Applicability of in vivo staging of regional amyloid burden in a cognitively normal cohort with subjective memory complaints: the INSIGHT-preAD study.

BACKGROUND:Current methods of amyloid PET interpretation based on the binary classification of global amyloid signal fail to identify early phases of amyloid deposition. A recent analysis of 18F-florbetapir PET data from the Alzheimer's disease Neuroimaging Initiative cohort suggested a hierarchical four-stage model of regional amyloid deposition that resembles neuropathologic estimates and can be used to stage an individual's amyloid burden in vivo. Here, we evaluated the validity of this in vivo amyloid staging model in an independent cohort of older people with subjective memory complaints (SMC). We further examined its potential association with subtle cognitive impairments in this population at elevated risk for Alzheimer's disease (AD). METHODS:The monocentric INSIGHT-preAD cohort includes 318 cognitively intact older individuals with SMC. All individuals underwent 18F-florbetapir PET scanning and extensive neuropsychological testing. We projected the regional amyloid uptake signal into the previously proposed hierarchical staging model of in vivo amyloid progression. We determined the adherence to this model across all cases and tested the association between increasing in vivo amyloid stage and cognitive performance using ANCOVA models. RESULTS:In total, 156 participants (49%) showed evidence of regional amyloid deposition, and all but 2 of these (99%) adhered to the hierarchical regional pattern implied by the in vivo amyloid progression model. According to a conventional binary classification based on global signal (SUVRCereb = 1.10), individuals in stages III and IV were classified as amyloid-positive (except one in stage III), but 99% of individuals in stage I and even 28% of individuals in stage II were classified as amyloid-negative. Neither in vivo amyloid stage nor conventional binary amyloid status was significantly associated with cognitive performance in this preclinical cohort. CONCLUSIONS:The proposed hierarchical staging scheme of PET-evidenced amyloid deposition generalizes well to data from an independent cohort of older people at elevated risk for AD. Future studies will determine the prognostic value of the staging approach for predicting longitudinal cognitive decline in older individuals at increased risk for AD

Comparing Multi-class, Binary and Hierarchical Machine Learning Classication schemes for variable stars

Upcoming synoptic surveys are set to generate an unprecedented amount of data. This requires an automatic framework that can quickly and efficiently provide classification labels for several new object classification challenges. Using data describing 11 types of variable stars from the Catalina Real-Time Transient Surveys (CRTS), we illustrate how to capture the most important information from computed features and describe detailed methods of how to robustly use Information Theory for feature selection and evaluation. We apply three Machine Learning (ML) algorithms and demonstrate how to optimize these classifiers via cross-validation techniques. For the CRTS dataset, we find that the Random Forest (RF) classifier performs best in terms of balanced-accuracy and geometric means. We demonstrate substantially improved classification results by converting the multi-class problem into a binary classification task, achieving a balanced-accuracy rate of $\sim$99 per cent for the classification of ${\delta}$-Scuti and Anomalous Cepheids (ACEP). Additionally, we describe how classification performance can be improved via converting a 'flat-multi-class' problem into a hierarchical taxonomy. We develop a new hierarchical structure and propose a new set of classification features, enabling the accurate identification of subtypes of cepheids, RR Lyrae and eclipsing binary stars in CRTS data.Comment: 16 pages, 11 figures, accepted for publication in MNRA

Data fusion with artificial neural networks (ANN) for classification of earth surface from microwave satellite measurements

A data fusion system with artificial neural networks (ANN) is used for fast and accurate classification of five earth surface conditions and surface changes, based on seven SSMI multichannel microwave satellite measurements. The measurements include brightness temperatures at 19, 22, 37, and 85 GHz at both H and V polarizations (only V at 22 GHz). The seven channel measurements are processed through a convolution computation such that all measurements are located at same grid. Five surface classes including non-scattering surface, precipitation over land, over ocean, snow, and desert are identified from ground-truth observations. The system processes sensory data in three consecutive phases: (1) pre-processing to extract feature vectors and enhance separability among detected classes; (2) preliminary classification of Earth surface patterns using two separate and parallely acting classifiers: back-propagation neural network and binary decision tree classifiers; and (3) data fusion of results from preliminary classifiers to obtain the optimal performance in overall classification. Both the binary decision tree classifier and the fusion processing centers are implemented by neural network architectures. The fusion system configuration is a hierarchical neural network architecture, in which each functional neural net will handle different processing phases in a pipelined fashion. There is a total of around 13,500 samples for this analysis, of which 4 percent are used as the training set and 96 percent as the testing set. After training, this classification system is able to bring up the detection accuracy to 94 percent compared with 88 percent for back-propagation artificial neural networks and 80 percent for binary decision tree classifiers. The neural network data fusion classification is currently under progress to be integrated in an image processing system at NOAA and to be implemented in a prototype of a massively parallel and dynamically reconfigurable Modular Neural Ring (MNR)

