Publications
A deep learning-based velocity dealiasing algorithm derived from the WSR-88D open radar product generator
July 1, 2023
Journal Article
Published in:
Artificial Intelligence for the Earth Systems, Vol. 2, Issue 3, July 2023.
Summary
Radial velocity estimates provided by Doppler weather radar are critical measurements used by operational forecasters for the detection and monitoring of life-impacting storms. The sampling methods used to produce these measurements are inherently susceptible to aliasing, which produces ambiguous velocity values in regions with high winds and needs to be corrected using a velocity dealiasing algorithm (VDA). In the United States, the Weather Surveillance Radar-1988 Doppler (WSR-88D) Open Radar Product Generator (ORPG) is a processing environment that provides a world-class VDA; however, this algorithm is complex and can be difficult to port to other radar systems outside the WSR-88D network. In this work, a deep neural network (DNN) is used to emulate the two-dimensional WSR-88D ORPG dealiasing algorithm. It is shown that a DNN, specifically a customized U-Net, is highly effective for building VDAs that are accurate, fast, and portable to multiple radar types. To train the DNN model, a large dataset is generated containing aligned samples of folded and dealiased velocity pairs. This dataset contains samples collected from WSR-88D Level-II and Level-III archives and uses the ORPG dealiasing algorithm output as a source of truth. Using this dataset, a U-Net is trained to produce the number of folds at each point of a velocity image. Several performance metrics are presented using WSR-88D data. The algorithm is also applied to other non-WSR-88D radar systems to demonstrate portability to other hardware/software interfaces. A discussion of the broad applicability of this method is presented, including how other Level-III algorithms may benefit from this approach.
Summary
Radial velocity estimates provided by Doppler weather radar are critical measurements used by operational forecasters for the detection and monitoring of life-impacting storms. The sampling methods used to produce these measurements are inherently susceptible to aliasing, which produces ambiguous velocity values in regions with high winds and needs to be...
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Detecting pathogen exposure during the non-symptomatic incubation period using physiological data: proof of concept in non-human primates
September 3, 2021
Journal Article
Published in:
Front Physiol., Vol. 12, September 2021, Article 691074.
Summary
Background and Objectives: Early warning of bacterial and viral infection, prior to the development of overt clinical symptoms, allows not only for improved patient care and outcomes but also enables faster implementation of public health measures (patient isolation and contact tracing). Our primary objectives in this effort are 3-fold. First, we seek to determine the upper limits of early warning detection through physiological measurements. Second, we investigate whether the detected physiological response is specific to the pathogen. Third, we explore the feasibility of extending early warning detection with wearable devices. Research Methods: For the first objective, we developed a supervised random forest algorithm to detect pathogen exposure in the asymptomatic period prior to overt symptoms (fever). We used high-resolution physiological telemetry data (aortic blood pressure, intrathoracic pressure, electrocardiograms, and core temperature) from non-human primate animal models exposed to two viral pathogens: Ebola and Marburg (N = 20). Second, to determine reusability across different pathogens, we evaluated our algorithm against three independent physiological datasets from non-human primate models (N = 13) exposed to three different pathogens: Lassa and Nipah viruses and Y. pestis. For the third objective, we evaluated performance degradation when the algorithm was restricted to features derived from electrocardiogram (ECG) waveforms to emulate data from a non-invasive wearable device. Results: First, our cross-validated random forest classifier provides a mean early warning of 51 ± 12 h, with an area under the receiver-operating characteristic curve (AUC) of 0.93 ± 0.01. Second, our algorithm achieved comparable performance when applied to datasets from different pathogen exposures – a mean early warning of 51 ± 14 h and AUC of 0.95 ± 0.01. Last, with a degraded feature set derived solely from ECG, we observed minimal degradation – a mean early warning of 46 ± 14 h and AUC of 0.91 ± 0.001. Conclusion: Under controlled experimental conditions, physiological measurements can provide over 2 days of early warning with high AUC. Deviations in physiological signals following exposure to a pathogen are due to the underlying host’s immunological response and are not specific to the pathogen. Pre-symptomatic detection is strong even when features are limited to ECG-derivatives, suggesting that this approach may translate to non-invasive wearable devices.
