Moussab/ORKG-training-evaluation-set huggingface dataset:
Research field: Natural Language Processing
Title: Web services-based text-mining demonstrates broad impacts for interoperability and process simplification
Abstract: The Critical Assessment of Information Extraction systems in Biology (BioCreAtIvE) challenge evaluation tasks collectively represent a community-wide effort to evaluate a variety of text-mining and information extraction systems applied to the biological domain. The BioCreative IV Workshop included five independent subject areas, including Track 3, which focused on named-entity recognition (NER) for the Comparative Toxicogenomics Database (CTD; http://ctdbase.org). Previously, CTD had organized document ranking and NER-related tasks for the BioCreative Workshop 2012; a key finding of that effort was that interoperability and integration complexity were major impediments to the direct application of the systems to CTD's text-mining pipeline. This underscored a prevailing problem with software integration efforts. Major interoperability-related issues included lack of process modularity, operating system incompatibility, tool configuration complexity and lack of standardization of high-level inter-process communications. One approach to potentially mitigate interoperability and general integration issues is the use of Web services to abstract implementation details; rather than integrating NER tools directly, HTTP-based calls from CTD's asynchronous, batch-oriented text-mining pipeline could be made to remote NER Web services for recognition of specific biological terms using BioC (an emerging family of XML formats) for inter-process communications. To test this concept, participating groups developed Representational State Transfer /BioC-compliant Web services tailored to CTD's NER requirements. Participants were provided with a comprehensive set of training materials. CTD evaluated results obtained from the remote Web service-based URLs against a test data set of 510 manually curated scientific articles. Twelve groups participated in the challenge. Recall, precision, balanced F-scores and response times were calculated. Top balanced F-scores for gene, chemical and disease NER were 61, 74 and 51%, respectively. Response times ranged from fractions-of-a-second to over a minute per article. We present a description of the challenge and summary of results, demonstrating how curation groups can effectively use interoperable NER technologies to simplify text-mining pipeline implementation. Database URL: http://ctdbase.org/
Extracted statement — Coarse-grained Entity type: Disease
Research field: Natural Language Processing
Title: An empirical evaluation of resources for the identification of diseases and adverse effects in biomedical literature
Abstract: The mentions of human health perturbations such as the diseases and adverse effects denote a special entity class in the biomedical literature. They help in understanding the underlying risk factors and develop a preventive rationale. The recognition of these named entities in texts through dictionary-based approaches relies on the availability of appropriate terminological resources. Although few resources are publicly available, not all are suitable for the text mining needs. Therefore, this work provides an overview of the well known resources with respect to human diseases and adverse effects such as the MeSH, MedDRA, ICD-10, SNOMED CT, and UMLS. Individual dictionaries are generated from these resources and their performance in recognizing the named entities is evaluated over a manually annotated corpus. In addition, the steps for curating the dictionaries, rule-based acronym disambiguation and their impact on the dictionary performance is discussed. The results show that the MedDRA and UMLS achieve the best recall. Besides this, MedDRA provides an additional benefit of achieving a higher precision. The combination of search results of all the dictionaries achieve a considerably high recall. The corpus is available on http://www.scai.fraunhofer.de/disease-ae-corpus.html
Extracted statement — Concept types: Disease
Research field: Natural Language Processing
Title: Assessing the state of the art in biomedical relation extraction: overview of the BioCreative V chemical-disease relation (CDR) task
Abstract: Manually curating chemicals, diseases and their relationships is significantly important to biomedical research, but it is plagued by its high cost and the rapid growth of the biomedical literature. In recent years, there has been a growing interest in developing computational approaches for automatic chemical-disease relation (CDR) extraction. Despite these attempts, the lack of a comprehensive benchmarking dataset has limited the comparison of different techniques in order to assess and advance the current state-of-the-art. To this end, we organized a challenge task through BioCreative V to automatically extract CDRs from the literature. We designed two challenge tasks: disease named entity recognition (DNER) and chemical-induced disease (CID) relation extraction. To assist system development and assessment, we created a large annotated text corpus that consisted of human annotations of chemicals, diseases and their interactions from 1500 PubMed articles. 