Publications
Comparison of two-talker attention decoding from EEG with nonlinear neural networks and linear methods
August 8, 2019
Conference Paper
Published in:
Sci. Rep., Vol. 9, No. 1, 8 August 2019, 11538.
R&D area:
R&D group:
Summary
Auditory attention decoding (AAD) through a brain-computer interface has had a flowering of developments since it was first introduced by Mesgarani and Chang (2012) using electrocorticograph recordings. AAD has been pursued for its potential application to hearing-aid design in which an attention-guided algorithm selects, from multiple competing acoustic sources, which should be enhanced for the listener and which should be suppressed. Traditionally, researchers have separated the AAD problem into two stages: reconstruction of a representation of the attended audio from neural signals, followed by determining the similarity between the candidate audio streams and the reconstruction. Here, we compare the traditional two-stage approach with a novel neural-network architecture that subsumes the explicit similarity step. We compare this new architecture against linear and non-linear (neural-network) baselines using both wet and dry electroencephalogram (EEG) systems. Our results indicate that the new architecture outperforms the baseline linear stimulus-reconstruction method, improving decoding accuracy from 66% to 81% using wet EEG and from 59% to 87% for dry EEG. Also of note was the finding that the dry EEG system can deliver comparable or even better results than the wet, despite the latter having one third as many EEG channels as the former. The 11-subject, wet-electrode AAD dataset for two competing, co-located talkers, the 11-subject, dry-electrode AAD dataset, and our software are available for further validation, experimentation, and modification.
Summary
Auditory attention decoding (AAD) through a brain-computer interface has had a flowering of developments since it was first introduced by Mesgarani and Chang (2012) using electrocorticograph recordings. AAD has been pursued for its potential application to hearing-aid design in which an attention-guided algorithm selects, from multiple competing acoustic sources, which...
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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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Detection and characterization of human trafficking networks using unsupervised scalable text template matching
December 10, 2018
Conference Paper
Published in:
Proc. IEEE Int. Conf. on Big Data, 10-13 December 2018, pp. 3111-20.
Summary
Human trafficking is a form of modern-day slavery affecting an estimated 40 million victims worldwide, primarily through the commercial sexual exploitation of women and children. In the last decade, the advertising of victims has moved from the streets to websites on the Internet, providing greater efficiency and anonymity for sex traffickers. This shift has allowed traffickers to list their victims in multiple geographic areas simultaneously, while also improving operational security by using multiple methods of electronic communication with buyers; complicating the ability of law enforcement to disrupt these illicit organizations. In this paper, we address this issue and present a novel unsupervised and scalable template matching algorithm for analyzing and detecting complex organizations operating on adult service websites. The algorithm uses only the advertisement content to uncover signature patterns in text that are indicative of organized activities and organizational structure. We apply this method to a large corpus of adult service advertisements retrieved from backpage.com, and show that the networks identified through the algorithm match well with surrogate truth data derived from phone number networks in the same corpus. Further exploration of the results show that the proposed method provides deeper insights into the complex structures of sex trafficking organizations, not possible through networks derived from phone numbers alone. This method provides a powerful new capability for law enforcement to more completely identify and gather evidence about trafficking networks and their operations.
Summary
Human trafficking is a form of modern-day slavery affecting an estimated 40 million victims worldwide, primarily through the commercial sexual exploitation of women and children. In the last decade, the advertising of victims has moved from the streets to websites on the Internet, providing greater efficiency and anonymity for sex...
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Large-scale Bayesian kinship analysis
September 25, 2018
Conference Paper
Published in:
IEEE High Performance Extreme Computing Conf., HPEC, 25-27 September 2018.
Summary
Kinship prediction in forensics is limited to first degree relatives due to the small number of short tandem repeat loci characterized. The Genetic Chain Rule for Probabilistic Kinship Estimation can leverage large panels of single nucleotide polymorphisms (SNPs) or sets of sequence linked SNPs, called haploblocks, to estimate more distant relationships between individuals. This method uses allele frequencies and Markov Chain Monte Carlo methods to determine kinship probabilities. Allele frequencies are a crucial input to this method. Since these frequencies are estimated from finite populations and many alleles are rare, a Bayesian extension to the algorithm has been developed to determine credible intervals for kinship estimates as a function of the certainty in allele frequency estimates. Generation of sufficiently large samples to accurately estimate credible intervals can take significant computational resources. In this paper, we leverage hundreds of compute cores to generate large numbers of Dirichlet random samples for Bayesian kinship prediction. We show that it is possible to generate 2,097,152 random samples on 32,768 cores at a rate of 29.68 samples per second. The ability to generate extremely large number of samples enables the computation of more statistically significant results from a Bayesian approach to kinship analysis.