Summary
Background and Objectives: Early warning of bacterial and viral infection, prior to the development of overt clinical symptoms, allows not only for improved patient care and outcomes but also enables faster implementation of public health measures (patient isolation and contact tracing). Our primary objectives in this effort are 3-fold. First...
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GraphChallenge.org triangle counting performance [e-print]
September 22, 2020
Conference Paper
Published in:
2020 IEEE High Performance Computing Conf., HPEC, 22-24 September 2020.
Summary
The rise of graph analytic systems has created a need for new ways to measure and compare the capabilities of graph processing systems. The MIT/Amazon/IEEE Graph Challenge has been developed to provide a well-defined community venue for stimulating research and highlighting innovations in graph analysis software, hardware, algorithms, and systems. GraphChallenge.org provides a wide range of preparsed graph data sets, graph generators, mathematically defined graph algorithms, example serial implementations in a variety of languages, and specific metrics for measuring performance. The triangle counting component of GraphChallenge.org tests the performance of graph processing systems to count all the triangles in a graph and exercises key graph operations found in many graph algorithms. In 2017, 2018, and 2019 many triangle counting submissions were received from a wide range of authors and organizations. This paper presents a performance analysis of the best performers of these submissions. These submissions show that their state-of-the-art triangle counting execution time, Ttri, is a strong function of the number of edges in the graph, Ne, which improved significantly from 2017 (Ttri \approx (Ne/10^8)^4=3) to 2018 (Ttri \approx Ne/10^9) and remained comparable from 2018 to 2019. Graph Challenge provides a clear picture of current graph analysis systems and underscores the need for new innovations to achieve high performance on very large graphs
Summary
The rise of graph analytic systems has created a need for new ways to measure and compare the capabilities of graph processing systems. The MIT/Amazon/IEEE Graph Challenge has been developed to provide a well-defined community venue for stimulating research and highlighting innovations in graph analysis software, hardware, algorithms, and systems...
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GraphChallenge.org sparse deep neural network performance [e-print]
September 22, 2020
Conference Paper
Published in:
2020 IEEE High Performance Computing Conf., HPEC, 22-24 September 2020.
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Summary
The MIT/IEEE/Amazon GraphChallenge.org encourages community approaches to developing new solutions for analyzing graphs and sparse data. Sparse AI analytics present unique scalability difficulties. The Sparse Deep Neural Network (DNN) Challenge draws upon prior challenges from machine learning, high performance computing, and visual analytics to create a challenge that is reflective of emerging sparse AI systems. The sparse DNN challenge is based on a mathematically well-defined DNN inference computation and can be implemented in any programming environment. In 2019 several sparse DNN challenge submissions were received from a wide range of authors and organizations. This paper presents a performance analysis of the best performers of these submissions. These submissions show that their state-of-the-art sparse DNN execution time, TDNN, is a strong function of the number of DNN operations performed, Nop. The sparse DNN challenge provides a clear picture of current sparse DNN systems and underscores the need for new innovations to achieve high performance on very large sparse DNNs.
Summary
The MIT/IEEE/Amazon GraphChallenge.org encourages community approaches to developing new solutions for analyzing graphs and sparse data. Sparse AI analytics present unique scalability difficulties. The Sparse Deep Neural Network (DNN) Challenge draws upon prior challenges from machine learning, high performance computing, and visual analytics to create a challenge that is reflective...
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75,000,000,000 streaming inserts/second using hierarchical hypersparse GraphBLAS matrices
May 18, 2020
Conference Paper
Published in:
2020 IEEE Intl. Parallel and Distributed Processing Symp. Workshops, IPDPSW, 18-22 May 2020.
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Summary
The SuiteSparse GraphBLAS C-library implements high performance hypersparse matrices with bindings to a variety of languages (Python, Julia, and Matlab/Octave). GraphBLAS provides a lightweight in-memory database implementation of hypersparse matrices that are ideal for analyzing many types of network data, while providing rigorous mathematical guarantees, such as linearity. Streaming updates of hypersparse matrices put enormous pressure on the memory hierarchy. This work benchmarks an implementation of hierarchical hypersparse matrices that reduces memory pressure and dramatically increases the update rate into a hypersparse matrices. The parameters of hierarchical hypersparse matrices rely on controlling the number of entries in each level in the hierarchy before an update is cascaded. The parameters are easily tunable to achieve optimal performance for a variety of applications. Hierarchical hypersparse matrices achieve over 1,000,000 updates per second in a single instance. Scaling to 31,000 instances of hierarchical hypersparse matrices arrays on 1,100 server nodes on the MIT SuperCloud achieved a sustained update rate of 75,000,000,000 updates per second. This capability allows the MIT SuperCloud to analyze extremely large streaming network data sets.
