Zixing Song

Yusong Wang, Jialun Shen, Zhihao Wu et al.

Graph Neural Networks (GNNs) have been widely adopted for Protein Representation Learning (PRL), as residue interaction networks can be naturally represented as graphs. Current GNN-based PRL methods typically rely on single-perspective graph construction strategies, which capture partial properties of residue interactions, resulting in incomplete protein representations. To address this limitation, we propose MMPG, a framework that constructs protein graphs from multiple perspectives and adaptively fuses them via Mixture of Experts (MoE) for PRL. MMPG constructs graphs from physical, chemical, and geometric perspectives to characterize different properties of residue interactions. To capture both perspective-specific features and their synergies, we develop an MoE module, which dynamically routes perspectives to specialized experts, where experts learn intrinsic features and cross-perspective interactions. We quantitatively verify that MoE automatically specializes experts in modeling distinct levels of interaction from individual representations, to pairwise inter-perspective synergies, and ultimately to a global consensus across all perspectives. Through integrating this multi-level information, MMPG produces superior protein representations and achieves advanced performance on four different downstream protein tasks.

Zixing Song, Irwin King

The emergent reasoning capabilities of Large Language Models (LLMs) offer a transformative paradigm for analyzing text-attributed graphs. While instruction tuning is the prevailing method for adapting pre-trained LLMs to graph learning tasks like node classification, it requires a substantial volume of annotated (INSTRUCTION, OUTPUT) pairs deriving from labeled nodes. This requirement is particularly prohibitive in the social domain, where obtaining expert labels for sensitive or evolving content is costly and slow. Furthermore, standard graph instruction tuning fails to exploit the vast amount of unlabeled nodes, which contain latent correlations due to edge connections that are beneficial for downstream predictions. To bridge this gap, we propose a novel Semi-supervised Instruction Tuning pipeline for Graph Learning, named SIT-Graph. Notably, SIT-Graph is model-agnostic and can be seamlessly integrated into any graph instruction tuning method that utilizes LLMs as the predictor. SIT-Graph operates via an iterative self-training process. Initially, the model is fine-tuned using instruction pairs constructed solely from the labeled nodes. Then it generates confidence-filtered pseudo-responses for unlabeled nodes to strategically augment the dataset for the next round of fine-tuning. Finally, this iterative refinement progressively aligns the LLM with the underlying node correlations. Extensive experiments demonstrate that when incorporated into state-of-the-art graph instruction tuning methods, SIT-Graph significantly enhances their performance on text-attributed graph benchmarks, achieving over 20% improvement under the low label ratio settings.