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.
A well known body of work, OpenIE @cite_18 @cite_0 @cite_10 @cite_15 aims to extract patterns between entity mentions in sentences, thereby discovering new surface forms which can be clustered @cite_12 @cite_9 in order to reveal new meaningful relationship types. In the biomedical domain, Percha and Altman attempt something similar by extracting and clustering dependency patterns between pairs of biomedical entities (e.g. chemical-gene, chemical-disease, gene-disease). Our work differs from these approaches in that we extract pairs for a pre-specified relationship type (either from scratch or by augmenting existing data written with specific guidelines), which is not guaranteed to correspond to a cluster of discovered surface forms.
@cite_18 @cite_9 @cite_0 @cite_15 @cite_10 @cite_12
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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. Extracting biomedical entities and their relations from text has important applications on biomedical research. Previous work primarily utilized feature-based pipeline models to process this task. Many efforts need to be made on feature engineering when feature-based models are employed. Moreover, pipeline models may suffer error propagation and are not able to utilize the interactions between subtasks. Therefore, we propose a neural joint model to extract biomedical entities as well as their relations simultaneously, and it can alleviate the problems above. Our model was evaluated on two tasks, i.e., the task of extracting adverse drug events between drug and disease entities, and the task of extracting resident relations between bacteria and location entities. Compared with the state-of-the-art systems in these tasks, our model improved the F1 scores of the first task by 5.1 in entity recognition and 8.0 in relation extraction, and that of the second task by 9.2 in relation extraction. The proposed model achieves competitive performances with less work on feature engineering. We demonstrate that the model based on neural networks is effective for biomedical entity and relation extraction. In addition, parameter sharing is an alternative method for neural models to jointly process this task. Our work can facilitate the research on biomedical text mining. Motivation: The abundance of biomedical literature has attracted significant interest in novel methods to automatically extract biomedical relations from the literature. Until recently, most research was focused on extracting binary relations such as protein–protein interactions and drug–disease relations. However, these binary relations cannot fully represent the original biomedical data. Therefore, there is a need for methods that can extract fine-grained and complex relations known as biomedical events. Results: In this article we propose a novel method to extract biomedical events from text. Our method consists of two phases. In the first phase, training data are mapped into structured representations. Based on that, templates are used to extract rules automatically. In the second phase, extraction methods are developed to process the obtained rules. When evaluated against the Genia event extraction abstract and full-text test datasets (Task 1), we obtain results with F-scores of 52.34 and 53.34, respectively, which are comparable to the state-of-the-art systems. Furthermore, our system achieves superior performance in terms of computational efficiency. Availability: Our source code is available for academic use at http: dl.dropbox.com u 10256952 BioEvent.zip Contact: [email protected] We develop a novel distant supervised model that integrates the results from open information extraction techniques to perform relation extraction task from biomedical literature. Unlike state-of-the-art models for relation extraction in biomedical domain which are mainly based on supervised methods, our approach does not require manually-labeled instances. In addition, our model incorporates a grouping strategy to take into consideration the coordinating structure among entities co-occurred in one sentence. We apply our approach to extract gene expression relationship between genes and brain regions from literature. Results show that our methods can achieve promising performance over baselines of Transductive Support Vector Machine and with non-grouping strategy. We propose an approach for extracting relations between entities from biomedical literature based solely on shallow linguistic information. We use a combination of kernel functions to integrate two different information sources: (i) the whole sentence where the relation appears, and (ii) the local contexts around the interacting entities. We performed experiments on extracting gene and protein interactions from two different data sets. The results show that our approach outperforms most of the previous methods based on syntactic and semantic information. 