34 teams worldwide participated in the CDR task: 16 (DNER) and 18 (CID). The best systems achieved an F-score of 86.46% for the DNER task—a result that approaches the human inter-annotator agreement (0.8875)—and an F-score of 57.03% for the CID task, the highest results ever reported for such tasks. When combining team results via machine learning, the ensemble system was able to further improve over the best team results by achieving 88.89% and 62.80% in F-score for the DNER and CID task, respectively. Additionally, another novel aspect of our evaluation is to test each participating system’s ability to return real-time results: the average response time for each team’s DNER and CID web service systems were 5.6 and 9.3 s, respectively. Most teams used hybrid systems for their submissions based on machining learning. Given the level of participation and results, we found our task to be successful in engaging the text-mining research community, producing a large annotated corpus and improving the results of automatic disease recognition and CDR extraction. Database URL: http://www.biocreative.org/tasks/biocreative-v/track-3-cdr/
Extracted statement — Number of development data mentions: Disease
Research field: Natural Language Processing
Title: Assessing the state of the art in biomedical relation extraction: overview of the BioCreative V chemical-disease relation (CDR) task
Abstract: Manually curating chemicals, diseases and their relationships is significantly important to biomedical research, but it is plagued by its high cost and the rapid growth of the biomedical literature. In recent years, there has been a growing interest in developing computational approaches for automatic chemical-disease relation (CDR) extraction. Despite these attempts, the lack of a comprehensive benchmarking dataset has limited the comparison of different techniques in order to assess and advance the current state-of-the-art. To this end, we organized a challenge task through BioCreative V to automatically extract CDRs from the literature. We designed two challenge tasks: disease named entity recognition (DNER) and chemical-induced disease (CID) relation extraction. To assist system development and assessment, we created a large annotated text corpus that consisted of human annotations of chemicals, diseases and their interactions from 1500 PubMed articles. 34 teams worldwide participated in the CDR task: 16 (DNER) and 18 (CID). The best systems achieved an F-score of 86.46% for the DNER task—a result that approaches the human inter-annotator agreement (0.8875)—and an F-score of 57.03% for the CID task, the highest results ever reported for such tasks. When combining team results via machine learning, the ensemble system was able to further improve over the best team results by achieving 88.89% and 62.80% in F-score for the DNER and CID task, respectively. Additionally, another novel aspect of our evaluation is to test each participating system’s ability to return real-time results: the average response time for each team’s DNER and CID web service systems were 5.6 and 9.3 s, respectively. Most teams used hybrid systems for their submissions based on machining learning. Given the level of participation and results, we found our task to be successful in engaging the text-mining research community, producing a large annotated corpus and improving the results of automatic disease recognition and CDR extraction. Database URL: http://www.biocreative.org/tasks/biocreative-v/track-3-cdr/
Extracted statement — Number of test data mentions: Disease
Research field: Natural Language Processing
Title: Assessing the state of the art in biomedical relation extraction: overview of the BioCreative V chemical-disease relation (CDR) task
Abstract: Manually curating chemicals, diseases and their relationships is significantly important to biomedical research, but it is plagued by its high cost and the rapid growth of the biomedical literature. In recent years, there has been a growing interest in developing computational approaches for automatic chemical-disease relation (CDR) extraction. Despite these attempts, the lack of a comprehensive benchmarking dataset has limited the comparison of different techniques in order to assess and advance the current state-of-the-art. To this end, we organized a challenge task through BioCreative V to automatically extract CDRs from the literature. We designed two challenge tasks: disease named entity recognition (DNER) and chemical-induced disease (CID) relation extraction. To assist system development and assessment, we created a large annotated text corpus that consisted of human annotations of chemicals, diseases and their interactions from 1500 PubMed articles. 34 teams worldwide participated in the CDR task: 16 (DNER) and 18 (CID). The best systems achieved an F-score of 86.46% for the DNER task—a result that approaches the human inter-annotator agreement (0.8875)—and an F-score of 57.03% for the CID task, the highest results ever reported for such tasks. When combining team results via machine learning, the ensemble system was able to further improve over the best team results by achieving 88.89% and 62.80% in F-score for the DNER and CID task, respectively. Additionally, another novel aspect of our evaluation is to test each participating system’s ability to return real-time results: the average response time for each team’s DNER and CID web service systems were 5.6 and 9.3 s, respectively. Most teams used hybrid systems for their submissions based on machining learning. Given the level of participation and results, we found our task to be successful in engaging the text-mining research community, producing a large annotated corpus and improving the results of automatic disease recognition and CDR extraction. Database URL: http://www.biocreative.org/tasks/biocreative-v/track-3-cdr/
