Bacteria Biotope Relation Extraction via Lexical Chains and Dependency Graphs (D19-57)
Copied to clipboard
| Challenge: | In this paper, we describe our approach for the Bacteria Biotopes relation extraction subtask in the BioNLP Shared Task 2019 . |
| Approach: | They propose a novel approach for dependency graph construction based on lexical chains . they then propose 'neuro network' model which uses short-term memories and syntax information . |
| Outcome: | The proposed approach achieves the best F1 (66.3%) in the official evaluation participated by 7 teams. |
Similar Papers
A Multi-Task Learning Framework for Extracting Bacteria Biotope Information (D19-57)
Copied to clipboard
| Challenge: | Existing methods to extract information from unstructured text are slow or expensive to get. |
| Approach: | They propose a multi-task transfer multi-learning method for Bacteria Biotope rel+ner task . they use BERT and pre-train it using mask language models and next sentence prediction . |
| Outcome: | The proposed method achieves the best performance on all metrics including slot error rate, precision and recall in the Bacteria Biotope rel+ner subtask. |
Integration of Deep Learning and Traditional Machine Learning for Knowledge Extraction from Biomedical Literature (D19-57)
Copied to clipboard
| Challenge: | BB system is among the top two systems in five of all six subtasks . knowledge about microbial diversity is crucial for the study of microbiome and bacteria . |
| Approach: | They present a system that uses word embedding and lexical features to perform entities recognition, normalization and relation extraction. |
| Outcome: | The proposed system achieves state-of-the-art in five of six subtasks and is among the top two in five. |
BOUN-ISIK Participation: An Unsupervised Approach for the Named Entity Normalization and Relation Extraction of Bacteria Biotopes (D19-57)
Copied to clipboard
| Challenge: | In 2011, the Bacteria Biotope Task was conducted for the first time as a part of the BioNLP Shared Task targeting the extraction of useful information regarding bacteria and their habitats. |
| Approach: | They propose two systems for the normalization of entities and the identification of relations between entities given a biomedical text. |
| Outcome: | The proposed method performs as good as deep learning based methods which require labeled data. |
Leveraging Dependency Forest for Neural Medical Relation Extraction (D19-1)
Copied to clipboard
| Challenge: | Existing methods for medical relation extraction use dependency syntax as a source of features. |
| Approach: | They propose a method to extract relational information from medical literature by using dependency forests. |
| Outcome: | The proposed method outperforms the standard tree-based methods in the medical domain. |
Syntax-aware Multi-task Graph Convolutional Networks for Biomedical Relation Extraction (D19-62)
Copied to clipboard
| Challenge: | 80% of the data sets for relation extraction tasks are negative instances, resulting in a lack of syntactic information between two entity mentions. |
| Approach: | They propose a graph convolutional networks model that incorporates dependency parsing and contextualized embedding to capture comprehensive contextual information. |
| Outcome: | The proposed model achieves state-of-the-art F-score on the 2013 drug-drug interaction extraction task. |
Exploiting the Syntax-Model Consistency for Neural Relation Extraction (2020.acl-main)
Copied to clipboard
| Challenge: | Existing deep learning models for Relation Extraction (RE) have limited generalization beyond the syntactic structures of the input sentences. |
| Approach: | They propose a deep learning model that uses dependency trees to extract syntactic importance of words for Relation Extraction. |
| Outcome: | The proposed model outperforms existing models on three RE benchmark datasets. |
Relation Extraction with Word Graphs from N-grams (2021.emnlp-main)
Copied to clipboard
| Challenge: | Recent studies for relation extraction (RE) leverage the dependency tree of the input sentence to improve performance. |
| Approach: | They propose to use a graph convolutional network to build a context graph without dependency parsers. |
| Outcome: | The proposed approach improves neural RE methods without dependency parsers on English benchmark datasets. |
A Novel Table-to-Graph Generation Approach for Document-Level Joint Entity and Relation Extraction (2023.acl-long)
Copied to clipboard
| Challenge: | Existing document-level relation extraction methods assume entities and their mentions are given beforehand, which is inadequate for real-world applications. |
| Approach: | They propose a table-to-graph generation model for joint extraction of entities and relations at document-level. |
| Outcome: | The proposed model surpasses existing methods by a large margin and achieves state-of-the-art results on a document-level relation extraction dataset. |
Linguistically Informed Relation Extraction and Neural Architectures for Nested Named Entity Recognition in BioNLP-OST 2019 (D19-57)
Copied to clipboard
| Challenge: | Named Entity Recognition (NER) and Relation Extraction (RE) are essential tools in distilling knowledge from biomedical literature. |
| Approach: | They propose to use Named Entities to perform nested entities extraction, Entity Normalization and Relation Extraction to generalize the approach to different languages. |
| Outcome: | The proposed approach can be generalized to different languages and showed it’s effectiveness for English and Spanish text. |
Graph Convolution over Multiple Dependency Sub-graphs for Relation Extraction (2020.coling-main)
Copied to clipboard
| Challenge: | Existing graph convolutional networks use pruned dependency trees to filter irrelevant nodes from sentence graphs. |
| Approach: | They propose to construct multiple sub-graphs from shortest dependency path and words linked to entities in the dependency parse to obtain more informative features useful for relation extraction. |
| Outcome: | The proposed method achieves state-of-the-art performance on a sentence-level relation extraction dataset and the SemEval 2010 Task 8 sentence- level relation extraction data. |