CLAMBER: A Benchmark of Identifying and Clarifying Ambiguous Information Needs in Large Language Models

Large language models (LLMs) are increasingly used to meet user information needs, but their effectiveness in dealing with user queries that contain various types of ambiguity remains unknown, ultimately risking user trust and satisfaction. To this end, we introduce CLAMBER, a benchmark for evaluating LLMs using a well-organized taxonomy. Building upon the taxonomy, we construct ~12K high-quality data to assess the strengths, weaknesses, and potential risks of various off-the-shelf LLMs. Our findings indicate the limited practical utility of current LLMs in identifying and clarifying ambiguous user queries, even enhanced by chain-of-thought (CoT) and few-shot prompting. These techniques may result in overconfidence in LLMs and yield only marginal enhancements in identifying ambiguity. Furthermore, current LLMs fall short in generating high-quality clarifying questions due to a lack of conflict resolution and inaccurate utilization of inherent knowledge. In this paper, CLAMBER presents a guidance and promotes further research on proactive and trustworthy LLMs. Our dataset is available at https://github.com/zt991211/CLAMBER

AUTODIFF: Autoregressive Diffusion Modeling for Structure-based Drug Design

Structure-based drug design (SBDD), which aims to generate molecules that can bind tightly to the target protein, is an essential problem in drug discovery, and previous approaches have achieved initial success. However, most existing methods still suffer from invalid local structure or unrealistic conformation issues, which are mainly due to the poor leaning of bond angles or torsional angles. To alleviate these problems, we propose AUTODIFF, a diffusion-based fragment-wise autoregressive generation model. Specifically, we design a novel molecule assembly strategy named conformal motif that preserves the conformation of local structures of molecules first, then we encode the interaction of the protein-ligand complex with an SE(3)-equivariant convolutional network and generate molecules motif-by-motif with diffusion modeling. In addition, we also improve the evaluation framework of SBDD by constraining the molecular weights of the generated molecules in the same range, together with some new metrics, which make the evaluation more fair and practical. Extensive experiments on CrossDocked2020 demonstrate that our approach outperforms the existing models in generating realistic molecules with valid structures and conformations while maintaining high binding affinity.