Summary
The SuiteSparse GraphBLAS C-library implements high performance hypersparse matrices with bindings to a variety of languages (Python, Julia, and Matlab/Octave). GraphBLAS provides a lightweight in-memory database implementation of hypersparse matrices that are ideal for analyzing many types of network data, while providing rigorous mathematical guarantees, such as linearity. Streaming updates...
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AI data wrangling with associative arrays [e-print]
January 18, 2020
Abstract
Published in:
Submitted to Northeast Database Day, NEDB 2020, https://arxiv.org/abs/2001.06731
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Summary
The AI revolution is data driven. AI "data wrangling" is the process by which unusable data is transformed to support AI algorithm development (training) and deployment (inference). Significant time is devoted to translating diverse data representations supporting the many query and analysis steps found in an AI pipeline. Rigorous mathematical representations of these data enables data translation and analysis optimization within and across steps. Associative array algebra provides a mathematical foundation that naturally describes the tabular structures and set mathematics that are the basis of databases. Likewise, the matrix operations and corresponding inference/training calculations used by neural networks are also well described by associative arrays. More surprisingly, a general denormalized form of hierarchical formats, such as XML and JSON, can be readily constructed. Finally, pivot tables, which are among the most widely used data analysis tools, naturally emerge from associative array constructors. A common foundation in associative arrays provides interoperability guarantees, proving that their operations are linear systems with rigorous mathematical properties, such as, associativity, commutativity, and distributivity that are critical to reordering optimizations.
Summary
The AI revolution is data driven. AI "data wrangling" is the process by which unusable data is transformed to support AI algorithm development (training) and deployment (inference). Significant time is devoted to translating diverse data representations supporting the many query and analysis steps found in an AI pipeline. Rigorous mathematical...
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Cultivating professional technical skills and understanding through hands-on online learning experiences
October 23, 2019
Conference Paper
Published in:
2019 IEEE Learning with MOOCS, LWMOOCS, 23-25 October 2019.
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Summary
Life-long learning is necessary for all professions because the technologies, tools and skills required for success over the course of a career expand and change. Professionals in science, technology, engineering and mathematics (STEM) fields face particular challenges as new multi-disciplinary methods, e.g. Machine Learning and Artificial Intelligence, mature to replace those learned in undergraduate or graduate programs. Traditionally, industry, professional societies and university programs have provided professional development. While these provide opportunities to develop deeper understanding in STEM specialties and stay current with new techniques, the constraints on formal classes and workshops preclude the possibility of Just-In-Time Mastery Learning, particularly for new domains. The MIT Lincoln Laboratory Supercomputing Center (LLSC) and MIT Supercloud teams have developed online course offerings specifically designed to provide a way for adult learners to build their own educational path based on their immediate needs, problems and schedules. To satisfy adult learners, the courses are formulated as a series of challenges and strategies. Using this perspective, the courses incorporate targeted theory supported by hands-on practice. The focus of this paper is the design of Mastery, Just-in-Time MOOC courses that address the full space of hands-on learning requirements, from digital to analog. The discussion centers on the design of project-based exercises for professional technical education courses. The case studies highlight examples from courses that incorporate practice ranging from the construction of a small radar used for real world data collection and processing to the development of high performance computing applications.
Summary
Life-long learning is necessary for all professions because the technologies, tools and skills required for success over the course of a career expand and change. Professionals in science, technology, engineering and mathematics (STEM) fields face particular challenges as new multi-disciplinary methods, e.g. Machine Learning and Artificial Intelligence, mature to replace...
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Sparse Deep Neural Network graph challenge
September 24, 2019
Conference Paper
Published in:
IEEE High Performance Extreme Computing Conf., HPEC, 24-26 September 2019.