Summary
Kinship prediction in forensics is limited to first degree relatives due to the small number of short tandem repeat loci characterized. The Genetic Chain Rule for Probabilistic Kinship Estimation can leverage large panels of single nucleotide polymorphisms (SNPs) or sets of sequence linked SNPs, called haploblocks, to estimate more distant...
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Detecting pathogen exposure during the non-symptomatic incubation period using physiological data
November 13, 2017
Journal Article
Published in:
bioRxiv preprint doi: https://doi-org.ezproxyberklee.flo.org/10.1101/218818, 13 November 2017.
Summary
Early pathogen exposure detection allows better patient care and faster implementation of public health measures (patient isolation, contact tracing). Existing exposure detection most frequently relies on overt clinical symptoms, namely fever, during the infectious prodromal period. We have developed a robust machine learning based method to better detect asymptomatic states during the incubation period using subtle, sub-clinical physiological markers. Starting with highresolution physiological waveform data from non-human primate studies of viral (Ebola, Marburg, Lassa, and Nipah viruses) and bacterial (Y. pestis) exposure, we processed the data to reduce short-term variability and normalize diurnal variations, then provided these to a supervised random forest classification algorithm and post-classifier declaration logic step to reduce false alarms. In most subjects detection is achieved well before the onset of fever; subject cross-validation across exposure studies (varying viruses, exposure routes, animal species, and target dose) lead to 51h mean early detection (at 0.93 area under the receiver-operating characteristic curve [AUCROC]). Evaluating the algorithm against entirely independent datasets for Lassa, Nipah, and Y. pestis exposures un-used in algorithm training and development yields a mean 51h early warning time (at AUCROC=0.95). We discuss which physiological indicators are most informative for early detection and options for extending this capability to limited datasets such as those available from wearable, non-invasive, ECG-based sensors.
Summary
Early pathogen exposure detection allows better patient care and faster implementation of public health measures (patient isolation, contact tracing). Existing exposure detection most frequently relies on overt clinical symptoms, namely fever, during the infectious prodromal period. We have developed a robust machine learning based method to better detect asymptomatic states...
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Cloud computing in tactical environments
October 23, 2017
Conference Paper
Published in:
MILCOM 2017, 23-25 October 2017.
Topic:
Summary
Ground personnel at the tactical edge often lack data and analytics that would increase their effectiveness. To address this problem, this work investigates methods to deploy cloud computing capabilities in tactical environments. Our approach is to identify representative applications and to design a system that spans the software/hardware stack to support such applications while optimizing the use of scarce resources. This paper presents our high-level design and the results of initial experiments that indicate the validity of our approach.
Summary
Ground personnel at the tactical edge often lack data and analytics that would increase their effectiveness. To address this problem, this work investigates methods to deploy cloud computing capabilities in tactical environments. Our approach is to identify representative applications and to design a system that spans the software/hardware stack to...
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A cloud-based brain connectivity analysis tool
September 12, 2017
Conference Paper
Published in:
HPEC 2017: IEEE Conf. on High Performance Extreme Computing, 12-14 September 2017.
Summary
With advances in high throughput brain imaging at the cellular and sub-cellular level, there is growing demand for platforms that can support high performance, large-scale brain data processing and analysis. In this paper, we present a novel pipeline that combines Accumulo, D4M, geohashing, and parallel programming to manage large-scale neuron connectivity graphs in a cloud environment. Our brain connectivity graph is represented using vertices (fiber start/end nodes), edges (fiber tracks), and the 3D coordinates of the fiber tracks. For optimal performance, we take the hybrid approach of storing vertices and edges in Accumulo and saving the fiber track 3D coordinates in flat files. Accumulo database operations offer low latency on sparse queries while flat files offer high throughput for storing, querying, and analyzing bulk data. We evaluated our pipeline by using 250 gigabytes of mouse neuron connectivity data. Benchmarking experiments on retrieving vertices and edges from Accumulo demonstrate that we can achieve 1-2 orders of magnitude speedup in retrieval time when compared to the same operation from traditional flat files. The implementation of graph analytics such as Breadth First Search using Accumulo and D4M offers consistent good performance regardless of data size and density, thus is scalable to very large dataset. Indexing of neuron subvolumes is simple and logical with geohashing-based binary tree encoding. This hybrid data management backend is used to drive an interactive web-based 3D graphical user interface, where users can examine the 3D connectivity map in a Google Map-like viewer. Our pipeline is scalable and extensible to other data modalities.
