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Background: In the healthcare domain today, despite the substantial adoption of electronic health information systems, a significant proportion of medical reports still exist in paper-based formats. As a result, there is a significant demand for the digitization of information from these paper-based reports. However, the digitization of paper-based laboratory reports into a structured data format can be challenging due to their non-standard layouts, which includes various data types such as text, numeric values, reference ranges, and units. Therefore, it is crucial to develop a highly scalable and lightweight technique that can effectively identify and extract information from laboratory test reports and convert them into a structured data format for downstream tasks. Methods: We developed an end-to-end Natural Language Processing (NLP)-based pipeline for extracting information from paper-based laboratory test reports. Our pipeline consists of two main modules: an optical character recognition (OCR) module and an information extraction (IE) module. The OCR module is applied to locate and identify text from scanned laboratory test reports using state-of-the-art OCR algorithms. The IE module is then used to extract meaningful information from the OCR results to form digitalized tables of the test reports. The IE module consists of five sub-modules, which are time detection, headline position, line normalization, Named Entity Recognition (NER) with a Conditional Random Fields (CRF)-based method, and step detection for multi-column. Finally, we evaluated the performance of the proposed pipeline on 153 laboratory test reports collected from Peking University First Hospital (PKU1). Results: In the OCR module, we evaluate the accuracy of text detection and recognition results at three different levels and achieved an averaged accuracy of 0.93. In the IE module, we extracted four laboratory test entities, including test item name, test result, test unit, and reference value range. The overall F1 score is 0.86 on the 153 laboratory test reports collected from PKU1. With a single CPU, the average inference time of each report is only 0.78 s. Conclusion: In this study, we developed a practical lightweight pipeline to digitalize and extract information from paper-based laboratory test reports in diverse types and with different layouts that can be adopted in real clinical environments with the lowest possible computing resources requirements. The high evaluation performance on the real-world hospital dataset validated the feasibility of the proposed pipeline. [ABSTRACT FROM AUTHOR]

Keyword extraction is the task of identifying important terms or phrase that are most representative of the source document. Although the process of automatic extraction of keywords from title is an old method, it was mainly for extraction from a single web document. Our approach differs from previous research works on keyword extraction in several aspects. For those who are non-expert of the scientific fields, understating scientific research trends is difficult. The purpose of this study is to develop an automatic method of obtaining overviews of a scientific field for non-experts by capturing research trends. This empirical study excavates significant term extraction using Natural Language Processing (NLP) tools. More than 15000 titles saved in a .csv file was our dataset and scripts written in Python were our process to compare how far significant terms of scientific title corpus are similar or different to the terms available in the abstract of that same scientific article corpus. A light-weight unsupervised title extractor, Yet Another Keyword Extractor (YAKE) was used to extract the results. Based on our analysis, it can be concluded that these algorithms can be used for other fields too by the non-experts of that subject field to perform automatic extraction of significant words and understanding trends. Our algorithm could be a solution to reduce the labour-intensive manual indexing process. [ABSTRACT FROM AUTHOR]

Background: A huge amount of research is carried out nowadays in Artificial Intelligence to propose automated ways to analyse medical data with the aim to support doctors in delivering medical diagnoses. However, a main issue of these approaches is the lack of transparency and interpretability of the achieved results, making it hard to employ such methods for educational purposes. It is therefore necessary to develop new frameworks to enhance explainability in these solutions. Results: In this paper, we present a novel full pipeline to generate automatically natural language explanations for medical diagnoses. The proposed solution starts from a clinical case description associated with a list of correct and incorrect diagnoses and, through the extraction of the relevant symptoms and findings, enriches the information contained in the description with verified medical knowledge from an ontology. Finally, the system returns a pattern-based explanation in natural language which elucidates why the correct (incorrect) diagnosis is the correct (incorrect) one. The main contribution of the paper is twofold: first, we propose two novel linguistic resources for the medical domain (i.e, a dataset of 314 clinical cases annotated with the medical entities from UMLS, and a database of biological boundaries for common findings), and second, a full Information Extraction pipeline to extract symptoms and findings from the clinical cases and match them with the terms in a medical ontology and to the biological boundaries. An extensive evaluation of the proposed approach shows the our method outperforms comparable approaches. Conclusions: Our goal is to offer AI-assisted educational support framework to form clinical residents to formulate sound and exhaustive explanations for their diagnoses to patients. [ABSTRACT FROM AUTHOR]

New discoveries and knowledge are summarized in thousands of published papers per year per scientific domain, making it incomprehensible for scientists to account for all available knowledge relevant for their studies. In this paper, we present ACCORDION (ACCelerating and Optimizing model RecommenDatIONs), a novel methodology and an expert system that retrieves and selects relevant knowledge from literature and databases to recommend models with correct structure and accurate behavior, enabling mechanistic explanations and predictions, and advancing understanding. ACCORDION introduces an approach that integrates knowledge retrieval, graph algorithms, clustering, simulation, and formal analysis. Here, we focus on biological systems, although the proposed methodology is applicable in other domains. We used ACCORDION in nine benchmark case studies and compared its performance with other previously published tools. We show that ACCORDION is: comprehensive, retrieving relevant knowledge from a range of literature sources through machine reading engines; very effective, reducing the error of the initial baseline model by more than 80%, recommending models that closely recapitulate desired behavior, and outperforming previously published tools; selective, recommending only the most relevant, contextspecific, and useful subset (15%-20%) of candidate knowledge in literature; diverse, accounting for several distinct criteria to recommend more than one solution, thus enabling alternative explanations or intervention directions. [ABSTRACT FROM AUTHOR]

Due to popular successes (e.g., ChatGPT) Artificial Intelligence (AI) is on everyone's lips today. When advances in biotechnology are combined with advances in AI unprecedented new potential solutions become available. This can help with many global problems and contribute to important Sustainability Development Goals. Current examples include Food Security, Health and Well-being, Clean Water, Clean Energy, Responsible Consumption and Production, Climate Action, Life below Water, or protect, restore and promote sustainable use of terrestrial ecosystems, sustainably manage forests, combat desertification, and halt and reverse land degradation and halt biodiversity loss. AI is ubiquitous in the life sciences today. Topics include a wide range from machine learning and Big Data analytics, knowledge discovery and data mining, biomedical ontologies, knowledge-based reasoning, natural language processing, decision support and reasoning under uncertainty, temporal and spatial representation and inference, and methodological aspects of explainable AI (XAI) with applications of biotechnology. In this pre-Editorial paper, we provide an overview of open research issues and challenges for each of the topics addressed in this special issue. Potential authors can directly use this as a guideline for developing their paper. • This pre-Editorial provides an overview of some hot topics in AI for life. • The benefit for the reader is to get a short, crisp, concise intro into AI. • Authors interested in this Special Issue will get a scope of topics. • The take away message is that in the future no biotechnology can do without AI. [ABSTRACT FROM AUTHOR]

