Main content area

A benchmark for comparing precision medicine methods in thyroid cancer diagnosis using tissue microarrays

Wang, Ching-Wei, Lee, Yu-Ching, Calista, Evelyne, Zhou, Fan, Zhu, Hongtu, Suzuki, Ryohei, Komura, Daisuke, Ishikawa, Shumpei, Cheng, Shih-Ping
Bioinformatics 2018 v.34 no.10 pp. 1767-1773
algorithms, bioinformatics, computer software, data collection, histopathology, image analysis, immunohistochemistry, lymph nodes, metastasis, microarray technology, models, mutation, patients, precision medicine, prediction, quantitative analysis, thyroid neoplasms
The aim of precision medicine is to harness new knowledge and technology to optimize the timing and targeting of interventions for maximal therapeutic benefit. This study explores the possibility of building AI models without precise pixel-level annotation in prediction of the tumor size, extrathyroidal extension, lymph node metastasis, cancer stage and BRAF mutation in thyroid cancer diagnosis, providing the patients’ background information, histopathological and immunohistochemical tissue images. A novel framework for objective evaluation of automatic patient diagnosis algorithms has been established under the auspices of the IEEE International Symposium on Biomedical Imaging 2017— A Grand Challenge for Tissue Microarray Analysis in Thyroid Cancer Diagnosis. Here, we present the datasets, methods and results of the challenge and lay down the principles for future uses of this benchmark. The main contributions of the challenge include the creation of the data repository of tissue microarrays; the creation of the clinical diagnosis classification data repository of thyroid cancer; and the definition of objective quantitative evaluation for comparison and ranking of the algorithms. With this benchmark, three automatic methods for predictions of the five clinical outcomes have been compared, and detailed quantitative evaluation results are presented in this paper. Based on the quantitative evaluation results, we believe automatic patient diagnosis is still a challenging and unsolved problem. The datasets and the evaluation software will be made available to the research community, further encouraging future developments in this field. ( Supplementary data are available at Bioinformatics online.