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A classification paradigm for distributed vertically partitioned data.

In general, pattern classification algorithms assume that all the features are available during the construction of a classifier and its subsequent use. In many practical situations, data are recorded in different servers that are geographically apart, and each server observes features of local interest. The underlying infrastructure and other logistics (such as access control) in many cases do not permit continual synchronization. Each server thus has a partial view of the data in the sense that feature subsets (not necessarily disjoint) are available at each server. In this article, we present a classification algorithm for this distributed vertically partitioned data. We assume that local classifiers can be constructed based on the local partial views of the data available at each server. These local classifiers can be any one of the many standard classifiers (e.g., neural networks, decision tree, k nearest neighbor). Often these local classifiers are constructed to support decision making at each location, and our focus is not on these individual local classifiers. Rather, our focus is constructing a classifier that can use these local classifiers to achieve an error rate that is as close as possible to that of a classifier having access to the entire feature set. We empirically demonstrate the efficacy of the proposed algorithm and also provide theoretical results quantifying the loss that results as compared to the situation where the entire feature set is available to any single classifier.

Abstracting and Indexing↗

Random forest similarity for protein-protein interaction prediction from multiple sources.

One of the most important, but often ignored, parts of any clustering and classification algorithm is the computation of the similarity matrix. This is especially important when integrating high throughput biological data sources because of the high noise rates and the many missing values. In this paper we present a new method to compute such similarities for the task of classifying pairs of proteins as interacting or not. Our method uses direct and indirect information about interaction pairs to constructs a random forest (a collection of decision tress) from a training set. The resulting forest is used to determine the similarity between protein pairs and this similarity is used by a classification algorithm (a modified kNN) to classify protein pairs. Testing the algorithm on yeast data indicates that it is able to improve coverage to 20% of interacting pairs with a false positive rate of 50%. These results compare favorably with all previously suggested methods for this task indicating the importance of robust similarity estimates.

Algorithms↗

[Study of serum proteome biomarkers with relation to the formation of portal vein tumor thrombi in hepatocellular carcinoma patients].

OBJECTIVE: To screen serum proteome biomarkers and establish predictive model with relation to the formation of portal vein tumor thrombi (PVTT) in hepatocellular carcinoma (HCC) patients. METHODS: Serum samples were collected from 135 HCC patients, which were divided, into training set (including 33 HCC patients with PVTT and 62 HCC patients without PVTT) and blind testing set (including 18 HCC patients with PVTT and 22 HCC patients without PVTT). Special serum protein or peptide pattern was determined by SELDI-TOF-MS measurement after treating the sample onto WCX2 protein chip for each case. The obtained data were analyzed by BioMarker Wizard software to screen serum proteome biomarkers with relation to the formation of PVTT, while decision tree classification algorithm and blind validation were determined by Biomarker Patterns Software. RESULTS: Ranging from 1100 to 30 000 at the m/z value, 100 protein features were detected in the serum protein pattern stably. Among them, 6 protein peaks with the m/z value of 3478, 1314, 1744, 1725, 2022 and 3380 were upregulated, 10 proteins peaks with the m/z value of 8901, 9353, 9415, 8773, 2766, 2745, 8697, 7773, 8569 and 1373 were downregulated respectively in the group of HCC with PVTT. The 7 candidate protein peaks with the m/z value of 3478, 2022, 8901, 9415, 8773, 2766 and 2745 were selected to establish predictive model by BPS with a sensitivity of 75.8% (25/33) and specificity of 82.3% (51/62). An accuracy of 87.5% (35/40), sensitivity of 100% (18/18), specificity of 77.3% (17/22), positive predictive value of 78.3% (18/23), and negative predictive value of 100% (17/17) were validated in blind testing set. CONCLUSION: Sixteen candidate proteome biomarkers may be related with the formation of PVTT in HCC patients. Decision tree classification algorithm may have great clinical significance in predicting the formation of PVTT.

