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Predicting how a drug-like molecule binds to a specific protein target is a core problem in drug discovery. An extremely fast computational binding method would enable key applications such as fast virtual screening or drug engineering. Existing methods are computationally expensive as they rely on heavy candidate sampling coupled with scoring, ranking, and fine-tuning steps. We challenge this paradigm with EquiBind, an SE(3)-equivariant geometric deep learning model performing direct-shot prediction of both i) the receptor binding location (blind docking) and ii) the ligand's bound pose and orientation. EquiBind achieves significant speed-ups and better quality compared to traditional and recent baselines. Further, we show extra improvements when coupling it with existing fine-tuning techniques at the cost of increased running time. Finally, we propose a novel and fast fine-tuning model that adjusts torsion angles of a ligand's rotatable bonds based on closed-form global minima of the von Mises angular distance to a given input atomic point cloud, avoiding previous expensive differential evolution strategies for energy minimization.

We hypothesize that due to the greedy nature of learning in multi-modal deep neural networks, these models tend to rely on just one modality while under-fitting the other modalities. Such behavior is counter-intuitive and hurts the models' generalization, as we observe empirically. To estimate the model's dependence on each modality, we compute the gain on the accuracy when the model has access to it in addition to another modality. We refer to this gain as the conditional utilization rate. In the experiments, we consistently observe an imbalance in conditional utilization rates between modalities, across multiple tasks and architectures. Since conditional utilization rate cannot be computed efficiently during training, we introduce a proxy for it based on the pace at which the model learns from each modality, which we refer to as the conditional learning speed. We propose an algorithm to balance the conditional learning speeds between modalities during training and demonstrate that it indeed addresses the issue of greedy learning. The proposed algorithm improves the model's generalization on three datasets: Colored MNIST, Princeton ModelNet40, and NVIDIA Dynamic Hand Gesture.

Unsupervised domain adaptation has recently emerged as an effective paradigm for generalizing deep neural networks to new target domains. However, there is still enormous potential to be tapped to reach the fully supervised performance. In this paper, we present a novel active learning strategy to assist knowledge transfer in the target domain, dubbed active domain adaptation. We start from an observation that energy-based models exhibit free energy biases when training (source) and test (target) data come from different distributions. Inspired by this inherent mechanism, we empirically reveal that a simple yet efficient energy-based sampling strategy sheds light on selecting the most valuable target samples than existing approaches requiring particular architectures or computation of the distances. Our algorithm, Energy-based Active Domain Adaptation (EADA), queries groups of targe data that incorporate both domain characteristic and instance uncertainty into every selection round. Meanwhile, by aligning the free energy of target data compact around the source domain via a regularization term, domain gap can be implicitly diminished. Through extensive experiments, we show that EADA surpasses state-of-the-art methods on well-known challenging benchmarks with substantial improvements, making it a useful option in the open world. Code is available at //github.com/BIT-DA/EADA.

Point cloud-based large scale place recognition is fundamental for many applications like Simultaneous Localization and Mapping (SLAM). Although many models have been proposed and have achieved good performance by learning short-range local features, long-range contextual properties have often been neglected. Moreover, the model size has also become a bottleneck for their wide applications. To overcome these challenges, we propose a super light-weight network model termed SVT-Net for large scale place recognition. Specifically, on top of the highly efficient 3D Sparse Convolution (SP-Conv), an Atom-based Sparse Voxel Transformer (ASVT) and a Cluster-based Sparse Voxel Transformer (CSVT) are proposed to learn both short-range local features and long-range contextual features in this model. Consisting of ASVT and CSVT, SVT-Net can achieve state-of-the-art on benchmark datasets in terms of both accuracy and speed with a super-light model size (0.9M). Meanwhile, two simplified versions of SVT-Net are introduced, which also achieve state-of-the-art and further reduce the model size to 0.8M and 0.4M respectively.

Most object recognition approaches predominantly focus on learning discriminative visual patterns while overlooking the holistic object structure. Though important, structure modeling usually requires significant manual annotations and therefore is labor-intensive. In this paper, we propose to "look into object" (explicitly yet intrinsically model the object structure) through incorporating self-supervisions into the traditional framework. We show the recognition backbone can be substantially enhanced for more robust representation learning, without any cost of extra annotation and inference speed. Specifically, we first propose an object-extent learning module for localizing the object according to the visual patterns shared among the instances in the same category. We then design a spatial context learning module for modeling the internal structures of the object, through predicting the relative positions within the extent. These two modules can be easily plugged into any backbone networks during training and detached at inference time. Extensive experiments show that our look-into-object approach (LIO) achieves large performance gain on a number of benchmarks, including generic object recognition (ImageNet) and fine-grained object recognition tasks (CUB, Cars, Aircraft). We also show that this learning paradigm is highly generalizable to other tasks such as object detection and segmentation (MS COCO). Project page: //github.com/JDAI-CV/LIO.

