Exploring QSAR Models for Activity-Cliff Prediction

Pairs of similar compounds that only differ by a small structural modification but exhibit a large difference in their binding affinity for a given target are known as activity cliffs (ACs). It has been hypothesised that quantitative structure-activity relationship (QSAR) models struggle to predict ACs and that ACs thus form a major source of prediction error. However, a study to explore the AC-prediction power of modern QSAR methods and its relationship to general QSAR-prediction performance is lacking. We systematically construct nine distinct QSAR models by combining three molecular representation methods (extended-connectivity fingerprints, physicochemical-descriptor vectors and graph isomorphism networks) with three regression techniques (random forests, k-nearest neighbours and multilayer perceptrons); we then use each resulting model to classify pairs of similar compounds as ACs or non-ACs and to predict the activities of individual molecules in three case studies: dopamine receptor D2, factor Xa, and SARS-CoV-2 main protease. We observe low AC-sensitivity amongst the tested models when the activities of both compounds are unknown, but a substantial increase in AC-sensitivity when the actual activity of one of the compounds is given. Graph isomorphism features are found to be competitive with or superior to classical molecular representations for AC-classification and can thus be employed as baseline AC-prediction models or simple compound-optimisation tools. For general QSAR-prediction, however, extended-connectivity fingerprints still consistently deliver the best performance. Our results provide strong support for the hypothesis that indeed QSAR methods frequently fail to predict ACs. We propose twin-network training for deep learning models as a potential future pathway to increase AC-sensitivity and thus overall QSAR performance.

Numerically Solving Parametric Families of High-Dimensional Kolmogorov Partial Differential Equations via Deep Learning

We present a deep learning algorithm for the numerical solution of parametric families of high-dimensional linear Kolmogorov partial differential equations (PDEs). Our method is based on reformulating the numerical approximation of a whole family of Kolmogorov PDEs as a single statistical learning problem using the Feynman-Kac formula. Successful numerical experiments are presented, which empirically confirm the functionality and efficiency of our proposed algorithm in the case of heat equations and Black-Scholes option pricing models parametrized by affine-linear coefficient functions. We show that a single deep neural network trained on simulated data is capable of learning the solution functions of an entire family of PDEs on a full space-time region. Most notably, our numerical observations and theoretical results also demonstrate that the proposed method does not suffer from the curse of dimensionality, distinguishing it from almost all standard numerical methods for PDEs.