Set Of Discriminative Features Research Articles

Towards automated discrimination of lipids versus peptides from full scan mass spectra

Although physicochemical fractionation techniques play a crucial role in the analysis of complex mixtures, they are not necessarily the best solution to separate specific molecular classes, such as lipids and peptides. Any physical fractionation step such as, for example, those based on liquid chromatography, will introduce its own variation and noise. In this paper we investigate to what extent the high sensitivity and resolution of contemporary mass spectrometers offers viable opportunities for computational separation of signals in full scan spectra. We introduce an automatic method that can discriminate peptide from lipid peaks in full scan mass spectra, based on their isotopic properties. We systematically evaluate which features maximally contribute to a peptide versus lipid classification. The selected features are subsequently used to build a random forest classifier that enables almost perfect separation between lipid and peptide signals without requiring ion fragmentation and classical tandem MS-based identification approaches. The classifier is trained on in silico data, but is also capable of discriminating signals in real world experiments. We evaluate the influence of typical data inaccuracies of common classes of mass spectrometry instruments on the optimal set of discriminant features. Finally, the method is successfully extended towards the classification of individual lipid classes from full scan mass spectral features, based on input data defined by the Lipid Maps Consortium.

Identification of non-coding RNAs with a new composite feature in the Hybrid Random Forest Ensemble algorithm.

To identify non-coding RNA (ncRNA) signals within genomic regions, a classification tool was developed based on a hybrid random forest (RF) with a logistic regression model to efficiently discriminate short ncRNA sequences as well as long complex ncRNA sequences. This RF-based classifier was trained on a well-balanced dataset with a discriminative set of features and achieved an accuracy, sensitivity and specificity of 92.11%, 90.7% and 93.5%, respectively. The selected feature set includes a new proposed feature, SCORE. This feature is generated based on a logistic regression function that combines five significant features—structure, sequence, modularity, structural robustness and coding potential—to enable improved characterization of long ncRNA (lncRNA) elements. The use of SCORE improved the performance of the RF-based classifier in the identification of Rfam lncRNA families. A genome-wide ncRNA classification framework was applied to a wide variety of organisms, with an emphasis on those of economic, social, public health, environmental and agricultural significance, such as various bacteria genomes, the Arthrospira (Spirulina) genome, and rice and human genomic regions. Our framework was able to identify known ncRNAs with sensitivities of greater than 90% and 77.7% for prokaryotic and eukaryotic sequences, respectively. Our classifier is available at http://ncrna-pred.com/HLRF.htm.

Projection transform on spatio-temporal context for action recognition

This paper discusses the task of human action recognition. This task is important to applications like video surveillance and video retrieval. Most of the existing local interest points based works on human action analysis, lost the information about spatio-temporal distribution of features and neglected the relationship between features and each defined actions. In this paper, through the analysis of feature distribution and their interactions over spatio-temporal domain, we propose a novel projection transform to take the two factors into account. A video sequence of human action in our perspective can be modeled by three types of features of spatio-temporal interest points: the global projection transform feature, the relative position distribution feature and the bag of visual words based feature. Then a new context-K-nearest-neighbor classifier is utilized to fuse them to form discriminative feature sets for action matching. In most of the case, our experiments have indicated that the novel method outperforms other previous published results on the Weizmann and KTH datasets.

A unified graphical models framework for automated mitosis detection in human embryos.

Time lapse microscopy has emerged as an important modality for studying human embryo development, as mitosis events can provide insight into embryo health and fate. Mitosis detection can happen through tracking of embryonic cells (tracking based), or from low level image features and classifiers (tracking free). Tracking based approaches are challenged by high dimensional search space, weak features, outliers, missing data, multiple deformable targets, and weak motion model. Tracking free approaches are data driven and complement tracking based approaches. We pose mitosis detection as augmented simultaneous segmentation and classification in a conditional random field (CRF) framework that combines both approaches. It uses a rich set of discriminative features and their spatiotemporal context. It performs a dual pass approximate inference that addresses the high dimensionality of tracking and combines results from both components. For 312 clinical sequences we measured division events to within 30 min and observed an improvement of 25.6% and a 32.9% improvement over purely tracking based and tracking free approach respectively, and close to an order of magnitude over a traditional particle filter. While our work was motivated by human embryo development, it can be extended to other detection problems in image sequences of evolving cell populations.

Automatic ROI selection in structural brain MRI using SOM 3D projection.

