In this paper, we propose a new data selection method which uses semi-supervised convolutional neural networks based on bitokens (Bi-SSCNNs) for training machine translation systems from a large bilingual corpus. In earlier work, we devised a data selection method based on semi-supervised convolutional neural networks (SSCNNs). The new method, Bi-SSCNN, is based on bitokens, which use bilingual information. When the new methods are tested on two translation tasks (Chinese-to-English and Arabic-to-English), they significantly outperform the other three data selection methods in the experiments. We also show that the Bi-SSCNN method is much more effective than other methods in preventing noisy sentence pairs from being chosen for training. More interestingly, this method only needs a tiny amount of in-domain data to train the selection model, which makes fine-grained topic-dependent translation adaptation possible. In the follow-up experiments, we find that neural machine translation (NMT) is more sensitive to noisy data than statistical machine translation (SMT). Therefore, Bi-SSCNN which can effectively screen out noisy sentence pairs, can benefit NMT much more than SMT.We observed a BLEU improvement over 3 points on an English-to-French WMT task when Bi-SSCNNs were used.