A forward pass through a sequence of strokes representing a handwritten equation is performed from the first stroke to the last stroke in the sequence. At each stroke, a path score is determined for a plurality of symbol-relation pairs that each represents a symbol and its spatial relation to a predecessor symbol. A symbol graph having nodes and links is constructed by backtracking through the strokes from the last stroke to the first stroke and assigning scores to the links based on the path scores for the symbol-relation pairs. The symbol graph is used to recognize a mathematical expression based in part on the scores for the links and the mathematical expression is stored.