Adult↗

Lymphoma discrimination by computerized triple matrix analysis of list mode data from three-color flow cytometric immunophenotypes of bone marrow aspirates.

BACKGROUND: The goal of this study was to evaluate a self-learning algorithm for the computer classification of information extracted from flow cytometric immunophenotype list mode files from high-grade non-Hodgkin's lymphoma (NHL), Hodgkin's disease (HD), and multiple myeloma (MM). Materials and Methods Bone marrow aspirates (BMA) were obtained from untreated NHL (n = 51), HD (n = 9), or MM (n = 13) patients. Bone marrow aspirates were not infiltrated in NHL and HD patients as confirmed by thorough histologic and cytologic investigation; however, MM patients showed an infiltration rate >50% by malignant myeloma cells. Peripheral blood leukocyte (PBL) samples were taken from age-matched healthy volunteers (n = 44) as easily available control material. A second control group of 15 healthy volunteers, from whom BMA and PBL samples were available, allowed us to differentiate whether the observed classification results on malignant samples were due to the malignant process or simply to the inherent differences between BMA and PBL. Bone marrow aspirates and PBL were analyzed by the same immunophenotyping antibody panel (CD45/14/20, CD4/8/3, kappa/CD19/5, lambda/CD19/5). The acquired list mode data files were analyzed and classified by the self-learning triple matrix classification algorithms CLASSIF1 following a priori separation of the data into a learning set and unknown test set. After completion of the learning phase, known patient samples were reclassified and unknown samples prospectively classified by the algorithm. RESULTS: Highly discriminatory information was extracted for the various lymphoma entities. The most discriminating information was encountered in antibody binding, antibody binding ratios, and relative antibody surface density parameters of leukocytes rather than in percentage frequencies of discrete leukocyte subpopulations. Samples from healthy controls were classified as normal in 97.2% of the cases, whereas those of NHL, HD, and MM patients were on average correctly classified in 80. 8% of the cases. CONCLUSIONS: Although no detectable lymphoma cells were present in BMA of NHL and HD patients, the CLASSIF1 classification of the immunophenotypes of morphologically normal cells provided a surprisingly good disease discrimination equal or better than that obtained by examining pathological lymph nodes according to the respective literature. The results are suggestive for a lymphoma-related and disease-specific antigen expression shift on normal hematopoietic bone marrow cells that can be used to discriminate the underlying disease (specificity of unspecific changes), i.e., in this case NHL from HD. Multiple myeloma patients were discriminated by changes on malignant as well as on normal bone marrow cells.

Algorithms↗

Stages of motivational readiness for physical activity: a comparison of different algorithms of classification.

OBJECTIVE: The aim of this study was to compare two approaches to classify individuals into stages of motivational readiness for physical activity and test which one was better explained by attitude and perceived behavioural control, as defined by Ajzen (1991). DESIGN: A survey of 20,430 respondents from a population-based sample. METHODS: The relevant variables were assessed in a self-administered questionnaire. The cluster approach consisted of combining both intention and behaviour in order to determine clusters of individuals; such clusters correspond to different stages of motivational readiness. The stage of change (SC) approach consisted of grouping the same individuals by using the SC variable of the Transtheoretical Model (TTM). RESULTS: The SC and cluster-solution approaches were replicated across four subsamples of the total number of respondents. Attitude and perceived behavioural control were more strongly associated with stage membership derived from four-cluster solution than with stage membership in the five categories assessed by the SC method. CONCLUSION: Stage of motivational readiness for physical activity, and possibly for other health-related behaviours, may usefully be characterized when both recent past behaviour and intention in the near future are simultaneously and explicitly taken into consideration.

Adolescent↗

Oriented 2-cell embeddings of a graph and their symmetry classification: generating algorithms and case study of the möbius-kantor graph.

