Igor T. Podolak

Tomasz Danel, Jan Łęski, Sabina Podlewska et al.

Despite the great popularity of virtual screening of existing compound libraries, the search for new potential drug candidates also takes advantage of generative protocols, where new compound suggestions are enumerated using various algorithms. To increase the activity potency of generative approaches, they have recently been coupled with molecular docking, a leading methodology of structure-based drug design. In this review, we summarize progress since docking-based generative models emerged. We propose a new taxonomy for these methods and discuss their importance for the field of computer-aided drug design. In addition, we discuss the most promising directions for further development of generative protocols coupled with docking.

Łukasz Struski, Michał B. Bednarczyk, Igor T. Podolak et al.

We present a novel technique for constructing differentiable order-type operations, including soft ranking, soft top-k selection, and soft permutations. Our approach leverages an efficient closed-form formula for the inverse of the function LapSum, defined as the sum of Laplace distributions. This formulation ensures low computational and memory complexity in selecting the highest activations, enabling losses and gradients to be computed in $O(n\log{}n)$ time. Through extensive experiments, we demonstrate that our method outperforms state-of-the-art techniques for high-dimensional vectors and large $k$ values. Furthermore, we provide efficient implementations for both CPU and CUDA environments, underscoring the practicality and scalability of our method for large-scale ranking and differentiable ordering problems.

Łukasz Struski, Michał Sadowski, Tomasz Danel et al.

Interpolating between points is a problem connected simultaneously with finding geodesics and study of generative models. In the case of geodesics, we search for the curves with the shortest length, while in the case of generative models we typically apply linear interpolation in the latent space. However, this interpolation uses implicitly the fact that Gaussian is unimodal. Thus the problem of interpolating in the case when the latent density is non-Gaussian is an open problem. In this paper, we present a general and unified approach to interpolation, which simultaneously allows us to search for geodesics and interpolating curves in latent space in the case of arbitrary density. Our results have a strong theoretical background based on the introduced quality measure of an interpolating curve. In particular, we show that maximising the quality measure of the curve can be equivalently understood as a search of geodesic for a certain redefinition of the Riemannian metric on the space. We provide examples in three important cases. First, we show that our approach can be easily applied to finding geodesics on manifolds. Next, we focus our attention in finding interpolations in pre-trained generative models. We show that our model effectively works in the case of arbitrary density. Moreover, we can interpolate in the subset of the space consisting of data possessing a given feature. The last case is focused on finding interpolation in the space of chemical compounds.