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Literature mining for context-specific molecular relations using multimodal representations (COMMODAR).

ABSTRACT: Biological contextual information helps understand various phenomena occurring in the biological systems consisting of complex molecular relations. The construction of context-specific relational resources vastly relies on laborious manual extraction from unstructured literature. In this paper, we propose COMMODAR, a machine learning-based literature mining framework for context-specific molecular relations using multimodal representations. The main idea of COMMODAR is the feature augmentation by the cooperation of multimodal representations for relation extraction. We leveraged biomedical domain knowledge as well as canonical linguistic information for more comprehensive representations of textual sources. The models based on multiple modalities outperformed those solely based on the linguistic modality. We applied COMMODAR to the 14 million PubMed abstracts and extracted 9214 context-specific molecular relations. All corpora, extracted data, evaluation results, and the implementation code are downloadable at https://github.com/jae-hyun-lee/commodar . CCS CONCEPTS: • Computing methodologies~Information extraction • Computing methodologies~Neural networks • Applied computing~Biological networks.

SUBMITTER: Lee J

PROVIDER: S-EPMC7586695 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature

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Literature mining for context-specific molecular relations using multimodal representations (COMMODAR).

Lee Jaehyun J Lee Doheon D Lee Kwang Hyung KH

BMC bioinformatics 20201026 Suppl 5

Biological contextual information helps understand various phenomena occurring in the biological systems consisting of complex molecular relations. The construction of context-specific relational resources vastly relies on laborious manual extraction from unstructured literature. In this paper, we propose COMMODAR, a machine learning-based literature mining framework for context-specific molecular relations using multimodal representations. The main idea of COMMODAR is the feature augmentation b ...[more]

PMID: 33106154

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Project description:A number of studies have explored the role of associative/event-based (thematic) and categorical (taxonomic) relations in the organization of object representations. Recent evidence suggests that thematic information may be particularly important in determining relationships between manipulable artifacts. However, although sensorimotor information is on many accounts an important component of manipulable artifact representations, little is known about the role that action may play during the processing of semantic relationships (particularly thematic relationships) between multiple objects. In this study, we assessed healthy and left hemisphere stroke participants to explore three questions relevant to object relationship processing. First, we assessed whether participants tended to favor thematic relations including action (Th+A, e.g., wine bottle-corkscrew), thematic relationships without action (Th-A, e.g., wine bottle-cheese), or taxonomic relationships (Tax, e.g., wine bottle-water bottle) when choosing between them in an association judgment task with manipulable artifacts. Second, we assessed whether the underlying constructs of event relatedness, action relatedness, and categorical relatedness determined the choices that participants made. Third, we assessed the hypothesis that degraded action knowledge and/or damage to temporo-parietal cortex, a region of the brain associated with the representation of action knowledge, would reduce the influence of action on the choice task. Experiment 1 showed that explicit ratings of event, action, and categorical relatedness were differentially predictive of healthy participants' choices, with action relatedness determining choices between Th+A and Th-A associations above and beyond event and categorical ratings. Experiment 2 focused more specifically on these Th+A vs. Th-A choices and demonstrated that participants with left temporo-parietal lesions, a brain region known to be involved in sensorimotor processing, were less likely than controls and tended to be less likely than patients with lesions sparing that region to use action relatedness in determining their choices. These data indicate that action knowledge plays a critical role in processing of thematic relations for manipulable artifacts.

Dataset Information

Literature mining for context-specific molecular relations using multimodal representations (COMMODAR).

Publications

Literature mining for context-specific molecular relations using multimodal representations (COMMODAR).

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