Information retrieval and text mining technologies for chemistry

Efficient access to chemical information contained in scientific literature, patents, technical reports, or the web is a pressing need shared by researchers and patent attorneys from different chemical disciplines. Retrieval of important chemical information in most cases starts with finding relevant documents for a particular chemical compound or family. Targeted retrieval of chemical documents is closely connected to the automatic recognition of chemical entities in the text, which commonly involves the extraction of the entire list of chemicals mentioned in a document, including any associated information. In this Review, we provide a comprehensive and in-depth description of fundamental concepts, technical implementations, and current technologies for meeting these information demands. A strong focus is placed on community challenges addressing systems performance, more particularly CHEMDNER and CHEMDNER patents tasks of BioCreative IV and V, respectively. Considering the growing interest in the construction of automatically annotated chemical knowledge bases that integrate chemical information and biological data, cheminformatics approaches for mapping the extracted chemical names into chemical structures and their subsequent annotation together with text mining applications for linking chemistry with biological information are also presented. Finally, future trends and current challenges are highlighted as a roadmap proposal for research in this emerging field.A.V. and M.K. acknowledge funding from the European Community’s Horizon 2020 Program (project reference: 654021 - OpenMinted). M.K. additionally acknowledges the Encomienda MINETAD-CNIO as part of the Plan for the Advancement of Language Technology. O.R. and J.O. thank the Foundation for Applied Medical Research (FIMA), University of Navarra (Pamplona, Spain). This work was partially funded by Consellería de Cultura, Educación e Ordenación Universitaria (Xunta de Galicia), and FEDER (European Union), and the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145-FEDER-006684). We thank Iñigo Garciá -Yoldi for useful feedback and discussions during the preparation of the manuscript.info:eu-repo/semantics/publishedVersio

Retrieving information from heterogeneous freight data sources to answer natural language queries

textThe ability to retrieve accurate information from databases without an extensive knowledge of the contents and organization of each database is extremely beneficial to the dissemination and utilization of freight data. The challenges, however, are: 1) correctly identifying only the relevant information and keywords from questions when dealing with multiple sentence structures, and 2) automatically retrieving, preprocessing, and understanding multiple data sources to determine the best answer to user’s query. Current named entity recognition systems have the ability to identify entities but require an annotated corpus for training which in the field of transportation planning does not currently exist. A hybrid approach which combines multiple models to classify specific named entities was therefore proposed as an alternative. The retrieval and classification of freight related keywords facilitated the process of finding which databases are capable of answering a question. Values in data dictionaries can be queried by mapping keywords to data element fields in various freight databases using ontologies. A number of challenges still arise as a result of different entities sharing the same names, the same entity having multiple names, and differences in classification systems. Dealing with ambiguities is required to accurately determine which database provides the best answer from the list of applicable sources. This dissertation 1) develops an approach to identify and classifying keywords from freight related natural language queries, 2) develops a standardized knowledge representation of freight data sources using an ontology that both computer systems and domain experts can utilize to identify relevant freight data sources, and 3) provides recommendations for addressing ambiguities in freight related named entities. Finally, the use of knowledge base expert systems to intelligently sift through data sources to determine which ones provide the best answer to a user’s question is proposed.Civil, Architectural, and Environmental Engineerin

