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In the recent years, the academic paper influence analysis has been widely studied due to its potential applications in the multiple areas of science information metric and retrieval. By identifying the academic influence of papers, authors, etc., we can directly support researchers to easily reach academic papers. These recommended candidate papers are not only highly relevant with their desired research topics but also highly-attended by the research community within these topics. For very recent years, the rapid developments of academic networks, like Google Scholar, Research Gate, CiteSeerX, etc., have significantly boosted the number of new published papers annually. It also helps to strengthen the borderless cooperation between researchers who are interested on the same research topics. However, these current academic networks still lack the capabilities of provisioning researchers deeper into most-influenced papers. They also largely ignore quite/irrelevant papers, which are not fully related with their current interest topics. Moreover, the distributions of topics within these academic papers are considered as varying and it is difficult to extract the main concentrated topics in these papers. Thus, it leads to challenges for researchers to find their appropriated/high-qualified reference resources while doing researches. To overcome this limitation, in this paper, we proposed a novel approach of paper influence analysis through their content-based and citation relationship-based analyses within the biographical network. In order to effectively extract the topic-based relevance from papers, we apply the integrated graph-based citation relationship analysis with topic modeling approach to automatically learn the distributions of keyword-based labeled topics in forms of unsupervised learning approach, named as TopCite. Then, we base on the constructed graph-based paper–topic structure to identify their relevancy levels. Upon the identified relevancy levels between papers, we can support for improving the accuracy performance of other bibliographic network mining tasks, such as paper similarity measurement, recommendation, etc. Extensive experiments in real-world AMiner bibliographic dataset demonstrate the effectiveness of our proposed ideas in this paper. [ABSTRACT FROM AUTHOR]

To address the issue of insufficient testing caused by the continuous reduction of software development cycles, many organizations maintain bug repositories and bug tracking systems to ensure real-time updates of bugs. However, each day, a large number of bugs is discovered and sent to the repository, which imposes a heavy workload on bug fixers. Therefore, effective bug deduplication and triage are of great significance in software development. This paper provides a comprehensive investigation and survey of the recent developments in bug deduplication and triage. The study begins by outlining the roadmap of the existing literature, including the research trends, mathematical models, methods, and commonly used datasets in recent years. Subsequently, the paper summarizes the general process of the methods from two perspectives—runtime information-based and bug report-based perspectives—and provides a detailed overview of the methodologies employed in relevant works. Finally, this paper presents a detailed comparison of the experimental results of various works in terms of usage methods, datasets, accuracy, recall rate, and F1 score. Drawing on key findings, such as the need to improve the accuracy of runtime information collection and refine the description information in bug reports, we propose several potential future research directions in the field, such as stack trace enrichment and the combination of new NLP models. [ABSTRACT FROM AUTHOR]

Much of the knowledge and information needed for enabling high-quality clinical research is stored in free-text format. Natural language processing (NLP) has been used to extract information from these sources at scale for several decades. This paper aims to present a comprehensive review of clinical NLP for the past 15 years in the UK to identify the community, depict its evolution, analyse methodologies and applications, and identify the main barriers. We collect a dataset of clinical NLP projects (n = 94; £ = 41.97 m) funded by UK funders or the European Union's funding programmes. Additionally, we extract details on 9 funders, 137 organisations, 139 persons and 431 research papers. Networks are created from timestamped data interlinking all entities, and network analysis is subsequently applied to generate insights. 431 publications are identified as part of a literature review, of which 107 are eligible for final analysis. Results show, not surprisingly, clinical NLP in the UK has increased substantially in the last 15 years: the total budget in the period of 2019–2022 was 80 times that of 2007–2010. However, the effort is required to deepen areas such as disease (sub-)phenotyping and broaden application domains. There is also a need to improve links between academia and industry and enable deployments in real-world settings for the realisation of clinical NLP's great potential in care delivery. The major barriers include research and development access to hospital data, lack of capable computational resources in the right places, the scarcity of labelled data and barriers to sharing of pretrained models. [ABSTRACT FROM AUTHOR]

