Large language models (LLMs) exhibit impressive capabilities but struggle with reasoning errors due to hallucinations and flawed logic. To investigate their internal representations of reasoning, we introduce ArrangementPuzzle, a novel puzzle dataset with structured solutions and automated stepwise correctness verification. We trained a classifier model on LLM activations on this dataset and found that it achieved over 80% accuracy in predicting reasoning correctness, implying that LLMs internally distinguish between correct and incorrect reasoning steps, with the strongest representations in middle-late Transformer layers. Further analysis reveals that LLMs encode abstract reasoning concepts within the middle activation layers of the transformer architecture, distinguishing logical from semantic equivalence. These findings provide insights into LLM reasoning mechanisms and contribute to improving AI reliability and interpretability, thereby offering the possibility to manipulate and refine LLM reasoning.

Large Language Models (LLMs) have demonstrated remarkable potential in advancing scientific knowledge and addressing complex challenges. In this work, we introduce OmniScience, a specialized large reasoning model for general science, developed through three key components: (1) domain adaptive pretraining on a carefully curated corpus of scientific literature, (2) instruction tuning on a specialized dataset to guide the model in following domain-specific tasks, and (3) reasoning-based knowledge distillation through fine-tuning to significantly enhance its ability to generate contextually relevant and logically sound responses. We demonstrate the versatility of OmniScience by developing a battery agent that efficiently ranks molecules as potential electrolyte solvents or additives. Comprehensive evaluations reveal that OmniScience is competitive with state-of-the-art large reasoning models on the GPQA Diamond and domain-specific battery benchmarks, while outperforming all public reasoning and non-reasoning models with similar parameter counts. We further demonstrate via ablation experiments that domain adaptive pretraining and reasoning-based knowledge distillation are critical to attain our performance levels, across benchmarks.