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Neural Machine Translation(NMT) has achieved notable results in high-resource languages, but still works poorly on low-resource languages. As times goes on, It is widely recognized that transfer learning methods are effective for low-resource language problems. However, existing transfer learning methods are typically based on the parent-child architecture, which does not adequately take advantages of helpful languages. In this paper, inspired by human transitive inference and learning ability, we handle this issue by proposing a new hierarchical transfer learning architecture for low-resource languages. In the architecture, the NMT model is trained in the unrelated high-resource language pair, the similar intermediate language pair and the low-resource language pair in turn. Correspondingly, the parameters are transferred and fine-tuned layer by layer for initialization. In this way, our hierarchical transfer learning architecture simultaneously combines the data volume advantages of high-resource languages and the syntactic similarity advantages of cognate languages. Specially, we utilize Byte Pair Encoding(BPE) and character-level embedding for data pre-processing, which effectively solve the problem of out of vocabulary(OOV). Experimental results on Uygur-Chinese and Turkish-English translation demonstrate the superiorities of the proposed architecture over the NMT model with parent-child architecture.INDEX TERMS Hierarchical transfer learning, low-resource problem, neural machine translation.

Transcription factors (TFs) play an important role in regulating gene expression, thus identification of the regions bound by them has become a fundamental step for molecular and cellular biology. In recent years, an increasing number of deep learning (DL) based methods have been proposed for predicting TF binding sites (TFBSs) and achieved impressive prediction performance. However, these methods mainly focus on predicting the sequence specificity of TF-DNA binding, which is equivalent to a sequence-level binary classification task, and fail to identify motifs and TFBSs accurately. In this paper, we developed a fully convolutional network coupled with global average pooling (FCNA), which by contrast is equivalent to a nucleotide-level binary classification task, to roughly locate TFBSs and accurately identify motifs. Experimental results on human ChIP-seq datasets show that FCNA outperforms other competing methods significantly. Besides, we find that the regions located by FCNA can be used by motif discovery tools to further refine the prediction performance. Furthermore, we observe that FCNA can accurately identify TF-DNA binding motifs across different cell lines and infer indirect TF-DNA bindings.

Transcription factors (TFs) play an important role in regulating gene expression, thus the identification of the sites bound by them has become a fundamental step for molecular and cellular biology. In this paper, we developed a deep learning framework leveraging existing fully convolutional neural networks (FCN) to predict TF-DNA binding signals at the base-resolution level (named as FCNsignal). The proposed FCNsignal can simultaneously achieve the following tasks: (i) modeling the base-resolution signals of binding regions; (ii) discriminating binding or non-binding regions; (iii) locating TF-DNA binding regions; (iv) predicting binding motifs. Besides, FCNsignal can also be used to predict opening regions across the whole genome. The experimental results on 53 TF ChIP-seq datasets and 6 chromatin accessibility ATAC-seq datasets show that our proposed framework outperforms some existing state-of-the-art methods. In addition, we explored to use the trained FCNsignal to locate all potential TF-DNA binding regions on a whole chromosome and predict DNA sequences of arbitrary length, and the results show that our framework can find most of the known binding regions and accept sequences of arbitrary length. Furthermore, we demonstrated the potential ability of our framework in discovering causal disease-associated single-nucleotide polymorphisms (SNPs) through a series of experiments.

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