Relational triple extraction, a fundamental procedure in natural language processing knowledge graph construction, assumes a crucial and irreplaceable role in the domain of academic research related to information extraction. In this paper, we propose a Double-Headed Entities and Relations Prediction (DERP) framework, which divides the entity recognition process into two stages: head entity recognition and tail entity recognition, using the obtained head and tail entities as inputs. By utilizing the corresponding relation and the corresponding entity, the DERP framework further incorporates a triple prediction module to improve the accuracy and completeness of the joint relation triple extraction. We conducted experiments on two English datasets, NYT and WebNLG, and two Chinese datasets, DuIE2.0 and CMeIE-V2, and compared the English dataset experimental results with those derived from ten baseline models. The experimental results demonstrate the effectiveness of our proposed DERP framework for triple extraction. [ABSTRACT FROM AUTHOR]

The mining of Tweets to develop datasets on recent issues, global challenges, pandemics, virus outbreaks, emerging technologies, and trending matters has been of significant interest to the scientific community in the recent past, as such datasets serve as a rich data resource for the investigation of different research questions. Furthermore, the virus outbreaks of the past, such as COVID-19, Ebola, Zika virus, and flu, just to name a few, were associated with various works related to the analysis of the multimodal components of Tweets to infer the different characteristics of conversations on Twitter related to these respective outbreaks. The ongoing outbreak of the monkeypox virus, declared a Global Public Health Emergency (GPHE) by the World Health Organization (WHO), has resulted in a surge of conversations about this outbreak on Twitter, which is resulting in the generation of tremendous amounts of Big Data. There has been no prior work in this field thus far that has focused on mining such conversations to develop a Twitter dataset. Furthermore, no prior work has focused on performing a comprehensive analysis of Tweets about this ongoing outbreak. To address these challenges, this work makes three scientific contributions to this field. First, it presents an open-access dataset of 556,427 Tweets about monkeypox that have been posted on Twitter since the first detected case of this outbreak. A comparative study is also presented that compares this dataset with 36 prior works in this field that focused on the development of Twitter datasets to further uphold the novelty, relevance, and usefulness of this dataset. Second, the paper reports the results of a comprehensive analysis of the Tweets of this dataset. This analysis presents several novel findings; for instance, out of all the 34 languages supported by Twitter, English has been the most used language to post Tweets about monkeypox, about 40,000 Tweets related to monkeypox were posted on the day WHO declared monkeypox as a GPHE, a total of 5470 distinct hashtags have been used on Twitter about this outbreak out of which #monkeypox is the most used hashtag, and Twitter for iPhone has been the leading source of Tweets about the outbreak. The sentiment analysis of the Tweets was also performed, and the results show that despite a lot of discussions, debate, opinions, information, and misinformation, on Twitter on various topics in this regard, such as monkeypox and the LGBTQI+ community, monkeypox and COVID-19, vaccines for monkeypox, etc., "neutral" sentiment was present in most of the Tweets. It was followed by "negative" and "positive" sentiments, respectively. Finally, to support research and development in this field, the paper presents a list of 50 open research questions related to the outbreak in the areas of Big Data, Data Mining, Natural Language Processing, and Machine Learning that may be investigated based on this dataset. [ABSTRACT FROM AUTHOR]

Problem solving applications require users to exercise caution in their data usage practices. Prior to installing these applications, users are encouraged to read and comprehend the terms of service, which address important aspects such as data privacy, processes, and policies (referred to as information elements). However, these terms are often lengthy and complex, making it challenging for users to fully grasp their content. Additionally, existing transparency analytics tools typically rely on the manual extraction of information elements, resulting in a time-consuming process. To address these challenges, this paper proposes a novel approach that combines information visualization and machine learning analyses to automate the retrieval of information elements. The methodology involves the creation and labeling of a dataset derived from multiple software terms of use. Machine learning models, including naïve Bayes, BART, and LSTM, are utilized for the classification of information elements and text summarization. Furthermore, the proposed approach is integrated into our existing visualization tool TranspVis to enable the automatic detection and display of software information elements. The system is thoroughly evaluated using a database-connected tool, incorporating various metrics and expert opinions. The results of our study demonstrate the promising potential of our approach, serving as an initial step in this field. Our solution not only addresses the challenge of extracting information elements from complex terms of service but also provides a foundation for future research in this area. [ABSTRACT FROM AUTHOR]

Natural language processing (NLP) technology has played a pivotal role in health monitoring as an important artificial intelligence method. As a key technology in NLP, relation triplet extraction is closely related to the performance of health monitoring. In this paper, a novel model is proposed for joint extraction of entities and relations, combining conditional layer normalization with the talking-head attention mechanism to strengthen the interaction between entity recognition and relation extraction. In addition, the proposed model utilizes position information to enhance the extraction accuracy of overlapping triplets. Experiments on the Baidu2019 and CHIP2020 datasets demonstrate that the proposed model can effectively extract overlapping triplets, which leads to significant performance improvements compared with baselines. [ABSTRACT FROM AUTHOR]

Entity relationship extraction is one of the key areas of information extraction and is an important research content in the field of natural language processing. Based on past research, this paper proposes a combined extraction model based on a multi-headed attention neural network. Based on the BERT training model architecture, this paper extracts textual entities and relations tasks. At the same time, it integrates the naming entity feature, the terminology labeling characteristics, and the training relationship. The multi-attention mechanism and improved neural structures are added to the model to enhance the characteristic extraction capacity of the model. By studying the parameters of the multi-head attention mechanism, it is shown that the optimal parameters of the multi-head attention are h = 8, dv = 16, and the classification effect of the model is the best at this time. After experimental analysis, comparing the traditional text entity relationship extraction model and the multi-head attention neural network joint extraction model, the model entity relationship extraction effect was evaluated from the aspects of comprehensive evaluation index F1, accuracy rate P, and system time consumed. Experiments show: First, in the accuracy indicator, Xception performance is best, reaching 87.7%, indicating that the model extraction feature effect is enhanced. Second, with the increase of the number of iterative times, the verification set curve and the training set curve have increased to 96% and 98%, respectively, and the model has a strong generalization ability. Third, the model completes the extraction of all data in the test set in 1005 ms, which is an acceptable speed. Therefore, the model test results in this article are good, with a strong practical value. [ABSTRACT FROM AUTHOR]

Background: Analyzing the unstructured textual data contained in electronic health records (EHRs) has always been a challenging task. Word embedding methods have become an essential foundation for neural network-based approaches in natural language processing (NLP), to learn dense and low-dimensional word representations from large unlabeled corpora that capture the implicit semantics of words. Models like Word2Vec, GloVe or FastText have been broadly applied and reviewed in the bioinformatics and healthcare fields, most often to embed clinical notes or activity and diagnostic codes. Visualization of the learned embeddings has been used in a subset of these works, whether for exploratory or evaluation purposes. However, visualization practices tend to be heterogeneous, and lack overall guidelines.Objective: This scoping review aims to describe the methods and strategies used to visualize medical concepts represented using word embedding methods. We aim to understand the objectives of the visualizations and their limits.Methods: This scoping review summarizes different methods used to visualize word embeddings in healthcare. We followed the methodology proposed by Arksey and O'Malley (Int J Soc Res Methodol 8:19-32, 2005) and by Levac et al. (Implement Sci 5:69, 2010) to better analyze the data and provide a synthesis of the literature on the matter.Results: We first obtained 471 unique articles from a search conducted in PubMed, MedRxiv and arXiv databases. 30 of these were effectively reviewed, based on our inclusion and exclusion criteria. 23 articles were excluded in the full review stage, resulting in the analysis of 7 papers that fully correspond to our inclusion criteria. Included papers pursued a variety of objectives and used distinct methods to evaluate their embeddings and to visualize them. Visualization also served heterogeneous purposes, being alternatively used as a way to explore the embeddings, to evaluate them or to merely illustrate properties otherwise formally assessed.Conclusions: Visualization helps to explore embedding results (further dimensionality reduction, synthetic representation). However, it does not exhaust the information conveyed by the embeddings nor constitute a self-sustaining evaluation method of their pertinence. [ABSTRACT FROM AUTHOR]

