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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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. 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. 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. Measuring the similarity between semantic relations that hold among entities is an important and necessary step in various Web related tasks such as relation extraction, information retrieval and analogy detection. For example, consider the case in which a person knows a pair of entities (e.g. Google, YouTube), between which a particular relation holds (e.g. acquisition). The person is interested in retrieving other such pairs with similar relations (e.g. Microsoft, Powerset). Existing keyword-based search engines cannot be applied directly in this case because, in keyword-based search, the goal is to retrieve documents that are relevant to the words used in a query -- not necessarily to the relations implied by a pair of words. We propose a relational similarity measure, using a Web search engine, to compute the similarity between semantic relations implied by two pairs of words. Our method has three components: representing the various semantic relations that exist between a pair of words using automatically extracted lexical patterns, clustering the extracted lexical patterns to identify the different patterns that express a particular semantic relation, and measuring the similarity between semantic relations using a metric learning approach. We evaluate the proposed method in two tasks: classifying semantic relations between named entities, and solving word-analogy questions. The proposed method outperforms all baselines in a relation classification task with a statistically significant average precision score of 0.74. Moreover, it reduces the time taken by Latent Relational Analysis to process 374 word-analogy questions from 9 days to less than 6 hours, with an SAT score of 51 . Universal schema builds a knowledge base (KB) of entities and relations by jointly embedding all relation types from input KBs as well as textual patterns expressing relations from raw text. In most previous applications of universal schema, each textual pattern is represented as a single embedding, preventing generalization to unseen patterns. Recent work employs a neural network to capture patterns' compositional semantics, providing generalization to all possible input text. In response, this paper introduces significant further improvements to the coverage and flexibility of universal schema relation extraction: predictions for entities unseen in training and multilingual transfer learning to domains with no annotation. We evaluate our model through extensive experiments on the English and Spanish TAC KBP benchmark, outperforming the top system from TAC 2013 slot-filling using no handwritten patterns or additional annotation. We also consider a multilingual setting in which English training data entities overlap with the seed KB, but Spanish text does not. Despite having no annotation for Spanish data, we train an accurate predictor, with additional improvements obtained by tying word embeddings across languages. Furthermore, we find that multilingual training improves English relation extraction accuracy. Our approach is thus suited to broad-coverage automated knowledge base construction in a variety of languages and domains. 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. We introduce a general framework which is suitable to capture the essence of compressed pattern matching according to various dictionary-based compressions. It is a formal system to represent a string by a pair of dictionary D and sequence S of phrases in D. The basic operations are concatenation, truncation, and repetition. We also propose a compressed pattern matching algorithm for the framework. The goal is to find all occurrences of a pattern in a text without decompression, which is one of the most active topics in string matching. Our framework includes such compression methods as Lempel-Ziv family (LZ77, LZSS, LZ78, LZW), RE-PAIR, SEQUITUR, and the static dictionary-based method. The proposed algorithm runs in O((||D|| + |S|)- height(D) + m2 + r) time with O(||D|| + m2) space, where ||D|| is the size of D, |S| is the number of tokens in S, height(D) is the maximum dependency of tokens in D, m is the pattern length, and r is the number of pattern occurrences. For a subclass of the framework that contains no truncation, the time complexity is O(||D|| + |S| + m2 + r). One of the most accurate methods in Question Answering (QA) uses off-line information extraction to find answers for frequently asked questions. It requires automatic extraction from text of all relation instances for relations that users frequently ask for. In this chapter, two methods are presented for learning relation instances for relations relevant in a closed and open domain (medical) QA system. Both methods try to learn automatic dependency paths that typically connect two arguments of a given relation. The first (lightly supervised) method starts from a seed list of argument instances, and extracts dependency paths from all sentences in which a seed pair occurs. This method works well for large text collections and for seeds which are easily identified, such as named entities, and is well-suited for open domain QA. A second experiment concentrates on medical relation extraction for the question answering module of the IMIX system. The IMIX corpus is relatively small and relation instances may contain complex noun phrases that do not occur frequently in the exact same form in the corpus. In this case, learning from annotated data is necessary. Dependency patterns enriched with semantic concept labels are shown to give accurate results for relations that are relevant for a medical QA system. Both methods improve the performance of the Dutch QA system Joost. 