Resource Constrained Maximum Path . Information Extraction ( IE ) is a process focused on automatic extraction of structured information from unstructured text sources . One open research field of IE relates to Named Entity Recognition ( NER ) , aimed at identifying and associating atomic elements in a given text to a predefined category such as names of persons , organizations , locations and so on . The foundations of NLP are diverse and include scientific fields such as electrical and electronic engineering , linguistics , and artificial intelligence . Some popular NLP applications are information extraction , machine translation , text summarization , and question answering . This dissertation proposes a new methodology using Answer Set programming ( ASP ) as our main formalism to predict Interpretable Semantic Textual Similarity ( iSTS ) with a rule-based approach focusing on hard-coded rules for our system , Inspire . This research proposed an approach of information extraction that combines bootstrapping approach with Ontology-Based Information Extraction ( OBIE ) . Bootstrapping approach using small seed of labelled data , is used to minimize human intervention on information extraction process , while the use of guide ontology for extracting classes , properties and instances , using for provide semantic content for semantic web . Combining both approaches expected to increase speed of extraction process and accuracy of extraction results . Ten participants each read 5,000 five-letter French words sampled in space-time within a 200 ms window . On the temporal dimension , our results show that two moments are especially important during the information extraction process . On the spatial dimension , we found a bias for the upper half of words . Now , there is interest in converting our personal desktops to structured databases , the knowledge in scientific publications to structured records , and harnessing the Internet for structured fact finding queries . Consequently , there are many different communities of researchers bringing in techniques from machine learning , databases , information retrieval , and computational linguistics for various aspects of the information extraction problem . This review is a survey of information extraction research of over two decades from these diverse communities . This paper addresses an information-extraction problem that aims to identify semantic relations among medical concepts ( problems , tests , and treatments ) in clinical text . The objectives of the paper are twofold . We introduce in particular a class of methods which use in a crucial way data compression techniques in order to define a measure of remoteness and distance between pairs of sequences of characters ( e.g. texts ) based on their relative information content . We also discuss in detail how specific features of data compression techniques could be used to introduce the notion of dictionary of a given sequence and of artificial text and we show how these new tools can be used for information extraction purposes . We point out the versatility and generality of our method that applies to any kind of corpora of character strings independently of the type of coding behind them . In the way biological data can be extracted , producing scientific knowledge , handling and mining huge information is at present a subject of incredible conspiracy and significance . Automation particularly in the information extraction step might be an essential technique to lessen the time important to finish an efficient research . However , the state of the art of automatically extricating information components from biological databases has not been all around portrayed . Entity recognition was based on Racine Pharma lexicon for drugs and Medical Dictionary for Regulatory Activities terminology for potential adverse events ( AEs ) . Natural language processing – based techniques automated the ADR information extraction ( relation between the drug and AE entities ) . The corpus of evaluation was a random sample of the messages containing drugs and/or AE concepts corresponding to recent pharmacovigilance alerts . The experiment was conducted on the data set of Thai Supreme Court 's cases , particularly about civil and criminal . For the information extraction part , the results showed that our system achieves more than 90 % of accuracy in terms of F1 . For the legal-case summarization part , experts evaluated that they are very satisfied with the summary provided by our system . The Fifth Message Understanding Conference ( MUC-5 ) involved the same tasks , domains and languages as the information extraction portion of the ARPA TIPSTER program . These tasks center on automatically filling object-oriented data structures , called templates , with information extracted from free text in news stories ( for discussion of templates and objects , see " Template Design for Information Extraction " in this volume ) . • We introduce a series of extractive evaluation models to automatically evaluate output generation performance , exploiting the fact that post - hoc information extraction is significantly easier than generation itself . • section : C. Information Extraction Details Data To form an information extraction dataset , we first sentence - tokenize the gold summary documents y 1:T using NLTK They are also the foundation of a class of output sensitive algorithms which use them to compute local community structure information in time sublinear to the size of the input graph [ reference ] . It is this connection to local structure that motivates us to use a stream of short random walks as our basic tool for extracting information from a network . In addition to capturing community information , using random walks as the basis for our algorithm gives us two other desirable properties . With this additional dynamic information , we should theoretically be able to improve facial expression accuracy . However , extracting information from videos has its own challenges . In following sub - sections , we briefly review standard approaches to facial expressions on both image and video - based approaches . First , contains additional information compared to since it is not filtered by . Thus a model that directly uses does not rely solely on for extracting information , due to the fact that it