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Mitigating the substantial undesirable impact of transportation systems on the environment is paramount. Thus, predicting Greenhouse Gas (GHG) emissions is one of the profound topics, especially with the emergence of intelligent transportation systems (ITS). We develop a deep learning framework to predict link-level GHG emission rate (ER) (in CO2eq gram/second) based on the most representative predictors, such as speed, density, and the GHG ER of previous time steps. In particular, various specifications of the long-short term memory (LSTM) networks with exogenous variables are examined and compared with clustering and the autoregressive integrated moving average (ARIMA) model with exogenous variables. The downtown Toronto road network is used as the case study and highly detailed data are synthesized using a calibrated traffic microsimulation and MOVES. It is found that LSTM specification with speed, density, GHG ER, and in-links speed from three previous minutes performs the best while adopting 2 hidden layers and when the hyper-parameters are systematically tuned. Adopting a 30 second updating interval improves slightly the correlation between true and predicted GHG ERs, but contributes negatively to the prediction accuracy as reflected on the increased root mean square error (RMSE) value. Efficiently predicting GHG emissions at a higher frequency with lower data requirements will pave the way to non-myopic eco-routing on large-scale road networks {to alleviate the adverse impact on the global warming