Molecular structure elucidation involves deducing a molecule’s structure from various types of spectral data, which is crucial in chemical experimental analysis. While large language models (LLMs) have shown remarkable proficiency in analyzing and reasoning through complex tasks, they still encounter substantial challenges in molecular structure elucidation. We identify that these challenges largely stem from LLMs’ limited grasp of specialized chemical knowledge. In this work, we introduce a Knowledge-enhanced reasoning framework for Molecular Structure Elucidation (K-MSE), leveraging Monte Carlo Tree Search for test-time scaling as a plugin. Specifically, we construct an external molecular substructure knowledge base to extend the LLMs’ coverage of the chemical structure space. Furthermore, we design a specialized molecule-spectrum scorer to act as a reward model for the reasoning process, addressing the issue of inaccurate solution evaluation in LLMs. Experimental results show that our approach significantly boosts performance, particularly gaining more than 20% improvement on both GPT-4o-mini and GPT-4o.

Large Language Models (LLMs) augmented with external tools have demonstrated remarkable capabilities in complex problem solving. Existing efforts for tool utilization typically involve an LLM agent that contains instructions on using the description of the available tools to determine and call the tools required to solve the problem. Inference Scaling techniques, such as chain-of-thought and tree-of-thought reasoning, are commonly used but require significant computational overhead and rendering such methods impractical in real-world applications. In this work, we recognize and formalize the critical role of instructions provided in agent prompts and tool descriptions—collectively referred to as *context*—and show that incomplete *context* is one of the reasons for this computational overhead.To fill this efficiency gap, we propose an optimization framework that jointly refines both the instructions provided in the agent prompt and tool description, enhancing their interaction. Experiments on StableToolBench and RestBench demonstrate that our optimized agents achieve superior efficiency while maintaining effectiveness. Our findings underscore the critical role of context optimization in improving LLM agents for tool utilization, paving the way for more responsive and cost-effective LLM agents. Our code is available at [https://github.com/Bingo-W/ToolOptimization](https://github.com/Bingo-W/ToolOptimization).

Augmenting Large Language Models (LLMs) with retrieved external knowledge has proven effective in improving the factual accuracy of generated responses. Despite their success, retrieval-augmented LLMs still face the distractibility issue, where the generated responses are negatively influenced by noise from both external and internal knowledge sources. In this paper, we introduce a novel, training-free decoding method guided by entropy considerations to mitigate this issue. Our approach utilizes entropy-based document-parallel ensemble decoding to prioritize low-entropy distributions from retrieved documents, thereby enhancing the extraction of relevant information of context. Additionally, it incorporates a contrastive decoding mechanism that contrasts the obtained low-entropy ensemble distribution with the high-entropy distribution derived from the model’s internal knowledge across layers, which ensures a greater emphasis on reliable external information. Extensive experiments on open-domain question answering datasets demonstrate the superiority of our method.