Antibody design is valuable for therapeutic usage and biological research. Existing deep-learning-based methods encounter several key issues: 1) incomplete context for Complementarity-Determining Regions (CDRs) generation; 2) incapability of capturing the entire 3D geometry of the input structure; 3) inefficient prediction of the CDR sequences in an autoregressive manner. In this paper, we propose Multi-channel Equivariant Attention Network (MEAN) to co-design 1D sequences and 3D structures of CDRs. To be specific, MEAN formulates antibody design as a conditional graph translation problem by importing extra components including the target antigen and the light chain of the antibody. Then, MEAN resorts to E(3)-equivariant message passing along with a proposed attention mechanism to better capture the geometrical correlation between different components. Finally, it outputs both the 1D sequences and 3D structure via a multi-round progressive full-shot scheme, which enjoys more efficiency and precision against previous autoregressive approaches. Specifically, the relative improvement to baselines is about 23% in antigen-binding CDR design and 34% for affinity optimization. Antibodies are Y-shaped proteins used by our immune system to capture specific pathogens. They show great potential in therapeutic usage and biological research for their strong specificity: each type of antibody usually binds to a unique kind of protein that is called antigen (Basu et al., 2019). The binding areas are mainly located at the so-called Complementarity-Determining Regions (CDRs) in antibodies (Kuroda et al., 2012). Therefore, the critical problem of antibody design is to identify CDRs that bind to a given antigen with desirable properties like high affinity and colloidal stability (Tiller & Tessier, 2015). There have been unremitting efforts made for antibody design by using deep generative models (Saka et al., 2021; Jin et al., 2021).

Predicting the binding sites of the target proteins plays a fundamental role in drug discovery. Most existing deep-learning methods consider a protein as a 3D image by spatially clustering its atoms into voxels and then feed the voxelized protein into a 3D CNN for prediction. However, the CNN-based methods encounter several critical issues: 1) defective in representing irregular protein structures; 2) sensitive to rotations; 3) insufficient to characterize the protein surface; 4) unaware of data distribution shift. To address the above issues, this work proposes EquiPocket, an E(3)-equivariant Graph Neural Network (GNN) for binding site prediction. In particular, EquiPocket consists of three modules: the first one to extract local geometric information for each surface atom, the second one to model both the chemical and spatial structure of the protein, and the last one to capture the geometry of the surface via equivariant message passing over the surface atoms. We further propose a dense attention output layer to better alleviate the data distribution shift effect incurred by the variable protein size. Extensive experiments on several representative benchmarks demonstrate the superiority of our framework to the state-of-the-art methods.

Molecule generation is central to a variety of applications. Current attention has been paid to approaching the generation task as subgraph prediction and assembling. Nevertheless, these methods usually rely on hand-crafted or external subgraph construction, and the subgraph assembling depends solely on local arrangement. In this paper, we define a novel notion, principal subgraph, that is closely related to the informative pattern within molecules. Interestingly, our proposed merge-and-update subgraph extraction method can automatically discover frequent principal subgraphs from the dataset, while previous methods are incapable of. Moreover, we develop a two-step subgraph assembling strategy, which first predicts a set of subgraphs in a sequence-wise manner and then assembles all generated subgraphs globally as the final output molecule. Built upon graph variational auto-encoder, our model is demonstrated to be effective in terms of several evaluation metrics and efficiency, compared with state-of-the-art methods on distribution learning and (constrained) property optimization tasks.

Pretraining molecular representation models without labels is fundamental to various applications. Conventional methods mainly process 2D molecular graphs and focus solely on 2D tasks, making their pretrained models incapable of characterizing 3D geometry and thus defective for downstream 3D tasks. In this work, we tackle 3D molecular pretraining in a complete and novel sense. In particular, we first propose to adopt an equivariant energy-based model as the backbone for pretraining, which enjoys the merits of fulfilling the symmetry of 3D space. Then we develop a node-level pretraining loss for force prediction, where we further exploit the Riemann-Gaussian distribution to ensure the loss to be E(3)-invariant, enabling more robustness. Moreover, a graph-level noise scale prediction task is also leveraged to further promote the eventual performance. We evaluate our model pretrained from a large-scale 3D dataset GEOM-QM9 on two challenging 3D benchmarks: MD17 and QM9. Experimental results demonstrate the efficacy of our method against current state-of-the-art pretraining approaches, and verify the validity of our design for each proposed component.

Keypoint detection and description play a central role in computer vision. Most existing methods are in the form of scene-level prediction, without returning the object classes of different keypoints. In this paper, we propose the object-centric formulation, which, beyond the conventional setting, requires further identifying which object each interest point belongs to. With such fine-grained information, our framework enables more downstream potentials, such as object-level matching and pose estimation in a clustered environment. To get around the difficulty of label collection in the real world, we develop a sim2real contrastive learning mechanism that can generalize the model trained in simulation to real-world applications. The novelties of our training method are three-fold: (i) we integrate the uncertainty into the learning framework to improve feature description of hard cases, e.g., less-textured or symmetric patches; (ii) we decouple the object descriptor into two output branches -- intra-object salience and inter-object distinctness, resulting in a better pixel-wise description; (iii) we enforce cross-view semantic consistency for enhanced robustness in representation learning. Comprehensive experiments on image matching and 6D pose estimation verify the encouraging generalization ability of our method from simulation to reality. Particularly for 6D pose estimation, our method significantly outperforms typical unsupervised/sim2real methods, achieving a closer gap with the fully supervised counterpart. Additional results and videos can be found at https://zhongcl-thu.github.io/rock/