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Summary
The MIT/IEEE/Amazon GraphChallenge.org encourages community approaches to developing new solutions for analyzing graphs and sparse data. Sparse AI analytics present unique scalability difficulties. The proposed Sparse Deep Neural Network (DNN) Challenge draws upon prior challenges from machine learning, high performance computing, and visual analytics to create a challenge that is reflective of emerging sparse AI systems. The Sparse DNN Challenge is based on a mathematically well-defined DNN inference computation and can be implemented in any programming environment. Sparse DNN inference is amenable to both vertex-centric implementations and array-based implementations (e.g., using the GraphBLAS.org standard). The computations are simple enough that performance predictions can be made based on simple computing hardware models. The input data sets are derived from the MNIST handwritten letters. The surrounding I/O and verification provide the context for each sparse DNN inference that allows rigorous definition of both the input and the output. Furthermore, since the proposed sparse DNN challenge is scalable in both problem size and hardware, it can be used to measure and quantitatively compare a wide range of present day and future systems. Reference implementations have been implemented and their serial and parallel performance have been measured. Specifications, data, and software are publicly available at GraphChallenge.org.
Summary
The MIT/IEEE/Amazon GraphChallenge.org encourages community approaches to developing new solutions for analyzing graphs and sparse data. Sparse AI analytics present unique scalability difficulties. The proposed Sparse Deep Neural Network (DNN) Challenge draws upon prior challenges from machine learning, high performance computing, and visual analytics to create a challenge that is...
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Optimizing the visualization pipeline of a 3-D monitoring and management system
September 24, 2019
Conference Paper
Published in:
2019 IEEE High Performance Computing Conf., HPEC, 24-26 September 2019.
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Summary
Monitoring and managing High Performance Computing (HPC) systems and environments generate an ever growing amount of data. Making sense of this data and generating a platform where the data can be visualized for system administrators and management to proactively identify system failures or understand the state of the system requires the platform to be as efficient and scalable as the underlying database tools used to store and analyze the data. In this paper we will show how we leverage Accumulo, d4m, and Unity to generate a 3-D visualization platform to monitor and manage the Lincoln Laboratory Supercomputer systems and how we have had to retool our approach to scale with our systems.
Summary
Monitoring and managing High Performance Computing (HPC) systems and environments generate an ever growing amount of data. Making sense of this data and generating a platform where the data can be visualized for system administrators and management to proactively identify system failures or understand the state of the system requires...
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Streaming 1.9 billion hyperspace network updates per second with D4M
September 24, 2019
Conference Paper
Published in:
2019 IEEE High Performance Computing Conf., HPEC, 24-26 September 2019.
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Summary
The Dynamic Distributed Dimensional Data Model (D4M) library implements associative arrays in a variety of languages (Python, Julia, and Matlab/Octave) and provides a lightweight in-memory database implementation of hypersparse arrays that are ideal for analyzing many types of network data. D4M relies on associative arrays which combine properties of spreadsheets, databases, matrices, graphs, and networks, while providing rigorous mathematical guarantees, such as linearity. Streaming updates of D4M associative arrays put enormous pressure on the memory hierarchy. This work describes the design and performance optimization of an implementation of hierarchical associative arrays that reduces memory pressure and dramatically increases the update rate into an associative array. The parameters of hierarchical associative arrays rely on controlling the number of entries in each level in the hierarchy before an update is cascaded. The parameters are easily tunable to achieve optimal performance for a variety of applications. Hierarchical arrays achieve over 40,000 updates per second in a single instance. Scaling to 34,000 instances of hierarchical D4M associative arrays on 1,100 server nodes on the MIT SuperCloud achieved a sustained update rate of 1,900,000,000 updates per second. This capability allows the MIT SuperCloud to analyze extremely large streaming network data sets.
Summary
The Dynamic Distributed Dimensional Data Model (D4M) library implements associative arrays in a variety of languages (Python, Julia, and Matlab/Octave) and provides a lightweight in-memory database implementation of hypersparse arrays that are ideal for analyzing many types of network data. D4M relies on associative arrays which combine properties of spreadsheets...
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