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arXiv 2023年

作者： Raghu, Aniruddh Chandak, Payal Alam, Ridwan Guttag, John Stultz, Collin M. Massachusetts Institute of Technology CambridgeMA United States Harvard-MIT Program in Health Sciences and Technology CambridgeMA United States

Self-supervised learning (SSL) for clinical time series data has received significant attention in recent literature, since these data are highly rich and provide important information about a patient’s physiological state. However, most existing SSL methods for clinical time series are limited in that they are designed for unimodal time series, such as a sequence of structured features (e.g., lab values and vitals signs) or an individual high-dimensional physiological signal (e.g., an electrocardiogram). These existing methods cannot be readily extended to model time series that exhibit multimodality, with structured features and high-dimensional data being recorded at each timestep in the sequence. In this work, we address this gap and propose a new SSL method — Sequential Multi-Dimensional SSL — where a SSL loss is applied both at the level of the entire sequence and at the level of the individual high-dimensional data points in the sequence in order to better capture information at both scales. Our strategy is agnostic to the specific form of loss function used at each level – it can be contrastive, as in SimCLR, or non-contrastive, as in VICReg. We evaluate our method on two real-world clinical datasets, where the time series contains sequences of (1) high-frequency electrocardiograms and (2) structured data from lab values and vitals signs. Our experimental results indicate that pre-training with our method and then fine-tuning on downstream tasks improves performance over baselines on both datasets, and in several settings, can lead to improvements across different self-supervised loss functions. Copyright © 2023, The Authors. All rights reserved.

关键词： Supervised learning

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Model-Based Insulin Sensitivity and Beta-Cell Function Estimation from Daily Continuous Glucose Monitoring

Model-Based Insulin Sensitivity and Beta-Cell Function Estim...

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Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)

作者： Elizabeth Healey Isaac Kohane Harvard-MIT Program in Health Sciences and Technology Cambridge MA USA Department of Biomedical Informatics Harvard Medical School Boston MA USA

ISBN: (数字)9798350371499

ISBN: (纸本)9798350371505

Type 2 diabetes (T2D) is a prevalent chronic illness with many different options for treatment management. Continuous glucose monitors (CGM) offer physiological data that clinicians can access when making treatment decisions. However, the utility of CGM in management of T2D remains an active area of research. In our work, we demonstrate the feasibility of exploiting raw daily CGM data to estimate the physiological parameters of insulin sensitivity and beta-cell function that correlate with estimates derived from laboratory findings. We use a peak extraction algorithm to extract peaks from daily CGM data and implement a model-based approach to infer physiological parameters. We demonstrate that the inferred parameter estimates of insulin sensitivity and beta-cell function correlate to the ground truth measurements as determined by an oral glucose tolerance test (OGTT).

关键词： Sensitivity Biological system modeling Estimation Data models Diabetes Data mining Insulin Engineering in medicine and biology

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A software tool for creating simulated outbreaks to benchmark surveillance systems

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BMC Medical Informatics and Decision Making 2005年第1期5卷 1-7页

作者： Cassa, Christopher A. Iancu, Karin Olson, Karen L. Mandl, Kenneth D. Children's Hospital Informatics Program Informatics Program - Mandl Group Children's Hospital Boston Boston MA 02115 1 Autumn St #721 United States Clinical Decision Making Group Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology Cambridge MA 02139 United States Harvard Medical School Boston MA 02115 United States Harvard/MIT Division of Health Sciences and Technology Cambridge MA 02139 United States

Background: Evaluating surveillance systems for the early detection of bioterrorism is particularly challenging when systems are designed to detect events for which there are few or no historical examples. One approach to benchmarking outbreak detection performance is to create semi-synthetic datasets containing authentic baseline patient data (noise) and injected artificial patient clusters, as signal. Methods: We describe a software tool, the AEGIS Cluster Creation Tool (AEGIS-CCT), that enables users to create simulated clusters with controlled feature sets, varying the desired cluster radius, density, distance, relative location from a reference point, and temporal epidemiological growth pattern. AEGIS-CCT does not require the use of an external geographical information system program for cluster creation. The cluster creation tool is an open source program, implemented in Java and is freely available under the Lesser GNU Public License at its Sourceforge website. Cluster data are written to files or can be appended to existing files so that the resulting file will include both existing baseline and artificially added cases. Multiple cluster file creation is an automated process in which multiple cluster files are created by varying a single parameter within a user-specified range. To evaluate the output of this software tool, sets of test clusters were created and graphically rendered. Results: Based on user-specified parameters describing the location, properties, and temporal pattern of simulated clusters, AEGIS-CCT created clusters accurately and uniformly. Conclusion: AEGIS-CCT enables the ready creation of datasets for benchmarking outbreak detection systems. It may be useful for automating the testing and validation of spatial and temporal cluster detection algorithms. © 2005 Cassa et al;licensee BioMed Central Ltd.