In the biomedical field due to tremendous medical research, every year the medical papers generated is very huge. In order to process these tremendous amounts of textual data, the information retrieval techniques are combined with machine learning methods like natural language processing (NLP) for finding the useful insights in data for NLP tasks. In this work, we have addressed the challenges involved in existing NLP techniques like Word2Vec, Doc2Vec, and Biosent2Vec and followed by the traditional classification of articles with Concept2Vec and random forest classification. Concept vector techniques are emerging methods in NLP and in information retrieval systems. Pretrained concept encoders are available in Machine learning, whereas no such exists in biomedical domain. In this paper a proposal on Concept2Vec trained from biomedical text is highlighted. Our work accurately emphasizes on the quality of semantics defined between the medical terms, which can help the medical practitioners in taking errorless decisions. In this work 20 thousand biomedical documents are considered for Concept2Vec embeddings and the proposed approach have shown best concept similarity in terms of relevant measures compared with existing approaches such as Word2Vec, global vectors (GloVe), fastText, and BioSentVec, bidirectional encoder representations from transformers (BERT), biomedical-BERT. [ABSTRACT FROM AUTHOR]

Biomedical-named entity recognition (bNER) is critical in biomedical informatics. It identifies biomedical entities with special meanings, such as people, places, and organizations, as predefined semantic types in electronic health records (EHR). bNER is essential for discovering novel knowledge using computational methods and Information Technology. Early bNER systems were configured manually to include domain-specific features and rules. However, these systems were limited in handling the complexity of the biomedical text. Recent advances in deep learning (DL) have led to the development of more powerful bNER systems. DL-based bNER systems can learn the patterns of biomedical text automatically, making them more robust and efficient than traditional rule-based systems. This paper reviews the healthcare domain of bNER, using DL techniques and artificial intelligence in clinical records, for mining treatment prediction. bNER-based tools are categorized systematically and represent the distribution of input, context, and tag (encoder/decoder). Furthermore, to create a labeled dataset for our machine learning sentiment analyzer to analyze the sentiment of a set of tweets, we used a manual coding approach and the multi-task learning method to bias the training signals with domain knowledge inductively. To conclude, we discuss the challenges facing bNER systems and future directions in the healthcare field. [ABSTRACT FROM AUTHOR]

Coreference Resolution is an essential task for Natural Language Processing (NLP) application, which has a paramount impact on the performance of text summarization, machine translation, text classification, and recognizing textual entailment. Mention Detection (MD) is the core component of the coreference resolution task and is additionally a process of extraction of all possible mentions from the text. Mention is referred to as a textual representation of entities in the text, such as Name, Nominal, and Pronominal mentions. The mentions appear in the text using different representations but indicating the same entity. The performance of an MD module positively affects the performance of NLP tasks such as Coreference resolution, Relation Extraction, Information retrieval, Information extraction, etc. Incorrect identification of mentions in the text severely affects the efficiency of the coreference resolution task. This paper aims to provide a comprehensive overview for the state of the art of mention detection approaches, which is utilized in the coreference resolution task and explains the importance of MD in Coreference resolution. The subsisting approaches are classified based on the underlying techniques adopted by each approach in three categories: Rule-based mention detection, Statistics-based mention detection, and Deep learning-based mention detection. The performance of deep learning is improving as more data and more powerful computing resources become available. This study endeavors to provide a comparative analysis of various mention detection approaches and help the researchers to assimilate knowledge about the mention detection approaches from sundry aspects. [ABSTRACT FROM AUTHOR]

The internet is surrounded by uncertain information which necessitates the usage of natural language processing and soft computing techniques to extract the relevant documents. The relevant results are retrieved using the query expansion technique which is mainly formulated using the machine learning or deep learning concepts in the existing literature. This paper presents a hybrid group mean-based optimizer-enhanced chimp optimization (GMBO-ECO) algorithm for pseudo-relevance-based query expansion, whereby the actual queries are expanded with their related keywords. The hybrid GMBO-ECO algorithm mainly expands the query based on the terms that have a strong interrelationship with the actual query. To generate the word embeddings, a Word2Vec paradigm is used which learns the word association from large text corpora. The useful context in the text is identified using the improved iterative deep learning framework which determines the user's intent for the current web search. This step reduces the mismatch of the words and improves the performance of query retrieval. The weak terms are eliminated and the candidate query terms for optimal query expansion are improved via an Okapi measure and cosine similarity techniques. The proposed methodology has been compared to the state-of-the-art methods with and without a query expansion approach. Moreover, the proposed optimal query expansion technique has shown a substantial improvement in terms of a normalized discounted cumulative gain of 0.87, a mean average precision of 0.35, and a mean reciprocal rank of 0.95. The experimental results show the efficiency of the proposed methodology in retrieving the appropriate response for information retrieval. The most common applications for the proposed method are search engines. [ABSTRACT FROM AUTHOR]

