Simple Linear Discriminant Analysis Research Articles

Oil Spills or Look-Alikes? Classification Rank of Surface Ocean Slick Signatures in Satellite Data

Linear discriminant analysis (LDA) is a mathematically robust multivariate data analysis approach that is sometimes used for surface oil slick signature classification. Our goal is to rank the effectiveness of LDAs to differentiate oil spills from look-alike slicks. We explored multiple combinations of (i) variables (size information, Meteorological-Oceanographic (metoc), geo-location parameters) and (ii) data transformations (non-transformed, cube root, log10). Active and passive satellite-based measurements of RADARSAT, QuikSCAT, AVHRR, SeaWiFS, and MODIS were used. Results from two experiments are reported and discussed: (i) an investigation of 60 combinations of several attributes subjected to the same data transformation and (ii) a survey of 54 other data combinations of three selected variables subjected to different data transformations. In Experiment 1, the best discrimination was reached using ten cube-transformed attributes: ~85% overall accuracy using six pieces of size information, three metoc variables, and one geo-location parameter. In Experiment 2, two combinations of three variables tied as the most effective: ~81% of overall accuracy using area (log transformed), length-to-width ratio (log- or cube-transformed), and number of feature parts (non-transformed). After verifying the classification accuracy of 114 algorithms by comparing with expert interpretations, we concluded that applying different data transformations and accounting for metoc and geo-location attributes optimizes the accuracies of binary classifiers (oil spill vs. look-alike slicks) using the simple LDA technique.

MCI Detection Using Kernel Eigen-Relative-Power Features of EEG Signals

Classification between individuals with mild cognitive impairment (MCI) and healthy controls (HC) based on electroencephalography (EEG) has been considered a challenging task to be addressed for the purpose of its early detection. In this study, we proposed a novel EEG feature, the kernel eigen-relative-power (KERP) feature, for achieving high classification accuracy of MCI versus HC. First, we introduced the relative powers (RPs) between pairs of electrodes across 21 different subbands of 2-Hz width as the features, which have not yet been used in previous MCI-HC classification studies. Next, the Fisher’s class separability criterion was applied to determine the best electrode pairs (five electrodes) as well as the frequency subbands for extracting the most sensitive RP features. The kernel principal component analysis (kernel PCA) algorithm was further performed to extract a few more discriminating nonlinear principal components from the optimal RPs, and these components form a KERP feature vector. Results carried out on 51 participants (24 MCI and 27 HC) show that the newly introduced subband RP feature showed superior classification performance to commonly used spectral power features, including the band power, single-electrode relative power, and also the RP based on the conventional frequency bands. A high leave-one-participant-out cross-validation (LOPO-CV) classification accuracy 86.27% was achieved by the RP feature, using a simple linear discriminant analysis (LDA) classifier. Moreover, with the same classifier, the proposed KERP further improved the accuracy to 88.24%. Finally, cascading the KERP feature to a nonlinear classifier, the support vector machine (SVM), yields a high MCI-HC classification accuracy of 90.20% (sensitivity = 87.50% and specificity = 92.59%). The proposed method demonstrated a high accuracy and a high usability (only five electrodes are required), and therefore, has great potential to further develop an EEG-based computer-aided diagnosis system that can be applied for the early detection of MCI.

ML-Based Identification of Structured Light Schemes under Free Space Jamming Threats for Secure FSO-Based Applications

This paper exploits for the first time the use of machine learning (ML) based techniques to identify complex structured light patterns under free space optics (FSO) jamming attacks for secure FSO-based applications. Five M-ary modulation schemes, construed using Laguerre and Hermite Gaussian (LG and HG) mode families, were used in this investigation. These include 8-ary LG, 8-ary superposition-LG, 16-ary HG, 16-ary LG and superposition-LG, and 32-ary LG and superposition-LG and HG formats. The work was conducted using experimental demonstrations for two different jammer positions. The convolutional neural network (CNN)-based ML method was utilized to differentiate between the stressed mode patterns. The experimental results show a 100% recognition accuracy for 8-ary LG, 8-ary superposition-LG, and 16-ary HG at 1, −2, and −2 dB signal-to-jammer ratios (SJR), respectively. For SJR values < 0 dB, the standard LG modes are the most affected by jamming and are not recommended for data transmission in such an environment. Besides, the accuracy of determining the jammer direction of arrival was investigated using CNN and a simpler classifier based on linear discriminant analysis (LDA). The results show that advanced networks (e.g., CNN) are required to achieve reliable performance of 100% direction determination accuracy, at −5 dB SJR, as opposed to 97%, at 2 dB SJR, for a simple LDA classifier.