Named Entity Recognition in Chinese Clinical Text

Objective: Named entity recognition (NER) is one of the fundamental tasks in natural language processing (NLP). In the medical domain, there have been a number of studies on NER in English clinical notes; however, very limited NER research has been done on clinical notes written in Chinese. The goal of this study is to develop corpora, methods, and systems for NER in Chinese clinical text. Materials and methods: To study entities in Chinese clinical text, we started with building annotated clinical corpora in Chinese. We developed an NER annotation guideline in Chinese by extending the one used in the 2010 i2b2 NLP challenge. We randomly selected 400 admission notes and 400 discharge summaries from Peking Union Medical College Hospital (PUMCH) in China. For each note, four types of entities including clinical problems, procedures, labs, and medications were annotated according to the developed guideline. In addition, an annotation tool was developed to assist two MD students to annotate Chinese clinical documents. A comparison of entity distribution between Chinese and English clinical notes (646 English and 400 Chinese discharge summaries) was performed using the annotated corpora, to identify the important features for NER. In the NER study, two-thirds of the 400 notes were used for training the NER systems and one-third were used for testing. We investigated the effects of different types of features including bag-of-characters, word segmentation, part-of-speech, and section information, with different machine learning (ML) algorithms including Conditional Random Fields (CRF), Support Vector Machines (SVM), Maximum Entropy (ME), and Structural Support Vector Machines (SSVM) on the Chinese clinical NER task. All classifiers were trained on the training dataset, evaluated on the test set, and microaveraged precision, recall, and F-measure were reported. Results: Our evaluation on the independent test set showed that most types of features were beneficial to Chinese NER systems, although the improvements were limited. By combining word segmentation and section information, the system achieved the highest performance, indicating that these two types of features are complementary to each other. When the same types of optimized features were used, CRF and SSVM outperformed SVM and ME. More specifically, SSVM reached the highest performance among the four algorithms, with F-measures of 93.51% and 90.01% for admission notes and discharge summaries respectively. Conclusions: In this study, we created large annotated datasets of Chinese admission notes and discharge summaries and then systematically evaluated different types of features (e.g., syntactic, semantic, and segmentation information) and four ML algorithms including CRF, SVM, SSVM, and ME for clinical NER in Chinese. To the best of our knowledge, this is one of the earliest comprehensive effort in Chinese clinical NER research and we believe it will provide valuable insights to NLP research in Chinese clinical text. Our results suggest that both word segmentation and section information improves NER in Chinese clinical text, and SSVM, a recent sequential labelling algorithm, outperformed CRF and other classification algorithms. Our best system achieved F-measures of 90.01% and 93.52% on Chinese discharge summaries and admission notes, respectively, indicating a promising start on Chinese NLP research

