| Challenge: | The Bacteria Biotope task focuses on the extraction of the locations and phenotypes of microorganisms from PubMed abstracts and full-text excerpts. |
| Approach: | They propose to use PubMed abstracts and full-text excerpts to extract the locations and phenotypes of microorganisms and to characterizations of these entities with respect to reference knowledge sources. |
| Outcome: | The proposed subtasks, the corpus characteristics, and the challenge organization are compared with the previous edition in 2016 and the results are presented in the second edition. |
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| 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. |
Integration of Deep Learning and Traditional Machine Learning for Knowledge Extraction from Biomedical Literature (D19-57)
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| 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. |
A Multi-Task Learning Framework for Extracting Bacteria Biotope Information (D19-57)
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| 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. |
Bacteria Biotope Relation Extraction via Lexical Chains and Dependency Graphs (D19-57)
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| 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. |
CRAFT Shared Tasks 2019 Overview — Integrated Structure, Semantics, and Coreference (D19-57)
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William Baumgartner, Michael Bada, Sampo Pyysalo, Manuel R. Ciosici, Negacy Hailu, Harrison Pielke-Lombardo, Michael Regan, Lawrence Hunter
| Challenge: | CRAFT corpus provides a unique foundation for integrating natural language processing (NLP) tasks involving structure, semantics, and coreference. |
| Approach: | They propose to use the CRAFT corpus to evaluate three fundamental language processing tasks over full-text biomedical articles. |
| Outcome: | The CRAFT corpus provides a unique foundation for integrating natural language processing tasks involving structure, semantics, and coreference. |
RDoC Task at BioNLP-OST 2019 (D19-57)
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| Challenge: | BioNLP-OST is an international competition organized to facilitate development and sharing of computational tasks of biomedical text mining and solutions to them. |
| Approach: | They propose a new mental health informatics task that is composed of two subtasks: information retrieval and sentence extraction. |
| Outcome: | The proposed task performed well on both tasks, but there are still challenges. |
Proceedings of the 5th Workshop on BioNLP Open Shared Tasks (D19-57)
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| Challenge: | a workshop organized by BioNLP-ST aims to share computational tasks of biomedical text mining and solutions to them. |
| Approach: | this year, six tasks are contributed by voluntary task organizers . they aim to promote the sharing of computational tasks of biomedical text mining . 43 reviewers selected 30 papers to be presented for the workshop . |
| Outcome: | the BioNLP Open Shared Tasks is organized to promote the sharing of computational tasks of biomedical text mining and solutions to them. |
Linguistically Informed Relation Extraction and Neural Architectures for Nested Named Entity Recognition in BioNLP-OST 2019 (D19-57)
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| 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. |
BioT5+: Towards Generalized Biological Understanding with IUPAC Integration and Multi-task Tuning (2024.findings-acl)
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Qizhi Pei, Lijun Wu, Kaiyuan Gao, Xiaozhuan Liang, Yin Fang, Jinhua Zhu, Shufang Xie, Tao Qin, Rui Yan
| Challenge: | BioT5+ is an extension of the BioT5, but lacked a nuanced understanding of molecular structures. |
| Approach: | They propose a new bio-entity modeling framework, BioT5+, which integrates IUPAC names and molecule data. |
| Outcome: | The proposed model bridges the gap between molecular representations and textual descriptions and improves the grounded reasoning of bio-text and bio-sequences. |
PubSE: A Hierarchical Model for Publication Extraction from Academic Homepages (D18-1)
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| Challenge: | Using a hierarchical model, we aim to extract all the publication strings from a researcher's homepage. |
| Approach: | They propose an end-to-end hierarchical model named PubSE based on Bi-LSTM-CRF and an alternating training method for training the model. |
| Outcome: | The proposed model outperforms the state-of-the-art models by 11.8% in F1-score on real data. |