Medication recommendation systems have gained significant attention in healthcare as a means of providing tailored and effective drug combinations based on patients' clinical information. However, existing approaches often suffer from fairness issues, as recommendations tend to be more accurate for patients with common diseases compared to those with rare conditions. In this paper, we propose a novel model called Robust and Accurate REcommendations for Medication (RAREMed), which leverages the pretrain-finetune learning paradigm to enhance accuracy for rare diseases. RAREMed employs a transformer encoder with a unified input sequence approach to capture complex relationships among disease and procedure codes. Additionally, it introduces two self-supervised pre-training tasks, namely Sequence Matching Prediction (SMP) and Self Reconstruction (SR), to learn specialized medication needs and interrelations among clinical codes. Experimental results on two real-world datasets demonstrate that RAREMed provides accurate drug sets for both rare and common disease patients, thereby mitigating unfairness in medication recommendation systems.

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