Information Extraction System Research Articles

Automatic Extraction of Lung Cancer Staging Information From Computed Tomography Reports: Deep Learning Approach.

BackgroundLung cancer is the leading cause of cancer deaths worldwide. Clinical staging of lung cancer plays a crucial role in making treatment decisions and evaluating prognosis. However, in clinical practice, approximately one-half of the clinical stages of lung cancer patients are inconsistent with their pathological stages. As one of the most important diagnostic modalities for staging, chest computed tomography (CT) provides a wealth of information about cancer staging, but the free-text nature of the CT reports obstructs their computerization.ObjectiveWe aimed to automatically extract the staging-related information from CT reports to support accurate clinical staging of lung cancer.MethodsIn this study, we developed an information extraction (IE) system to extract the staging-related information from CT reports. The system consisted of the following three parts: named entity recognition (NER), relation classification (RC), and postprocessing (PP). We first summarized 22 questions about lung cancer staging based on the TNM staging guideline. Next, three state-of-the-art NER algorithms were implemented to recognize the entities of interest. Next, we designed a novel RC method using the relation sign constraint (RSC) to classify the relations between entities. Finally, a rule-based PP module was established to obtain the formatted answers using the results of NER and RC.ResultsWe evaluated the developed IE system on a clinical data set containing 392 chest CT reports collected from the Department of Thoracic Surgery II in the Peking University Cancer Hospital. The experimental results showed that the bidirectional encoder representation from transformers (BERT) model outperformed the iterated dilated convolutional neural networks-conditional random field (ID-CNN-CRF) and bidirectional long short-term memory networks-conditional random field (Bi-LSTM-CRF) for NER tasks with macro-F1 scores of 80.97% and 90.06% under the exact and inexact matching schemes, respectively. For the RC task, the proposed RSC showed better performance than the baseline methods. Further, the BERT-RSC model achieved the best performance with a macro-F1 score of 97.13% and a micro-F1 score of 98.37%. Moreover, the rule-based PP module could correctly obtain the formatted results using the extractions of NER and RC, achieving a macro-F1 score of 94.57% and a micro-F1 score of 96.74% for all the 22 questions.ConclusionsWe conclude that the developed IE system can effectively and accurately extract information about lung cancer staging from CT reports. Experimental results show that the extracted results have significant potential for further use in stage verification and prediction to facilitate accurate clinical staging.

Synthetic data for annotation and extraction of family history information from clinical text

BackgroundThe limited availability of clinical texts for Natural Language Processing purposes is hindering the progress of the field. This article investigates the use of synthetic data for the annotation and automated extraction of family history information from Norwegian clinical text. We make use of incrementally developed synthetic clinical text describing patients’ family history relating to cases of cardiac disease and present a general methodology which integrates the synthetically produced clinical statements and annotation guideline development. The resulting synthetic corpus contains 477 sentences and 6030 tokens. In this work we experimentally assess the validity and applicability of the annotated synthetic corpus using machine learning techniques and furthermore evaluate the system trained on synthetic text on a corpus of real clinical text, consisting of de-identified records for patients with genetic heart disease.ResultsFor entity recognition, an SVM trained on synthetic data had class weighted precision, recall and F1-scores of 0.83, 0.81 and 0.82, respectively. For relation extraction precision, recall and F1-scores were 0.74, 0.75 and 0.74.ConclusionsA system for extraction of family history information developed on synthetic data generalizes well to real, clinical notes with a small loss of accuracy. The methodology outlined in this paper may be useful in other situations where limited availability of clinical text hinders NLP tasks. Both the annotation guidelines and the annotated synthetic corpus are made freely available and as such constitutes the first publicly available resource of Norwegian clinical text.

