Computer Science Research Works

Permanent URI for this collectionhttp://hdl.handle.net/1903/1593

Browse

Filters

2012 - 201922020 - 20254

Settings

Author: search.filters.author.Cummings, Michael P.Start date: 2010

Search Results

Now showing 1 - 6 of 6
  • Thumbnail Image
    Item
    Supplementary material for Applying Wearable Sensors and Machine Learning to the Diagnostic Challenge of Distinguishing Parkinson's Disease from Other Forms of Parkinsonism
    (2025) Khalil, Rana M.; Shulman, Lisa M.; Gruber-Baldini, Ann L.; Reich, Stephen G.; Savitt, Joseph M.; Hausdorff, Jeffrey M.; von Coelln, Rainer; Cummings, Michael P.
    Parkinson's Disease (PD) and other forms of parkinsonism share motor symptoms, including tremor, bradykinesia, and rigidity. This overlap in the clinical presentation creates a diagnostic challenge, underscoring the need for objective differentiation. However, applying machine learning (ML) to clinical datasets faces challenges such as imbalanced class distributions, small sample sizes for non-PD parkinsonism, and heterogeneity within the non-PD group. This study analyzed wearable sensor data from 260 PD participants and 18 individuals with etiologically diverse forms of non-PD parkinsonism during clinical mobility tasks, using a single sensor placed on the lower-back. We evaluated the performance of ML models in distinguishing these two groups and identified the most informative mobility tasks for classification. Additionally, we examined clinical characteristics of misclassified participants and presented case studies of common challenges in clinical practice, including diagnostic uncertainty at the initial visit and changes in diagnosis over time. We also suggested potential steps to address dataset challenges which limited the models' performance. We demonstrate that ML-based analysis is a promising approach for distinguishing idiopathic PD from non-PD parkinsonism, though its accuracy remains below that of expert clinicians. Using the Timed Up and Go test as a single mobility task outperformed the use of all tasks combined, achieving a balanced accuracy of 78.2%. We also identified differences in some clinical scores between participants correctly and falsely classified by our models. These findings demonstrate the feasibility of using ML and wearable sensors for differentiating PD from other parkinsonian disorders, addressing key challenges in diagnosis, and streamlining diagnostic workflows.
  • Thumbnail Image
    Item
    Supplementary material for machine learning and statistical analyses of sensor data reveal variability between repeated trials in Parkinson’s disease mobility assessments
    (2024) Khalil, Rana M.; Shulman, Lisa M.; Gruber-Baldini, Ann L.; Shakya, Sunita; Hausdorff, Jeffrey M.; von Coelln, Rainer; Cummings, Michael P.
    Mobility tasks like the Timed Up and Go test (TUG), cognitive TUG (cogTUG), and walking with turns provide insight into motor control, balance, and cognitive functions affected by Parkinson’s disease (PD). We assess the test-retest reliability of these tasks in 262 PD participants and 50 controls by evaluating machine learning models based on wearable sensor-derived measures and statistical metrics. This evaluation examines total duration, subtask duration, and other quantitative measures across two trials. We show that the diagnostic accuracy for distinguishing PD from controls decreases by a mean of 1.8% between the first and the second trial, suggesting that task repetition may not be necessary for accurate diagnosis. Although the total duration remains relatively consistent between trials (intraclass correlation coefficient (ICC) = 0.62 to 0.95), greater variability is seen in subtask duration and sensor-derived measures, reflected in machine learning performance and statistical differences. Our findings also show that this variability differs not only between controls and PD participants but also among groups with varying levels of PD severity, indicating the need to consider population characteristics. Relying solely on total task duration and conventional statistical metrics to gauge the reliability of mobility tasks may fail to reveal nuanced variations in movement.
  • Thumbnail Image
    Item
    Supplementary material for Machine learning analysis of wearable sensor data from mobility testing distinguishes Parkinson's disease from other forms of parkinsonism
    (2024-03-13) Khalil, Rana M.; Shulman, Lisa M.; Gruber-Baldini, Ann L.; Hausdorff, Jeffrey M.; von Coelln, Rainer; Cummings, Michael P.; Cummings, Michael P.
    Parkinson's Disease (PD) and other forms of parkinsonism share characteristic motor symptoms, including tremor, bradykinesia, and rigidity. This overlap in the clinical presentation creates a diagnostic challenge, underscoring the need for objective differentiation tools. In this study, we analyzed wearable sensor data collected during mobility testing from 260 PD participants and 18 participants with etiologically diverse forms of parkinsonism. Our findings illustrate that machine learning-based analysis of data from a single wearable sensor can effectively distinguish idiopathic PD from non-PD parkinsonism with a balanced accuracy of 83.5%, comparable to expert diagnosis. Moreover, we found that diagnostic performance can be improved through severity-based partitioning of participants, achieving a balanced accuracy of 95.9%, 91.2% and 100% for mild, moderate and severe cases, respectively. Beyond its diagnostic implications, our results suggest the possibility of streamlining the testing protocol by using the Timed Up and Go test as a single mobility task. Furthermore, we present a detailed analysis of several case studies of challenging scenarios commonly encountered in clinical practice, including diagnostic uncertainty at the initial visit, and changes in clinical diagnosis at a subsequent visit. Together, these findings demonstrate the potential of applying machine learning on sensor-based measures of mobility to distinguish between PD and other forms of parkinsonism.
