Why Deep Models Often cannot Beat Non-deep Counterparts on Molecular Property Prediction?

Molecular property prediction (MPP) is a crucial task in the drug discovery pipeline, which has recently gained considerable attention thanks to advances in deep neural networks. However, recent research has revealed that deep models struggle to beat traditional non-deep ones on MPP. In this study, we benchmark 12 representative models (3 non-deep models and 9 deep models) on 14 molecule datasets. Through the most comprehensive study to date, we make the following key observations: \textbf{(\romannumeral 1)} Deep models are generally unable to outperform non-deep ones; \textbf{(\romannumeral 2)} The failure of deep models on MPP cannot be solely attributed to the small size of molecular datasets. What matters is the irregular molecule data pattern; \textbf{(\romannumeral 3)} In particular, tree models using molecular fingerprints as inputs tend to perform better than other competitors. Furthermore, we conduct extensive empirical investigations into the unique patterns of molecule data and inductive biases of various models underlying these phenomena.

OpenSTL: A Comprehensive Benchmark of Spatio-Temporal Predictive Learning

Spatio-temporal predictive learning is a learning paradigm that enables models to learn spatial and temporal patterns by predicting future frames from given past frames in an unsupervised manner. Despite remarkable progress in recent years, a lack of systematic understanding persists due to the diverse settings, complex implementation, and difficult reproducibility. Without standardization, comparisons can be unfair and insights inconclusive. To address this dilemma, we propose OpenSTL, a comprehensive benchmark for spatio-temporal predictive learning that categorizes prevalent approaches into recurrent-based and recurrent-free models. OpenSTL provides a modular and extensible framework implementing various state-of-the-art methods. We conduct standard evaluations on datasets across various domains, including synthetic moving object trajectory, human motion, driving scenes, traffic flow and weather forecasting. Based on our observations, we provide a detailed analysis of how model architecture and dataset properties affect spatio-temporal predictive learning performance. Surprisingly, we find that recurrent-free models achieve a good balance between efficiency and performance than recurrent models. Thus, we further extend the common MetaFormers to boost recurrent-free spatial-temporal predictive learning. We open-source the code and models at https://github.com/chengtan9907/OpenSTL.

Quantifying the Knowledge in GNNs for Reliable Distillation into MLPs

To bridge the gaps between topology-aware Graph Neural Networks (GNNs) and inference-efficient Multi-Layer Perceptron (MLPs), GLNN proposes to distill knowledge from a well-trained teacher GNN into a student MLP. Despite their great progress, comparatively little work has been done to explore the reliability of different knowledge points (nodes) in GNNs, especially their roles played during distillation. In this paper, we first quantify the knowledge reliability in GNN by measuring the invariance of their information entropy to noise perturbations, from which we observe that different knowledge points (1) show different distillation speeds (temporally); (2) are differentially distributed in the graph (spatially). To achieve reliable distillation, we propose an effective approach, namely Knowledge-inspired Reliable Distillation (KRD), that models the probability of each node being an informative and reliable knowledge point, based on which we sample a set of additional reliable knowledge points as supervision for training student MLPs. Extensive experiments show that KRD improves over the vanilla MLPs by 12.62% and outperforms its corresponding teacher GNNs by 2.16% averaged over 7 datasets and 3 GNN architectures.

Dink-Net: Neural Clustering on Large Graphs

Deep graph clustering, which aims to group the nodes of a graph into disjoint clusters with deep neural networks, has achieved promising progress in recent years. However, the existing methods fail to scale to the large graph with million nodes. To solve this problem, a scalable deep graph clustering method (Dink-Net) is proposed with the idea of dilation and shrink. Firstly, by discriminating nodes, whether being corrupted by augmentations, representations are learned in a self-supervised manner. Meanwhile, the cluster centres are initialized as learnable neural parameters. Subsequently, the clustering distribution is optimized by minimizing the proposed cluster dilation loss and cluster shrink loss in an adversarial manner. By these settings, we unify the two-step clustering, i.e., representation learning and clustering optimization, into an end-to-end framework, guiding the network to learn clustering-friendly features. Besides, Dink-Net scales well to large graphs since the designed loss functions adopt the mini-batch data to optimize the clustering distribution even without performance drops. Both experimental results and theoretical analyses demonstrate the superiority of our method. Compared to the runner-up, Dink-Net achieves 9.62% NMI improvement on the ogbn-papers100M dataset with 111 million nodes and 1.6 billion edges. The source code is released at https://github.com/yueliu1999/Dink-Net. Besides, a collection (papers, codes, and datasets) of deep graph clustering is shared at https://github.com/yueliu1999/Awesome-Deep-Graph-Clustering.

Knowledge-Design: Pushing the Limit of Protein Deign via Knowledge Refinement

Recent studies have shown competitive performance in protein design that aims to find the amino acid sequence folding into the desired structure. However, most of them disregard the importance of predictive confidence, fail to cover the vast protein space, and do not incorporate common protein knowledge. After witnessing the great success of pretrained models on diverse protein-related tasks and the fact that recovery is highly correlated with confidence, we wonder whether this knowledge can push the limits of protein design further. As a solution, we propose a knowledge-aware module that refines low-quality residues. We also introduce a memory-retrieval mechanism to save more than 50\% of the training time. We extensively evaluate our proposed method on the CATH, TS50, and TS500 datasets and our results show that our Knowledge-Design method outperforms the previous PiFold method by approximately 9\% on the CATH dataset. Specifically, Knowledge-Design is the first method that achieves 60+\% recovery on CATH, TS50 and TS500 benchmarks. We also provide additional analysis to demonstrate the effectiveness of our proposed method. The code will be publicly available.