We discuss a method to derive all symmetry-distinct oriented 2-cell embeddings of a given graph and classify them based on their symmetry. As an example, we apply the algorithm to the highly symmetrical trivalent Möbius-Kantor graph. Considering the derived 2-cell embeddings as carbon networks leads to some interesting negative curvature carbon allotropes.

Journal Article↗

The deviated nose: optimizing results using a simplified classification and algorithmic approach.

The deviated nose presents a particular challenge to the rhinoplasty surgeon because, frequently, both a functional problem (airway obstruction) and an aesthetic problem must be addressed. An approach to the deviated nose is presented that relies on accurate preoperative planning and precise intraoperative execution of corrective measures to return the nasal dorsum to midline, restore dorsal aesthetic lines, and maintain airway patency. The principles of correction include wide exposure through the open approach, release of all deforming forces to the septum, straightening of the septum while maintaining an adequate dorsal and caudal strut, restoring long-term support, reducing the hypertrophied turbinates, and performing controlled stable percutaneous osteotomies. An operative algorithm is described that emphasizes simplicity and reproducibility, and case studies demonstrate the results that can be achieved with this approach.

Adult↗

Approximate Statistical Tests for Comparing Supervised Classification Learning Algorithms.

This article reviews five approximate statistical tests for determining whether one learning algorithm outperforms another on a particular learning task. These tests are compared experimentally to determine their probability of incorrectly detecting a difference when no difference exists (type I error). Two widely used statistical tests are shown to have high probability of type I error in certain situations and should never be used: a test for difference of two proportions and a paired-differences t test based on taking several random train-test splits. A third test, a paired-differences t test based on 10-fold cross-validation, exhibits somewhat elevated probability of type I error. A fourth test, McNemar's test, is shown to have low type I error. The fifth test is a new test, 5 x 2 cv, based on five iterations of twofold cross-validation. Experiments show that this test also has acceptable type I error. The article also measures the power (ability to detect algorithm differences when they do exist) of these tests. The cross-validated t test is the most powerful. The 5 x 2 cv test is shown to be slightly more powerful than McNemar's test. The choice of the best test is determined by the computational cost of running the learning algorithm. For algorithms that can be executed only once, McNemar's test is the only test with acceptable type I error. For algorithms that can be executed 10 times, the 5 x 2 cv test is recommended, because it is slightly more powerful and because it directly measures variation due to the choice of training set.

Journal Article↗

Classification of postoperative cardiac patients: comparative evaluation of four algorithms.

Four classification algorithms based on Bayes' rule for minimum error are compared by evaluating their ability to recognize high- and normal-risk cardio-surgical patients. These algorithms differ in the modelling of the probability density function (pdf) for each class and include: (a) two parametric algorithms based on the assumption of normal pdf; (b) two non-parametric algorithms using Parzen multidimensional approximation of pdf with normal kernels. In each case, classes with both equal and different covariance matrices were considered. A set of 200 patients in the 6 h immediately following cardiac surgery has been used to test the performance of the algorithms. For each patient the three measured variables most effective in representing the difference between the two classes were considered. We found that the two algorithms which explicitly incorporate the information on the different sample covariance between the physiological variables existing in the two classes generally provide better recognition of high- and normal-risk patients. Of these two algorithms the parametric one appears extremely attractive for practical applications, since it exhibits slightly better performance in spite of its great simplicity.

Algorithms↗

Principal components null space analysis for image and video classification.