This paper proposes an interactive dialog system, called AidIR, to aid information retrieval. AidIR allows users to retrieve information on diseases resulting from coronaviruses and diseases transmitted by vector mosquitoes with natural language interaction and Line chat media. In a subjective evaluation, we asked 20 users to rate the intuitiveness, usability, and user experience of AidIR with a range between −2 and 2. Moreover, we also asked these users to answer yes–no questions to evaluate AidIR and provide feedback. The average scores of intuitiveness, usability, and user experience are 0.8, 0.8, and 1.05, respectively. The yes–no questions demonstrated that AidIR is better than systems using the graphical user interface in mobile phones and single-turn dialog systems. According to user feedback, AidIR is more convenient for information retrieval. Moreover, we designed a new loss function to jointly train a BERT model for domain classification and sequence label tasks. The accuracy of both tasks is 92%. Finally, we trained the dialog policy network with supervised learning tasks and deployed the reinforcement learning algorithm to allow AidIR to continue learning the dialog policy. [ABSTRACT FROM AUTHOR]

In the era of rapid paper publications in various venues, automatic citation recommendations would be highly useful to researchers when they write papers. Local citation recommendation aims to recommend possible papers to cite given local citation contexts. Previous work mainly computes the similarity score between citation contexts and cited papers on a one-to-one basis, which is quite time-consuming. We train a pair of neural network encoders that map citation contexts and all possible cited papers to the same vector space, respectively. After that, we index the positions of all cited papers in the vector space. This makes our process for searching recommended papers considerably faster. On the other hand, existing methods tend to recommend papers that are highly similar to each other, which makes recommendations lack diversity. Therefore, we extend our algorithm to perform multi-topic recommendations. We generate multi-topic training examples based on the index we mentioned earlier. Furthermore, we specially design a multi-group contrastive learning method to train our model so that it can distinguish different topics. Empirical experiments show that our model outperforms previous methods by a wide margin. Our model is also light weighted and has been deployed online so that researchers can use it to obtain recommended citations for their own paper in real-time. • Proposed FLCR algorithm with sentence-transformer & k-d tree. • Introduced multi-topic citation recommendation for diverse contexts. • Developed large-scale dataset with 1.7 million citation contexts for evaluation. • Demonstrated significant performance improvement over previous methods. • Deployed demo for real-time citation recommendations. [ABSTRACT FROM AUTHOR]

We study the problem of entity salience by proposing the design and implementation of Swat, a system that identifies the salient Wikipedia entities occurring in an input document. Swat consists of several modules that are able to detect and classify on‐the‐fly Wikipedia entities as salient or not, based on a large number of syntactic, semantic, and latent features properly extracted via a supervised process, which has been trained over millions of examples drawn from the New York Times corpus. The validation process is performed through a large experimental assessment, eventually showing that Swat improves known solutions over all publicly available datasets. We release Swat via an API that we describe and comment in the paper to ease its use in other software. [ABSTRACT FROM AUTHOR]

In the emerging information retrieval world, the selection of keywords and the generation of queries are very critical for the efficient retrieval. The most new-generations database applications request keen interface to upgrade productive connections among various databases and the clients. Majority of the accessible interfaces for databases should be intelligent and also should understand natural language expressions. The paper deals with, the mapping of natural language queries which is in spoken form, and converting into words forming the foundation of SQL. We give a general framework for a smart database interface which could be linked to any database. One of the most striking features of this interface is domain-independence. The smart interface employs speech recognition techniques to convert spoken language input into text. Then a semantic matching technique is employed in converting natural language query to SQL words, complemented by using dictionary and a set of production rules. The dictionary consists of semantics sets for columns and tables. The identified type of query, query-word tuple is memorized and sent through a convolution neural network for better construction. This work tries to use natural language processing techniques, parsing and POS tagging to identify semantic structures of inputs. The natural language techniques are used to increase the production of unambiguous queries and speed in detecting and identifying the important parts in a query. [ABSTRACT FROM AUTHOR]

Language models (LMs) such as BERT and GPT have revolutionized natural language processing (NLP). However, the medical field faces challenges in training LMs due to limited data access and privacy constraints imposed by regulations like the Health Insurance Portability and Accountability Act (HIPPA) and the General Data Protection Regulation (GDPR). Federated learning (FL) offers a decentralized solution that enables collaborative learning while ensuring data privacy. In this study, we evaluated FL on 2 biomedical NLP tasks encompassing 8 corpora using 6 LMs. Our results show that: (1) FL models consistently outperformed models trained on individual clients' data and sometimes performed comparably with models trained with polled data; (2) with the fixed number of total data, FL models training with more clients produced inferior performance but pre-trained transformer-based models exhibited great resilience. (3) FL models significantly outperformed pre-trained LLMs with few-shot prompting. [ABSTRACT FROM AUTHOR]

