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
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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. Extracting relations from text corpora is an important task with wide applications. However, it becomes particularly challenging when focusing on weakly-supervised relation extraction, that is, utilizing a few relation instances (i.e., a pair of entities and their relation) as seeds to extract from corpora more instances of the same relation. Existing distributional approaches leverage the corpus-level co-occurrence statistics of entities to predict their relations, and require large amount of labeled instances to learn effective relation classifiers. Alternatively, pattern-based approaches perform boostrapping or apply neural networks to model the local contexts, but still rely on large amount of labeled instances to build reliable models. In this paper, we study the integration of distributional and pattern-based methods in a weakly-supervised setting such that the two kinds of methods can provide complementary supervision for each other to build an effective, unified model. We propose a novel framework with a distributional module and a pattern module. During training, the distributional module helps the pattern module discriminate between the informative patterns and other patterns, and the pattern module generates some highly-confident instances to improve the distributional module. The whole framework can be effectively optimized by iterating between improving the pattern module and updating the distributional module. We conduct experiments on two tasks: knowledge base completion and corpus-level relation extraction. Experimental results prove the effectiveness of our framework over many competitive baselines. The wealth of interaction information provided in biomedical articles motivated the implementation of text mining approaches to automatically extract biomedical relations. This paper presents an unsupervised method based on pattern clustering and sentence parsing to deal with biomedical relation extraction. Pattern clustering algorithm is based on Polynomial Kernel method, which identifies interaction words from unlabeled data; these interaction words are then used in relation extraction between entity pairs. Dependency parsing and phrase structure parsing are combined for relation extraction. Based on the semi-supervised KNN algorithm, we extend the proposed unsupervised approach to a semi-supervised approach by combining pattern clustering, dependency parsing and phrase structure parsing rules. We evaluated the approaches on two different tasks: (1) Protein–protein interactions extraction, and (2) Gene–suicide association extraction. The evaluation of task (1) on the benchmark dataset (AImed corpus) showed that our proposed unsupervised approach outperformed three supervised methods. The three supervised methods are rule based, SVM based, and Kernel based separately. The proposed semi-supervised approach is superior to the existing semi-supervised methods. The evaluation on gene–suicide association extraction on a smaller dataset from Genetic Association Database and a larger dataset from publicly available PubMed showed that the proposed unsupervised and semi-supervised methods achieved much higher F-scores than co-occurrence based method. The goal of relation extraction is to detect relations between two entities in free text. In a sentence, a relation instance usually comprises a small number of words, which yields a sparse feature representation. To make better use of limited information in a relation instance, parsing trees and combined features are employed widely to capture the local dependencies of relation instances. However, the performance of parsing tree-based systems is often degraded by chunking or parsing errors. Combined features are used widely, but few studies have addressed how features can be combined to achieve optimal performance. Thus, in this study, we propose a feature assembly method for relation extraction. Six types of candidate features (head noun, POS tag, n-gram, omni-word, etc.) are employed as atomic features and six constraint conditions (singleton, position, syntax, etc.) are used to combine these features in different settings. Depending on the utilization of candidate features, different constraint conditions can be explored to achieve the optimal extraction performance. Our method is effective for capturing local dependencies and it reduces the errors caused by inaccurate parsing. We tested the proposed method using the ACE 2005 Chinese and English corpora, and it achieved state-of-the-art performance, where it was significantly superior to existing methods. While relation extraction has traditionally been viewed as a task relying solely on textual data, recent work has shown that by taking as input existing facts in the form of entity-relation triples from both knowledge bases and textual data, the performance of relation extraction can be improved significantly. Following this new paradigm, we propose a tensor decomposition approach for knowledge base embedding that is highly scalable, and is especially suitable for relation extraction. By leveraging relational domain knowledge about entity type information, our learning algorithm is significantly faster than previous approaches and is better able to discover new relations missing from the database. In addition, when applied to a relation extraction task, our approach alone is comparable to several existing systems, and improves the weighted mean average precision of a state-of-theart method by 10 points when used as a subcomponent. We present a novel approach to relation extraction, based on the observation that the information required to