Pulmonary hypertension (PH) in newborns and infants is a complex condition associated with several pulmonary, cardiac, and systemic diseases contributing to morbidity and mortality. Thus, accurate and early detection of PH and the classification of its severity is crucial for appropriate and successful management. Using echocardiography, the primary diagnostic tool in pediatrics, human assessment is both time-consuming and expertise-demanding, raising the need for an automated approach. Little effort has been directed towards automatic assessment of PH using echocardiography, and the few proposed methods only focus on binary PH classification on the adult population. In this work, we present an explainable multi-view video-based deep learning approach to predict and classify the severity of PH for a cohort of 270 newborns using echocardiograms. We use spatio-temporal convolutional architectures for the prediction of PH from each view, and aggregate the predictions of the different views using majority voting. Our results show a mean F1-score of 0.84 for severity prediction and 0.92 for binary detection using 10-fold cross-validation and 0.63 for severity prediction and 0.78 for binary detection on the held-out test set. We complement our predictions with saliency maps and show that the learned model focuses on clinically relevant cardiac structures, motivating its usage in clinical practice. To the best of our knowledge, this is the first work for an automated assessment of PH in newborns using echocardiograms.

Hanna Ragnarsdottir^*, Ece Özkan Elsen^*, Holger Michel^*, Kieran Chin-Cheong, Laura Manduchi, Sven Wellmann^†, Julia E. Vogt^†
* denotes shared first authorship, ^† denotes shared last authorship

International Journal of Computer Vision

06.02.2024

LinkDOI

Appendicitis is among the most frequent reasons for pediatric abdominal surgeries. Previous decision support systems for appendicitis have focused on clinical, laboratory, scoring, and computed tomography data and have ignored abdominal ultrasound, despite its noninvasive nature and widespread availability. In this work, we present interpretable machine learning models for predicting the diagnosis, management and severity of suspected appendicitis using ultrasound images. Our approach utilizes concept bottleneck models (CBM) that facilitate interpretation and interaction with high-level concepts understandable to clinicians. Furthermore, we extend CBMs to prediction problems with multiple views and incomplete concept sets. Our models were trained on a dataset comprising 579 pediatric patients with 1709 ultrasound images accompanied by clinical and laboratory data. Results show that our proposed method enables clinicians to utilize a human-understandable and intervenable predictive model without compromising performance or requiring time-consuming image annotation when deployed. For predicting the diagnosis, the extended multiview CBM attained an AUROC of 0.80 and an AUPR of 0.92, performing comparably to similar black-box neural networks trained and tested on the same dataset.

Ricards Marcinkevics^*, Patricia Reis Wolfertstetter^*, Ugne Klimiene^*, Kieran Chin-Cheong, Alyssia Paschke, Julia Zerres, Markus Denzinger, David Niederberger, Sven Wellmann, Ece Özkan Elsen^†, Christian Knorr^†, Julia E. Vogt^†
* denotes shared first authorship, ^† denotes shared last authorship

Medical Image Analysis

01.01.2024

LinkDOICode

Background: The overarching goal of blood glucose forecasting is to assist individuals with type 1 diabetes (T1D) in avoiding hyper- or hypoglycemic conditions. While deep learning approaches have shown promising results for blood glucose forecasting in adults with T1D, it is not known if these results generalize to children. Possible reasons are physical activity (PA), which is often unplanned in children, as well as age and development of a child, which both have an effect on the blood glucose level. Materials and Methods: In this study, we collected time series measurements of glucose levels, carbohydrate intake, insulin-dosing and physical activity from children with T1D for one week in an ethics approved prospective observational study, which included daily physical activities. We investigate the performance of state-of-the-art deep learning methods for adult data—(dilated) recurrent neural networks and a transformer—on our dataset for short-term (30  min) and long-term (2  h) prediction. We propose to integrate static patient characteristics, such as age, gender, BMI, and percentage of basal insulin, to account for the heterogeneity of our study group. Results: Integrating static patient characteristics (SPC) proves beneficial, especially for short-term prediction. LSTMs and GRUs with SPC perform best for a prediction horizon of 30  min (RMSE of 1.66  mmol/l), a vanilla RNN with SPC performs best across different prediction horizons, while the performance significantly decays for long-term prediction. For prediction during the night, the best method improves to an RMSE of 1.50  mmol/l. Overall, the results for our baselines and RNN models indicate that blood glucose forecasting for children conducting regular physical activity is more challenging than for previously studied adult data. Conclusion: We find that integrating static data improves the performance of deep-learning architectures for blood glucose forecasting of children with T1D and achieves promising results for short-term prediction. Despite these improvements, additional clinical studies are warranted to extend forecasting to longer-term prediction horizons.

