MonoNet: enhancing interpretability in neural networks via monotonic features

MOTIVATION: Being able to interpret and explain the predictions made by a machine learning model is of fundamental importance. Unfortunately, a trade-off between accuracy and interpretability is often observed. As a result, the interest in developing more transparent yet powerful models has grown considerably over the past few years. Interpretable models are especially needed in high-stake scenarios, such as computational biology and medical informatics, where erroneous or biased models’ predictions can have deleterious consequences for a patient. Furthermore, understanding the inner workings of a model can help increase the trust in the model. RESULTS: We introduce a novel structurally constrained neural network, MonoNet, which is more transparent, while still retaining the same learning capabilities of traditional neural models. MonoNet contains monotonically connected layers that ensure monotonic relationships between (high-level) features and outputs. We show how, by leveraging the monotonic constraint in conjunction with other post hoc strategies, we can interpret our model. To demonstrate our model’s capabilities, we train MonoNet to classify cellular populations in a single-cell proteomic dataset. We also demonstrate MonoNet’s performance in other benchmark datasets in different domains, including non-biological applications (in the Supplementary Material). Our experiments show how our model can achieve good performance, while providing at the same time useful biological insights about the most important biomarkers. We finally carry out an information-theoretical analysis to show how the monotonic constraint actively contributes to the learning process of the model. AVAILABILITY AND IMPLEMENTATION: Code and sample data are available at https://github.com/phineasng/mononet. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Advances online.