Geological reports are frequently used by geologists involved in geological surveys and scientific research to record the results and outcomes of geological surveys. With such a rich data source, a substantial amount of knowledge has yet to be mined and analyzed. This paper focuses on automatically information extraction from geological reports, namely, geological named entity recognition. Geological named entity recognition has an important role in data mining, knowledge discovery and Knowledge graph construction. Existing general named entity recognition models/tools are limited in the domain of geoscience due to the various language irregularities associated with geological text, such as informal sentence structures, several domain‐geoscience words, large character lengths and multiple combinations of independent words. We present Bidirectional encoder representations from transformers (BERT)‐(Bidirectional gated recurrent unit network) BiGRU‐ (Conditional random field) CRF, which is a deep learning‐based geological named entity recognition model that is designed specifically with these linguistic irregularities in mind. Based on the pretrained language model, an integrated deep learning model incorporating BERT, BiGRU and CRF is constructed to obtain character vectors rich in semantic information through the BERT pretrained language model to alleviate for the lack of specificity of static word vectors (e.g., word2vec) and to improve the extraction capability of complex geological entities. We demonstrate our proposed model by applying it to four test datasets, including a geoscience NER data set from regional geological reports, and by comparing its performance with those of five baseline models. Plain Language Summary: Geological named entity recognition has an important role in information extraction and knowledge discovery. This paper presents BERT‐BiGRU‐CRF, which is a deep learning‐based geological named entity recognition model that is designed specifically with these linguistic irregularities in mind. We hope that our approach will serve as an alternative method that deserves further study. Key Points: A named entity recognition model based on BERT‐BiGRU‐CRF is proposed and a set of detailed experimental tests on domain data setOur model is compared in detail with four other mainstream models, and experiments demonstrate that our model obtains better performanceWe share the source code of BERT‐BiGRU‐CRF and the annotated test data [ABSTRACT FROM AUTHOR]

Archaeological site text is the main carrier of archaeological data at present, which contains rich information. How to efficiently extract useful knowledge from the massive unstructured archaeological site texts is of great significance for the mining and reuse of archaeological information. According to the site information (such as name, location, cultural type, dynasty, etc.) recorded in the Chinese archaeological site text, this paper combines deep learning and natural language processing techniques to study the information extraction method for automatically obtaining the spatio-temporal information of sites. The initial construction of the corpus of Chinese archaeological site text is completed for the first time, and the corpus is input into the Bidirectional Long Short-Term Memory with Conditional Random Fields (BiLSTM-CRF) entity recognition model and Bidirectional Gated Recurrent Units with Dual Attention (BiGRU-Dual Attention) relationship extraction model for training. The F1 values of BiLSTM-CRF model and BiGRU-Dual Attention model on the test set reach 87.87% and 88.05%, respectively. The study demonstrates that the information extraction method proposed in this paper is feasible for the Chinese archaeological site texts, which promotes the establishment of knowledge graphs in archaeology and provides new methods and ideas for the development of information mining technology in archaeology. [ABSTRACT FROM AUTHOR]

The text matching is a basic task of NLP and is important for tasks such as text retrieval, question answering, and so forth. The development of pre‐trained language models has promoted the progress of text matching tasks. However, due to the natural particularity of Chinese characters and expressions, the Chinese text matching tasks still have problems such as word segmentation difficulty, serious semantic loss, and model instability. In this paper, we propose the DAINet model, which includes DMM, AA and IO modules. We use the Dynamic Multi‐Mask module (DMM) to enhance the completeness of word segmentation. Then we use the Augmented Adversarial module (AA) to further extraction of semantic information. Finally, we use the Integrated Output module (IO) for a more stable output. We conducted experiments on LCQMC, BQ and Xiaobu datasets and compared the results with seven strong baseline models. The results showed that DAINet model made great improvement, including improving ACC value of BQ dataset to 86.0%+0.8%, AUC value to 93.9%+0.8%, ACC value of LCQMC dataset to 88.7%+1.1% and AUC value to 97.2%+1.0%. The ACC value of Xiaobu dataset was improved to 83.2%+1.3% and the AUC value was improved to 91.7%+2.2%. Further ablation experiment results show that the proposed DMM, AA and IO modules have good adaptability and improvement over existing models. [ABSTRACT FROM AUTHOR]

Recent advances in Artificial Intelligence (AI) have sparked renewed interest in its potential to improve education. However, AI is a loose umbrella term that refers to a collection of methods, capabilities, and limitations--many of which are often not explicitly articulated by researchers, education technology companies, or other AI developers. In this paper, we seek to clarify what "AI" is and the potential it holds to both advance and hamper educational opportunities that may improve the human condition. We offer a basic introduction to different methods and philosophies underpinning AI, discuss recent advances, explore applications to education, and highlight key limitations and risks. We conclude with a set of questions that educationalists may ask as they encounter AI in their research and practice. Our hope is to make often jargon-laden terms and concepts accessible, so that all are equipped to understand, interrogate, and ultimately shape the development of human-centered AI in education. [ABSTRACT FROM AUTHOR]

According to the natural language perspective, UGC has been significantly used for the screening of key nodes in knowledge discovery and strategic investment. This article presents a new research framework that is proposed for the decomposition of UGC knowledge feature extraction into topic recognition and language analysis, mainly. For visual analysis of associated topics, the LDAvis approach is utilized. Then, risk features of UGC knowledge are assigned according to language attribution. Based on previous studies, the risk attribute lexicon is further updated by judging semantic distance through word vectors. This research uses platform data and individual stock data as samples for subject recognition and knowledge feature extraction. A regression model is constructed based on the panel data after natural language processing to verify the feedback effect of the market at strategic risk measurement. It can be found from the conclusion that the change in market behavior is regular and correlates with the change in the UGC risk degree of individual stocks. The purpose of this paper is to examine the value of UGC in investment decision-making from the perspective of knowledge discovery. The research content can provide a reference for data mining, fintech, strategic risk monitoring, and other related works. [ABSTRACT FROM AUTHOR]