MotifRetro: Exploring the Combinability-Consistency Trade-offs in retrosynthesis via Dynamic Motif Editing

Is there a unified framework for graph-based retrosynthesis prediction? Through analysis of full-, semi-, and non-template retrosynthesis methods, we discovered that they strive to strike an optimal balance between combinability and consistency: \textit{Should atoms be combined as motifs to simplify the molecular editing process, or should motifs be broken down into atoms to reduce the vocabulary and improve predictive consistency?} Recent works have studied several specific cases, while none of them explores different combinability-consistency trade-offs. Therefore, we propose MotifRetro, a dynamic motif editing framework for retrosynthesis prediction that can explore the entire trade-off space and unify graph-based models. MotifRetro comprises two components: RetroBPE, which controls the combinability-consistency trade-off, and a motif editing model, where we introduce a novel LG-EGAT module to dynamiclly add motifs to the molecule. We conduct extensive experiments on USPTO-50K to explore how the trade-off affects the model performance and finally achieve state-of-the-art performance.

Extracting Low-/High- Frequency Knowledge from Graph Neural Networks and Injecting it into MLPs: An Effective GNN-to-MLP Distillation Framework

Recent years have witnessed the great success of Graph Neural Networks (GNNs) in handling graph-related tasks. However, MLPs remain the primary workhorse for practical industrial applications due to their desirable inference efficiency and scalability. To reduce their gaps, one can directly distill knowledge from a well-designed teacher GNN to a student MLP, which is termed as GNN-to-MLP distillation. However, the process of distillation usually entails a loss of information, and ``which knowledge patterns of GNNs are more likely to be left and distilled into MLPs?" becomes an important question. In this paper, we first factorize the knowledge learned by GNNs into low- and high-frequency components in the spectral domain and then derive their correspondence in the spatial domain. Furthermore, we identified a potential information drowning problem for existing GNN-to-MLP distillation, i.e., the high-frequency knowledge of the pre-trained GNNs may be overwhelmed by the low-frequency knowledge during distillation; we have described in detail what it represents, how it arises, what impact it has, and how to deal with it. In this paper, we propose an efficient Full-Frequency GNN-to-MLP (FF-G2M) distillation framework, which extracts both low-frequency and high-frequency knowledge from GNNs and injects it into MLPs. Extensive experiments show that FF-G2M improves over the vanilla MLPs by 12.6% and outperforms its corresponding teacher GNNs by 2.6% averaged over six graph datasets and three common GNN architectures.

FM-ViT: Flexible Modal Vision Transformers for Face Anti-Spoofing

The availability of handy multi-modal (i.e., RGB-D) sensors has brought about a surge of face anti-spoofing research. However, the current multi-modal face presentation attack detection (PAD) has two defects: (1) The framework based on multi-modal fusion requires providing modalities consistent with the training input, which seriously limits the deployment scenario. (2) The performance of ConvNet-based model on high fidelity datasets is increasingly limited. In this work, we present a pure transformer-based framework, dubbed the Flexible Modal Vision Transformer (FM-ViT), for face anti-spoofing to flexibly target any single-modal (i.e., RGB) attack scenarios with the help of available multi-modal data. Specifically, FM-ViT retains a specific branch for each modality to capture different modal information and introduces the Cross-Modal Transformer Block (CMTB), which consists of two cascaded attentions named Multi-headed Mutual-Attention (MMA) and Fusion-Attention (MFA) to guide each modal branch to mine potential features from informative patch tokens, and to learn modality-agnostic liveness features by enriching the modal information of own CLS token, respectively. Experiments demonstrate that the single model trained based on FM-ViT can not only flexibly evaluate different modal samples, but also outperforms existing single-modal frameworks by a large margin, and approaches the multi-modal frameworks introduced with smaller FLOPs and model parameters.

High-dimensional Clustering onto Hamiltonian Cycle

Clustering aims to group unlabelled samples based on their similarities. It has become a significant tool for the analysis of high-dimensional data. However, most of the clustering methods merely generate pseudo labels and thus are unable to simultaneously present the similarities between different clusters and outliers. This paper proposes a new framework called High-dimensional Clustering onto Hamiltonian Cycle (HCHC) to solve the above problems. First, HCHC combines global structure with local structure in one objective function for deep clustering, improving the labels as relative probabilities, to mine the similarities between different clusters while keeping the local structure in each cluster. Then, the anchors of different clusters are sorted on the optimal Hamiltonian cycle generated by the cluster similarities and mapped on the circumference of a circle. Finally, a sample with a higher probability of a cluster will be mapped closer to the corresponding anchor. In this way, our framework allows us to appreciate three aspects visually and simultaneously - clusters (formed by samples with high probabilities), cluster similarities (represented as circular distances), and outliers (recognized as dots far away from all clusters). The experiments illustrate the superiority of HCHC.