has access to the raw information , as in temporal connections . In other words , no longer has to take all responsibility for selecting useful features for both horizontal and vertical transitions , and the burden of selecting information is shared with . DEFINITION Extraction , Transformation , and Loading ( ETL ) processes are responsible for the operations taking place in the back stage of a data warehouse architecture . In a high level description of an ETL process , first , the data are extracted from the source data stores that can be On-Line Transaction Processing ( OLTP ) or legacy systems , files under any format , web pages , various kinds of documents ( e.g. , spreadsheets and text documents ) or even data coming in a streaming fashion . Definition extraction is the task to identify definitional sentences automatically from unstructured text . The task can be used in the aspects of ontology generation , relation extraction and question answering . The Case of Indirect Taxes.- 10 - First Workshop on Search Techniques for Constraint Satisfaction ( STCS 2007).- Efficient and Tight Upper Bounds for Haplotype Inference by Pure Parsimony Using Delayed Haplotype Selection.- GRASPER.- 11 - Second Workshop on Text Mining and Applications ( TEMA 2007).- Text Segmentation Using Context Overlap.- Automatic Extraction of Definitions in Portuguese : A Rule-Based Approach.- N-Grams and Morphological Normalization in Text Classification : A Comparison on a Croatian-English Parallel Corpus.- Detection of Strange and Wrong Automatic Part-of-Speech Tagging.- New Techniques for Relevant Word Ranking and Extraction . During the last few years , a lot of researches have focused on automatic definition extraction in the context of question answering systems . Although , these researches have been conducted for different languages , no research has been proposed for Arabic . In this paper we present the results of an experiment in automatic concept and definition extraction from written sources of law using relatively simple natural language and standard semantic web technology . The software was tested on six laws from the tax domain . So in this study an semi-automatic building approach of domain ontology based on text mining is brought forward , which is to extract concepts , concept definition and relationships between concepts from textbooks or scientific materials with text-oriented intelligent information processing technology and with the help of subject experts and knowledge engineers . This approach is constituted of the selection of document materials , the text processing of document materials , the concepts relation marking , the formal representation and storage and the evaluation of knowledge database , including the technologies of information extraction , Chinese word segmentation , automatic term extraction and automatic term definition extraction . At last , according to the learning resource requirement in Teachers Training of educational technology capability , the authors took the curriculum of Instructional Design as study case and built the domain ontology of instructional design with semi-automatic building approach of domain ontology based on text mining . In this paper , a terminological framework , both theoretical and methodological , backed by empirical data , is proposed in order to highlight the particular questions to which attention should be paid when conceiving an evaluation scheme for definition extraction ( DE ) in terminology . The premise is that not just any information is relevant to defining a given concept in a given expert domain . To address those issues , this paper proposes a solution to perform the automatic extraction of definitional patterns from multi-domain definitional sentences of Wikipedia . Our method FIND-SS is modified based on FIND-S algorithm and solves the definition extraction problems of cross-domain corpora . Find-SS adopts a " the more similar the higher priority " scheme to improve the learning performance . So far , these approaches have been evaluated using different collections and gold standard datasets , which prevented comparative performance assessments . To facilitate future research on the task of identifier definition extraction , we make three contributions . First , we provide an automated evaluation framework , which uses the dataset and gold standard of the NTCIR-11 Math Retrieval Wikipedia task . However , unlike the biomedical literature , clinical notes have many abbreviations without their full forms available in the text or without standard definitions in dictionaries due to the nature of the documents . This causes difficulties in adapting traditional approaches for abbreviation disambiguation such as classification among fixed candidates or pattern-based definition extraction . Because of this reason , we consider the task as search problem and propose an approach with two steps : a ) exploring possible full form candidates from various resources and b ) choosing most acceptable one among retrieved candidates by ranking . The soft match includes definition memberhood calculation and similarity calculation based on Vector Space Model , and then combined the two algorithms together . The experiment achieves good results , and offers effective method for the research of term definition extraction . Joint extraction of entities and relations is an important task in information extraction . To tackle this problem , we firstly propose a novel tagging scheme that can convert the joint extraction task to a tagging problem . On the other side , in order to obtain large training data for methods of supervised learning , distant supervision are used in previous work whereas largely suffer from noisy labeling problem . To solve these problems , we propose a reinforcement learning framework for joint extraction of entities and relations . First , we construct a relation extractor based on a tagging scheme to extract entities and relations jointly . Both entity and relation extraction can benefit from being performed jointly , allowing each task to correct the errors of the other . We present a new method for joint entity and relation extraction using a graph we call a " card-pyramid . " This graph compactly encodes all possible entities and relations in a sentence , reducing the task of their joint extraction