Increasing the depth of GCN, which is expected to permit more expressivity, is shown to incur performance detriment especially on node classification. The main cause of this lies in over-smoothing. The over-smoothing issue drives the output of GCN towards a space that contains limited distinguished information among nodes, leading to poor expressivity. Several works on refining the architecture of deep GCN have been proposed, but it is still unknown in theory whether or not these refinements are able to relieve over-smoothing. In this paper, we first theoretically analyze how general GCNs act with the increase in depth, including generic GCN, GCN with bias, ResGCN, and APPNP. We find that all these models are characterized by a universal process: all nodes converging to a cuboid. Upon this theorem, we propose DropEdge to alleviate over-smoothing by randomly removing a certain number of edges at each training epoch. Theoretically, DropEdge either reduces the convergence speed of over-smoothing or relieves the information loss caused by dimension collapse. Experimental evaluations on simulated dataset have visualized the difference in over-smoothing between different GCNs. Moreover, extensive experiments on several real benchmarks support that DropEdge consistently improves the performance on a variety of both shallow and deep GCNs.

Graph Identification (GI) has long been researched in graph learning and is essential in certain applications (e.g. social community detection). Specifically, GI requires to predict the label/score of a target graph given its collection of node features and edge connections. While this task is common, more complex cases arise in practice---we are supposed to do the inverse thing by, for example, grouping similar users in a social network given the labels of different communities. This triggers an interesting thought: can we identify nodes given the labels of the graphs they belong to? Therefore, this paper defines a novel problem dubbed Inverse Graph Identification (IGI), as opposed to GI. Upon a formal discussion of the variants of IGI, we choose a particular case study of node clustering by making use of the graph labels and node features, with an assistance of a hierarchical graph that further characterizes the connections between different graphs. To address this task, we propose Gaussian Mixture Graph Convolutional Network (GMGCN), a simple yet effective method that makes the node-level message passing process using Graph Attention Network (GAT) under the protocol of GI and then infers the category of each node via a Gaussian Mixture Layer (GML). The training of GMGCN is further boosted by a proposed consensus loss to take advantage of the structure of the hierarchical graph. Extensive experiments are conducted to test the rationality of the formulation of IGI. We verify the superiority of the proposed method compared to other baselines on several benchmarks we have built up. We will release our codes along with the benchmark data to facilitate more research attention to the IGI problem.

The crux of molecular property prediction is to generate meaningful representations of the molecules. One promising route is to exploit the molecular graph structure through Graph Neural Networks (GNNs). It is well known that both atoms and bonds significantly affect the chemical properties of a molecule, so an expressive model shall be able to exploit both node (atom) and edge (bond) information simultaneously. Guided by this observation, we present Multi-View Graph Neural Network (MV-GNN), a multi-view message passing architecture to enable more accurate predictions of molecular properties. In MV-GNN, we introduce a shared self-attentive readout component and disagreement loss to stabilize the training process. This readout component also renders the whole architecture interpretable. We further boost the expressive power of MV-GNN by proposing a cross-dependent message passing scheme that enhances information communication of the two views, which results in the MV-GNN^cross variant. Lastly, we theoretically justify the expressiveness of the two proposed models in terms of distinguishing non-isomorphism graphs. Extensive experiments demonstrate that MV-GNN models achieve remarkably superior performance over the state-of-the-art models on a variety of challenging benchmarks. Meanwhile, visualization results of the node importance are consistent with prior knowledge, which confirms the interpretability power of MV-GNN models.

This paper studies Learning from Observations (LfO) for imitation learning with access to state-only demonstrations. In contrast to Learning from Demonstration (LfD) that involves both action and state supervision, LfO is more practical in leveraging previously inapplicable resources (e.g. videos), yet more challenging due to the incomplete expert guidance. In this paper, we investigate LfO and its difference with LfD in both theoretical and practical perspectives. We first prove that the gap between LfD and LfO actually lies in the disagreement of inverse dynamics models between the imitator and the expert, if following the modeling approach of GAIL. More importantly, the upper bound of this gap is revealed by a negative causal entropy which can be minimized in a model-free way. We term our method as Inverse-Dynamics-Disagreement-Minimization (IDDM) which enhances the conventional LfO method through further bridging the gap to LfD. Considerable empirical results on challenging benchmarks indicate that our method attains consistent improvements over other LfO counterparts.

With the great success of Graph Neural Networks (GNNs) towards representation learning on graph-structure data, the robustness of GNNs against adversarial attack inevitably becomes a central problem in graph learning domain. Regardless of the fruitful progress, current works suffer from two main limitations: First, the attack method required to be developed case by case; Second, most of them are restricted to the white-box attack. This paper promotes current frameworks in a more general and flexible sense -- we demand only one single method to attack various kinds of GNNs and this attacker is black box driven. To this end, we begin by investigating the theoretical connections between different kinds of GNNs in a principled way and integrate different GNN models into a unified framework, dubbed as General Spectral Graph Convolution. As such, a generalized adversarial attacker is proposed towards two families of GNNs: Convolution-based model and sampling-based model. More interestingly, our attacker does not require any knowledge of the target classifiers used in GNNs. Extensive experimental results validate the effectiveness of our method on several benchmark datasets. Particularly by using our attack, even small graph perturbations like one-edge flip is able to consistently make a strong attack in performance to different GNN models.