Real-time and distributed applications for dictionary-based data compression

The greedy approach to dictionary-based static text compression can be executed by a finite state machine. When it is applied in parallel to different blocks of data independently, there is no lack of robustness even on standard large scale distributed systems with input files of arbitrary size. Beyond standard large scale, a negative effect on the compression effectiveness is caused by the very small size of the data blocks. A robust approach for extreme distributed systems is presented in this paper, where this problem is fixed by overlapping adjacent blocks and preprocessing the neighborhoods of the boundaries. Moreover, we introduce the notion of pseudo-prefix dictionary, which allows optimal compression by means of a real-time semi-greedy procedure and a slight improvement on the compression ratio obtained by the distributed implementations

A Compression Technique Exploiting References for Data Synchronization Services

Department of Computer Science and EngineeringIn a variety of network applications, there exists significant amount of shared data between two end hosts. Examples include data synchronization services that replicate data from one node to another. Given that shared data may have high correlation with new data to transmit, we question how such shared data can be best utilized to improve the efficiency of data transmission. To answer this, we develop an encoding technique, SyncCoding, that effectively replaces bit sequences of the data to be transmitted with the pointers to their matching bit sequences in the shared data so called references. By doing so, SyncCoding can reduce data traffic, speed up data transmission, and save energy consumption for transmission. Our evaluations of SyncCoding implemented in Linux show that it outperforms existing popular encoding techniques, Brotli, LZMA, Deflate, and Deduplication. The gains of SyncCoding over those techniques in the perspective of data size after compression in a cloud storage scenario are about 12.4%, 20.1%, 29.9%, and 61.2%, and are about 78.3%, 79.6%, 86.1%, and 92.9% in a web browsing scenario, respectively.ope

Large-scale compression of genomic sequence databases with the Burrows-Wheeler transform

Motivation The Burrows-Wheeler transform (BWT) is the foundation of many algorithms for compression and indexing of text data, but the cost of computing the BWT of very large string collections has prevented these techniques from being widely applied to the large sets of sequences often encountered as the outcome of DNA sequencing experiments. In previous work, we presented a novel algorithm that allows the BWT of human genome scale data to be computed on very moderate hardware, thus enabling us to investigate the BWT as a tool for the compression of such datasets. Results We first used simulated reads to explore the relationship between the level of compression and the error rate, the length of the reads and the level of sampling of the underlying genome and compare choices of second-stage compression algorithm. We demonstrate that compression may be greatly improved by a particular reordering of the sequences in the collection and give a novel `implicit sorting' strategy that enables these benefits to be realised without the overhead of sorting the reads. With these techniques, a 45x coverage of real human genome sequence data compresses losslessly to under 0.5 bits per base, allowing the 135.3Gbp of sequence to fit into only 8.2Gbytes of space (trimming a small proportion of low-quality bases from the reads improves the compression still further). This is more than 4 times smaller than the size achieved by a standard BWT-based compressor (bzip2) on the untrimmed reads, but an important further advantage of our approach is that it facilitates the building of compressed full text indexes such as the FM-index on large-scale DNA sequence collections.Comment: Version here is as submitted to Bioinformatics and is same as the previously archived version. This submission registers the fact that the advanced access version is now available at http://bioinformatics.oxfordjournals.org/content/early/2012/05/02/bioinformatics.bts173.abstract . Bioinformatics should be considered as the original place of publication of this article, please cite accordingl

Tight and simple Web graph compression

Analysing Web graphs has applications in determining page ranks, fighting Web spam, detecting communities and mirror sites, and more. This study is however hampered by the necessity of storing a major part of huge graphs in the external memory, which prevents efficient random access to edge (hyperlink) lists. A number of algorithms involving compression techniques have thus been presented, to represent Web graphs succinctly but also providing random access. Those techniques are usually based on differential encodings of the adjacency lists, finding repeating nodes or node regions in the successive lists, more general grammar-based transformations or 2-dimensional representations of the binary matrix of the graph. In this paper we present two Web graph compression algorithms. The first can be seen as engineering of the Boldi and Vigna (2004) method. We extend the notion of similarity between link lists, and use a more compact encoding of residuals. The algorithm works on blocks of varying size (in the number of input lines) and sacrifices access time for better compression ratio, achieving more succinct graph representation than other algorithms reported in the literature. The second algorithm works on blocks of the same size, in the number of input lines, and its key mechanism is merging the block into a single ordered list. This method achieves much more attractive space-time tradeoffs.Comment: 15 page

Adapting End-to-End Speech Recognition for Readable Subtitles

Automatic speech recognition (ASR) systems are primarily evaluated on transcription accuracy. However, in some use cases such as subtitling, verbatim transcription would reduce output readability given limited screen size and reading time. Therefore, this work focuses on ASR with output compression, a task challenging for supervised approaches due to the scarcity of training data. We first investigate a cascaded system, where an unsupervised compression model is used to post-edit the transcribed speech. We then compare several methods of end-to-end speech recognition under output length constraints. The experiments show that with limited data far less than needed for training a model from scratch, we can adapt a Transformer-based ASR model to incorporate both transcription and compression capabilities. Furthermore, the best performance in terms of WER and ROUGE scores is achieved by explicitly modeling the length constraints within the end-to-end ASR system.Comment: IWSLT 202