assert a relationship between two named entities in the same sentence is typically captured by the shortest path between the two entities in the dependency graph. Experiments on extracting top-level relations from the ACE (Automated Content Extraction) newspaper corpus show that the new shortest path dependency kernel outperforms a recent approach based on dependency tree kernels. This paper proposes a novel approach for relation extraction from free text which is trained to jointly use information from the text and from existing knowledge. Our model is based on scoring functions that operate by learning low-dimensional embeddings of words, entities and relationships from a knowledge base. We empirically show on New York Times articles aligned with Freebase relations that our approach is able to efficiently use the extra information provided by a large subset of Freebase data (4M entities, 23k relationships) to improve over methods that rely on text features alone. Entity relation detection is a form of information extraction that finds predefined relations between pairs of entities in text. This paper describes a relation detection approach that combines clues from different levels of syntactic processing using kernel methods. Information from three different levels of processing is considered: tokenization, sentence parsing and deep dependency analysis. Each source of information is represented by kernel functions. Then composite kernels are developed to integrate and extend individual kernels so that processing errors occurring at one level can be overcome by information from other levels. We present an evaluation of these methods on the 2004 ACE relation detection task, using Support Vector Machines, and show that each level of syntactic processing contributes useful information for this task. When evaluated on the official test data, our approach produced very competitive ACE value scores. We also compare the SVM with KNN on different kernels. We present a novel approach to relation extraction that integrates information across documents, performs global inference and requires no labelled text. In particular, we tackle relation extraction and entity identification jointly. We use distant supervision to train a factor graph model for relation extraction based on an existing knowledge base (Freebase, derived in parts from Wikipedia). For inference we run an efficient Gibbs sampler that leads to linear time joint inference. We evaluate our approach both for an indomain (Wikipedia) and a more realistic out-of-domain (New York Times Corpus) setting. For the in-domain setting, our joint model leads to 4 higher precision than an isolated local approach, but has no advantage over a pipeline. For the out-of-domain data, we benefit strongly from joint modelling, and observe improvements in precision of 13 over the pipeline, and 15 over the isolated baseline. While tuple extraction for a given relation has been an active research area, its dual problem of pattern search-- to find and rank patterns in a principled way-- has not been studied explicitly. In this paper, we propose and address the problem of pattern search, in addition to tuple extraction. As our objectives, we stress reusability for pattern search and scalability of tuple extraction, such that our approach can be applied to very large corpora like the Web. As the key foundation, we propose a conceptual model PRDualRank to capture the notion of precision and recall for both tuples and patterns in a principled way, leading to the "rediscovery" of the Pattern-Relation Duality-- the formal quantification of the reinforcement between patterns and tuples with the metrics of precision and recall. We also develop a concrete framework for PRDualRank, guided by the principles of a perfect sampling process over a complete corpus. Finally, we evaluated our framework over the real Web. Experiments show that on all three target relations our principled approach greatly outperforms the previous state-of-the-art system in both effectiveness and efficiency. In particular, we improved optimal F-score by up to 64 . Given a set @math of @math strings of total length @math , our task is to report the "most relevant"strings for a given query pattern @math . This involves somewhat more advanced query functionality than the usual pattern matching, as some notion of "most relevant" is involved. In information retrieval literature, this task is best achieved by using inverted indexes. However, inverted indexes work only for some predefined set of patterns. In the pattern matching community, the most popular pattern-matching data structures are suffix trees and suffix arrays. However, a typical suffix tree search involves going through all the occurrences of the pattern over the entire string collection, which might be a lot more than the required relevant documents. The first formal framework to study such kind of retrieval problems was given by [Muthukrishnan, 2002]. He considered two metrics for relevance: frequency and proximity. He took a threshold-based approach on these metrics and gave data structures taking @math words of space. We study this problem in a slightly different framework of reporting the top @math most relevant documents (in sorted order) under similar and more general relevance metrics. Our framework gives linear space data structure with optimal query times for arbitrary score functions. As a corollary, it improves the space utilization for the problems in [Muthukrishnan, 2002] while maintaining optimal query performance. We also develop compressed variants of these data structures for several specific relevance metrics. Information extraction systems usually require two dictionaries: a semantic lexicon and a dictionary of extraction patterns for the