Extracted statement — Number of training data mentions: Disease
Research field: Natural Language Processing
Title: Assessing the state of the art in biomedical relation extraction: overview of the BioCreative V chemical-disease relation (CDR) task
Abstract: Manually curating chemicals, diseases and their relationships is significantly important to biomedical research, but it is plagued by its high cost and the rapid growth of the biomedical literature. In recent years, there has been a growing interest in developing computational approaches for automatic chemical-disease relation (CDR) extraction. Despite these attempts, the lack of a comprehensive benchmarking dataset has limited the comparison of different techniques in order to assess and advance the current state-of-the-art. To this end, we organized a challenge task through BioCreative V to automatically extract CDRs from the literature. We designed two challenge tasks: disease named entity recognition (DNER) and chemical-induced disease (CID) relation extraction. To assist system development and assessment, we created a large annotated text corpus that consisted of human annotations of chemicals, diseases and their interactions from 1500 PubMed articles. 34 teams worldwide participated in the CDR task: 16 (DNER) and 18 (CID). The best systems achieved an F-score of 86.46% for the DNER task—a result that approaches the human inter-annotator agreement (0.8875)—and an F-score of 57.03% for the CID task, the highest results ever reported for such tasks. When combining team results via machine learning, the ensemble system was able to further improve over the best team results by achieving 88.89% and 62.80% in F-score for the DNER and CID task, respectively. Additionally, another novel aspect of our evaluation is to test each participating system’s ability to return real-time results: the average response time for each team’s DNER and CID web service systems were 5.6 and 9.3 s, respectively. Most teams used hybrid systems for their submissions based on machining learning. Given the level of participation and results, we found our task to be successful in engaging the text-mining research community, producing a large annotated corpus and improving the results of automatic disease recognition and CDR extraction. Database URL: http://www.biocreative.org/tasks/biocreative-v/track-3-cdr/
Extracted statement — Concept types: diseases
Research field: Natural Language Processing
Title: MS MARCO: A Human Generated MAchine Reading COmprehension Dataset
Abstract: This paper presents our recent work on the design and development of a new, large scale dataset, which we name MS MARCO, for MAchine Reading COmprehension. This new dataset is aimed to overcome a number of well-known weaknesses of previous publicly available datasets for the same task of reading comprehension and question answering. In MS MARCO, all questions are sampled from real anonymized user queries. The context passages, from which answers in the dataset are derived, are extracted from real web documents using the most advanced version of the Bing search engine. The answers to the queries are human generated. Finally, a subset of these queries has multiple answers. We aim to release one million queries and the corresponding answers in the dataset, which, to the best of our knowledge, is the most comprehensive real-world dataset of its kind in both quantity and quality. We are currently releasing 100,000 queries with their corresponding answers to inspire work in reading comprehension and question answering along with gathering feedback from the research community.
Extracted statement — Type of knowledge source: Documents
Research field: Natural Language Processing
Title: A Hierarchical Attention Retrieval Model for Healthcare Question Answering
Abstract: The growth of the Web in recent years has resulted in the development of various online platforms that provide healthcare information services. These platforms contain an enormous amount of information, which could be beneficial for a large number of people. However, navigating through such knowledgebases to answer specific queries of healthcare consumers is a challenging task. A majority of such queries might be non-factoid in nature, and hence, traditional keyword-based retrieval models do not work well for such cases. Furthermore, in many scenarios, it might be desirable to get a short answer that sufficiently answers the query, instead of a long document with only a small amount of useful information. In this paper, we propose a neural network model for ranking documents for question answering in the healthcare domain. The proposed model uses a deep attention mechanism at word, sentence, and document levels, for efficient retrieval for both factoid and non-factoid queries, on documents of varied lengths. Specifically, the word-level cross-attention allows the model to identify words that might be most relevant for a query, and the hierarchical attention at sentence and document levels allows it to do effective retrieval on both long and short documents. We also construct a new large-scale healthcare question-answering dataset, which we use to evaluate our model. Experimental evaluation results against several state-of-the-art baselines show that our model outperforms the existing retrieval techniques.