Machine learning algorithms applied to text categorization mostly employ the Bag of Words (BoW) representation to describe the content of the documents. This method has been successfully used in many applications, but it is known to have several limitations. One way of improving text representation is usage of Wikipedia as the lexical knowledge base - an approach that has already shown promising results in many research studies. In this paper we propose three path-based measures for computing document relatedness in the conceptual space formed by the hierarchical organization of a Wikipedia Category Graph (WCG). We compare the proposed approaches with the standard Path Length method to establish the best relatedness measure for the WCG representation. To test overall WCG efficiency, we compare the proposed representations with the BoW method. The evaluation was performed with two different types of clustering algorithms (OPTICS and K-Means), used for categorization of keyword-based search results. The experiments have shown that our approach outperforms the standard Path Length approach, and the WCG representation achieves better results than BoW. [ABSTRACT FROM AUTHOR]

Nowadays, universities (on-site and online) have a large competition in order to attract more students. In this panorama, learning analytics can be a very useful tool since it allows instructors (and university managers) to get a more thorough view of their context, to better understand the environment, and to identify potential improvements. In order to perform analytics efficiently, it is necessary to have as much information as possible about the instructional context. The paper proposes a novel approach to gather information from different aspects within courses. In particular, the approach applies natural language processing (NLP) techniques to analyze the course's materials and discover what concepts are taught, their relevancy in the course and their alignment with the learning outcomes of the course. The contribution of the paper is a semiautomatic system that allows obtaining a better understanding of courses. A validation experiment on a master of the Open University of Catalonia is presented in order to show the quality of the results. The system can be used to analyze the suitability of course's materials and to enrich and contextualize other analytical processes. [ABSTRACT FROM AUTHOR]

Twitter is one of the major social media platforms today to study human behaviours by analysing their interactions. To ensure popularity of the tweet, the focus should be on the content of the tweet that results in numerous followings of that message with sufficient number of likes and retweets. The high quality of tweets, increases the online reputation of the users who post it. If a user can get the prediction of likes and retweets on his text before posting it on the internet, it would improve the popularity of the tweet from information sharing perspective. In this paper we employed different machine learning classifiers like SVM, Naïve Bayes, Logistic Regression, Random Forest, and Neural Network, on top of two different text processing approaches used in NLP (natural language processing), namely bag-of-words (TFIDF) and word embeddings (Doc2Vec), to check how many likes and retweets can a tweet generate. The results obtained indicate that all the models performed 10-15% better with the bag-of-word technique. [ABSTRACT FROM AUTHOR]

• Our approach outperforms previous ones in identifying different query types. • Our approach has practical advantages related to the reduced number of features. • RandomForest outperformed other algorithms with 99.6% accuracy. In real-life classification problems, prior information about the problem and expert knowledge about the domain are often used to obtain reliable and consistent solutions. This is especially true in fields where the data is ambiguous, such as text, in which the same words can be used in seemingly similar texts, but have a different meaning. A promising avenue for text classification is machine learning, which has been shown to perform well in a variety of applications including query classification and sentiment analysis. Many of the proposed approaches rely on the bag-of-words representation, which loses the information about the structure of the text. In this paper, we propose a Customised Grammar Framework for text classification, which exploits domain-related information and a new way to represent text as a series of syntactic categories forming syntactic patterns. The framework employs a formal grammar approach for transforming the text into the syntactic patterns representation. We applied the framework for the query classification problem and our results show that our approach outperforms previous ones in terms of classification performance. [ABSTRACT FROM AUTHOR]

Natural Language Processing (NLP) is very important in modern data processing taking into consideration different sources, forms and purpose of data as well as information in different areas our industry, administration, public and private life. Our studies concern Natural Language Processing techniques in biomedical field. The increasing volume of information stored in medical health record databases both in natural language and in structured forms is creating increasing challenges for information retrieval (IR) technologies. The paper presents the comparison study of chosen Named Entity Recognition techniques for biomedical field. [ABSTRACT FROM AUTHOR]