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. We explore unsupervised approaches to relation extraction between two named entities; for instance, the semantic bornIn relation between a person and location entity. Concretely, we propose a series of generative probabilistic models, broadly similar to topic models, each which generates a corpus of observed triples of entity mention pairs and the surface syntactic dependency path between them. The output of each model is a clustering of observed relation tuples and their associated textual expressions to underlying semantic relation types. Our proposed models exploit entity type constraints within a relation as well as features on the dependency path between entity mentions. We examine effectiveness of our approach via multiple evaluations and demonstrate 12 error reduction in precision over a state-of-the-art weakly supervised baseline. Abstract Biomedical relation extraction can automatically extract high-quality biomedical relations from biomedical texts, which is a vital step for the mining of biomedical knowledge hidden in the literature. Recurrent neural networks (RNNs) and convolutional neural networks (CNNs) are two major neural network models for biomedical relation extraction. Neural network-based methods for biomedical relation extraction typically focus on the sentence sequence and employ RNNs or CNNs to learn the latent features from sentence sequences separately. However, RNNs and CNNs have their own advantages for biomedical relation extraction. Combining RNNs and CNNs may improve biomedical relation extraction. In this paper, we present a hybrid model for the extraction of biomedical relations that combines RNNs and CNNs. First, the shortest dependency path (SDP) is generated based on the dependency graph of the candidate sentence. To make full use of the SDP, we divide the SDP into a dependency word sequence and a relation sequence. Then, RNNs and CNNs are employed to automatically learn the features from the sentence sequence and the dependency sequences, respectively. Finally, the output features of the RNNs and CNNs are combined to detect and extract biomedical relations. We evaluate our hybrid model using five public (protein-protein interaction) PPI corpora and a (drug-drug interaction) DDI corpus. The experimental results suggest that the advantages of RNNs and CNNs in biomedical relation extraction are complementary. Combining RNNs and CNNs can effectively boost biomedical relation extraction performance. 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. Many biomedical relation extraction approaches are based on supervised machine learning, requiring an annotated corpus. Distant supervision aims at training a classifier by combining a knowledge base with a corpus, reducing the amount of manual effort necessary. This is particularly useful for biomedicine because many databases and ontologies have been made available for many biological processes, while the availability of annotated corpora is still limited. We studied the extraction of microRNA-gene relations from text. MicroRNA regulation is an important biological process due to its close association with human diseases. The proposed method, IBRel, is based on distantly supervised multi-instance learning. We evaluated IBRel on three datasets, and the results were compared with a co-occurrence approach as well as a supervised machine learning algorithm. While supervised learning outperformed on two of those datasets, IBRel obtained an F-score 28.3 percentage points higher on the dataset for which there was no training set developed specifically. To demonstrate the applicability of IBRel, we used it to extract 27 miRNA-gene relations from recently published papers about cystic fibrosis. Our results demonstrate that our method can be successfully used to extract relations from literature about a biological process without an annotated corpus. The source code and data used in this study are available at https: github.com AndreLamurias IBRel. Given a set of documents from a specific domain (e.g., medical research journals), how do we automatically build a Knowledge Graph (KG) for that domain? Automatic identification of relations and their schemas, i.e., type signature of arguments of relations (e.g., undergo(Patient, Surgery)), is an important first step towards this goal. We refer to this problem as Relation Schema Induction (RSI). In this paper, we propose Schema Induction using Coupled Tensor Factorization (SICTF), a novel tensor factorization method for relation schema induction. SICTF factorizes Open Information Extraction (OpenIE) triples extracted from a domain corpus along with additional side information in a principled way to induce relation schemas. To the best of our knowledge, this is the first application of tensor factorization for the RSI problem. Through extensive experiments on multiple real-world datasets, we find that SICTF is not only more accurate than state-of-the-art baselines, but also significantly faster (about 14x faster). The vast number of published medical documents is considered a vital source for relationship discovery. This paper presents a statistical unsupervised system, called BioNoculars, for extracting protein-protein interactions from biomedical text. BioNoculars uses graph-based mutual reinforcement to make use of redundancy in data to construct extraction patterns in a domain independent fashion. The system was tested using MEDLINE abstract for which the protein-protein interactions that they contain are listed in the database of interacting proteins and protein-protein interactions (DIPPPI). The system reports an F-Measure of 0.55 on test MEDLINE abstracts. © 2013 Association for Computational Linguistics. Traditional relation extraction predicts relations within some fixed and finite target schema. Machine learning approaches to this task require either manual annotation or, in the case of distant supervision, existing structured sources of the same schema. The need for existing datasets can be avoided by using a universal schema: the union of all involved