domain. We present a multilevel bootstrapping algorithm that generates both the semantic lexicon and extraction patterns simultaneously. As input, our technique requires only unannotated training texts and a handful of seed words for a category. We use a mutual bootstrapping technique to alternately select the best extraction pattern for the category and bootstrap its extractions into the semantic lexicon, which is the basis for selecting the next extraction pattern. To make this approach more robust, we add a second level of bootstrapping (metabootstrapping) that retains only the most reliable lexicon entries produced by mutual bootstrapping and then restarts the process. We evaluated this multilevel bootstrapping technique on a collection of corporate web pages and a corpus of terrorism news articles. The algorithm produced high-quality dictionaries for several semantic categories. Entity recognition is an important but challenging research problem. In reality, many text collections are from specific, dynamic, or emerging domains, which poses significant new challenges for entity recognition with increase in name ambiguity and context sparsity, requiring entity detection without domain restriction. In this paper, we investigate entity recognition (ER) with distant-supervision and propose a novel relation phrase-based ER framework, called ClusType, that runs data-driven phrase mining to generate entity mention candidates and relation phrases, and enforces the principle that relation phrases should be softly clustered when propagating type information between their argument entities. Then we predict the type of each entity mention based on the type signatures of its co-occurring relation phrases and the type indicators of its surface name, as computed over the corpus. Specifically, we formulate a joint optimization problem for two tasks, type propagation with relation phrases and multi-view relation phrase clustering. Our experiments on multiple genres---news, Yelp reviews and tweets---demonstrate the effectiveness and robustness of ClusType, with an average of 37 improvement in F1 score over the best compared method. Traditional approaches to Relation Extraction from text require manually defining the relations to be extracted. We propose here an approach to automatically discovering relevant relations, given a large text corpus plus an initial ontology defining hundreds of noun categories (e.g., Athlete, Musician, Instrument). Our approach discovers frequently stated relations between pairs of these categories, using a two step process. For each pair of categories (e.g., Musician and Instrument) it first co-clusters the text contexts that connect known instances of the two categories, generating a candidate relation for each resulting cluster. It then applies a trained classifier to determine which of these candidate relations is semantically valid. Our experiments apply this to a text corpus containing approximately 200 million web pages and an ontology containing 122 categories from the NELL system [, 2010b], producing a set of 781 proposed candidate relations, approximately half of which are semantically valid. We conclude this is a useful approach to semi-automatic extension of the ontology for large-scale information extraction systems such as NELL. We present an incremental joint framework to simultaneously extract entity mentions and relations using structured perceptron with efficient beam-search. A segment-based decoder based on the idea of semi-Markov chain is adopted to the new framework as opposed to traditional token-based tagging. In addition, by virtue of the inexact search, we developed a number of new and effective global features as soft constraints to capture the interdependency among entity mentions and relations. Experiments on Automatic Content Extraction (ACE) 1 corpora demonstrate that our joint model significantly outperforms a strong pipelined baseline, which attains better performance than the best-reported end-to-end system. This paper contributes a joint embedding model for predicting relations between a pair of entities in the scenario of relation inference. It differs from most stand-alone approaches which separately operate on either knowledge bases or free texts. The proposed model simultaneously learns low-dimensional vector representations for both triplets in knowledge repositories and the mentions of relations in free texts, so that we can leverage the evidence both resources to make more accurate predictions. We use NELL to evaluate the performance of our approach, compared with cutting-edge methods. Results of extensive experiments show that our model achieves significant improvement on relation extraction. Distant supervised relation extraction is an efficient approach to scale relation extraction to very large corpora, and has been widely used to find novel relational facts from plain text. Recent studies on neural relation extraction have shown great progress on this task via modeling the sentences in low-dimensional spaces, but seldom considered syntax information to model the entities. In this paper, we propose to learn syntax-aware entity embedding for neural relation extraction. First, we encode the context of entities on a dependency tree as sentence-level entity embedding based on tree-GRU. Then, we utilize both intra-sentence and inter-sentence attentions to obtain sentence set-level entity embedding over all sentences containing the focus entity pair. Finally, we combine both sentence embedding and entity embedding for relation classification. We conduct experiments on a widely used real-world dataset and the experimental results show that our model can make full use of all informative instances and achieve state-of-the-art performance of relation extraction.