Integrating Natural Language Processing and Machine Learning Algorithms to Categorize Oncologic Response in Radiology Reports
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A significant volume of medical data remains unstructured. Natural language processing (NLP) and machine learning (ML) techniques have shown to successfully extract insights from radiology reports. However, the codependent effects of NLP and ML in this context have not been well-studied. Between April 1, 2015 and November 1, 2016, 9418 cross-sectional abdomen/pelvis CT and MR examinations containing our internal structured reporting element for cancer were separated into four categories: Progression, Stable Disease, Improvement, or No Cancer. We combined each of three NLP techniques with five ML algorithms to predict the assigned label using the unstructured report text and compared the performance of each combination. The three NLP algorithms included term frequency-inverse document frequency (TF-IDF), term frequency weighting (TF), and 16-bit feature hashing. The ML algorithms included logistic regression (LR), random decision forest (RDF), one-vs-all support vector machine (SVM), one-vs-all Bayes point machine (BPM), and fully connected neural network (NN). The best-performing NLP model consisted of tokenized unigrams and bigrams with TF-IDF. Increasing N-gram length yielded little to no added benefit for most ML algorithms. With all parameters optimized, SVM had the best performance on the test dataset, with 90.6 average accuracy and F score of 0.813. The interplay between ML and NLP algorithms and their effect on interpretation accuracy is complex. The best accuracy is achieved when both algorithms are optimized concurrently.
KeywordsNatural language processing Machine learning Structured reporting Informatics
This study received no funding support from a grant agency.
Compliance with Ethical Standards
Conflict of Interest
Po-Hao Chen is a co-founder of Alphametric Health LLC. Maya Galperin-Aizenberg, Hanna Zafar, and Tessa S. Cook declare that they have no conflicts of interest.
For this type of study formal consent is not required.
- 4.Cai T, Giannopoulos AA, Yu S, Kelil T, Ripley B, Kumamaru KK et al.: Natural language processing technologies in radiology research and clinical applications. Radiogr Rev Publ Radiol Soc N Am Inc. 36(1):176–191, 2016Google Scholar
- 6.Kocbek S, Cavedon L, Martinez D, Bain C, Mac Manus C, Haffari G et al.: Text mining electronic hospital records to automatically classify admissions against disease: measuring the impact of linking data sources. J Biomed Inform., 2016Google Scholar
- 7.Rajaraman A, Ullman JD: Mining of massive datasets [Internet]. Cambridge: Cambridge University Press, 2011, [cited 2017 May 24]. Available from: http://ebooks.cambridge.org/ref/id/CBO9781139058452 CrossRefGoogle Scholar
- 10.Weinberger K, Dasgupta A, Langford J, Smola A, Attenberg J: Feature hashing for large scale multitask learning. In ACM Press; 2009 [cited 2017 May 24]. p. 1–8. Available from: http://portal.acm.org/citation.cfm?doid=1553374.1553516
- 11.Hassanpour S, Langlotz CP. Unsupervised Topic Modeling in a Large Free Text Radiology Report Repository. J Digit Imaging. 29(1):59–62, 2016.Google Scholar
- 12.Hassanpour S, Langlotz CP. Information extraction from multi-institutional radiology reports. Artif Intell Med. 66:29–39, 2016.Google Scholar
- 17.Wang Z, He Y, Jiang M: A Comparison among Three Neural Networks for Text Classification. In IEEE; 2006 [cited 2017 May 29]. Available from: http://ieeexplore.ieee.org/document/4129218/
- 20.Bird S, Klein E, Loper E: Natural language processing with Python, 1st edition. Beijing: O’Reilly, 2009, 479 pGoogle Scholar
- 21.Lipton ZC, Elkan C, Naryanaswamy B: Optimal thresholding of classifiers to maximize F1 measure. Mach Learn Knowl Discov Databases Eur Conf ECML PKDD Proc ECML PKDD Conf. 8725:225–239, 2014Google Scholar
- 24.Pennington J, Socher R, Manning C. Glove: global vectors for word representation. In association for computational linguistics; 2014 [cited 2017 Sep 2]. p. 1532–43. Available from: http://aclweb.org/anthology/D14-1162
- 25.Mikolov T, Chen K, Corrado G, Dean J. Efficient Estimation of Word Representations in Vector Space. ICLR Workshop. 2013 Jan 16;Google Scholar
- 26.Zhang W, Yoshida T, Tang X. TFIDF, LSI and multi-word in information retrieval and text categorization. In IEEE; 2008 [cited 2017 May 29]. p. 108–13. Available from: http://ieeexplore.ieee.org/document/4811259/
- 28.Joachims T: Text categorization with support vector machines: learning with many relevant features. In: Nédellec C, Rouveirol C Eds. Machine learning: ECML-98 [Internet]. Berlin: Springer Berlin Heidelberg, 1998, pp. 137–142 [cited 2017 May 29] Available from: http://link.springer.com/10.1007/BFb0026683 CrossRefGoogle Scholar
- 31.Wei W, Marmor R, Singh S, Wang S, Demner-Fushman D, Kuo T-T et al.: Finding related publications: extending the set of terms used to assess article similarity. AMIA Jt Summits Transl Sci Proc AMIA Jt Summits Transl Sci. 2016:225–234, 2016Google Scholar