With the rise of knowledge graph (KG), question answering over knowledge base (KBQA) has attracted increasing attention in recent years. Despite much research has been conducted on this topic, it is still challenging to apply KBQA technology in industry because business knowledge and real-world questions can be rather complicated. In this paper, we present AliMe-KBQA, a bold attempt to apply KBQA in the E-commerce customer service field. To handle real knowledge and questions, we extend the classic "subject-predicate-object (SPO)" structure with property hierarchy, key-value structure and compound value type (CVT), and enhance traditional KBQA with constraints recognition and reasoning ability. We launch AliMe-KBQA in the Marketing Promotion scenario for merchants during the "Double 11" period in 2018 and other such promotional events afterwards. Online results suggest that AliMe-KBQA is not only able to gain better resolution and improve customer satisfaction, but also becomes the preferred knowledge management method by business knowledge staffs since it offers a more convenient and efficient management experience.

Graph convolutional network (GCN) has been successfully applied to many graph-based applications; however, training a large-scale GCN remains challenging. Current SGD-based algorithms suffer from either a high computational cost that exponentially grows with number of GCN layers, or a large space requirement for keeping the entire graph and the embedding of each node in memory. In this paper, we propose Cluster-GCN, a novel GCN algorithm that is suitable for SGD-based training by exploiting the graph clustering structure. Cluster-GCN works as the following: at each step, it samples a block of nodes that associate with a dense subgraph identified by a graph clustering algorithm, and restricts the neighborhood search within this subgraph. This simple but effective strategy leads to significantly improved memory and computational efficiency while being able to achieve comparable test accuracy with previous algorithms. To test the scalability of our algorithm, we create a new Amazon2M data with 2 million nodes and 61 million edges which is more than 5 times larger than the previous largest publicly available dataset (Reddit). For training a 3-layer GCN on this data, Cluster-GCN is faster than the previous state-of-the-art VR-GCN (1523 seconds vs 1961 seconds) and using much less memory (2.2GB vs 11.2GB). Furthermore, for training 4 layer GCN on this data, our algorithm can finish in around 36 minutes while all the existing GCN training algorithms fail to train due to the out-of-memory issue. Furthermore, Cluster-GCN allows us to train much deeper GCN without much time and memory overhead, which leads to improved prediction accuracy---using a 5-layer Cluster-GCN, we achieve state-of-the-art test F1 score 99.36 on the PPI dataset, while the previous best result was 98.71 by [16]. Our codes are publicly available at //github.com/google-research/google-research/tree/master/cluster_gcn.

Graph neural networks (GNNs) are a popular class of machine learning models whose major advantage is their ability to incorporate a sparse and discrete dependency structure between data points. Unfortunately, GNNs can only be used when such a graph-structure is available. In practice, however, real-world graphs are often noisy and incomplete or might not be available at all. With this work, we propose to jointly learn the graph structure and the parameters of graph convolutional networks (GCNs) by approximately solving a bilevel program that learns a discrete probability distribution on the edges of the graph. This allows one to apply GCNs not only in scenarios where the given graph is incomplete or corrupted but also in those where a graph is not available. We conduct a series of experiments that analyze the behavior of the proposed method and demonstrate that it outperforms related methods by a significant margin.

Dynamic programming (DP) solves a variety of structured combinatorial problems by iteratively breaking them down into smaller subproblems. In spite of their versatility, DP algorithms are usually non-differentiable, which hampers their use as a layer in neural networks trained by backpropagation. To address this issue, we propose to smooth the max operator in the dynamic programming recursion, using a strongly convex regularizer. This allows to relax both the optimal value and solution of the original combinatorial problem, and turns a broad class of DP algorithms into differentiable operators. Theoretically, we provide a new probabilistic perspective on backpropagating through these DP operators, and relate them to inference in graphical models. We derive two particular instantiations of our framework, a smoothed Viterbi algorithm for sequence prediction and a smoothed DTW algorithm for time-series alignment. We showcase these instantiations on two structured prediction tasks and on structured and sparse attention for neural machine translation.

Spectral clustering is a leading and popular technique in unsupervised data analysis. Two of its major limitations are scalability and generalization of the spectral embedding (i.e., out-of-sample-extension). In this paper we introduce a deep learning approach to spectral clustering that overcomes the above shortcomings. Our network, which we call SpectralNet, learns a map that embeds input data points into the eigenspace of their associated graph Laplacian matrix and subsequently clusters them. We train SpectralNet using a procedure that involves constrained stochastic optimization. Stochastic optimization allows it to scale to large datasets, while the constraints, which are implemented using a special-purpose output layer, allow us to keep the network output orthogonal. Moreover, the map learned by SpectralNet naturally generalizes the spectral embedding to unseen data points. To further improve the quality of the clustering, we replace the standard pairwise Gaussian affinities with affinities leaned from unlabeled data using a Siamese network. Additional improvement can be achieved by applying the network to code representations produced, e.g., by standard autoencoders. Our end-to-end learning procedure is fully unsupervised. In addition, we apply VC dimension theory to derive a lower bound on the size of SpectralNet. State-of-the-art clustering results are reported on the Reuters dataset. Our implementation is publicly available at //github.com/kstant0725/SpectralNet .