Motivation
Mixed molecular data combines continuous and categorical features of the same samples, such as OMICS profiles with genotypes, diagnoses, or patient sex. Like all high dimensional molecular data it is prone to incorrect values that can stem from various sources as for example the technical limitations of the measurement devices, errors in the sample preparation or contamination. Most anomaly detection algorithms identify complete samples as outliers or anomalies. However, in most cases, not all measurements of those samples are erroneous but only a few one-dimensional features within the samples are incorrect. These one-dimensional data errors are continuous measurements that are either located outside or inside the normal ranges of their features but in both cases show atypical values given all other continuous and categorical features in the sample. Additionally, categorical anomalies can occur for example when the genotype or diagnosis was submitted wrongly.
Results
We introduce ADMIRE (Anomaly Detection using MIxed gRaphical modEls), a novel approach for the detection and correction of anomalies in mixed high dimensional data. Hereby, we focus on the detection of single (one-dimensional) data errors in the categorical and continuous features of a sample. For that the joint distribution of continuous and categorical features is learned by Mixed Graphical Models, anomalies are detected by the difference between measured and model-based estimations and are corrected using imputation. We evaluated ADMIRE in simulation and by screening for anomalies in one of our own metabolic data sets. In simulation experiments ADMIRE outperformed the state-of-the-art methods Local Outlier Factor, stray and Isolation Forest.
Availability
All data and code is available at https://github.com/spang-lab/adadmire. ADMIRE is implemented in a python package called adadmire which can be found at https://pypi.org/project/adadmire.