This paper presents a method for selecting Regions of Interest (ROI) in brain Magnetic Resonance Imaging (MRI) for diagnostic purposes, using statistical learning and vector quantization techniques. The proposed method models the distribution of GM and WM tissues grouping the voxels belonging to each tissue in ROIs associated to a specific neurological disorder. Tissue distribution of normal and abnormal images is modelled by a Self-Organizing map (SOM), generating a set of representative prototypes, and the receptive field (RF) of each SOM prototype defines a ROI. Moreover, the proposed method computes the relative importance of each ROI by means of its discriminative power. The devised method has been assessed using 818 images from the Alzheimer's disease Neuroimaging Initiative (ADNI) which were previously segmented through Statistical Parametric Mapping (SPM). The proposed algorithm was used over these images to parcel ROIs associated to the Alzheimer's Disease (AD). Additionally, this method can be used to extract a reduced set of discriminative features for classification, since it compresses discriminative information contained in the brain. Voxels marked by ROIs which were computed using the proposed method, yield classification results up to 90% of accuracy for controls (CN) and Alzheimer's disease (AD) patients, and 84% of accuracy for Mild Cognitive Impairment (MCI) and AD patients.

Identifying scientific artefacts in biomedical literature: The Evidence Based Medicine use case

Evidence Based Medicine (EBM) provides a framework that makes use of the current best evidence in the domain to support clinicians in the decision making process. In most cases, the underlying foundational knowledge is captured in scientific publications that detail specific clinical studies or randomised controlled trials. Over the course of the last two decades, research has been performed on modelling key aspects described within publications (e.g., aims, methods, results), to enable the successful realisation of the goals of EBM. A significant outcome of this research has been the PICO (Population/Problem–Intervention–Comparison–Outcome) structure, and its refined version PIBOSO (Population–Intervention–Background–Outcome–Study Design–Other), both of which provide a formalisation of these scientific artefacts. Subsequently, using these schemes, diverse automatic extraction techniques have been proposed to streamline the knowledge discovery and exploration process in EBM. In this paper, we present a Machine Learning approach that aims to classify sentences according to the PIBOSO scheme. We use a discriminative set of features that do not rely on any external resources to achieve results comparable to the state of the art. A corpus of 1000 structured and unstructured abstracts – i.e., the NICTA-PIBOSO corpus – is used for training and testing. Our best CRF classifier achieves a micro-average F-score of 90.74% and 87.21%, respectively, over structured and unstructured abstracts, which represents an increase of 25.48 percentage points and 26.6 percentage points in F-score when compared to the best existing approaches.

Learned geometric features of 3D range data for human and tree recognition

A new method of obtaining geometric features of three-dimensional range data for human and tree recognition in an off-road environment is described. The learning algorithm AdaBoost is used to select a set of discriminative features from a very large set of potential geometric features. The proposed geometric feature can be considered as a generalisation of the geometric feature used in previous studies. The experimental results for human and tree recognition show that the proposed method outperforms the other methods.

Multi-label classification for colon cancer using histopathological images

Colon cancer classification has a significant guidance value in clinical diagnoses and medical prognoses. The classification of colon cancers with high accuracy is the premise of efficient treatment. Our task is to build a system for colon cancer detection and classification based on slide histopathological images. Some former researches focus on single label classification. Through analyzing large amount of colon cancer images, we found that one image may contain cancer regions of multiple types. Therefore, we reformulated the task as multi-label problem. Four kinds of features (Color Histogram, Gray-Level Co-occurrence Matrix, Histogram of Oriented Gradients and Euler number) were introduced to compose our discriminative feature set, extracted from our dataset that includes six single categories and four multi-label categories. In order to evaluate the performance and make comparison with our multi-label model, three commonly used multi-classification methods were designed in our experiment including one-against-all SVM (OAA), one-against-one SVM (OAO) and multi-structure SVM. Four indicators (Precision, Recall, F-measure, and Accuracy) under 3-fold cross-validation were used to validate the performance of our approach. Experiment results show that the precision, recall and F-measure of multi-label method as 73.7%, 68.2%, and 70.8% with all features, which are higher than the other three classifiers. These results demonstrate the effectiveness and efficiency of our method on colon histopathological images analysis.

