Haochen Xue

Mingyu Jin, Haochen Xue, Zhenting Wang et al.

The prediction of protein-protein interactions (PPIs) is crucial for understanding biological functions and diseases. Previous machine learning approaches to PPI prediction mainly focus on direct physical interactions, ignoring the broader context of nonphysical connections through intermediate proteins, thus limiting their effectiveness. The emergence of Large Language Models (LLMs) provides a new opportunity for addressing this complex biological challenge. By transforming structured data into natural language prompts, we can map the relationships between proteins into texts. This approach allows LLMs to identify indirect connections between proteins, tracing the path from upstream to downstream. Therefore, we propose a novel framework ProLLM that employs an LLM tailored for PPI for the first time. Specifically, we propose Protein Chain of Thought (ProCoT), which replicates the biological mechanism of signaling pathways as natural language prompts. ProCoT considers a signaling pathway as a protein reasoning process, which starts from upstream proteins and passes through several intermediate proteins to transmit biological signals to downstream proteins. Thus, we can use ProCoT to predict the interaction between upstream proteins and downstream proteins. The training of ProLLM employs the ProCoT format, which enhances the model's understanding of complex biological problems. In addition to ProCoT, this paper also contributes to the exploration of embedding replacement of protein sites in natural language prompts, and instruction fine-tuning in protein knowledge datasets. We demonstrate the efficacy of ProLLM through rigorous validation against benchmark datasets, showing significant improvement over existing methods in terms of prediction accuracy and generalizability. The code is available at: https://github.com/MingyuJ666/ProLLM.

Xi Zhu, Haochen Xue, Ziwei Zhao et al.

Text-Attributed Graphs (TAGs), where each node is associated with text descriptions, are ubiquitous in real-world scenarios. They typically exhibit distinctive structure and domain-specific knowledge, motivating the development of a Graph Foundation Model (GFM) that generalizes across diverse graphs and tasks. Despite large efforts to integrate Large Language Models (LLMs) and Graph Neural Networks (GNNs) for TAGs, existing approaches suffer from decoupled architectures with two-stage alignment, limiting their synergistic potential. Even worse, existing methods assign out-of-vocabulary (OOV) tokens to graph nodes, leading to graph-specific semantics, token explosion, and incompatibility with task-oriented prompt templates, which hinders cross-graph and cross-task transferability. To address these challenges, we propose PromptGFM, a versatile GFM for TAGs grounded in graph vocabulary learning. PromptGFM comprises two key components: (1) Graph Understanding Module, which explicitly prompts LLMs to replicate the finest GNN workflow within the text space, facilitating seamless GNN-LLM integration and elegant graph-text alignment; (2) Graph Inference Module, which establishes a language-based graph vocabulary ensuring expressiveness, transferability, and scalability, enabling readable instructions for LLM fine-tuning. Extensive experiments demonstrate our superiority and transferability across diverse graphs and tasks. The code is available at this: https://github.com/agiresearch/PromptGFM.

Wenyue Hua, Kaijie Zhu, Lingyao Li et al.

This study intends to systematically disentangle pure logic reasoning and text understanding by investigating the contrast across abstract and contextualized logical problems from a comprehensive set of domains. We explore whether LLMs demonstrate genuine reasoning capabilities across various domains when the underlying logical structure remains constant. We focus on two main questions (1) Can abstract logical problems alone accurately benchmark an LLM's reasoning ability in real-world scenarios, disentangled from contextual support in practical settings? (2) Does fine-tuning LLMs on abstract logic problem generalize to contextualized logic problems and vice versa? To investigate these questions, we focus on standard propositional logic, specifically propositional deductive and abductive logic reasoning. In particular, we construct instantiated datasets for deductive and abductive reasoning with 4 levels of difficulty, encompassing 12 distinct categories or domains based on the categorization of Wikipedia. Our experiments aim to provide insights into disentangling context in logical reasoning and the true reasoning capabilities of LLMs and their generalization potential. The code and dataset are available at: https://github.com/agiresearch/ContextHub.

Minghao Guo, Xi Zhu, Haochen Xue et al.

Graph Neural Networks (GNNs) have achieved remarkable success in graph-based learning by propagating information among neighbor nodes via predefined aggregation mechanisms. However, such fixed schemes often suffer from two key limitations. First, they cannot handle the imbalance in node informativeness -- some nodes are rich in information, while others remain sparse. Second, predefined message passing primarily leverages local structural similarity while ignoring global semantic relationships across the graph, limiting the model's ability to capture distant but relevant information. We propose Retrieval-augmented Graph Agentic Network (ReaGAN), an agent-based framework that empowers each node with autonomous, node-level decision-making. Each node acts as an agent that independently plans its next action based on its internal memory, enabling node-level planning and adaptive message propagation. Additionally, retrieval-augmented generation (RAG) allows nodes to access semantically relevant content and build global relationships in the graph. ReaGAN achieves competitive performance under few-shot in-context settings using a frozen LLM backbone without fine-tuning, showcasing the potential of agentic planning and local-global retrieval in graph learning.

Yulong Li, Yuxuan Zhang, Feilong Tang et al.

Sign language is the primary communication mode for 72 million hearing-impaired individuals worldwide, necessitating effective bidirectional Sign Language Production and Sign Language Translation systems. However, functional bidirectional systems require a unified linguistic environment, hindered by the lack of suitable unified datasets, particularly those providing the necessary pose information for accurate Sign Language Production (SLP) evaluation. Concurrently, current SLP evaluation methods like back-translation ignore pose accuracy, and high-quality coordinated generation remains challenging. To create this crucial environment and overcome these challenges, we introduce CNText2Sign and CNSign, which together constitute the first unified dataset aimed at supporting bidirectional accessibility systems for Chinese sign language; CNText2Sign provides 15,000 natural language-to-sign mappings and standardized skeletal keypoints for 8,643 vocabulary items supporting pose assessment. Building upon this foundation, we propose the AuraLLM model, which leverages a decoupled architecture with CNText2Sign's pose data for novel direct gesture accuracy assessment. The model employs retrieval augmentation and Cascading Vocabulary Resolution to handle semantic mapping and out-of-vocabulary words and achieves all-scenario production with controllable coordination of gestures and facial expressions via pose-conditioned video synthesis. Concurrently, our Sign Language Translation model SignMST-C employs targeted self-supervised pretraining for dynamic feature capture, achieving new SOTA results on PHOENIX2014-T with BLEU-4 scores up to 32.08. AuraLLM establishes a strong performance baseline on CNText2Sign with a BLEU-4 score of 50.41 under direct evaluation.