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Python for Data Mining in Computer and System Sciences, M. Sc. Course

A selection from Stockholm University publication database

• A clustering framework for patient phenotyping with application to adverse drug events

  2020. Maria Bampa, Panagiotis Papapetrou, Jaakko Hollmén. 2020 IEEE 33rd International Symposium on Computer-Based Medical Systems (CBMS), 177-182

  Conference

  We present a clustering framework for identifying patient groups with Adverse Drug Reactions from Electronic Health Records (EHRs). The increased adoption of EHRs has brought changes in the way drug safety surveillance is carried out and plays an important role in effective drug regulation. Unsupervised machine learning methods using EHRs as their input can identify patients that share common meaningful information, without the need for expert input. In this work, we propose a generalized framework that exploits the strengths of different clustering algorithms and via clustering aggregation identifies consensus patient cluster profiles. Moreover, the inherent hierarchical structure of diagnoses and medication codes is exploited. We assess the statistical significance of the produced clusterings by applying a randomization technique that keeps the data distribution margins fixed, as we are interested in evaluating information that is not conveyed by the marginal distributions. The experimental findings suggest that the framework produces medically meaningful patient groups with regard to adverse drug events by investigating two use-cases, i.e., aplastic anaemia and drug-induced skin eruption.

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• Aggregate-Eliminate-Predict

  2019. Maria Bampa, Panagiotis Papapetrou.

  We study the problem of detecting adverse drug events in electronic healthcare records. The challenge in this work is to aggregate heterogeneous data types involving diagnosis codes, drug codes, as well as lab measurements. An earlier framework proposed for the same problem demonstrated promising predictive performance for the random forest classifier by using only lab measurements as data features. We extend this framework, by additionally including diagnosis and drug prescription codes, concurrently. In addition, we employ a recursive feature selection mechanism on top, that extracts the top-k most important features. Our experimental evaluation on five medical datasets of adverse drug events and six different classifiers, suggests that the integration of these additional features provides substantial and statistically significant improvements in terms of AUC, while employing medically relevant features.

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• Mining Adverse Drug Events Using Multiple Feature Hierarchies and Patient History Windows

  2019. Maria Bampa, Panagiotis Papapetrou. 19th IEEE International Conference on Data Mining Workshops

  Conference

  We study the problem of detecting adverse drug events in electronic health records. The challenge is this work is to aggregate heterogeneous data types involving lab measurements, diagnoses codes and medications codes. An earlier framework proposed for the same problem demonstrated promising predictive performance for the random forest classifier by using only lab measurements as data features. We extend this framework, by additionally including diagnosis and drug prescription codes, concurrently. In addition, we employ the concept of hierarchies of clinical codes as proposed by another work, in order to exploit the inherently complex nature of the medical data. Moreover, we extended the state-of-the-art by considering variable patient history lengths before the occurrence of an ADE event rather than a patient history of an arbitrary length. Our experimental evaluation on eight medical datasets of adverse drug events, five different patient history lengths, and six different classifiers, suggests that the integration of these additional features on the different window lengths provides significant improvements in terms of AUC while employing medically relevant features.

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Show all publications by Maria Bampa at Stockholm University