Motivation Graph embedding learning that aims to automatically learn low-dimensional node representations, has drawn increasing attention in recent years. To date, most recent graph embedding methods are evaluated on social and information networks and are not comprehensively studied on biomedical networks under systematic experiments and analyses. On the other hand, for a variety of biomedical network analysis tasks, traditional techniques such as matrix factorization (which can be seen as a type of graph embedding methods) have shown promising results, and hence there is a need to systematically evaluate the more recent graph embedding methods (e.g. random walk-based and neural network-based) in terms of their usability and potential to further the state-of-the-art. Results We select 11 representative graph embedding methods and conduct a systematic comparison on 3 important biomedical link prediction tasks: drug-disease association (DDA) prediction, drug–drug interaction (DDI) prediction, protein–protein interaction (PPI) prediction; and 2 node classification tasks: medical term semantic type classification, protein function prediction. Our experimental results demonstrate that the recent graph embedding methods achieve promising results and deserve more attention in the future biomedical graph analysis. Compared with three state-of-the-art methods for DDAs, DDIs and protein function predictions, the recent graph embedding methods achieve competitive performance without using any biological features and the learned embeddings can be treated as complementary representations for the biological features. By summarizing the experimental results, we provide general guidelines for properly selecting graph embedding methods and setting their hyper-parameters for different biomedical tasks. Availability and implementation As part of our contributions in the paper, we develop an easy-to-use Python package with detailed instructions, BioNEV, available at: https://github.com/xiangyue9607/BioNEV, including all source code and datasets, to facilitate studying various graph embedding methods on biomedical tasks. Supplementary information Supplementary data are available at Bioinformatics online.

To accelerate software development, much research has been performed to help people understand and reuse the huge amount of available code resources. Two important tasks have been widely studied: code retrieval, which aims to retrieve code snippets relevant to a given natural language query from a code base, and code annotation, where the goal is to annotate a code snippet with a natural language description. Despite their advancement in recent years, the two tasks are mostly explored separately. In this work, we investigate a novel perspective of Code annotation for Code retrieval (hence called "CoaCor"), where a code annotation model is trained to generate a natural language annotation that can represent the semantic meaning of a given code snippet and can be leveraged by a code retrieval model to better distinguish relevant code snippets from others. To this end, we propose an effective framework based on reinforcement learning, which explicitly encourages the code annotation model to generate annotations that can be used for the retrieval task. Through extensive experiments, we show that code annotations generated by our framework are much more detailed and more useful for code retrieval, and they can further improve the performance of existing code retrieval models significantly. 1

Tables are pervasive on the Web. Informative web tables range across a large variety of topics, which can naturally serve as a significant resource to satisfy user information needs. Driven by such observations, in this paper, we investigate an important yet largely under-addressed problem: Given millions of tables, how to precisely retrieve table cells to answer a user question. This work proposes a novel table cell search framework to attack this problem. We first formulate the concept of a relational chain which connects two cells in a table and represents the semantic relation between them. With the help of search engine snippets, our framework generates a set of relational chains pointing to potentially correct answer cells. We further employ deep neural networks to conduct more fine-grained inference on which relational chains best match the input question and finally extract the corresponding answer cells. Based on millions of tables crawled from the Web, we evaluate our framework in the open-domain question answering (QA) setting, using both the well-known WebQuestions dataset and user queries mined from Bing search engine logs. On WebQuestions, our framework is comparable to state-of-the-art QA systems based on knowledge bases (KBs), while on Bing queries, it outperforms other systems with a 56.7% relative gain. Moreover, when combined with results from our framework, KB-based QA performance can obtain a relative improvement of 28.1% to 66.7%, demonstrating that web tables supply rich knowledge that might not exist or is difficult to be identified in existing KBs.

We present a semi-automated framework for constructing factoid question answering (QA) datasets, where an array of question characteristics are formalized, including structure complexity, function, commonness, answer cardinality, and paraphrasing. Instead of collecting questions and manually characterizing them, we employ a reverse procedure, first generating a kind of graph-structured logical forms from a knowledge base, and then converting them into questions. Our work is the first to generate questions with explicitly specified characteristics for QA evaluation. We construct a new QA dataset with over 5,000 logical form-question pairs, associated with answers from the knowledge base, and show that datasets constructed in this way enable finegrained analyses of QA systems. The dataset can be found in https://github.com/ ysu1989/GraphQuestions.

Most recent question answering (QA) systems query largescale knowledge bases (KBs) to answer a question, after parsing and transforming natural language questions to KBsexecutable forms (e.g., logical forms). As a well-known fact, KBs are far from complete, so that information required to answer questions may not always exist in KBs. In this paper, we develop a new QA system that mines answers directly from the Web, and meanwhile employs KBs as a significant auxiliary to further boost the QA performance.Specifically, to the best of our knowledge, we make the first attempt to link answer candidates to entities in Freebase, during answer candidate generation. Several remarkable advantages follow: (1) Redundancy among answer candidates is automatically reduced. (2) The types of an answer candidate can be effortlessly determined by those of its corresponding entity in Freebase. (3) Capitalizing on the rich information about entities in Freebase, we can develop semantic features for each answer candidate after linking them to Freebase. Particularly, we construct answer-type related features with two novel probabilistic models, which directly evaluate the appropriateness of an answer candidate's types under a given question. Overall, such semantic features turn out to play significant roles in determining the true answers from the large answer candidate pool. The experimental results show that across two testing datasets, our QA system achieves an 18% ∼ 54% improvement under F1 metric, compared with various existing QA systems.