Can we trust the reasoning traces that large reasoning models (LRMs) produce? We investigate whether these traces faithfully reflect what drives model outputs, and whether models will honestly report their influence. We introduce Thought Injection, a method that injects synthetic reasoning snippets into a model’s reasoning trace, then measures whether the model follows the injected reasoning and acknowledges doing so. Across 45,000 samples from three LRMs, we find that injected hints reliably alter outputs, confirming that reasoning traces causally shape model behavior. However, when asked to explain their changed answers, models overwhelmingly refuse to disclose the influence: non-disclosure exceeds 90% for extreme hints across 30,000 follow-up samples. Instead of acknowledging the injected reasoning, models fabricate aligned-appearing but unrelated explanations. Activation analysis reveals that sycophancy- and deception-related directions are strongly activated during these fabrications, suggesting systematic patterns rather than incidental failures. Our findings reveal a gap between the reasoning LRMs follow and the reasoning they report, raising concern that aligned-appearing explanations may not be equivalent to genuine alignment.

Understanding scientific papers requires more than answering isolated questions or summarizing content. It involves an integrated reasoning process that grounds textual and visual information, interprets experimental evidence, synthesizes information across sources, and critically evaluates scientific claims. However, existing benchmarks typically assess these abilities in isolation, making it difficult to evaluate scientific paper understanding as a unified set of interacting cognitive abilities. In this work, we introduce PaperMind , a benchmark designed to evaluate integrated and agent-oriented scientific reasoning over research papers. PaperMind is constructed from real scientific papers across seven domains, including agriculture, biology, chemistry, computer science, medicine, physics, and economics. It comprises four complementary task families that collectively operationalize distinct cognitive facets of scientific paper reasoning, including multimodal grounding, experimental interpretation, cross-source evidence reasoning, and critical assessment. By analyzing model behavior across multiple tasks, PaperMind enables a diagnostic evaluation of integrated scientific reasoning behaviors that are difficult to assess through isolated task evaluations. Extensive experiments on both open-source and closed-source multimodal LLMs reveal consistent performance gaps across tasks, highlighting persistent challenges in integrated scientific reasoning and critique. Our benchmark and dataset are available at https://github.com/Yanjun-Zhao/PaperMind.

Puns play a vital role in academic research due to their distinct structure and clear definition, which aid in the comprehensive analysis of linguistic humor. However, the understanding of puns in large language models (LLMs) has not been thoroughly examined, limiting their use in creative writing and humor creation. In this paper, we leverage three popular tasks, i.e., pun recognition, explanation and generation to systematically evaluate the capabilities of LLMs in pun understanding. In addition to adopting the automated evaluation metrics from prior research, we introduce new evaluation methods and metrics that are better suited to the in-context learning paradigm of LLMs. These new metrics offer a more rigorous assessment of an LLM’s ability to understand puns and align more closely with human cognition than previous metrics. Our findings reveal the “lazy pun generation” pattern and identify the primary challenges LLMs encounter in understanding puns.