Parkinsonism-related features of neuronal discharge in primates

Parkinson's disease is known to be associated with abnormal electrical spiking activities of basal ganglia neurons, including changes in firing rate, bursting activities and oscillatory firing patterns and changes in entropy. We explored the relative importance of these measures through optimal feature selection and discrimination analysis methods. We identified key characteristics of basal ganglia activity that predicted whether the neurons were recorded in the normal or parkinsonian state. Starting with 29 features extracted from the spike timing of neurons recorded in normal and parkinsonian monkeys in the internal or external segment of the globus pallidus or the subthalamic nucleus (STN), we used a method that incorporates a support vector machine algorithm to find feature combinations that optimally discriminate between the normal and parkinsonian states. Our results demonstrate that the discrimination power of combinations of specific features is higher than that of single features, or of all features combined, and that the most discriminative feature sets differ substantially between basal ganglia structures. Each nucleus or class of neurons in the basal ganglia may react differently to the parkinsonian condition, and the features used to describe this state should be adapted to the neuron type under study. The feature that was overall most predictive of the parkinsonian state in our data set was a high STN intraburst frequency. Interestingly, this feature was not correlated with parameters describing oscillatory firing properties in recordings made in the normal condition but was significantly correlated with spectral power in specific frequency bands in recordings from the parkinsonian state (specifically with power in the 8-13 Hz band).

Prediction of protein-protein interactions from amino acid sequences with ensemble extreme learning machines and principal component analysis

BackgroundProtein-protein interactions (PPIs) play crucial roles in the execution of various cellular processes and form the basis of biological mechanisms. Although large amount of PPIs data for different species has been generated by high-throughput experimental techniques, current PPI pairs obtained with experimental methods cover only a fraction of the complete PPI networks, and further, the experimental methods for identifying PPIs are both time-consuming and expensive. Hence, it is urgent and challenging to develop automated computational methods to efficiently and accurately predict PPIs.ResultsWe present here a novel hierarchical PCA-EELM (principal component analysis-ensemble extreme learning machine) model to predict protein-protein interactions only using the information of protein sequences. In the proposed method, 11188 protein pairs retrieved from the DIP database were encoded into feature vectors by using four kinds of protein sequences information. Focusing on dimension reduction, an effective feature extraction method PCA was then employed to construct the most discriminative new feature set. Finally, multiple extreme learning machines were trained and then aggregated into a consensus classifier by majority voting. The ensembling of extreme learning machine removes the dependence of results on initial random weights and improves the prediction performance.ConclusionsWhen performed on the PPI data of Saccharomyces cerevisiae, the proposed method achieved 87.00% prediction accuracy with 86.15% sensitivity at the precision of 87.59%. Extensive experiments are performed to compare our method with state-of-the-art techniques Support Vector Machine (SVM). Experimental results demonstrate that proposed PCA-EELM outperforms the SVM method by 5-fold cross-validation. Besides, PCA-EELM performs faster than PCA-SVM based method. Consequently, the proposed approach can be considered as a new promising and powerful tools for predicting PPI with excellent performance and less time.

Keyword spotting using an evolutionary-based classifier and discriminative features

Keyword spotting refers to detection of all occurrences of any given keyword in input speech utterances. In this paper, we define a keyword spotter as a binary classifier that separates a class of sentences containing a target keyword from a class of sentences which do not include the target keyword. In order to discriminate the mentioned classes, an efficient classification method and a suitable feature set are to be studied. For the classification method, we propose an evolutionary algorithm to train the separating hyper-plane between the two classes. As our discriminative feature set, we propose two confidence measure functions. The first confidence measure function computes the possibility of phonemes presence in the speech frames, and the second one determines the duration of each phoneme. We define these functions based on the acoustic, spectral and statistical features of speech. The results on TIMIT indicate that the proposed evolutionary-based discriminative keyword spotter has lower computational complexity and higher speed in both test and train phases, in comparison to the SVM-based discriminative keyword spotter. Additionally, the proposed system is robust in noisy conditions.

Automated Feature Set Selection and Its Application to MCC Identification in Digital Mammograms for Breast Cancer Detection

We propose a fully automated algorithm that is able to select a discriminative feature set from a training database via sequential forward selection (SFS), sequential backward selection (SBS), and F-score methods. We applied this scheme to microcalcifications cluster (MCC) detection in digital mammograms for early breast cancer detection. The system was able to select features fully automatically, regardless of the input training mammograms used. We tested the proposed scheme using a database of 111 clinical mammograms containing 1,050 microcalcifications (MCs). The accuracy of the system was examined via a free response receiver operating characteristic (fROC) curve of the test dataset. The system performance for MC identifications was Az = 0.9897, the sensitivity was 92%, and 0.65 false positives (FPs) were generated per image for MCC detection.