to jointly labeling its nodes . We develop a new paradigm for the task of joint entity relation extraction . It first identifies entity spans , then performs a joint inference on entity types and relation types . State-of-the-art entity relation recognition systems are built using deep recurrent neural networks which often does not capture the symbolic knowledge or the logical constraints in the problem . The main contribution of this paper is an end-to-end neural model for joint entity relation extraction which incorporates a novel loss function . This novel loss function encodes the constraint information in the problem to guide the model training effectively . T he Arabic Language needs to perform more researches in information extraction domain and hence we introduce this research . The experiment is concerned with extraction entities and entities relation extraction from the Arabic text . We used in our experiment text from Arabic news in Egyptian Arabic newswire . Joint extraction of entities and their relations from the text is an essential issue in automatic knowledge graph construction , which is also known as the joint extraction of relational triplets . The relational triplets in sentence are complicated , multiple and different relational triplets may have overlaps , which is commonly seen in reality . We present a novel attention-based recurrent neural network for joint extraction of entity mentions and relations . We show that attention along with long short term memory ( LSTM ) network can extract semantic relations between entity mentions without having access to dependency trees . We propose a neural network model for joint extraction of named entities and relations between them , without any hand-crafted features . The key contribution of our model is to extend a BiLSTM-CRF-based entity recognition model with a deep biaffine attention layer to model second-order interactions between latent features for relation classification , specifically attending to the role of an entity in a directional relationship . Furthermore , we incorporate hierarchical multi-head attention mechanisms into the joint extraction model to capture vital semantic information from the available texts . Experiments show that the proposed approach consistently achieves significant improvements on joint extraction task of entities and relations as compared with strong baselines . However , previous models are not effective or ignore to model this property . In this work , to effectively leverage class ties , we propose to make joint relation extraction with a unified model that integrates convolutional neural network ( CNN ) with a general pairwise ranking framework , in which three novel ranking loss functions are introduced . Additionally , an effective method is presented to relieve the severe class imbalance problem from NR ( not relation ) for model training . The syndrome-gene relationships are discovered based on the syndrome-disease relationships extracted from TCM literature and the disease-gene relationships in MEDLINE . Based on the bubble-bootstrapping and relation weight computing methods , we have developed a prototype system called MeDisco/3S , which has name entity and relation extraction , and online analytical processing ( OLAP ) capabilities , to perform the integrative mining process . RESULTS We have got about 200,000 syndrome-gene relations , which could help generate syndrome-based gene networks , and help analyze the functional knowledge of genes from syndrome perspective . We leverage popular tools of Open Information Extraction ( OpenIE ) and dependency parser for this purpose . OpenIE refers to the extraction of entity relations from the open - domain text . In OpenIE , a fact is typically interpreted as a relation triple consisting of ( subject ; predicate ; object ) . BioConceptVec covers over 400,000 biomedical concepts mentioned in the literature and is of the largest among the publicly available biomedical concept embeddings to date . To evaluate the validity and utility of BioConceptVec , we respectively performed two intrinsic evaluations ( identifying related concepts based on drug-gene and gene-gene interactions ) and two extrinsic evaluations ( protein-protein interaction prediction and drug-drug interaction extraction ) , collectively using over 25 million instances from nine independent datasets ( 17 million instances from six intrinsic evaluation tasks and 8 million instances from three extrinsic evaluation tasks ) , which is , by far , the most comprehensive to our best knowledge . The intrinsic evaluation results demonstrate that BioConceptVec consistently has , by a large margin , better performance than existing concept embeddings in identifying similar and related concepts . We propose a multi-task learning framework to jointly model relation identification and classification tasks to propagate supervision signals from each other and apply a focal loss to focus training on ambiguous mention pairs . By applying these two strategies , experiments show that our model achieves state-of-the-art F-score on the 2013 drug-drug interaction extraction task . Since more and more new drug products come into the market , it is difficult to collect such information by manual . We take part in the Drug-Drug Interaction ( DDI ) Extraction from Drug Labels challenge of Text Analysis Conference ( TAC ) 2018 , choosing task1 and task2 to automatically extract DDI related mentions and DDI relations respectively . Instead of regarding task1 as named entity recognition ( NER ) task and regarding task2 as relation extraction ( RE ) task then solving it in a pipeline , we propose a two step joint model to detect DDI and it ’s related mentions jointly . DrugNerAR , a drug anaphora resolution system is presented to address the problem of co-referring expressions in pharmacological literature . This development is part of a larger and innovative study about automatic drug-drug interaction extraction . Besides , a corpus has been developed in order to analyze the phenomena and evaluate the current approach . In this thesis , we have conducted a detailed study about various information extraction techniques applied to biomedical domain . Based on this study , we have proposed two different approximations for the extraction of drug-drug interactions from texts . The