Background: Relationships between bio-entities (genes, proteins, diseases, etc.) constitute a significant part of our knowledge. Most of this information is documented as unstructured text in different forms, such as books, articles and on-line pages. Automatic extraction of such information and storing it in structured form could help researchers more easily access such information and also make it possible to incorporate it in advanced integrative analysis. In this study, we developed a novel approach to extract bio-entity relationships information using Nature Language Processing (NLP) and a graph-theoretic algorithm. Methods: Our method, called GRGT (Grammatical Relationship Graph for Triplets), not only extracts the pairs of terms that have certain relationships, but also extracts the type of relationship (the word describing the relationships). In addition, the directionality of the relationship can also be extracted. Our method is based on the assumption that a triplet exists for a pair of interactions. A triplet is defined as two terms (entities) and an interaction word describing the relationship of the two terms in a sentence. We first use a sentence parsing tool to obtain the sentence structure represented as a dependency graph where words are nodes and edges are typed dependencies. The shortest paths among the pairs of words in the triplet are then extracted, which form the basis for our information extraction method. Flexible pattern matching scheme was then used to match a triplet graph with unknown relationship to those triplet graphs with labels (True or False) in the database. Results: We applied the method on three benchmark datasets to extract the protein-protein-interactions (PPIs), and obtained better precision than the top performing methods in literature. Conclusions: We have developed a method to extract the protein-protein interactions from biomedical literature. PPIs extracted by our method have higher precision among other methods, suggesting that our method can be used to effectively extract PPIs and deposit them into databases. Beyond extracting PPIs, our method could be easily extended to extracting relationship information between other bio-entities.
more »
« less
Entity-Aware Dependency-Based Deep Graph Attention Network for Comparative Preference Classification
This paper studies the task of comparative preference classification (CPC). Given two entities in a sentence, our goal is to classify whether the first (or the second) entity is preferred over the other or no comparison is expressed at all between the two entities. Existing works either do not learn entity-aware representations well and fail to deal with sentences involving multiple entity pairs or use sequential modeling approaches that are unable to capture long-range dependencies between the entities. Some also use traditional machine learning approaches that do not generalize well. This paper proposes a novel Entity-aware Dependency-based Deep Graph Attention Network (ED-GAT) that employs a multi-hop graph attention over a dependency graph sentence representation to leverage both the semantic information from word embeddings and the syntactic information from the dependency graph to solve the problem. Empirical evaluation shows that the proposed model achieves the state-of-the-art performance in comparative preference classification.
more »
« less
- Award ID(s):
- 1838770
- NSF-PAR ID:
- 10195694
- Date Published:
- Journal Name:
- Proceedings of the 58th Annual Meeting of the Association for Computational Linguistics
- Page Range / eLocation ID:
- 5782 to 5788
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
The continuing growth of scientific publications has posed a double-challenge to researchers, to not only grasp the overall research trends in a scientific domain, but also get down to research details embedded in a collection of core papers. Existing work on science mapping provides multiple tools to visualize research trends in domain on macro-level, and work from the digital humanities have proposed text visualization of documents, topics, sentences, and words on micro-level. However, existing micro-level text visualizations are not tailored for scientific paper corpus, and cannot support meso-level scientific reading, which aligns a set of core papers based on their research progress, before drilling down to individual papers. To bridge this gap, the present paper proposes LitStoryTeller+, an interactive system under a unified framework that can support both meso-level and micro-level scientific paper visual storytelling. More specifically, we use entities (concepts and terminologies) as basic visual elements, and visualize entity storylines across papers and within a paper borrowing metaphors from screen play. To identify entities and entity communities, named entity recognition and community detection are performed. We also employ a variety of text mining methods such as extractive text summarization and comparative sentence classification to provide rich textual information supplementary to our visualizations. We also propose a top-down story-reading strategy that best takes advantage of our system. Two comprehensive hypothetical walkthroughs to explore documents from the computer science domain and history domain with our system demonstrate the effectiveness of our story-reading strategy and the usefulness of LitStoryTeller+.more » « less
-
Recent literature focuses on utilizing the entity information in the sentence-level relation extraction (RE), but this risks leaking superficial and spurious clues of relations. As a result, RE still suffers from unintended entity bias, i.e., the spurious correlation between entity mentions (names) and relations. Entity bias can mislead the RE models to extract the relations that do not exist in the text. To combat this issue, some previous work masks the entity mentions to prevent the RE models from over-fitting entity mentions. However, this strategy degrades the RE performance because it loses the semantic information of entities. In this paper, we propose the CoRE (Counterfactual Analysis based Relation Extraction) debiasing method that guides the RE models to focus on the main effects of textual context without losing the entity information. We first construct a causal graph for RE, which models the dependencies between variables in RE models. Then, we propose to conduct counterfactual analysis on our causal graph to distill and mitigate the entity bias, that captures the causal effects of specific entity mentions in each instance. Note that our CoRE method is model-agnostic to debias existing RE systems during inference without changing their training processes. Extensive experimental results demonstrate that our CoRE yields significant gains on both effectiveness and generalization for RE. The source code is provided at: https://github.com/vanoracai/CoRE.more » « less
-
In this paper, we propose to use a set of simple, uniform in architecture LSTM-based models to recover different kinds of temporal relations from text. Using the shortest dependency path between entities as input, the same architecture is implemented to extract intra-sentence, cross-sentence, and document creation time relations. A “double-checking” technique reverses entity pairs in classification, boosting the recall of positive cases and reducing misclassifications between opposite classes. An efficient pruning algorithm resolves conflicts globally. Evaluated on QA-TempEval (SemEval2015 Task 5), our proposed technique outperforms state-of-the-art methods by a large margin. We also conduct intrinsic evaluation and post state-of-the-art results on Timebank-Dense.more » « less
-
null (Ed.)Definition Extraction (DE) is one of the well-known topics in Information Extraction that aims to identify terms and their corresponding definitions in unstructured texts. This task can be formalized either as a sentence classification task (i.e., containing term-definition pairs or not) or a sequential labeling task (i.e., identifying the boundaries of the terms and definitions). The previous works for DE have only focused on one of the two approaches, failing to model the inter-dependencies between the two tasks. In this work, we propose a novel model for DE that simultaneously performs the two tasks in a single framework to benefit from their inter-dependencies. Our model features deep learning architectures to exploit the global structures of the input sentences as well as the semantic consistencies between the terms and the definitions, thereby improving the quality of the representation vectors for DE. Besides the joint inference between sentence classification and sequential labeling, the proposed model is fundamentally different from the prior work for DE in that the prior work has only employed the local structures of the input sentences (i.e., word-to-word relations), and not yet considered the semantic consistencies between terms and definitions. In order to implement these novel ideas, our model presents a multi-task learning framework that employs graph convolutional neural networks and predicts the dependency paths between the terms and the definitions. We also seek to enforce the consistency between the representations of the terms and definitions both globally (i.e., increasing semantic consistency between the representations of the entire sentences and the terms/definitions) and locally (i.e., promoting the similarity between the representations of the terms and the definitions). The extensive experiments on three benchmark datasets demonstrate the effectiveness of our approach.1more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Conference Paper:
- https://doi.org/10.18653/v1/2020.acl-main.512
