TY - JOUR

T1 - Using convolutional neural network to measure the physiological age of Caenorhabditis elegans

AU - Lin, Jiunn Liang

AU - Kuo, Wei-Liang

AU - Huang, Yi Hao

AU - Jong, Tai Lang

AU - Hsu, Ao-Lin

AU - Hsu, Wen Hsing

PY - 2021/12/8

Y1 - 2021/12/8

N2 - Caenorhabditis elegans ( C. elegans ) is a popular and excellent model for studies of aging due to its short lifespan. Methods for precisely measuring the physiological age of C. elegans are critically needed, especially for antiaging drug screening and genetic screening studies. The effects of various antiaging interventions on the rate of aging in the early stage of the aging process can be determined based on the quantification of physiological age. However, in general, the age of C. elegans is evaluated via human visual inspection of morphological changes based on personal experience and subjective judgment. For example, the rate of motor activity decay has been used to predict lifespan in early- to mid-stage aging. Using image processing, the physiological age of C. elegans can be measured and then classified into periods or classes from childhood to elderhood (e.g., 3 periods comprising days 0–2, 4–6 and 10–12) by using texture entropy (Shamir, L. et al., 2009). Our dataset consists of 913 microscopic images of C. elegans , with approximately 60 images per day from day 1 to day 14 of adulthood. We present quantitative methods to measure the physiological age of C. elegans with convolution neural networks (CNNs), which can measure age with a granularity of days rather than periods. The methods achieved a mean absolute error (MAE) of less than 1 day for the measured age of C. elegans . In our experiments, we found that after training and testing our dataset, 5 popular CNN models, 50-layer residual network (ResNet50), InceptionV3, InceptionResNetV2, 16-layer Visual Geometry Group network (VGG16) and MobileNet, measured the physiological age of C. elegans with an average testing MAE of 1.58 days. Furthermore, based on the results, we propose two models, one model for linear regression analysis and the other model for logistic regression, that combine a CNN model and a new attribute: curved_or_straight. The linear regression analysis model achieved a test MAE of 0.94 days; the logistic regression model achieved an accuracy of 84.78 percent with an error tolerance of 1 day.

AB - Caenorhabditis elegans ( C. elegans ) is a popular and excellent model for studies of aging due to its short lifespan. Methods for precisely measuring the physiological age of C. elegans are critically needed, especially for antiaging drug screening and genetic screening studies. The effects of various antiaging interventions on the rate of aging in the early stage of the aging process can be determined based on the quantification of physiological age. However, in general, the age of C. elegans is evaluated via human visual inspection of morphological changes based on personal experience and subjective judgment. For example, the rate of motor activity decay has been used to predict lifespan in early- to mid-stage aging. Using image processing, the physiological age of C. elegans can be measured and then classified into periods or classes from childhood to elderhood (e.g., 3 periods comprising days 0–2, 4–6 and 10–12) by using texture entropy (Shamir, L. et al., 2009). Our dataset consists of 913 microscopic images of C. elegans , with approximately 60 images per day from day 1 to day 14 of adulthood. We present quantitative methods to measure the physiological age of C. elegans with convolution neural networks (CNNs), which can measure age with a granularity of days rather than periods. The methods achieved a mean absolute error (MAE) of less than 1 day for the measured age of C. elegans . In our experiments, we found that after training and testing our dataset, 5 popular CNN models, 50-layer residual network (ResNet50), InceptionV3, InceptionResNetV2, 16-layer Visual Geometry Group network (VGG16) and MobileNet, measured the physiological age of C. elegans with an average testing MAE of 1.58 days. Furthermore, based on the results, we propose two models, one model for linear regression analysis and the other model for logistic regression, that combine a CNN model and a new attribute: curved_or_straight. The linear regression analysis model achieved a test MAE of 0.94 days; the logistic regression model achieved an accuracy of 84.78 percent with an error tolerance of 1 day.

U2 - 10.1109/TCBB.2020.2971992

DO - 10.1109/TCBB.2020.2971992

M3 - Article

C2 - 32031946

SN - 1545-5963

VL - 18

SP - 2724

EP - 2732

JO - IEEE/ACM Transactions on Computational Biology and Bioinformatics

JF - IEEE/ACM Transactions on Computational Biology and Bioinformatics

IS - 6

ER -