关键词： Geographic Information System Cluster Point Syndromic Surveillance Geographic Information System Software Patient Cluster

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The Ceres Human Exploration and Transit Architecture (CHEATA): A Mission Architecture for Small Bodies Exploration 73

The Ceres Human Exploration and Transit Architecture (CHEATA...

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73rd International Astronautical Congress, IAC 2022

作者： Todd, Jessica Gentgen, Chloe Porter, Allison Bellisle, Rachel Martell, Benjamin Hoffman, Jeffrey Department of Aeronautics and Astronautics Massachusetts Institute of Technology 77 Massachusetts Ave CambridgeMA02139 United States MIT-WHOI Joint Program in Oceanography/Applied Ocean Science and Engineering Woods Hole Oceanographic Institution Woods HoleMA United States Harvard-MIT Health Sciences and Technology Massachusetts Institute of Technology 77 Massachusetts Ave CambridgeMA02139 United States

The Ceres Human Exploration and Transit Architecture (CHEATA) is a conceptual mission developed to enable human exploration of Ceres and other small bodies in the asteroid belt. These small bodies present tempting targets for future human exploration, providing insight into the evolution of our solar system, potentially containing environments of interest to astrobiologists, and acting as water- and mineral-rich stepping stones for outer solar system exploration. Minimizing radiation exposure and mission duration while maximizing surface science operations on the surface of Ceres was the critical driving requirement for this design reference mission. Key elements of the design include (1) a low gravity hopping vehicle using vacuum retro-propulsion and LOX/Methane propellant, taking advantage of the low gravity environment for regional exploration and surface operations on Ceres, (2) a bimodal nuclear thermal propulsion (NTP) system that utilizes liquid hydrogen and a reusable CERMET core, and (3) an active high-temperature superconducting magnet system, complemented by a passive high-density polyethylene system, to mitigate crew exposure to galactic cosmic radiation and solar energetic particle events. A transit habitat vehicle is assembled in cislunar space and used to ferry astronauts to Ceres orbit. The study also details breakdowns of the human countermeasures employed to address the effects of microgravity and isolation. The CHEATA mission concept was initially presented at the IEEE Aerospace Conference in 2022. The mission architecture has been updated to now include the design of additional spacecraft and habitation subsystems. These include the design of an Environmental Control and Life Support System, secondary propulsion for corrections, small maneuvers, and attitude control, but also more in-depth power and thermal management systems. The propellant storage was refined with the inclusion of zero boil-off technology for the Liquid Hydrogen tanks. A detail

关键词： Liquefied gases

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An unsupervised classification method for inferring original case locations from low-resolution disease maps

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International Journal of health Geographics 2006年第1期5卷 1-7页

作者： Brownstein, John S. Cassa, Christopher A. Kohane, Isaac S. Mandl, Kenneth D. Children's Hospital Informatics Program Harvard-MIT Division of Health Sciences and Technology Boston MA 1 Autumn St. United States Division of Emergency Medicine Children's Hospital Boston Boston MA 300 Longwood Ave. United States Department of Pediatrics Harvard Medical School Boston MA 300 Longwood Ave. United States

Background: Widespread availability of geographic information systems software has facilitated the use of disease mapping in academia, government and private sector. Maps that display the address of affected patients are often exchanged in public forums, and published in peer-reviewed journal articles. As previously reported, a search of figure legends in five major medical journals found 19 articles from 1994-2004 that identify over 19,000 patient addresses. In this report, a method is presented to evaluate whether patient privacy is being breached in the publication of low-resolution disease maps. Results: To demonstrate the effect, a hypothetical low-resolution map of geocoded patient addresses was created and the accuracy with which patient addresses can be resolved is described. Through georeferencing and unsupervised classification of the original image, the method precisely re-identified 26% (144/550) of the patient addresses from a presentation quality map and 79% (432/550) from a publication quality map. For the presentation quality map, 99.8% of the addresses were within 70 meters (approximately one city block length) of the predicted patient location, 51.6% of addresses were identified within five buildings, 70.7% within ten buildings and 93% within twenty buildings. For the publication quality map, all addresses were within 14 meters and 11 buildings of the predicted patient location. Conclusion: This study demonstrates that lowering the resolution of a map displaying geocoded patient addresses does not sufficiently protect patient addresses from re-identification. Guidelines to protect patient privacy, including those of medical journals, should reflect policies that ensure privacy protection when spatial data are displayed or published. © 2006 Brownstein et al;licensee BioMed Central Ltd.

