MolDeTox: Evaluating Language Model's Stepwise Fragment Editing for Molecular Detoxification

Large Language Models (LLMs) and Vision Language Models (VLMs) have recently shown promising capabilities in various scientific domain. In particular, these advances have opened new opportunities in drug discovery, where the ability to understand and modify molecular structures is critical for optimizing drug properties such as efficacy and toxicity. However, existing models and benchmarks often overlook toxicity-related challenges, focusing primarily on general property optimization without adequately addressing safety concerns. In addition, even existing toxicity repair benchmarks suffer from limited data diversity, low structural validity of generated molecules, and heavy reliance on proxy models for toxicity assessment. To address these limitations, we propose MolDeTox, a novel benchmark for molecular detoxification, designed to enable fine-grained and reliable evaluation of toxicity-aware molecular optimization across stepwise tasks. We evaluate a wide range of general-purpose LLMs and VLMs under diverse settings, and demonstrate that understanding and generating molecules at the fragment-level improves structural validity and enhances the quality of generated molecules. Moreover, through detailed task-level performance analysis, MolDeTox provides an interpretable benchmark that enables a deeper understanding of the detoxification process. Our dataset is available at : https://huggingface.co/datasets/MolDeTox/MolDeTox

ToxReason: A Benchmark for Mechanistic Chemical Toxicity Reasoning via Adverse Outcome Pathway

Recent advances in large language models (LLMs) have enabled molecular reasoning for property prediction. However, toxicity arises from complex biological mechanisms beyond chemical structure, necessitating mechanistic reasoning for reliable prediction. Despite its importance, current benchmarks fail to systematically evaluate this capability. LLMs can generate fluent but biologically unfaithful explanations, making it difficult to assess whether predicted toxicities are grounded invalid mechanisms. To bridge this gap, we introduce ToxReason, a benchmark grounded in the Adverse Outcome Pathway (AOP) that evaluates organ-level toxicity reasoning across multiple organs. ToxReason integrates experimental drug-target interaction evidence with toxicity labels, requiring models to infer both toxic outcomes and their underlying mechanisms from Molecular Initiating Event (MIE) to Adverse Outcome (AO). Using ToxReason, we evaluate toxicity prediction performance and reasoning quality across diverse LLMs. We find that strong predictive performance does not necessarily imply reliable reasoning. Furthermore, we show that reasoning-aware training improves mechanistic reasoning and, consequently, toxicity prediction performance. Together, these results underscore the necessity of integrating reasoning into both evaluation and training for trustworthy toxicity modeling.

When Choices Become Priors: Contrastive Decoding for Scientific Figure Multiple-Choice QA

Scientific figure multiple-choice question answering (MCQA) requires models to reason over diverse visual evidence, ranging from charts and multipanel figures to microscopy and biomedical images. However, this setting suffers from a distinctive bias: answer choices themselves can act as priors, steering multimodal models toward scientifically plausible options even when the figure supports a different answer. We investigate this failure mode through a simple question: what if decoding explicitly discounts what the model would prefer from text alone, so as to favor figure-grounded evidence? To this end, we propose SCICON, a training-free decoding method that scores each candidate by subtracting a text-only option score from its image-conditioned counterpart. Unlike prior contrastive decoding approaches that mitigate hallucinations by contrasting original inputs with distorted images or perturbed instructions, SCICON directly targets the choice-induced prior encoded in candidate text. Across three scientific figure QA benchmarks and three model backbones, SCICON consistently improves accuracy over standard decoding baselines. These results show that decoding against choice-induced priors is an effective and simple way to improve figure-grounded reasoning in scientific MCQA.

CLAG: Adaptive Memory Organization via Agent-Driven Clustering for Small Language Model Agents

Large language model agents heavily rely on external memory to support knowledge reuse and complex reasoning tasks. Yet most memory systems store experiences in a single global retrieval pool which can gradually dilute or corrupt stored knowledge. This problem is especially pronounced for small language models (SLMs), which are highly vulnerable to irrelevant context. We introduce CLAG, a CLustering-based AGentic memory framework where an SLM agent actively organizes memory by clustering. CLAG employs an SLM-driven router to assign incoming memories to semantically coherent clusters and autonomously generates cluster-specific profiles, including topic summaries and descriptive tags, to establish each cluster as a self-contained functional unit. By performing localized evolution within these structured neighborhoods, CLAG effectively reduces cross-topic interference and enhances internal memory density. During retrieval, the framework utilizes a two-stage process that first filters relevant clusters via their profiles, thereby excluding distractors and reducing the search space. Experiments on multiple QA datasets with three SLM backbones show that CLAG consistently improves answer quality and robustness over prior memory systems for agents, remaining lightweight and efficient.