Yalou Huang

YaoGong Zhang, YingJie Xu, Xin Fan et al.

Background: Mining gene modules from genomic data is an important step to detect gene members of pathways or other relations such as protein-protein interactions. In this work, we explore the plausibility of detecting gene modules by factorizing gene-phenotype associations from a phenotype ontology rather than the conventionally used gene expression data. In particular, the hierarchical structure of ontology has not been sufficiently utilized in clustering genes while functionally related genes are consistently associated with phenotypes on the same path in the phenotype ontology. Results: We propose a hierarchal Nonnegative Matrix Factorization (NMF)-based method, called Consistent Multiple Nonnegative Matrix Factorization (CMNMF), to factorize genome-phenome association matrix at two levels of the hierarchical structure in phenotype ontology for mining gene functional modules. CMNMF constrains the gene clusters from the association matrices at two consecutive levels to be consistent since the genes are annotated with both the child phenotype and the parent phenotype in the consecutive levels. CMNMF also restricts the identified phenotype clusters to be densely connected in the phenotype ontology hierarchy. In the experiments on mining functionally related genes from mouse phenotype ontology and human phenotype ontology, CMNMF effectively improved clustering performance over the baseline methods. Gene ontology enrichment analysis was also conducted to reveal interesting gene modules. Conclusions: Utilizing the information in the hierarchical structure of phenotype ontology, CMNMF can identify functional gene modules with more biological significance than the conventional methods. CMNMF could also be a better tool for predicting members of gene pathways and protein-protein interactions. Availability: https://github.com/nkiip/CMNMF

Chen Xing, Wei Wu, Yu Wu et al.

We study multi-turn response generation in chatbots where a response is generated according to a conversation context. Existing work has modeled the hierarchy of the context, but does not pay enough attention to the fact that words and utterances in the context are differentially important. As a result, they may lose important information in context and generate irrelevant responses. We propose a hierarchical recurrent attention network (HRAN) to model both aspects in a unified framework. In HRAN, a hierarchical attention mechanism attends to important parts within and among utterances with word level attention and utterance level attention respectively. With the word level attention, hidden vectors of a word level encoder are synthesized as utterance vectors and fed to an utterance level encoder to construct hidden representations of the context. The hidden vectors of the context are then processed by the utterance level attention and formed as context vectors for decoding the response. Empirical studies on both automatic evaluation and human judgment show that HRAN can significantly outperform state-of-the-art models for multi-turn response generation.

Chen Xing, Wei Wu, Yu Wu et al.

We consider incorporating topic information into the sequence-to-sequence framework to generate informative and interesting responses for chatbots. To this end, we propose a topic aware sequence-to-sequence (TA-Seq2Seq) model. The model utilizes topics to simulate prior knowledge of human that guides them to form informative and interesting responses in conversation, and leverages the topic information in generation by a joint attention mechanism and a biased generation probability. The joint attention mechanism summarizes the hidden vectors of an input message as context vectors by message attention, synthesizes topic vectors by topic attention from the topic words of the message obtained from a pre-trained LDA model, and let these vectors jointly affect the generation of words in decoding. To increase the possibility of topic words appearing in responses, the model modifies the generation probability of topic words by adding an extra probability item to bias the overall distribution. Empirical study on both automatic evaluation metrics and human annotations shows that TA-Seq2Seq can generate more informative and interesting responses, and significantly outperform the-state-of-the-art response generation models.