An Intelligent Arabic Sign Language Recognition System Using a Pair of LMCs With GMM Based Classification

In this paper, we propose a dual leap motion controllers (LMC)-based Arabic sign language recognition system. More specifically, we introduce the concept of using both front and side LMCs to cater for the challenges of finger occlusions and missing data. For feature extraction, an optimum set of geometric features is selected from both controllers, while for classification, we used both a Bayesian approach with a Gaussian mixture model (GMM) and a simple linear discriminant analysis (LDA) approach. To combine the information from the two LMCs, we introduce an evidence-based fusion approach; namely, the Dempster–Shafer (DS) theory of evidence. Data were collected from two native adult signers, for 100 isolated Arabic dynamic signs. Ten observations were collected for each of the signs. The proposed framework uses an intelligent strategy to handle the case of missing data from one or both controllers. A recognition accuracy of about 92% was achieved. The proposed system outperforms state-of-the-art glove-based systems and single-sensor-based techniques.

Plant leaf tooth feature extraction.

Leaf tooth can indicate several systematically informative features and is extremely useful for circumscribing fossil leaf taxa. Moreover, it can help discriminate species or even higher taxa accurately. Previous studies extract features that are not strictly defined in botany; therefore, a uniform standard to compare the accuracies of various feature extraction methods cannot be used. For efficient and automatic retrieval of plant leaves from a leaf database, in this study, we propose an image-based description and measurement of leaf teeth by referring to the leaf structure classification system in botany. First, image preprocessing is carried out to obtain a binary map of plant leaves. Then, corner detection based on the curvature scale-space (CSS) algorithm is used to extract the inflection point from the edges; next, the leaf tooth apex is extracted by screening the convex points; then, according to the definition of the leaf structure, the characteristics of the leaf teeth are described and measured in terms of number of orders of teeth, tooth spacing, number of teeth, sinus shape, and tooth shape. In this manner, data extracted from the algorithm can not only be used to classify plants, but also provide scientific and standardized data to understand the history of plant evolution. Finally, to verify the effectiveness of the extraction method, we used simple linear discriminant analysis and multiclass support vector machine to classify leaves. The results show that the proposed method achieves high accuracy that is superior to that of other methods.

Incremental Linear Discriminant Analysis: A Fast Algorithm and Comparisons.

It has always been a challenging task to develop a fast and an efficient incremental linear discriminant analysis (ILDA) algorithm. For this purpose, we conduct a new study for linear discriminant analysis (LDA) in this paper and develop a new ILDA algorithm. We propose a new batch LDA algorithm called LDA/QR. LDA/QR is a simple and fast LDA algorithm, which is obtained by computing the economic QR factorization of the data matrix followed by solving a lower triangular linear system. The relationship between LDA/QR and uncorrelated LDA (ULDA) is also revealed. Based on LDA/QR, we develop a new incremental LDA algorithm called ILDA/QR. The main features of our ILDA/QR include that: 1) it can easily handle the update from one new sample or a chunk of new samples; 2) it has efficient computational complexity and space complexity; and 3) it is very fast and always achieves competitive classification accuracy compared with ULDA algorithm and existing ILDA algorithms. Numerical experiments based on some real-world data sets demonstrate that our ILDA/QR is very efficient and competitive with the state-of-the-art ILDA algorithms in terms of classification accuracy, computational complexity, and space complexity.

A Climatological Baseline for Assessing the Skill of Tropical Cyclone Phase Forecasts

Abstract A simple linear discriminant analysis scheme using climatological predictors is derived for the Atlantic basin as a no-skill baseline for operational phase forecasts from the National Hurricane Center (NHC). The model with independent data correctly classifies 80% of the cases at 12 h, and this value decreases to about 45% by 60 h, remaining steady thereafter. Using the same cases, NHC-issued phase predictions were more frequently accurate than the baseline, so their forecasts are said to have skill.

Methodological approach from the Best Overall Team in the sbv IMPROVER Diagnostic Signature Challenge

The sbv IMPROVER Diagnostic Signature Challenge used crowdsourcing to identify the best methods to classify clinical samples using transcriptomics data. Participating teams used public microarray data sets to develop prediction models in four disease areas, and then made predictions on blinded test data generated by the organizers. Here we describe the approach of the team for the Perinatology Research Branch (Team PRB; AL Tarca, R Romero), that was awarded the best performing entrant prize out of 54 entrants. The key elements of our approach included: (1) selection of training data sets by trial and error; (2) removal of batch effects by pre-processing the test and training data together; (3) the use of statistical significance and magnitude of change to select biomarkers; and (4) optimization of the number of biomarkers via the cross-validated performance of a simple linear discriminant analysis (LDA) model. Not only were our resulting models ranked consistently high, but they also generated parsimoniou...

