This paper focuses on how to take advantage of external knowledge bases (KBs) to improve recurrent neural networks for machine reading. Traditional methods that exploit knowledge from KBs encode knowledge as discrete indicator features. Not only do these features generalize poorly, but they require task-specific feature engineering to achieve good performance. We propose KBLSTM, a novel neural model that leverages continuous representations of KBs to enhance the learning of recurrent neural networks for machine reading. To effectively integrate background knowledge with information from the currently processed text, our model employs an attention mechanism with a sentinel to adaptively decide whether to attend to background knowledge and which information from KBs is useful. Experimental results show that our model achieves accuracies that surpass the previous state-of-the-art results for both entity extraction and event extraction on the widely used ACE2005 dataset.
Knowledge of the creation date of documents facilitates several tasks such as summarization, event extraction, temporally focused information extraction etc. Unfortunately, for most of the documents on the Web, the time-stamp metadata is either missing or can't be trusted. Thus, predicting creation time from document content itself is an important task. In this paper, we propose Attentive Deep Document Dater (AD3), an attention-based neural document dating system which utilizes both context and temporal information in documents in a flexible and principled manner. We perform extensive experimentation on multiple real-world datasets to demonstrate the effectiveness of AD3 over neural and non-neural baselines.
The advancement of biomedical named entity recognition (BNER) and biomedical relation extraction (BRE) researches promotes the development of text mining in biological domains. As a cornerstone of BRE, robust BNER system is required to identify the mentioned NEs in plain texts for further relation extraction stage. However, the current BNER corpora, which play important roles in these tasks, paid less attention to achieve the criteria for BRE task. In this study, we present Revised JNLPBA corpus, the revision of JNLPBA corpus, to broaden the applicability of a NER corpus from BNER to BRE task. We preserve the original entity types including protein, DNA, RNA, cell line and cell type while all the abstracts in JNLPBA corpus are manually curated by domain experts again basis on the new annotation guideline focusing on the specific NEs instead of general terms. Simultaneously, several imperfection issues in JNLPBA are pointed out and made up in the new corpus. To compare the adaptability of different NER systems in Revised JNLPBA and JNLPBA corpora, the F1-measure was measured in three open sources NER systems including BANNER, Gimli and NERSuite. In the same circumstance, all the systems perform average 10% better in Revised JNLPBA than in JNLPBA. Moreover, the cross-validation test is carried out which we train the NER systems on JNLPBA/Revised JNLPBA corpora and access the performance in both protein-protein interaction extraction (PPIE) and biomedical event extraction (BEE) corpora to confirm that the newly refined Revised JNLPBA is a competent NER corpus in biomedical relation application. The revised JNLPBA corpus is freely available at iasl-btm.iis.sinica.edu.tw/BNER/Content/Revised_JNLPBA.zip.
The previous work for event extraction has mainly focused on the predictions for event triggers and argument roles, treating entity mentions as being provided by human annotators. This is unrealistic as entity mentions are usually predicted by some existing toolkits whose errors might be propagated to the event trigger and argument role recognition. Few of the recent work has addressed this problem by jointly predicting entity mentions, event triggers and arguments. However, such work is limited to using discrete engineering features to represent contextual information for the individual tasks and their interactions. In this work, we propose a novel model to jointly perform predictions for entity mentions, event triggers and arguments based on the shared hidden representations from deep learning. The experiments demonstrate the benefits of the proposed method, leading to the state-of-the-art performance for event extraction.
Topic models are widely used for thematic structure discovery in text. But traditional topic models often require dedicated inference procedures for specific tasks at hand. Also, they are not designed to generate word-level semantic representations. To address these limitations, we propose a topic modeling approach based on Generative Adversarial Nets (GANs), called Adversarial-neural Topic Model (ATM). The proposed ATM models topics with Dirichlet prior and employs a generator network to capture the semantic patterns among latent topics. Meanwhile, the generator could also produce word-level semantic representations. To illustrate the feasibility of porting ATM to tasks other than topic modeling, we apply ATM for open domain event extraction. Our experimental results on the two public corpora show that ATM generates more coherence topics, outperforming a number of competitive baselines. Moreover, ATM is able to extract meaningful events from news articles.
Named entity recognition (NER), which focuses on the extraction of semantically meaningful named entities and their semantic classes from text, serves as an indispensable component for several down-stream natural language processing (NLP) tasks such as relation extraction and event extraction. Dependency trees, on the other hand, also convey crucial semantic-level information. It has been shown previously that such information can be used to improve the performance of NER (Sasano and Kurohashi 2008, Ling and Weld 2012). In this work, we investigate on how to better utilize the structured information conveyed by dependency trees to improve the performance of NER. Specifically, unlike existing approaches which only exploit dependency information for designing local features, we show that certain global structured information of the dependency trees can be exploited when building NER models where such information can provide guided learning and inference. Through extensive experiments, we show that our proposed novel dependency-guided NER model performs competitively with models based on conventional semi-Markov conditional random fields, while requiring significantly less running time.
