Microarray gene expression data generally suffers from missing value problem due to a variety of experimental reasons. Since the missing data points can adversely affect downstream analysis, many algorithms have been proposed to impute missing values. In this survey, we provide a comprehensive review of existing missing value imputation algorithms, focusing on their underlying algorithmic techniques and how they utilize local or global information from within the data, or their use of domain knowledge during imputation. In addition, we describe how the imputation results can be validated and the different ways to assess the performance of different imputation algorithms, as well as a discussion on some possible future research directions. It is hoped that this review will give the readers a good understanding of the current development in this field and inspire them to come up with the next generation of imputation algorithms.

Background: The DNA microarray technology allows the measurement of expression levels of thousands of genes under tens/hundreds of different conditions. In microarray data, genes with similar functions usually co-express under certain conditions only [1]. Thus, biclustering which clusters genes and conditions simultaneously is preferred over the traditional clustering technique in discovering these coherent genes. Various biclustering algorithms have been developed using different bicluster formulations. Unfortunately, many useful formulations result in NP-complete problems. In this article, we investigate an efficient method for identifying a popular type of biclusters called additive model. Furthermore, parallel coordinate (PC) plots are used for bicluster visualization and analysis. Results: We develop a novel and efficient biclustering algorithm which can be regarded as a greedy version of an existing algorithm known as pCluster algorithm. By relaxing the constraint in homogeneity, the proposed algorithm has polynomial-time complexity in the worst case instead of exponential-time complexity as in the pCluster algorithm. Experiments on artificial datasets verify that our algorithm can identify both additive-related and multiplicative-related biclusters in the presence of overlap and noise. Biologically significant biclusters have been validated on the yeast cell-cycle expression dataset using Gene Ontology annotations. Comparative study shows that the proposed approach outperforms several existing biclustering algorithms. We also provide an interactive exploratory tool based on PC plot visualization for determining the parameters of our biclustering algorithm. Conclusion: We have proposed a novel biclustering algorithm which works with PC plots for an interactive exploratory analysis of gene expression data. Experiments show that the biclustering algorithm is efficient and is capable of detecting co-regulated genes. The interactive analysis enables an optimum parameter determination in the biclustering algorithm so as to achieve the best result. In future, we will modify the proposed algorithm for other bicluster models such as the coherent evolution model.

An image segmentation algorithm based on adaptive fuzzy c-means (FCM) clustering is presented in this paper. In the conventional FCM clustering algorithm, cluster assignment is based solely on the distribution of pixel attributes in the feature space, and does not take into consideration the spatial distribution of pixels in an image. By introducing a novel dissimilarity index in the modified FCM objective function, the new adaptive fuzzy clustering algorithm is capable of utilizing local contextual information to impose local spatial continuity, thus exploiting the high inter-pixel correlation inherent in most real-world images. The incorporation of local spatial continuity allows the suppression of noise and helps to resolve classification ambiguity. To account for smooth intensity variation within each homogenous region in an image, a multiplicative field is introduced to each of the fixed FCM cluster prototype. The multiplicative field effectively makes the fixed cluster prototype adaptive to slow smooth within-cluster intensity variation, and allows homogenous regions with slow smooth intensity variation to be segmented as a whole. Experimental results with synthetic and real color images have shown the effectiveness of the proposed algorithm.

Summary: BiVisu is an open-source software tool for detecting and visualizing biclusters embedded in a gene expression matrix. Through the use of appropriate coherence relations, BiVisu can detect constant, constant-row, constant-column, additive-related as well as multiplicative-related biclusters. The biclustering results are then visualized under a 2D setting for easy inspection. In particular, parallel coordinate (PC) plots for each bicluster are displayed, from which objective and subjective cluster quality evaluation can be performed. Availability: BiVisu has been developed in Matlab and is available at http://www.eie.polyu.edu.hk/~nflaw/Biclustering/ Contact:k.o.cheng@polyu.edu.hk

Source camera identification has long been a hot topic in the field of image forensics. Besides conventional feature engineering algorithms developed based on studying the traces left upon shooting, several deep-learning-based methods have also emerged recently. However, identification performance is susceptible to image content and is far from satisfactory for small image patches in real demanding applications. In this paper, an efficient patch-level source camera identification method is proposed based on a convolutional neural network. First, in order to obtain improved robustness with reduced training cost, representative patches are selected according to multiple criteria for enhanced diversity in training data. Second, a fine-grained multiscale deep residual prediction module is proposed to reduce the impact of scene content. Finally, a modified VGG network is proposed for source camera identification at brand, model, and instance levels. A more critical patch-level evaluation protocol is also proposed for fair performance comparison. Abundant experimental results show that the proposed method achieves better results as compared with the state-of-the-art algorithms.