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. A complex relation is any n-ary relation in which some of the arguments may be be unspecified. We present here a simple two-stage method for extracting complex relations between named entities in text. The first stage creates a graph from pairs of entities that are likely to be related, and the second stage scores maximal cliques in that graph as potential complex relation instances. We evaluate the new method against a standard baseline for extracting genomic variation relations from biomedical text. Web extraction systems attempt to use the immense amount of unlabeled text in the Web in order to create large lists of entities and relations. Unlike traditional Information Extraction methods, the Web extraction systems do not label every mention of the target entity or relation, instead focusing on extracting as many different instances as possible while keeping the precision of the resulting list reasonably high. SRES is a self-supervised Web relation extraction system that learns powerful extraction patterns from unlabeled text, using short descriptions of the target relations and their attributes. SRES automatically generates the training data needed for its pattern-learning component. The performance of SRES is further enhanced by classifying its output instances using the properties of the instances and the patterns. The features we use for classification and the trained classification model are independent from the target relation, which we demonstrate in a series of experiments. We also compare the performance of SRES to the performance of the state-of-the-art KnowItAll system, and to the performance of its pattern learning component, which learns simpler pattern language than SRES. Statistical methods to extract translational equivalents from non-parallel corpora hold the promise of ensuring the required coverage and domain customisation of lexicons as well as accelerating their compilation and maintenance. A challenge for these methods are rare, less common words and expressions, which often have low corpus frequencies. However, it is rare words such as newly introduced terminology and named entities that present the main interest for practical lexical acquisition. In this article, we study possibilities of improving the extraction of low-frequency equivalents from bilingual comparable corpora. Our work is carried out in the general framework which discovers equivalences between words of different languages using similarities between their occurrence patterns found in respective monolingual corpora. We develop a method that aims to compensate for insufficient amounts of corpus evidence on rare words: prior to measuring cross-language similarities, the method uses same-language corpus data to model co-occurrence vectors of rare words by predicting their unseen co-occurrences and smoothing rare, unreliable ones. Our experimental evaluation demonstrates that the proposed method delivers a consistent and significant improvement on the conventional approach to this task. Determining semantic similarity between texts is important in many tasks in information retrieval such as search, query suggestion, automatic summarization and image finding. Many approaches have been suggested, based on lexical matching, handcrafted patterns, syntactic parse trees, external sources of structured semantic knowledge and distributional semantics. However, lexical features, like string matching, do not capture semantic similarity beyond a trivial level. Furthermore, handcrafted patterns and external sources of structured semantic knowledge cannot be assumed to be available in all circumstances and for all domains. Lastly, approaches depending on parse trees are restricted to syntactically well-formed texts, typically of one sentence in length. We investigate whether determining short text similarity is possible using only semantic features---where by semantic we mean, pertaining to a representation of meaning---rather than relying on similarity in lexical or syntactic representations. We use word embeddings, vector representations of terms, computed from unlabelled data, that represent terms in a semantic space in which proximity of vectors can be interpreted as semantic similarity. We propose to go from word-level to text-level semantics by combining insights from methods based on external sources of semantic knowledge with word embeddings. A novel feature of our approach is that an arbitrary number of word embedding sets can be incorporated. We derive multiple types of meta-features from the comparison of the word vectors for short text pairs, and from the vector means of their respective word embeddings. The features representing labelled short text pairs are used to train a supervised learning algorithm. We use the trained model at testing time to predict the semantic similarity of new, unlabelled pairs of short texts We show on a publicly available evaluation set commonly used for the task of semantic similarity that our method outperforms baseline methods that work under the same conditions. We present a new kernel method for extracting semantic relations between entities in natural language text, based on a generalization of subsequence kernels. This kernel uses three types of subsequence patterns that are typically employed in natural language to assert relationships between two entities. Experiments on extracting protein interactions from biomedical corpora and top-level relations from newspaper