Conditional Antibody Design as 3D Equivariant Graph Translation

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) incapable 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), an end-to-end model that is able 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 against previous autoregressive approaches. Our method significantly surpasses state-of-the-art models in sequence and structure modeling, antigen-binding antibody design, and binding affinity optimization. Specifically, the relative improvement to baselines is about 22% in antigen-binding CDR design and 34% for affinity optimization.

3D Equivariant Molecular Graph Pretraining

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 merit 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. The experimental results support the better efficacy of our method against current state-of-the-art pretraining approaches, and verify the validity of our design for each proposed component.

Similarity-aware Positive Instance Sampling for Graph Contrastive Pre-training

Graph instance contrastive learning has been proved as an effective task for Graph Neural Network (GNN) pre-training. However, one key issue may seriously impede the representative power in existing works: Positive instances created by current methods often miss crucial information of graphs or even yield illegal instances (such as non-chemically-aware graphs in molecular generation). To remedy this issue, we propose to select positive graph instances directly from existing graphs in the training set, which ultimately maintains the legality and similarity to the target graphs. Our selection is based on certain domain-specific pair-wise similarity measurements as well as sampling from a hierarchical graph encoding similarity relations among graphs. Besides, we develop an adaptive node-level pre-training method to dynamically mask nodes to distribute them evenly in the graph. We conduct extensive experiments on $13$ graph classification and node classification benchmark datasets from various domains. The results demonstrate that the GNN models pre-trained by our strategies can outperform those trained-from-scratch models as well as the variants obtained by existing methods.

SNAKE: Shape-aware Neural 3D Keypoint Field

Detecting 3D keypoints from point clouds is important for shape reconstruction, while this work investigates the dual question: can shape reconstruction benefit 3D keypoint detection? Existing methods either seek salient features according to statistics of different orders or learn to predict keypoints that are invariant to transformation. Nevertheless, the idea of incorporating shape reconstruction into 3D keypoint detection is under-explored. We argue that this is restricted by former problem formulations. To this end, a novel unsupervised paradigm named SNAKE is proposed, which is short for shape-aware neural 3D keypoint field. Similar to recent coordinate-based radiance or distance field, our network takes 3D coordinates as inputs and predicts implicit shape indicators and keypoint saliency simultaneously, thus naturally entangling 3D keypoint detection and shape reconstruction. We achieve superior performance on various public benchmarks, including standalone object datasets ModelNet40, KeypointNet, SMPL meshes and scene-level datasets 3DMatch and Redwood. Intrinsic shape awareness brings several advantages as follows. (1) SNAKE generates 3D keypoints consistent with human semantic annotation, even without such supervision. (2) SNAKE outperforms counterparts in terms of repeatability, especially when the input point clouds are down-sampled. (3) the generated keypoints allow accurate geometric registration, notably in a zero-shot setting. Codes are available at https://github.com/zhongcl-thu/SNAKE

Multimodal Token Fusion for Vision Transformers

Many adaptations of transformers have emerged to address the single-modal vision tasks, where self-attention modules are stacked to handle input sources like images. Intuitively, feeding multiple modalities of data to vision transformers could improve the performance, yet the inner-modal attentive weights may also be diluted, which could thus undermine the final performance. In this paper, we propose a multimodal token fusion method (TokenFusion), tailored for transformer-based vision tasks. To effectively fuse multiple modalities, TokenFusion dynamically detects uninformative tokens and substitutes these tokens with projected and aggregated inter-modal features. Residual positional alignment is also adopted to enable explicit utilization of the inter-modal alignments after fusion. The design of TokenFusion allows the transformer to learn correlations among multimodal features, while the single-modal transformer architecture remains largely intact. Extensive experiments are conducted on a variety of homogeneous and heterogeneous modalities and demonstrate that TokenFusion surpasses state-of-the-art methods in three typical vision tasks: multimodal image-to-image translation, RGB-depth semantic segmentation, and 3D object detection with point cloud and images.

