Ruosong Ye

Ruosong Ye, Caiqi Zhang, Runhui Wang et al. · cambridge

The emergence of large-scale pre-trained language models has revolutionized various AI research domains. Transformers-based Large Language Models (LLMs) have gradually replaced CNNs and RNNs to unify fields of computer vision and natural language processing. Compared with independent data samples such as images, videos or texts, graphs usually contain rich structural and relational information. Meanwhile, language, especially natural language, being one of the most expressive mediums, excels in describing complex structures. However, existing work on incorporating graph problems into the generative language modeling framework remains very limited. Considering the rising prominence of LLMs, it becomes essential to explore whether LLMs can also replace GNNs as the foundation model for graphs. In this paper, we propose InstructGLM (Instruction-finetuned Graph Language Model) with highly scalable prompts based on natural language instructions. We use natural language to describe multi-scale geometric structure of the graph and then instruction finetune an LLM to perform graph tasks, which enables Generative Graph Learning. Our method surpasses all GNN baselines on ogbn-arxiv, Cora and PubMed datasets, underscoring its effectiveness and sheds light on generative LLMs as new foundation model for graph machine learning. Our code is open-sourced at https://github.com/agiresearch/InstructGLM.

Kai Mei, Xi Zhu, Wujiang Xu et al.

LLM-based intelligent agents face significant deployment challenges, particularly related to resource management. Allowing unrestricted access to LLM or tool resources can lead to inefficient or even potentially harmful resource allocation and utilization for agents. Furthermore, the absence of proper scheduling and resource management mechanisms in current agent designs hinders concurrent processing and limits overall system efficiency. To address these challenges, this paper proposes the architecture of AIOS (LLM-based AI Agent Operating System) under the context of managing LLM-based agents. It introduces a novel architecture for serving LLM-based agents by isolating resources and LLM-specific services from agent applications into an AIOS kernel. This AIOS kernel provides fundamental services (e.g., scheduling, context management, memory management, storage management, access control) for runtime agents. To enhance usability, AIOS also includes an AIOS SDK, a comprehensive suite of APIs designed for utilizing functionalities provided by the AIOS kernel. Experimental results demonstrate that using AIOS can achieve up to 2.1x faster execution for serving agents built by various agent frameworks. The source code is available at https://github.com/agiresearch/AIOS.

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.

Yang Zhou, Mingyu Zhao, Zhenting Wang et al.

We present M^3-Bench, the first benchmark for evaluating multimodal tool use under the Model Context Protocol. The benchmark targets realistic, multi-hop and multi-threaded workflows that require visual grounding and textual reasoning, cross-tool dependencies, and persistence of intermediate resources across steps. We introduce a similarity-driven alignment that serializes each tool call, embeds signatures with a sentence encoder, and performs similarity-bucketed Hungarian matching to obtain auditable one-to-one correspondences. On top of this alignment, we report interpretable metrics that decouple semantic fidelity from workflow consistency. The benchmark spans 28 servers with 231 tools, and provides standardized trajectories curated through an Executor & Judge pipeline with human verification; an auxiliary four large language models (LLMs) judge ensemble reports end-task Task Completion and information grounding. Evaluations of representative state-of-the-art Multimodal LLMs (MLLMs) reveal persistent gaps in multimodal MCP tool use, particularly in argument fidelity and structure consistency, underscoring the need for methods that jointly reason over images, text, and tool graphs. Our Benchmark's anonymous repository is at https://github.com/EtaYang10th/Open-M3-Bench

Yu'an Chen, Ruosong Ye, Ziyang Tao et al.

Deep reinforcement learning (DRL) algorithms have proven effective in robot navigation, especially in unknown environments, by directly mapping perception inputs into robot control commands. However, most existing methods ignore the local minimum problem in navigation and thereby cannot handle complex unknown environments. In this paper, we propose the first DRL-based navigation method modeled by a semi-Markov decision process (SMDP) with continuous action space, named Adaptive Forward Simulation Time (AFST), to overcome this problem. Specifically, we reduce the dimensions of the action space and improve the distributed proximal policy optimization (DPPO) algorithm for the specified SMDP problem by modifying its GAE to better estimate the policy gradient in SMDPs. Experiments in various unknown environments demonstrate the effectiveness of AFST.