Expression cartography of human tissues using self organizing maps

Background: The availability of parallel, high-throughput microarray and sequencing experiments poses a challenge how to best arrange and to analyze the obtained heap of multidimensional data in a concerted way. Self organizing maps (SOM), a machine learning method, enables the parallel sample- and gene-centered view on the data combined with strong visualization and second-level analysis capabilities. The paper addresses aspects of the method with practical impact in the context of expression analysis of complex data sets.
Results: The method was applied to generate a SOM characterizing the whole genome expression profiles of 67 healthy human tissues selected from ten tissue categories (adipose, endocrine, homeostasis, digestion, exocrine, epithelium, sexual reproduction, muscle, immune system and nervous tissues). SOM mapping reduces the dimension of expression data from ten thousands of genes to a few thousands of metagenes where each metagene acts as representative of a minicluster of co-regulated single genes. Tissue-specific and common properties shared between groups of tissues emerge as a handful of localized spots in the tissue maps collecting groups of co-regulated and co-expressed metagenes. The functional context of the spots was discovered using overrepresentation analysis with respect to pre-defined gene sets of known functional impact. We found that tissue related spots typically contain enriched populations of gene sets well corresponding to molecular processes in the respective tissues. Analysis techniques normally used at the gene-level such as two-way hierarchical clustering provide a better signal-to-noise ratio and a better representativeness of the method if applied to the metagenes. Metagene-based clustering analyses aggregate the tissues into essentially three clusters containing nervous, immune system and the remaining tissues. 
Conclusions: The global view on the behavior of a few well-defined modules of correlated and differentially expressed genes is more intuitive and more informative than the separate discovery of the expression levels of hundreds or thousands of individual genes. The metagene approach is less sensitive to a priori selection of genes. It can detect a coordinated expression pattern whose components would not pass single-gene significance thresholds and it is able to extract context-dependent patterns of gene expression in complex data sets.
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Quality Adaptive Least Squares Trained Filters for Video Compression Artifacts Removal Using a No-reference Block Visibility Metric

Compression artifacts removal is a challenging problem because videos can be compressed at different qualities. In this paper, a least squares approach that is self-adaptive to the visual quality of the input sequence is proposed. For compression artifacts, the visual quality of an image is measured by a no-reference block visibility metric. According to the blockiness visibility of an input image, an appropriate set of filter coefficients that are trained beforehand is selected for optimally removing coding artifacts and reconstructing object details. The performance of the proposed algorithm is evaluated on a variety of sequences compressed at different qualities in comparison to several other deblocking techniques. The proposed method outperforms the others significantly both objectively and subjectively

Expression cartography of human tissues using self organizing maps

Background: The availability of parallel, high-throughput microarray and sequencing experiments poses a challenge how to best arrange and to analyze the obtained heap of multidimensional data in a concerted way. Self organizing maps (SOM), a machine learning method, enables the parallel sample- and gene-centered view on the data combined with strong visualization and second-level analysis capabilities. The paper addresses aspects of the method with practical impact in the context of expression analysis of complex data sets.
Results: The method was applied to generate a SOM characterizing the whole genome expression profiles of 67 healthy human tissues selected from ten tissue categories (adipose, endocrine, homeostasis, digestion, exocrine, epithelium, sexual reproduction, muscle, immune system and nervous tissues). SOM mapping reduces the dimension of expression data from ten thousands of genes to a few thousands of metagenes where each metagene acts as representative of a minicluster of co-regulated single genes. Tissue-specific and common properties shared between groups of tissues emerge as a handful of localized spots in the tissue maps collecting groups of co-regulated and co-expressed metagenes. The functional context of the spots was discovered using overrepresentation analysis with respect to pre-defined gene sets of known functional impact. We found that tissue related spots typically contain enriched populations of gene sets well corresponding to molecular processes in the respective tissues. Analysis techniques normally used at the gene-level such as two-way hierarchical clustering provide a better signal-to-noise ratio and a better representativeness of the method if applied to the metagenes. Metagene-based clustering analyses aggregate the tissues into essentially three clusters containing nervous, immune system and the remaining tissues. 
Conclusions: The global view on the behavior of a few well-defined modules of correlated and differentially expressed genes is more intuitive and more informative than the separate discovery of the expression levels of hundreds or thousands of individual genes. The metagene approach is less sensitive to a priori selection of genes. It can detect a coordinated expression pattern whose components would not pass single-gene significance thresholds and it is able to extract context-dependent patterns of gene expression in complex data sets.
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Perceptually-Driven Video Coding with the Daala Video Codec

The Daala project is a royalty-free video codec that attempts to compete with the best patent-encumbered codecs. Part of our strategy is to replace core tools of traditional video codecs with alternative approaches, many of them designed to take perceptual aspects into account, rather than optimizing for simple metrics like PSNR. This paper documents some of our experiences with these tools, which ones worked and which did not. We evaluate which tools are easy to integrate into a more traditional codec design, and show results in the context of the codec being developed by the Alliance for Open Media.Comment: 19 pages, Proceedings of SPIE Workshop on Applications of Digital Image Processing (ADIP), 201

Adapting x264 to asynchronous video telephony for the Deaf

Deaf people want to communicate remotely with sign language. Sign language requires sufficient video quality to be intelligible. Internet-based real-time video tools do not provide that quality. Our approach is to use asynchronous transmission to maintain video quality. Unfortunately, this entails a corresponding increase in latency. To reduce latency as much as possible, we sought to adapt a synchronous video codec to an asynchronous video application. First we compared several video codecs with subjective and objective metrics. This paper describes the process by which we chose x264 and integrated it into a Deaf telephony video application, and experimented to configure x264 optimally for the asynchronous environment.Telkom, Cisco, THRIP, SANPADDepartment of HE and Training approved lis