Social media (e.g., Twitter and Facebook) can be regarded as vital sources of information during disasters to improve situational awareness (SA) and disaster management since they play a significant role in the rapid spread of information in the event of a disaster. Due to the volume of data is far beyond the capabilities of manual examination, existing works utilize natural language processing methods based on keywords, or classification models relying on features derived from text and other metadata (e.g., user profiles) to extract social media data contributing to SA and automatically categorize them into the relevant classes (e.g., damage and donation). However, the design of the classification schema and the associated information extraction methods are far less than straightforward and highly depend on: (1) the event type, (2) the study or analysis purpose, and (3) the social media platform used. To this end, this paper reviews the literature for extracting social media data and provides an overview of classification schemas that have been used to assess SA in events involving natural hazards from five different analytical perspectives (content, temporal, user, sentiment, and spatiotemporal) by discussing the prevalent topic categories, disaster event types, purpose of studies, and platforms utilized from each schema. Finally, this paper summarizes classification methods, and platforms that are most commonly used for each disaster event type, and outlines a research agenda with recommendations for future innovations. [ABSTRACT FROM AUTHOR]

Background: Manually extracted data points from health records are collated on an institutional, provincial, and national level to facilitate clinical research. However, the labour-intensive clinical chart review process puts an increasing burden on healthcare system budgets. Therefore, an automated information extraction system is needed to ensure the timeliness and scalability of research data.Methods: We used a dataset of 100 synoptic operative and 100 pathology reports, evenly split into 50 reports in training and test sets for each report type. The training set guided our development of a Natural Language Processing (NLP) extraction pipeline system, which accepts scanned images of operative and pathology reports. The system uses a combination of rule-based and transfer learning methods to extract numeric encodings from text. We also developed visualization tools to compare the manual and automated extractions. The code for this paper was made available on GitHub.Results: A test set of 50 operative and 50 pathology reports were used to evaluate the extraction accuracies of the NLP pipeline. Gold standard, defined as manual extraction by expert reviewers, yielded accuracies of 90.5% for operative reports and 96.0% for pathology reports, while the NLP system achieved overall 91.9% (operative) and 95.4% (pathology) accuracy. The pipeline successfully extracted outcomes data pertinent to breast cancer tumor characteristics (e.g. presence of invasive carcinoma, size, histologic type), prognostic factors (e.g. number of lymph nodes with micro-metastases and macro-metastases, pathologic stage), and treatment-related variables (e.g. margins, neo-adjuvant treatment, surgical indication) with high accuracy. Out of the 48 variables across operative and pathology codebooks, NLP yielded 43 variables with F-scores of at least 0.90; in comparison, a trained human annotator yielded 44 variables with F-scores of at least 0.90.Conclusions: The NLP system achieves near-human-level accuracy in both operative and pathology reports using a minimal curated dataset. This system uniquely provides a robust solution for transparent, adaptable, and scalable automation of data extraction from patient health records. It may serve to advance breast cancer clinical research by facilitating collection of vast amounts of valuable health data at a population level. [ABSTRACT FROM AUTHOR]

With the increasing popularity of open-source platforms, software data is easily available from various open-source tools like GitHub, CVS, SVN, etc. More than 80 percent of the data present in them is unstructured. Mining data from these repositories helps project managers, developers and businesses, in getting interesting insights. Most of the software artefacts present in these repositories are in the natural language form, which makes natural language processing (NLP) an important part of mining to get the useful results. The paper reviews the application of NLP techniques in the field of Mining Software Repositories (MSR). The paper mainly focuses on sentiment analysis, summarization, traceability, norms mining and mobile analytics. The paper presents the major NLP works performed in this area by surveying the research papers from 2000 to 2018. The paper firstly describes the major artefacts present in the software repositories where the NLP techniques have been applied. Next, the paper presents some popular open-source NLP tools that have been used to perform NLP tasks. Later the paper discusses, in brief, the research state of NLP in MSR field. The paper also lists down the various challenges along with the pointers for future work in this field of research and finally the conclusion. [ABSTRACT FROM AUTHOR]

Large volumes of publications are being produced in biomedical sciences nowadays with ever-increasing speed. To deal with the large amount of unstructured text data, effective natural language processing (NLP) methods need to be developed for various tasks such as document classification and information extraction. BioCreative Challenge was established to evaluate the effectiveness of information extraction methods in biomedical domain and facilitate their development as a community-wide effort. In this paper, we summarize our work and what we have learned from the latest round, BioCreative Challenge VII, where we participated in all five tracks. Overall, we found three key components for achieving high performance across a variety of NLP tasks: (1) pre-trained NLP models; (2) data augmentation strategies and (3) ensemble modelling. These three strategies need to be tailored towards the specific tasks at hands to achieve high-performing baseline models, which are usually good enough for practical applications. When further combined with task-specific methods, additional improvements (usually rather small) can be achieved, which might be critical for winning competitions. Database URL : https://doi.org/10.1093/database/baac066 [ABSTRACT FROM AUTHOR]

Background: A lot of medical mentions can be extracted from a huge amount of medical texts. In order to make use of these medical mentions, a prerequisite step is to link those medical mentions to a medical domain knowledge base (KB). This linkage of mention to a well-defined, unambiguous KB is a necessary part of the downstream application such as disease diagnosis and prescription of drugs. Such demand becomes more urgent in colloquial and informal situations like online medical consultation, where the medical language is more casual and vaguer. In this article, we propose an unsupervised method to link the Chinese medical symptom mentions to the ICD10 classification in a colloquial background.Methods: We propose an unsupervised entity linking model using multi-instance learning (MIL). Our approach builds on a basic unsupervised entity linking method (named BEL), which is an embedding similarity-based EL model in this paper, and uses MIL training paradigm to boost the performance of BEL. First, we construct a dataset from an unlabeled large-scale Chinese medical consultation corpus with the help of BEL. Subsequently, we use a variety of encoders to obtain the representations of mention-context and the ICD10 entities. Then the representations are fed into a ranking network to score candidate entities.Results: We evaluate the proposed model on the test dataset annotated by professional doctors. The evaluation results show that our method achieves 60.34% accuracy, exceeding the fundamental BEL by 1.72%.Conclusions: We propose an unsupervised entity linking method to the entity linking in the medical domain, using MIL training manner. We annotate a test set for evaluation. The experimental results show that our model behaves better than the fundamental model BEL, and provides an insight for future research. [ABSTRACT FROM AUTHOR]