first approximation proposes a hybrid approach , which combines shallow parsing and pattern matching to extract relations between drugs from biomedical texts . This paper presents a system for identify generic drug names in biomedical texts . The identification of drug names is the first step of the process involved in the development of a system aimed at the automatic extraction of drug-drug interactions in biomedical texts . A drug-drug interaction occurs when one drug influences the level or activity of another drug . Abstract Since Drug-drug interactions ( DDIs ) can cause adverse effects when patients take two or more drugs and therefore increase health care costs , the extraction of DDIs is an important research area in patient safety . To improve the performance of Drug – drug interaction extraction ( DDIE ) , we present a novel two-stage method in this paper . It first identifies the positive instances using a feature based binary classifier , and then a Long Short Term Memory ( LSTM ) based classifier is used to classify the positive instances into specific category . The Drug-Drug Reaction Extraction at NIST TAC 2018 conference aims to extract information on drug reactions from drug labels . In this paper , we describe the PE-TU ’ model participated in mention extraction task . These heuristics are based on the default PR structure and linguistic expressions signaling temporal and conditional markers . They are integrated in a system for drug extraction from hospital Patient Records ( PRs ) in Bulgarian language . Present evaluation results are summarized as well . In this study , a method based on co-occurrence is used as the underlying relationship extraction method for its simplicity . It can be replaced by or combined with more advanced methods such as machine learning or natural language processing approaches to further improve the performance of the drug-gene relationship extraction from free text . Our method is not limited to extracting a drug-gene relationship ; it can be generalized to extract other types of relationships when related background knowledge bases exist . In the biomedical domain , typical entity types include disease , chemical , gene and protein . Biomedical named entity recognition ( BioNER ) is an essential building block of many downstream text mining applications such as extracting drug - drug interactions and disease - treatment relations . BioNER is also used when building a sophisticated biomedical entity search tool that enables users to pose complex queries to search for bio - entities . While most span errors tend to come from subjective annotations , or can be easily fixed by non - experts , bio - entity errors are difficult to detect , even for biomedical researchers . Also , for biomedical text mining methods , such as drug - drug interaction extraction , span errors can cause minor errors but bio - entity errors could lead to completely different results . In CollaboNet , each expert model is trained on a single entity type dataset , and their training inputs are a concatenation of word embeddings and outputs of the other expert models .
Resource Constrained Maximum Path . Information Extraction ( IE ) is a process focused on automatic extraction of structured information from unstructured text sources . One open research field of IE relates to Named Entity Recognition ( NER ) , aimed at identifying and associating atomic elements in a given text to a predefined category such as names of persons , organizations , locations and so on .
The foundations of NLP are diverse and include scientific fields such as electrical and electronic engineering , linguistics , and artificial intelligence . Some popular NLP applications are information extraction , machine translation , text summarization , and question answering . This dissertation proposes a new methodology using Answer Set programming ( ASP ) as our main formalism to predict Interpretable Semantic Textual Similarity ( iSTS ) with a rule-based approach focusing on hard-coded rules for our system , Inspire .
This research proposed an approach of information extraction that combines bootstrapping approach with Ontology-Based Information Extraction ( OBIE ) . Bootstrapping approach using small seed of labelled data , is used to minimize human intervention on information extraction process , while the use of guide ontology for extracting classes , properties and instances , using for provide semantic content for semantic web . Combining both approaches expected to increase speed of extraction process and accuracy of extraction results .
Ten participants each read 5,000 five-letter French words sampled in space-time within a 200 ms window . On the temporal dimension , our results show that two moments are especially important during the information extraction process . On the spatial dimension , we found a bias for the upper half of words .
Now , there is interest in converting our personal desktops to structured databases , the knowledge in scientific publications to structured records , and harnessing the Internet for structured fact finding queries . Consequently , there are many different communities of researchers bringing in techniques from machine learning , databases , information retrieval , and computational linguistics for various aspects of the information extraction problem . This review is a survey of information extraction research of over two decades from these diverse communities .
This paper addresses an information-extraction problem that aims to identify semantic relations among medical concepts ( problems , tests , and treatments ) in clinical text . The objectives of the paper are twofold .
We introduce in particular a class of methods which use in a crucial way data compression techniques in order to define a measure of remoteness and distance between pairs of sequences of characters ( e.g. texts ) based on their relative information content . We also discuss in detail how specific features of data compression techniques could be used to introduce the notion of dictionary of a given sequence and of artificial text and we show how these new tools can be used for information extraction purposes . We point out the versatility and generality of our method that applies to any kind of corpora of character strings independently of the type of coding behind them .
