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Recently, the neural machine translation systems showed their promising performance and surpassed the phrase-based systems for most translation tasks. Retreating into conventional concepts machine translation while utilizing effective neural models is vital for comprehending the leap accomplished by neural machine translation over phrase-based methods. This work proposes a direct HMM with neural network-based lexicon and alignment models, which are trained jointly using the Baum-Welch algorithm. The direct HMM is applied to rerank the n-best list created by a state-of-the-art phrase-based translation system and it provides improvements by up to 1.0% Bleu scores on two different translation tasks.