This thesis describes a new optimisation and new heuristics for automatically marking up XML documents. These are implemented in CEM, using PPMmodels. CEM is significantly more general than previous systems, marking up large numbers of hierarchical tags, using n-gram models for large n and a variety of escape methods. Four corpora are discussed, including the bibliography corpus of 14682 bibliographies laid out in seven standard styles using the BIBTEX system and markedup in XML with every field from the original BIBTEX. Other corpora include the ROCLING Chinese text segmentation corpus, the Computists’ Communique corpus and the Reuters’ corpus. A detailed examination is presented of the methods of evaluating mark up algorithms, including computation complexity measures and correctness measures from the fields of information retrieval, string processing, machine learning and information theory. A new taxonomy of markup complexities is established and the properties of each taxon are examined in relation to the complexity of marked-up documents. The performance of the new heuristics and optimisation is examined using the four corpora.