Document image layout analysis via explicit edge embedding network

Layout analysis from a document image plays an important role in document content understanding and information extraction systems. While many existing methods focus on learning knowledge with convolutional networks directly from color channels, we argue the importance of high-frequency structures in document images, especially edge information. In this paper, we present a novel document layout analysis framework with the Explicit Edge Embedding Network (E3Net). Specifically, the proposed network contains the edge embedding block and dynamic skip connection block to produce detailed features, as well as a lightweight fully convolutional subnet as the backbone for the effectiveness of the framework. The edge embedding block is designed to explicitly incorporate the edge information from the document images. The dynamic skip connection block aims to learn both color and edge representations with learnable weights. In contrast to the previous methods, we harness the model by using a synthetic document approach to overcome data scarcity. The combination of data augmentation and edge embedding is important toward a more compact representation than directly using the training images with only color channels. We conduct experiments using the proposed framework on three document layout analysis benchmarks and demonstrate its superiority in terms of effectiveness and efficiency over previous approaches.

Ship Berthing Information Extraction System Using Three-Dimensional Light Detection and Ranging Data

Safe and efficient berthing is essential to ensure maritime transportation and the safety of ships and ports. Three-dimensional (3D) light detection and ranging (LiDAR) can monitor and support ship berthing because it provides abundant target information and offers excellent advantages in measuring accuracy. Hence, a berthing information extraction system has been developed based on 3D LiDAR. Principal component analysis is used to calculate a ship’s heading and the normal vector, and the feature points of the bow and stern are determined. The segments passing through the points are obtained via region growing. The bow and stern are recognized by the similarity of the normal vector of the segments and ship’s heading according to the positions of the ship relative to the berth through visibility analysis. Qualitative and quantitative calculated analyses of the distance, velocity, and approach angle of the dynamic ship’s bow and stern relative to the dock are performed based on the feature points of 3D LiDAR data. A laser scanner, used as the detection unit, efficiently monitored the Ro–Ro ship Ocean Island berthing at Lushun Port in field experiments. On-site applications demonstrated the feasibility and effectiveness of the proposed method for the recognition of dynamic ship target and ensuring safe ship berthing.

AMFormulaS: an intelligent retrieval system for traditional Chinese medicine formulas

BackgroundFormula is an important means of traditional Chinese medicine (TCM) to treat diseases and has great research significance. There are many formula databases, but accessing rich information efficiently is difficult due to the small-scale data and lack of intelligent search engine.MethodsWe selected 38,000 formulas from a semi-structured database, and then segmented text, extracted information, and standardized terms. After that, we constructed a structured formula database based on ontology and an intelligent retrieval engine by calculating the weight of decoction pieces of formulas.ResultsThe intelligent retrieval system named AMFormulaS (means Ancient and Modern Formula system) was constructed based on the structured database, ontology, and intelligent retrieval engine, so the retrieval and statistical analysis of formulas and decoction pieces were realized.ConclusionsAMFormulaS is a large-scale intelligent retrieval system which includes a mass of formula data, efficient information extraction system and search engine. AMFormulaS could provide users with efficient retrieval and comprehensive data support. At the same time, the statistical analysis of the system can enlighten scientific research ideas and support patent review as well as new drug research and development.

Towards Robust Visual Information Extraction in Real World: New Dataset and Novel Solution

Visual Information Extraction (VIE) has attracted considerable attention recently owing to its various advanced applications such as document understanding, automatic marking and intelligent education. Most existing works decoupled this problem into several independent sub-tasks of text spotting (text detection and recognition) and information extraction, which completely ignored the high correlation among them during optimization. In this paper, we propose a robust Visual Information Extraction System (VIES) towards real-world scenarios, which is an unified end-to-end trainable framework for simultaneous text detection, recognition and information extraction by taking a single document image as input and outputting the structured information. Specifically, the information extraction branch collects abundant visual and semantic representations from text spotting for multimodal feature fusion and conversely, provides higher-level semantic clues to contribute to the optimization of text spotting. Moreover, regarding the shortage of public benchmarks, we construct a fully-annotated dataset called EPHOIE (https://github.com/HCIILAB/EPHOIE), which is the first Chinese benchmark for both text spotting and visual information extraction. EPHOIE consists of 1,494 images of examination paper head with complex layouts and background, including a total of 15,771 Chinese handwritten or printed text instances. Compared with the state-of-the-art methods, our VIES shows significant superior performance on the EPHOIE dataset and achieves a 9.01% F-score gain on the widely used SROIE dataset under the end-to-end scenario.