关键词： Global Position System Privacy Protection Unsupervised Classification Apartment Building Housing Density

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Helping high-risk youth move through high-risk periods: personally controlled health records for improving social and health care transitions

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Journal of diabetes science and technology 2011年第1期5卷 47-54页

作者： Elissa R Weitzman Liljana Kaci Maryanne Quinn Kenneth D Mandl Children's Hospital Informatics Program at the Harvard-MIT Division of Health Sciences and Technology Children's Hospital Boston Boston Massachusetts 02215 USA. elissa.weitzman@childrens.harvard.edu

BACKGROUND:New patient-centered information technologies are needed to address risks associated with health care transitions for adolescents and young adults with diabetes, including systems that support individual and structural impediments to self- and clinical-care. METHODS:We describe the personally controlled health record (PCHR) system platform and its key structural capabilities and assess its alignment with tenets of the chronic care model (CCM) and the social-behavioral and health care ecologies within which adolescents and young adults with diabetes mature. RESULTS:Configured as Web-based platforms, PCHRs can support a new class of patient-facing applications that serve as monitoring and support systems for adolescents navigating complex social, developmental, and health care transitions. The approach can enable supportive interventions tailored to individual patient needs to boost adherence, self-management, and monitoring. CONCLUSIONS:The PCHR platform is a paradigm shift for the organization of health information systems and is consistent with the CCM and conceptualizations of patient- and family-centered care for diabetes. Advancing the approach augers well for improvement around health care transitions for youth and also requires that we address (i) structural barriers impacting diabetes care for maturing youth; (ii) challenges around health and technology literacy; (iii) privacy and confidentiality issues, including sharing of health information within family and institutional systems; and (iv) needs for evaluation around uptake, impacts, and outcomes.

关键词： adherence consumer informatics diabetes health information technology patient medical record systems personally controlled health records self-management transitions type 1 diabetes

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Phenotype Prediction by Integrative Network Analysis of SNP and Gene Expression Microarrays

Phenotype Prediction by Integrative Network Analysis of SNP ...

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Annual International Conference of the IEEE Engineering in Medicine and Biology Society

作者： Hsun-Hsien Chang Michael McGeachie Children's Hospital Informatics Program Harvard-MIT Division of Health Sciences and Technology Harvard Medical School Channing Lab Brigham and Women's Hospital Harvard Medical School

ISBN: (纸本)9781424441211

A long-term goal of biomedical research is to decipher how genetic processes influence disease formation. Ubiquitous and advancing microarray technology can measure millions of DNA structural variants (single-nucleotide polymorphisms, or SNPs) and thousands of gene transcripts (RNA expression microarrays) in cells. Both of these information modalities can be brought to bear on disease etiology. This paper develops a Bayesian network-based approach to integrate SNP and expression microarray data. The network models SNP-gene interactions using a phenotype-centric network. Inferring the network consists of two steps: variable selection and network learning. The learned network illustrates how functionally dependent SNPs and genes influence each other, and also serves as a predictor of the phenotype. The application of the proposed method to a pediatric acute lymphoblastic leukemia dataset demonstrates the feasibility of our approach and its impact on biological investigation and clinical practice.

关键词： Single nucleotide polymorphism sequence number protection Microarray Genetic Processes microarray technology L1 Acute Lymphoblastic Leukemia Biomedical Research Network analysis Genetic Transcription clinical practice gene interaction

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Using Topology of the Metabolic Network to Predict Viability of Mutant Strains

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Genome Biology 2005年第13期6卷 1-30页

作者： Zeba Wunderlich Leonid Mirny Biophysics Program Harvard University 77 Massachusetts Avenue 16-361 Cambridge MA 02139 USA Harvard-MIT Division of Health Sciences & Technology Massachusetts Institute of Technology 77 Massachusetts Avenue 16-343 Cambridge MA 02139 USA

BackgroundUnderstanding the relationships between the structure (topology) andfunction of biological networks is a central question of systems biology. The idea thattopology is a major determinant of systems function ... 详细信息

Background

Understanding the relationships between the structure (topology) andfunction of biological networks is a central question of systems biology. The idea thattopology is a major determinant of systems function has become an attractive andhighly-disputed hypothesis. While the structural analysis of interaction networksdemonstrates a correlation between the topological properties of a node (protein, gene)in the network and its functional essentiality, the analysis of metabolic networks fails tofind such correlations. In contrast, approaches utilizing both the topology andbiochemical parameters of metabolic networks, e.g. flux balance analysis (FBA), aremore successful in predicting phenotypes of knock-out strains.

