A Study on Clustering for Clustering Based Image De-Noising

In this paper, the problem of de-noising of an image contaminated with Additive White Gaussian Noise (AWGN) is studied. This subject is an open problem in signal processing for more than 50 years. Local methods suggested in recent years, have obtained better results than global methods. However by more intelligent training in such a way that first, important data is more effective for training, second, clustering in such way that training blocks lie in low-rank subspaces, we can design a dictionary applicable for image de-noising and obtain results near the state of the art local methods. In the present paper, we suggest a method based on global clustering of image constructing blocks. As the type of clustering plays an important role in clustering-based de-noising methods, we address two questions about the clustering. The first, which parts of the data should be considered for clustering? and the second, what data clustering method is suitable for de-noising.? Then clustering is exploited to learn an over complete dictionary. By obtaining sparse decomposition of the noisy image blocks in terms of the dictionary atoms, the de-noised version is achieved. In addition to our framework, 7 popular dictionary learning methods are simulated and compared. The results are compared based on two major factors: (1) de-noising performance and (2) execution time. Experimental results show that our dictionary learning framework outperforms its competitors in terms of both factors.Comment: 9 pages, 8 figures, Journal of Information Systems and Telecommunications (JIST

Bayesian wavelet de-noising with the caravan prior

According to both domain expert knowledge and empirical evidence, wavelet coefficients of real signals tend to exhibit clustering patterns, in that they contain connected regions of coefficients of similar magnitude (large or small). A wavelet de-noising approach that takes into account such a feature of the signal may in practice outperform other, more vanilla methods, both in terms of the estimation error and visual appearance of the estimates. Motivated by this observation, we present a Bayesian approach to wavelet de-noising, where dependencies between neighbouring wavelet coefficients are a priori modelled via a Markov chain-based prior, that we term the caravan prior. Posterior computations in our method are performed via the Gibbs sampler. Using representative synthetic and real data examples, we conduct a detailed comparison of our approach with a benchmark empirical Bayes de-noising method (due to Johnstone and Silverman). We show that the caravan prior fares well and is therefore a useful addition to the wavelet de-noising toolbox.Comment: 32 pages, 15 figures, 4 table

Groundtruthing next-gen sequencing for microbial ecology-biases and errors in community structure estimates from PCR amplicon pyrosequencing

Analysis of microbial communities by high-throughput pyrosequencing of SSU rRNA gene PCR amplicons has transformed microbial ecology research and led to the observation that many communities contain a diverse assortment of rare taxa-a phenomenon termed the Rare Biosphere. Multiple studies have investigated the effect of pyrosequencing read quality on operational taxonomic unit (OTU) richness for contrived communities, yet there is limited information on the fidelity of community structure estimates obtained through this approach. Given that PCR biases are widely recognized, and further unknown biases may arise from the sequencing process itself, a priori assumptions about the neutrality of the data generation process are at best unvalidated. Furthermore, post-sequencing quality control algorithms have not been explicitly evaluated for the accuracy of recovered representative sequences and its impact on downstream analyses, reducing useful discussion on pyrosequencing reads to their diversity and abundances. Here we report on community structures and sequences recovered for in vitro-simulated communities consisting of twenty 16S rRNA gene clones tiered at known proportions. PCR amplicon libraries of the V3-V4 and V6 hypervariable regions from the in vitro-simulated communities were sequenced using the Roche 454 GS FLX Titanium platform. Commonly used quality control protocols resulted in the formation of OTUs with >1% abundance composed entirely of erroneous sequences, while over-aggressive clustering approaches obfuscated real, expected OTUs. The pyrosequencing process itself did not appear to impose significant biases on overall community structure estimates, although the detection limit for rare taxa may be affected by PCR amplicon size and quality control approach employed. Meanwhile, PCR biases associated with the initial amplicon generation may impose greater distortions in the observed community structure

Community Structure Detection in Complex Networks with Partial Background Information

Constrained clustering has been well-studied in the unsupervised learning society. However, how to encode constraints into community structure detection, within complex networks, remains a challenging problem. In this paper, we propose a semi-supervised learning framework for community structure detection. This framework implicitly encodes the must-link and cannot-link constraints by modifying the adjacency matrix of network, which can also be regarded as de-noising the consensus matrix of community structures. Our proposed method gives consideration to both the topology and the functions (background information) of complex network, which enhances the interpretability of the results. The comparisons performed on both the synthetic benchmarks and the real-world networks show that the proposed framework can significantly improve the community detection performance with few constraints, which makes it an attractive methodology in the analysis of complex networks

Wavelet based joint denoising of depth and luminance images

In this paper we present a new method for joint denoising of depth and luminance images produced by time-of-flight camera. Here we assume that the sequence does not contain outlier points which can be present in the depth images. Our method first performs estimation of noise and signal covariance matrices and then performs vector denoising. Two versions of the algorithm are presented, depending on the method used for the classification of the image contexts. Denoising results are compared with the ground truth images obtained by averaging of the multiple frames of the still scene