Shyh Wei Teng

PTP1B regulates Eph receptor function and trafficking

Changes in protein tyrosine phosphatase 1B expression affect duration and amplitude of EphA3 phosphorylation and cell surface concentration.

Differential prioritization between relevance and redundancy in correlation-based feature selection techniques for multiclass gene expression data

BackgroundDue to the large number of genes in a typical microarray dataset, feature selection looks set to play an important role in reducing noise and computational cost in gene expression-based tissue classification while improving accuracy at the same time. Surprisingly, this does not appear to be the case for all multiclass microarray datasets. The reason is that many feature selection techniques applied on microarray datasets are either rank-based and hence do not take into account correlations between genes, or are wrapper-based, which require high computational cost, and often yield difficult-to-reproduce results. In studies where correlations between genes are considered, attempts to establish the merit of the proposed techniques are hampered by evaluation procedures which are less than meticulous, resulting in overly optimistic estimates of accuracy.ResultsWe present two realistically evaluated correlation-based feature selection techniques which incorporate, in addition to the two existing criteria involved in forming a predictor set (relevance and redundancy), a third criterion called the degree of differential prioritization (DDP). DDP functions as a parameter to strike the balance between relevance and redundancy, providing our techniques with the novel ability to differentially prioritize the optimization of relevance against redundancy (and vice versa). This ability proves useful in producing optimal classification accuracy while using reasonably small predictor set sizes for nine well-known multiclass microarray datasets.ConclusionFor multiclass microarray datasets, especially the GCM and NCI60 datasets, DDP enables our filter-based techniques to produce accuracies better than those reported in previous studies which employed similarly realistic evaluation procedures.

Image indexing and retrieval based on vector quantization

To effectively utilize information stored in a digital image library, effective image indexing and retrieval techniques are essential. This paper proposes an image indexing and retrieval technique based on the compressed image data using vector quantization (VQ). By harnessing the characteristics of VQ, the proposed technique is able to capture the spatial relationships of pixels when indexing the image. Experimental results illustrate the robustness of the proposed technique and also show that its retrieval performance is higher compared with existing color-based techniques.

Differential prioritization in feature selection and classifier aggregation for multiclass microarray datasets

The high dimensionality of microarray datasets endows the task of multiclass tissue classification with various difficulties—the main challenge being the selection of features deemed relevant and non-redundant to form the predictor set for classifier training. The necessity of varying the emphases on relevance and redundancy, through the use of the degree of differential prioritization (DDP) during the search for the predictor set is also of no small importance. Furthermore, there are several types of decomposition technique for the feature selection (FS) problem—all-classes-at-once, one-vs.-all (OVA) or pairwise (PW). Also, in multiclass problems, there is the need to consider the type of classifier aggregation used—whether non-aggregated (a single machine), or aggregated (OVA or PW). From here, first we propose a systematic approach to combining the distinct problems of FS and classification. Then, using eight well-known multiclass microarray datasets, we empirically demonstrate the effectiveness of the DDP in various combinations of FS decomposition types and classifier aggregation methods. Aided by the variable DDP, feature selection leads to classification performance which is better than that of rank-based or equal-priorities scoring methods and accuracies higher than previously reported for benchmark datasets with large number of classes. Finally, based on several criteria, we make general recommendations on the optimal choice of the combination of FS decomposition type and classifier aggregation method for multiclass microarray datasets.

Improved Symmetric-SIFT for Multi-modal Image Registration

Multi-modal image registration has received significant research attention over the past decade. Symmetric-SIFT is a recently proposed local description technique that can be used for registering multi-modal images. It is based on a well-known general image registration technique named Scale Invariant Feature Transform (SIFT). Symmetric-SIFT, however, achieves this invariance to multi-modality at the cost of losing important information. In this paper, we show how this loss may adversely affect the accuracy of registration results. We then propose an improvement to Symmetric-SIFT to overcome the problem. Our experimental results show that the proposed technique can improve the number of true matches by up to 10 times and overall matching accuracy by up to 30%.