Alexander Marx, Francesco Di Stefano, Heike Leutheuser, Kieran Chin-Cheong, Marc Pfister, Marie-Anne Burckhardt, Sara Bachmann^†, Julia E. Vogt^†
† denotes shared last authorship

Frontiers in Pediatrics

14.12.2023

LinkDOI

Appendicitis is among the most frequent reasons for pediatric abdominal surgeries. With recent advances in machine learning, data-driven decision support could help clinicians diagnose and manage patients while reducing the number of non-critical surgeries. However, previous decision support systems for appendicitis have focused on clinical, laboratory, scoring, and computed tomography data and have ignored the use of abdominal ultrasound, despite its noninvasive nature and widespread availability. In this work, we present interpretable machine learning models for predicting the diagnosis, management and severity of suspected appendicitis using ultrasound images. To this end, our approach utilizes concept bottleneck models (CBM) that facilitate interpretation and interaction with high-level concepts that are understandable to clinicians. Furthermore, we extend CBMs to prediction problems with multiple views and incomplete concept sets. Our models were trained on a dataset comprising 579 pediatric patients with 1709 ultrasound images accompanied by clinical and laboratory data. Results show that our proposed method enables clinicians to utilize a human-understandable and intervenable predictive model without compromising performance or requiring time-consuming image annotation when deployed.

Ricards Marcinkevics^*, Patricia Reis Wolfertstetter^*, Ugne Klimiene^*, Kieran Chin-Cheong, Alyssia Paschke, Julia Zerres, Markus Denzinger, David Niederberger, Sven Wellmann, Ece Özkan Elsen^†, Christian Knorr^†, Julia E. Vogt^†
* denotes shared first authorship, ^† denotes shared last authorship

Workshop on Machine Learning for Multimodal Healthcare Data, Co-located with ICML 2023

29.07.2023

Multimodal variational autoencoders (VAEs) have shown promise as efficient generative models for weakly-supervised data. Yet, despite their advantage of weak supervision, they exhibit a gap in generative quality compared to unimodal VAEs, which are completely unsupervised. In an attempt to explain this gap, we uncover a fundamental limitation that applies to a large family of mixture-based multimodal VAEs. We prove that the sub-sampling of modalities enforces an undesirable upper bound on the multimodal ELBO and thereby limits the generative quality of the respective models. Empirically, we showcase the generative quality gap on both synthetic and real data and present the tradeoffs between different variants of multimodal VAEs. We find that none of the existing approaches fulfills all desired criteria of an effective multimodal generative model when applied on more complex datasets than those used in previous benchmarks. In summary, we identify, formalize, and validate fundamental limitations of VAE-based approaches for modeling weakly-supervised data and discuss implications for real-world applications.

Imant Daunhawer, Thomas M. Sutter, Kieran Chin-Cheong, Emanuele Palumbo, Julia E. Vogt

The Tenth International Conference on Learning Representations, ICLR 2022

07.04.2022

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Constrained clustering has gained significant attention in the field of machine learning as it can leverage prior information on a growing amount of only partially labeled data. Following recent advances in deep generative models, we propose a novel framework for constrained clustering that is intuitive, interpretable, and can be trained efficiently in the framework of stochastic gradient variational inference. By explicitly integrating domain knowledge in the form of probabilistic relations, our proposed model (DC-GMM) uncovers the underlying distribution of data conditioned on prior clustering preferences, expressed as pairwise constraints. These constraints guide the clustering process towards a desirable partition of the data by indicating which samples should or should not belong to the same cluster. We provide extensive experiments to demonstrate that DC-GMM shows superior clustering performances and robustness compared to state-of-the-art deep constrained clustering methods on a wide range of data sets. We further demonstrate the usefulness of our approach on two challenging real-world applications.

