Information Extraction in the Medical Domain

2015 ◽  
Vol 8 (2) ◽  
pp. 1-15 ◽  
Author(s):  
Aicha Ghoulam ◽  
Fatiha Barigou ◽  
Ghalem Belalem
Keyword(s):  
Natural Language ◽  
Information Extraction ◽  
Language Processing ◽  
Personal Information ◽  
Recognition Task ◽  
Relation Extraction ◽  
Entity Recognition ◽  
Machine Learning Techniques ◽  
Literature Mining ◽  
Advantages And Disadvantages

Information Extraction (IE) is a natural language processing (NLP) task whose aim is to analyse texts written in natural language to extract structured and useful information such as named entities and semantic relations between them. Information extraction is an important task in a diverse set of applications like bio-medical literature mining, customer care, community websites, personal information management and so on. In this paper, the authors focus only on information extraction from clinical reports. The two most fundamental tasks in information extraction are discussed; namely, named entity recognition task and relation extraction task. The authors give details about the most used rule/pattern-based and machine learning techniques for each task. They also make comparisons between these techniques and summarize the advantages and disadvantages of each one.

scholarly journals Building Graph for Events and Time in Natural Language Text

2020 ◽  
Vol 9 (3) ◽  
pp. 581-586
Keyword(s):  
Natural Language Processing ◽  
Natural Language ◽  
Information Extraction ◽  
Language Processing ◽  
Question Answering ◽  
Relation Extraction ◽  
Event Extraction ◽  
Event Time ◽  
Time Graph ◽  
Question Answering Systems

Events and time are two major key terms in natural language processing due to the various event-oriented tasks these are become an essential terms in information extraction. In natural language processing and information extraction or retrieval event and time leads to several applications like text summaries, documents summaries, and question answering systems. In this paper, we present events-time graph as a new way of construction for event-time based information from text. In this event-time graph nodes are events, whereas edges represent the temporal and co-reference relations between events. In many of the previous researches of natural language processing mainly individually focused on extraction tasks and in domain-specific way but in this work we present extraction and representation of the relationship between events- time by representing with event time graph construction. Our overall system construction is in three-step process that performs event extraction, time extraction, and representing relation extraction. Each step is at a performance level comparable with the state of the art. We present Event extraction on MUC data corpus annotated with events mentions on which we train and evaluate our model. Next, we present time extraction the model of times tested for several news articles from Wikipedia corpus. Next is to represent event time relation by representation by next constructing event time graphs. Finally, we evaluate the overall quality of event graphs with the evaluation metrics and conclude the observations of the entire work

scholarly journals ENCADEAr: ENCADEAmento automático de notícias

2015 ◽  
Vol 7 (1) ◽  
Author(s):  
Carla Abreu ◽  
Jorge Teixeira ◽  
Eugénio Oliveira
Keyword(s):  
Natural Language Processing ◽  
Natural Language ◽  
Information Extraction ◽  
Supervised Learning ◽  
Language Processing ◽  
Name Entity Recognition ◽  
Entity Recognition ◽  
Name Entity ◽  
Supervised Learning Algorithms ◽  
Processing Information

This work aims at defining and evaluating different techniques to automatically build temporal news sequences. The approach proposed is composed by three steps: (i) near duplicate documents detention; (ii) keywords extraction; (iii) news sequences creation. This approach is based on: Natural Language Processing, Information Extraction, Name Entity Recognition and supervised learning algorithms. The proposed methodology got a precision of 93.1% for news chains sequences creation.

scholarly journals DeNERT-KG: Named Entity and Relation Extraction Model Using DQN, Knowledge Graph, and BERT

2020 ◽  
Vol 10 (18) ◽  
pp. 6429
Author(s):  
SungMin Yang ◽  
SoYeop Yoo ◽  
OkRan Jeong
Keyword(s):  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Language Model ◽  
Named Entity Recognition ◽  
Relation Extraction ◽  
Entity Recognition ◽  
Knowledge Graph ◽  
Named Entity ◽  
Artificial Intelligence Technology