In the way biological data can be extracted , producing scientific knowledge , handling and mining huge information is at present a subject of incredible conspiracy and significance . Automation particularly in the information extraction step might be an essential technique to lessen the time important to finish an efficient research . However , the state of the art of automatically extricating information components from biological databases has not been all around portrayed .
Entity recognition was based on Racine Pharma lexicon for drugs and Medical Dictionary for Regulatory Activities terminology for potential adverse events ( AEs ) . Natural language processing – based techniques automated the ADR information extraction ( relation between the drug and AE entities ) . The corpus of evaluation was a random sample of the messages containing drugs and/or AE concepts corresponding to recent pharmacovigilance alerts .
The experiment was conducted on the data set of Thai Supreme Court 's cases , particularly about civil and criminal . For the information extraction part , the results showed that our system achieves more than 90 % of accuracy in terms of F1 . For the legal-case summarization part , experts evaluated that they are very satisfied with the summary provided by our system .
The Fifth Message Understanding Conference ( MUC-5 ) involved the same tasks , domains and languages as the information extraction portion of the ARPA TIPSTER program . These tasks center on automatically filling object-oriented data structures , called templates , with information extracted from free text in news stories ( for discussion of templates and objects , see " Template Design for Information Extraction " in this volume ) .
• We introduce a series of extractive evaluation models to automatically evaluate output generation performance , exploiting the fact that post - hoc information extraction is significantly easier than generation itself . •
section : C. Information Extraction Details Data To form an information extraction dataset , we first sentence - tokenize the gold summary documents y 1:T using NLTK
They are also the foundation of a class of output sensitive algorithms which use them to compute local community structure information in time sublinear to the size of the input graph [ reference ] . It is this connection to local structure that motivates us to use a stream of short random walks as our basic tool for extracting information from a network . In addition to capturing community information , using random walks as the basis for our algorithm gives us two other desirable properties .
With this additional dynamic information , we should theoretically be able to improve facial expression accuracy . However , extracting information from videos has its own challenges . In following sub - sections , we briefly review standard approaches to facial expressions on both image and video - based approaches .
First , contains additional information compared to since it is not filtered by . Thus a model that directly uses does not rely solely on for extracting information , due to the fact that it has access to the raw information , as in temporal connections . In other words , no longer has to take all responsibility for selecting useful features for both horizontal and vertical transitions , and the burden of selecting information is shared with .
DEFINITION Extraction , Transformation , and Loading ( ETL ) processes are responsible for the operations taking place in the back stage of a data warehouse architecture . In a high level description of an ETL process , first , the data are extracted from the source data stores that can be On-Line Transaction Processing ( OLTP ) or legacy systems , files under any format , web pages , various kinds of documents ( e.g. , spreadsheets and text documents ) or even data coming in a streaming fashion .
Definition extraction is the task to identify definitional sentences automatically from unstructured text . The task can be used in the aspects of ontology generation , relation extraction and question answering .
The Case of Indirect Taxes.- 10 - First Workshop on Search Techniques for Constraint Satisfaction ( STCS 2007).- Efficient and Tight Upper Bounds for Haplotype Inference by Pure Parsimony Using Delayed Haplotype Selection.- GRASPER.- 11 - Second Workshop on Text Mining and Applications ( TEMA 2007).- Text Segmentation Using Context Overlap.- Automatic Extraction of Definitions in Portuguese : A Rule-Based Approach.- N-Grams and Morphological Normalization in Text Classification : A Comparison on a Croatian-English Parallel Corpus.- Detection of Strange and Wrong Automatic Part-of-Speech Tagging.- New Techniques for Relevant Word Ranking and Extraction .
During the last few years , a lot of researches have focused on automatic definition extraction in the context of question answering systems . Although , these researches have been conducted for different languages , no research has been proposed for Arabic .
In this paper we present the results of an experiment in automatic concept and definition extraction from written sources of law using relatively simple natural language and standard semantic web technology . The software was tested on six laws from the tax domain .
So in this study an semi-automatic building approach of domain ontology based on text mining is brought forward , which is to extract concepts , concept definition and relationships between concepts from textbooks or scientific materials with text-oriented intelligent information processing technology and with the help of subject experts and knowledge engineers . This approach is constituted of the selection of document materials , the text processing of document materials , the concepts relation marking , the formal representation and storage and the evaluation of knowledge database , including the technologies of information extraction , Chinese word segmentation , automatic term extraction and automatic term definition extraction . At last , according to the learning resource requirement in Teachers Training of educational technology capability , the authors took the curriculum of Instructional Design as study case and built the domain ontology of instructional design with semi-automatic building approach of domain ontology based on text mining .
