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Predicting ankle moment trajectory with adaptive weighted ensemble of LSTM network
November 1, 2022
Conference Paper
Published in:
2022 IEEE High Perf. Extreme Comp. Conf. (HPEC), 19-23 September 2022, DOI: 10.1109/HPEC55821.2022.9926370.
Summary
Estimations of ankle moments can provide clinically helpful information on the function of lower extremities and further lead to insight on patient rehabilitation and assistive wearable exoskeleton design. Current methods for estimating ankle moments leave room for improvement, with most recent cutting-edge methods relying on machine learning models trained on wearable sEMG and IMU data. While machine learning eliminates many practical challenges that troubled more traditional human body models for this application, we aim to expand on prior work that showed the feasibility of using LSTM models by employing an ensemble of LSTM networks. We present an adaptive weighted LSTM ensemble network and demonstrate its performance during standing, walking, running, and sprinting. Our result show that the LSTM ensemble outperformed every single LSTM model component within the ensemble. Across every activity, the ensemble reduced median root mean squared error (RMSE) by 0.0017-0.0053 N. m/kg, which is 2.7 – 10.3% lower than the best performing single LSTM model. Hypothesis testing revealed that most reductions in RMSE were statistically significant between the ensemble and other single models across all activities and subjects. Future work may analyze different trajectory lengths and different combinations of LSTM submodels within the ensemble.
Summary
Estimations of ankle moments can provide clinically helpful information on the function of lower extremities and further lead to insight on patient rehabilitation and assistive wearable exoskeleton design. Current methods for estimating ankle moments leave room for improvement, with most recent cutting-edge methods relying on machine learning models trained on...
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Relationships between cognitive factors and gait strategy during exoskeleton-augmented walking
November 12, 2021
Conference Paper
Published in:
Proc. Human Factors and Ergonomics Society Annual Mtg, HFES, Vol. 65, No. 1, 2021.
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Summary
Individual variation in exoskeleton-augmented gait strategy may arise from differences in cognitive factors, e.g., ability to respond quickly to stimuli or complete tasks under divided attention. Gait strategy is defined as different approaches to achieving gait priorities (e.g., walking without falling) and is observed via changes in gait characteristics like normalized stride length or width. Changes indicate shifting priorities like increasing stability or coordination with an exoskeleton. Relationships between cognitive factors and exoskeleton gait characteristics were assessed. Cognitive factors were quantified using a modified Simon task and a speed achievement task on a self-paced treadmill with and without a secondary go/no-go task. Individuals with faster reaction times and decreased ability to maintain a given speed tended to prioritize coordination with an exoskeleton over gait stability. These correlations indicate relationships between cognitive factors and individual exoskeleton-augmented gait strategy that should be further investigated to understand variation in exoskeleton use.
Summary
Individual variation in exoskeleton-augmented gait strategy may arise from differences in cognitive factors, e.g., ability to respond quickly to stimuli or complete tasks under divided attention. Gait strategy is defined as different approaches to achieving gait priorities (e.g., walking without falling) and is observed via changes in gait characteristics like...
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Geographic source estimation using airborne plant environmental DNA in dust
August 10, 2021
Journal Article
Published in:
Scientific Reports
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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 of dust components, we developed a pipeline that utilizes the airborne plant environmental DNA (eDNA) in settled dust to estimate geographic origin. Metabarcoding of settled airborne eDNA was used to identify plant species whose 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 was achieved with 66.7% (16 of 24 samples). For broader demonstration, citizen-collected dust samples collected from 31 diverse U.S. sites were analyzed, and trace plant eDNA provided relevant regional attribution information on provenance in 32.2% of samples. This showed that analysis of airborne plant eDNA in settled 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 of dust components, we developed a pipeline that utilizes the airborne plant environmental DNA (eDNA) in settled dust to...
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Human balance models optimized using a large-scale, parallel architecture with applications to mild traumatic brain injury
September 22, 2020
Conference Paper
Published in:
2020 IEEE High Performance Extreme Computing Conf., HPEC, 22-24 September 2020.
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Summary
Static and dynamic balance are frequently disrupted through brain injuries. The impairment can be complex and for mild traumatic brain injury (mTBI) can be undetectable by standard clinical tests. Therefore, neurologically relevant modeling approaches are needed for detection and inference of mechanisms of injury. The current work presents models of static and dynamic balance that have a high degree of correspondence. Emphasizing structural similarity between the domains facilitates development of both. Furthermore, particular attention is paid to components of sensory feedback and sensory integration to ground mechanisms in neurobiology. Models are adapted to fit experimentally collected data from 10 healthy control volunteers and 11 mild traumatic brain injury volunteers. Through an analysis by synthesis approach whose implementation was made possible by a state-of-the-art high performance computing system, we derived an interpretable, model based feature set that could classify mTBI and controls in a static balance task with an ROC AUC of 0.72.