Along with studies on artificial intelligence technology, research is also being carried out actively in the field of natural language processing to understand and process people’s language, in other words, natural language. For computers to learn on their own, the skill of understanding natural language is very important. There are a wide variety of tasks involved in the field of natural language processing, but we would like to focus on the named entity registration and relation extraction task, which is considered to be the most important in understanding sentences. We propose DeNERT-KG, a model that can extract subject, object, and relationships, to grasp the meaning inherent in a sentence. Based on the BERT language model and Deep Q-Network, the named entity recognition (NER) model for extracting subject and object is established, and a knowledge graph is applied for relation extraction. Using the DeNERT-KG model, it is possible to extract the subject, type of subject, object, type of object, and relationship from a sentence, and verify this model through experiments.

scholarly journals Learning adaptive representations for entity recognition in the biomedical domain

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ivano Lauriola ◽  
Fabio Aiolli ◽  
Alberto Lavelli ◽  
Fabio Rinaldi
Keyword(s):  
Machine Learning ◽  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Machine Learning Algorithms ◽  
Entity Recognition ◽  
Machine Learning Techniques ◽  
Hybrid Architecture ◽  
Biomedical Domain ◽  
Word Embeddings

Abstract Background Named Entity Recognition is a common task in Natural Language Processing applications, whose purpose is to recognize named entities in textual documents. Several systems exist to solve this task in the biomedical domain, based on Natural Language Processing techniques and Machine Learning algorithms. A crucial step of these applications is the choice of the representation which describes data. Several representations have been proposed in the literature, some of which are based on a strong knowledge of the domain, and they consist of features manually defined by domain experts. Usually, these representations describe the problem well, but they require a lot of human effort and annotated data. On the other hand, general-purpose representations like word-embeddings do not require human domain knowledge, but they could be too general for a specific task. Results This paper investigates methods to learn the best representation from data directly, by combining several knowledge-based representations and word embeddings. Two mechanisms have been considered to perform the combination, which are neural networks and Multiple Kernel Learning. To this end, we use a hybrid architecture for biomedical entity recognition which integrates dictionary look-up (also known as gazetteers) with machine learning techniques. Results on the CRAFT corpus clearly show the benefits of the proposed algorithm in terms of F1 score. Conclusions Our experiments show that the principled combination of general, domain specific, word-, and character-level representations improves the performance of entity recognition. We also discussed the contribution of each representation in the final solution.

scholarly journals Natural Language Processing Model for Automatic Analysis of Cybersecurity-Related Documents

Symmetry ◽  
2020 ◽  
Vol 12 (3) ◽  
pp. 354
Author(s):  
Tiberiu-Marian Georgescu
Keyword(s):  
Machine Learning ◽  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Web Application ◽  
Named Entity Recognition ◽  
Relation Extraction ◽  
Entity Recognition ◽  
Model Based ◽  
The Way

This paper describes the development and implementation of a natural language processing model based on machine learning which performs cognitive analysis for cybersecurity-related documents. A domain ontology was developed using a two-step approach: (1) the symmetry stage and (2) the machine adjustment. The first stage is based on the symmetry between the way humans represent a domain and the way machine learning solutions do. Therefore, the cybersecurity field was initially modeled based on the expertise of cybersecurity professionals. A dictionary of relevant entities was created; the entities were classified into 29 categories and later implemented as classes in a natural language processing model based on machine learning. After running successive performance tests, the ontology was remodeled from 29 to 18 classes. Using the ontology, a natural language processing model based on a supervised learning model was defined. We trained the model using sets of approximately 300,000 words. Remarkably, our model obtained an F1 score of 0.81 for named entity recognition and 0.58 for relation extraction, showing superior results compared to other similar models identified in the literature. Furthermore, in order to be easily used and tested, a web application that integrates our model as the core component was developed.

Natural language processing and machine learning as practical toolsets for archival processing

2020 ◽  
Vol 30 (2) ◽  
pp. 155-174
Author(s):  
Tim Hutchinson
Keyword(s):  
Machine Learning ◽  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Entity Recognition ◽  
Machine Learning Techniques ◽  
Learning Tools ◽  
Functional Requirements ◽  
Content Type ◽  
Archival Processing