In this paper , a terminological framework , both theoretical and methodological , backed by empirical data , is proposed in order to highlight the particular questions to which attention should be paid when conceiving an evaluation scheme for definition extraction ( DE ) in terminology . The premise is that not just any information is relevant to defining a given concept in a given expert domain .
To address those issues , this paper proposes a solution to perform the automatic extraction of definitional patterns from multi-domain definitional sentences of Wikipedia . Our method FIND-SS is modified based on FIND-S algorithm and solves the definition extraction problems of cross-domain corpora . Find-SS adopts a " the more similar the higher priority " scheme to improve the learning performance .
So far , these approaches have been evaluated using different collections and gold standard datasets , which prevented comparative performance assessments . To facilitate future research on the task of identifier definition extraction , we make three contributions . First , we provide an automated evaluation framework , which uses the dataset and gold standard of the NTCIR-11 Math Retrieval Wikipedia task .
However , unlike the biomedical literature , clinical notes have many abbreviations without their full forms available in the text or without standard definitions in dictionaries due to the nature of the documents . This causes difficulties in adapting traditional approaches for abbreviation disambiguation such as classification among fixed candidates or pattern-based definition extraction . Because of this reason , we consider the task as search problem and propose an approach with two steps : a ) exploring possible full form candidates from various resources and b ) choosing most acceptable one among retrieved candidates by ranking .
The soft match includes definition memberhood calculation and similarity calculation based on Vector Space Model , and then combined the two algorithms together . The experiment achieves good results , and offers effective method for the research of term definition extraction .
Joint extraction of entities and relations is an important task in information extraction . To tackle this problem , we firstly propose a novel tagging scheme that can convert the joint extraction task to a tagging problem .
On the other side , in order to obtain large training data for methods of supervised learning , distant supervision are used in previous work whereas largely suffer from noisy labeling problem . To solve these problems , we propose a reinforcement learning framework for joint extraction of entities and relations . First , we construct a relation extractor based on a tagging scheme to extract entities and relations jointly .
Both entity and relation extraction can benefit from being performed jointly , allowing each task to correct the errors of the other . We present a new method for joint entity and relation extraction using a graph we call a " card-pyramid . " This graph compactly encodes all possible entities and relations in a sentence , reducing the task of their joint extraction to jointly labeling its nodes .
We develop a new paradigm for the task of joint entity relation extraction . It first identifies entity spans , then performs a joint inference on entity types and relation types .
State-of-the-art entity relation recognition systems are built using deep recurrent neural networks which often does not capture the symbolic knowledge or the logical constraints in the problem . The main contribution of this paper is an end-to-end neural model for joint entity relation extraction which incorporates a novel loss function . This novel loss function encodes the constraint information in the problem to guide the model training effectively .
T he Arabic Language needs to perform more researches in information extraction domain and hence we introduce this research . The experiment is concerned with extraction entities and entities relation extraction from the Arabic text . We used in our experiment text from Arabic news in Egyptian Arabic newswire .
Joint extraction of entities and their relations from the text is an essential issue in automatic knowledge graph construction , which is also known as the joint extraction of relational triplets . The relational triplets in sentence are complicated , multiple and different relational triplets may have overlaps , which is commonly seen in reality .
We present a novel attention-based recurrent neural network for joint extraction of entity mentions and relations . We show that attention along with long short term memory ( LSTM ) network can extract semantic relations between entity mentions without having access to dependency trees .
We propose a neural network model for joint extraction of named entities and relations between them , without any hand-crafted features . The key contribution of our model is to extend a BiLSTM-CRF-based entity recognition model with a deep biaffine attention layer to model second-order interactions between latent features for relation classification , specifically attending to the role of an entity in a directional relationship .
Furthermore , we incorporate hierarchical multi-head attention mechanisms into the joint extraction model to capture vital semantic information from the available texts . Experiments show that the proposed approach consistently achieves significant improvements on joint extraction task of entities and relations as compared with strong baselines .
However , previous models are not effective or ignore to model this property . In this work , to effectively leverage class ties , we propose to make joint relation extraction with a unified model that integrates convolutional neural network ( CNN ) with a general pairwise ranking framework , in which three novel ranking loss functions are introduced . Additionally , an effective method is presented to relieve the severe class imbalance problem from NR ( not relation ) for model training .
