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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. 

Abstract Real-world grasp detection is challenging due to the stochasticity in grasp dynamics and the noise in hardware. Ideally, the system would adapt to the real world by training directly on physical systems. However, this is generally difficult due to the large amount of training data required by most grasp learning models. In this paper, we note that the planar grasp function is $\textrm{SE}(2)$ -equivariant and demonstrate that this structure can be used to constrain the neural network used during learning. This creates an inductive bias that can significantly improve the sample efficiency of grasp learning and enable end-to-end training from scratch on a physical robot with as few as 600 grasp attempts. We call this method Symmetric Grasp learning (SymGrasp) and show that it can learn to grasp “from scratch” in less that 1.5 h of physical robot time. This paper represents an expanded and revised version of the conference paper Zhu et al. (2022). 

In robotic manipulation, acquiring samples is extremely expensive because it often requires interacting with the real world. Traditional image-level data augmentation has shown the potential to improve sample efficiency in various machine learning tasks. However, image-level data augmentation is insufficient for an imitation learning agent to learn good manipulation policies in a reasonable amount of demonstrations. We propose Simulation-augmented Equivariant Imitation Learning (SEIL), a method that combines a novel data augmentation strategy of supplementing expert trajectories with simulated transitions and an equivariant model that exploits the O(2) symmetry in robotic manipulation. Experimental evaluations demonstrate that our method can learn non-trivial manipulation tasks within ten demonstrations and outperform the baselines by a significant margin. 

Robotic pick and place tasks are symmetric under translations and rotations of both the object to be picked and the desired place pose. For example, if the pick object is rotated or translated, then the optimal pick action should also rotate or translate. The same is true for the place pose; if the desired place pose changes, then the place action should also transform accordingly. A recently proposed pick and place framework known as Transporter Net (Zeng, Florence, Tompson, Welker, Chien, Attarian, Armstrong, Krasin, Duong, Sindhwani et al., 2021) captures some of these symmetries, but not all. This paper analytically studies the symmetries present in planar robotic pick and place and proposes a method of incorporating equivariant neural models into Transporter Net in a way that captures all symmetries. The new model, which we call Equivariant Transporter Net, is equivariant to both pick and place symmetries and can immediately generalize pick and place knowledge to different pick and place poses. We evaluate the new model empirically and show that it is much more sample-efficient than the non-symmetric version, resulting in a system that can imitate demonstrated pick and place behavior using very few human demonstrations on a variety of imitation learning tasks.