Read alignment using deep neural networks

2019 Spring.Includes bibliographical references.Read alignment is the process of mapping short DNA sequences into the reference genome. With the advent of consecutively evolving "next generation" sequencing technologies, the need for sequence alignment tools appeared. Many scientific communities and the companies marketing the sequencing technologies developed a whole spectrum of read aligners/mappers for different error profiles and read length characteristics. Among the most recent successfully marketed sequencing technologies are Oxford Nanopore and PacBio SMRT sequencing, which are considered top players because of their extremely long reads and low cost. However, the reads may contain error up to 20% that are not generally uniformly distributed. To deal with that level of error rate and read length, proximity preserving hashing techniques, such as Minhash and Minimizers, were utilized to quickly map a read to the target region of the reference sequence. Subsequently, a variant of global or local alignment dynamic programming is then used to give the final alignment. In this research work, we train a Deep Neural Network (DNN) to yield a hashing scheme for the highly erroneous long reads, which is deemed superior to Minhash for mapping the reads. We implemented that idea to build a read alignment tool: DNNAligner. We evaluated the performance of our aligner against the popular read aligners in the bioinformatics community currently — minimap2, bwa-mem and graphmap. Our results show that the performance of DNNAligner is comparable to other tools without any code optimization or integration of other advanced features. Moreover, DNN exhibits superior performance in comparison with Minhashon neighborhood classification

Structural Graph-based Metamodel Matching

Data integration has been, and still is, a challenge for applications processing multiple heterogeneous data sources. Across the domains of schemas, ontologies, and metamodels, this imposes the need for mapping specifications, i.e. the task of discovering semantic correspondences between elements. Support for the development of such mappings has been researched, producing matching systems that automatically propose mapping suggestions. However, especially in the context of metamodel matching the result quality of state of the art matching techniques leaves room for improvement. Although the traditional approach of pair-wise element comparison works on smaller data sets, its quadratic complexity leads to poor runtime and memory performance and eventually to the inability to match, when applied on real-world data. The work presented in this thesis seeks to address these shortcomings. Thereby, we take advantage of the graph structure of metamodels. Consequently, we derive a planar graph edit distance as metamodel similarity metric and mining-based matching to make use of redundant information. We also propose a planar graph-based partitioning to cope with large-scale matching. These techniques are then evaluated using real-world mappings from SAP business integration scenarios and the MDA community. The results demonstrate improvement in quality and managed runtime and memory consumption for large-scale metamodel matching

Multiple Media Correlation: Theory and Applications

This thesis introduces multiple media correlation, a new technology for the automatic alignment of multiple media objects such as text, audio, and video. This research began with the question: what can be learned when multiple multimedia components are analyzed simultaneously? Most ongoing research in computational multimedia has focused on queries, indexing, and retrieval within a single media type. Video is compressed and searched independently of audio, text is indexed without regard to temporal relationships it may have to other media data. Multiple media correlation provides a framework for locating and exploiting correlations between multiple, potentially heterogeneous, media streams. The goal is computed synchronization, the determination of temporal and spatial alignments that optimize a correlation function and indicate commonality and synchronization between media objects. The model also provides a basis for comparison of media in unrelated domains. There are many real-world applications for this technology, including speaker localization, musical score alignment, and degraded media realignment. Two applications, text-to-speech alignment and parallel text alignment, are described in detail with experimental validation. Text-to-speech alignment computes the alignment between a textual transcript and speech-based audio. The presented solutions are effective for a wide variety of content and are useful not only for retrieval of content, but in support of automatic captioning of movies and video. Parallel text alignment provides a tool for the comparison of alternative translations of the same document that is particularly useful to the classics scholar interested in comparing translation techniques or styles. The results presented in this thesis include (a) new media models more useful in analysis applications, (b) a theoretical model for multiple media correlation, (c) two practical application solutions that have wide-spread applicability, and (d) Xtrieve, a multimedia database retrieval system that demonstrates this new technology and demonstrates application of multiple media correlation to information retrieval. This thesis demonstrates that computed alignment of media objects is practical and can provide immediate solutions to many information retrieval and content presentation problems. It also introduces a new area for research in media data analysis