Extracting Family History Information From Electronic Health Records: Natural Language Processing Analysis.

BackgroundThe 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.ObjectiveThe aim of this study is to develop automated methods that enable access to FH data through natural language processing.MethodsWe 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.ResultsOur 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 (P<.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%.ConclusionsOur 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.

A Hybrid Model for Family History Information Identification and Relation Extraction: Development and Evaluation of an End-to-End Information Extraction System.

BackgroundFamily history information is important to assess the risk of inherited medical conditions. Natural language processing has the potential to extract this information from unstructured free-text notes to improve patient care and decision making. We describe the end-to-end information extraction system the Medical University of South Carolina team developed when participating in the 2019 National Natural Language Processing Clinical Challenge (n2c2)/Open Health Natural Language Processing (OHNLP) shared task.ObjectiveThis task involves identifying mentions of family members and observations in electronic health record text notes and recognizing the 2 types of relations (family member-living status relations and family member-observation relations). Our system aims to achieve a high level of performance by integrating heuristics and advanced information extraction methods. Our efforts also include improving the performance of 2 subtasks by exploiting additional labeled data and clinical text-based embedding models.MethodsWe present a hybrid method that combines machine learning and rule-based approaches. We implemented an end-to-end system with multiple information extraction and attribute classification components. For entity identification, we trained bidirectional long short-term memory deep learning models. These models incorporated static word embeddings and context-dependent embeddings. We created a voting ensemble that combined the predictions of all individual models. For relation extraction, we trained 2 relation extraction models. The first model determined the living status of each family member. The second model identified observations associated with each family member. We implemented online gradient descent models to extract related entity pairs. As part of postchallenge efforts, we used the BioCreative/OHNLP 2018 corpus and trained new models with the union of these 2 datasets. We also pretrained language models using clinical notes from the Medical Information Mart for Intensive Care (MIMIC-III) clinical database.ResultsThe voting ensemble achieved better performance than individual classifiers. In the entity identification task, our top-performing system reached a precision of 78.90% and a recall of 83.84%. Our natural language processing system for entity identification took 3rd place out of 17 teams in the challenge. We ranked 4th out of 9 teams in the relation extraction task. Our system substantially benefited from the combination of the 2 datasets. Compared to our official submission with F1 scores of 81.30% and 64.94% for entity identification and relation extraction, respectively, the revised system yielded significantly better performance (P<.05) with F1 scores of 86.02% and 72.48%, respectively.ConclusionsWe demonstrated that a hybrid model could be used to successfully extract family history information recorded in unstructured free-text notes. In this study, our approach to entity identification as a sequence labeling problem produced satisfactory results. Our postchallenge efforts significantly improved performance by leveraging additional labeled data and using word vector representations learned from large collections of clinical notes.

An Ontology-Based Information Extraction System for Organic Farming

In the existing farming system, information is obtained manually, and most times, farmers act based on their discretion. Sometimes, farmers rely on information from experts and extension officers for decision making. In recent times, a lot of information systems are available with relevant information on organic farming practices; however, such information is scattered in different context, form, and media all over the internet, making their retrieval difficult. The use of ontology with the aid of a conceptual scheme makes the comprehensive and detailed formalization of any subject domain possible. This study is aimed at acquiring, storing, and providing organic farming-based information available to current and intending software developer who may wish to develop applications for farmers. It employs information extraction (IE) and ontology development techniques to develop an ontology-based information extraction (OBIE) system called ontology-based information extraction system for organic farming (OBIESOF). The knowledge base was built using protégé editor; Java was used for the implementation of the ontology knowledge base with the aid of the high-level application programming language for working web ontology language application program interface (OWL API). In contrast, HermiT was used to checking the consistencies of the ontology and for submitting queries in order to verify their validity. The queries were expressed in description logic (DL) query language. The authors tested the capability of the ontology to respond to user queries by posing instances of the competency questions from DL query interface. The answers generated by the ontology were promising and serve as positive pointers to its usefulness as a knowledge repository.

