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- Creators: Arizona State University
Description
Identifying chemical compounds that inhibit bacterial infection has recently gained a considerable amount of attention given the increased number of highly resistant bacteria and the serious health threat it poses around the world. With the development of automated microscopy and image analysis systems, the process of identifying novel therapeutic drugs can generate an immense amount of data - easily reaching terabytes worth of information. Despite increasing the vast amount of data that is currently generated, traditional analytical methods have not increased the overall success rate of identifying active chemical compounds that eventually become novel therapeutic drugs. Moreover, multispectral imaging has become ubiquitous in drug discovery due to its ability to provide valuable information on cellular and sub-cellular processes using florescent reagents. These reagents are often costly and toxic to cells over an extended period of time causing limitations in experimental design. Thus, there is a significant need to develop a more efficient process of identifying active chemical compounds.
This dissertation introduces novel machine learning methods based on parallelized cellomics to analyze interactions between cells, bacteria, and chemical compounds while reducing the use of fluorescent reagents. Machine learning analysis using image-based high-content screening (HCS) data is compartmentalized into three primary components: (1) \textit{Image Analytics}, (2) \textit{Phenotypic Analytics}, and (3) \textit{Compound Analytics}. A novel software analytics tool called the Insights project is also introduced. The Insights project fully incorporates distributed processing, high performance computing, and database management that can rapidly and effectively utilize and store massive amounts of data generated using HCS biological assessments (bioassays). It is ideally suited for parallelized cellomics in high dimensional space.
Results demonstrate that a parallelized cellomics approach increases the quality of a bioassay while vastly decreasing the need for control data. The reduction in control data leads to less fluorescent reagent consumption. Furthermore, a novel proposed method that uses single-cell data points is proven to identify known active chemical compounds with a high degree of accuracy, despite traditional quality control measurements indicating the bioassay to be of poor quality. This, ultimately, decreases the time and resources needed in optimizing bioassays while still accurately identifying active compounds.
This dissertation introduces novel machine learning methods based on parallelized cellomics to analyze interactions between cells, bacteria, and chemical compounds while reducing the use of fluorescent reagents. Machine learning analysis using image-based high-content screening (HCS) data is compartmentalized into three primary components: (1) \textit{Image Analytics}, (2) \textit{Phenotypic Analytics}, and (3) \textit{Compound Analytics}. A novel software analytics tool called the Insights project is also introduced. The Insights project fully incorporates distributed processing, high performance computing, and database management that can rapidly and effectively utilize and store massive amounts of data generated using HCS biological assessments (bioassays). It is ideally suited for parallelized cellomics in high dimensional space.
Results demonstrate that a parallelized cellomics approach increases the quality of a bioassay while vastly decreasing the need for control data. The reduction in control data leads to less fluorescent reagent consumption. Furthermore, a novel proposed method that uses single-cell data points is proven to identify known active chemical compounds with a high degree of accuracy, despite traditional quality control measurements indicating the bioassay to be of poor quality. This, ultimately, decreases the time and resources needed in optimizing bioassays while still accurately identifying active compounds.
ContributorsTrevino, Robert (Author) / Liu, Huan (Thesis advisor) / Lamkin, Thomas J (Committee member) / He, Jingrui (Committee member) / Lee, Joohyung (Committee member) / Arizona State University (Publisher)
Created2016
Description
With the exponential growth in video content over the period of the last few years, analysis of videos is becoming more crucial for many applications such as self-driving cars, healthcare, and traffic management. Most of these video analysis application uses deep learning algorithms such as convolution neural networks (CNN) because of their high accuracy in object detection. Thus enhancing the performance of CNN models become crucial for video analysis. CNN models are computationally-expensive operations and often require high-end graphics processing units (GPUs) for acceleration. However, for real-time applications in an energy-thermal constrained environment such as traffic management, GPUs are less preferred because of their high power consumption, limited energy efficiency. They are challenging to fit in a small place.
To enable real-time video analytics in emerging large scale Internet of things (IoT) applications, the computation must happen at the network edge (near the cameras) in a distributed fashion. Thus, edge computing must be adopted. Recent studies have shown that field-programmable gate arrays (FPGAs) are highly suitable for edge computing due to their architecture adaptiveness, high computational throughput for streaming processing, and high energy efficiency.
This thesis presents a generic OpenCL-defined CNN accelerator architecture optimized for FPGA-based real-time video analytics on edge. The proposed CNN OpenCL kernel adopts a highly pipelined and parallelized 1-D systolic array architecture, which explores both spatial and temporal parallelism for energy efficiency CNN acceleration on FPGAs. The large fan-in and fan-out of computational units to the memory interface are identified as the limiting factor in existing designs that causes scalability issues, and solutions are proposed to resolve the issue with compiler automation. The proposed CNN kernel is highly scalable and parameterized by three architecture parameters, namely pe_num, reuse_fac, and vec_fac, which can be adapted to achieve 100% utilization of the coarse-grained computation resources (e.g., DSP blocks) for a given FPGA. The proposed CNN kernel is generic and can be used to accelerate a wide range of CNN models without recompiling the FPGA kernel hardware. The performance of Alexnet, Resnet-50, Retinanet, and Light-weight Retinanet has been measured by the proposed CNN kernel on Intel Arria 10 GX1150 FPGA. The measurement result shows that the proposed CNN kernel, when mapped with 100% utilization of computation resources, can achieve a latency of 11ms, 84ms, 1614.9ms, and 990.34ms for Alexnet, Resnet-50, Retinanet, and Light-weight Retinanet respectively when the input feature maps and weights are represented using 32-bit floating-point data type.
To enable real-time video analytics in emerging large scale Internet of things (IoT) applications, the computation must happen at the network edge (near the cameras) in a distributed fashion. Thus, edge computing must be adopted. Recent studies have shown that field-programmable gate arrays (FPGAs) are highly suitable for edge computing due to their architecture adaptiveness, high computational throughput for streaming processing, and high energy efficiency.
This thesis presents a generic OpenCL-defined CNN accelerator architecture optimized for FPGA-based real-time video analytics on edge. The proposed CNN OpenCL kernel adopts a highly pipelined and parallelized 1-D systolic array architecture, which explores both spatial and temporal parallelism for energy efficiency CNN acceleration on FPGAs. The large fan-in and fan-out of computational units to the memory interface are identified as the limiting factor in existing designs that causes scalability issues, and solutions are proposed to resolve the issue with compiler automation. The proposed CNN kernel is highly scalable and parameterized by three architecture parameters, namely pe_num, reuse_fac, and vec_fac, which can be adapted to achieve 100% utilization of the coarse-grained computation resources (e.g., DSP blocks) for a given FPGA. The proposed CNN kernel is generic and can be used to accelerate a wide range of CNN models without recompiling the FPGA kernel hardware. The performance of Alexnet, Resnet-50, Retinanet, and Light-weight Retinanet has been measured by the proposed CNN kernel on Intel Arria 10 GX1150 FPGA. The measurement result shows that the proposed CNN kernel, when mapped with 100% utilization of computation resources, can achieve a latency of 11ms, 84ms, 1614.9ms, and 990.34ms for Alexnet, Resnet-50, Retinanet, and Light-weight Retinanet respectively when the input feature maps and weights are represented using 32-bit floating-point data type.
ContributorsDua, Akshay (Author) / Ren, Fengbo (Thesis advisor) / Ogras, Umit Y. (Committee member) / Seo, Jae-Sun (Committee member) / Arizona State University (Publisher)
Created2019