Abstract

Promoters are DNA sequences containing regulatory elements required to guide and modulate the transcription initiation of the gene. Predicting promoter sequences in genomic sequences is a significant task in genome annotation and understanding transcriptional regulation. In the past decade many methods with many feature extraction schemes have been proposed for the prediction of eukaryotic and prokaryotic promoters. Still there is great need for more accurate and faster methods. In this paper we employed extreme learning machine algorithm (ELM), for promoter prediction in DNA sequences of H. sapiens, D. melanogaster, A. thaliana, C. elegans and E. coli. We extracted dinucleotide and CpG island features, and achieved accuracy above 90 % for all the five species. Performance is compared with the feed forward back propagation algorithm (BP) and support vector machines (SVM) and the …

Abstract

Task: The task is a probabilistic learning task as described in Pasquereau et al., 2007 where four visual cues are associated with different reward probabilities (0.00, 0.33, 0.66 & 1.00). A trial is made of the simultaneous presentation of two random cues with equal salience at two random positions. Some time after the presentation, a switch in the cortex activities is observed, representing the decision taken. After the model has chosen one cue or the other, a reward is given according to the probability associated with the chosen cue. Connections between the cortex and the striatum are then modified using a reinforcement learning rule based on the reward signal. The model is trained over 120 trials such that each combination of cues is presented equal number of times at uniformly sampled positions and the model performance reaches at least 0.9 measuring the ration of optimal choices. The decision switch and the performance are identical to the results when primates are tested with same task. Learning is then disabled and the model is tested using always the same pair of cues A (P (R)= 1) and B (P (R)= 0.33) in the presence of external factors. We study how, despite reward based learning, visual salience of the stimuli and the temporal difference between stimulus presentations affect the model to take a sub-optimal decision.