scholarly journals Integrating Speculation Detection and Deep Learning to Extract Lung Cancer Diagnosis from Clinical Notes

2021 ◽  
Vol 11 (2) ◽  
pp. 865
Author(s):  
Oswaldo Solarte Pabón ◽  
Maria Torrente ◽  
Mariano Provencio ◽  
Alejandro Rodríguez-Gonzalez ◽  
Ernestina Menasalvas
Keyword(s):  
Lung Cancer ◽  
Deep Learning ◽  
Cancer Diagnosis ◽  
Hybrid Approach ◽  
Named Entity Recognition ◽  
Entity Recognition ◽  
Clinical Notes ◽  
Named Entity ◽  
Lung Cancer Diagnosis ◽  
Diagnosis Date

Despite efforts to develop models for extracting medical concepts from clinical notes, there are still some challenges in particular to be able to relate concepts to dates. The high number of clinical notes written for each single patient, the use of negation, speculation, and different date formats cause ambiguity that has to be solved to reconstruct the patient’s natural history. In this paper, we concentrate on extracting from clinical narratives the cancer diagnosis and relating it to the diagnosis date. To address this challenge, a hybrid approach that combines deep learning-based and rule-based methods is proposed. The approach integrates three steps: (i) lung cancer named entity recognition, (ii) negation and speculation detection, and (iii) relating the cancer diagnosis to a valid date. In particular, we apply the proposed approach to extract the lung cancer diagnosis and its diagnosis date from clinical narratives written in Spanish. Results obtained show an F-score of 90% in the named entity recognition task, and a 89% F-score in the task of relating the cancer diagnosis to the diagnosis date. Our findings suggest that speculation detection is together with negation detection a key component to properly extract cancer diagnosis from clinical notes.

Computer-Aided Lung Cancer Diagnosis Approaches Based on Deep Learning

2018 ◽  
Vol 30 (1) ◽  
pp. 90 ◽  
Author(s):  
Peng Zhang ◽  
Xinnan Xu ◽  
Hongwei Wang ◽  
Yuanli Feng ◽  
Haozhe Feng ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Deep Learning ◽  
Cancer Diagnosis ◽  
Lung Cancer Diagnosis ◽  
Computer Aided

Named Entity Recognition and Relation Extraction

2021 ◽  
Vol 54 (1) ◽  
pp. 1-39
Author(s):  
Zara Nasar ◽  
Syed Waqar Jaffry ◽  
Muhammad Kamran Malik
Keyword(s):  
Deep Learning ◽  
State Of The Art ◽  
Named Entity Recognition ◽  
Relation Extraction ◽  
The State ◽  
Entity Recognition ◽  
Joint Models ◽  
Named Entity ◽  
Textual Data ◽  
Benchmark Datasets

With the advent of Web 2.0, there exist many online platforms that result in massive textual-data production. With ever-increasing textual data at hand, it is of immense importance to extract information nuggets from this data. One approach towards effective harnessing of this unstructured textual data could be its transformation into structured text. Hence, this study aims to present an overview of approaches that can be applied to extract key insights from textual data in a structured way. For this, Named Entity Recognition and Relation Extraction are being majorly addressed in this review study. The former deals with identification of named entities, and the latter deals with problem of extracting relation between set of entities. This study covers early approaches as well as the developments made up till now using machine learning models. Survey findings conclude that deep-learning-based hybrid and joint models are currently governing the state-of-the-art. It is also observed that annotated benchmark datasets for various textual-data generators such as Twitter and other social forums are not available. This scarcity of dataset has resulted into relatively less progress in these domains. Additionally, the majority of the state-of-the-art techniques are offline and computationally expensive. Last, with increasing focus on deep-learning frameworks, there is need to understand and explain the under-going processes in deep architectures.

Chemical Named Entity Recognition Using Deep Learning Techniques

2021 ◽  
pp. 59-73
Author(s):  
Hema R. ◽  
Ajantha Devi
Keyword(s):  
Deep Learning ◽  
Chemical Elements ◽  
Data Extraction ◽  
Named Entity Recognition ◽  
Entity Recognition ◽  
Related Data ◽  
Named Entity ◽  
Chemical Structures ◽  
Learning Techniques ◽  
Chemical Named Entity Recognition

Chemical entities can be represented in different forms like chemical names, chemical formulae, and chemical structures. Because of the different classification frameworks for chemical names, the task of distinguishing proof or extraction of chemical elements with less ambiguous is considered a major test. Compound named entity recognition (NER) is the initial phase in any chemical-related data extraction strategy. The majority of the chemical NER is done utilizing dictionary-based, rule-based, and machine learning procedures. Recently, deep learning methods have evolved, and, in this chapter, the authors sketch out the various deep learning techniques applied for chemical NER. First, the authors introduced the fundamental concepts of chemical named entity recognition, the textual contents of chemical documents, and how these chemicals are represented in chemical literature. The chapter concludes with the strengths and weaknesses of the above methods and also the types of the chemical entities extracted.

scholarly journals Deep Learning-Based Named Entity Recognition and Knowledge Graph Construction for Geological Hazards

2019 ◽  
Vol 9 (1) ◽  
pp. 15 ◽  
Author(s):  
Runyu Fan ◽  
Lizhe Wang ◽  
Jining Yan ◽  
Weijing Song ◽  
Yingqian Zhu ◽  
...  
Keyword(s):  
Deep Learning ◽  
Large Scale ◽  
Conditional Random Field ◽  
Named Entity Recognition ◽  
Entity Recognition ◽  
Knowledge Graph ◽  
Geological Hazard ◽  
Geological Hazards ◽  
Named Entity ◽  
Corpus Construction

Constructing a knowledge graph of geological hazards literature can facilitate the reuse of geological hazards literature and provide a reference for geological hazard governance. Named entity recognition (NER), as a core technology for constructing a geological hazard knowledge graph, has to face the challenges that named entities in geological hazard literature are diverse in form, ambiguous in semantics, and uncertain in context. This can introduce difficulties in designing practical features during the NER classification. To address the above problem, this paper proposes a deep learning-based NER model; namely, the deep, multi-branch BiGRU-CRF model, which combines a multi-branch bidirectional gated recurrent unit (BiGRU) layer and a conditional random field (CRF) model. In an end-to-end and supervised process, the proposed model automatically learns and transforms features by a multi-branch bidirectional GRU layer and enhances the output with a CRF layer. Besides the deep, multi-branch BiGRU-CRF model, we also proposed a pattern-based corpus construction method to construct the corpus needed for the deep, multi-branch BiGRU-CRF model. Experimental results indicated the proposed deep, multi-branch BiGRU-CRF model outperformed state-of-the-art models. The proposed deep, multi-branch BiGRU-CRF model constructed a large-scale geological hazard literature knowledge graph containing 34,457 entities nodes and 84,561 relations.

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