Summary
Static and dynamic balance are frequently disrupted through brain injuries. The impairment can be complex and for mild traumatic brain injury (mTBI) can be undetectable by standard clinical tests. Therefore, neurologically relevant modeling approaches are needed for detection and inference of mechanisms of injury. The current work presents models of...
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COVID-19: famotidine, histamine, mast cells, and mechanisms [eprint]
May 23, 2020
Journal Article
Published in:
Research Square, preprint, 23 May 2020.
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Summary
SARS-CoV-2 infection is required for COVID-19, but many signs and symptoms of COVID-19 differ from common acute viral diseases. Currently, there are no pre- or post-exposure prophylactic COVID-19 medical countermeasures. Clinical data suggest that famotidine may mitigate COVID-19 disease, but both mechanism of action and rationale for dose selection remain obscure. We explore several plausible avenues of activity including antiviral and host-mediated actions. We propose that the principal famotidine mechanism of action for COVID-19 involves on-target histamine receptor H2 activity, and that development of clinical COVID-19 involves dysfunctional mast cell activation and histamine release.
Summary
SARS-CoV-2 infection is required for COVID-19, but many signs and symptoms of COVID-19 differ from common acute viral diseases. Currently, there are no pre- or post-exposure prophylactic COVID-19 medical countermeasures. Clinical data suggest that famotidine may mitigate COVID-19 disease, but both mechanism of action and rationale for dose selection remain...
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Medical countermeasures analysis of 2019-nCoV and vaccine risks for antibody-dependent enhancement (ADE)
March 8, 2020
Journal Article
Published in:
https://www.preprints.org/manuscript/202003.0138/v1
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Summary
Background: In 80% of patients, COVID-19 presents as mild disease. 20% of cases develop severe (13%) or critical (6%) illness. More severe forms of COVID-19 present as clinical severe acute respiratory syndrome, but include a T-predominant lymphopenia, high circulating levels of proinflammatory cytokines and chemokines, accumulation of neutrophils and macrophages in lungs, and immune dysregulation including immunosuppression. Methods: All major SARS-CoV-2 proteins were characterized using an amino acid residue variation analysis method. Results predict that most SARS-CoV-2 proteins are evolutionary constrained, with the exception of the spike (S) protein extended outer surface. Results were interpreted based on known SARS-like coronavirus virology and pathophysiology, with a focus on medical countermeasure development implications. Findings: Non-neutralizing antibodies to variable S domains may enable an alternative infection pathway via Fc receptor-mediated uptake. This may be a gating event for the immune response dysregulation observed in more severe COVID-19 disease. Prior studies involving vaccine candidates for FCoV SARS-CoV-1 and Middle East Respiratory Syndrome coronavirus (MERS-CoV) demonstrate vaccination-induced antibody-dependent enhancement of disease (ADE), including infection of phagocytic antigen presenting cells (APC). T effector cells are believed to play an important role in controlling coronavirus infection; pan-T depletion is present in severe COVID-19 disease and may be accelerated by APC infection. Sequence and structural conservation of S motifs suggests that SARS and MERS vaccine ADE risks may foreshadow SARS-CoV-2 S-based vaccine risks. Autophagy inhibitors may reduce APC infection and T-cell depletion. Amino acid residue variation analysis identifies multiple constrained domains suitable as T cell vaccine targets. Evolutionary constraints on proven antiviral drug targets present in SARS-CoV-1 and SARS-CoV-2 may reduce risk of developing antiviral drug escape mutants. Interpretation: Safety testing of COVID-19 S protein-based B cell vaccines in animal models is strongly encouraged prior to clinical trials to reduce risk of ADE upon virus exposure.
Summary
Background: In 80% of patients, COVID-19 presents as mild disease. 20% of cases develop severe (13%) or critical (6%) illness. More severe forms of COVID-19 present as clinical severe acute respiratory syndrome, but include a T-predominant lymphopenia, high circulating levels of proinflammatory cytokines and chemokines, accumulation of neutrophils and macrophages...
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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/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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