Qi Liu

Hanchen Wang, Jean Kaddour, Shengchao Liu et al. · stanford

Graph Self-Supervised Learning (GSSL) provides a robust pathway for acquiring embeddings without expert labelling, a capability that carries profound implications for molecular graphs due to the staggering number of potential molecules and the high cost of obtaining labels. However, GSSL methods are designed not for optimisation within a specific domain but rather for transferability across a variety of downstream tasks. This broad applicability complicates their evaluation. Addressing this challenge, we present "Molecular Graph Representation Evaluation" (MOLGRAPHEVAL), generating detailed profiles of molecular graph embeddings with interpretable and diversified attributes. MOLGRAPHEVAL offers a suite of probing tasks grouped into three categories: (i) generic graph, (ii) molecular substructure, and (iii) embedding space properties. By leveraging MOLGRAPHEVAL to benchmark existing GSSL methods against both current downstream datasets and our suite of tasks, we uncover significant inconsistencies between inferences drawn solely from existing datasets and those derived from more nuanced probing. These findings suggest that current evaluation methodologies fail to capture the entirety of the landscape.

Zaixi Zhang, Qi Liu, Chee-Kong Lee et al.

Designing molecules with desirable physiochemical properties and functionalities is a long-standing challenge in chemistry, material science, and drug discovery. Recently, machine learning-based generative models have emerged as promising approaches for \emph{de novo} molecule design. However, further refinement of methodology is highly desired as most existing methods lack unified modeling of 2D topology and 3D geometry information and fail to effectively learn the structure-property relationship for molecule design. Here we present MolCode, a roto-translation equivariant generative framework for \underline{Mol}ecular graph-structure \underline{Co-de}sign. In MolCode, 3D geometric information empowers the molecular 2D graph generation, which in turn helps guide the prediction of molecular 3D structure. Extensive experimental results show that MolCode outperforms previous methods on a series of challenging tasks including \emph{de novo} molecule design, targeted molecule discovery, and structure-based drug design. Particularly, MolCode not only consistently generates valid (99.95$\%$ Validity) and diverse (98.75$\%$ Uniqueness) molecular graphs/structures with desirable properties, but also generate drug-like molecules with high affinity to target proteins (61.8$\%$ high-affinity ratio), which demonstrates MolCode's potential applications in material design and drug discovery. Our extensive investigation reveals that the 2D topology and 3D geometry contain intrinsically complementary information in molecule design, and provide new insights into machine learning-based molecule representation and generation.

Jiaxian Yan, Zaixi Zhang, Kai Zhang et al.

Molecular docking is a key computational tool utilized to predict the binding conformations of small molecules to protein targets, which is fundamental in the design of novel drugs. Despite recent advancements in geometric deep learning-based approaches leading to improvements in blind docking efficiency, these methods have encountered notable challenges, such as limited generalization performance on unseen proteins, the inability to concurrently address the settings of blind docking and site-specific docking, and the frequent occurrence of physical implausibilities such as inter-molecular steric clash. In this study, we introduce DeltaDock, a robust and versatile framework designed for efficient molecular docking to overcome these challenges. DeltaDock operates in a two-step process: rapid initial complex structures sampling followed by multi-scale iterative refinement of the initial structures. In the initial stage, to sample accurate structures with high efficiency, we develop a ligand-dependent binding site prediction model founded on large protein models and graph neural networks. This model is then paired with GPU-accelerated sampling algorithms. The sampled structures are updated using a multi-scale iterative refinement module that captures both protein-ligand atom-atom interactions and residue-atom interactions in the following stage. Distinct from previous geometric deep learning methods that are conditioned on the blind docking setting, DeltaDock demonstrates superior performance in both blind docking and site-specific docking settings. Comprehensive experimental results reveal that DeltaDock consistently surpasses baseline methods in terms of docking accuracy. Furthermore, it displays remarkable generalization capabilities and proficiency for predicting physically valid structures, thereby attesting to its robustness and reliability in various scenarios.

Rui Lv, Zaixi Zhang, Kai Zhang et al.

Graph In-Context Learning, with the ability to adapt pre-trained graph models to novel and diverse downstream graphs without updating any parameters, has gained much attention in the community. The key to graph in-context learning is to perform downstream graphs conditioned on chosen prompt examples. Existing methods randomly select subgraphs or edges as prompts, leading to noisy graph prompts and inferior model performance. Additionally, due to the gap between pre-training and testing graphs, when the number of classes in the testing graphs is much greater than that in the training, the in-context learning ability will also significantly deteriorate. To tackle the aforementioned challenges, we develop a multi-stage adaptive prompt optimization method GraphPrompter, which optimizes the entire process of generating, selecting, and using graph prompts for better in-context learning capabilities. Firstly, Prompt Generator introduces a reconstruction layer to highlight the most informative edges and reduce irrelevant noise for graph prompt construction. Furthermore, in the selection stage, Prompt Selector employs the $k$-nearest neighbors algorithm and pre-trained selection layers to dynamically choose appropriate samples and minimize the influence of irrelevant prompts. Finally, we leverage a Prompt Augmenter with a cache replacement strategy to enhance the generalization capability of the pre-trained model on new datasets. Extensive experiments show that GraphPrompter effectively enhances the in-context learning ability of graph models. On average across all the settings, our approach surpasses the state-of-the-art baselines by over 8%. Our code is released at https://github.com/karin0018/GraphPrompter.

