Multimodal Large Language Models (MLLMs) excel at recognizing individual visual elements and reasoning over simple linear diagrams. However, when faced with complex topological structures involving branching paths, converging flows, and cyclic dependencies, their reasoning capabilities degrade sharply, even on tasks as basic as counting endpoints. Existing benchmarks fail to probe this gap, focusing on semantic comprehension rather than structural reasoning. We introduce **ReactBench**, a benchmark that reveals fundamental limitations in structural reasoning through chemical reaction diagrams. These real-world scientific diagrams offer an ideal testbed because they naturally span diverse structures from linear chains to cyclic graphs, while requiring both precise local recognition and coherent global reasoning. Our benchmark comprises 1,618 expert-annotated QA pairs across four hierarchical task dimensions. Extensive evaluation across 24 MLLMs reveals a significant performance gap exceeding 30% between anchor-based tasks and holistic structural reasoning tasks.

Large language models (LLMs) are increasingly applied to scientific research, yet existing evaluations often fail to reflect the fine-grained capabilities required in practice. Most benchmarks are manually curated or domain-generic, limiting scalability and alignment with real scientific use cases. In this paper, we propose a new framework named SciCustom to address the problem. It enables the custom construction of benchmarks from large-scale scientific data to evaluate application-specific scientific capabilities in LLMs. SciCustom first organizes scientific knowledge into ontology-grounded knowledge units with controlled granularity and trains a tagger to map large-scale data instances into this knowledge space. Given a custom requirement, relevant knowledge units are identified via voting-based multi-model consensus. These units enable relevance-aware benchmark retrieval via binary search, followed by proxy subset selection and data-grounded benchmark generation for efficient evaluation. Experiments in chemistry and healthcare demonstrate that SciCustom reveals fine-grained differences in LLM scientific capabilities that standard benchmarks overlook, while requiring neither expert annotation nor synthetic question generation. This work provides a scalable and application-aware foundation for benchmarking scientific capabilities in LLMs.

With the extensive deployment of Large Language Models (LLMs), ensuring their safety has become increasingly critical. However, existing defense methods often struggle with two key issues: (i) inadequate defense capabilities, particularly in domain-specific scenarios like chemistry, where a lack of specialized knowledge can lead to the generation of harmful responses to malicious queries. (ii) over-defensiveness, which compromises the general utility and responsiveness of LLMs. To mitigate these issues, we introduce a multi-agents-based defense framework, Guide for Defense (G4D), which leverages accurate external information to provide an unbiased summary of user intentions and analytically grounded safety response guidance. Extensive experiments on popular jailbreak attacks and benign datasets show that our G4D can enhance LLM’s robustness against jailbreak attacks on general and domain-specific scenarios without compromising the model’s general functionality.

In recent years, protein-text models have gained significant attention for their potential in protein generation and understanding. Current approaches focus on integrating protein-related knowledge into large language models through continued pretraining and multi-modal alignment, enabling simultaneous comprehension of textual descriptions and protein sequences. Through a thorough analysis of existing model architectures and text-based protein understanding benchmarks, we identify significant data leakage issues present in current benchmarks. Moreover, conventional metrics derived from natural language processing fail to assess the model’s performance in this domain accurately. To address these limitations, we reorganize existing datasets and introduce a novel evaluation framework based on biological entities. Motivated by our observation, we propose a retrieval-enhanced method, which significantly outperforms fine-tuned LLMs for protein-to-text generation and shows accuracy and efficiency in training-free scenarios. Our code and data will be available.