Texture classification using multimodal Invariant Local Binary Pattern

As texture information among pixels can be effectively represented using Local binary patterns (LBPs), image descriptors built using LBPs or its variants have been frequently used for various image analysis applications, e.g. medical image and texture image classification and retrieval. However, neither LBP nor any of its existing variants can be used to build descriptors for classifying multimodal images effectively. This is because the same object when captured in different modalities may result in opposite pixel intensity in some corresponding parts of the images, which in turn will cause their descriptors to be very different. To solve this problem, we propose a novel modality invariant texture descriptor which is built by modifying the standard procedure for building LBP. In this paper, we explain how the proposed descriptor can be built efficiently. We also demonstrate empirically that compared to all the state of the art LBP-based descriptors, the proposed descriptor achieves better accuracy for classifying multimodal images.

Relevance, redundancy and differential prioritization in feature selection for multiclass gene expression data

The large number of genes in microarray data makes feature selection techniques more crucial than ever. From various ranking-based filter procedures to classifier-based wrapper techniques, many studies have devised their own flavor of feature selection techniques. Only a handful of the studies delved into the effect of redundancy in the predictor set on classification accuracy, and even fewer on the effect of varying the importance between relevance and redundancy. We present a filter-based feature selection technique which incorporates the three elements of relevance, redundancy and differential prioritization. With the aid of differential prioritization, our feature selection technique is capable of achieving better accuracies than those of previous studies, while using fewer genes in the predictor set. At the same time, the pitfalls of over-optimistic estimates of accuracy are avoided through the use of a more realistic evaluation procedure than the internal leave-one-out-cross-validation.

Achieving High Multi-Modal Registration Performance Using Simplified Hough-Transform with Improved Symmetric-SIFT

The traditional way of using Hough Transform with SIFT is for the purpose of reliable object recognition. However, it cannot be effectively applied to image registration in the same way as the recall rate can be significantly lower. In this paper, we propose an alternative implementation of Hough Transform that can be used with Improved Symmetric-SIFT for multi-modal image registration. Our experimental results show that the proposed technique of applying Hough Transform can significantly improve the key-point matching as well as registration accuracy by utilizing aggregated information from key-points throughout the input images.

An Enhancement to SIFT-Based Techniques for Image Registration

Symmetric-SIFT is a recently proposed local technique used for registering multimodal images. It is based on a well-known general image registration technique named Scale Invariant Feature Transform (SIFT). Symmetric SIFT makes use of the gradient magnitude information at the image’s key regions to build the descriptors. In this paper, we highlight an issue with how the magnitude information is used in this process. This issue may result in similar descriptors being built to represent regions in images that are visually different. To address this issue, we have proposed two new strategies for weighting the descriptors. Our experimental results show that Symmetric-SIFT descriptors built using our proposed strategies can lead to better registration accuracy than descriptors built using the original Symmetric-SIFT technique. The issue highlighted and the two strategies proposed are also applicable to the general SIFT technique.

Characteristics of predictor sets found using differential prioritization

BackgroundFeature selection plays an undeniably important role in classification problems involving high dimensional datasets such as microarray datasets. For filter-based feature selection, two well-known criteria used in forming predictor sets are relevance and redundancy. However, there is a third criterion which is at least as important as the other two in affecting the efficacy of the resulting predictor sets. This criterion is the degree of differential prioritization (DDP), which varies the emphases on relevance and redundancy depending on the value of the DDP. Previous empirical works on publicly available microarray datasets have confirmed the effectiveness of the DDP in molecular classification. We now propose to establish the fundamental strengths and merits of the DDP-based feature selection technique. This is to be done through a simulation study which involves vigorous analyses of the characteristics of predictor sets found using different values of the DDP from toy datasets designed to mimic real-life microarray datasets.ResultsA simulation study employing analytical measures such as the distance between classes before and after transformation using principal component analysis is implemented on toy datasets. From these analyses, the necessity of adjusting the differential prioritization based on the dataset of interest is established. This conclusion is supported by comparisons against both simplistic rank-based selection and state-of-the-art equal-priorities scoring methods, which demonstrates the superiority of the DDP-based feature selection technique. Reapplying similar analyses to real-life multiclass microarray datasets provides further confirmation of our findings and of the significance of the DDP for practical applications.ConclusionThe findings have been achieved based on analytical evaluations, not empirical evaluation involving classifiers, thus providing further basis for the usefulness of the DDP and validating the need for unequal priorities on relevance and redundancy during feature selection for microarray datasets, especially highly multiclass datasets.