Optimizing support vector machines and autoregressive integrated moving average methods for heart rate variability data correction

Heart rate variability (HRV) is the variation in time between successive heartbeats and can be used as an indirect measure of autonomic nervous system (ANS) activity. During physical exercise, movement of the measuring device can cause artifacts in the HRV data, severely affecting the analysis of the HRV data. Current methods used for data artifact correction perform insufficiently when HRV is measured during exercise. In this paper we propose the use of autoregressive integrated moving average (ARIMA) and support vector regression (SVR) for HRV data artifact correction. Since both methods are only trained on previous data points, they can be applied not only for correction (i.e., gap filling), but also prediction (i.e., forecasting future values). Our paper describes: • why HRV is difficult to predict and why ARIMA and SVR might be valuable options. • finding the best hyperparameters for using ARIMA and SVR to correct HRV data, including which criterion to use for choosing the best model. • which correction method should be used given the data at hand.publishedVersio

Recurrent Neural Networks for Artifact Correction in HRV Data During Physical Exercise

In this paper, we propose the use of recurrent neural networks (RNNs) for artifact correction and analysis of heart rate variability (HRV) data. HRV can be a valuable metric for determining the function of the heart and the autonomic nervous system. When measured during exercise, motion artifacts present a significant challenge. Several methods for artifact correction have previously been proposed, none of them applying machine learning, and each presenting some limitations regarding an accurate representation of HRV metrics. RNNs offer the ability to capture patterns that might otherwise not be detected, yielding predictions where no prior physiological assumptions are needed. A hyperparameter search has been carried out to determine the best network configuration and the most important hyperparameters. The approach was tested on two extensive multi-subject data sets, one from a recreational bicycle race and the other from a laboratory experiment. The results demonstrate that RNNs outperform by order of magnitude existing methods with respect to the calculation of derived HRV metrics. However, they are not able to accurately fill in individual missing RR intervals in sequence. Future research should pursue improvements in the prediction of RR interval lengths and reduction in necessary training data.publishedVersio

3D Masked Modelling Advances Lesion Classification in Axial T2w Prostate MRI

Masked Image Modelling (MIM) has been shown to be an efficient self-supervised learning (SSL) pre-training paradigm when paired with transformer architectures and in the presence of a large amount of unlabelled natural images. The combination of the difficulties in accessing and obtaining large amounts of labeled data and the availability of unlabelled data in the medical imaging domain makes MIM an interesting approach to advance deep learning (DL) applications based on 3D medical imaging data. Nevertheless, SSL and, in particular, MIM applications with medical imaging data are rather scarce and there is still uncertainty around the potential of such a learning paradigm in the medical domain. We study MIM in the context of Prostate Cancer (PCa) lesion classification with T2 weighted (T2w) axial magnetic resonance imaging (MRI) data. In particular, we explore the effect of using MIM when coupled with convolutional neural networks (CNNs) under different conditions such as different masking strategies, obtaining better results in terms of AUC than other pre-training strategies like ImageNet weight initialization.publishedVersio

Invasive cancerous area detection in non-muscle invasive bladder cancer whole slide images

Bladder cancer patients’ stratification into risk groups relies on grade, stage and clinical factors. For non-muscle invasive bladder cancer, T1 tumours that invade the subepithelial tissue are high-risk lesions with a high probability to progress into an aggressive muscle-invasive disease. Detecting invasive cancerous areas is the main factor for dictating the treatment strategy for the patient. However, defining invasion is often subject to intra/interobserver variability among pathologists, thus leading to over or undertreatment. Computer-aided diagnosis systems can help pathologists reduce overheads and erratic reproducibility. We propose a multi-scale model that detects invasive cancerous areas patterns across the whole slide image. The model extracts tiles of different tissue types at multiple magnification levels and processes them to predict invasive patterns based on local and regional information for accurate T1 staging. Our proposed method yields an F1 score of 71.9, in controlled settings 74.9, and without infiltration 90.0.acceptedVersio

A probabilistic function to model the relationship between quality of chest compressions and the physiological response for patients in cardiac arrest