Smoothing Matters: Momentum Transformer for Domain Adaptive Semantic Segmentation

After the great success of Vision Transformer variants (ViTs) in computer vision, it has also demonstrated great potential in domain adaptive semantic segmentation. Unfortunately, straightforwardly applying local ViTs in domain adaptive semantic segmentation does not bring in expected improvement. We find that the pitfall of local ViTs is due to the severe high-frequency components generated during both the pseudo-label construction and features alignment for target domains. These high-frequency components make the training of local ViTs very unsmooth and hurt their transferability. In this paper, we introduce a low-pass filtering mechanism, momentum network, to smooth the learning dynamics of target domain features and pseudo labels. Furthermore, we propose a dynamic of discrepancy measurement to align the distributions in the source and target domains via dynamic weights to evaluate the importance of the samples. After tackling the above issues, extensive experiments on sim2real benchmarks show that the proposed method outperforms the state-of-the-art methods. Our codes are available at https://github.com/alpc91/TransDA

Equivariant Graph Mechanics Networks with Constraints

Learning to reason about relations and dynamics over multiple interacting objects is a challenging topic in machine learning. The challenges mainly stem from that the interacting systems are exponentially-compositional, symmetrical, and commonly geometrically-constrained. Current methods, particularly the ones based on equivariant Graph Neural Networks (GNNs), have targeted on the first two challenges but remain immature for constrained systems. In this paper, we propose Graph Mechanics Network (GMN) which is combinatorially efficient, equivariant and constraint-aware. The core of GMN is that it represents, by generalized coordinates, the forward kinematics information (positions and velocities) of a structural object. In this manner, the geometrical constraints are implicitly and naturally encoded in the forward kinematics. Moreover, to allow equivariant message passing in GMN, we have developed a general form of orthogonality-equivariant functions, given that the dynamics of constrained systems are more complicated than the unconstrained counterparts. Theoretically, the proposed equivariant formulation is proved to be universally expressive under certain conditions. Extensive experiments support the advantages of GMN compared to the state-of-the-art GNNs in terms of prediction accuracy, constraint satisfaction and data efficiency on the simulated systems consisting of particles, sticks and hinges, as well as two real-world datasets for molecular dynamics prediction and human motion capture.

Sound Adversarial Audio-Visual Navigation

Audio-visual navigation task requires an agent to find a sound source in a realistic, unmapped 3D environment by utilizing egocentric audio-visual observations. Existing audio-visual navigation works assume a clean environment that solely contains the target sound, which, however, would not be suitable in most real-world applications due to the unexpected sound noise or intentional interference. In this work, we design an acoustically complex environment in which, besides the target sound, there exists a sound attacker playing a zero-sum game with the agent. More specifically, the attacker can move and change the volume and category of the sound to make the agent suffer from finding the sounding object while the agent tries to dodge the attack and navigate to the goal under the intervention. Under certain constraints to the attacker, we can improve the robustness of the agent towards unexpected sound attacks in audio-visual navigation. For better convergence, we develop a joint training mechanism by employing the property of a centralized critic with decentralized actors. Experiments on two real-world 3D scan datasets, Replica, and Matterport3D, verify the effectiveness and the robustness of the agent trained under our designed environment when transferred to the clean environment or the one containing sound attackers with random policy. Project: \url{https://yyf17.github.io/SAAVN}.

Geometrically Equivariant Graph Neural Networks: A Survey

Many scientific problems require to process data in the form of geometric graphs. Unlike generic graph data, geometric graphs exhibit symmetries of translations, rotations, and/or reflections. Researchers have leveraged such inductive bias and developed geometrically equivariant Graph Neural Networks (GNNs) to better characterize the geometry and topology of geometric graphs. Despite fruitful achievements, it still lacks a survey to depict how equivariant GNNs are progressed, which in turn hinders the further development of equivariant GNNs. To this end, based on the necessary but concise mathematical preliminaries, we analyze and classify existing methods into three groups regarding how the message passing and aggregation in GNNs are represented. We also summarize the benchmarks as well as the related datasets to facilitate later researches for methodology development and experimental evaluation. The prospect for future potential directions is also provided.