Dataset Information

Feasibility of the deep learning method for estimating the ventilatory threshold with electrocardiography data.

ABSTRACT: Regular aerobic physical activity is of utmost importance in maintaining a good health status and preventing cardiovascular diseases (CVDs). Although cardiopulmonary exercise testing (CPX) is an essential examination for noninvasive estimation of ventilatory threshold (VT), defined as the clinically equivalent to aerobic exercise, its evaluation requires an expensive respiratory gas analyzer and expertize. To address these inconveniences, this study investigated the feasibility of a deep learning (DL) algorithm with single-lead electrocardiography (ECG) for estimating the aerobic exercise threshold. Two hundred sixty consecutive patients with CVDs who underwent CPX were analyzed. Single-lead ECG data were stored as time-series voltage data with a sampling rate of 1000?Hz. The data of preprocessed ECG and time point at VT calculated by respiratory gas analyzer were used to train a neural network. The trained model was applied on an independent test cohort, and the DL threshold (DLT; a time of VT estimated through the DL algorithm) was calculated. We compared the correlation between oxygen uptake of the VT (VT-VO₂) and the DLT (DLT-VO₂). Our DL model showed that the DLT-VO₂ was confirmed to be significantly correlated with the VT-VO₂ (r?=?0.875; P?P?>?0.05), which displayed strong agreements between the VT and the DLT. The DL algorithm using single-lead ECG data enabled accurate estimation of VT in patients with CVDs. The DL algorithm may be a novel way for estimating aerobic exercise threshold.

SUBMITTER: Miura K

PROVIDER: S-EPMC7596490 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Feasibility of the deep learning method for estimating the ventilatory threshold with electrocardiography data.

Miura Kotaro K Goto Shinichi S Katsumata Yoshinori Y Ikura Hidehiko H Shiraishi Yasuyuki Y Sato Kazuki K Fukuda Keiichi K

NPJ digital medicine 20201029

Regular aerobic physical activity is of utmost importance in maintaining a good health status and preventing cardiovascular diseases (CVDs). Although cardiopulmonary exercise testing (CPX) is an essential examination for noninvasive estimation of ventilatory threshold (VT), defined as the clinically equivalent to aerobic exercise, its evaluation requires an expensive respiratory gas analyzer and expertize. To address these inconveniences, this study investigated the feasibility of a deep learnin ...[more]

PMID: 33145437

Similar Datasets

Project description:Proteins interact with small molecules to modulate several important cellular functions. Many acute diseases were cured by small molecule binding in the active site of protein either by inhibition or activation. Currently, there are several docking programs to estimate the binding position and the binding orientation of protein-ligand complex. Many scoring functions were developed to estimate the binding strength and predict the effective protein-ligand binding. While the accuracy of current scoring function is limited by several aspects, the solvent effect, entropy effect, and multibody effect are largely ignored in traditional machine learning methods. In this paper, we proposed a new deep neural network-based model named DeepBindRG to predict the binding affinity of protein-ligand complex, which learns all the effects, binding mode, and specificity implicitly by learning protein-ligand interface contact information from a large protein-ligand dataset. During the initial data processing step, the critical interface information was preserved to make sure the input is suitable for the proposed deep learning model. While validating our model on three independent datasets, DeepBindRG achieves root mean squared error (RMSE) value of pKa (-logKd or -logKi) about 1.6-1.8 and R value around 0.5-0.6, which is better than the autodock vina whose RMSE value is about 2.2-2.4 and R value is 0.42-0.57. We also explored the detailed reasons for the performance of DeepBindRG, especially for several failed cases by vina. Furthermore, DeepBindRG performed better for four challenging datasets from DUD.E database with no experimental protein-ligand complexes. The better performance of DeepBindRG than autodock vina in predicting protein-ligand binding affinity indicates that deep learning approach can greatly help with the drug discovery process. We also compare the performance of DeepBindRG with a 4D based deep learning method "pafnucy", the advantage and limitation of both methods have provided clues for improving the deep learning based protein-ligand prediction model in the future.

