Knowledge base construction is crucial for summarising, understanding and inferring relationships between biomedical entities. However, for many practical applications such as drug discovery, the scarcity of relevant facts (e.g. gene X is therapeutic target for disease Y) severely limits a domain expert's ability to create a usable knowledge base, either directly or by training a relation extraction model. In this paper, we present a simple and effective method of extracting new facts with a pre-specified binary relationship type from the biomedical literature, without requiring any training data or hand-crafted rules. Our system discovers, ranks and presents the most salient patterns to domain experts in an interpretable form. By marking patterns as compatible with the desired relationship type, experts indirectly batch-annotate candidate pairs whose relationship is expressed with such patterns in the literature. Even with a complete absence of seed data, experts are able to discover thousands of high-quality pairs with the desired relationship within minutes. When a small number of relevant pairs do exist - even when their relationship is more general (e.g. gene X is biologically associated with disease Y) than the relationship of interest - our system leverages them in order to i) learn a better ranking of the patterns to be annotated or ii) generate weakly labelled pairs in a fully automated manner. We evaluate our method both intrinsically and via a downstream knowledge base completion task, and show that it is an effective way of constructing knowledge bases when few or no relevant facts are already available.
The idea of extracting entity pairs by discovering textual patterns dates back to early work on bootstrapping for relation extraction with the DIPRE system @cite_1 . This system was designed to find co-occurrences of seed entity pairs of a known relationship type inside unlabelled text, then extract simple patterns (exact string matches) from these occurrences and use them to discover new entity pairs. introduced a pattern evaluation methodology based on the precision of a pattern on the set of entity pairs which had already been discovered; they also used the dot product between word vectors instead of an exact string match to allow for slight variations in text. Later work @cite_3 @cite_2 @cite_5 has proposed more sophisticated pattern extraction methods (based on dependency graphs or kernel methods on word vectors) and different pattern evaluation frameworks (document relevance scores).
@cite_5 @cite_1 @cite_3 @cite_2
2251405440 2055261195 2595918108 2587809655
Bootstrapped pattern learning for entity extraction usually starts with seed entities and iteratively learns patterns and entities from unlabeled text. Patterns are scored by their ability to extract more positive entities and less negative entities. A problem is that due to the lack of labeled data, unlabeled entities are either assumed to be negative or are ignored by the existing pattern scoring measures. In this paper, we improve pattern scoring by predicting the labels of unlabeled entities. We use various unsupervised features based on contrasting domain-specific and general text, and exploiting distributional similarity and edit distances to learned entities. Our system outperforms existing pattern scoring algorithms for extracting drug-andtreatment entities from four medical forums. Dictionary-based entity extraction has attracted much attention from the database community recently, which locates sub strings in a document into predefined entities (e.g., person names or locations). To improve extraction recall, a recent trend is to provide approximate matching between sub strings of the document and entities by tolerating minor errors. In this paper we study dictionary-based approximate entity extraction with edit-distance constraints. Existing methods have several limitations. First, they need to tune many parameters to achieve high performance. Second, they are inefficient for large edit-distance thresholds. We propose a trie-based method to address these problems. We first partition each entity into a set of segments, and then use a trie structure to index segments. To extract similar entities, we search segments from the document, and extend the matching segments in both entities and the document to find similar pairs. We develop an extension-based method to efficiently find similar string pairs by extending the matching segments. We optimize our partition scheme and select the best partition strategy to improve the extraction performance. Experimental results show that our method achieves much higher performance compared with state-of-the-art studies. Mining textual patterns in news, tweets, papers, and many other kinds of text corpora has been an active theme in text mining and NLP research. Previous studies adopt a dependency parsing-based pattern discovery approach. However, the parsing results lose rich context around entities in the patterns, and the process is costly for a corpus of large scale. In this study, we propose a novel typed textual pattern structure, called meta pattern, which is extended to a frequent, informative, and precise subsequence pattern in certain context. We propose an efficient framework, called MetaPAD, which discovers meta patterns from massive corpora with three techniques: (1) it develops a context-aware segmentation method to carefully determine the boundaries of patterns with a learnt pattern quality assessment function, which avoids costly dependency parsing and generates high-quality patterns; (2) it identifies and groups synonymous meta patterns from multiple facets---their types, contexts, and extractions; and (3) it examines type distributions of entities in the instances extracted by each group of patterns, and looks for appropriate type levels to make discovered patterns precise. Experiments demonstrate that our proposed framework discovers high-quality typed textual patterns efficiently from different genres of massive corpora and facilitates information extraction. Entity and relation extraction is a task that combines detecting entity mentions and recognizing entities' semantic relationships from unstructured text. We propose a hybrid neural network model to extract entities and their relationships without any handcrafted features. The hybrid neural network contains a novel bidirectional encoder-decoder LSTM module (BiLSTM-ED) for entity extraction and a CNN module for relation classification. The contextual information of entities obtained in BiLSTM-ED further pass though to CNN module to improve the relation classification. We conduct experiments on the public dataset ACE05 (Automatic Content Extraction program) to verify the effectiveness of our method. The method we proposed achieves the state-of-the-art results on entity and relation extraction task. (C) 2017 Elsevier B.V. All rights reserved.