Event extraction is of practical utility in natural language processing. In the real world, it is a common phenomenon that multiple events existing in the same sentence, where extracting them are more difficult than extracting a single event. Previous works on modeling the associations between events by sequential modeling methods suffer a lot from the low efficiency in capturing very long-range dependencies. In this paper, we propose a novel Jointly Multiple Events Extraction (JMEE) framework to jointly extract multiple event triggers and arguments by introducing syntactic shortcut arcs to enhance information flow and attention-based graph convolution networks to model graph information. The experiment results demonstrate that our proposed framework achieves competitive results compared with state-of-the-art methods.
We present a system for rapidly customizing event extraction capability to find new event types and their arguments. The system allows a user to find, expand and filter event triggers for a new event type by exploring an unannotated corpus. The system will then automatically generate mention-level event annotation automatically, and train a Neural Network model for finding the corresponding event. Additionally, the system uses the ACE corpus to train an argument model for extracting Actor, Place, and Time arguments for any event types, including ones not seen in its training data. Experiments show that with less than 10 minutes of human effort per event type, the system achieves good performance for 67 novel event types. The code, documentation, and a demonstration video will be released as open source on github.com.
Supervised event extraction systems are limited in their accuracy due to the lack of available training data. We present a method for self-training event extraction systems by bootstrapping additional training data. This is done by taking advantage of the occurrence of multiple mentions of the same event instances across newswire articles from multiple sources. If our system can make a highconfidence extraction of some mentions in such a cluster, it can then acquire diverse training examples by adding the other mentions as well. Our experiments show significant performance improvements on multiple event extractors over ACE 2005 and TAC-KBP 2015 datasets.
Background: Given the importance of relation or event extraction from biomedical research publications to support knowledge capture and synthesis, and the strong dependency of approaches to this information extraction task on syntactic information, it is valuable to understand which approaches to syntactic processing of biomedical text have the highest performance. Results: We perform an empirical study comparing state-of-the-art traditional feature-based and neural network-based models for two core natural language processing tasks of part-of-speech (POS) tagging and dependency parsing on two benchmark biomedical corpora, GENIA and CRAFT. To the best of our knowledge, there is no recent work making such comparisons in the biomedical context; specifically no detailed analysis of neural models on this data is available. Experimental results show that in general, the neural models outperform the feature-based models on two benchmark biomedical corpora GENIA and CRAFT. We also perform a task-oriented evaluation to investigate the influences of these models in a downstream application on biomedical event extraction, and show that better intrinsic parsing performance does not always imply better extrinsic event extraction performance. Conclusion: We have presented a detailed empirical study comparing traditional feature-based and neural network-based models for POS tagging and dependency parsing in the biomedical context, and also investigated the influence of parser selection for a biomedical event extraction downstream task. Availability of data and material: We make the retrained models available at https://github.com/datquocnguyen/BioPosDep
We propose a novel neural network model for joint part-of-speech (POS) tagging and dependency parsing. Our model extends the well-known BIST graph-based dependency parser (Kiperwasser and Goldberg, 2016) by incorporating a BiLSTM-based tagging component to produce automatically predicted POS tags for the parser. On the benchmark English Penn treebank, our model obtains strong UAS and LAS scores at 94.51% and 92.87%, respectively, producing 1.5+% absolute improvements to the BIST graph-based parser, and also obtaining a state-of-the-art POS tagging accuracy at 97.97%. Furthermore, experimental results on parsing 61 "big" Universal Dependencies treebanks from raw texts show that our model outperforms the baseline UDPipe (Straka and Strakov\'a, 2017) with 0.8% higher average POS tagging score and 3.6% higher average LAS score. In addition, with our model, we also obtain state-of-the-art downstream task scores for biomedical event extraction and opinion analysis applications. Our code is available together with all pre-trained models at: https://github.com/datquocnguyen/jPTDP
The problem of spatiotemporal event visualization based on reports entails subtasks ranging from named entity recognition to relationship extraction and mapping of events. We present an approach to event extraction that is driven by data mining and visualization goals, particularly thematic mapping and trend analysis. This paper focuses on bridging the information extraction and visualization tasks and investigates topic modeling approaches. We develop a static, finite topic model and examine the potential benefits and feasibility of extending this to dynamic topic modeling with a large number of topics and continuous time. We describe an experimental test bed for event mapping that uses this end-to-end information retrieval system, and report preliminary results on a geoinformatics problem: tracking of methamphetamine lab seizure events across time and space.
