Podolak, Igor T.
LapSum -- One Method to Differentiate Them All: Ranking, Sorting and Top-k Selection
Struski, Łukasz, Bednarczyk, Michał B., Podolak, Igor T., Tabor, Jacek
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.
Docking-based generative approaches in the search for new drug candidates
Danel, Tomasz, Łęski, Jan, Podlewska, Sabina, Podolak, Igor T.
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.