Training-free Measures Based on Algorithmic Probability Identify High Nucleosome Occupancy in DNA Sequences

We introduce and study a set of training-free methods of information-theoretic and algorithmic complexity nature applied to DNA sequences to identify their potential capabilities to determine nucleosomal binding sites. We test our measures on well-studied genomic sequences of different sizes drawn from different sources. The measures reveal the known in vivo versus in vitro predictive discrepancies and uncover their potential to pinpoint (high) nucleosome occupancy. We explore different possible signals within and beyond the nucleosome length and find that complexity indices are informative of nucleosome occupancy. We compare against the gold standard (Kaplan model) and find similar and complementary results with the main difference that our sequence complexity approach. For example, for high occupancy, complexity-based scores outperform the Kaplan model for predicting binding representing a significant advancement in predicting the highest nucleosome occupancy following a training-free approach.Comment: 8 pages main text (4 figures), 12 total with Supplementary (1 figure

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

Reconfigurable-Hardware Accelerated Stream Aggregation

High throughput and low latency stream aggregation is essential for many applications that analyze massive volumes of data in real-time. Incoming data need to be stored in a single sliding-window before processing, in cases where incremental aggregations are wasteful or not possible at all. However, storing all incoming values in a single-window puts tremendous pressure on the memory bandwidth and capacity. GPU and CPU memory management is inefficient for this task as it introduces unnecessary data movement that wastes bandwidth. FPGAs can make more efficient use of their memory but existing approaches employ only on-chip memory and therefore, can only support small problem sizes (i.e. small sliding windows and number of keys) due to the limited capacity. This thesis addresses the above limitations of stream processing systems by proposing techniques for accelerating single sliding-window stream aggregation using FPGAs to achieve line-rate processing throughput and ultra low latency. It does so first by building accelerators using FPGAs and second, by alleviating the memory pressure posed by single-window stream aggregation. The initial part of this thesis presents the accelerators for both windowing policies, namely, tuple- and time-\ua0based, using Maxeler\u27s DataFlow Engines\ua0(DFEs) which have a direct feed of incoming data from the network as well as direct access to off-chip DRAM. Compared to state-of-the-art stream processing software system, the DFEs offer 1-2 orders of magnitude higher processing throughput and 4 orders of magnitude lower latency. The later part of this thesis focuses on alleviating the memory pressure due to the various steps in single-window stream aggregation. Updating the window with new incoming values and reading it to feed the aggregation functions are the two primary steps in stream aggregation. The high on-chip SRAM bandwidth enables line-rate processing, but only for small problem sizes due to the limited capacity. The larger off-chip DRAM size supports larger problems, but falls short on performance due to lower bandwidth. In order to bridge this gap, this thesis introduces a specialized memory hierarchy for stream aggregation. It employs Multi-Level Queues (MLQs) spanning across multiple memory levels with different characteristics to offer both high bandwidth and capacity. In doing so, larger stream aggregation problems can be supported at line-rate performance, outperforming existing competing solutions. Compared to designs with only on-chip memory, our approach supports 4 orders of magnitude larger problems. Compared to designs that use only DRAM, our design achieves up to 8x higher throughput. Finally, this thesis aims to alleviate the memory pressure due to the window-aggregation step. Although window-updates can be supported efficiently using MLQs, frequent window-aggregations remain a performance bottleneck. This thesis addresses this problem by introducing StreamZip, a dataflow stream aggregation engine that is able to compress the sliding-windows. StreamZip deals with a number of data and control dependency challenges to integrate a compressor in the stream aggregation pipeline and alleviate the memory pressure posed by frequent aggregations. In doing so, StreamZip offers higher throughput as well as larger effective window capacity to support larger problems. StreamZip supports diverse compression algorithms offering both lossless and lossy compression to fixed- as well as floating- point numbers. Compared to designs using MLQs, StreamZip lossless and lossy designs achieve up to 7.5x and 22x higher throughput, while improving the effective memory capacity by up to 5x and 23x, respectively