With the rapid development of the Internet and information technology, people are able to create multimedia data such as pictures or videos anytime and anywhere. Efficient multimedia processing tools are needed for the vast video data. The video moment localization task aims to locate the video moment which best matches the query in the untrimmed video. Existing text-guided methods only consider single-scale text features, which cannot fully represent the semantic features of text, and also do not consider the masking of crucial information in the video by text information when using text to guide the extraction of video features. To solve the above problems, we propose a video moment localization network based on text multi-semantic clues guidance. Specifically, we first design a text encoder based on fusion gate to better capture the semantic information in the text through multi-semantic clues composed of word embedding, local features and global features. Then text guidance module guides the extraction of video features by text semantic features to highlight the video features related to text semantics. Experimental results on two datasets, Charades-STA and ActivityNet Captions, show that our approach provides significant improvements over state-of-the-art methods. [ABSTRACT FROM AUTHOR]

Rising incidence and mortality of cancer have led to an incremental amount of research in the field. To learn from preexisting data, it has become important to capture maximum information related to disease type, stage, treatment, and outcomes. Medical imaging reports are rich in this kind of information but are only present as free text. The extraction of information from such unstructured text reports is labor-intensive. The use of Natural Language Processing (NLP) tools to extract information from radiology reports can make it less time-consuming as well as more effective. In this study, we have developed and compared different models for the classification of lung carcinoma reports using clinical concepts. This study was approved by the institutional ethics committee as a retrospective study with a waiver of informed consent. A clinical concept-based classification pipeline for lung carcinoma radiology reports was developed using rule-based as well as machine learning models and compared. The machine learning models used were XGBoost and two more deep learning model architectures with bidirectional long short-term neural networks. A corpus consisting of 1700 radiology reports including computed tomography (CT) and positron emission tomography/computed tomography (PET/CT) reports were used for development and testing. Five hundred one radiology reports from MIMIC-III Clinical Database version 1.4 was used for external validation. The pipeline achieved an overall F1 score of 0.94 on the internal set and 0.74 on external validation with the rule-based algorithm using expert input giving the best performance. Among the machine learning models, the Bi-LSTM_dropout model performed better than the ML model using XGBoost and the Bi-LSTM_simple model on internal set, whereas on external validation, the Bi-LSTM_simple model performed relatively better than other 2. This pipeline can be used for clinical concept-based classification of radiology reports related to lung carcinoma from a huge corpus and also for automated annotation of these reports. [ABSTRACT FROM AUTHOR]

This paper describes our approach to developing the Turkish PropBank by adopting the semantic role-labeling guidelines of the original PropBank and using the translation of the English Penn-TreeBank as a resource. We discuss the semantic annotation process of the PropBank and language-specific cases for Turkish, the tools we have developed for annotation, and quality control for multiuser annotation. In the current phase of the project, more than 9500 sentences are semantically analyzed and predicate-argument information is extracted for 1330 verbs and 1914 verb senses. Our plan is to annotate 17,000 sentences by the end of 2017. [ABSTRACT FROM AUTHOR]

Automatic Question Answering (QA) has been successfully applied in various domains such as search engines and chatbots. Biomedical QA (BQA), as an emerging QA task, enables innovative applications to effectively perceive, access, and understand complex biomedical knowledge. There have been tremendous developments of BQA in the past two decades, which we classify into five distinctive approaches: classic, information retrieval, machine reading comprehension, knowledge base, and question entailment approaches. In this survey, we introduce available datasets and representative methods of each BQA approach in detail. Despite the developments, BQA systems are still immature and rarely used in real-life settings. We identify and characterize several key challenges in BQA that might lead to this issue, and we discuss some potential future directions to explore. [ABSTRACT FROM AUTHOR]

The epidemic spread of fake news is a side effect of the expansion of social networks to circulate news, in contrast to traditional mass media such as newspapers, magazines, radio, and television. Human inefficiency to distinguish between true and false facts exposes fake news as a threat to logical truth, democracy, journalism, and credibility in government institutions. In this paper, we survey methods for preprocessing data in natural language, vectorization, dimensionality reduction, machine learning, and quality assessment of information retrieval. We also contextualize the identification of fake news, and we discuss research initiatives and opportunities. [ABSTRACT FROM AUTHOR]