Jiaxian Yan, Zaixi Zhang, Jintao Zhu et al.

Molecular docking, a technique for predicting ligand binding poses, is crucial in structure-based drug design for understanding protein-ligand interactions. Recent advancements in docking methods, particularly those leveraging geometric deep learning (GDL), have demonstrated significant efficiency and accuracy advantages over traditional sampling methods. Despite these advancements, current methods are often tailored for specific docking settings, and limitations such as the neglect of protein side-chain structures, difficulties in handling large binding pockets, and challenges in predicting physically valid structures exist. To accommodate various docking settings and achieve accurate, efficient, and physically reliable docking, we propose a novel two-stage docking framework, DeltaDock, consisting of pocket prediction and site-specific docking. We innovatively reframe the pocket prediction task as a pocket-ligand alignment problem rather than direct prediction in the first stage. Then we follow a bi-level coarse-to-fine iterative refinement process to perform site-specific docking. Comprehensive experiments demonstrate the superior performance of DeltaDock. Notably, in the blind docking setting, DeltaDock achieves a 31\% relative improvement over the docking success rate compared with the previous state-of-the-art GDL model. With the consideration of physical validity, this improvement increases to about 300\%.

Weiyin Gong, Kai Zhang, Yanghai Zhang et al.

Multimodal intent recognition (MIR) seeks to accurately interpret user intentions by integrating verbal and non-verbal information across video, audio and text modalities. While existing approaches prioritize text analysis, they often overlook the rich semantic content embedded in non-verbal cues. This paper presents a novel Wavelet-Driven Multimodal Intent Recognition(WDMIR) framework that enhances intent understanding through frequency-domain analysis of non-verbal information. To be more specific, we propose: (1) a wavelet-driven fusion module that performs synchronized decomposition and integration of video-audio features in the frequency domain, enabling fine-grained analysis of temporal dynamics; (2) a cross-modal interaction mechanism that facilitates progressive feature enhancement from bimodal to trimodal integration, effectively bridging the semantic gap between verbal and non-verbal information. Extensive experiments on MIntRec demonstrate that our approach achieves state-of-the-art performance, surpassing previous methods by 1.13% on accuracy. Ablation studies further verify that the wavelet-driven fusion module significantly improves the extraction of semantic information from non-verbal sources, with a 0.41% increase in recognition accuracy when analyzing subtle emotional cues.

Jinjiang Guo, Qi Liu, Han Guo et al.

Robust and efficient interpretation of QSAR methods is quite useful to validate AI prediction rationales with subjective opinion (chemist or biologist expertise), understand sophisticated chemical or biological process mechanisms, and provide heuristic ideas for structure optimization in pharmaceutical industry. For this purpose, we construct a multi-layer self-attention based Graph Neural Network framework, namely Ligandformer, for predicting compound property with interpretation. Ligandformer integrates attention maps on compound structure from different network blocks. The integrated attention map reflects the machine's local interest on compound structure, and indicates the relationship between predicted compound property and its structure. This work mainly contributes to three aspects: 1. Ligandformer directly opens the black-box of deep learning methods, providing local prediction rationales on chemical structures. 2. Ligandformer gives robust prediction in different experimental rounds, overcoming the ubiquitous prediction instability of deep learning methods. 3. Ligandformer can be generalized to predict different chemical or biological properties with high performance. Furthermore, Ligandformer can simultaneously output specific property score and visible attention map on structure, which can support researchers to investigate chemical or biological property and optimize structure efficiently. Our framework outperforms over counterparts in terms of accuracy, robustness and generalization, and can be applied in complex system study.

Zaixi Zhang, Qi Liu, Hao Wang et al.

Predicting molecular properties with data-driven methods has drawn much attention in recent years. Particularly, Graph Neural Networks (GNNs) have demonstrated remarkable success in various molecular generation and prediction tasks. In cases where labeled data is scarce, GNNs can be pre-trained on unlabeled molecular data to first learn the general semantic and structural information before being fine-tuned for specific tasks. However, most existing self-supervised pre-training frameworks for GNNs only focus on node-level or graph-level tasks. These approaches cannot capture the rich information in subgraphs or graph motifs. For example, functional groups (frequently-occurred subgraphs in molecular graphs) often carry indicative information about the molecular properties. To bridge this gap, we propose Motif-based Graph Self-supervised Learning (MGSSL) by introducing a novel self-supervised motif generation framework for GNNs. First, for motif extraction from molecular graphs, we design a molecule fragmentation method that leverages a retrosynthesis-based algorithm BRICS and additional rules for controlling the size of motif vocabulary. Second, we design a general motif-based generative pre-training framework in which GNNs are asked to make topological and label predictions. This generative framework can be implemented in two different ways, i.e., breadth-first or depth-first. Finally, to take the multi-scale information in molecular graphs into consideration, we introduce a multi-level self-supervised pre-training. Extensive experiments on various downstream benchmark tasks show that our methods outperform all state-of-the-art baselines.

Jean Kaddour, Yuchen Zhu, Qi Liu et al.

We address the estimation of conditional average treatment effects (CATEs) for structured treatments (e.g., graphs, images, texts). Given a weak condition on the effect, we propose the generalized Robinson decomposition, which (i) isolates the causal estimand (reducing regularization bias), (ii) allows one to plug in arbitrary models for learning, and (iii) possesses a quasi-oracle convergence guarantee under mild assumptions. In experiments with small-world and molecular graphs we demonstrate that our approach outperforms prior work in CATE estimation.