Project description:BackgroundVentilatory anaerobic threshold (VAT) is a useful submaximal measure of exercise tolerance; however, it must be visually determined. We developed a new mathematical method to objectively determine VAT.MethodsWe employed two retrospective population data sets (A/B). Data A (from 128 healthy subjects, patients with cardiovascular risk factors, and cardiac subjects at institution A, who underwent symptom-limited cardiopulmonary exercise testing) were used to develop the method. Data B (from 163 cardiac patients at institution B, who underwent pre-/post-rehabilitation submaximal exercise testing) were used to apply the developed method. VAT (by V-slope) was visually determined (vVAT), assuming that the pre-VAT segment is parallel to the respiratory exchange ratio (R) = 1 line.ResultsFirst, from data A, exponential fitting of ramp V-slope data yielded the equation y = ba x, where a is the slope of the exponential function: a smaller value signified a less steep curve, representing less VCO2 against VO2. Next, a tangential line parallel to R = 1 was drawn. The x-axis value of the contact point was the derived VAT, termed the expVAT (VCO2) (calculated as LN (1/[b*LN(a)]/LN(a). This point represents an instantaneous ΔVCO2/ΔVO2 of 1.0. Second, in a similar way, the relation of VO2 vs. VE (minute ventilation) was fitted exponentially. The tangent line that crosses zero was drawn and the x-axis value was termed expVAT (VE) (calculated as 1/LN(a). For data A, the correlation coefficients (r) of vVAT versus VAT (CO2), and VAT (VE) were 0.924 and 0.903, respectively (p < 0.001), with no significant difference between mean values with the limits of agreement (1.96*SD of the pair difference) being ±276 and ± 278 mL/min, respectively. expVAT (VCO2) and expVAT (VE) significantly correlated with VO2peak (r = 0.971, r = 0.935, p < 0.001). For data B, after cardiac rehabilitation, expVAT (CO2) and exp. (VE) (mL/min) increased from 641 ± 185 to 685 ± 201 and from 696 ± 182 to 727 ± 209, respectively (p < 0.001, p < 0.008), while vVAT increased from 673 ± 191 to 734 ± 226 (p < 0.001). During submaximal testing, expVAT (VCO2) underestimated VAT, whereas expVAT (VE) did not.ConclusionsTwo new mathematically-derived estimates to determine VAT are promising because they yielded an objective VAT that significantly correlated with VO2peak, and detected training effect as well as visual VAT did.

Project description:SummaryIn recent years, SWATH-MS has become the proteomic method of choice for data-independent-acquisition, as it enables high proteome coverage, accuracy and reproducibility. However, data analysis is convoluted and requires prior information and expert curation. Furthermore, as quantification is limited to a small set of peptides, potentially important biological information may be discarded. Here we demonstrate that deep learning can be used to learn discriminative features directly from raw MS data, eliminating hence the need of elaborate data processing pipelines. Using transfer learning to overcome sample sparsity, we exploit a collection of publicly available deep learning models already trained for the task of natural image classification. These models are used to produce feature vectors from each mass spectrometry (MS) raw image, which are later used as input for a classifier trained to distinguish tumor from normal prostate biopsies. Although the deep learning models were originally trained for a completely different classification task and no additional fine-tuning is performed on them, we achieve a highly remarkable classification performance of 0.876 AUC. We investigate different types of image preprocessing and encoding. We also investigate whether the inclusion of the secondary MS2 spectra improves the classification performance. Throughout all tested models, we use standard protein expression vectors as gold standards. Even with our naïve implementation, our results suggest that the application of deep learning and transfer learning techniques might pave the way to the broader usage of raw mass spectrometry data in real-time diagnosis.Availability and implementationThe open source code used to generate the results from MS images is available on GitHub: https://ibm.biz/mstransc. The raw MS data underlying this article cannot be shared publicly for the privacy of individuals that participated in the study. Processed data including the MS images, their encodings, classification labels and results can be accessed at the following link: https://ibm.box.com/v/mstc-supplementary.Supplementary informationSupplementary data are available at Bioinformatics online.

Project description:Left ventricular hypertrophy is a significant independent risk factor for all-cause mortality and morbidity, and an accurate diagnosis at an early stage of heart change is clinically significant. Electrocardiography is the most convenient, economical, and non-invasive method for screening in primary care. However, the coincidence rate of the actual left ventricular hypertrophy and diagnostic findings was low, consequently increasing the interest in algorithms using big data and deep learning. We attempted to diagnose left ventricular hypertrophy using big data and deep learning algorithms, and aimed to confirm its diagnostic power according to the differences between males and females. This retrospective study used electrocardiographs obtained at Yonsei University Wonju Severance Christian Hospital, Wonju, Korea, from October 2010 to February 2020. Binary classification was performed for primary screening for left ventricular hypertrophy. Three datasets were used for the experiment: the male, female, and entire dataset. A cutoff for binary classification was defined as the meaningful as a screening test (<132 g/m2 vs. ≥132 g/m2, <109 g/m2 vs. ≥109 g/m2). Six types of input were used for the classification tasks. We attempted to determine whether electrocardiography had predictive power for left ventricular hypertrophy diagnosis. For the entire dataset, the model achieved an area under the receiver operating characteristic (AUROC) curve of 0.836 (95% CI, 0.833-838) with a sensitivity of 78.37% (95% CI, 76.79-79.95). For the male dataset, the AUROC was 0.826 (95% CI, 0.822-830) with a sensitivity of 76.73% (95% CI, 75.14-78.33). For the female dataset, the AUROC was 0.772 (95% CI, 0.769-775) with a sensitivity of 72.90% (95% CI, 70.33-75.46). Our model confirmed that left ventricular hypertrophy can be classified to some extent using electrocardiography, demographics, and electrocardiography features. In particular, a learning environment that considered gender differences was constructed. Consequently, the difference in diagnostic power between men and women was confirmed. Our model will help patients with suspected left ventricular hypertrophy to undergo screening tests at a low cost. In addition, our research and attempts will show the expected effect that gender-consideration approaches can help with various currently proposed diagnostic methods.

Dataset Information

Feasibility of the deep learning method for estimating the ventilatory threshold with electrocardiography data.

Publications

Feasibility of the deep learning method for estimating the ventilatory threshold with electrocardiography data.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets