Structure-based drug design (SBDD) aims to generate potential drugs that can bind to a target protein and is greatly expedited by the aid of AI techniques in generative models. However, a lack of systematic understanding persists due to the diverse settings, complex implementation, difficult reproducibility, and task singularity. Firstly, the absence of standardization can lead to unfair comparisons and inconclusive insights. To address this dilemma, we propose CBGBench, a comprehensive benchmark for SBDD, that unifies the task as a generative graph completion, analogous to fill-in-the-blank of the 3D complex binding graph. By categorizing existing methods based on their attributes, CBGBench facilitates a modular and extensible framework that implements cutting-edge methods. Secondly, a single de novo molecule generation task can hardly reflect their capabilities. To broaden the scope, we adapt these models to a range of tasks essential in drug design, considered sub-tasks within the graph fill-in-the-blank tasks. These tasks include the generative designation of de novo molecules, linkers, fragments, scaffolds, and sidechains, all conditioned on the structures of protein pockets. Our evaluations are conducted with fairness, encompassing comprehensive perspectives on interaction, chemical properties, geometry authenticity, and substructure validity. We further provide insights with analysis from empirical studies. Our results indicate that there is potential for further improvements on many tasks, with optimization in network architectures, and effective incorporation of chemical prior knowledge. Finally, to lower the barrier to entry and facilitate further developments in the field, we also provide a single [codebase](https://github.com/EDAPINENUT/CBGBench) that unifies the discussed models, data pre-processing, training, sampling, and evaluation.

Recent years have witnessed great success in handling graph-related tasks with graph neural networks (GNNs). However, most existing GNNs are based on message passing to perform feature aggregation and transformation, where the structural information is explicitly involved in the forward propagation by coupling with node features through graph convolution at each layer. As a result, subtle feature noise or structure perturbation may cause severe error propagation, resulting in extremely poor robustness. In this article, we rethink the roles played by graph structural information in graph data training and identify that message passing is not the only path to modeling structural information. Inspired by this, we propose a simple but effective graph structure self-contrasting (GSSC) framework that learns graph structural information without message passing. The proposed framework is based purely on multilayer perceptrons (MLPs), where the structural information is only implicitly incorporated as prior knowledge to guide the computation of supervision signals, substituting the explicit message propagation as in GNNs. Specifically, it first applies structural sparsification (STR-Sparse) to remove potentially uninformative or noisy edges in the neighborhood, and then performs structural self-contrasting (STR-Contrast) in the sparsified neighborhood to learn robust node representations. Finally, STR-Sparse and self-contrasting are formulated as a bilevel optimization problem and solved in a unified framework. Extensive experiments have qualitatively and quantitatively demonstrated that the GSSC framework can produce truly encouraging performance with better generalization and robustness than other leading competitors. Codes are publicly available at: https://github.com/LirongWu/GSSC.

Recent years have witnessed great success in handling graph-related tasks with Graph Neural Networks (GNNs). Despite their greatacademicsuccess, Multi-Layer Perceptrons (MLPs) remain the primary workhorse for practicalindustrialapplications. One reason for such an academic-industry gap is the neighborhood-fetching latency incurred by data dependency in GNNs. To reduce their gaps, Graph Knowledge Distillation (GKD) is proposed, usually based on a standard teacher-student architecture, to distill knowledge from a large teacher GNN into a lightweight student GNN or MLP. However, we found in this paper that neither teachers nor GNNs are necessary for graph knowledge distillation. We propose aTeacher-FreeGraphSelf-Distillation(TGS) framework that does not require any teacher model or GNNs during both training and inference. More importantly, the proposed TGS framework is purely based on MLPs, where structural information is only implicitly used to guidedual knowledge self-distillationbetween the target node and its neighborhood. As a result, TGS enjoys the benefits of graph topology awareness in training but is free from data dependency in inference. Extensive experiments have shown that the performance of vanilla MLPs can be greatly improved with dual self-distillation, e.g., TGS improves over vanilla MLPs by 15.54% on average and outperforms state-of-the-art GKD algorithms on six real-world datasets. In terms of inference speed, TGS infers 75×-89× faster than existing GNNs and 16×-25× faster than classical inference acceleration methods.

High-dimensional data analysis for exploration and discovery includes two fundamental tasks: deep clustering and data visualization. When these two associated tasks are done separately, as is often the case thus far, disagreements can occur among the tasks in terms of geometry preservation. Namely, the clustering process is often accompanied by the corruption of the geometric structure, whereas visualization aims to preserve the data geometry for better interpretation. Therefore, how to achieve deep clustering and data visualization in an end-to-end unified framework is an important but challenging problem. In this article, we propose a novel neural network-based method, called deep clustering and visualization (DCV), to accomplish the two associated tasks end-to-end to resolve their disagreements. The DCV framework consists of two nonlinear dimensionality reduction (NLDR) transformations: 1) one from the input data space to latent feature space for clustering and 2) the other from the latent feature space to the final 2-D space for visualization. Importantly, the first NLDR transformation is mainly optimized by one Clustering Loss, allowing arbitrary corruption of the geometric structure for better clustering, while the second NLDR transformation is optimized by one Geometry-Preserving Loss to recover the corrupted geometry for better visualization. Extensive comparative results show that the DCV framework outperforms other leading clustering-visualization algorithms in terms of both quantitative evaluation metrics and qualitative visualization.

Jiangbin Zheng, Yile Wang, Ge Wang, Jun Xia, Yufei Huang, Guojiang Zhao, Yue Zhang, Stan Li. Proceedings of the 60th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers). 2022.