Xinmeng Li

Xinmeng Li, Hao Zhu, Li-ping Liu et al.

A key challenge in metabolomics is annotating measured spectra from a biological sample with chemical identities. Currently, only a small fraction of measurements can be assigned identities. Two complementary computational approaches have emerged to address the annotation problem: mapping candidate molecules to spectra, and mapping query spectra to molecular candidates. In essence, the candidate molecule with the spectrum that best explains the query spectrum is recommended as the target molecule. Despite candidate ranking being fundamental in both approaches, no prior works utilized rank learning tasks in determining the target molecule. We propose a novel machine learning model, Ensemble Spectral Prediction (ESP), for metabolite annotation. ESP takes advantage of prior neural network-based annotation models that utilize multilayer perceptron (MLP) networks and Graph Neural Networks (GNNs). Based on the ranking results of the MLP and GNN-based models, ESP learns a weighting for the outputs of MLP and GNN spectral predictors to generate a spectral prediction for a query molecule. Importantly, training data is stratified by molecular formula to provide candidate sets during model training. Further, baseline MLP and GNN models are enhanced by considering peak dependencies through multi-head attention mechanism and multi-tasking on spectral topic distributions. ESP improves average rank by 41% and 30% over the MLP and GNN baselines, respectively, demonstrating remarkable performance gain over state-of-the-art neural network approaches. We show that annotation performance, for ESP and other models, is a strong function of the number of molecules in the candidate set and their similarity to the target molecule.

Xinmeng Li, Li-ping Liu, Soha Hassoun

Despite experimental and curation efforts, the extent of enzyme promiscuity on substrates continues to be largely unexplored and under documented. Recommender systems (RS), which are currently unexplored for the enzyme-substrate interaction prediction problem, can be utilized to provide enzyme recommendations for substrates, and vice versa. The performance of Collaborative-Filtering (CF) recommender systems however hinges on the quality of embedding vectors of users and items (enzymes and substrates in our case). Importantly, enhancing CF embeddings with heterogeneous auxiliary data, specially relational data (e.g., hierarchical, pairwise, or groupings), remains a challenge. We propose an innovative general RS framework, termed Boost-RS, that enhances RS performance by "boosting" embedding vectors through auxiliary data. Specifically, Boost-RS is trained and dynamically tuned on multiple relevant auxiliary learning tasks Boost-RS utilizes contrastive learning tasks to exploit relational data. To show the efficacy of Boost-RS for the enzyme-substrate prediction interaction problem, we apply the Boost-RS framework to several baseline CF models. We show that each of our auxiliary tasks boosts learning of the embedding vectors, and that contrastive learning using Boost-RS outperforms attribute concatenation and multi-label learning. We also show that Boost-RS outperforms similarity-based models. Ablation studies and visualization of learned representations highlight the importance of using contrastive learning on some of the auxiliary data in boosting the embedding vectors.

Wansen Wu, Tao Chang, Xinmeng Li

Vision-Language Navigation (VLN) tasks require an agent to follow human language instructions to navigate in previously unseen environments. This challenging field involving problems in natural language processing, computer vision, robotics, etc., has spawn many excellent works focusing on various VLN tasks. This paper provides a comprehensive survey and an insightful taxonomy of these tasks based on the different characteristics of language instructions in these tasks. Depending on whether the navigation instructions are given for once or multiple times, this paper divides the tasks into two categories, i.e., single-turn and multi-turn tasks. For single-turn tasks, we further subdivide them into goal-oriented and route-oriented based on whether the instructions designate a single goal location or specify a sequence of multiple locations. For multi-turn tasks, we subdivide them into passive and interactive tasks based on whether the agent is allowed to question the instruction or not. These tasks require different capabilities of the agent and entail various model designs. We identify progress made on the tasks and look into the limitations of existing VLN models and task settings. Finally, we discuss several open issues of VLN and point out some opportunities in the future, i.e., incorporating knowledge with VLN models and implementing them in the real physical world.

Xinmeng Li, Wansen Wu, Long Qin et al.

Evaluating the quality of a dialogue system is an understudied problem. The recent evolution of evaluation method motivated this survey, in which an explicit and comprehensive analysis of the existing methods is sought. We are first to divide the evaluation methods into three classes, i.e., automatic evaluation, human-involved evaluation and user simulator based evaluation. Then, each class is covered with main features and the related evaluation metrics. The existence of benchmarks, suitable for the evaluation of dialogue techniques are also discussed in detail. Finally, some open issues are pointed out to bring the evaluation method into a new frontier.

Xinmeng Li, Mamoun Alazab, Qian Li et al.

Knowledge graph question answering is an important technology in intelligent human-robot interaction, which aims at automatically giving answer to human natural language question with the given knowledge graph. For the multi-relation question with higher variety and complexity, the tokens of the question have different priority for the triples selection in the reasoning steps. Most existing models take the question as a whole and ignore the priority information in it. To solve this problem, we propose question-aware memory network for multi-hop question answering, named QA2MN, to update the attention on question timely in the reasoning process. In addition, we incorporate graph context information into knowledge graph embedding model to increase the ability to represent entities and relations. We use it to initialize the QA2MN model and fine-tune it in the training process. We evaluate QA2MN on PathQuestion and WorldCup2014, two representative datasets for complex multi-hop question answering. The result demonstrates that QA2MN achieves state-of-the-art Hits@1 accuracy on the two datasets, which validates the effectiveness of our model.