Jing Tang

Qifan Zhang, Xiaobin Hong, Jianheng Tang et al.

Large Language Models (LLMs) have demonstrated strong reasoning abilities, making them suitable for complex tasks such as graph computation. Traditional reasoning steps paradigm for graph problems is hindered by unverifiable steps, limited long-term reasoning, and poor generalization to graph variations. To overcome these limitations, we introduce GCoder, a code-based LLM designed to enhance problem-solving in generalized graph computation problems. Our method involves constructing an extensive training dataset, GraphWild, featuring diverse graph formats and algorithms. We employ a multi-stage training process, including Supervised Fine-Tuning (SFT) and Reinforcement Learning from Compiler Feedback (RLCF), to refine model capabilities. For unseen tasks, a hybrid retrieval technique is used to augment performance. Experiments demonstrate that GCoder outperforms GPT-4o, with an average accuracy improvement of 16.42% across various graph computational problems. Furthermore, GCoder efficiently manages large-scale graphs with millions of nodes and diverse input formats, overcoming the limitations of previous models focused on the reasoning steps paradigm. This advancement paves the way for more intuitive and effective graph problem-solving using LLMs. Code and data are available at here: https://github.com/Bklight999/WWW25-GCoder/tree/master.

Yuhan Chen, Yihong Luo, Yifan Song et al.

Despite extensive research efforts focused on OOD detection on images, OOD detection on nodes in graph learning remains underexplored. The dependence among graph nodes hinders the trivial adaptation of existing approaches on images that assume inputs to be i.i.d. sampled, since many unique features and challenges specific to graphs are not considered, such as the heterophily issue. Recently, GNNSafe, which considers node dependence, adapted energy-based detection to the graph domain with state-of-the-art performance, however, it has two serious issues: 1) it derives node energy from classification logits without specifically tailored training for modeling data distribution, making it less effective at recognizing OOD data; 2) it highly relies on energy propagation, which is based on homophily assumption and will cause significant performance degradation on heterophilic graphs, where the node tends to have dissimilar distribution with its neighbors. To address the above issues, we suggest training EBMs by MLE to enhance data distribution modeling and remove energy propagation to overcome the heterophily issues. However, training EBMs via MLE requires performing MCMC sampling on both node feature and node neighbors, which is challenging due to the node interdependence and discrete graph topology. To tackle the sampling challenge, we introduce DeGEM, which decomposes the learning process into two parts: a graph encoder that leverages topology information for node representations and an energy head that operates in latent space. Extensive experiments validate that DeGEM, without OOD exposure during training, surpasses previous state-of-the-art methods, achieving an average AUROC improvement of 6.71% on homophilic graphs and 20.29% on heterophilic graphs, and even outperform methods trained with OOD exposure. Our code is available at: https://github.com/draym28/DeGEM.

Renyi Zhou, Huimin Zhu, Jing Tang et al.

Achieving precise control over a molecule's biological activity-encompassing targeted activation/inhibition, cooperative multi-target modulation, and off-target toxicity mitigation-remains a critical challenge in de novo drug design. However, existing generative methods primarily focus on producing molecules with a single desired activity, lacking integrated mechanisms for the simultaneous management of multiple intended and unintended molecular interactions. Here, we propose ActivityDiff, a generative approach based on the classifier-guidance technique of diffusion models. It leverages separately trained drug-target classifiers for both positive and negative guidance, enabling the model to enhance desired activities while minimizing harmful off-target effects. Experimental results show that ActivityDiff effectively handles essential drug design tasks, including single-/dual-target generation, fragment-constrained dual-target design, selective generation to enhance target specificity, and reduction of off-target effects. These results demonstrate the effectiveness of classifier-guided diffusion in balancing efficacy and safety in molecular design. Overall, our work introduces a novel paradigm for achieving integrated control over molecular activity, and provides ActivityDiff as a versatile and extensible framework.

Qifan Zhang, Nuo Chen, Zehua Li et al.

Large Language Models (LLMs) have made remarkable strides in reasoning tasks, yet their performance often falters on novel and complex problems. Domain-specific continued pretraining (CPT) methods, such as those tailored for mathematical reasoning, have shown promise but lack transferability to broader reasoning tasks. In this work, we pioneer the use of Graph Problem Reasoning (GPR) to enhance the general reasoning capabilities of LLMs. GPR tasks, spanning pathfinding, network analysis, numerical computation, and topological reasoning, require sophisticated logical and relational reasoning, making them ideal for teaching diverse reasoning patterns. To achieve this, we introduce GraphPile, the first large-scale corpus specifically designed for CPT using GPR data. Spanning 10.9 billion tokens across 23 graph tasks, the dataset includes chain-of-thought, program-of-thought, trace of execution, and real-world graph data. Using GraphPile, we train GraphMind on popular base models Llama 3 and 3.1, as well as Gemma 2, achieving up to 4.9 percent higher accuracy in mathematical reasoning and up to 21.2 percent improvement in non-mathematical reasoning tasks such as logical and commonsense reasoning. By being the first to harness GPR for enhancing reasoning patterns and introducing the first dataset of its kind, our work bridges the gap between domain-specific pretraining and universal reasoning capabilities, advancing the adaptability and robustness of LLMs.