Int. J. Data Mining and Bioinformatics, Vol. 1, No. 2, 2006 111 Copyright © 2006 Inderscience Enterprises Ltd. Dynamic algorithm for inferring qualitative models of Gene Regulatory Networks Yun Zheng* and Chee Keong Kwoh Bioinformatics Research Center, School of Computer Engineering, Nanyang Technological University, Nanyang Avenue, Singapore 639798 E-mail: pg04325488@ntu.edu.sg E-mail: asckkwoh@ntu.edu.sg *Corresponding author Abstract: We introduce a novel algorithm, DFL (Discrete Function Learning), for reconstructing qualitative models of Gene Regulatory Networks (GRNs) from gene expression data in this paper. We analyse its complexity of O(k ⋅ N ⋅ n 2 ) on the average and its data requirements. The experiments of synthetic Boolean networks show that the DFL algorithm is more efficient than current algorithms without loss of prediction performances. The results of yeast cell cycle gene expression data show that the DFL algorithm can identify biologically significant models with reasonable accuracy, sensitivity and high precision with respect to the literature evidences. Keywords: algorithm; Gene Regulatory Networks (GRNs); qualitative models; mutual information; entropy. Reference to this paper should be made as follows: Zheng, Y. and Kwoh, C.K. (2006) ‘Dynamic algorithm for inferring qualitative models of Gene Regulatory Networks’, Int. J. Data Mining and Bioinformatics, Vol. 1, No. 2, pp.111–137. Biographical notes: Yun Zheng is currently pursuing his PhD at Bioinformatics Research Center of Nanyang Technological University in Singapore. His research interests include learning theory, information theory, modelling gene regulatory networks, classification, feature selection, Bayesian networks, statistical methods for analysis of microarray gene expression data. Chee Keong Kwoh is an Associate Professor of Computer Engineering at Nanyang Technological University in Singapore. His research interests include applying statistical learning theory in bioinformatics research, statistical learning theory, particularly in protein-protein interaction networks; probabilistic inference, numerical expert systems, particularly in the area of probabilistic reasoning; and augmented reality systems and image processing in biomedical applications. He was the Deputy Director of Biomedical Engineering Research Centre, NTU (between 1997–2003) and has been the Director, MSc in Bioinformatics since 2002.