Publications
Axon tracing and centerline detection using topologically-aware 3D U-nets
July 11, 2022
Journal Article
Published in:
2022 44th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), 2022, pp. 238-242
Summary
As advances in microscopy imaging provide an ever clearer window into the human brain, accurate reconstruction of neural connectivity can yield valuable insight into the relationship between brain structure and function. However, human manual tracing is a slow and laborious task, and requires domain expertise. Automated methods are thus needed to enable rapid and accurate analysis at scale. In this paper, we explored deep neural networks for dense axon tracing and incorporated axon topological information into the loss function with a goal to improve the performance on both voxel-based segmentation and axon centerline detection. We evaluated three approaches using a modified 3D U-Net architecture trained on a mouse brain dataset imaged with light sheet microscopy and achieved a 10% increase in axon tracing accuracy over previous methods. Furthermore, the addition of centerline awareness in the loss function outperformed the baseline approach across all metrics, including a boost in Rand Index by 8%.
Summary
As advances in microscopy imaging provide an ever clearer window into the human brain, accurate reconstruction of neural connectivity can yield valuable insight into the relationship between brain structure and function. However, human manual tracing is a slow and laborious task, and requires domain expertise. Automated methods are thus needed...
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Fun as a strategic advantage: applying lessons in engagement from commercial games to military logistics training
July 1, 2022
Journal Article
Published in:
Train., Educ., Learn. Sci., Vol. 59, 2022, p. 180-7.
Topic:
Summary
Digital games offer many elements to augment traditional classroom lectures and reading assignments. They enable players to explore concepts through repeat play in a low-risk environment, and allow players to integrate feedback given during gameplay and evaluate their own performance. Commercial games leverage a number of features to engage players and hold their attention. But do those engagement-improving methods have a place in instructional environments with a captive and motivated audience? Our experience building a logistics supply chain training game for the Marine Corps University suggests that yes; applying lessons in engagement from commercial games can both help improve player experience with the learning environment, and potentially improve learning outcomes.
Summary
Digital games offer many elements to augment traditional classroom lectures and reading assignments. They enable players to explore concepts through repeat play in a low-risk environment, and allow players to integrate feedback given during gameplay and evaluate their own performance. Commercial games leverage a number of features to engage players...
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Geographic source estimation using airborne plant environmental DNA in dust
May 14, 2021
Journal Article
Published in:
Sci. Rep., Vol. 11, No. 1, 10 August 2021, 16238.
Summary
Information obtained from the analysis of dust, particularly biological particles such as pollen, plant parts, and fungal spores, has great utility in forensic geolocation. As an alternative to manual microscopic analysis, we developed a pipeline that utilizes the environmental DNA (eDNA) from plants in dust samples to estimate previous sample location(s). The species of plant-derived eDNA within dust samples were identified using metabarcoding and their geographic distributions were then derived from occurrence records in the USGS Biodiversity in Service of Our Nation (BISON) database. The distributions for all plant species identified in a sample were used to generate a probabilistic estimate of the sample source. With settled dust collected at four U.S. sites over a 15-month period, we demonstrated positive regional geolocation (within 600 km2 of the collection point) with 47.6% (20 of 42) of the samples analyzed. Attribution accuracy and resolution was dependent on the number of plant species identified in a dust sample, which was greatly affected by the season of collection. In dust samples that yielded a minimum of 20 identified plant species, positive regional attribution improved to 66.7% (16 of 24 samples). Using dust samples collected from 31 different U.S. sites, trace plant eDNA provided relevant regional attribution information on provenance in 32.2%. This demonstrated that analysis of plant eDNA in dust can provide an accurate estimate regional provenance within the U.S., and relevant forensic information, for a substantial fraction of samples analyzed.
Summary
Information obtained from the analysis of dust, particularly biological particles such as pollen, plant parts, and fungal spores, has great utility in forensic geolocation. As an alternative to manual microscopic analysis, we developed a pipeline that utilizes the environmental DNA (eDNA) from plants in dust samples to estimate previous sample...
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Automatic detection of influential actors in disinformation networks
January 7, 2021
Journal Article
Published in:
Proc. Natl. Acad. Sci., Vol. 118, No. 4, January 2021, e2011216118.
