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

Rank, select and access in grammar-compressed strings

Given a string $S$ of length $N$ on a fixed alphabet of $\sigma$ symbols, a grammar compressor produces a context-free grammar $G$ of size $n$ that generates $S$ and only $S$. In this paper we describe data structures to support the following operations on a grammar-compressed string: \mbox{rank}_c(S,i) (return the number of occurrences of symbol $c$ before position $i$ in $S$); \mbox{select}_c(S,i) (return the position of the $i$th occurrence of $c$ in $S$); and \mbox{access}(S,i,j) (return substring $S[i,j]$). For rank and select we describe data structures of size $O(n\sigma\log N)$ bits that support the two operations in $O(\log N)$ time. We propose another structure that uses $O(n\sigma\log (N/n)(\log N)^{1+\epsilon})$ bits and that supports the two queries in $O(\log N/\log\log N)$, where $\epsilon>0$ is an arbitrary constant. To our knowledge, we are the first to study the asymptotic complexity of rank and select in the grammar-compressed setting, and we provide a hardness result showing that significantly improving the bounds we achieve would imply a major breakthrough on a hard graph-theoretical problem. Our main result for access is a method that requires $O(n\log N)$ bits of space and $O(\log N+m/\log_\sigma N)$ time to extract $m=j-i+1$ consecutive symbols from $S$. Alternatively, we can achieve $O(\log N/\log\log N+m/\log_\sigma N)$ query time using $O(n\log (N/n)(\log N)^{1+\epsilon})$ bits of space. This matches a lower bound stated by Verbin and Yu for strings where $N$ is polynomially related to $n$.Comment: 16 page

Compressed indexing data structures for biological sequences

Ph.DDOCTOR OF PHILOSOPH

Indexes and Computation over Compressed Structured Data (Dagstuhl Seminar 13232)

This report documents the program and the outcomes of Dagstuhl Seminar 13232 "Indexes and Computation over Compressed Structured Data"

Parallel Construction of Wavelet Trees on Multicore Architectures

The wavelet tree has become a very useful data structure to efficiently represent and query large volumes of data in many different domains, from bioinformatics to geographic information systems. One problem with wavelet trees is their construction time. In this paper, we introduce two algorithms that reduce the time complexity of a wavelet tree's construction by taking advantage of nowadays ubiquitous multicore machines. Our first algorithm constructs all the levels of the wavelet in parallel in $O(n)$ time and $O(n\lg\sigma + \sigma\lg n)$ bits of working space, where $n$ is the size of the input sequence and $\sigma$ is the size of the alphabet. Our second algorithm constructs the wavelet tree in a domain-decomposition fashion, using our first algorithm in each segment, reaching $O(\lg n)$ time and $O(n\lg\sigma + p\sigma\lg n/\lg\sigma)$ bits of extra space, where $p$ is the number of available cores. Both algorithms are practical and report good speedup for large real datasets.Comment: This research has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sk{\l}odowska-Curie Actions H2020-MSCA-RISE-2015 BIRDS GA No. 69094