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The coordinated activities of muscles during reaching movements can be characterized by appropriate analysis of simultaneously-recorded surface electromyograms (sEMGs). Many recent sEMG studies have analyzed muscle synergies using statistical methods such as Independent Component Analysis, which commonly assume a small set of influences upstream of the muscles (e.g., originating from the motor cortex) produce the sEMG signals. Traditionally only the amplitude of the sEMG signal was investigated. Here, we present a fundamentally different approach and model sEMG signals after the effects of amplitude have been minimized. We develop the framework of Bayesian networks (BNs) for modeling muscle activities and for analyzing the overall muscle network structure. Instead of assuming that synergies may be independently activated, we assume that neuronal activity driving a given muscle may be conditionally dependent upon neurons driving other muscles. We call the resulting interactions between muscle activity patterns ldquodependent synergiesrdquo. The learned BN networks were explored for the purpose of classification across subjects based on hand dominance or affliction by stroke. Network structure features were investigated as classification input features and it was determined that specific edge connection patterns of 3-node subnetworks were selectively recruited during reaching movements and were differentially recruited after stroke compared to normal control subjects. The resulting classification was robust to inter-subject and within-group variability and yielded excellent classification performance. The proposed framework extends muscle synergy analysis and provides a framework for thinking about muscle activity interactions in motor control.