Deep Learning-Based Knowledge Graph Generation for COVID-19

Many attempts have been made to construct new domain-specific knowledge graphs using the existing knowledge base of various domains. However, traditional “dictionary-based” or “supervised” knowledge graph building methods rely on predefined human-annotated resources of entities and their relationships. The cost of creating human-annotated resources is high in terms of both time and effort. This means that relying on human-annotated resources will not allow rapid adaptability in describing new knowledge when domain-specific information is added or updated very frequently, such as with the recent coronavirus disease-19 (COVID-19) pandemic situation. Therefore, in this study, we propose an Open Information Extraction (OpenIE) system based on unsupervised learning without a pre-built dataset. The proposed method obtains knowledge from a vast amount of text documents about COVID-19 rather than a general knowledge base and add this to the existing knowledge graph. First, we constructed a COVID-19 entity dictionary, and then we scraped a large text dataset related to COVID-19. Next, we constructed a COVID-19 perspective language model by fine-tuning the bidirectional encoder representations from transformer (BERT) pre-trained language model. Finally, we defined a new COVID-19-specific knowledge base by extracting connecting words between COVID-19 entities using the BERT self-attention weight from COVID-19 sentences. Experimental results demonstrated that the proposed Co-BERT model outperforms the original BERT in terms of mask prediction accuracy and metric for evaluation of translation with explicit ordering (METEOR) score.

ABioNER: A BERT‐Based Model for Arabic Biomedical Named‐Entity Recognition

The web is being loaded daily with a huge volume of data, mainly unstructured textual data, which increases the need for information extraction and NLP systems significantly. Named‐entity recognition task is a key step towards efficiently understanding text data and saving time and effort. Being a widely used language globally, English is taking over most of the research conducted in this field, especially in the biomedical domain. Unlike other languages, Arabic suffers from lack of resources. This work presents a BERT‐based model to identify biomedical named entities in the Arabic text data (specifically disease and treatment named entities) that investigates the effectiveness of pretraining a monolingual BERT model with a small‐scale biomedical dataset on enhancing the model understanding of Arabic biomedical text. The model performance was compared with two state‐of‐the‐art models (namely, AraBERT and multilingual BERT cased), and it outperformed both models with 85% F1‐score.

Design of e-commerce cluster information classification and extraction system based on relevant vector machine

Aiming at the problems of low accuracy and long time-consuming in traditional classification and extraction system, this paper studies and designs an e-commerce clustering information classificatio...

Design of e-commerce cluster information classification and extraction system based on relevant vector machine

Design of e-commerce cluster information classification and extraction system based on relevant vector machine

Intelligent Web Information Extraction Model for Agricultural Product Quality and Safety System

With the development of society, people pay more and more attention to the safety of food, and relevant laws and policies are gradually introduced and being improved. The research and development of agricultural product quality and safety system has become a research hot spot, and how to obtain the Web information of the system effectively and quickly is the focus of the research, so it is essential to carry out the intelligent extraction of Web information for agricultural product quality and safety system. The purpose of this paper is to solve the problem of how to efficiently extract the Web information of the agricultural product quality and safety system. By studying the Web information extraction methods of various systems, the paper makes a detailed analysis and research on how to realize the efficient and intelligent extraction of the Web information of the agricultural product quality and safety system. This paper analyzes in detail all kinds of template information extraction algorithms used at present, and systematically discusses a set of schemes that can automatically extract the Web information of agricultural product quality and safety system according to the template. The research results show that the proposed scheme is a dynamically extensible information extraction system, which can independently implement dynamic configuration templates according to different requirements without changing the code. Compared with the general way, the Web information extraction speed of agricultural product quality safety system is increased by 25%, the accuracy is increased by 12%, and the recall rate is increased by 30%.

A Face Recognition System Using ACO-BPNN Model for Optimizing the Teaching Management System.