The syndrome-gene relationships are discovered based on the syndrome-disease relationships extracted from TCM literature and the disease-gene relationships in MEDLINE . Based on the bubble-bootstrapping and relation weight computing methods , we have developed a prototype system called MeDisco/3S , which has name entity and relation extraction , and online analytical processing ( OLAP ) capabilities , to perform the integrative mining process . RESULTS We have got about 200,000 syndrome-gene relations , which could help generate syndrome-based gene networks , and help analyze the functional knowledge of genes from syndrome perspective .
We leverage popular tools of Open Information Extraction ( OpenIE ) and dependency parser for this purpose . OpenIE refers to the extraction of entity relations from the open - domain text . In OpenIE , a fact is typically interpreted as a relation triple consisting of ( subject ; predicate ; object ) .
BioConceptVec covers over 400,000 biomedical concepts mentioned in the literature and is of the largest among the publicly available biomedical concept embeddings to date . To evaluate the validity and utility of BioConceptVec , we respectively performed two intrinsic evaluations ( identifying related concepts based on drug-gene and gene-gene interactions ) and two extrinsic evaluations ( protein-protein interaction prediction and drug-drug interaction extraction ) , collectively using over 25 million instances from nine independent datasets ( 17 million instances from six intrinsic evaluation tasks and 8 million instances from three extrinsic evaluation tasks ) , which is , by far , the most comprehensive to our best knowledge . The intrinsic evaluation results demonstrate that BioConceptVec consistently has , by a large margin , better performance than existing concept embeddings in identifying similar and related concepts .
We propose a multi-task learning framework to jointly model relation identification and classification tasks to propagate supervision signals from each other and apply a focal loss to focus training on ambiguous mention pairs . By applying these two strategies , experiments show that our model achieves state-of-the-art F-score on the 2013 drug-drug interaction extraction task .
Since more and more new drug products come into the market , it is difficult to collect such information by manual . We take part in the Drug-Drug Interaction ( DDI ) Extraction from Drug Labels challenge of Text Analysis Conference ( TAC ) 2018 , choosing task1 and task2 to automatically extract DDI related mentions and DDI relations respectively . Instead of regarding task1 as named entity recognition ( NER ) task and regarding task2 as relation extraction ( RE ) task then solving it in a pipeline , we propose a two step joint model to detect DDI and it ’s related mentions jointly .
DrugNerAR , a drug anaphora resolution system is presented to address the problem of co-referring expressions in pharmacological literature . This development is part of a larger and innovative study about automatic drug-drug interaction extraction . Besides , a corpus has been developed in order to analyze the phenomena and evaluate the current approach .
In this thesis , we have conducted a detailed study about various information extraction techniques applied to biomedical domain . Based on this study , we have proposed two different approximations for the extraction of drug-drug interactions from texts . The first approximation proposes a hybrid approach , which combines shallow parsing and pattern matching to extract relations between drugs from biomedical texts .
This paper presents a system for identify generic drug names in biomedical texts . The identification of drug names is the first step of the process involved in the development of a system aimed at the automatic extraction of drug-drug interactions in biomedical texts . A drug-drug interaction occurs when one drug influences the level or activity of another drug .
Abstract Since Drug-drug interactions ( DDIs ) can cause adverse effects when patients take two or more drugs and therefore increase health care costs , the extraction of DDIs is an important research area in patient safety . To improve the performance of Drug – drug interaction extraction ( DDIE ) , we present a novel two-stage method in this paper . It first identifies the positive instances using a feature based binary classifier , and then a Long Short Term Memory ( LSTM ) based classifier is used to classify the positive instances into specific category .
The Drug-Drug Reaction Extraction at NIST TAC 2018 conference aims to extract information on drug reactions from drug labels . In this paper , we describe the PE-TU ’ model participated in mention extraction task .
These heuristics are based on the default PR structure and linguistic expressions signaling temporal and conditional markers . They are integrated in a system for drug extraction from hospital Patient Records ( PRs ) in Bulgarian language . Present evaluation results are summarized as well .
In this study , a method based on co-occurrence is used as the underlying relationship extraction method for its simplicity . It can be replaced by or combined with more advanced methods such as machine learning or natural language processing approaches to further improve the performance of the drug-gene relationship extraction from free text . Our method is not limited to extracting a drug-gene relationship ; it can be generalized to extract other types of relationships when related background knowledge bases exist .
In the biomedical domain , typical entity types include disease , chemical , gene and protein . Biomedical named entity recognition ( BioNER ) is an essential building block of many downstream text mining applications such as extracting drug - drug interactions and disease - treatment relations . BioNER is also used when building a sophisticated biomedical entity search tool that enables users to pose complex queries to search for bio - entities .