corpora demonstrate the advantages of this approach. We compare two different types of extraction patterns for automatically deriving semantic information from text: lexical patterns, built from words and word class information, and dependency patterns with syntactic information obtained from a full parser. We are particularly interested in whether the richer linguistic information provided by a parser allows for a better performance of subsequent information extraction work. We evaluate automatic extraction of hypernym information from text and conclude that the application of dependency patterns does not lead to substantially higher precision and recall scores than using lexical patterns. To evaluate how much a pair of entities or documents are similar is a common problem for current applications. Most approaches for this problem are based on the co-occurrence. However, different terms or words may represent the same entity or similar semantic in the real world since a concept often has more than one way of expression. Existing works always focus on computing semantic relatedness of words. But relatedness cannot reflect the similarity most of the time, on the other hand, most of their corpus are from common data sources such as Wikipedia and are not useful for the specialized vocabulary. In this paper, we propose a novel unsupervised approach for evaluating the semantic similarity between words by mapping texts to vector space and computing prior information. In our approach, we construct a model that can identify the words representing the same entity in special context even though they don't belong to the same concept. At last, we construct a network of words in which paths between words can reflect the evolution process of concepts. Our experimental results show that that our approach gives an effective solution to discover the semantic relationship between words, especially for words in specialty domains. Semantic taxonomies such as WordNet provide a rich source of knowledge for natural language processing applications, but are expensive to build, maintain, and extend. Motivated by the problem of automatically constructing and extending such taxonomies, in this paper we present a new algorithm for automatically learning hypernym (is-a) relations from text. Our method generalizes earlier work that had relied on using small numbers of hand-crafted regular expression patterns to identify hypernym pairs. Using "dependency path" features extracted from parse trees, we introduce a general-purpose formalization and generalization of these patterns. Given a training set of text containing known hypernym pairs, our algorithm automatically extracts useful dependency paths and applies them to new corpora to identify novel pairs. On our evaluation task (determining whether two nouns in a news article participate in a hypernym relationship), our automatically extracted database of hypernyms attains both higher precision and higher recall than WordNet. We address the issue of extracting implicit and explicit relationships between entities in biomedical text. We argue that entities seldom occur in text in their simple form and that relationships in text relate the modified, complex forms of entities with each other. We present a rule-based method for (1) extraction of such complex entities and (2) relationships between them and (3) the conversion of such relationships into RDF. Furthermore, we present results that clearly demonstrate the utility of the generated RDF in discovering knowledge from text corpora by means of locating paths composed of the extracted relationships. Hypernym discovery aims to extract such noun pairs that one noun is a hypernym of the other. Most previous methods are based on lexical patterns but perform badly on opendomain data. Other work extracts hypernym relations from encyclopedias but has limited coverage. This paper proposes a simple yet effective distant supervision framework for Chinese open-domain hypernym discovery. Given an entity name, we try to discover its hypernyms by leveraging knowledge from multiple sources, i.e., search engine results, encyclopedias, and morphology of the entity name. First, we extract candidate hypernyms from the above sources. Then, we apply a statistical ranking model to select correct hypernyms. A set of novel features is proposed for the ranking model. We also present a heuristic strategy to build a large-scale noisy training data for the model without human annotation. Experimental results demonstrate that our approach outperforms the state-of-the-art methods on a manually labeled test dataset. Modern models of relation extraction for tasks like ACE are based on supervised learning of relations from small hand-labeled corpora. We investigate an alternative paradigm that does not require labeled corpora, avoiding the domain dependence of ACE-style algorithms, and allowing the use of corpora of any size. Our experiments use Freebase, a large semantic database of several thousand relations, to provide distant supervision. For each pair of entities that appears in some Freebase relation, we find all sentences containing those entities in a large unlabeled corpus and extract textual features to train a relation classifier. Our algorithm combines the advantages of supervised IE (combining 400,000 noisy pattern features in a probabilistic classifier) and unsupervised IE (extracting large numbers of relations from large corpora of any domain). Our model is able to extract 10,000 instances of 102 relations at a precision of 67.6 . We also analyze feature performance, showing that syntactic parse features are particularly helpful for relations that are ambiguous or lexically distant in their expression.