Imbalance Learning for Variable Star Classification

The accurate automated classification of variable stars into their respective sub-types is difficult. Machine learning based solutions often fall foul of the imbalanced learning problem, which causes poor generalisation performance in practice, especially on rare variable star sub-types. In previous work, we attempted to overcome such deficiencies via the development of a hierarchical machine learning classifier. This 'algorithm-level' approach to tackling imbalance, yielded promising results on Catalina Real-Time Survey (CRTS) data, outperforming the binary and multi-class classification schemes previously applied in this area. In this work, we attempt to further improve hierarchical classification performance by applying 'data-level' approaches to directly augment the training data so that they better describe under-represented classes. We apply and report results for three data augmentation methods in particular: Randomly Augmented Sampled Light curves from magnitude Error (RASLE), augmenting light curves with Gaussian Process modelling (GpFit) and the Synthetic Minority Over-sampling Technique (SMOTE). When combining the 'algorithm-level' (i.e. the hierarchical scheme) together with the 'data-level' approach, we further improve variable star classification accuracy by 1-4%. We found that a higher classification rate is obtained when using GpFit in the hierarchical model. Further improvement of the metric scores requires a better standard set of correctly identified variable stars and, perhaps enhanced features are needed

New KEGG pathway-based interpretable features for classifying ageing-related mouse proteins

Motivation: The incidence of ageing-related diseases has been constantly increasing in the last decades, raising the need for creating effective methods to analyze ageing-related protein data. These methods should have high predictive accuracy and be easily interpretable by ageing experts. To enable this, one needs interpretable classification models (supervised machine learning) and features with rich biological meaning. In this paper we propose two interpretable feature types based on Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and compare them with traditional feature types in hierarchical classification (a more challenging classification task regarding predictive performance) and binary classification (a classification task producing easier to interpret classification models). As far as we know, this work is the first to: (i) explore the potential of the KEGG pathway data in the hierarchical classification setting, (i) use the graph structure of KEGG pathways to create a feature type that quantifies the influence of a current protein on another specific protein within a KEGG pathway graph and (iii) propose a method for interpreting the classification models induced using KEGG features. Results: We performed tests measuring predictive accuracy considering hierarchical and binary class labels extracted from the Mouse Phenotype Ontology. One of the KEGG feature types leads to the highest predictive accuracy among five individual feature types across three hierarchical classification algorithms. Additionally, the combination of the two KEGG feature types proposed in this work results in one of the best predictive accuracies when using the binary class version of our datasets, at the same time enabling the extraction of knowledge from ageing-related data using quantitative influence information

On automatic emotion classification using acoustic features

In this thesis, we describe extensive experiments on the classification of emotions from speech using acoustic features. This area of research has important applications in human computer interaction. We have thoroughly reviewed the current literature and present our results on some of the contemporary emotional speech databases. The principal focus is on creating a large set of acoustic features, descriptive of different emotional states and finding methods for selecting a subset of best performing features by using feature selection methods. In this thesis we have looked at several traditional feature selection methods and propose a novel scheme which employs a preferential Borda voting strategy for ranking features. The comparative results show that our proposed scheme can strike a balance between accurate but computationally intensive wrapper methods and less accurate but computationally less intensive filter methods for feature selection. By using the selected features, several schemes for extending the binary classifiers to multiclass classification are tested. Some of these classifiers form serial combinations of binary classifiers while others use a hierarchical structure to perform this task. We describe a new hierarchical classification scheme, which we call Data-Driven Dimensional Emotion Classification (3DEC), whose decision hierarchy is based on non-metric multidimensional scaling (NMDS) of the data. This method of creating a hierarchical structure for the classification of emotion classes gives significant improvements over other methods tested. The NMDS representation of emotional speech data can be interpreted in terms of the well-known valence-arousal model of emotion. We find that this model does not givea particularly good fit to the data: although the arousal dimension can be identified easily, valence is not well represented in the transformed data. From the recognitionresults on these two dimensions, we conclude that valence and arousal dimensions are not orthogonal to each other. In the last part of this thesis, we deal with the very difficult but important topic of improving the generalisation capabilities of speech emotion recognition (SER) systems over different speakers and recording environments. This topic has been generally overlooked in the current research in this area. First we try the traditional methods used in automatic speech recognition (ASR) systems for improving the generalisation of SER in intra– and inter–database emotion classification. These traditional methods do improve the average accuracy of the emotion classifier. In this thesis, we identify these differences in the training and test data, due to speakers and acoustic environments, as a covariate shift. This shift is minimised by using importance weighting algorithms from the emerging field of transfer learning to guide the learning algorithm towards that training data which gives better representation of testing data. Our results show that importance weighting algorithms can be used to minimise the differences between the training and testing data. We also test the effectiveness of importance weighting algorithms on inter–database and cross-lingual emotion recognition. From these results, we draw conclusions about the universal nature of emotions across different languages