Cardiopulmonary resuscitation quality (CPRQ) parameters can be derived from electric signals obtained during resuscitation. We propose to model a probabilistic relationship between CPRQ parameters and the physiological response as judged by ECG-features, to guide therapy in a clinical context. A total of 821 compression sequences were extracted from 394 out-of-hospital resuscitation episodes. Sequences were categorized as effective if the post sequence cardiac rhythm had better prognosis than the pre-sequence rhythm by a positive difference, otherwise as non effective if the difference was negative. CPRQ parameters related to depth and rate were calculated. Three alternative approaches were designed for the binary classifier based on the CPRQ parameters: quadratic discriminant analysis (QDA), logistic regression (LR) and artificial neural networks (ANN). The positive class discriminant function defined the probability of effective compressions (Pec). The classification accuracies were around 0.6 for all three models. The highest probability estimates of effective chest compressions corresponded to the depth (5–6 cm) and rate (100–120 min −1 ) currently recommended in the CPR guidelines. We have proposed a novel method to relate the quality of chest compressions to the physiologic response to CPR.acceptedVersio

Duration of elevated heart rate Is an important predictor of exercise-induced troponin elevation

Background The precise mechanisms causing cardiac troponin (cTn) increase after exercise remain to be determined. The aim of this study was to investigate the impact of heart rate (HR) on exercise‐induced cTn increase by using sports watch data from a large bicycle competition. Methods and Results Participants were recruited from NEEDED (North Sea Race Endurance Exercise Study). All completed a 91‐km recreational mountain bike race (North Sea Race). Clinical status, ECG, blood pressure, and blood samples were obtained 24 hours before and 3 and 24 hours after the race. Participants (n=177) were, on average, 44 years old; 31 (18%) were women. Both cTnI and cTnT increased in all individuals, reaching the highest level (of the 3 time points assessed) at 3 hours after the race (P150 beats per minute was a significant predictor of both cTnI and cTnT, at both 3 and 24 hours after exercise. Neither mean HR nor mean HR in percentage of maximum HR was a significant predictor of the cTn response at 3 and 24 hours after exercise. Conclusions The duration of elevated HR is an important predictor of physiological exercise‐induced cTn elevation.publishedVersio

Factors Affecting the Course of Resuscitation From Cardiac Arrest With Pulseless Electrical Activity in Children and Adolescents

Background: Although in-hospital pediatric cardiac arrests and cardiopulmonary resuscitation occur >15,000/year in the US, few studies have assessed which factors affect the course of resuscitation in these patients. We investigated transitions from Pulseless Electrical Activity (PEA) to Ventricular Fibrillation/pulseless Ventricular Tachycardia (VF/pVT), Return of Spontaneous Circulation (ROSC) and recurrences from ROSC to PEA in children and adolescents with in-hospital cardiac arrest. Methods: Episodes of cardiac arrest at the Children's Hospital of Philadelphia were prospectively registered. Defibrillators that recorded chest compression depth/rate and ventilation rate were applied. CPR variables, patient characteristics and etiology, and dynamic factors (e.g. the proportion of time spent in PEA or ROSC) were entered as time-varying covariates for the transition intensities under study. Results: In 67 episodes of CPR in 59 patients (median age 15 years) with cardiac arrest, there were 52 transitions from PEA to ROSC, 22 transitions from PEA to VF/pVT, and 23 recurrences of PEA from ROSC. Except for a nearly significant effect of mean compression depth beyond a threshold of 5.7 cm, only dynamic factors that evolved during CPR favored a transition from PEA to ROSC. The latter included a lower proportion of PEA over the last 5 min and a higher proportion of ROSC over the last 5 min. Factors associated with PEA to VF/pVT development were age, weight, the proportion spent in VF/pVT or PEA the last 5 min, and the general transition intensity, while PEA recurrence from ROSC only depended on the general transition intensity. Conclusion: The clinical course during pediatric cardiac arrest was mainly influenced by dynamic factors associated with time in PEA and ROSC. Transitions from PEA to ROSC seemed to be favored by deeper compressions.publishedVersio

A Multiscale Approach for Whole-Slide Image Segmentation of five Tissue Classes in Urothelial Carcinoma Slides