Existing construction monitoring systems rely on designated personnel to compare a planned procedure in the instructional documents with an execution procedure on the jobsite. It requires major human efforts and is time-consuming, costly, and human error–prone. To reduce manual efforts in collecting information from construction procedural documents, selecting appropriate sensing techniques to collect data on the jobsite, and giving in-time feedback for progress monitoring and compliance checking, the authors: (1) proposed a semantic rule-based information extraction (IE) method to extract construction execution steps from construction procedural documents automatically; (2) developed a construction procedure and data collection (CPDC) ontology to classify construction site information and provide guidance on selecting sensing techniques for collecting jobsite data based on the extracted information; and (3) proposed a construction procedural data integration (CPDI) framework, which could integrate textual data and sensing data to conduct construction execution steps compliance checking automatically. The proposed IE method offers a novel way to retrieve construction activities (e.g., install door and prepare surface) from the construction procedural documents that are an important source of information but were seldom analyzed in previous research. It focuses on extracting construction execution steps, which supports the incorporation of execution sequence information into construction jobsite management. A novel information classification application based on a newly developed CPDC ontology is provided to support IE. The IE results provide a new instrument for selecting sensing techniques based on different construction site data categories. The proposed method is developed to support a targeted unified CPDI framework that integrates the following: natural language processing (NLP) and sensing techniques to automatically extract, analyze, and process both planned procedures from textual data from construction procedural documents and executed procedures from sensing data of construction jobsites. It also can be extended to any domain applications that contain textual information and site activity information that needs to be matched or compared. In this paper, the authors focus on the NLP-based textual information extraction of the construction procedural documents, introduced the detailed steps involved, and proposed a CPDI framework on top of and as an application of the IE method. An experiment was conducted to evaluate the IE method with a set of open-source specifications. Comparing it to a manually developed gold standard, 97.08% precision and 93.23% recall were achieved using the proposed IE method for the extraction of construction execution steps. A qualitative analysis on sensing technique selection based on the IE results was also performed. The proposed IE method can be applied to the automation of construction site management tasks (e.g., construction monitoring) that integrates both textual information and sensing data to support construction decision-makings. It enables the transformation of construction monitoring/control from a human-intensive process to an automated one. [ABSTRACT FROM AUTHOR]

Relation classification is an important semantic processing task in the field of natural language processing (NLP). Data sources generally adopt remote monitoring strategies to automatically generate large-scale training data, which inevitably causes label noise problems. At the same time, another challenge is that important information can appear at any place in the sentence. This paper presents a sentence-level joint relation classification model. The model has two modules: a reinforcement learning (RL) agent and a joint network model. In particular, we combine bidirectional long short-term memory (Bi-LSTM) and attention mechanism as a joint model to process the text features of sentences and classify the relation between two entities. At the same time, we introduce an attention mechanism to discover hidden information in sentences. The joint training of the two modules solves the noise problem in relation extraction, sentence-level information extraction, and relation classification. Experimental results demonstrate that the model can effectively deal with data noise and achieve better relation classification performance at the sentence level. [ABSTRACT FROM AUTHOR]

Background: Controlled vocabularies are fundamental resources for information extraction from clinical texts using natural language processing (NLP). Standard language resources available in the healthcare domain such as the UMLS metathesaurus or SNOMED CT are widely used for this purpose, but with limitations such as lexical ambiguity of clinical terms. However, most of them are unambiguous within text limited to a given clinical specialty. This is one rationale besides others to classify clinical text by the clinical specialty to which they belong.Results: This paper addresses this limitation by proposing and applying a method that automatically extracts Spanish medical terms classified and weighted per sub-domain, using Spanish MEDLINE titles and abstracts as input. The hypothesis is biomedical NLP tasks benefit from collections of domain terms that are specific to clinical subdomains. We use PubMed queries that generate sub-domain specific corpora from Spanish titles and abstracts, from which token n-grams are collected and metrics of relevance, discriminatory power, and broadness per sub-domain are computed. The generated term set, called Spanish core vocabulary about clinical specialties (SCOVACLIS), was made available to the scientific community and used in a text classification problem obtaining improvements of 6 percentage points in the F-measure compared to the baseline using Multilayer Perceptron, thus demonstrating the hypothesis that a specialized term set improves NLP tasks.Conclusion: The creation and validation of SCOVACLIS support the hypothesis that specific term sets reduce the level of ambiguity when compared to a specialty-independent and broad-scope vocabulary. [ABSTRACT FROM AUTHOR]

The recent years have witnessed a rapid increase in the number of scientific articles in biomedical domain. These literature are mostly available and readily accessible in electronic format. The domain knowledge hidden in them is critical for biomedical research and applications, which makes biomedical literature mining (BLM) techniques highly demanding. Numerous efforts have been made on this topic from both biomedical informatics (BMI) and computer science (CS) communities. The BMI community focuses more on the concrete application problems and thus prefer more interpretable and descriptive methods, while the CS community chases more on superior performance and generalization ability, thus more sophisticated and universal models are developed. The goal of this paper is to provide a review of the recent advances in BLM from both communities and inspire new research directions. [ABSTRACT FROM AUTHOR]

A variety of detailed data about geological topics and geoscience knowledge are buried in the geoscience literature and rarely used. Named entity recognition (NER) provides both opportunities and challenges to leverage this wealth of data in the geoscience literature for data analysis and further information extraction. Existing NER models and techniques are mainly based on rule‐based and supervised approaches, and developing such systems requires a costly manual effort. In this paper, we first design a generic stepwise framework for domain‐specific NER. Following this framework, domain‐specific entities and domain‐general words are collected and selected as seed terms. Normalization and grouping processes are then applied to these seed terms for further analysis. A random extraction algorithm based on a unigram language model is used to generate a large‐scale training data set consisting of probabilistically labeled pseudosentences. Each generated sentence is then used as input to the self‐training and learning algorithm. Experimental results on two constructed data sets demonstrate that the proposed model effectively recognizes and identifies geological named entities. Plain Language Summary: Existing entity recognition and classification methods are less functional for automatic geological name entity recognition. In this paper, we propose a stepwise unsupervised approach to geological name entity recognition in geological reports that requires no labeled data. This approach dynamically adapts to extract and identify unseen instances. We hope that our approach will serve as an alternative method that deserves further study. Key Points: Geological named entities are extracted from unstructured Chinese geoscience reports using deep learningThe proposed framework can be easily extended to other subject domains through fine‐tuningA training data set is constructed based on both domain‐specific entities and domain‐general words [ABSTRACT FROM AUTHOR]

Purpose: This paper aims to better understand a large number of papers in the medical domain of Alzheimer's disease (AD) and related diseases using the machine reading approach. Design/methodology/approach: The study uses the topic modeling method to obtain an overview of the field, and employs open information extraction to further comprehend the field at a specific fact level. Findings: Several topics within the AD research field are identified, such as the Human Immunodeficiency Virus (HIV)/Acquired Immune Deficiency Syndrome (AIDS), which can help answer the question of how AIDS/HIV and AD are very different yet related diseases. Research limitations: Some manual data cleaning could improve the study, such as removing incorrect facts found by open information extraction. Practical implications: This study uses the literature to answer specific questions on a scientific domain, which can help domain experts find interesting and meaningful relations among entities in a similar manner, such as to discover relations between AD and AIDS/HIV. Originality/value: Both the overview and specific information from the literature are obtained using two distinct methods in a complementary manner. This combination is novel because previous work has only focused on one of them, and thus provides a better way to understand an important scientific field using data-driven methods. [ABSTRACT FROM AUTHOR]

Sentiment Analysis or in particular social network analysis (SNA) is a new research area which is increased explosively. This domain has become a very active research issue in data mining and natural language processing. Sentiment analysis (opinion mining) consists in analyzing and extracting emotions, opinions or attitudes from product's reviews, movie's reviews, etc., and classify them into classes such as positive, negative and neutral, or extract the degree of importance (polarity). In this paper, we propose a new hybrid approach for classifying tweets into classes based on fuzzy logic and a lexicon based approach using SentiWordnet. Our approach consists in classifying tweets according to three classes: positive, negative or neutral, using SentiWordNet and the fuzzy logic with its three important steps: Fuzzification, Rule Inference/aggregation, and Defuzzification. The dataset of tweets to classify and the result of the classification are stored in the Hadoop Distributed File System (HDFS), and we use the Hadoop MapReduce for the application of our proposal. [ABSTRACT FROM AUTHOR]

