Chemical reasoning language models are expected to derive molecular answers through faithful chain-of-thought (CoT). However, across four reasoning model families and twelve chemistry tasks, hallucination is widespread and largely decoupled from answer correctness: correct answers often coexist with fabricated structural claims absent from the relevant molecules. Yet this does not make the reasoning trace computationally irrelevant. Attribution analyses suggest a shared scratchpad function expressed in model-specific forms: Chem-R and ether-0 rely on fragmented SMILES drafts, whereas ChemDFM-R emphasizes scaffold, positional, and naming cues. Notably, perturbing Chem-R's SMILES sketches degrades generation, showing that structural drafts can be causally load-bearing even when verbal structural claims are largely inert. Together, these results show that chemical CoT is neither a faithful explanation nor merely a post-hoc rationalization, but a hallucination-prone molecular scratchpad. This finding cautions against treating CoT as direct evidence of faithful reasoning and motivates process-level supervision beyond answer-only evaluation.
Jiatong Li, Yuxuan Ren, Weida Wang et al.· 1 citation
Adversarial purification is a defense technique that employs generative models to remove adversarial perturbations. Current methods often rely on powerful generators, typically diffusion models, and focus on reducing the gap between adversarial and clean samples in the feature space, while overlooking semantic correlation within a single sample. To address this issue, we explore adversarial purification from the perspective of preserving semantic relationships among image patches. We employ an Attentive Mask Reconstruction Model (AMRM), which shows superior performance. Our theoretical and experimental analysis reveals that AMRM is highly sensitive to adversarial noise, as such noise significantly distorts patch relationships. Based on this observation, we propose AMRM-Pure, a purification framework that denoises adversarial inputs by preserving patch-level semantics, and formulate this process as a tractable optimization problem with respect to the input. To further enhance robustness, we finetune AMRM-Pure with classification loss to strengthen semantic consistency. We apply our insight to two AMRM architectures, including Mask Autoencoder (MAE) and MaskDiT. Extensive experiments confirm the effectiveness of our method, establishing new state-of-the-art performance across multiple benchmarks.
Zhihao Dou, Zhiqiang Gao, Dongfei Cui et al.· 0 citations
The proposed Chem-R, a general Chemical Reasoning model designed to emulate the deliberative processes of chemists, achieves state-of-the-art performance on comprehensive benchmarks, surpassing leading LLMs, including Gemini-3-Pro and Kimi-k2.5.
Weida Wang, Benteng Chen, Di Zhang et al.· Proceedings of the 32nd ACM...· 0 citations
A Molecular Perturbation framework that generates syntax-valid structural variants of training molecules under controlled Graph Edit Distance (GED) to probe the manifold regularity of molecular LLMs and suggests that it can partially expand the local trust region and offer a promising direction for stabilizing molecular LLMs against structural variation.
Jiatong Li, Weida Wang, Changmeng Zheng et al.· 0 citations