ترغب بنشر مسار تعليمي؟ اضغط هنا

Inter-sentence Relation Extraction for Associating Biological Context with Events in Biomedical Texts

80   0   0.0 ( 0 )
 نشر من قبل Enrique Noriega-Atala
 تاريخ النشر 2018
  مجال البحث الهندسة المعلوماتية
والبحث باللغة English




اسأل ChatGPT حول البحث

We present an analysis of the problem of identifying biological context and associating it with biochemical events in biomedical texts. This constitutes a non-trivial, inter-sentential relation extraction task. We focus on biological context as descriptions of the species, tissue type and cell type that are associated with biochemical events. We describe the properties of an annotated corpus of context-event relations and present and evaluate several classifiers for context-event association trained on syntactic, distance and frequency features.



قيم البحث

اقرأ أيضاً

105 - Qingyu Chen , Yifan Peng , 2018
Sentence embeddings have become an essential part of todays natural language processing (NLP) systems, especially together advanced deep learning methods. Although pre-trained sentence encoders are available in the general domain, none exists for bio medical texts to date. In this work, we introduce BioSentVec: the first open set of sentence embeddings trained with over 30 million documents from both scholarly articles in PubMed and clinical notes in the MIMIC-III Clinical Database. We evaluate BioSentVec embeddings in two sentence pair similarity tasks in different text genres. Our benchmarking results demonstrate that the BioSentVec embeddings can better capture sentence semantics compared to the other competitive alternatives and achieve state-of-the-art performance in both tasks. We expect BioSentVec to facilitate the research and development in biomedical text mining and to complement the existing resources in biomedical word embeddings. BioSentVec is publicly available at https://github.com/ncbi-nlp/BioSentVec
99 - Wenxuan Zhou , Muhao Chen 2021
Sentence-level relation extraction (RE) aims at identifying the relationship between two entities in a sentence. Many efforts have been devoted to this problem, while the best performing methods are still far from perfect. In this paper, we revisit t wo problems that affect the performance of existing RE models, namely entity representation and noisy or ill-defined labels. Our improved baseline model, incorporated with entity representations with typed markers, achieves an F1 of 74.6% on TACRED, significantly outperforms previous SOTA methods. Furthermore, the presented new baseline achieves an F1 of 91.1% on the refined Re-TACRED dataset, demonstrating that the pre-trained language models achieve unexpectedly high performance on this task. We release our code to the community for future research.
Past work in relation extraction has focused on binary relations in single sentences. Recent NLP inroads in high-value domains have sparked interest in the more general setting of extracting n-ary relations that span multiple sentences. In this paper , we explore a general relation extraction framework based on graph long short-term memory networks (graph LSTMs) that can be easily extended to cross-sentence n-ary relation extraction. The graph formulation provides a unified way of exploring different LSTM approaches and incorporating various intra-sentential and inter-sentential dependencies, such as sequential, syntactic, and discourse relations. A robust contextual representation is learned for the entities, which serves as input to the relation classifier. This simplifies handling of relations with arbitrary arity, and enables multi-task learning with related relations. We evaluate this framework in two important precision medicine settings, demonstrating its effectiveness with both conventional supervised learning and distant supervision. Cross-sentence extraction produced larger knowledge bases. and multi-task learning significantly improved extraction accuracy. A thorough analysis of various LSTM approaches yielded useful insight the impact of linguistic analysis on extraction accuracy.
The recent advancement of pre-trained Transformer models has propelled the development of effective text mining models across various biomedical tasks. However, these models are primarily learned on the textual data and often lack the domain knowledg e of the entities to capture the context beyond the sentence. In this study, we introduced a novel framework that enables the model to learn multi-omnics biological information about entities (proteins) with the help of additional multi-modal cues like molecular structure. Towards this, rather developing modality-specific architectures, we devise a generalized and optimized graph based multi-modal learning mechanism that utilizes the GraphBERT model to encode the textual and molecular structure information and exploit the underlying features of various modalities to enable end-to-end learning. We evaluated our proposed method on ProteinProtein Interaction task from the biomedical corpus, where our proposed generalized approach is observed to be benefited by the additional domain-specific modality.
112 - Chris Quirk , Hoifung Poon 2016
The growing demand for structured knowledge has led to great interest in relation extraction, especially in cases with limited supervision. However, existing distance supervision approaches only extract relations expressed in single sentences. In gen eral, cross-sentence relation extraction is under-explored, even in the supervised-learning setting. In this paper, we propose the first approach for applying distant supervision to cross- sentence relation extraction. At the core of our approach is a graph representation that can incorporate both standard dependencies and discourse relations, thus providing a unifying way to model relations within and across sentences. We extract features from multiple paths in this graph, increasing accuracy and robustness when confronted with linguistic variation and analysis error. Experiments on an important extraction task for precision medicine show that our approach can learn an accurate cross-sentence extractor, using only a small existing knowledge base and unlabeled text from biomedical research articles. Compared to the existing distant supervision paradigm, our approach extracted twice as many relations at similar precision, thus demonstrating the prevalence of cross-sentence relations and the promise of our approach.

الأسئلة المقترحة

التعليقات
جاري جلب التعليقات جاري جلب التعليقات
سجل دخول لتتمكن من متابعة معايير البحث التي قمت باختيارها
mircosoft-partner

هل ترغب بارسال اشعارات عن اخر التحديثات في شمرا-اكاديميا