of advanced computer vision approaches and is a productive research topic in this field due to the limited means of representing the features and machine learning techniques for classification. Fruits and vegetables offer significant inter and intra class variance in weight, shape, size, colour and texture which makes the classification challenging. The applications of effective fruit and vegetable classification have significant importance in daily life e.g. crop estimation, fruit classification, robotic harvesting, fruit quality assessment, etc. One potential application for this fruit and vegetable classification capability is for supermarket self-checkouts. Increasingly, supermarkets are introducing self-checkouts in stores to make the checkout process easier and faster. However, there are a number of challenges with this as all goods cannot readily be sold with packaging and barcodes, for instance loose fresh items (e.g. fruits and vegetables). Adding barcodes to these types of items individually is impractical and pre-packaging limits the freedom of choice when selecting fruits and vegetables and creates additional waste, hence reducing customer satisfaction. The current situation, which relies on customers correctly identifying produce themselves leaves open the potential for incorrect billing either due to inadvertent error, or due to intentional fraudulent misclassification resulting in financial losses for the store. To address this identified problem, the main goals of this PhD work are: (a) exploring the types of visual and non-visual sensors that could be incorporated into a self-checkout system for classification of fruits and vegetables, (b) determining a suitable feature representation method for fresh produce items available at supermarkets, (c) identifying optimal machine learning techniques for classification within this context and (d) evaluating our work relative to the state-of-the-art object classification results presented in the literature. An in-depth analysis of related computer vision literature and techniques is performed to identify and implement the possible solutions. A progressive process distribution approach is used for this project where the task of computer vision based fruit and vegetables classification is divided into pre-processing and classification techniques. Different classification techniques have been implemented and evaluated as possible solution for this problem. Both visual and non-visual features of fruit and vegetables are exploited to perform the classification. Novel classification techniques have been carefully developed to deal with the complex and highly variant physical features of fruit and vegetables while taking advantages of both visual and non-visual features. The capability of classification techniques is tested in individual and ensemble manner to achieved the higher effectiveness. Significant results have been obtained where it can be concluded that the fruit and vegetables classification is complex task with many challenges involved. It is also observed that a larger dataset can better comprehend the complex variant features of fruit and vegetables. Complex multidimensional features can be extracted from the larger datasets to generalise on higher number of classes. However, development of a larger multiclass dataset is an expensive and time consuming process. The effectiveness of classification techniques can be significantly improved by subtracting the background occlusions and complexities. It is also worth mentioning that ensemble of simple and less complicated classification techniques can achieve effective results even if applied to less number of features for smaller number of classes. The combination of visual and nonvisual features can reduce the struggle of a classification technique to deal with higher number of classes with similar physical features. Classification of fruit and vegetables with similar physical features (i.e. colour and texture) needs careful estimation and hyper-dimensional embedding of visual features. Implementing rigorous classification penalties as loss function can achieve this goal at the cost of time and computational requirements. There is a significant need to develop larger datasets for different fruit and vegetables related computer vision applications. Considering more sophisticated loss function penalties and discriminative hyper-dimensional features embedding techniques can significantly improve the effectiveness of the classification techniques for the fruit and vegetables applications

Class-Level Refactoring Prediction by Ensemble Learning with Various Feature Selection Techniques

Background: Refactoring is changing a software system without affecting the software functionality. The current researchers aim i to identify the appropriate method(s) or class(s) that needs to be refactored in object-oriented software. Ensemble learning helps to reduce prediction errors by amalgamating different classifiers and their respective performances over the original feature data. Other motives are added in this paper regarding several ensemble learners, errors, sampling techniques, and feature selection techniques for refactoring prediction at the class level. Objective: This work aims to develop an ensemble-based refactoring prediction model with structural identification of source code metrics using different feature selection techniques and data sampling techniques to distribute the data uniformly. Our model finds the best classifier after achieving fewer errors during refactoring prediction at the class level. Methodology: At first, our proposed model extracts a total of 125 software metrics computed from object-oriented software systems processed for a robust multi-phased feature selection method encompassing Wilcoxon significant text, Pearson correlation test, and principal component analysis (PCA). The proposed multi-phased feature selection method retains the optimal features characterizing inheritance, size, coupling, cohesion, and complexity. After obtaining the optimal set of software metrics, a novel heterogeneous ensemble classifier is developed using techniques such as ANN-Gradient Descent, ANN-Levenberg Marquardt, ANN-GDX, ANN-Radial Basis Function; support vector machine with different kernel functions such as LSSVM-Linear, LSSVM-Polynomial, LSSVM-RBF, Decision Tree algorithm, Logistic Regression algorithm and extreme learning machine (ELM) model are used as the base classifier. In our paper, we have calculated four different errors i.e., Mean Absolute Error (MAE), Mean magnitude of Relative Error (MORE), Root Mean Square Error (RMSE), and Standard Error of Mean (SEM). Result: In our proposed model, the maximum voting ensemble (MVE) achieves better accuracy, recall, precision, and F-measure values (99.76, 99.93, 98.96, 98.44) as compared to the base trained ensemble (BTE) and it experiences less errors (MAE = 0.0057, MORE = 0.0701, RMSE = 0.0068, and SEM = 0.0107) during its implementation to develop the refactoring model. Conclusions: Our experimental result recommends that MVE with upsampling can be implemented to improve the performance of the refactoring prediction model at the class level. Furthermore, the performance of our model with different data sampling techniques and feature selection techniques has been shown in the form boxplot diagram of accuracy, F-measure, precision, recall, and area under the curve (AUC) parameters.publishedVersio

Discriminative Appearance Models for Face Alignment

The proposed face alignment algorithm uses local gradient features as the appearance representation. These features are obtained by pixel value comparison, which provide robustness against changes in illumination, as well as partial occlusion and local deformation due to the locality. The adopted features are modeled in three discriminative methods, which correspond to different alignment cost functions. The discriminative appearance modeling alleviate the generalization problem to some extent

Efficient Learning Machines

Computer scienc

Bioinformatics framework for genotyping microarray data analysis

Functional genomics is a flourishing science enabled by recent technological breakthroughs in high-throughput instrumentation and microarray data analysis. Genotyping microarrays establish the genotypes of DNA sequences containing single nucleotide polymorphisms (SNPs), and can help biologists probe the functions of different genes and/or construct complex gene interaction networks. The enormous amount of data from these experiments makes it infeasible to perform manual processing to obtain accurate and reliable results in daily routines. Advanced algorithms as well as an integrated software toolkit are needed to help perform reliable and fast data analysis. The author developed a MatlabTM based software package, called TIMDA (a Toolkit for Integrated Genotyping Microarray Data Analysis), for fully automatic, accurate and reliable genotyping microarray data analysis. The author also developed new algorithms for image processing and genotype-calling. The modular design of TIMDA allows satisfactory extensibility and maintainability. TIMDA is open source (URL: http://timda.SF.net and can be easily customized by users to meet their particular needs. The quality and reproducibility of results in image processing and genotype-calling and the ease of customization indicate that TIMDA is a useful package for genomics research