Extracted statement — Type of knowledge source: Documents
Research field: Natural Language Processing
Title: Analyzing the Dynamics of Research by Extracting Key Aspects of Scientific Papers
Abstract: We present a method for characterizing a research work in terms of its focus, domain of application, and techniques used. We show how tracing these aspects over time provides a novel measure of the influence of research communities on each other. We extract these characteristics by matching semantic extraction patterns, learned using bootstrapping, to the dependency trees of sentences in an article’s
Extracted statement — Concept types: Domain
Research field: Natural Language Processing
Title: The STEM-ECR Dataset: Grounding Scientific Entity References in STEM Scholarly Content to Authoritative Encyclopedic and Lexicographic Sources
Abstract: We introduce the STEM (Science, Technology, Engineering, and Medicine) Dataset for Scientific Entity Extraction, Classification, and Resolution, version 1.0 (STEM-ECR v1.0). The STEM-ECR v1.0 dataset has been developed to provide a benchmark for the evaluation of scientific entity extraction, classification, and resolution tasks in a domain-independent fashion. It comprises abstracts in 10 STEM disciplines that were found to be the most prolific ones on a major publishing platform. We describe the creation of such a multidisciplinary corpus and highlight the obtained findings in terms of the following features: 1) a generic conceptual formalism for scientific entities in a multidisciplinary scientific context; 2) the feasibility of the domain-independent human annotation of scientific entities under such a generic formalism; 3) a performance benchmark obtainable for automatic extraction of multidisciplinary scientific entities using BERT-based neural models; 4) a delineated 3-step entity resolution procedure for human annotation of the scientific entities via encyclopedic entity linking and lexicographic word sense disambiguation; and 5) human evaluations of Babelfy returned encyclopedic links and lexicographic senses for our entities. Our findings cumulatively indicate that human annotation and automatic learning of multidisciplinary scientific concepts as well as their semantic disambiguation in a wide-ranging setting as STEM is reasonable.
Extracted statement — Data domains: Engineering
Research field: Natural Language Processing
Title: SemEval-2020 Task 3: Graded Word Similarity in Context
Abstract: This paper presents the Graded Word Similarity in Context (GWSC) task which asked participants to predict the effects of context on human perception of similarity in English, Croatian, Slovene and Finnish. We received 15 submissions and 11 system description papers. A new dataset (CoSimLex) was created for evaluation in this task: it contains pairs of words, each annotated within two different contexts. Systems beat the baselines by significant margins, but few did well in more than one language or subtask. Almost every system employed a Transformer model, but with many variations in the details: WordNet sense embeddings, translation of contexts, TF-IDF weightings, and the automatic creation of datasets for fine-tuning were all used to good effect.
Extracted statement — Language: English
Research field: Natural Language Processing
Title: A Hierarchical Attention Retrieval Model for Healthcare Question Answering
Abstract: The growth of the Web in recent years has resulted in the development of various online platforms that provide healthcare information services. These platforms contain an enormous amount of information, which could be beneficial for a large number of people. However, navigating through such knowledgebases to answer specific queries of healthcare consumers is a challenging task. A majority of such queries might be non-factoid in nature, and hence, traditional keyword-based retrieval models do not work well for such cases. Furthermore, in many scenarios, it might be desirable to get a short answer that sufficiently answers the query, instead of a long document with only a small amount of useful information. In this paper, we propose a neural network model for ranking documents for question answering in the healthcare domain. The proposed model uses a deep attention mechanism at word, sentence, and document levels, for efficient retrieval for both factoid and non-factoid queries, on documents of varied lengths. Specifically, the word-level cross-attention allows the model to identify words that might be most relevant for a query, and the hierarchical attention at sentence and document levels allows it to do effective retrieval on both long and short documents. We also construct a new large-scale healthcare question-answering dataset, which we use to evaluate our model. Experimental evaluation results against several state-of-the-art baselines show that our model outperforms the existing retrieval techniques.
Extracted statement — Question Types: Factoid
Research field: Natural Language Processing
Title: Question Answering Benchmarks for Wikidata
Abstract: Wikidata is becoming an increasingly important knowledge base whose usage is spreading in the research community. However, most question answering systems evaluation datasets rely on Freebase or DBpedia. We present two new datasets in order to train and benchmark QA systems over Wikidata. The first is a translation of the popular SimpleQuestions dataset to Wikidata, the second is a dataset created by collecting user feedbacks.
Extracted statement — Knowledge Base: Freebase
Research field: Natural Language Processing
Title: Large-scale semantic parsing via schema matching and lexicon extension
Abstract: Supervised training procedures for semantic parsers produce high-quality semantic parsers, but they have difficulty scaling to large databases because of the sheer number of logical constants for which they must see labeled training data. We present a technique for developing semantic parsers for large databases based on a reduction to standard supervised training algorithms, schema matching, and pattern learning. Leveraging techniques from each of these areas, we develop a semantic parser for Freebase that is capable of parsing questions with an F1 that improves by 0.42 over a purely-supervised learning algorithm.
Extracted statement — Type of knowledge source: Freebase