Retrieval-augmented generation (RAG) systems often struggle with narrative-rich documents and event-centric reasoning, particularly when synthesizing information across multiple sources. We present EventRAG, a novel framework that enhances text generation through structured event representations. We first construct an Event Knowledge Graph by extracting events and merging semantically equivalent nodes across documents, while expanding under-connected relationships. We then employ an iterative retrieval and inference strategy that explicitly captures temporal dependencies and logical relationships across events. Experiments on UltraDomain and MultiHopRAG benchmarks show EventRAG’s superiority over baseline RAG systems, with substantial gains in generation effectiveness, logical consistency, and multi-hop reasoning accuracy. Our work advances RAG systems by integrating structured event semantics with iterative inference, particularly benefiting scenarios requiring temporal and logical reasoning across documents.

Protein language models have emerged as powerful tools for sequence generation, offering substantial advantages in functional optimization and denovo design. However, these models also present significant risks of generating harmful protein sequences, such as those that enhance viral transmissibility or evade immune responses. These concerns underscore critical biosafety and ethical challenges. To address these issues, we propose a Knowledge-guided Preference Optimization (KPO) framework that integrates prior knowledge via a Protein Safety Knowledge Graph. This framework utilizes an efficient graph pruning strategy to identify preferred sequences and employs reinforcement learning to minimize the risk of generating harmful proteins. Experimental results demonstrate that KPO effectively reduces the likelihood of producing hazardous sequences while maintaining high functionality, offering a robust safety assurance framework for applying generative models in biotechnology.

The past years have witnessed a proliferation of large language models (LLMs). Yet, reliable evaluation of LLMs is challenging due to the inaccuracy of standard metrics in human perception of text quality and the inefficiency in sampling informative test examples for human evaluation. This paper presents a sample-efficient human evaluation method for LLMs based on the principle of MAximum Discrepancy (MAD) competition. MAD automatically selects a small set of informative input instructions, each of which maximizes the discrepancy of two LLMs’ reponses, which are subsequently subject to three-alternative forced choice by human subjects. The pairwise comparison results of multiple LLMs are then aggregated into a global ranking using the Elo rating system. We compare eight representative LLMs in terms of four skills: knowledge understanding, mathematical reasoning, writing, and coding. Experimental results show that the proposed method reliably achieves the “golden” ranking of LLMs with a minimum set of input instructions, which in turn reveal their relative strengths and weaknesses, and offers valuable insights for further LLM advancement.

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.

Recent advancements in large language models (LLMs) have highlighted their potential across a variety of tasks, but their performance still heavily relies on the design of effective prompts. Existing methods for automatic prompt optimization face two challenges: lack of diversity, limiting the exploration of valuable and innovative directions and semantic drift, where optimizations for one task can degrade performance in others. To address these issues, we propose Residual Optimization Tree (RiOT), a novel framework for automatic prompt optimization. RiOT iteratively refines prompts through text gradients, generating multiple semantically diverse candidates at each step, and selects the best prompt using perplexity. Additionally, RiOT incorporates the text residual connection to mitigate semantic drift by selectively retaining beneficial content across optimization iterations. A tree structure efficiently manages the optimization process, ensuring scalability and flexibility. Extensive experiments across five benchmarks — covering commonsense, mathematical, logical, temporal, and semantic reasoning — demonstrate that RiOT outperforms both previous prompt optimization methods and manual prompting. Code will be released.

The ability to understand a user’s underlying needs is critical for conversational systems, especially with limited input from users in a conversation. Thus, in such a domain, Asking Clarification Questions (ACQs) to reveal users’ true intent from their queries or utterances arise as an essential task. However, it is noticeable that a key limitation of the existing ACQs studies is their incomparability, from inconsistent use of data, distinct experimental setups and evaluation strategies. Therefore, in this paper, to assist the development of ACQs techniques, we comprehensively analyse the current ACQs research status, which offers a detailed comparison of publicly available datasets, and discusses the applied evaluation metrics, joined with benchmarks for multiple ACQs-related tasks. In particular, given a thorough analysis of the ACQs task, we discuss a number of corresponding research directions for the investigation of ACQs as well as the development of conversational systems.