  • Thumbnail Image
    Item
    Supplementary material for machine learning analysis of data from a simplified mobility testing procedure with a single sensor and single task accurately differentiates Parkinson's disease from controls
    (2023) Khalil, Rana M.; Shulman, Lisa M.; Gruber-Baldini, Ann L.; Shakya, Sunita; von Coelln, Rainer; Cummings, Michael P.; Fenderson, Rebecca; van Hoven, Maxwell; Hausdorff, Jeffrey M.; Cummings, Michael P.
    Quantitative mobility analysis using wearable sensors, while promising as a diagnostic tool for Parkinson's disease (PD), is not commonly applied in clinical settings. Major obstacles include uncertainty regarding the best protocol for instrumented mobility testing and subsequent data processing, as well as the added workload and complexity of this multi-step process. To simplify sensor-based mobility testing in diagnosing PD, we analyzed data from 262 PD participants and 50 controls performing several motor tasks wearing a sensor on the lower back containing a triaxial accelerometer and a triaxial gyroscope. Using ensembles of heterogeneous machine learning models incorporating a range of classifiers trained on a large set of sensor features, we show that our models effectively differentiate between participants with PD and controls, both for mixed-stage PD (92.6% accuracy) and a group selected for mild PD only (89.4% accuracy). Omitting algorithmic segmentation of complex mobility tasks decreased the diagnostic accuracy of our models, as did the inclusion of kinesiological features. Feature importance analysis revealed Timed Up & Go (TUG) tasks to contribute highest-yield predictive features, with only minor decrease in accuracy for models based on cognitive TUG as a single mobility task. Our machine learning approach facilitates major simplification of instrumented mobility testing without compromising predictive performance.
  • Thumbnail Image
    Item
    Can RNA-Seq Resolve the Rapid Radiation of Advanced Moths and Butterflies (Hexapoda: Lepidoptera: Apoditrysia)? An Exploratory Study
    (PLoS One, 2013-12-04) Bazinet, Adam L.; Cummings, Michael P.; Mitter, Kim T.; Mitter, Charles W.
    Recent molecular phylogenetic studies of the insect order Lepidoptera have robustly resolved family-level divergences within most superfamilies, and most divergences among the relatively species-poor early-arising superfamilies. In sharp contrast, relationships among the superfamilies of more advanced moths and butterflies that comprise the mega-diverse clade Apoditrysia (ca. 145,000 spp.) remain mostly poorly supported. This uncertainty, in turn, limits our ability to discern the origins, ages and evolutionary consequences of traits hypothesized to promote the spectacular diversification of Apoditrysia. Low support along the apoditrysian “backbone” probably reflects rapid diversification. If so, it may be feasible to strengthen resolution by radically increasing the gene sample, but case studies have been few. We explored the potential of next-generation sequencing to conclusively resolve apoditrysian relationships. We used transcriptome RNA-Seq to generate 1579 putatively orthologous gene sequences across a broad sample of 40 apoditrysians plus four outgroups, to which we added two taxa from previously published data. Phylogenetic analysis of a 46-taxon, 741-gene matrix, resulting from a strict filter that eliminated ortholog groups containing any apparent paralogs, yielded dramatic overall increase in bootstrap support for deeper nodes within Apoditrysia as compared to results from previous and concurrent 19-gene analyses. High support was restricted mainly to the huge subclade Obtectomera broadly defined, in which 11 of 12 nodes subtending multiple superfamilies had bootstrap support of 100%. The strongly supported nodes showed little conflict with groupings from previous studies, and were little affected by changes in taxon sampling, suggesting that they reflect true signal rather than artifacts of massive gene sampling. In contrast, strong support was seen at only 2 of 11 deeper nodes among the “lower”, non-obtectomeran apoditrysians. These represent a much harder phylogenetic problem, for which one path to resolution might include further increase in gene sampling, together with improved orthology assignments.
  • Thumbnail Image
    Item
    A comparative evaluation of sequence classification programs
    (2012-05-10) Bazinet, Adam L.; Cummings, Michael P.
    Background: A fundamental problem in modern genomics is to taxonomically or functionally classify DNA sequence fragments derived from environmental sampling (i.e., metagenomics). Several different methods have been proposed for doing this effectively and efficiently, and many have been implemented in software. In addition to varying their basic algorithmic approach to classification, some methods screen sequence reads for ’barcoding genes’ like 16S rRNA, or various types of protein-coding genes. Due to the sheer number and complexity of methods, it can be difficult for a researcher to choose one that is well-suited for a particular analysis. Results: We divided the very large number of programs that have been released in recent years for solving the sequence classification problem into three main categories based on the general algorithm they use to compare a query sequence against a database of sequences. We also evaluated the performance of the leading programs in each category on data sets whose taxonomic and functional composition is known. Conclusions: We found significant variability in classification accuracy, precision, and resource consumption of sequence classification programs when used to analyze various metagenomics data sets. However, we observe some general trends and patterns that will be useful to researchers who use sequence classification programs.