Muscle computer interfaces for driver distraction reduction

Driver distraction is regarded as a significant contributor to motor-vehicle crashes. One of the important factors contributing to driver distraction was reported to be the handling and reaching of in-car electronic equipment and controls that usually requires taking the drivers’ hands off the wheel and eyes off the road. To minimize the amount of such distraction, we present a new control scheme that senses and decodes the human muscles signals, denoted as Electromyogram (EMG), associated with different fingers postures/pressures, and map that to different commands to control external equipment, without taking hands off the wheel. To facilitate such a scheme, the most significant step is the extraction of a set of highly discriminative feature set that can well separate between the different EMG-based actions and to do so in a computationally efficient manner. In this paper, an accurate and efficient method based on Fuzzy Neighborhood Discriminant Analysis (FNDA), is proposed for discriminant feature extraction and then extended to the channel selection problem. Unlike existing methods, the objective of the proposed FNDA is to preserve the local geometrical and discriminant structures, while taking into account the contribution of the samples to the different classes. The method also aims to efficiently overcome the singularity problems of classical LDA by employing the QR-decomposition. Practical real-time experiments with eight EMG sensors attached on the human forearm of eight subjects indicated that up to fourteen classes of fingers postures/pressures can be classified with <7% error on average, proving the significance of the proposed method.

Fusion of Directional Spatial Discriminant Features for Face Recognition

Abstract Feature level fusion is one of the most important techniques, used to improve the performance of a face recognition system. This paper presents an approach of fusion of directional spatial discriminant features for face recognition. The key idea of the proposed method is to fuse the facial features lie along the horizontal, vertical and diagonal directions. So that this fused feature vector can contain more discriminant information than the individual facial feature lie along single direction. However due to fusion the size of fused feature vector is become larger which may increase complexity of the classifier. To optimize this lower dimensional discriminant features are again extracted from this large fused feature vector. In our experiment, we apply G-2DFLD method on the original images to extract the discriminant features. Then original images are converted into diagonal images and another set of discriminant features, representing the diagonal information, are extracted by using the G-2DFLD method. The original and diagonal features vectors are then fused to form a large feature vector. The dimension of this large fused feature vector is then reduced by PCA method and this resultant reduced feature vector is used for classification and recognition by Radial Basis Function-Neural Networks (RBF-NN). Experiments on the AT&T (formally known as ORL database) face database indicate the competitive performance of the proposed method, as compared to some existing subspaces-based methods. Click here and insert your abstract text.

SPECTRAL REGRESSION DISCRIMINANT ANALYSIS FOR HYPERSPECTRAL IMAGE CLASSIFICATION

Abstract. Dimensionality reduction algorithms, which aim to select a small set of efficient and discriminant features, have attracted great attention for Hyperspectral Image Classification. The manifold learning methods are popular for dimensionality reduction, such as Locally Linear Embedding, Isomap, and Laplacian Eigenmap. However, a disadvantage of many manifold learning methods is that their computations usually involve eigen-decomposition of dense matrices which is expensive in both time and memory. In this paper, we introduce a new dimensionality reduction method, called Spectral Regression Discriminant Analysis (SRDA). SRDA casts the problem of learning an embedding function into a regression framework, which avoids eigen-decomposition of dense matrices. Also, with the regression based framework, different kinds of regularizes can be naturally incorporated into our algorithm which makes it more flexible. It can make efficient use of data points to discover the intrinsic discriminant structure in the data. Experimental results on Washington DC Mall and AVIRIS Indian Pines hyperspectral data sets demonstrate the effectiveness of the proposed method.

An efficient diagnosis system for detection of Parkinson’s disease using fuzzy k-nearest neighbor approach

In this paper, we present an effective and efficient diagnosis system using fuzzy k-nearest neighbor (FKNN) for Parkinson’s disease (PD) diagnosis. The proposed FKNN-based system is compared with the support vector machines (SVM) based approaches. In order to further improve the diagnosis accuracy for detection of PD, the principle component analysis was employed to construct the most discriminative new feature sets on which the optimal FKNN model was constructed. The effectiveness of the proposed system has been rigorously estimated on a PD data set in terms of classification accuracy, sensitivity, specificity and the area under the receiver operating characteristic (ROC) curve (AUC). Experimental results have demonstrated that the FKNN-based system greatly outperforms SVM-based approaches and other methods in the literature. The best classification accuracy (96.07%) obtained by the FKNN-based system using a 10-fold cross validation method can ensure a reliable diagnostic model for detection of PD. Promisingly, the proposed system might serve as a new candidate of powerful tools for diagnosing PD with excellent performance.

