Extracting time expressions from free text is a fundamental task for many applications. We analyze time expressions from four different datasets and find that only a small group of words are used to express time information and that the words in time expressions demonstrate similar syntactic behaviour. Based on the findings, we propose a type-based approach named SynTime 1 for time expression recognition. Specifically, we define three main syntactic token types, namely time token, modifier, and numeral, to group time-related token regular expressions. On the types we design general heuristic rules to recognize time expressions. In recognition, SynTime first identifies time tokens from raw text, then searches their surroundings for modifiers and numerals to form time segments, and finally merges the time segments to time expressions. As a lightweight rule-based tagger, SynTime runs in real time, and can be easily expanded by simply adding keywords for the text from different domains and different text types. Experiments on benchmark datasets and tweets data show that SynTime outperforms state-of-the-art methods.

We find from four datasets that time expressions are formed by loose structure and the words used to express time information can differentiate time expressions from common text. The findings drive us to design a learning method named TOMN to model time expressions. TOMN defines a constituent-based tagging scheme named TOMN scheme with four tags, namely T, O, M, and N, indicating the constituents of time expression, namely Time token, Modifier, Numeral, and the words Outside time expression. In modeling, TOMN assigns a word with a TOMN tag under conditional random fields with minimal features. Essentially, our constituent-based TOMN scheme overcomes the problem of inconsistent tag assignment that is caused by the conventional position-based tagging schemes (e.g., BIO scheme and BILOU scheme). Experiments show that TOMN is equally or more effective than state-of-the-art methods on various datasets, and much more robust on cross-datasets. Moreover, our analysis can explain many empirical observations in other works about time expression recognition and named entity recognition.

Background: Semantic similarity between Gene Ontology (GO) terms is a fundamental measure for many bioinformatics applications, such as determining functional similarity between genes or proteins. Most previous research exploited information content to estimate the semantic similarity between GO terms; recently some research exploited word embeddings to learn vector representations for GO terms from a large-scale corpus. In this paper, we proposed a novel method, named GO2Vec, that exploits graph embeddings to learn vector representations for GO terms from GO graph. GO2Vec combines the information from both GO graph and GO annotations, and its learned vectors can be applied to a variety of bioinformatics applications, such as calculating functional similarity between proteins and predicting protein-protein interactions. Results: We conducted two kinds of experiments to evaluate the quality of GO2Vec: (1) functional similarity between proteins on the Collaborative Evaluation of GO-based Semantic Similarity Measures (CESSM) dataset and (2) prediction of protein-protein interactions on the Yeast and Human datasets from the STRING database. Experimental results demonstrate the effectiveness of GO2Vec over the information content-based measures and the word embedding-based measures. Conclusion: Our experimental results demonstrate the effectiveness of using graph embeddings to learn vector representations from undirected GO and GOA graphs. Our results also demonstrate that GO annotations provide useful information for computing the similarity between GO terms and between proteins.

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Background Protein–protein interaction (PPI) prediction is an important task towards the understanding of many bioinformatics functions and applications, such as predicting protein functions, gene-disease associations and disease-drug associations. However, many previous PPI prediction researches do not consider missing and spurious interactions inherent in PPI networks. To address these two issues, we define two corresponding tasks, namely missing PPI prediction and spurious PPI prediction, and propose a method that employs graph embeddings that learn vector representations from constructed Gene Ontology Annotation (GOA) graphs and then use embedded vectors to achieve the two tasks. Our method leverages on information from both term–term relations among GO terms and term-protein annotations between GO terms and proteins, and preserves properties of both local and global structural information of the GO annotation graph. Results We compare our method with those methods that are based on information content (IC) and one method that is based on word embeddings, with experiments on three PPI datasets from STRING database. Experimental results demonstrate that our method is more effective than those compared methods. Conclusion Our experimental results demonstrate the effectiveness of using graph embeddings to learn vector representations from undirected GOA graphs for our defined missing and spurious PPI tasks.