Reasoning large language models (LLMs) have recently made much progress in complex problem-solving, leveraging internal reasoning (or thought) to guide their solution generation. However, existing LLM-based counseling agents, including those using Motivational Interviewing (MI), generate responses without explicitly aligning thoughts with counseling techniques, limiting their effectiveness. We propose MIThinker, a lightweight thinking model that generates therapeutic thoughts to guide MI counseling agents in strategy selection and response generation. To overcome the lack of annotated thought data, we introduce AugR1-MI, an automated pipeline that reverse-engineers counselor's thoughts from observed responses. Through two-stage training combining supervised fine-tuning and reinforcement learning, MIThinker demonstrates improved theory-of-mind assessment and strategy alignment. Comprehensive evaluations show that MindfulMI, our agent leveraging MIThinker, achieves MI competency comparable to state-of-the-art systems with an order of magnitude less computation.
Rare diseases affect millions of individuals worldwide, yet timely diagnosis remains a major public health challenge due to scarcity of specialized clinical expertise. While large language models (LLMs) show promise to support rare disease diagnosis, current models are constrained by insufficient clinical deployability, limited clinically grounded evidence, and scarcity of training data. Here we present RaDaR (Rare Disease navigatoR), an open-source, compact reasoning LLM (32B parameters) for rare disease diagnosis. RaDaR was trained with 49,170 publicly available free-text cases and 104,666 synthetic cases with reasoning-enhanced training. RaDaR showed the strongest performance among evaluated open-source models, including the 671B DeepSeek-R1, across public benchmarks and four external validation centers. In a retrospective cohort, RaDaR prioritized the final diagnosis before documented clinical suspicion in 61.06 percent of cases, corresponding to a potential lead time of 1.87 months and 50.18 percent of the within-center interval. In a randomized physician-assistance trial, RaDaR assistance improved physicians' rare-disease diagnostic accuracy by 21.44 percentage points compared with internet search alone. Synthetic-data ablations suggested that phenotype-anchored narratives provide useful training signal for long-tail rare diseases, with a monotonic scaling trend within the tested data range. Together, RaDaR and its development and validation framework provide a deployable rare-disease reasoning model and a reproducible development framework for diagnostic AI under data scarcity.