A Named Entity Recognition (NER) plays a noteworthy role in Natural Language Processing (NLP) research, since it makes available the detection of proper nouns in unstructured texts. NER makes easier searching, retrieving, and extracting information seeing as the significant information in texts is usually sited around proper names. This paper suggests an efficient approach that can identify Named Entities (NE) in Arabic texts without the need for morphological or syntactic analysis or gazetteers. The goal of our approach is to provide a general framework for Arabic NE recognition. Within this framework; the system learns the recognition of NE automatically and induces NE systematically, starting from sample NE instances as seeds. This method takes advantage from the web, the approach learns from a web corpus. The seeds are used to identify the contexts in the web denoting NE and then the contexts identify new NE. Thorough experimental evaluation of our approach, the performances measured by recall, precision and f-measure conducted to recognize NE are promising. We obtained an overall rate of F-measure equal to 83%. [ABSTRACT FROM AUTHOR]

Toponym recognition, or the challenge of detecting place names that have a similar referent, is involved in a number of activities connected to geographical information retrieval and geographical information sciences. This research focuses on recognizing Chinese toponyms from social media communications. While broad named entity recognition methods are frequently used to locate places, their accuracy is hampered by the many linguistic abnormalities seen in social media posts, such as informal sentence constructions, name abbreviations, and misspellings. In this study, we describe a Chinese toponym identification model based on a hybrid neural network that was created with these linguistic inconsistencies in mind. Our method adds a number of improvements to a standard bidirectional recurrent neural network model to help with location detection in social media messages. We demonstrate the results of a wide-ranging evaluation of the performance of different supervised machine learning methods, which have the natural advantage of avoiding human design features. A set of controlled experiments with four test datasets (one constructed and three public datasets) demonstrates the performance of supervised machine learning that can achieve good results on the task, significantly outperforming seven baseline models. [ABSTRACT FROM AUTHOR]

Optical character recognition (OCR) is one of the most popular techniques used for converting printed documents into machine-readable ones. While OCR engines can do well with modern text, their performance is unfortunately significantly reduced on historical materials. Additionally, many texts have already been processed by various out-of-date digitisation techniques. As a consequence, digitised texts are noisy and need to be post-corrected. This article clarifies the importance of enhancing quality of OCR results by studying their effects on information retrieval and natural language processing applications. We then define the post-OCR processing problem, illustrate its typical pipeline, and review the state-of-the-art post-OCR processing approaches. Evaluation metrics, accessible datasets, language resources, and useful toolkits are also reported. Furthermore, the work identifies the current trend and outlines some research directions of this field. [ABSTRACT FROM AUTHOR]

Information retrieval IR is the process of finding information (generally documents) that matches the needs of the user. One way to improve the search effectiveness, as well as the quality of text categorization is to build an effective stemmer that helps to match users’ queries with relevant documents in IR and reduce the space of textual representation in TC. This has been always an interesting research topic in IR and TC. We can define stemming as the process of reducing inflected and derived words to their reduced forms (stems or roots). Many stemmers have been developed for different languages, but there is always many weaknesses and problems. In the present work, we have developed a multilingual stemming approach, based on the extraction of the word root and that exploits the technique of n-grams of characters. Our experiments have been done on three languages which are: Arabic, English, and French. [ABSTRACT FROM AUTHOR]

Traditional clinical named entity recognition methods fail to balance the effectiveness of feature extraction of unstructured text and the complexity of neural network models. We propose a model based on ALBERT and a multihead attention (MHA) mechanism to solve this problem. Structurally, the model first obtains character-level word embeddings through the ALBERT pretraining language model, then inputs the word embeddings into the iterated dilated convolutional neural network model to quickly extract global semantic information, and decodes the predicted labels through conditional random fields to obtain the optimal label sequence. Also, we apply the MHA mechanism to capture intercharacter dependencies from multiple aspects. Furthermore, we use the RAdam optimizer to boost the convergence speed and improve the generalization ability of our model. Experimental results show that our model achieves an F1 score of 85.63% on the CCKS-2019 dataset—an increase of 4.36% compared to the baseline model. [ABSTRACT FROM AUTHOR]