schemas (surface form predicates as in OpenIE, and relations in the schemas of preexisting databases). This schema has an almost unlimited set of relations (due to surface forms), and supports integration with existing structured data (through the relation types of existing databases). To populate a database of such schema we present matrix factorization models that learn latent feature vectors for entity tuples and relations. We show that such latent models achieve substantially higher accuracy than a traditional classification approach. More importantly, by operating simultaneously on relations observed in text and in pre-existing structured DBs such as Freebase, we are able to reason about unstructured and structured data in mutually-supporting ways. By doing so our approach outperforms stateof- the-Art distant supervision. With the increasing automation of health care information processing, it has become crucial to extract meaningful information from textual notes in electronic medical records. One of the key challenges is to extract and normalize entity mentions. State-of-the-art approaches have focused on the recognition of entities that are explicitly mentioned in a sentence. However, clinical documents often contain phrases that indicate the entities but do not contain their names. We term those implicit entity mentions and introduce the problem of implicit entity recognition (IER) in clinical documents. We propose a solution to IER that leverages entity definitions from a knowledge base to create entity models, projects sentences to the entity models and identifies implicit entity mentions by evaluating semantic similarity between sentences and entity models. The evaluation with 857 sentences selected for 8 different entities shows that our algorithm outperforms the most closely related unsupervised solution. The similarity value calculated by our algorithm proved to be an effective feature in a supervised learning setting, helping it to improve over the baselines, and achieving F1 scores of .81 and .73 for different classes of implicit mentions. Our gold standard annotations are made available to encourage further research in the area of IER. 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. 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. Distantly supervised relation extraction has been widely used to find novel relational facts from plain text. To predict the relation between a pair of two target entities, existing methods solely rely on those direct sentences containing both entities. In fact, there are also many sentences containing only one of the target entities, which provide rich and useful information for relation extraction. To address this issue, we build inference chains between two target entities via intermediate entities, and propose a path-based neural relation extraction model to encode the relational semantics from both direct sentences and inference chains. Experimental results on real-world datasets show that, our model can make full use of those sentences containing only one target entity, and achieves significant and consistent improvements on relation extraction as compared with baselines. The source code of this paper can be obtained from https: github.com thunlp PathNRE. This paper presents a generative model for the automatic discovery of relations between entities in electronic medical records. The model discovers relation instances and their types by determining which context tokens express the relation. Additionally, the valid semantic classes for each type of relation are determined. We show that the model produces clusters of relation trigger words which better correspond with manually annotated relations than several existing clustering techniques. The discovered relations reveal some of the implicit semantic structure present in patient records. 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. Recognizing visual relationships among any pair of localized objects is pivotal for image understanding. Previous studies have shown remarkable progress in exploiting linguistic priors or external textual information to improve the performance. In this work, we investigate an orthogonal perspective based on feature interactions. We show that by encouraging deep message propagation and interactions between local object features and global predicate features, one can achieve compelling performance in recognizing complex relationships without using any linguistic priors. To this end, we present two new pooling cells to encourage feature interactions: (i) Contrastive ROI Pooling Cell, which has a unique deROI pooling that inversely pools local object features to the corresponding area of global predicate features. (ii) Pyramid ROI Pooling Cell, which broadcasts global predicate features to reinforce local object features.The two cells constitute a Spatiality-Context-Appearance Module (SCA-M), which can be further stacked consecutively to form our final Zoom-Net.We further shed light on how one could resolve ambiguous and noisy object and predicate annotations by Intra-Hierarchical trees (IH-tree). Extensive experiments conducted on Visual Genome dataset demonstrate the effectiveness of our feature-oriented approach compared to state-of-the-art methods (Acc@1 11.42 from 8.16 ) that depend on explicit modeling of linguistic interactions. We further show that SCA-M can be incorporated seamlessly into existing approaches to improve the performance by a large margin. The source code will be released on this https URL.