Background: Free-text sections of pathology reports contain the most important information from a diagnostic standpoint. However, this information is largely underutilized for computer-based analytics. The vast majority of NLP-based methods lack a capacity to accurately extract complex diagnostic entities and relationships among them as well as to provide an adequate knowledge representation for downstream data-mining applications. Methods: In this paper, we introduce a novel informatics pipeline that extends open information extraction (openIE) techniques with artificial intelligence (AI) based modeling to extract and transform complex diagnostic entities and relationships among them into Knowledge Graphs (KGs) of relational triples (RTs). Results: Evaluation studies have demonstrated that the pipeline's output significantly differs from a random process. The semantic similarity with original reports is high (Mean Weighted Overlap of 0.83). The precision and recall of extracted RTs based on experts' assessment were 0.925 and 0.841 respectively (P <0.0001). Inter-rater agreement was significant at 93.6% and inter-rated reliability was 81.8%. Conclusion: The results demonstrated important properties of the pipeline such as high accuracy, minimality and adequate knowledge representation. Therefore, we conclude that the pipeline can be used in various downstream data-mining applications to assist diagnostic medicine. [ABSTRACT FROM AUTHOR]

Online discussions about software applications and services that take place on web-based communication platforms represent an invaluable knowledge source for diverse software engineering tasks, including requirements elicitation. The amount of research work on developing effective tool-supported analysis methods is rapidly increasing, as part of the so called software analytics. Textual messages in App store reviews, tweets, online discussions taking place in mailing lists and user forums, are processed by combining natural language techniques to filter out irrelevant data; text mining and machine learning algorithms to classify messages into different categories, such as bug report and feature request. Our research objective is to exploit a linguistic technique based on speech-acts for the analysis of online discussions with the ultimate goal of discovering requirements-relevant information. In this paper, we present a revised and extended version of the speech-acts based analysis technique, which we previously presented at CAiSE 2017, together with a detailed experimental characterisation of its properties. Datasets used in the experimental evaluation are taken from a widely used open source software project (161120 textual comments), as well as from an industrial project in the home energy management domain. We make them available for experiment replication purposes. On these datasets, our approach is able to successfully classify messages into Feature/Enhancement and Other, with F-measure of 0.81 and 0.84 respectively. We also found evidence that there is an association between types of speech-acts and categories of issues, and that there is correlation between some of the speech-acts and issue priority, thus motivating further research on the exploitation of our speech-acts based analysis technique in semi-automated multi-criteria requirements prioritisation. [ABSTRACT FROM AUTHOR]

Nowadays, it is really important and crucial to follow the new biomedical knowledge that is presented in scientific literature. To this end, Information Extraction pipelines can help to automatically extract meaningful relations from textual data that further require additional checks by domain experts. In the last two decades, a lot of work has been performed for extracting relations between phenotype and health concepts, however, the relations with food entities which are one of the most important environmental concepts have never been explored. In this study, we propose FooDis, a novel Information Extraction pipeline that employs state-of-the-art approaches in Natural Language Processing to mine abstracts of biomedical scientific papers and automatically suggests potential cause or treat relations between food and disease entities in different existing semantic resources. A comparison with already known relations indicates that the relations predicted by our pipeline match for 90% of the food-disease pairs that are common in our results and the NutriChem database, and 93% of the common pairs in the DietRx platform. The comparison also shows that the FooDis pipeline can suggest relations with high precision. The FooDis pipeline can be further used to dynamically discover new relations between food and diseases that should be checked by domain experts and further used to populate some of the existing resources used by NutriChem and DietRx. • A novel Information Extraction pipeline for mining scientific literature. • Suggestion of cause or treat relations between food and disease entities. • Linking food and disease entities from various knowledge bases. [ABSTRACT FROM AUTHOR]

The paper presents an Object Oriented Analysis and Design (OOAD) approach to modeling, reasoning and a database query based approach to processing and solving addition-subtraction (Add-Sub) type arithmetic Mathematical Word Problems (MWP) of elementary school level. The system identifies and extracts the key entities in a word problem like owners, items and their attributes and quantities, verbs, from all the input sentences, using a rule based Information Extraction (IE) approach based on Semantic Role Labeling (SRL) technique. These information are then stored in predefined templates which are further modeled to represent an MWP in the object-oriented paradigm and processed using query based approach to generate the answer. These kind of applications are based on Natural Language Processing (NLP), Natural Language Understanding (NLU) and Artificial Intelligence (AI), and can be used as intelligent dynamic mathematical tutoring tools as part of E-Learning systems, Learning Management Systems, on-line education, etc. The proposed object oriented mathematical word problem solver can solve arithmetic MWPs involving only addition-subtraction operations and it has produced an accuracy of 94.35% on a subset of the AI2 arithmetic questions dataset. [ABSTRACT FROM AUTHOR]

Abstract Social media, particularly Twitter, is increasingly used to improve resilience during extreme weather events/emergency management situations, including floods: by communicating potential risks and their impacts, and informing agencies and responders. In this paper, we developed a prototype national-scale Twitter data mining pipeline for improved stakeholder situational awareness during flooding events across Great Britain, by retrieving relevant social geodata, grounded in environmental data sources (flood warnings and river levels). With potential users we identified and addressed three research questions to develop this application, whose components constitute a modular architecture for real-time dashboards. First, polling national flood warning and river level Web data sources to obtain at-risk locations. Secondly, real-time retrieval of geotagged tweets, proximate to at-risk areas. Thirdly, filtering flood-relevant tweets with natural language processing and machine learning libraries, using word embeddings of tweets. We demonstrated the national-scale social geodata pipeline using over 420,000 georeferenced tweets obtained between 20 and 29th June 2016. Highlights • Prototype real-time social geodata pipeline for flood events and demonstration dataset. • National-scale flood warnings/river levels set 'at-risk areas' in Twitter API queries. • Monitoring multiple locations (without keywords) retrieved current, geotagged tweets. • Novel application of word embeddings in flooding context identified relevant tweets. • Pipeline extracts tweets to visualise using open-source libraries (SciKit Learn/Gensim). [ABSTRACT FROM AUTHOR]

Background: Free-text sections of pathology reports contain the most important information from a diagnostic standpoint. However, this information is largely underutilized for computer-based analytics. The vast majority of NLP-based methods lack a capacity to accurately extract complex diagnostic entities and relationships among them as well as to provide an adequate knowledge representation for downstream data-mining applications. Methods: In this paper, we introduce a novel informatics pipeline that extends open information extraction (openIE) techniques with artificial intelligence (AI) based modeling to extract and transform complex diagnostic entities and relationships among them into Knowledge Graphs (KGs) of relational triples (RTs). Results: Evaluation studies have demonstrated that the pipeline's output significantly differs from a random process. The semantic similarity with original reports is high (Mean Weighted Overlap of 0.83). The precision and recall of extracted RTs based on experts' assessment were 0.925 and 0.841 respectively (P <0.0001). Inter-rater agreement was significant at 93.6% and inter-rated reliability was 81.8%. Conclusion: The results demonstrated important properties of the pipeline such as high accuracy, minimality and adequate knowledge representation. Therefore, we conclude that the pipeline can be used in various downstream data-mining applications to assist diagnostic medicine. [ABSTRACT FROM AUTHOR]