While most span errors tend to come from subjective annotations , or can be easily fixed by non - experts , bio - entity errors are difficult to detect , even for biomedical researchers . Also , for biomedical text mining methods , such as drug - drug interaction extraction , span errors can cause minor errors but bio - entity errors could lead to completely different results . In CollaboNet , each expert model is trained on a single entity type dataset , and their training inputs are a concatenation of word embeddings and outputs of the other expert models .
Named Entity Recognition: Resource Constrained Maximum Path Learning logic rules from text using statistical methods for natural language processing Ekstraksi Informasi Halaman Web Menggunakan Pendekatan Bootstrapping pada Ontology-Based Information Extraction Reading between Eye Saccades Information Extraction Detecting concept relations in clinical text: Insights from a state-of-the-art model Artificial sequences and complexity measures Pubmedinfo Crawler: Data Extraction System from PUBMED for Fast Research The Adverse Drug Reactions From Patient Reports in Social Media Project: Protocol for an Evaluation Against a Gold Standard An information extraction framework for legal documents: A case study of Thai Supreme Court verdicts Tasks, domains, and languages Challenges in Data-to-Document Generation DeepWalk: online learning of social representations Covariance Pooling for Facial Expression Recognition Cell-aware Stacked LSTMs for Modeling Sentences Extraction, Transformation, and Loading Definition Extraction with LSTM Recurrent Neural Networks Progress in Artificial Intelligence, 13th Portuguese Conference on Aritficial Intelligence, EPIA 2007, Workshops: GAIW, AIASTS, ALEA, AMITA, BAOSW, BI, CMBSB, IROBOT, MASTA, STCS, and TEMA, Guimarães, Portugal, December 3-7, 2007, Proceedings An Automatic Definition Extraction in Arabic Language Automatic Extraction of Legal Concepts and Definitions Semi-automatic Building Approach of Domain Ontology Based on Text Mining:A Case Study of Building Instructional Design Domain Ontology A Proposal for a Framework to Evaluate Feature Relevance for Terminographic Definitions Automatic Learning Common Definitional Patterns from Multi-domain Wikipedia Pages Evaluating and Improving the Extraction of Mathematical Identifier Definitions Using Candidate Exploration and Ranking for Abbreviation Resolution in Clinical Document Research on Extraction of Term Definition Joint Extraction of Entities and Relations Based on a Novel Graph Scheme Reinforcement Learning for Joint Extraction of Entities and Relations Joint Entity and Relation Extraction Using Card-Pyramid Parsing Joint Type Inference on Entities and Relations via Graph Convolutional Networks Semantic Loss Application to Entity Relation Recognition Information Extraction from Arabic News A Deep Neural Network Model for Joint Entity and Relation Extraction Going out on a limb: Joint Extraction of Entity Mentions and Relations without Dependency Trees End-to-end neural relation extraction using deep biaffine attention Enhancing Joint Entity and Relation Extraction with Language Modeling and Hierarchical Attention Jointly Extracting Relations with Class Ties via Effective Deep Ranking Integrative mining of traditional Chinese medicine literature and MEDLINE for functional gene networks Faithful to the Original: Fact Aware Neural Abstractive Summarization BioConceptVec: Creating and evaluating literature-based biomedical concept embeddings on a large scale Syntax-aware Multi-task Graph Convolutional Networks for Biomedical Relation Extraction Two Step Joint Model for Drug Drug Interaction Extraction DrugNerAR: linguistic rule-based anaphora resolver for drug-drug interaction extraction in pharmacological documents Application of information extraction techniques to pharmacological domain : extracting drug-drug interactions Identifying and annotating generic drug names Drug-drug interaction extraction from biomedical literature using support vector machine and long short term memory networks PE-TU Participation at TAC 2018 Drug-Drug Interaction Extraction from Drug Labels Contextualization in Automatic Extraction of Drugs from Hospital Patient Records A knowledge-driven conditional approach to extract pharmacogenomics specific drug-gene relationships from free text CollaboNet: collaboration of deep neural networks for biomedical named entity recognition
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MUC EMNLP KDD '14 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition Workshops (CVPRW) ACML Encyclopedia of Database Systems (2nd ed.) CCL NLDB JURIX ICDM Workshops CLEF ICHI IJCAI ICANN (2) CoNLL ACL (1) ACL (1) ECIR (1) APWeb/WAIM (1) AAAI LOUHI@EMNLP TAC DTMBIO TAC MIE BMC Bioinformatics
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