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Identifying novel drug-target interactions is a critical and rate-limiting step in drug discovery. While deep learning models have been proposed to accelerate the identification process, here we show that state-of-the-art models fail to generalize to novel (i.e., never-before-seen) structures. We unveil the mechanisms responsible for this shortcoming, demonstrating how models rely on shortcuts that leverage the topology of the protein-ligand bipartite network, rather than learning the node features. Here we introduce AI-Bind, a pipeline that combines network-based sampling strategies with unsupervised pre-training to improve binding predictions for novel proteins and ligands. We validate AI-Bind predictions via docking simulations and comparison with recent experimental evidence, and step up the process of interpreting machine learning prediction of protein-ligand binding by identifying potential active binding sites on the amino acid sequence. AI-Bind is a high-throughput approach to identify drug-target combinations with the potential of becoming a powerful tool in drug discovery. 

Learning multi-agent dynamics is a core AI problem with broad applications in robotics and autonomous driving. While most existing works focus on deterministic prediction, producing probabilistic forecasts to quantify uncertainty and assess risks is critical for downstream decision-making tasks such as motion planning and collision avoidance. Multi-agent dynamics often contains internal symmetry. By leveraging symmetry, specifically rotation equivariance, we can improve not only the prediction accuracy but also uncertainty calibration. We introduce Energy Score, a proper scoring rule, to evaluate probabilistic predictions. We propose a novel deep dynamics model, Probabilistic Equivariant Continuous COnvolution (PECCO) for probabilistic prediction of multi-agent trajectories. PECCO extends equivariant continuous convolution to model the joint velocity distribution of multiple agents. It uses dynamics integration to propagate the uncertainty from velocity to position. On both synthetic and real-world datasets, PECCO shows significant improvements in accuracy and calibration compared to non-equivariant baselines. 

A tool that could suggest new personalized research directions and ideas by taking insights from the scientific literature could profoundly accelerate the progress of science. A field that might benefit from such an approach is artificial intelligence (AI) research, where the number of scientific publications has been growing exponentially over recent years, making it challenging for human researchers to keep track of the progress. Here we use AI techniques to predict the future research directions of AI itself. We introduce a graph-based benchmark based on real-world data—the Science4Cast benchmark, which aims to predict the future state of an evolving semantic network of AI. For that, we use more than 143,000 research papers and build up a knowledge network with more than 64,000 concept nodes. We then present ten diverse methods to tackle this task, ranging from pure statistical to pure learning methods. Surprisingly, the most powerful methods use a carefully curated set of network features, rather than an end-to-end AI approach. These results indicate a great potential that can be unleashed for purely ML approaches without human knowledge. Ultimately, better predictions of new future research directions will be a crucial component of more advanced research suggestion tools.

 

Incorporating symmetry as an inductive bias into neural network architecture has led to improvements in generalization, data efficiency, and physical consistency in dynamics modeling. Methods such as CNNs or equivariant neural networks use weight tying to enforce symmetries such as shift invariance or rotational equivariance. However, despite the fact that physical laws obey many symmetries, real-world dynamical data rarely conforms to strict mathematical symmetry either due to noisy or incomplete data or to symmetry breaking features in the underlying dynamical system. We explore approximately equivariant networks which are biased towards preserving symmetry but are not strictly constrained to do so. By relaxing equivariance constraints, we find that our models can outperform both baselines with no symmetry bias and baselines with overly strict symmetry in both simulated turbulence domains and real-world multi-stream jet flow.