On Entity Embeddings for Ordinal Features as Representation Learning in Recurrence Prediction of Urothelial Bladder Cancer.

BACKGROUND: Urothelial Bladder Cancer (UBC) is a common cancer with a high risk of recurrence, which is influenced by the TNM classification, grading, age, and other factors. Recent studies demonstrate reliable and accurate recurrence prediction using Machine Learning (ML) algorithms and even outperform traditional approaches. However, most ML algorithms cannot process categorical input features, which must first be encoded into numerical values. Choosing the appropriate encoding strategy has a significant impact on the prediction quality. OBJECTIVE: We investigate the impact of encoding strategies for ordinal features in the prediction quality of ML algorithms. METHOD: We compare three different encoding strategies namely one-hot, ordinal, and entity embedding in predicting the 2-year recurrence in UBC patients using an artificial neural network. We use ordered categorical and numerical data of UBC patients provided by the Cancer Registry Rhineland-Palatinate. RESULTS: We show superior prediction quality using entity embedding encoding with 84.6% precision, an overall accuracy of 73.8%, and 68.9% AUC on testing data over 100 epochs after 30 runs compared to one-hot and ordinal encoding. CONCLUSION: We confirm the superiority of entity embedding encoding as it could provide a more detailed and accurate representation of ordinal features in numerical scales. This can lead to enhanced generalizability, resulting in significantly improved prediction quality.

On relevant features for the recurrence prediction of urothelial carcinoma of the bladder.

BACKGROUND: Urothelial bladder cancer (UBC) is characterized by a high recurrence rate, which is predicted by scoring systems. However, recent studies show the superiority of Machine Learning (ML) models. Nevertheless, these ML approaches are rarely used in medical practice because most of them are black-box models, that cannot adequately explain how a prediction is made. OBJECTIVE: We investigate the global feature importance of different ML models. By providing information on the most relevant features, we can facilitate the use of ML in everyday medical practice. DESIGN, SETTING, AND PARTICIPANTS: The data is provided by the cancer registry Rhineland-Palatinate gGmbH, Germany. It consists of numerical and categorical features of 1,944 patients with UBC. We retrospectively predict 2-year recurrence through ML models using Support Vector Machine, Gradient Boosting, and Artificial Neural Network. We then determine the global feature importance using performance-based Permutation Feature Importance (PFI) and variance-based Feature Importance Ranking Measure (FIRM). RESULTS: We show reliable recurrence prediction of UBC with 82.02% to 83.89% F1-Score, 83.95% to 84.49% Precision, and an overall performance of 69.20% to 70.82% AUC on testing data, depending on the model. Gradient Boosting performs best among all black-box models with an average F1-Score (83.89%), AUC (70.82%), and Precision (83.95%). Furthermore, we show consistency across PFI and FIRM by identifying the same features as relevant across the different models. These features are exclusively therapeutic measures and are consistent with findings from both medical research and clinical trials. CONCLUSIONS: We confirm the superiority of ML black-box models in predicting UBC recurrence compared to more traditional logistic regression. In addition, we present an approach that increases the explanatory power of black-box models by identifying the underlying influence of input features, thus facilitating the use of ML in clinical practice and therefore providing improved recurrence prediction through the application of black-box models.