We present a new classification algorithm, principal component null space analysis (PCNSA), which is designed for classification problems like object recognition where different classes have unequal and nonwhite noise covariance matrices. PCNSA first obtains a principal components subspace (PCA space) for the entire data. In this PCA space, it finds for each class "i," an Mi-dimensional subspace along which the class' intraclass variance is the smallest. We call this subspace an approximate null space (ANS) since the lowest variance is usually "much smaller" than the highest. A query is classified into class "i" if its distance from the class' mean in the class' ANS is a minimum. We derive upper bounds on classification error probability of PCNSA and use these expressions to compare classification performance of PCNSA with that of subspace linear discriminant analysis (SLDA). We propose a practical modification of PCNSA called progressive-PCNSA that also detects "new" (untrained classes). Finally, we provide an experimental comparison of PCNSA and progressive PCNSA with SLDA and PCA and also with other classification algorithms-linear SVMs, kernel PCA, kernel discriminant analysis, and kernel SLDA, for object recognition and face recognition under large pose/expression variation. We also show applications of PCNSA to two classification problems in video--an action retrieval problem and abnormal activity detection.

Algorithms↗

Sensorimotor rhythm-based brain-computer interface (BCI): feature selection by regression improves performance.

People can learn to control electroencephalogram (EEG) features consisting of sensorimotor rhythm amplitudes and can use this control to move a cursor in one or two dimensions to a target on a screen. In the standard one-dimensional application, the cursor moves horizontally from left to right at a fixed rate while vertical cursor movement is continuously controlled by sensorimotor rhythm amplitude. The right edge of the screen is divided among 2-6 targets, and the user's goal is to control vertical cursor movement so that the cursor hits the correct target when it reaches the right edge. Up to the present, vertical cursor movement has been a linear function of amplitude in a specific frequency band [i.e., 8-12 Hz (mu) or 18-26 Hz (beta)] over left and/or right sensorimotor cortex. The present study evaluated the effect of controlling cursor movement with a weighted combination of these amplitudes in which the weights were determined by an regression algorithm on the basis of the user's past performance. Analyses of data obtained from a representative set of trained users indicated that weighted combinations of sensorimotor rhythm amplitudes could support cursor control significantly superior to that provided by a single feature. Inclusion of an interaction term further improved performance. Subsequent online testing of the regression algorithm confirmed the improved performance predicted by the offline analyses. The results demonstrate the substantial value for brain-computer interface applications of simple multivariate linear algorithms. In contrast to many classification algorithms, such linear algorithms can easily incorporate multiple signal features, can readily adapt to changes in the user's control of these features, and can accommodate additional targets without major modifications.

Adult↗

Using 12-lead ECG and synthesized VCG in detection of right ventricular hypertrophy with terminal right conduction delay versus partial right bundle branch block in the pediatric population.

In pediatric electrocardiogram (ECG) analysis, mild right ventricular hypertrophy (RVH) and especially mild RVH with terminal right conduction delay (RVHtcd) are often confused with partial right bundle branch block (PRBBB). This is problematic for computer ECG analysis algorithms and even for most experienced pediatric cardiologists. This study was designed to achieve better classification of mild RVHtcd and PRBBB by combining the 12-lead synthesized vectocardiogram (VCG) transverse plane measurements with scalar ECG measurements. Pediatric ECGs used in the study were recorded with 15 leads and a 500 Hz sampling rate at the Lucile Salter Packard Children's Hospital, Stanford University Medical Center. Out of 4,200 ECGs collected consecutively over a period of 18 months, 447 RVH, 335 RBBB and 589 Normal were interpreted by expert pediatric cardiologists, and were included in the study. Statistical comparison of ECG and VCG measurements were done in stratified ECG sets (412) that have a visually indistinguishable waveform pattern, 117 RVHtcd, 96 PRBBB and 199 normal, showed significant differences in initial and terminal vectors in the transverse plane. The mean angle of the initial vector was anterior (57.2 degrees +/- 41.8) in the normal group, left anterior in the PRBBB group (34.4 degrees +/- 39.5) and in the RVHtcd group (31.9 degrees +/- 41.0) and. The mean angle of the terminal vector was right anterior (158.3 degrees +/- 36.8) in the PRBBB group, rightward (179.7 degrees +/- 29.9) in the RVHtcd group and right posterior (212.6 degrees +/- 37.8) in the normal group. These are clearly applicable features for a classification algorithm. Significantly improved classification results were obtained from a new algorithm using combined ECG and VCG measurements versus an existing algorithm. The limitation of this study stems from the unavailability of a more reliable gold standard. It may be necessary to used body surface potentials obtained with a large number of electrodes to accurately differentiate the study groups.

