Accelerating molecular docking -- the process of predicting how molecules bind to protein targets -- could boost small-molecule drug discovery and revolutionize medicine. Unfortunately, current molecular docking tools are too slow to screen potential drugs against all relevant proteins, which often results in missed drug candidates or unexpected side effects occurring in clinical trials. To address this gap, we introduce RapidDock, an efficient transformer-based model for blind molecular docking. RapidDock achieves at least a $100 \times$ speed advantage over existing methods without compromising accuracy. On the Posebusters and DockGen benchmarks, our method achieves $52.1\%$ and $44.0\%$ success rates ($\text{RMSD}<2$\r{A}), respectively. The average inference time is $0.04$ seconds on a single GPU, highlighting RapidDock's potential for large-scale docking studies. We examine the key features of RapidDock that enable leveraging the transformer architecture for molecular docking, including the use of relative distance embeddings of $3$D structures in attention matrices, pre-training on protein folding, and a custom loss function invariant to molecular symmetries.

Computational Intelligence (CI) is a sub-branch of Artificial Intelligence paradigm focusing on the study of adaptive mechanisms to enable or facilitate intelligent behavior in complex and changing environments. There are several paradigms of CI [like artificial neural networks, evolutionary computations, swarm intelligence, artificial immune systems, fuzzy systems and many others], each of these has its origins in biological systems [biological neural systems, natural Darwinian evolution, social behavior, immune system, interactions of organisms with their environment]. Most of those paradigms evolved into separate machine learning (ML) techniques, where probabilistic methods are used complementary with CI techniques in order to effectively combine elements of learning, adaptation, evolution and Fuzzy logic to create heuristic algorithms that are, in some sense, intelligent. The current trend is to develop consensus techniques, since no single machine learning algorithms is superior to others in all possible situations. In order to overcome this problem several meta-approaches were proposed in ML focusing on the integration of results from different methods into single prediction. We discuss here the Landau theory for the nonlinear equation that can describe the adaptive integration of information acquired from an ensemble of independent learning agents. The influence of each individual agent on other learners is described similarly to the social impact theory. The final decision outcome for the consensus system is calculated using majority rule in the stationary limit, yet the minority solutions can survive inside the majority population as the complex intermittent clusters of opposite opinion.

We discuss here the mean-field theory for a cellular automata model of meta-learning. The meta-learning is the process of combining outcomes of individual learning procedures in order to determine the final decision with higher accuracy than any single learning method. Our method is constructed from an ensemble of interacting, learning agents, that acquire and process incoming information using various types, or different versions of machine learning algorithms. The abstract learning space, where all agents are located, is constructed here using a fully connected model that couples all agents with random strength values. The cellular automata network simulates the higher level integration of information acquired from the independent learning trials. The final classification of incoming input data is therefore defined as the stationary state of the meta-learning system using simple majority rule, yet the minority clusters that share opposite classification outcome can be observed in the system. Therefore, the probability of selecting proper class for a given input data, can be estimated even without the prior knowledge of its affiliation. The fuzzy logic can be easily introduced into the system, even if learning agents are build from simple binary classification machine learning algorithms by calculating the percentage of agreeing agents.

We present here an introduction to Brainstorming approach, that was recently proposed as a consensus meta-learning technique, and used in several practical applications in bioinformatics and chemoinformatics. The consensus learning denotes heterogeneous theoretical classification method, where one trains an ensemble of machine learning algorithms using different types of input training data representations. In the second step all solutions are gathered and the consensus is build between them. Therefore no early solution, given even by a generally low performing algorithm, is not discarder until the late phase of prediction, when the final conclusion is drawn by comparing different machine learning models. This final phase, i.e. consensus learning, is trying to balance the generality of solution and the overall performance of trained model.