Welcome

We work on developing and extending new machine learning techniques for precision medicine, the life sciences and clinical data analysis. This field is exciting and challenging because new methods for a better understanding of diseases are enormous important. The field of action comprises many areas such as prediction of response to treatment in personalized medicine, (sparse) biomarker detection, tumor classification or the understanding of interactions between genes or groups of genes. The challenge lies not only in developing fast, robust and reliable systems but also in systems that are easy to interpret and usable in clinical practice.

News


Alexander and Ricards win best paper at ICDH2021

Congratulations to Alexander H. Hatteland and  Ricards Marcinkevics for winning best paper at ICDH2021 with their paper Exploring Relationships…


MDS Group organizing the Research2Clinics workshop at NeurIPS 2021

The Medical Data Science group is proud to help organize the Research2Clinics workshop at NeuIPS 2021. Please see the call for papers here.


Julia Vogt interviews with NZZ, Tagesschau and SRF Radio 1

Read, watch and listen to Julia Vogt's latest interviews


Publications


Abstract

Estimating conditional mutual information (CMI) is an essential yet challenging step in many machine learning and data mining tasks. Estimating CMI from data that contains both discrete and continuous variables, or even discrete-continuous mixture variables, is a particularly hard problem. In this paper, we show that CMI for such mixture variables, defined based on the Radon-Nikodym derivate, can be written as a sum of entropies, just like CMI for purely discrete or continuous data. Further, we show that CMI can be consistently estimated for discrete-continuous mixture variables by learning an adaptive histogram model. In practice, we estimate such a model by iteratively discretizing the continuous data points in the mixture variables. To evaluate the performance of our estimator, we benchmark it against state-of-the-art CMI estimators as well as evaluate it in a causal discovery setting.

Authors

Alexander Marx, Lincen Yang, Matthijs van Leeuwen

Submitted

Proceedings of the SIAM International Conference on Data Mining (SDM)

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Abstract

Background: Current strategies for risk stratification and prediction of neonatal early-onset sepsis (EOS) are inefficient and lack diagnostic performance. The aim of this study was to use machine learning to analyze the diagnostic accuracy of risk factors (RFs), clinical signs and biomarkers and to develop a prediction model for culture-proven EOS. We hypothesized that the contribution to diagnostic accuracy of biomarkers is higher than of RFs or clinical signs. Study Design: Secondary analysis of the prospective international multicenter NeoPInS study. Neonates born after completed 34 weeks of gestation with antibiotic therapy due to suspected EOS within the first 72 hours of life participated. Primary outcome was defined as predictive performance for culture-proven EOS with variables known at the start of antibiotic therapy. Machine learning was used in form of a random forest classifier. Results: One thousand six hundred eighty-five neonates treated for suspected infection were analyzed. Biomarkers were superior to clinical signs and RFs for prediction of culture-proven EOS. C-reactive protein and white blood cells were most important for the prediction of the culture result. Our full model achieved an area-under-the-receiver-operating-characteristic-curve of 83.41% (+/-8.8%) and an area-under-the-precision-recall-curve of 28.42% (+/-11.5%). The predictive performance of the model with RFs alone was comparable with random. Conclusions: Biomarkers have to be considered in algorithms for the management of neonates suspected of EOS. A 2-step approach with a screening tool for all neonates in combination with our model in the preselected population with an increased risk for EOS may have the potential to reduce the start of unnecessary antibiotics.

Authors

Martin Stocker, Imant Daunhawer, Wendy van Herk, Salhab el Helou, Sourabh Dutta, Frank A. B. A.Schuerman, Rita K. van den Tooren-de Groot, ; Jantien W. Wieringa, Jan Janota, Laura H. van der Meer-Kappelle, Rob Moonen, Sintha D. Sie, Esther de Vries, Albertine E. Donker, Urs Zimmerman, Luregn J. Schlapbach, Amerik C. de Mol, Angelique Hoffmann-Haringsma, Madan Roy, Maren Tomaske, René F. Kornelisse, Juliette van Gijsel, Frans B. Plötz, Sven Wellmann, Niek B Achten, Dirk Lehnick, Annemarie M. C. van Rossum, Julia E. Vogt

Submitted

The Pediatric Infectious Disease Journal

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Abstract

Autonomic peripheral activity is partly governed by brain autonomic centers. However, there is still a lot of uncertainties regarding the precise link between peripheral and central autonomic biosignals. Clarifying these links could have a profound impact on the interpretability, and thus usefulness, of peripheral autonomic biosignals captured with wearable devices. In this study, we take advantage of a unique dataset consisting of intracranial stereo-electroencephalography (SEEG) and peripheral biosignals acquired simultaneously for several days from four subjects undergoing epilepsy monitoring. Compared to previous work, we apply a deep neural network to explore high-dimensional nonlinear correlations between the cerebral brainwaves and variations in heart rate and electrodermal activity (EDA). Further, neural network explainability methods were applied to identify most relevant brainwave frequencies, brain regions and temporal information to predict a specific biosignal. Strongest brain-peripheral correlations were observed from contacts located in the central autonomic network, in particular in the alpha, theta and 52 to 58 Hz frequency band. Furthermore, a temporal delay of 12 to 14 s between SEEG and EDA signal was observed. Finally, we believe that this pilot study demonstrates a promising approach to mapping brain-peripheral relationships in a data-driven manner by leveraging the expressiveness of deep neural networks.

Authors

Alexander H. Hatteland, Ricards Marcinkevics, Renaud Marquis, Thomas Frick, Ilona Hubbard, Julia E. Vogt, Thomas Brunschwiler, Philippe Ryvlin

Submitted

IEEE International Conference on Digital Health, ICDH 2021

Abstract

Survival analysis has gained significant attention in the medical domain and has many far-reaching applications. Although a variety of machine learning methods have been introduced for tackling time-to-event prediction in unstructured data with complex dependencies, clustering of survival data remains an under-explored problem. The latter is particularly helpful in discovering patient subpopulations whose survival is regulated by different generative mechanisms, a critical problem in precision medicine. To this end, we introduce a novel probabilistic approach to cluster survival data in a variational deep clustering setting. Our proposed method employs a deep generative model to uncover the underlying distribution of both the explanatory variables and the potentially censored survival times. We compare our model to the related work on survival clustering in comprehensive experiments on a range of synthetic, semi-synthetic, and real-world datasets. Our proposed method performs better at identifying clusters and is competitive at predicting survival times in terms of the concordance index and relative absolute error. To further demonstrate the usefulness of our approach, we show that our method identifies meaningful clusters from an observational cohort of hemodialysis patients that are consistent with previous clinical findings.

Authors

Laura Manduchi, Ricards Marcinkevics, Michela C. Massi, Verena Gotta, Timothy Müller, Flavio Vasella, Marian C. Neidert, Marc Pfister, Julia E. Vogt

Submitted

Arxiv

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Abstract

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.

Authors

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

Submitted

arXiv

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