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This study investigated using the stress wave method to predict the properties of thermally modified wood by means of an adaptive neuro-fuzzy inference system (ANFIS) and neural network (NN) modeling. The stress wave was detected using a pair of accelerometers and an acoustic emission (AE) sensor, and the effect of heat treatment (HT) on the physical and mechanical properties of wood as well as wave velocity and AE signal is discussed. The AE signal was processed in the time and time-frequency domains using wavelet analysis and different features were extracted for network training. The auto-associative NN is used as a dimensional reduction method to decrease the dimension of the extracted AE features and enhance the ANFIS performance. It was shown that while the stress wave velocity using the accelerometer did not result in an accurate model, the network performance significantly increased when trained with the AE features. The AE signal exhibited a significant correlation with wood treatment and porosity. The best ANFIS performance corresponded to predicting the wood swelling coefficient, equilibrium moisture content (EMC) and water absorption (WA), respectively. However, the AE signal did not seem suitable for predicting the wood density and hardness. The performance of ANFIS was compared with the “group method of data handling” (GMDH) NN. Both the ANFIS and GMDH networks showed higher accuracy than the multivariate linear regression (MVLR) model.