A phrase is a natural, meaningful, and essential semantic unit. In topic modeling, visualizing phrases for individual topics is an effective way to explore and understand unstructured text corpora. However, from phrase quality and topical cohesion perspectives, the outcomes of existing approaches remain to be improved. Usually, the process of topical phrase mining is twofold: phrase mining and topic modeling. For phrase mining, existing approaches often suffer from order sensitive and inappropriate segmentation problems, which make them often extract inferior quality phrases. For topic modeling, traditional topic models do not fully consider the constraints induced by phrases, which may weaken the cohesion. Moreover, existing approaches often suffer from losing domain terminologies since they neglect the impact of domain-level topical distribution. In this paper, we propose an efficient method for high quality and cohesive topical phrase mining. A high quality phrase should satisfy frequency, phraseness, completeness, and appropriateness criteria. In our framework, we integrate quality guaranteed phrase mining method, a novel topic model incorporating the constraint of phrases, and a novel document clustering method into an iterative framework to improve both phrase quality and topical cohesion. We also describe efficient algorithmic designs to execute these methods efficiently. The empirical verification demonstrates that our method outperforms the state-of-the-art methods from the aspects of both interpretability and efficiency. [ABSTRACT FROM AUTHOR]

Background: Biomedical semantic indexing is important for information retrieval and many other research fields in bioinformatics. It annotates biomedical citations with Medical Subject Headings. In face of unbalanced category distribution in the training data, sampling methods are difficult to apply for semantic indexing task. Results: In this paper, we present a novel deep serial multi-task learning model. The primary task treats the biomedical semantic indexing as a multi-label text classification issue that considers the relations of the labels. The auxiliary task is a regression task that predicts the MeSH number of the citation and provides hints for the network to make it converge faster. The experimental results on the BioASQ-Task5A open dataset show that our model outperforms the state-of-the-art solution "MTI", proposed by the US National Library of Medicine. Further, it not only achieves the highest precision among all the solutions in BioASQ-Task5A but also has faster convergence speed compared with some naive deep learning methods. Conclusions: Rather than parallel in an ordinary multi-task structure, the tasks in our model are serial and tightly coupled. It can achieve satisfied performance without any handcrafted feature. [ABSTRACT FROM AUTHOR]

The BLEU metric has been widely used in NLP for over 15 years to evaluate NLP systems, especially in machine translation and natural language generation. I present a structured review of the evidence on whether BLEU is a valid evaluation technique—in other words, whether BLEU scores correlate with real-world utility and user-satisfaction of NLP systems; this review covers 284 correlations reported in 34 papers. Overall, the evidence supports using BLEU for diagnostic evaluation of MT systems (which is what it was originally proposed for), but does not support using BLEU outside of MT, for evaluation of individual texts, or for scientific hypothesis testing. [ABSTRACT FROM AUTHOR]

[Display omitted] • We attach a top-down path to the feature Pyramid Network (FPN). • We designed a fast table parsing method (GTab). • A novel semantic similarity matching model is designed. • A translation-based graph structure-driven Q&A approach is proposed. The geological reports contain various tables, and can offer mineral element content data and stratum detailed information. Geological tabular information extraction and its semantic fusion with text is of great significance in converting and fusing geological unstructured data into structured knowledge to guide cognitive intelligence analysis in the geoscience domain. While the performance of general tools and existing table structure analysis methods is limited due to the various merged cells and diagonally split table headers. To address this issue, we propose a novel approach based on the improved Mask R-CNN model to identify and parse the forms. The geological table parsing network constructed in this paper consists of two key steps: (1) A cell feature augmentation (CFA) module to learn the contextual features for identifying cells of different sizes. (2) A table parsing method (GTab) to parse the table header cells with split lines. We compare the proposed method with commonly used table parsing methods on our constructed geological table dataset. Our models are easily integrated into a prototype system to provide joint information processing and analysis. [ABSTRACT FROM AUTHOR]

Emotion analysis and emotion cause extraction are key research tasks in natural language processing and public opinion mining. This paper presents a rule-based approach to emotion cause component detection for Chinese micro-blogs. Our research has important scientific values on social network knowledge discovery and data mining. It also has a great potential in analyzing the psychological processes of consumers. Firstly, this paper proposes a rule-based system underlying the conditions that trigger emotions based on an emotional model. Secondly, this paper extracts the corresponding cause events in fine-grained emotions from the results of events, actions of agents and aspects of objects. Meanwhile, it is reasonable to get the proportions of different cause components under different emotions by constructing the emotional lexicon and identifying different linguistic features, and the proposed approach is based on Bayesian probability. Finally, this paper presents the experiments on an emotion corpus of Chinese micro-blogs. The experimental results validate the feasibility of the approach. The existing problems and the further works are also present at the end. [ABSTRACT FROM AUTHOR]

With the spurt of online user-generated contents on web, sentiment analysis has become a very active research issue in data mining and natural language processing. As the most important indicator of sentiment, sentiment words which convey positive and negative polarity are quite instrumental for sentiment analysis. However, most of the existing methods for identifying polarity of sentiment words only consider the positive and negative polarity by the Cantor set, and no attention is paid to the fuzziness of the polarity intensity of sentiment words. In order to improve the performance, we propose a fuzzy computing model to identify the polarity of Chinese sentiment words in this paper. There are three major contributions in this paper. Firstly, we propose a method to compute polarity intensity of sentiment morphemes and sentiment words. Secondly, we construct a fuzzy sentiment classifier and propose two different methods to compute the parameter of the fuzzy classifier. Thirdly, we conduct extensive experiments on four sentiment words datasets and three review datasets, and the experimental results indicate that our model performs better than the state-of-the-art methods. [ABSTRACT FROM AUTHOR]