Linear Discriminant Analysis Based on L1-Norm Maximization

Linear discriminant analysis (LDA) is a well-known dimensionality reduction technique, which is widely used for many purposes. However, conventional LDA is sensitive to outliers because its objective function is based on the distance criterion using L2-norm. This paper proposes a simple but effective robust LDA version based on L1-norm maximization, which learns a set of local optimal projection vectors by maximizing the ratio of the L1-norm-based between-class dispersion and the L1-norm-based within-class dispersion. The proposed method is theoretically proved to be feasible and robust to outliers while overcoming the singular problem of the within-class scatter matrix for conventional LDA. Experiments on artificial datasets, standard classification datasets and three popular image databases demonstrate the efficacy of the proposed method.

Automating Digital Leaf Measurement: The Tooth, the Whole Tooth, and Nothing but the Tooth

Many species of plants produce leaves with distinct teeth around their margins. The presence and nature of these teeth can often help botanists to identify species. Moreover, it has long been known that more species native to colder regions have teeth than species native to warmer regions. It has therefore been suggested that fossilized remains of leaves can be used as a proxy for ancient climate reconstruction. Similar studies on living plants can help our understanding of the relationships. The required analysis of leaves typically involves considerable manual effort, which in practice limits the number of leaves that are analyzed, potentially reducing the power of the results. In this work, we describe a novel algorithm to automate the marginal tooth analysis of leaves found in digital images. We demonstrate our methods on a large set of images of whole herbarium specimens collected from Tilia trees (also known as lime, linden or basswood). We chose the genus Tilia as its constituent species have toothed leaves of varied size and shape. In a previous study we extracted leaves automatically from a set of images. Our new algorithm locates teeth on the margins of such leaves and extracts features such as each tooth’s area, perimeter and internal angles, as well as counting them. We evaluate an implementation of our algorithm’s performance against a manually analyzed subset of the images. We found that the algorithm achieves an accuracy of 85% for counting teeth and 75% for estimating tooth area. We also demonstrate that the automatically extracted features are sufficient to identify different species of Tilia using a simple linear discriminant analysis, and that the features relating to teeth are the most useful.

A hybrid system for distortion classification and image quality evaluation

Numerous Image Quality Measures (IQMs) have been proposed in the literature with different degrees of success. While some IQMs are more efficient for particular artifacts, they are inefficient for others. The researchers in this field agree that there is no universal IQM which can efficiently estimate image quality across all degradations. In this paper, we overcome this limitation by proposing a new approach based on a degradation classification scheme allowing the selection of the “most appropriate” IQM for each type of degradation. To achieve this, each degradation type is considered here as a particular class and the problem is then formulated as a pattern recognition task. The classification of different degradations is performed using simple Linear Discriminant Analysis (LDA). The proposed system is developed to cover a very large set of possible degradations commonly found in practical applications. The proposed method is evaluated in terms of recognition accuracy of degradation type and overall image quality assessment with excellent results compared to traditional approaches. An improvement of around 15% (in terms of correlation with subjective measures) is achieved across different databases.

LIBP-Pred: web server for lipid binding proteins using structural network parameters; PDB mining of human cancer biomarkers and drug targets in parasites and bacteria

Lipid-Binding Proteins (LIBPs) or Fatty Acid-Binding Proteins (FABPs) play an important role in many diseases such as different types of cancer, kidney injury, atherosclerosis, diabetes, intestinal ischemia and parasitic infections. Thus, the computational methods that can predict LIBPs based on 3D structure parameters became a goal of major importance for drug-target discovery, vaccine design and biomarker selection. In addition, the Protein Data Bank (PDB) contains 3000+ protein 3D structures with unknown function. This list, as well as new experimental outcomes in proteomics research, is a very interesting source to discover relevant proteins, including LIBPs. However, to the best of our knowledge, there are no general models to predict new LIBPs based on 3D structures. We developed new Quantitative Structure-Activity Relationship (QSAR) models based on 3D electrostatic parameters of 1801 different proteins, including 801 LIBPs. We calculated these electrostatic parameters with the MARCH-INSIDE software and they correspond to the entire protein or to specific protein regions named core, inner, middle, and surface. We used these parameters as inputs to develop a simple Linear Discriminant Analysis (LDA) classifier to discriminate 3D structure of LIBPs from other proteins. We implemented this predictor in the web server named LIBP-Pred, freely available at , along with other important web servers of the Bio-AIMS portal. The users can carry out an automatic retrieval of protein structures from PDB or upload their custom protein structural models from their disk created with LOMETS server. We demonstrated the PDB mining option performing a predictive study of 2000+ proteins with unknown function. Interesting results regarding the discovery of new Cancer Biomarkers in humans or drug targets in parasites have been discussed here in this sense.

