Heartbeat Anomaly Detection using Adversarial Oversampling

Cardiovascular diseases are one of the most common causes of death in the world. Prevention, knowledge of previous cases in the family, and early detection is the best strategy to reduce this fact. Different machine learning approaches to automatic diagnostic are being proposed to this task. As in most health problems, the imbalance between examples and classes is predominant in this problem and affects the performance of the automated solution. In this paper, we address the classification of heartbeats images in different cardiovascular diseases. We propose a two-dimensional Convolutional Neural Network for classification after using a InfoGAN architecture for generating synthetic images to unbalanced classes. We call this proposal Adversarial Oversampling and compare it with the classical oversampling methods as SMOTE, ADASYN, and RandomOversampling. The results show that the proposed approach improves the classifier performance for the minority classes without harming the performance in the balanced classes

Fr\'echet ChemNet Distance: A metric for generative models for molecules in drug discovery

The new wave of successful generative models in machine learning has increased the interest in deep learning driven de novo drug design. However, assessing the performance of such generative models is notoriously difficult. Metrics that are typically used to assess the performance of such generative models are the percentage of chemically valid molecules or the similarity to real molecules in terms of particular descriptors, such as the partition coefficient (logP) or druglikeness. However, method comparison is difficult because of the inconsistent use of evaluation metrics, the necessity for multiple metrics, and the fact that some of these measures can easily be tricked by simple rule-based systems. We propose a novel distance measure between two sets of molecules, called Fr\'echet ChemNet distance (FCD), that can be used as an evaluation metric for generative models. The FCD is similar to a recently established performance metric for comparing image generation methods, the Fr\'echet Inception Distance (FID). Whereas the FID uses one of the hidden layers of InceptionNet, the FCD utilizes the penultimate layer of a deep neural network called ChemNet, which was trained to predict drug activities. Thus, the FCD metric takes into account chemically and biologically relevant information about molecules, and also measures the diversity of the set via the distribution of generated molecules. The FCD's advantage over previous metrics is that it can detect if generated molecules are a) diverse and have similar b) chemical and c) biological properties as real molecules. We further provide an easy-to-use implementation that only requires the SMILES representation of the generated molecules as input to calculate the FCD. Implementations are available at: https://www.github.com/bioinf-jku/FCDComment: Implementations are available at: https://www.github.com/bioinf-jku/FC