Results

We reconcile these seemingly conflicting results by showing that the topologyof E. coli's metabolic network is, in fact, sufficient to predict the viability of knock-outstrains with accuracy comparable to FBA on a large, unbiased dataset of mutants. Thissurprising result is obtained by introducing a novel topology-based measure of networktransport: synthetic accessibility. We also show that other popular topology-basedcharacteristics like node degree, graph diameter, and node usage (betweenness) fail topredict the viability of mutant strains. The success of synthetic accessibilitydemonstrates its ability to capture the essential properties of the metabolic network,such as the branching of chemical reactions and the directed transport of material frominputs to outputs.

Conclusions

Our results (1) strongly support a link between the topology and functionof biological networks; (2) in agreement with recent genetic studies, emphasize theminimal role of flux re-routing in providing robustness of mutant strain

关键词： Mutant Strain System Biology Metabolic Network Additional Data File Topological Property

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A Distinctive Platform System to Study the Effects of a Vestibular Prosthesis on Nonhuman Primate Postural Control

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Journal of Engineering and Science in Medical Diagnostics and Therapy 2018年第2期1卷 021004页

作者： Thompson, Lara A. Haburcakova, Csilla Lewis, Richard F. Mem. ASME Biomedical Engineering Program Department of Mechanical Engineering School of Engineering and Applied Sciences 4200 Connecticut Avenue NW WashingtonDC20008 United States University of the District of Columbia Harvard-MIT Division of Health Sciences and Technology Massachusetts Institute of Technology 77 Massachusetts Avenue CambridgeMA02138 United States Jenks Vestibular Physiology Laboratory Massachusetts Eye and Ear Infirmary BostonMA02139 United States Departments of Otology and Laryngology and Neurology Harvard Medical School BostonMA02139 United States

The purpose of this paper is to describe novel experiments and methodologies utilizing a distinctive balance platform system to investigate postural responses for moderate to severe vestibular loss and invasive vestibular prosthesis-assisted nonhuman primates (rhesus monkeys). For several millions of vestibular loss sufferers in the U.S., daily living is severely affected in that common everyday tasks, such as getting out of bed at night, maintaining balance on a moving bus, or walking on an uneven surface, may cause a loss of stability leading to falls and injury. Aside from loss of balance, blurred vision and vertigo (perceived spinning sensation) are also debilitating in vestibular-impaired individuals. Although the need for vestibular rehabilitative solutions is apparent, postural responses for a broad range of peripheral vestibular function, and for various stationary and moving support conditions, have not been systematically investigated. For the investigation of implants and prostheses that are being developed toward implementation in humans, nonhuman primates are a key component. The measurement system used in this research was unique. Our platform system facilitated the study of rhesus monkey posture for stationary support surface conditions (quiet stance and head turns) and for dynamic support surface conditions (pseudorandom roll tilts of the support surface). Further, the platform system was used to systematically study postural responses that will serve as baseline measures for future vestibular-focused human and nonhuman primate posture studies. © 2018 by ASME.

关键词： Prosthetics

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Characterization of shape and deformation of tympanic membranes by dual-wavelength lensless digital holography

Characterization of shape and deformation of tympanic membra...

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2011 SEM Annual Conference on Experimental and Applied Mechanics

作者： Lu, Weina Furlong, Cosme Rosowski, John J. Cheng, Jeffrey T. Merchant, Saumil N. Center for Holographic Studies and Laser Micro-mechaTronics Department of Mechanical Engineering Worcester Polytechnic Institute Worcester MA United States Eaton-Peabody Laboratory Massachusetts Eye and Ear Infirmary Boston MA 02114 United States Speech and Hearing Bioscience and Technology Program MIT-Harvard Division of Health Sciences and Technology Cambridge MA United States

ISBN: (纸本)9781461402183

We are developing an advanced computer-controlled digital optoelectronic holographic system (DOEHS) with the ability to measure both shape and acoustically induced deformations of the tympanic membrane of several species, including humans. The DOEHS consists of laser delivery (LD), optical head (OH), and computing platform (CP) subsystems. The LD subsystem houses two tunable near-infrared laser sources, an acoustic modulator to enable stroboscopic illumination, and laser-to-fiber mechanisms to couple light into one single mode polarization maintaining fiber. The output of the LD subsystem is delivered into the OH subsystem through the polarized maintaining fiber (PM), which is arranged to perform imaging and measurements by phase-shifting lensless digital holography. A high-resolution digital camera, contained within the OH subsystem, is used for image recording at high-rates while the CP subsystem acquires and processes images in either time-averaged or double-exposure holographic modes. Shape measurements are performed by double-exposure mode with a different laser source used in each one of the exposures whereas deformation measurements are obtained by using a single laser source. We present preliminary results of our investigations of acoustically induced motions on tympanic membrane and the transfer of these motions to the ossicular chain, including results on sample preparation for measurements with the DOEHS.

关键词： Infrared devices

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