Abstract: A system (100) is extracting targeted medical information from clinical notes stored in memory (120). The system (100) includes a preprocessing module (120a) configured to retrieve from the memory (120) a sequence of clinical texts of electronic health records, and to tokenize the sequence of clinical texts to obtain a sequence of input tokens. The system (100) further includes a sequence to structure model module (120b) configured to transform, using a trained natural language based transformer, the sequence of input tokens into a sequence of structured output tokens. The system (100) further includes a post-processing unit (110) configured to obtain annotated text-label pairs of the clinical texts from the structure output tokens.