74980
PLS and SVD based penalized logistic regression for cancer classification using microarray data
Accurate cancer prediction is important for treatment of cancers. The combination of two dimension reduction methods, partial least squares (PLS) and singular value decomposition (SVD), with the penalized logistic regression (PLR) has created powerful classifiers for cancer prediction using microarray data. Comparing with support vector machine (SVM) on seven publicly available cancer datasets, the new algorithms can achieve very good performance and run much faster. They also have the advantage that the probabilities of predictions can be directly given. PLS based PLR is also combined with recursive feature elimination (RFE) to select a 16-gene subset for acute leukemia cancer classification. The testing error on this subset of genes is empirically zero.
45019016
A Simplified Algorithm for Testing Microprocessors
Abstract In this paper, we present a number of algorithms to test the instruction decoding function of microprocessors. The algorithms are based on the knowledge of some timing and control information available to users through microprocessor manuals and data sheets. The tests are functional in nature. We also establish the order of complexity of the algorithms presented in this paper. As an example, the test complexity for a microprocessor is computed and the results are compared with a known algorithm.
7641777
GBNet: Deciphering regulatory rules in the co-regulated genes using a Gibbs sampler enhanced Bayesian network approach
BackgroundCombinatorial regulation of transcription factors (TFs) is important in determining the complex gene expression patterns particularly in higher organisms. Deciphering regulatory rules between cooperative TFs is a critical step towards understanding the mechanisms of combinatorial regulation.ResultsWe present here a Bayesian network approach called GBNet to search for DNA motifs that may be cooperative in transcriptional regulation and the sequence constraints that these motifs may satisfy. We showed that GBNet outperformed the other available methods in the simulated and the yeast data. We also demonstrated the usefulness of GBNet on learning regulatory rules between YY1, a human TF, and its co-factors. Most of the rules learned by GBNet on YY1 and co-factors were supported by literature. In addition, a spacing constraint between YY1 and E2F was also supported by independent TF binding experiments.ConclusionWe thus conclude that GBNet is a useful tool for deciphering the "grammar" of transcriptional regulation.
31019926
A Functional Testing Method for Microprocessors
A method is presented for functional testing of microprocessors. First, a control fault model at the RTL (register transfer language) level is developed. Based on this model, the authors establish testing requirements for control faults. They present two test procedures to verify the write and read sequences, and use the write and read sequences to test each instruction in the microprocessor. By utilizing k-out-of-m codes, they use fewer tests to cover more faults, thereby reducing the test generation time. >
19415028
Unified model in identity subspace for face recognition
Human faces have two important characteristics: (1) They are similar objects and the specific, variations of each face are similar to each other; (2) They are nearly bilateral symmetric. Exploiting the two important properties, we build a unified model in identity subspace (UMIS) as a novel technique for face recognition from only one example image per person. An identity subspace spanned by bilateral symmetric bases, which compactly encodes identity information. is presented. The unified model, trained on an obtained training set with multiple samples per class from a known people groupA, can be generalized well to facial images of unknown individuals, and can be used to recognize facial images from an unknown people groupB with only one sample per subject. Extensive experimental results on two public databases (the Yale database and the Bern database) and our own database (the ICT-JDL database) demonstrate that the UMIS approach is significantly effective and robust for face recognition.
62074016
Dimension Reduction-Based Penalized Logistic Regression for Cancer Classification Using Microarray Data
The use of penalized logistic regression for cancer classification using microarray expression data is presented. Two dimension reduction methods are respectively combined with the penalized logistic regression so that both the classification accuracy and computational speed are enhanced. Two other machine-learning methods, support vector machines and least-squares regression, have been chosen for comparison. It is shown that our methods have achieved at least equal or better results. They also have the advantage that the output probability can be explicitly given and the regression coefficients are easier to interpret. Several other aspects, such as the selection of penalty parameters and components, pertinent to the application of our methods for cancer classification are also discussed.
17743882
Morphometric Analysis of Brain Structures for Improved Discrimination
We perform discriminative analysis of brain structures using morphometric information. Spherical harmonics technique and point distribution model are used for shape description. Classification is performed using linear discriminants and support vector machines with several feature selection approaches. We consider both inclusion and exclusion of volume information in the discrimination. We perform extensive experimental studies by applying different combinations of techniques to hippocampal data in schizophrenia and achieve best jackknife classification accuracies of 95% (whole set) and 90% (right-handed males), respectively. Our results find that the left hippocampus is a better predictor than the right in the complete dataset, but that the right hippocampus is a stronger predictor than the left in the right-handed male subset. We also propose a new method for visualization of discriminative patterns.
6802677
A surface-based approach for classification of 3D neuroanatomic structures
We present a new framework for 3D surface object classification that combines a powerful shape description method with suitable pattern classification techniques. Spherical harmonic parameterization and normalization techniques are used to describe a surface shape and derive a dual high dimensional landmark representation. A point distribution model is applied to reduce the dimensionality. Fisher's linear discriminants and support vector machines are used for classification. Several feature selection schemes are proposed for learning better classifiers. After showing the effectiveness of this framework using simulated shape data, we apply it to real hippocampal data in schizophrenia and perform extensive experimental studies by examining different combinations of techniques. We achieve best leave-one-out cross-validation accuracies of 93% (whole set, N = 56) and 90% (right-handed males, N = 39), respectively, which are competitive with the best results in previous studies using different techniques on similar types of data. Furthermore, to help medical diagnosis in practice, we employ a threshold-free receiver operating characteristic (ROC) approach as an alternative evaluation of classification results as well as propose a new method for visualizing discriminative patterns.
14935665
Optimal Matrix Computing Using Vector Division with Sub-word Parallel
Available computing is expected to be effective and efficient in ubiquitous multimedia services. And, matrix multiplication is particular to ubiquitous computing such as image transformation so that it is urgent to exploit potential parallelism as well as data reuse in matrix multiplication. Therefore, based on synchronized data triggered architecture (SDTA), we propose a method of parallel vector division (PVD) as well as sub-word parallel (SWP) supported on SDTA to optimize the matrix computation on specified architecture. Experimental results show that PVD with SWP is suitable for matrix multiplication on SDTA instruction set architecture. Besides, we could extend the proposed model into other data-intensive computing on SDTA.
29817800
Mining Flexible Multiple-Level Association Rules in All Concept Hierarchies (Extended Abstract)
We introduce the problem of mining FML (flexible multiple-level) association rules in all concept hierarchies related to a set of user-interested database attributes, as interesting association rules among data items may occur at multiple levels of multiple relevant concept hierarchies. We present a complete classification of all FML rules and show that direct application of previous research can find only a small part of strong FML rules. We propose an efficient method to generate all strong FML rules in all concept hierarchies.
635773
Surface Alignment of 3D Spherical Harmonic Models: Application to Cardiac MRI Analysis
The spherical harmonic (SPHARM) description is a powerful surface modeling technique that can model arbitrarily shaped but simply connected 3D objects and has been used in many applications in medical imaging. Previous SPHARM techniques use the first order ellipsoid for establishing surface correspondence and aligning objects. However, this first order information may not be sufficient in many cases; a more general method for establishing surface correspondence would be to minimize the mean squared distance between two corresponding surfaces. In this paper, a new surface matching algorithm is proposed for 3D SPHARM models to achieve this goal. This algorithm employs a useful rotational property of spherical harmonic basis functions for a fast implementation. Applications of medical image analysis (e.g., spatio-temporal modeling of heart shape changes) are used to demonstrate this approach. Theoretical proofs and experimental results show that our approach is an accurate and flexible surface correspondence alignment method.