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This article is part of the supplement: Proceedings of the Second International Symposium on Languages in Biology and Medicine (LBM) 2007

Open Access Open Badges Proceedings

Automatic construction of rule-based ICD-9-CM coding systems

Richárd Farkas1 and György Szarvas2

Author Affiliations

1 Research Group on Artificial Intelligence of the Hungarian Academy of Sciences, Aradi Vértanúk tere 1., Szeged, Hungary

2 University of Szeged, Department of Informatics, Human Language Technology Group, Árpád tér 2., Szeged, Hungary

BMC Bioinformatics 2008, 9(Suppl 3):S10  doi:10.1186/1471-2105-9-S3-S10

Published: 11 April 2008



In this paper we focus on the problem of automatically constructing ICD-9-CM coding systems for radiology reports. ICD-9-CM codes are used for billing purposes by health institutes and are assigned to clinical records manually following clinical treatment. Since this labeling task requires expert knowledge in the field of medicine, the process itself is costly and is prone to errors as human annotators have to consider thousands of possible codes when assigning the right ICD-9-CM labels to a document. In this study we use the datasets made available for training and testing automated ICD-9-CM coding systems by the organisers of an International Challenge on Classifying Clinical Free Text Using Natural Language Processing in spring 2007. The challenge itself was dominated by entirely or partly rule-based systems that solve the coding task using a set of hand crafted expert rules. Since the feasibility of the construction of such systems for thousands of ICD codes is indeed questionable, we decided to examine the problem of automatically constructing similar rule sets that turned out to achieve a remarkable accuracy in the shared task challenge.


Our results are very promising in the sense that we managed to achieve comparable results with purely hand-crafted ICD-9-CM classifiers. Our best model got a 90.26% F measure on the training dataset and an 88.93% F measure on the challenge test dataset, using the micro-averaged Fβ=1 measure, the official evaluation metric of the International Challenge on Classifying Clinical Free Text Using Natural Language Processing. This result would have placed second in the challenge, with a hand-crafted system achieving slightly better results.


Our results demonstrate that hand-crafted systems – which proved to be successful in ICD-9-CM coding – can be reproduced by replacing several laborious steps in their construction with machine learning models. These hybrid systems preserve the favourable aspects of rule-based classifiers like good performance, and their development can be achieved rapidly and requires less human effort. Hence the construction of such hybrid systems can be feasible for a set of labels one magnitude bigger, and with more labeled data.