Purpose This study aims to provide an overview of recent efforts relating to natural language processing (NLP) and machine learning applied to archival processing, particularly appraisal and sensitivity reviews, and propose functional requirements and workflow considerations for transitioning from experimental to operational use of these tools. Design/methodology/approach The paper has four main sections. 1) A short overview of the NLP and machine learning concepts referenced in the paper. 2) A review of the literature reporting on NLP and machine learning applied to archival processes. 3) An overview and commentary on key existing and developing tools that use NLP or machine learning techniques for archives. 4) This review and analysis will inform a discussion of functional requirements and workflow considerations for NLP and machine learning tools for archival processing. Findings Applications for processing e-mail have received the most attention so far, although most initiatives have been experimental or project based. It now seems feasible to branch out to develop more generalized tools for born-digital, unstructured records. Effective NLP and machine learning tools for archival processing should be usable, interoperable, flexible, iterative and configurable. Originality/value Most implementations of NLP for archives have been experimental or project based. The main exception that has moved into production is ePADD, which includes robust NLP features through its named entity recognition module. This paper takes a broader view, assessing the prospects and possible directions for integrating NLP tools and techniques into archival workflows.

scholarly journals Relation Extraction With Clause-Based Open Information Extraction

2021 ◽  
Author(s):  
Duc Thuan Vo
Keyword(s):  
Natural Language ◽  
Information Extraction ◽  
Language Processing ◽  
Question Answering ◽  
Relation Extraction ◽  
Linguistic Knowledge ◽  
Dependency Parsing ◽  
Grammatical Structure ◽  
Open Information Extraction ◽  
Wide Range

Information Extraction (IE) is one of the challenging tasks in natural language processing. The goal of relation extraction is to discover the relevant segments of information in large numbers of textual documents such that they can be used for structuring data. IE aims at discovering various semantic relations in natural language text and has a wide range of applications such as question answering, information retrieval, knowledge presentation, among others. This thesis proposes approaches for relation extraction with clause-based Open Information Extraction that use linguistic knowledge to capture a variety of information including semantic concepts, words, POS tags, shallow and full syntax, dependency parsing in rich syntactic and semantic structures.<div>Within the plethora of Open Information Extraction that focus on the use of syntactic and dependency parsing for the purposes of detecting relations, incoherent and uninformative relation extractions can still be found. The extracted relations can be erroneous at times and fail to have a meaningful interpretation. As such, we first propose refinements to the grammatical structure of syntactic and dependency parsing with clause structures and clause types in an effort to generate propositions that can be deemed as meaningful extractable relations. Second, considering that choosing the most efficient seeds are pivotal to the success of the bootstrapping process when extracting relations, we propose an extended clause-based pattern extraction method with selftraining for unsupervised relation extraction. The proposed self-training algorithm relies on the clause-based approach to extract a small set of seed instances in order to identify and derive new patterns. Third, we employ matrix factorization and collaborative filtering for relation extraction. To avoid the need for manually predefined schemas, we employ the notion of universal schemas that is formed as a collection of patterns derived from Open Information Extraction tools as well as from relation schemas of pre-existing datasets. While previous systems have trained relations only for entities, we exploit advanced features from relation characteristics such as clause types and semantic topics for predicting new relation instances. Finally, we present an event network representation for temporal and causal event relation extraction that benefits from existing Open IE systems to generate a set of triple relations that are then used to build an event network. The event network is bootstrapped by labeling the temporal and causal disposition of events that are directly linked to each other. The event network can be systematically traversed to identify temporal and causal relations between indirectly connected events. <br></div>

scholarly journals Extracting Family History Information From Electronic Health Records: Natural Language Processing Analysis (Preprint)

2020 ◽  
Author(s):  
Maciej Rybinski ◽  
Xiang Dai ◽  
Sonit Singh ◽  
Sarvnaz Karimi ◽  
Anthony Nguyen
Keyword(s):  
Natural Language Processing ◽  
Family History ◽  
Natural Language ◽  
Information Extraction ◽  
Learning Strategies ◽  
Language Processing ◽  
Entity Recognition ◽  
Free Text ◽  
Shared Task ◽  
Data Set