Adolescent↗

Bayesian automatic relevance determination algorithms for classifying gene expression data.

MOTIVATION: We investigate two new Bayesian classification algorithms incorporating feature selection. These algorithms are applied to the classification of gene expression data derived from cDNA microarrays. RESULTS: We demonstrate the effectiveness of the algorithms on three gene expression datasets for cancer, showing they compare well with alternative kernel-based techniques. By automatically incorporating feature selection, accurate classifiers can be constructed utilizing very few features and with minimal hand-tuning. We argue that the feature selection is meaningful and some of the highlighted genes appear to be medically important.

Algorithms↗

Diagnosis of gastric carcinoma by classification on feature projections.

A new classification algorithm, called benefit maximizing classifier on feature projections (BCFP), is developed and applied to the problem of diagnosis of gastric carcinoma. The domain contains records of patients with known diagnosis through gastroscopy results. Given a training set of such records, the BCFP classifier learns how to differentiate a new case in the domain. BCFP represents a concept in the form of feature projections on each feature dimension separately. Classification in the BCFP algorithm is based on a voting among the individual predictions made on each feature. In the gastric carcinoma domain, a lesion can be an indicator of one of nine different levels of gastric carcinoma, from early to late stages. The benefit of correct classification of early levels is much more than that of late cases. Also, the costs of wrong classifications are not symmetric. In the training phase, the BCFP algorithm learns classification rules that maximize the benefit of classification. In the querying phase, using these rules, the BCFP algorithm tries to make a prediction maximizing the benefit. A genetic algorithm is applied to select the relevant features. The performance of the BCFP algorithm is evaluated in terms of accuracy and running time. The rules induced are verified by experts of the domain.

Adolescent↗

Automated recognition of spontaneous versus voluntary cough.

Cough or cough epochs may be an important and persistent symptom in many respiratory diseases requiring both a continuous and objective observation. The research presented in this paper is aimed at assessing a blind data-based classification between 'spontaneous' and 'voluntary' human cough on individual sound samples. Cough sounds were registered in the free acoustic field on 3 pathological and 9 healthy non-smoking subjects, all aged between 20 and 30. Each sound is represented by the normalized power spectral density (PSD). Different transformations of the cough PSD-vector are chosen as input features to the classification algorithm. An experimental error rate comparison between different neural and fuzzy classification networks is performed. All evaluated algorithms used the Euclidean metric. This resulted in a correct class-discrimination between 'spontaneous' and 'voluntary' cough for 96% of the cough database.

Acoustics↗

Using the EM algorithm to train neural networks: misconceptions and a new algorithm for multiclass classification.

The expectation-maximization (EM) algorithm has been of considerable interest in recent years as the basis for various algorithms in application areas of neural networks such as pattern recognition. However, there exists some misconceptions concerning its application to neural networks. In this paper, we clarify these misconceptions and consider how the EM algorithm can be adopted to train multilayer perceptron (MLP) and mixture of experts (ME) networks in applications to multiclass classification. We identify some situations where the application of the EM algorithm to train MLP networks may be of limited value and discuss some ways of handling the difficulties. For ME networks, it is reported in the literature that networks trained by the EM algorithm using iteratively reweighted least squares (IRLS) algorithm in the inner loop of the M-step, often performed poorly in multiclass classification. However, we found that the convergence of the IRLS algorithm is stable and that the log likelihood is monotonic increasing when a learning rate smaller than one is adopted. Also, we propose the use of an expectation-conditional maximization (ECM) algorithm to train ME networks. Its performance is demonstrated to be superior to the IRLS algorithm on some simulated and real data sets.

Algorithms↗