The Abstract Meaning Representation (AMR) is a representation for open-domain rich semantics, with potential use in fields like event extraction and machine translation. Node generation, typically done using a simple dictionary lookup, is currently an important limiting factor in AMR parsing. We propose a small set of actions that derive AMR subgraphs by transformations on spans of text, which allows for more robust learning of this stage. Our set of construction actions generalize better than the previous approach, and can be learned with a simple classifier. We improve on the previous state-of-the-art result for AMR parsing, boosting end-to-end performance by 3 F$_1$ on both the LDC2013E117 and LDC2014T12 datasets.
Many models in natural language processing define probabilistic distributions over linguistic structures. We argue that (1) the quality of a model' s posterior distribution can and should be directly evaluated, as to whether probabilities correspond to empirical frequencies, and (2) NLP uncertainty can be projected not only to pipeline components, but also to exploratory data analysis, telling a user when to trust and not trust the NLP analysis. We present a method to analyze calibration, and apply it to compare the miscalibration of several commonly used models. We also contribute a coreference sampling algorithm that can create confidence intervals for a political event extraction task.
This document describes the Odin framework, which is a domain-independent platform for developing rule-based event extraction models. Odin aims to be powerful (the rule language allows the modeling of complex syntactic structures) and robust (to recover from syntactic parsing errors, syntactic patterns can be freely mixed with surface, token-based patterns), while remaining simple (some domain grammars can be up and running in minutes), and fast (Odin processes over 100 sentences/second in a real-world domain with over 200 rules). Here we include a thorough definition of the Odin rule language, together with a description of the Odin API in the Scala language, which allows one to apply these rules to arbitrary texts.
We propose an approach for biomedical information extraction that marries the advantages of machine learning models, e.g., learning directly from data, with the benefits of rule-based approaches, e.g., interpretability. Our approach starts by training a feature-based statistical model, then converts this model to a rule-based variant by converting its features to rules, and "snapping to grid" the feature weights to discrete votes. In doing so, our proposal takes advantage of the large body of work in machine learning, but it produces an interpretable model, which can be directly edited by experts. We evaluate our approach on the BioNLP 2009 event extraction task. Our results show that there is a small performance penalty when converting the statistical model to rules, but the gain in interpretability compensates for that: with minimal effort, human experts improve this model to have similar performance to the statistical model that served as starting point.
We describe challenges and advantages unique to coreference resolution in the biomedical domain, and a sieve-based architecture that leverages domain knowledge for both entity and event coreference resolution. Domain-general coreference resolution algorithms perform poorly on biomedical documents, because the cues they rely on such as gender are largely absent in this domain, and because they do not encode domain-specific knowledge such as the number and type of participants required in chemical reactions. Moreover, it is difficult to directly encode this knowledge into most coreference resolution algorithms because they are not rule-based. Our rule-based architecture uses sequentially applied hand-designed "sieves", with the output of each sieve informing and constraining subsequent sieves. This architecture provides a 3.2% increase in throughput to our Reach event extraction system with precision parallel to that of the stricter system that relies solely on syntactic patterns for extraction.
Events and entities are closely related; entities are often actors or participants in events and events without entities are uncommon. The interpretation of events and entities is highly contextually dependent. Existing work in information extraction typically models events separately from entities, and performs inference at the sentence level, ignoring the rest of the document. In this paper, we propose a novel approach that models the dependencies among variables of events, entities, and their relations, and performs joint inference of these variables across a document. The goal is to enable access to document-level contextual information and facilitate context-aware predictions. We demonstrate that our approach substantially outperforms the state-of-the-art methods for event extraction as well as a strong baseline for entity extraction.
A lot of prior work on event extraction has exploited a variety of features to represent events. Such methods have several drawbacks: 1) the features are often specific for a particular domain and do not generalize well; 2) the features are derived from various linguistic analyses and are error-prone; and 3) some features may be expensive and require domain expert. In this paper, we develop a Chinese event extraction system that uses word embedding vectors to represent language, and deep neural networks to learn the abstract feature representation in order to greatly reduce the effort of feature engineering. In addition, in this framework, we leverage large amount of unlabeled data, which can address the problem of limited labeled corpus for this task. Our experiments show that our proposed method performs better compared to the system using rich language features, and using unlabeled data benefits the word embeddings. This study suggests the potential of DNN and word embedding for the event extraction task.
Biomedical events describe complex interactions between various biomedical entities. Event trigger is a word or a phrase which typically signifies the occurrence of an event. Event trigger identification is an important first step in all event extraction methods. However many of the current approaches either rely on complex hand-crafted features or consider features only within a window. In this paper we propose a method that takes the advantage of recurrent neural network (RNN) to extract higher level features present across the sentence. Thus hidden state representation of RNN along with word and entity type embedding as features avoid relying on the complex hand-crafted features generated using various NLP toolkits. Our experiments have shown to achieve state-of-art F1-score on Multi Level Event Extraction (MLEE) corpus. We have also performed category-wise analysis of the result and discussed the importance of various features in trigger identification task.