Reviewing the metabolomics literature is becoming increasingly difficult because of the rapid expansion of relevant journal literature. Text-mining technologies are therefore needed to facilitate more efficient literature reviews. Here we contribute a standardised corpus of full-text publications from metabolomics studies and describe the development of two metabolite named entity recognition (NER) methods. These methods are based on Bidirectional Long Short-Term Memory (BiLSTM) networks and each incorporate different transfer learning techniques (for tokenisation and word embedding). Our first model (MetaboListem) follows prior methodology using GloVe word embeddings. Our second model exploits BERT and BioBERT for embedding and is named TABoLiSTM (Transformer-Affixed BiLSTM). The methods are trained on a novel corpus annotated using rule-based methods, and evaluated on manually annotated metabolomics articles. MetaboListem (F1-score 0.890, precision 0.892, recall 0.888) and TABoLiSTM (BioBERT version: F1-score 0.909, precision 0.926, recall 0.893) have achieved state-of-the-art performance on metabolite NER. A training corpus with full-text sentences from >1000 full-text Open Access metabolomics publications with 105,335 annotated metabolites was created, as well as a manually annotated test corpus (19,138 annotations). This work demonstrates that deep learning algorithms are capable of identifying metabolite names accurately and efficiently in text. The proposed corpus and NER algorithms can be used for metabolomics text-mining tasks such as information retrieval, document classification and literature-based discovery and are available from the omicsNLP GitHub repository. [ABSTRACT FROM AUTHOR]

This paper tackles the issue of analyst bias in performance of comparative political analyses on political discourse, by leveraging data and machine-learning over human prior knowledge. The case studied is characterization of the issue of migration in the Croatian political discourse, which was chosen arbitrarily. We developed a machine-learning system that identifies most prominent features in the Croatian political discourse, with regards to migration and were interested solo in comparative political analysis in political science. This system does not rely on human judgement on the part of the researchers, and can be thus considered to be “objective”, short of possible sampling or selection bias. It is replicable. If provided, the same dataset and algorithm used, same conclusions should be reached by any scientist. This result was achieved by creating a text corpus from news items and press releases extracted from the websites of Croatian political parties currently represented in the Parliament. Available and collected data consist of public announcements mainly from IDS (Istarski Demokratski Sabor / Istrian Democratic Assambly), SDSS (Samostalna Demokratska Srpska Stranka / Independed Democratic Serb Party) and HSLS (Hrvatska Socijalno Liberalna Stranka / Croatian Social Liberal Party). Data analyzed suggests three dominant phrases of the research process. All political parties had similar political stand towards pointed out issues. Three most significant phrases were determined. First phrase is related to words “Demography” and “Reduction” and finding suggest that most analyzed articles relates towards migration of Croatian citizens in connection to economic hardships of some kind. Phrase two is related to words “Border” and “Croatia-Serbia” which strongly indicates relation to migration and is related towards inter-Balkan migration, mostly connected with consequences of the Croatian War of Independence from 1990’s, and is of most interest to SDSS, a Serb minority party in Croatia. Phrase three is related towards Marrakesh Agreement (Global Compact for Safe, Orderly and Regular Migration), where most of analyzed data shows that parties have a constructive but ambivalent stance towards migration from the third countries. Research conducted on available data, shows that wide spread international migration is not in the focus of most Croatian political parties, while topics and interest for inter-Balkan and Croatian economic/political migration dominates Croatian political spectre

Synthetic speech's applications sector is rapidly growing, as well as the quality of TTS systems is continuously improving. Speech synthesis solutions are becoming relatively cheap for average users, making them more appropriate for regular usage, especially as NLP, Machine Learning, and Artificial Intelligence continue to develop where Synthetic speech may also be utilised in a variety of industries, and with effective integration, money can indeed be saved. [ABSTRACT FROM AUTHOR]

As resources for conservation are limited, gathering and analysing information from digital platforms can help investigate the global biodiversity crisis in a cost‐efficient manner. Development and application of methods for automated content analysis of digital data sources are especially important in the context of investigating human–nature interactions.In this study, we introduce novel application methods to automatically collect and analyse textual data on species of conservation concern from digital platforms. An end‐to‐end pipeline is constructed that begins from searching and downloading news articles about species listed in Appendix I of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) along with news articles from specific Twitter handles and proceeds with implementing natural language processing and machine learning methods to filter and retain only relevant articles. A crucial aspect here is the automatic annotation of training data, which can be challenging in many machine learning applications. A Named Entity Recognition model is then used to extract additional relevant information for each article.The data collected over a 1‐month period included 15,088 articles focusing on 585 species listed in Appendix I of CITES. The accuracy of the neural network to detect relevant articles was 95.91% while the Named Entity recognition model helped extract information on prices, location and quantities of traded animals and plants. A regularly updated database, which can be queried and analysed for various research purposes and to inform conservation decision making, is generated by the system.The results demonstrate that natural language processing can be used successfully to extract information from digital text content. The proposed methods can be applied to multiple digital data platforms at the same time and used to investigate human–nature interactions in conservation science and practice. [ABSTRACT FROM AUTHOR]