Identification of important image features for pork and turkey ham classification using colour and wavelet texture features and genetic selection

A method to discriminate between various grades of pork and turkey ham was developed using colour and wavelet texture features. Image analysis methods originally developed for predicting the palatability of beef were applied to rapidly identify the ham grade. With high quality digital images of 50-94 slices per ham it was possible to identify the greyscale that best expressed the differences between the various ham grades. The best 10 discriminating image features were then found with a genetic algorithm. Using the best 10 image features, simple linear discriminant analysis models produced 100% correct classifications for both pork and turkey on both calibration and validation sets.

Extensions of simple component analysis and simple linear discriminant analysis using genetic algorithms

Extensions of Simple Component Analysis are proposed. Two methods are obtained: a new Simple Component Analysis and a Simple Linear Discriminant Analysis. These two methodologies use Genetic Algorithms, optimize a criterion (derived from the usual method) and add constraints. The objective is to obtain loadings constituted of a small number of integers determining blocks of variables. The programs implementing the methods have been developed using the R © language. Four applications are made and show a good robustness of the algorithms and a proximity to the optimal solution (from the usual PCA and LDA).

Study of the feasibility of distinguishing cigarettes of different brands using an Adaboost algorithm and near-infrared spectroscopy

The feasibility of utilizing an Adaboost algorithm in conjuction with near-infrared (NIR) spectroscopy to automatically distinguish cigarettes of different brands was explored. Simple linear discriminant analysis (LDA) was used as the base algorithm to train all weak classifiers in Adaboost. Both principal component analysis (PCA) and its kernel version (kernel principal component analysis, KPCA) were used for feature extraction and were also compared to each other. The influence of the training set size on the final classification model was also investigated. Using a case study, it was demonstrated that Adaboost coupled with PCA or KPCA can obviously improve the ability to discriminate between samples that cannot be separated by a single linear classifier. However, in term of the overall performance, KPCA appears preferable to PCA for feature extraction, especially when the samples used for training are relatively small. The results also indicate that more training samples should be applied, if possible, in order to fully demonstrate the superiority of Adaboost. It seems that the use of an Adaboost algorithm in conjunction with NIR spectroscopy in combination with KPCA for feature extraction comprises a promising tool for distinguishing cigarettes of different brands, especially in situations where there is an obvious overlap between the NIR spectra afforded by cigarettes of different brands.

Dynamic variable selection in SNP genotype autocalling from APEX microarray data

BackgroundSingle nucleotide polymorphisms (SNPs) are DNA sequence variations, occurring when a single nucleotide – adenine (A), thymine (T), cytosine (C) or guanine (G) – is altered. Arguably, SNPs account for more than 90% of human genetic variation. Our laboratory has developed a highly redundant SNP genotyping assay consisting of multiple probes with signals from multiple channels for a single SNP, based on arrayed primer extension (APEX). This mini-sequencing method is a powerful combination of a highly parallel microarray with distinctive Sanger-based dideoxy terminator sequencing chemistry. Using this microarray platform, our current genotype calling system (known as SNP Chart) is capable of calling single SNP genotypes by manual inspection of the APEX data, which is time-consuming and exposed to user subjectivity bias.ResultsUsing a set of 32 Coriell DNA samples plus three negative PCR controls as a training data set, we have developed a fully-automated genotyping algorithm based on simple linear discriminant analysis (LDA) using dynamic variable selection. The algorithm combines separate analyses based on the multiple probe sets to give a final posterior probability for each candidate genotype. We have tested our algorithm on a completely independent data set of 270 DNA samples, with validated genotypes, from patients admitted to the intensive care unit (ICU) of St. Paul's Hospital (plus one negative PCR control sample). Our method achieves a concordance rate of 98.9% with a 99.6% call rate for a set of 96 SNPs. By adjusting the threshold value for the final posterior probability of the called genotype, the call rate reduces to 94.9% with a higher concordance rate of 99.6%. We also reversed the two independent data sets in their training and testing roles, achieving a concordance rate up to 99.8%.ConclusionThe strength of this APEX chemistry-based platform is its unique redundancy having multiple probes for a single SNP. Our model-based genotype calling algorithm captures the redundancy in the system considering all the underlying probe features of a particular SNP, automatically down-weighting any 'bad data' corresponding to image artifacts on the microarray slide or failure of a specific chemistry. In this regard, our method is able to automatically select the probes which work well and reduce the effect of other so-called bad performing probes in a sample-specific manner, for any number of SNPs.