Summary
With advances in high throughput brain imaging at the cellular and sub-cellular level, there is growing demand for platforms that can support high performance, large-scale brain data processing and analysis. In this paper, we present a novel pipeline that combines Accumulo, D4M, geohashing, and parallel programming to manage large-scale neuron...
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A linear algebra approach to fast DNA mixture analysis using GPUs
September 12, 2017
Conference Paper
Published in:
HPEC 2017: IEEE Conf. on High Performance Extreme Computing, 12-14 September 2017.
Summary
Analysis of DNA samples is an important step in forensics, and the speed of analysis can impact investigations. Comparison of DNA sequences is based on the analysis of short tandem repeats (STRs), which are short DNA sequences of 2-5 base pairs. Current forensics approaches use 20 STR loci for analysis. The use of single nucleotide polymorphisms (SNPs) has utility for analysis of complex DNA mixtures. The use of tens of thousands of SNPs loci for analysis poses significant computational challenges because the forensic analysis scales by the product of the loci count and number of DNA samples to be analyzed. In this paper, we discuss the implementation of a DNA sequence comparison algorithm by re-casting the algorithm in terms of linear algebra primitives. By developing an overloaded matrix multiplication approach to DNA comparisons, we can leverage advances in GPU hardware and algorithms for Dense Generalized Matrix-Multiply (DGEMM) to speed up DNA sample comparisons. We show that it is possible to compare 2048 unknown DNA samples with 20 million known samples in under 6 seconds using a NVIDIA K80 GPU.
Summary
Analysis of DNA samples is an important step in forensics, and the speed of analysis can impact investigations. Comparison of DNA sequences is based on the analysis of short tandem repeats (STRs), which are short DNA sequences of 2-5 base pairs. Current forensics approaches use 20 STR loci for analysis...
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Detecting virus exposure during the pre-symptomatic incubation period using physiological data
March 3, 2017
Journal Article
Published in:
Science Translational Medicine (submitted), 3 March 2017.
Summary
Early pathogen exposure detection allows better patient care and faster implementation of public health measures (patient isolation, contact tracing). Existing exposure detection most frequently relies on overt clinical symptoms, namely fever, during the infectious prodromal period. We have developed a robust machine learning method to better detect asymptomatic states during the incubation period using subtle, sub-clinical physiological markers. Using high-resolution physiological data from non-human primate studies of Ebola and Marburg viruses, we pre-processed the data to reduce short-term variability and normalize diurnal variations, then provided these to a supervised random forest classification algorithm. In most subjects detection is achieved well before the onset of fever; subject cross-validation lead to 52±14h mean early detection (at >0.90 area under the receiver-operating characteristic curve). Cross-cohort tests across pathogens and exposure routes also lead to successful early detection (28±16h and 43±22h, respectively). We discuss which physiological indicators are most informative for early detection and options for extending this capability to lower data resolution and wearable, non-invasive sensors.
Summary
Early pathogen exposure detection allows better patient care and faster implementation of public health measures (patient isolation, contact tracing). Existing exposure detection most frequently relies on overt clinical symptoms, namely fever, during the infectious prodromal period. We have developed a robust machine learning method to better detect asymptomatic states during...
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Benchmarking SciDB data import on HPC systems
September 13, 2016
Conference Paper
Published in:
HPEC 2016: IEEE Conf. on High Performance Extreme Computing, 13-15 September 2016.
Summary
SciDB is a scalable, computational database management system that uses an array model for data storage. The array data model of SciDB makes it ideally suited for storing and managing large amounts of imaging data. SciDB is designed to support advanced analytics in database, thus reducing the need for extracting data for analysis. It is designed to be massively parallel and can run on commodity hardware in a high performance computing (HPC) environment. In this paper, we present the performance of SciDB using simulated image data. The Dynamic Distributed Dimensional Data Model (D4M) software is used to implement the benchmark on a cluster running the MIT SuperCloud software stack. A peak performance of 2.2M database inserts per second was achieved on a single node of this system. We also show that SciDB and the D4M toolbox provide more efficient ways to access random sub-volumes of massive datasets compared to the traditional approaches of reading volumetric data from individual files. This work describes the D4M and SciDB tools we developed and presents the initial performance results. This performance was achieved by using parallel inserts, a in-database merging of arrays as well as supercomputing techniques, such as distributed arrays and single-program-multiple-data programming.
Summary
SciDB is a scalable, computational database management system that uses an array model for data storage. The array data model of SciDB makes it ideally suited for storing and managing large amounts of imaging data. SciDB is designed to support advanced analytics in database, thus reducing the need for extracting...
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