Comparing temporal behavior of fast objective video quality measures on a large-scale database

In many application scenarios, video quality assessment is required to be fast and reasonably accurate. The characterisation of objective algorithms by subjective assessment is well established but limited due to the small number of test samples. Verification using large-scale objectively annotated databases provides a complementary solution. In this contribution, three simple but fast measures are compared regarding their agreement on a large-scale database. In contrast to subjective experiments, not only sequence-wise but also framewise agreement can be analyzed. Insight is gained into the behavior of the measures with respect to 5952 different coding configurations of High Efficiency Video Coding (HEVC). Consistency within a video sequence is analyzed as well as across video sequences. The results show that the occurrence of discrepancies depends mostly on the configured coding structure and the source content. The detailed observations stimulate questions on the combined usage of several video quality measures for encoder optimization

Full Reference Objective Quality Assessment for Reconstructed Background Images

With an increased interest in applications that require a clean background image, such as video surveillance, object tracking, street view imaging and location-based services on web-based maps, multiple algorithms have been developed to reconstruct a background image from cluttered scenes. Traditionally, statistical measures and existing image quality techniques have been applied for evaluating the quality of the reconstructed background images. Though these quality assessment methods have been widely used in the past, their performance in evaluating the perceived quality of the reconstructed background image has not been verified. In this work, we discuss the shortcomings in existing metrics and propose a full reference Reconstructed Background image Quality Index (RBQI) that combines color and structural information at multiple scales using a probability summation model to predict the perceived quality in the reconstructed background image given a reference image. To compare the performance of the proposed quality index with existing image quality assessment measures, we construct two different datasets consisting of reconstructed background images and corresponding subjective scores. The quality assessment measures are evaluated by correlating their objective scores with human subjective ratings. The correlation results show that the proposed RBQI outperforms all the existing approaches. Additionally, the constructed datasets and the corresponding subjective scores provide a benchmark to evaluate the performance of future metrics that are developed to evaluate the perceived quality of reconstructed background images.Comment: Associated source code: https://github.com/ashrotre/RBQI, Associated Database: https://drive.google.com/drive/folders/1bg8YRPIBcxpKIF9BIPisULPBPcA5x-Bk?usp=sharing (Email for permissions at: ashrotreasuedu

Structural RNA Homology Search and Alignment Using Covariance Models

Functional RNA elements do not encode proteins, but rather function directly as RNAs. Many different types of RNAs play important roles in a wide range of cellular processes, including protein synthesis, gene regulation, protein transport, splicing, and more. Because important sequence and structural features tend to be evolutionarily conserved, one way to learn about functional RNAs is through comparative sequence analysis - by collecting and aligning examples of homologous RNAs and comparing them. Covariance models: CMs) are powerful computational tools for homology search and alignment that score both the conserved sequence and secondary structure of an RNA family. However, due to the high computational complexity of their search and alignment algorithms, searches against large databases and alignment of large RNAs like small subunit ribosomal RNA: SSU rRNA) are prohibitively slow. Large-scale alignment of SSU rRNA is of particular utility for environmental survey studies of microbial diversity which often use the rRNA as a phylogenetic marker of microorganisms. In this work, we improve CM methods by making them faster and more sensitive to remote homology. To accelerate searches, we introduce a query-dependent banding: QDB) technique that makes scoring sequences more efficient by restricting the possible lengths of structural elements based on their probability given the model. We combine QDB with a complementary filtering method that quickly prunes away database subsequences deemed unlikely to receive high CM scores based on sequence conservation alone. To increase search sensitivity, we apply two model parameterization strategies from protein homology search tools to CMs. As judged by our benchmark, these combined approaches yield about a 250-fold speedup and significant increase in search sensitivity compared with previous implementations. To accelerate alignment, we apply a method that uses a fast sequence-based alignment of a target sequence to determine constraints for the more expensive CM sequence- and structure-based alignment. This technique reduces the time required to align one SSU rRNA sequence from about 15 minutes to 1 second with a negligible effect on alignment accuracy. Collectively, these improvements make CMs more powerful and practical tools for RNA homology search and alignment

The Parallelism Motifs of Genomic Data Analysis

Genomic data sets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share this data with the research community, but some of these genomic data analysis problems require large scale computational platforms to meet both the memory and computational requirements. These applications differ from scientific simulations that dominate the workload on high end parallel systems today and place different requirements on programming support, software libraries, and parallel architectural design. For example, they involve irregular communication patterns such as asynchronous updates to shared data structures. We consider several problems in high performance genomics analysis, including alignment, profiling, clustering, and assembly for both single genomes and metagenomes. We identify some of the common computational patterns or motifs that help inform parallelization strategies and compare our motifs to some of the established lists, arguing that at least two key patterns, sorting and hashing, are missing

Likelihood-based inference of B-cell clonal families

The human immune system depends on a highly diverse collection of antibody-making B cells. B cell receptor sequence diversity is generated by a random recombination process called "rearrangement" forming progenitor B cells, then a Darwinian process of lineage diversification and selection called "affinity maturation." The resulting receptors can be sequenced in high throughput for research and diagnostics. Such a collection of sequences contains a mixture of various lineages, each of which may be quite numerous, or may consist of only a single member. As a step to understanding the process and result of this diversification, one may wish to reconstruct lineage membership, i.e. to cluster sampled sequences according to which came from the same rearrangement events. We call this clustering problem "clonal family inference." In this paper we describe and validate a likelihood-based framework for clonal family inference based on a multi-hidden Markov Model (multi-HMM) framework for B cell receptor sequences. We describe an agglomerative algorithm to find a maximum likelihood clustering, two approximate algorithms with various trade-offs of speed versus accuracy, and a third, fast algorithm for finding specific lineages. We show that under simulation these algorithms greatly improve upon existing clonal family inference methods, and that they also give significantly different clusters than previous methods when applied to two real data sets