Laura Manduchi, Kieran Chin-Cheong, Holger Michel, Sven Wellmann, Julia E. Vogt

Accepted at NeurIPS 2021

14.12.2021

Unplanned hospital readmissions are a burden to patients and increase healthcare costs. A wide variety of machine learning (ML) models have been suggested to predict unplanned hospital readmissions. These ML models were often specifically trained on patient populations with certain diseases. However, it is unclear whether these specialized ML models—trained on patient subpopulations with certain diseases or defined by other clinical characteristics—are more accurate than a general ML model trained on an unrestricted hospital cohort. In this study based on an electronic health record cohort of consecutive inpatient cases of a single tertiary care center, we demonstrate that accurate prediction of hospital readmissions may be obtained by general, disease-independent, ML models. This general approach may substantially decrease the cost of development and deployment of respective ML models in daily clinical routine, as all predictions are obtained by the use of a single model.

Thomas Sutter, Jan A Roth, Kieran Chin-Cheong, Balthasar L Hug, Julia E Vogt

Journal of the American Medical Informatics Association

18.12.2020

LinkDOI

Electronic Health Records (EHRs) are commonly used by the machine learning community for research on problems specifically related to health care and medicine. EHRs have the advantages that they can be easily distributed and contain many features useful for e.g. classification problems. What makes EHR data sets different from typical machine learning data sets is that they are often very sparse, due to their high dimensionality, and often contain heterogeneous (mixed) data types. Furthermore, the data sets deal with sensitive information, which limits the distribution of any models learned using them, due to privacy concerns. For these reasons, using EHR data in practice presents a real challenge. In this work, we explore using Generative Adversarial Networks to generate synthetic, heterogeneous EHRs with the goal of using these synthetic records in place of existing data sets for downstream classification tasks. We will further explore applying differential privacy (DP) preserving optimization in order to produce DP synthetic EHR data sets, which provide rigorous privacy guarantees, and are therefore shareable and usable in the real world. The performance (measured by AUROC, AUPRC and accuracy) of our model's synthetic, heterogeneous data is very close to the original data set (within 3 - 5% of the baseline) for the non-DP model when tested in a binary classification task. Using strong (1,10^-5) DP, our model still produces data useful for machine learning tasks, albeit incurring a roughly 17% performance penalty in our tested classification task. We additionally perform a sub-population analysis and find that our model does not introduce any bias into the synthetic EHR data compared to the baseline in either male/female populations, or the 0-18, 19-50 and 51+ age groups in terms of classification performance for either the non-DP or DP variant.

Kieran Chin-Cheong, Thomas M. Sutter, Julia E. Vogt

Arxiv

07.06.2020

Link

Electronic Health Records (EHRs) are commonly used by the machine learning community for research on problems specifically related to health care and medicine. EHRs have the advantages that they can be easily distributed and contain many features useful for e.g. classification problems. What makes EHR data sets different from typical machine learning data sets is that they are often very sparse, due to their high dimensionality, and often contain heterogeneous data types. Furthermore, the data sets deal with sensitive information, which limits the distribution of any models learned using them, due to privacy concerns. In this work, we explore using Generative Adversarial Networks to generate synthetic, \textit{heterogeneous} EHRs with the goal of using these synthetic records in place of existing data sets. We will further explore applying differential privacy (DP) preserving optimization in order to produce differentially private synthetic EHR data sets, which provide rigorous privacy guarantees, and are therefore more easily shareable. The performance of our model's synthetic, heterogeneous data is very close to the original data set (within 4.5%) for the non-DP model. Although around 20% worse, the DP synthetic data is still usable for machine learning tasks.

Kieran Chin-Cheong, Thomas Sutter, Julia E. Vogt

Machine Learning for Health (ML4H) Workshop, NeurIPS 2019

12.12.2019