Philipp Renz

Philipp Renz, Kurt Cutajar, Niall Twomey et al.

Low-count time series describe sparse or intermittent events, which are prevalent in large-scale online platforms that capture and monitor diverse data types. Several distinct challenges surface when modelling low-count time series, particularly low signal-to-noise ratios (when anomaly signatures are provably undetectable), and non-uniform performance (when average metrics are not representative of local behaviour). The time series anomaly detection community currently lacks explicit tooling and processes to model and reliably detect anomalies in these settings. We address this gap by introducing a novel generative procedure for creating benchmark datasets comprising of low-count time series with anomalous segments. Via a mixture of theoretical and empirical analysis, our work explains how widely-used algorithms struggle with the distribution overlap between normal and anomalous segments. In order to mitigate this shortcoming, we then leverage our findings to demonstrate how anomaly score smoothing consistently improves performance. The practical utility of our analysis and recommendation is validated on a real-world dataset containing sales data for retail stores.

Markus Hofmarcher, Andreas Mayr, Elisabeth Rumetshofer et al.

Due to the current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, there is an urgent need for novel therapies and drugs. We conducted a large-scale virtual screening for small molecules that are potential CoV-2 inhibitors. To this end, we utilized "ChemAI", a deep neural network trained on more than 220M data points across 3.6M molecules from three public drug-discovery databases. With ChemAI, we screened and ranked one billion molecules from the ZINC database for favourable effects against CoV-2. We then reduced the result to the 30,000 top-ranked compounds, which are readily accessible and purchasable via the ZINC database. Additionally, we screened the DrugBank using ChemAI to allow for drug repurposing, which would be a fast way towards a therapy. We provide these top-ranked compounds of ZINC and DrugBank as a library for further screening with bioassays at https://github.com/ml-jku/sars-cov-inhibitors-chemai.

Kristina Preuer, Philipp Renz, Thomas Unterthiner et al.

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 Fréchet 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 Fréchet 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/FCD

Philipp Seidl, Philipp Renz, Natalia Dyubankova et al.

Finding synthesis routes for molecules of interest is an essential step in the discovery of new drugs and materials. To find such routes, computer-assisted synthesis planning (CASP) methods are employed which rely on a model of chemical reactivity. In this study, we model single-step retrosynthesis in a template-based approach using modern Hopfield networks (MHNs). We adapt MHNs to associate different modalities, reaction templates and molecules, which allows the model to leverage structural information about reaction templates. This approach significantly improves the performance of template relevance prediction, especially for templates with few or zero training examples. With inference speed several times faster than that of baseline methods, we improve predictive performance for top-k exact match accuracy for $\mathrm{k}\geq5$ in the retrosynthesis benchmark USPTO-50k.