With the increasing popularity of large scale Knowledge Graph (KG)s, many applications such as semantic analysis, search and question answering need to link entity mentions in texts to entities in KGs. Because of the polysemy problem in natural language, entity disambiguation is thus a key problem in current research. Existing disambiguation methods have considered entity prominence, context similarity and entity-entity relatedness to discriminate ambiguous entities, which are mainly working on document or paragraph level texts containing rich contextual information, and based on lexical matching for computing context similarity. When meeting short texts containing limited contextual information, such as web queries, questions and tweets, those conventional disambiguation methods are not good at handling single entity mention and measuring context similarity. In order to enhance the performance of disambiguation methods based on context similarity with such short texts, we propose SCSNED method for disambiguation based on semantic similarity between contextual words and informative words of entities in KGs. Specially, we exploit the effectiveness of both knowledge-based and corpus-based semantic similarity methods for entity disambiguation with SCSNED. Moreover, we propose a Category2Vec embedding model based on joint learning of word and category embedding, in order to compute word-category similarity for entity disambiguation. We show the effectiveness of these proposed methods with illustrative examples, and evaluate their effectiveness in a comparative experiment for entity disambiguation in real world web queries, questions and tweets. The experimental results have identified the effectiveness of different semantic similarity methods, and demonstrated the improvement of semantic similarity methods in SCSNED and Category2Vec over the conventional context similarity baseline. We further compare the proposed approaches with the state of the art entity disambiguation systems and show the performances of the proposed approaches are among the best performing systems. In addition, one important feature of the proposed approaches using semantic similarity, is the potential application on any existing KGs since they mainly use common features of entity descriptions and categories. Another contribution of the paper is an updated survey on background of entity disambiguation in KGs and semantic similarity methods. [ABSTRACT FROM AUTHOR]

Summary: Second use of clinical data commonly involves annotating biomedical text with terminologies and ontologies. The National Center for Biomedical Ontology Annotator is a frequently used annotation service, originally designed for biomedical data, but not very suitable for clinical text annotation. In order to add new functionalities to the NCBO Annotator without hosting or modifying the original Web service, we have designed a proxy architecture that enables seamless extensions by pre-processing of the input text and parameters, and post processing of the annotations. We have then implemented enhanced functionalities for annotating and indexing free text such as: scoring, detection of context (negation, experiencer, temporality), new output formats and coarse-grained concept recognition (with UMLS Semantic Groups). In this paper, we present the NCBO Annotator+, a Web service which incorporates these new functionalities as well as a small set of evaluation results for concept recognition and clinical context detection on two standard evaluation tasks (Clef eHealth 2017, SemEval 2014). [ABSTRACT FROM AUTHOR]

Abstract: In this paper, we describe an open information extraction pipeline based on ReVerb for extracting knowledge from French text. We put it to the test by using the information triples extracted to build an entity classifier, ie, a system able to label a given instance with its type (for instance, Michel Foucault is a philosopher). The classifier requires little supervision. One novel aspect of this study is that we show how general domain information triples (extracted from French Wikipedia) can be used for deriving new knowledge from domain‐specific documents unrelated to Wikipedia, in our case scholarly articles focusing on the humanities. We believe that the present study is the first that focuses on such a cross‐domain, recall‐oriented approach in open information extraction. While our system's performance shows room for improvement, manual assessments show that the task is quite hard, even for a human, in part because of the cross‐domain aspect of the problem we tackle. [ABSTRACT FROM AUTHOR]

Relation extraction is an important task in the field of natural language processing. In this paper, we describe our approach for the BioCreative VI Task 5: text mining chemical–protein interactions. We investigate multiple deep neural network (DNN) models, including convolutional neural networks, recurrent neural networks (RNNs) and attention-based (ATT-) RNNs (ATT-RNNs) to extract chemical–protein relations. Our experimental results indicate that ATT-RNN models outperform the same models without using attention and the ATT-gated recurrent unit (ATT-GRU) achieves the best performing micro average F1 score of 0.527 on the test set among the tested DNNs. In addition, the result of word-level attention weights also shows that attention mechanism is effective on selecting the most important trigger words when trained with semantic relation labels without the need of semantic parsing and feature engineering. The source code of this work is available at https://github.com/ohnlp/att-chemprot. [ABSTRACT FROM AUTHOR]

Unstructured texts dominate data in construction projects. With the achievements of natural language processing (NLP) techniques, mining unstructured text data for smart construction has become increasingly significant. To understand state-of-the-art NLP for smart construction, uncover related issues, and propose potential improvements, this paper presents a comprehensive review of bottom-level techniques and mainstream applications of NLP in the industry. In total, 124 journal articles published in the last two decades are reviewed. NLP involves five core steps supported by various techniques, e.g., syntactic parsing, heuristic rules, machine learning, and deep learning. NLP has been applied for information extraction and exchanging and many downstream applications to facilitate management and decision-making. The role of NLP in smart construction and current challenges for fully reaping its benefits are discussed, and four research directions are identified, i.e., improving relation extraction, realising knowledge base auto-development, integrating multi-modal information, and achieving an accuracy-efficiency trade-off by developing an NLP application framework. It is envisioned that outcomes of this paper can assist both researchers and industrial practitioners with appreciating the research and practice frontier of NLP for smart construction and soliciting the latest NLP techniques. • An in-depth review of natural language processing (NLP) for smart construction is conducted. • 124 journal articles published in 2000–2021 are manually reviewed. • Bottom-level NLP techniques are thoroughly introduced. • NLP is used to extract and exchange information and to support downstream applications. • The role of NLP in smart construction, current challenges, and future directions are provided. [ABSTRACT FROM AUTHOR]

Background: Knowledge engineering for ontological knowledgebases is resource and time intensive. To alleviate these issues, especially for novices, automated tools from the natural language domain can assist in the development process of ontologies. We focus towards the development of ontologies for the public health domain and use patient-centric sources from MedlinePlus related to HPV-causing cancers.Methods: This paper demonstrates the use of a lightweight open information extraction (OIE) tool to derive accurate knowledge triples that can lead to the seeding of an ontological knowledgebase. We developed a custom application, which interfaced with an information extraction software library, to help facilitate the tasks towards producing knowledge triples from textual sources.Results: The results of our efforts generated accurate extractions ranging from 80-89% precision. These triples can later be transformed to OWL/RDF representation for our planned ontological knowledgebase.Conclusions: OIE delivers an effective and accessible method towards the development ontologies. [ABSTRACT FROM AUTHOR]

As the prevalence of social media on the Internet, opinion mining has become an essential approach to analyzing so many data. Various applications appear in a wide range of industrial domains. Meanwhile, opinions have diverse expressions which bring along research challenges. Both of the practical demands and research challenges make opinion mining an active research area in recent years. In this paper, we present a review of Natural Language Processing (NLP) techniques for opinion mining. First, we introduce general NLP techniques which are required for text preprocessing. Second, we investigate the approaches of opinion mining for different levels and situations. Then we introduce comparative opinion mining and deep learning approaches for opinion mining. Opinion summarization and advanced topics are introduced later. Finally, we discuss some challenges and open problems related to opinion mining. [ABSTRACT FROM AUTHOR]

Named Entity Recognition (NER) is a key NLP task, which is all the more challenging on Web and user-generated content with their diverse and continuously changing language. This paper aims to quantify how this diversity impacts state-of-the-art NER methods, by measuring named entity (NE) and context variability, feature sparsity, and their effects on precision and recall. In particular, our findings indicate that NER approaches struggle to generalise in diverse genres with limited training data. Unseen NEs, in particular, play an important role, which have a higher incidence in diverse genres such as social media than in more regular genres such as newswire. Coupled with a higher incidence of unseen features more generally and the lack of large training corpora, this leads to significantly lower F 1 scores for diverse genres as compared to more regular ones. We also find that leading systems rely heavily on surface forms found in training data, having problems generalising beyond these, and offer explanations for this observation. [ABSTRACT FROM AUTHOR]