The basic idea of face recognition technology is to compare the matching degree between the standard face image marked with identity information and the static or dynamic face collected from the actual scene, which includes two main research contents: face feature extraction and face feature recognition. Traditional identification generally proves who we are through certificates, passwords, or certificates plus passwords. With the development of science and technology, face recognition technology will occupy an increasingly important position. Inspired by the human brain, the artificial neural network (ANN) is an information extraction system based on imitating the basic function and structure of the human brain and abstracted by physical and mathematical research methods. Based on the traditional BP neural network model, this paper proposes an ant colony algorithm-enabled BP neural network (ACO-BPNN) model and applies it to face recognition. Experimental results show that, similar to other face recognition techniques, the facial feature location needs to adapt to various changes of faces to the maximum extent, so the recognition and classification effect of the whole face feature extracted from the whole face image on the changes of such partial areas is not good, while the local feature extraction method based on ACO-BPNN can achieve a good recognition and classification effect.

Resume extraction with conditional random field method

Information extraction resume is a system used to carry out the automatic information extraction process on resumes of prospective employees to obtain key information including information on names, skills, educational experience, work experience, awards which are the main components in a curriculum vitae of prospective employees. Conditional Random Field (CRF) is one method that can be used to extract information. The step taken in the information extraction process is an annotation documents, tokenization, labeling on each token in the document, feature extraction, and the formation of models that will be used at the classification stage. In this study a system was built that could be used to extract CVs from users in pdf format. This study uses a CV from LinkedIn. Information extraction is done using 15 features and 11 classes. The evaluation of information extraction system for the employee’s resume has a precision value of 85,052%, a recall value of 85,052%, and an f-measure of 78,527%.

Advanced Information Extraction System based on Unstructured Mammogram Reports

Advanced Information Extraction System based on Unstructured Mammogram Reports

A Silver Standard Biomedical Corpus for Arabic Language

The rapidly growing data in many areas, as well as in the biomedical domain, require the assistance of information extraction systems to acquire the much needed knowledge about specific entities such as proteins, drugs, or diseases practically within a short time. Annotated corpora serve the purpose of facilitating the process of building NLP systems. While colossal work has been done in this area for English language, other languages like Arabic seem to lack these resources, especially in the healthcare area. Therefore, in this work, we present a method to develop a silver standard medical corpus for the Arabic language with a dictionary as a minimal supervision tool. The corpus contains 49,856 sentences tagged with 13 entity types corresponding to a subset of UMLS (Unified Medical Language System) concept types. The evaluation of a subset of corpus showed the efficiency of the method used to annotate it with 90% accuracy.

Information Extraction from Text Intensive and Visually Rich Banking Documents

Document types, where visual and textual information plays an important role in their analysis and understanding, pose a new and attractive area for information extraction research. Although cheques, invoices, and receipts have been studied in some previous multi-modal studies, banking documents present an unexplored area due to the naturalness of the text they possess in addition to their visual richness. This article presents the first study which uses visual and textual information for deep-learning based information extraction on text-intensive and visually rich scanned documents which are, in this instance, unstructured banking documents, or more precisely, money transfer orders. The impact of using different neural word representations (i.e., FastText, ELMo, and BERT) on IE subtasks (namely, named entity recognition and relation extraction stages), positional features of words on document images and auxiliary learning with some other tasks are investigated. The article proposes a new relation extraction algorithm based on graph factorization to solve the complex relation extraction problem where the relations within documents are n-ary, nested, document-level, and previously indeterminate in quantity. Our experiments revealed that the use of deep learning algorithms yielded around 10 percentage points improvement on the IE sub-tasks. The inclusion of word positional features yielded around 3 percentage points of improvement in some specific information fields. Similarly, our auxiliary learning experiments yielded around 2 percentage points of improvement on some information fields associated with the specific transaction type detected by our auxiliary task. The integration of the information extraction system into a real banking environment reduced cycle times substantially. When compared to the manual workflow, document processing pipeline shortened book-to-book money transfers to 10 minutes (from 29 min.) and electronic fund transfers (EFT) to 17 minutes (from 41 min.) respectively.

The Study of Accuracy Characteristics of Information Extraction System Under Conditions of Change of State of the Working Signals Propagation Path and A-Priori Uncertainty About the Informative Parameters of Objects on the Sighting Surface

The Study of Accuracy Characteristics of Information Extraction System Under Conditions of Change of State of the Working Signals Propagation Path and A-Priori Uncertainty About the Informative Parameters of Objects on the Sighting Surface