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Background and Objective: Question answering (QA), the identification of short accurate answers to users questions written in natural language expressions, is a longstanding issue widely studied over the last decades in the open-domain. However, it still remains a real challenge in the biomedical domain as the most of the existing systems support a limited amount of question and answer types as well as still require further efforts in order to improve their performance in terms of precision for the supported questions. Here, we present a semantic biomedical QA system named SemBioNLQA which has the ability to handle the kinds of yes/no, factoid, list, and summary natural language questions.Methods: This paper describes the system architecture and an evaluation of the developed end-to-end biomedical QA system named SemBioNLQA, which consists of question classification, document retrieval, passage retrieval and answer extraction modules. It takes natural language questions as input, and outputs both short precise answers and summaries as results. The SemBioNLQA system, dealing with four types of questions, is based on (1) handcrafted lexico-syntactic patterns and a machine learning algorithm for question classification, (2) PubMed search engine and UMLS similarity for document retrieval, (3) the BM25 model, stemmed words and UMLS concepts for passage retrieval, and (4) UMLS metathesaurus, BioPortal synonyms, sentiment analysis and term frequency metric for answer extraction.Results and Conclusion: Compared with the current state-of-the-art biomedical QA systems, SemBioNLQA, a fully automated system, has the potential to deal with a large amount of question and answer types. SemBioNLQA retrieves quickly users' information needs by returning exact answers (e.g., "yes", "no", a biomedical entity name, etc.) and ideal answers (i.e., paragraph-sized summaries of relevant information) for yes/no, factoid and list questions, whereas it provides only the ideal answers for summary questions. Moreover, experimental evaluations performed on biomedical questions and answers provided by the BioASQ challenge especially in 2015, 2016 and 2017 (as part of our participation), show that SemBioNLQA achieves good performances compared with the most current state-of-the-art systems and allows a practical and competitive alternative to help information seekers find exact and ideal answers to their biomedical questions. The SemBioNLQA source code is publicly available at https://github.com/sarrouti/sembionlqa. [ABSTRACT FROM AUTHOR]

Software tools now are essential to research and applications in the biomedical domain. However, existing software repositories are mainly built using manual curation, which is time-consuming and unscalable. This study took the initiative to manually annotate software names in 1,120 MEDLINE abstracts and titles and used this corpus to develop and evaluate machine learning–based named entity recognition systems for biomedical software. Specifically, two strategies were proposed for feature engineering: (1) domain knowledge features and (2) unsupervised word representation features of clustered and binarized word embeddings. Our best system achieved an F-measure of 91.79% for recognizing software from titles and an F-measure of 86.35% for recognizing software from both titles and abstracts using inexact matching criteria. We then created a biomedical software catalog with 19,557 entries using the developed system. This study demonstrates the feasibility of using natural language processing methods to automatically build a high-quality software index from biomedical literature. [ABSTRACT FROM AUTHOR]

Existing keyword-based search techniques suffer from limitations owing to unknown, mismatched, and obscure vocabulary. These challenges are particularly prevalent in social media, where slang, jargon, and memetics are abundant. We develop a new technique, Archetype-Based Modeling and Search, that can mitigate these challenges as they are encountered in social media. This technique learns to identify new relevant documents based on a specified set of archetypes from which both vocabulary and relevance information are extracted. We present a case study from the social media data from Reddit, by using authors from/r/Opiates to characterize discourse around opioid use and to find additional relevant authors on this topic. [ABSTRACT FROM AUTHOR]

Unstructured and semi-structured radiology reports represent an underutilized trove of information for machine learning (ML)-based clinical informatics applications, including abnormality tracking systems, research cohort identification, point-of-care summarization, semi-automated report writing, and as a source of weak data labels for training image processing systems. Clinical ML systems must be interpretable to ensure user trust. To create interpretable models applicable to all of these tasks, we can build general-purpose systems which extract all relevant human-level assertions or "facts" documented in reports; identifying these facts is an information extraction (IE) task. Previous IE work in radiology has focused on a limited set of information, and extracts isolated entities (i.e., single words such as "lesion" or "cyst") rather than complete facts, which require the linking of multiple entities and modifiers. Here, we develop a prototype system to extract all useful information in abdominopelvic radiology reports (findings, recommendations, clinical history, procedures, imaging indications and limitations, etc.), in the form of complete, contextualized facts. We construct an information schema to capture the bulk of information in reports, develop real-time ML models to extract this information, and demonstrate the feasibility and performance of the system. [ABSTRACT FROM AUTHOR]