BACKGROUND The prognosis, diagnosis, and treatment of many genetic disorders and familial diseases significantly improve if the family history (FH) of a patient is known. Such information is often written in the free text of clinical notes. OBJECTIVE The aim of this study is to develop automated methods that enable access to FH data through natural language processing. METHODS We performed information extraction by using transformers to extract disease mentions from notes. We also experimented with rule-based methods for extracting family member (FM) information from text and coreference resolution techniques. We evaluated different transfer learning strategies to improve the annotation of diseases. We provided a thorough error analysis of the contributing factors that affect such information extraction systems. RESULTS Our experiments showed that the combination of domain-adaptive pretraining and intermediate-task pretraining achieved an F1 score of 81.63% for the extraction of diseases and FMs from notes when it was tested on a public shared task data set from the National Natural Language Processing Clinical Challenges (N2C2), providing a statistically significant improvement over the baseline (<i>P</i><.001). In comparison, in the 2019 N2C2/Open Health Natural Language Processing Shared Task, the median F1 score of all 17 participating teams was 76.59%. CONCLUSIONS Our approach, which leverages a state-of-the-art named entity recognition model for disease mention detection coupled with a hybrid method for FM mention detection, achieved an effectiveness that was close to that of the top 3 systems participating in the 2019 N2C2 FH extraction challenge, with only the top system convincingly outperforming our approach in terms of precision.

scholarly journals A Relation-Specific Attention Network for Joint Entity and Relation Extraction

2020 ◽  
Author(s):  
Yue Yuan ◽  
Xiaofei Zhou ◽  
Shirui Pan ◽  
Qiannan Zhu ◽  
Zeliang Song ◽  
...  
Keyword(s):  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
State Of The Art ◽  
Relation Extraction ◽  
Attention Mechanism ◽  
Important Task ◽  
Entity Recognition ◽  
Attention Network ◽  
Public Datasets

Joint extraction of entities and relations is an important task in natural language processing (NLP), which aims to capture all relational triplets from plain texts. This is a big challenge due to some of the triplets extracted from one sentence may have overlapping entities. Most existing methods perform entity recognition followed by relation detection between every possible entity pairs, which usually suffers from numerous redundant operations. In this paper, we propose a relation-specific attention network (RSAN) to handle the issue. Our RSAN utilizes relation-aware attention mechanism to construct specific sentence representations for each relation, and then performs sequence labeling to extract its corresponding head and tail entities. Experiments on two public datasets show that our model can effectively extract overlapping triplets and achieve state-of-the-art performance.

scholarly journals Relation Extraction With Clause-Based Open Information Extraction

2021 ◽  
Author(s):  
Duc Thuan Vo
Keyword(s):  
Natural Language ◽  
Information Extraction ◽  
Language Processing ◽  
Question Answering ◽  
Relation Extraction ◽  
Linguistic Knowledge ◽  
Dependency Parsing ◽  
Grammatical Structure ◽  
Open Information Extraction ◽  
Wide Range

Information Extraction (IE) is one of the challenging tasks in natural language processing. The goal of relation extraction is to discover the relevant segments of information in large numbers of textual documents such that they can be used for structuring data. IE aims at discovering various semantic relations in natural language text and has a wide range of applications such as question answering, information retrieval, knowledge presentation, among others. This thesis proposes approaches for relation extraction with clause-based Open Information Extraction that use linguistic knowledge to capture a variety of information including semantic concepts, words, POS tags, shallow and full syntax, dependency parsing in rich syntactic and semantic structures.<div>Within the plethora of Open Information Extraction that focus on the use of syntactic and dependency parsing for the purposes of detecting relations, incoherent and uninformative relation extractions can still be found. The extracted relations can be erroneous at times and fail to have a meaningful interpretation. As such, we first propose refinements to the grammatical structure of syntactic and dependency parsing with clause structures and clause types in an effort to generate propositions that can be deemed as meaningful extractable relations. Second, considering that choosing the most efficient seeds are pivotal to the success of the bootstrapping process when extracting relations, we propose an extended clause-based pattern extraction method with selftraining for unsupervised relation extraction. The proposed self-training algorithm relies on the clause-based approach to extract a small set of seed instances in order to identify and derive new patterns. Third, we employ matrix factorization and collaborative filtering for relation extraction. To avoid the need for manually predefined schemas, we employ the notion of universal schemas that is formed as a collection of patterns derived from Open Information Extraction tools as well as from relation schemas of pre-existing datasets. While previous systems have trained relations only for entities, we exploit advanced features from relation characteristics such as clause types and semantic topics for predicting new relation instances. Finally, we present an event network representation for temporal and causal event relation extraction that benefits from existing Open IE systems to generate a set of triple relations that are then used to build an event network. The event network is bootstrapped by labeling the temporal and causal disposition of events that are directly linked to each other. The event network can be systematically traversed to identify temporal and causal relations between indirectly connected events. <br></div>

Sign in / Sign up

Export Citation Format

Share Document