Biologically Inspired Object Tracking Using Center-Surround Saliency Mechanisms

A biologically inspired discriminant object tracker is proposed. It is argued that discriminant tracking is a consequence of top-down tuning of the saliency mechanisms that guide the deployment of visual attention. The principle of discriminant saliency is then used to derive a tracker that implements a combination of center-surround saliency, a spatial spotlight of attention, and feature-based attention. In this framework, the tracking problem is formulated as one of continuous target-background classification, implemented in two stages. The first, or learning stage, combines a focus of attention (FoA) mechanism, and bottom-up saliency to identify a maximally discriminant set of features for target detection. The second, or detection stage, uses a feature-based attention mechanism and a target-tuned top-down discriminant saliency detector to detect the target. Overall, the tracker iterates between learning discriminant features from the target location in a video frame and detecting the location of the target in the next. The statistics of natural images are exploited to derive an implementation which is conceptually simple and computationally efficient. The saliency formulation is also shown to establish a unified framework for classifier design, target detection, automatic tracker initialization, and scale adaptation. Experimental results show that the proposed discriminant saliency tracker outperforms a number of state-of-the-art trackers in the literature.

An efficient framework for location-based scene matching in image databases

SIFT-based methods have been widely used for scene matching of photos taken at particular locations or places of interest. These methods are typically very time consuming due to the large number and high dimensionality of features used, making them unfeasible for use in consumer image collections containing a large number of images where computational power is limited and a fast response is desired. Considerable computational savings can be realized if images containing signature elements of particular locations can be automatically identified from the large number of images and only these representative images used for scene matching. We propose an efficient framework incorporating a set of discriminative image features that effectively enables us to select representative images for fast location-based scene matching. These image features are used for classifying images into good or bad candidates for scene matching, using different classification approaches. Furthermore, the image features created from our framework can facilitate the process of using sub-images for location-based scene matching with SIFT features. The experimental results demonstrate the effectiveness of our approach compared with the traditional SIFT-, PCA-SIFT-, and SURF-based approaches by reducing the computational time by an order of magnitude.

A Computer Aided Diagnosis System for Thyroid Disease Using Extreme Learning Machine

In this paper, we present an effective and efficient computer aided diagnosis (CAD) system based on principle component analysis (PCA) and extreme learning machine (ELM) to assist the task of thyroid disease diagnosis. The CAD system is comprised of three stages. Focusing on dimension reduction, the first stage applies PCA to construct the most discriminative new feature set. After then, the system switches to the second stage whose target is model construction. ELM classifier is explored to train an optimal predictive model whose parameters are optimized. As we known, the number of hidden neurons has an important role in the performance of ELM, so we propose an experimental method to hunt for the optimal value. Finally, the obtained optimal ELM model proceeds to perform the thyroid disease diagnosis tasks using the most discriminative new feature set and the optimal parameters. The effectiveness of the resultant CAD system (PCA-ELM) has been rigorously estimated on a thyroid disease dataset which is taken from UCI machine learning repository. We compare it with other related methods in terms of their classification accuracy. Experimental results demonstrate that PCA-ELM outperforms other ones reported so far by 10-fold cross-validation method, with the mean accuracy of 97.73% and with the maximum accuracy of 98.1%. Besides, PCA-ELM performs much faster than support vector machines (SVM) based CAD system. Consequently, the proposed method PCA-ELM can be considered as a new powerful tools for diagnosing thyroid disease with excellent performance and less time.

Online multiple instance gradient feature selection for robust visual tracking

In this paper, we focus on learning an adaptive appearance model robustly and effectively for object tracking. There are two important factors to affect object tracking, the one is how to represent the object using a discriminative appearance model, the other is how to update appearance model in an appropriate manner. In this paper, following the state-of-the-art tracking techniques which treat object tracking as a binary classification problem, we firstly employ a new gradient-based Histogram of Oriented Gradient (HOG) feature selection mechanism under Multiple Instance Learning (MIL) framework for constructing target appearance model, and then propose a novel optimization scheme to update such appearance model robustly. This is an unified framework that not only provides an efficient way of selecting the discriminative feature set which forms a powerful appearance model, but also updates appearance model in online MIL Boost manner which could achieve robust tracking overcoming the drifting problem. Experiments on several challenging video sequences demonstrate the effectiveness and robustness of our proposal.