Summary
The weaponization of digital communications and social media to conduct disinformation campaigns at immense scale, speed, and reach presents new challenges to identify and counter hostile influence operations (IO). This paper presents an end-to-end framework to automate detection of disinformation narratives, networks, and influential actors. The framework integrates natural language processing, machine learning, graph analytics, and a novel network causal inference approach to quantify the impact of individual actors in spreading IO narratives. We demonstrate its capability on real-world hostile IO campaigns with Twitter datasets collected during the 2017 French presidential elections, and known IO accounts disclosed by Twitter. Our system detects IO accounts with 96% precision, 79% recall, and 96% area-under-the-PR-curve, maps out salient network communities, and discovers high-impact accounts that escape the lens of traditional impact statistics based on activity counts and network centrality. Results are corroborated with independent sources of known IO accounts from U.S. Congressional reports, investigative journalism, and IO datasets provided by Twitter.
Summary
The weaponization of digital communications and social media to conduct disinformation campaigns at immense scale, speed, and reach presents new challenges to identify and counter hostile influence operations (IO). This paper presents an end-to-end framework to automate detection of disinformation narratives, networks, and influential actors. The framework integrates natural language...
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Automated posterior interval evaluation for inference in probabilistic programming
October 22, 2020
Conference Paper
Published in:
Intl. Conf. on Probabilistic Programming, PROBPROG, 22 October 2020.
Summary
In probabilistic inference, credible intervals constructed from posterior samples provide ranges of likely values for continuous parameters of interest. Intuitively, an inference procedure is optimal if it produces the most precise posterior intervals that cover the true parameter value with the expected frequency in repeated experiments. We present theories and methods for automating posterior interval evaluation of inference performance in probabilistic programming using two metrics: 1.) truth coverage, and 2.) ratio of the empirical over the ideal interval widths. Demonstrating with inference on popular regression and state-space models, we show how the metrics provide effective comparisons between different inference procedures, and capture the effects of collinearity and model misspecification. Overall, we claim such automated interval evaluation can accelerate the robust design and comparison of probabilistic inference programs by directly diagnosing how accurately and precisely they can estimate parameters of interest.
Summary
In probabilistic inference, credible intervals constructed from posterior samples provide ranges of likely values for continuous parameters of interest. Intuitively, an inference procedure is optimal if it produces the most precise posterior intervals that cover the true parameter value with the expected frequency in repeated experiments. We present theories and...
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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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Leveraging linear algebra to count and enumerate simple subgraphs
September 22, 2020
Conference Paper
Published in:
2020 IEEE High Performance Extreme Computing Conf., HPEC, 22-24 September 2020.
Summary
Even though subgraph counting and subgraph matching are well-known NP-Hard problems, they are foundational building blocks for many scientific and commercial applications. In order to analyze graphs that contain millions to billions of edges, distributed systems can provide computational scalability through search parallelization. One recent approach for exposing graph algorithm parallelization is through a linear algebra formulation and the use of the matrix multiply operation, which conceptually is equivalent to a massively parallel graph traversal. This approach has several benefits, including 1) a mathematically-rigorous foundation, and 2) ability to leverage specialized linear algebra accelerators and high-performance libraries. In this paper, we explore and define a linear algebra methodology for performing exact subgraph counting and matching for 4-vertex subgraphs excluding the clique. Matches on these simple subgraphs can be joined as components for a larger subgraph. With thorough analysis, we demonstrate that the linear algebra formulation leverages path aggregation which allows it to be up 2x to 5x more efficient in traversing the search space and compressing the results as compared to tree-based subgraph matching techniques.
Summary
Even though subgraph counting and subgraph matching are well-known NP-Hard problems, they are foundational building blocks for many scientific and commercial applications. In order to analyze graphs that contain millions to billions of edges, distributed systems can provide computational scalability through search parallelization. One recent approach for exposing graph algorithm...