In pathology labs worldwide, we see an increasing number of tissue samples that need to be assessed without the same increase in the number of pathologists. Computational pathology, where digital scans of histological samples called whole-slide images (WSI) are processed by computational tools, can be of help for the pathologists and is gaining research interests. Most research effort has been given to classify slides as being cancerous or not, localization of cancerous regions, and to the “big-four” in cancer: breast, lung, prostate, and bowel. Urothelial carcinoma, the most common form of bladder cancer, is expensive to follow up due to a high risk of recurrence, and grading systems have a high degree of inter- and intra-observer variability. The tissue samples of urothelial carcinoma contain a mixture of damaged tissue, blood, stroma, muscle, and urothelium, where it is mainly muscle and urothelium that is diagnostically relevant. A coarse segmentation of these tissue types would be useful to i) guide pathologists to the diagnostic relevant areas of the WSI, and ii) use as input in a computer-aided diagnostic (CAD) system. However, little work has been done on segmenting tissue types in WSIs, and on computational pathology for urothelial carcinoma in particular. In this work, we are using convolutional neural networks (CNN) for multiscale tile-wise classification and coarse segmentation, including both context and detail, by using three magnification levels: 25x, 100x, and 400x. 28 models were trained on weakly labeled data from 32 WSIs, where the best model got an F1-score of 96.5% across six classes. The multiscale models were consistently better than the single-scale models, demonstrating the benefit of combining multiple scales. No tissue-class ground-truth for complete WSIs exist, but the best models were used to segment seven unseen WSIs where the results were manually inspected by a pathologist and are considered as very promising.publishedVersio

Texture-based probability mapping for automatic scar assessment in late gadolinium-enhanced cardiovascular magnetic resonance images

Purpose To evaluate a novel texture-based probability mapping (TPM) method for scar size estimation in LGE-CMRI. Methods This retrospective proof-of-concept study included chronic myocardial scars from 52 patients. The TPM was compared with three signal intensity-based methods: manual segmentation, full-width-half-maximum (FWHM), and 5-standard deviation (5-SD). TPM is generated using machine learning techniques, expressing the probability of scarring in pixels. The probability is derived by comparing the texture of the 3 × 3 pixel matrix surrounding each pixel with reference dictionaries from patients with established myocardial scars. The Sørensen-Dice coefficient was used to find the optimal TPM range. A non-parametric test was used to test the correlation between infarct size and remodeling parameters. Bland-Altman plots were performed to assess agreement among the methods. Results The study included 52 patients (76.9% male; median age 64.5 years (54, 72.5)). A TPM range of 0.328–1.0 was found to be the optimal probability interval to predict scar size compared to manual segmentation, median dice (25th and 75th percentiles)): 0.69(0.42–0.81). There was no significant difference in the scar size between TPM and 5-SD. However, both 5-SD and TPM yielded larger scar sizes compared with FWHM (p < 0.001 and p = 0.002). There were strong correlations between scar size measured by TPM, and left ventricular ejection fraction (LVEF, r = −0.76, p < 0.001), left ventricular end-diastolic volume index (r = 0.73, p < 0.001), and left ventricular end-systolic volume index (r = 0.75, p < 0.001). Conclusion The TPM method is comparable with current SI-based methods, both for the scar size assessment and the relationship with left ventricular remodeling when applied on LGE-CMRI.publishedVersio

Optimizing support vector machines and autoregressive integrated moving average methods for heart rate variability data correction

Heart rate variability (HRV) is the variation in time between successive heartbeats and can be used as an indirect measure of autonomic nervous system (ANS) activity. During physical exercise, movement of the measuring device can cause artifacts in the HRV data, severely affecting the analysis of the HRV data. Current methods used for data artifact correction perform insufficiently when HRV is measured during exercise. In this paper we propose the use of autoregressive integrated moving average (ARIMA) and support vector regression (SVR) for HRV data artifact correction. Since both methods are only trained on previous data points, they can be applied not only for correction (i.e., gap filling), but also prediction (i.e., forecasting future values). Our paper describes: • why HRV is difficult to predict and why ARIMA and SVR might be valuable options. • finding the best hyperparameters for using ARIMA and SVR to correct HRV data, including which criterion to use for choosing the best model. • which correction method should be used given the data at hand