Described is a multi-path handwriting recognition framework based upon stroke segmentation, symbol recognition, two-dimensional structure analysis and semantic structure analysis. Electronic pen input corresponding to handwritten input (e.g., a chemical expression) is recognized and output via a data structure, which may include multiple recognition candidates. A recognition framework performs stroke segmentation and symbol recognition on the input, and analyzes the structure of the input to output the data structure corresponding to recognition results. For chemical expressions, the structural analysis may perform a conditional sub-expression analysis for inorganic expressions, or organic bond detection, connection relationship analysis, organic atom determination and/or conditional sub-expression analysis for organic expressions. The structural analysis also performs subscript, superscript analysis and character determination. Further analysis may be performed, e.g., chemical valence analysis and/or semantic structure analysis.