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Data trust methodology: a blockchain-based approach to instrumenting complex systems
August 5, 2020
Technical Report
Published in:
MIT Lincoln Laboratory Report TR-1256
Summary
Increased data sharing and interoperability has created challenges in maintaining a level of trust and confidence in Department of Defense (DoD) systems. As tightly-coupled, unique, static, and rigorously validated mission processing solutions have been supplemented with newer, more dynamic, and complex counterparts, mission effectiveness has been impacted. On the one hand, newer deeper processing with more diverse data inputs can offer resilience against overconfident decisions under rapidly changing conditions. On the other hand, the multitude of diverse methods for reaching a decision may be in apparent conflict and decrease decision confidence. This has sometimes manifested itself in the presentation of simultaneous, divergent information to high-level decision makers. In some important specific instances, this has caused the operators to be less efficient in determining the best course of action. In this paper, we will describe an approach to more efficiently and effectively leverage new data sources and processing solutions, without requiring redesign of each algorithm or the system itself. We achieve this by instrumenting the processing chains with an enterprise blockchain framework. Once instrumented, we can collect, verify, and validate data processing chains by tracking data provenance using smart contracts to add dynamically calculated metadata to an immutable and distributed ledger. This noninvasive approach to verification and validation in data sharing environments has the power to improve decision confidence at larger scale than manual approaches, such as consulting individual developer subject matter experts to understand system behavior. In this paper, we will present our study of the following: 1. Types of information (i.e., knowledge) that are supplied and leveraged by decision makers and operational contextualized data processes (Figure 1) 2. Benefits to verifying data provenance, integrity, and validity within an operational processing chain 3. Our blockchain technology framework coupled with analytical techniques which leverage a verification and validation capability that could be deployed into existing DoD data-processing systems with insignificant performance and operational interference.
Summary
Increased data sharing and interoperability has created challenges in maintaining a level of trust and confidence in Department of Defense (DoD) systems. As tightly-coupled, unique, static, and rigorously validated mission processing solutions have been supplemented with newer, more dynamic, and complex counterparts, mission effectiveness has been impacted. On the one...
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Toward an autonomous aerial survey and planning system for humanitarian aid and disaster response
March 7, 2020
Conference Paper
Published in:
IEEE Aerospace Conf., 7-14 March 2020.
Summary
In this paper we propose an integrated system concept for autonomously surveying and planning emergency response for areas impacted by natural disasters. Referred to as AASAPS-HADR, this system is composed of a network of ground stations and autonomous aerial vehicles interconnected by an ad hoc emergency communication network. The system objectives are three-fold: to provide situational awareness of the evolving disaster event, to generate dispatch and routing plans for emergency vehicles, and to provide continuous communication networks which augment pre-existing communication infrastructure that may have been damaged or destroyed. Lacking development in previous literature, we give particular emphasis to the situational awareness objective of disaster response by proposing an autonomous aerial survey that is tasked with assessing damage to existing road networks, detecting and locating human victims, and providing a cursory assessment of casualty types that can be used to inform medical response priorities. In this paper we provide a high-level system design concept, identify existing AI perception and planning algorithms that most closely suit our purposes as well as technology gaps within those algorithms, and provide initial experimental results for non-contact health monitoring using real-time pose recognition algorithms running on a Nvidia Jetson TX2 mounted on board a quadrotor UAV. Finally we provide technology development recommendations for future phases of the AASAPS-HADR system.
Summary
In this paper we propose an integrated system concept for autonomously surveying and planning emergency response for areas impacted by natural disasters. Referred to as AASAPS-HADR, this system is composed of a network of ground stations and autonomous aerial vehicles interconnected by an ad hoc emergency communication network. The system...
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The Human Trafficking Technology Roadmap: a targeted development strategy for the Department of Homeland Security
July 31, 2019
Technical Report
Published in:
MIT Lincoln Laboratory Report
Summary
Human trafficking is a form of modern-day slavery that involves the use of force, fraud, or coercion for the purposes of involuntary labor and sexual exploitation. It affects tens of million of victims worldwide and generates tens of billions of dollars in illicit profits annually. While agencies across the U.S. Government employ a diverse range of resources to combat human trafficking in the U.S. and abroad, trafficking operations remain challenging to measure, investigate, and interdict. Within the Department of Homeland Security, the Science and Technology Directorate is addressing these challenges by incorporating computational social science research into their counter-human trafficking approach. As part of this approach, the Directorate tasked an interdisciplinary team of national security researchers at the Massachusetts Institute of Technology's Lincoln Laboratory, a federally funded research and development center, to undertake a detailed examination of the human trafficking response across the Homeland Security Enterprise. The first phase of this effort was a government-wide systems analysis of major counter-trafficking thrust areas, including law enforcement and prosecution; public health and emergency medicine; victim services; and policy and legislation. The second phase built on this systems analysis to develop a human trafficking technology roadmap and implementation strategy for the Science and Technology Directorate, which is presented in this document.
Summary
Human trafficking is a form of modern-day slavery that involves the use of force, fraud, or coercion for the purposes of involuntary labor and sexual exploitation. It affects tens of million of victims worldwide and generates tens of billions of dollars in illicit profits annually. While agencies across the U.S...
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