DILS 2015: Data Integration in the Life Sciences pp 240-250 | Cite as
SPIRIT-ML: A Machine Learning Platform for Deriving Knowledge from Biomedical Datasets
Abstract
SPIRIT-ML (Software Platform for Integrated Research Information and Transformation - Machine Learning) is a synergistic and flexible machine learning component of integrated research informatics platform, SPIRIT, being developed at City of Hope. SPIRIT-ML is being developed to analyze varied data analysis problems in biomedical and clinical datasets to further translational research. An interactive interface, broad spectrum of data driven learning models, multiple cross-validation techniques, visualization methods and reporting metrics constitute the platform.
Keywords
Machine learning Translational research PlatformNotes
Acknowledgments
The authors would like to thank Dr. Joyce Niland, Dr. Haiqing Li and Dr. Weizhong Zhu for their input and feedback.
References
- 1.Ross, M.E., Zhou, X., et al.: Classification of pediatric acute lymphoblastic leukemia by gene expression profiling. Blood 102(8), 2951–2959 (2003)CrossRefGoogle Scholar
- 2.Cleophas, T.J., Zwinderman, A.H.: Machine Learning in Medicine. Springer, Netherlands (2013)CrossRefGoogle Scholar
- 3.Wolberg, W.H., Mangasarian, O.L.: Multisurface method of pattern separation for medical diagnosis applied to breast cytology. PNAS 87, 9193–9196 (1990)CrossRefMATHGoogle Scholar
- 4.Zhang, J.: Selecting typical instances in instance-based learning. In: Proceedings of the Ninth International Machine Learning Conference, Aberdeen, Scotland, pp. 470–479. Morgan Kaufmann (1992)Google Scholar
- 5.Friedman, N., Geiger, D., Goldszmidt, M.: Bayesian network classifiers. Mach. Learn. 29(2–3), 131–163 (1997)CrossRefMATHGoogle Scholar
- 6.Kaufman, L., Rousseeuw, P.J.: Finding Groups in Data: An Introduction to Cluster Analysis. Wiley, New York (1990)CrossRefGoogle Scholar
- 7.Hartigan, J.A.: Clustering Algorithms. Wiley, New York (1975)MATHGoogle Scholar
- 8.Breiman, L., Freidman, J., Stone, C.J., Olshen, R.A.: Classification and Regression Trees. Chapman and Hall/CRC, Boca Raton (1984)MATHGoogle Scholar
- 9.Kuhn, M., Johnson, K.: Applied Predictive Modeling. Springer, New York (2013)CrossRefMATHGoogle Scholar
- 10.Cortes, C., Vapnik, V.: Support-vector network. Mach. Learn. 20, 1–25 (1995)Google Scholar
- 11.Werbos, P.J.: Beyond Regression: New Tools for Prediction and Analysis in the Behavioral Sciences. Ph.D. thesis, Harvard University (1974)Google Scholar
- 12.Breiman, L.: Random forests. Mach. Learn. 45(1), 5–32 (2001)CrossRefMATHGoogle Scholar
- 13.Nagarajan, R., Scutari, M., Lebre, S.: Bayesian Networks in R: with Applications in Systems Biology. Springer, New York (2013)CrossRefGoogle Scholar
- 14.Kohavi, R.: A study of cross-validation and bootstrap for accuracy estimation and model selection. In: Proceedings of the Fourteenth International Joint Conference on Artificial Intelliegence, vol. 2(12), pp. 1137–1143 (1995)Google Scholar
- 15.Powers, D.M.W.: Evaluation: from precision, recall and F-measure to ROC, informedness, markedness and correlation. J. Mach. Learn. Technol. 2(1), 37–63 (2011)MathSciNetGoogle Scholar
- 16.Amazon Web Services Machine Learning. http://aws.amazon.com/machine-learning/
- 17.H\(_2\)O - the open source predictive analytics platform. http://0xdata.com/product/
- 18.The Apache Mahout. http://mahout.apache.org/
- 19.Waikato Environment for Knowledge Analysis (WEKA). http://www.cs.waikato.ac.nz/ml/weka/
- 20.Pipeline Pilot platform. http://accelrys.com/products/pipeline-pilot/
- 21.Hugin, the decision support tool. http://www.hugin.com/productsservices/products/academic/researcher