Event Detection and Tracking Detection of Dangerous Events on Social Media

Online social media platforms have become essential tools for communication and information exchange in our lives. It is used for connecting with people and sharing information. This phenomenon has been intensively studied in the past decade to investigate users’ sentiments for different scenarios and purposes. As the technology advanced and popularity increased, it led to the use of different terms referring to similar topics which often result in confusion. We study such trends and intend to propose a uniform solution that deals with the subject clearly. We gather all these ambiguous terms under the umbrella of the most recent and popular terms to reach a concise verdict. Many events have been addressed in recent works that cover only specific types and domains of events. For the sake of keeping things simple and practical, the events that are extreme, negative, and dangerous are grouped under the name Dangerous Events (DE). These dangerous events are further divided into three main categories of action-based, scenario-based, and sentiments-based dangerous events to specify their characteristics. We then propose deep-learning-based models to detect events that are dangerous in nature. The deep-learning models that include BERT, RoBERTa, and XLNet provide valuable results that can effectively help solve the issue of detecting dangerous events using various dimensions. Even though the models perform well, the main constraint of fewer available event datasets and lower quality of certain events data affects the performance of these models can be tackled by handling the issue accordingly.As plataformas online de redes sociais tornaram-se ferramentas essenciais para a comunicação, conexão com outros, e troca de informação nas nossas vidas. Este fenómeno tem sido intensamente estudado na última década para investigar os sentimentos dos utilizadores em diferentes cenários e para vários propósitos. Contudo, a utilização dos meios de comunicação social tornou-se mais complexa e num fenómeno mais vasto devido ao envolvimento de múltiplos intervenientes, tais como empresas, grupos e outras organizações. À medida que a tecnologia avançou e a popularidade aumentou, a utilização de termos diferentes referentes a tópicos semelhantes gerou confusão. Por outras palavras, os modelos são treinados segundo a informação de termos e âmbitos específicos. Portanto, a padronização é imperativa. O objetivo deste trabalho é unir os diferentes termos utilizados em termos mais abrangentes e padronizados. O perigo pode ser uma ameaça como violência social, desastres naturais, danos intelectuais ou comunitários, contágio, agitação social, perda económica, ou apenas a difusão de ideologias odiosas e violentas. Estudamos estes diferentes eventos e classificamos-los em tópicos para que a ténica de deteção baseada em tópicos possa ser concebida e integrada sob o termo Evento Perigosos (DE). Consequentemente, definimos o termo proposto “Eventos Perigosos” (Dangerous Events) e dividimo-lo em três categorias principais de modo a especificar as suas características. Sendo estes denominados Eventos Perigosos, Eventos Perigosos de nível superior, e Eventos Perigosos de nível inferior. O conjunto de dados MAVEN foi utilizado para a obtenção de conjuntos de dados para realizar a experiência. Estes conjuntos de dados são filtrados manualmente com base no tipo de eventos para separar eventos perigosos de eventos gerais. Os modelos de transformação BERT, RoBERTa, e XLNet foram utilizados para classificar dados de texto consoante a respetiva categoria de Eventos Perigosos. Os resultados demonstraram que o desempenho do BERT é superior a outros modelos e pode ser eficazmente utilizado para a tarefa de deteção de Eventos Perigosos. Salienta-se que a abordagem de divisão dos conjuntos de dados aumentou significativamente o desempenho dos modelos. Existem diversos métodos propostos para a deteção de eventos. A deteção destes eventos (ED) são maioritariamente classificados na categoria de supervisonado e não supervisionados, como demonstrado nos metódos supervisionados, estão incluidos support vector machine (SVM), Conditional random field (CRF), Decision tree (DT), Naive Bayes (NB), entre outros. Enquanto a categoria de não supervisionados inclui Query-based, Statisticalbased, Probabilistic-based, Clustering-based e Graph-based. Estas são as duas abordagens em uso na deteção de eventos e são denonimados de document-pivot and feature-pivot. A diferença entre estas abordagens é na sua maioria a clustering approach, a forma como os documentos são utilizados para caracterizar vetores, e a similaridade métrica utilizada para identificar se dois documentos correspondem ao mesmo evento ou não. Além da deteção de eventos, a previsão de eventos é um problema importante mas complicado que engloba diversas dimensões. Muitos destes eventos são difíceis de prever antes de se tornarem visíveis e ocorrerem. Como um exemplo, é impossível antecipar catástrofes naturais, sendo apenas detetáveis após o seu acontecimento. Existe um número limitado de recursos em ternos de conjuntos de dados de eventos. ACE 2005, MAVEN, EVIN são alguns dos exemplos de conjuntos de dados disponíveis para a deteção de evnetos. Os trabalhos recentes demonstraram que os Transformer-based pre-trained models (PTMs) são capazes de alcançar desempenho de última geração em várias tarefas de NLP. Estes modelos são pré-treinados em grandes quantidades de texto. Aprendem incorporações para as palavras da língua ou representações de vetores de modo a que as palavras que se relacionem se agrupen no espaço vectorial. Um total de três transformadores diferentes, nomeadamente BERT, RoBERTa, e XLNet, será utilizado para conduzir a experiência e tirar a conclusão através da comparação destes modelos. Os modelos baseados em transformação (Transformer-based) estão em total sintonia utilizando uma divisão de 70,30 dos conjuntos de dados para fins de formação e teste/validação. A sintonização do hiperparâmetro inclui 10 epochs, 16 batch size, e o optimizador AdamW com taxa de aprendizagem 2e-5 para BERT e RoBERTa e 3e-5 para XLNet. Para eventos perigosos, o BERT fornece 60%, o RoBERTa 59 enquanto a XLNet fornece apenas 54% de precisão geral. Para as outras experiências de configuração de eventos de alto nível, o BERT e a XLNet dão 71% e 70% de desempenho com RoBERTa em relação aos outros modelos com 74% de precisão. Enquanto para o DE baseado em acções, DE baseado em cenários, e DE baseado em sentimentos, o BERT dá 62%, 85%, e 81% respetivamente; RoBERTa com 61%, 83%, e 71%; a XLNet com 52%, 81%, e 77% de precisão. Existe a necessidade de clarificar a ambiguidade entre os diferentes trabalhos que abordam problemas similares utilizando termos diferentes. A ideia proposta de referir acontecimentos especifícos como eventos perigosos torna mais fácil a abordagem do problema em questão. No entanto, a escassez de conjunto de dados de eventos limita o desempenho dos modelos e o progresso na deteção das tarefas. A disponibilidade de uma maior quantidade de informação relacionada com eventos perigosos pode melhorar o desempenho do modelo existente. É evidente que o uso de modelos de aprendizagem profunda, tais como como BERT, RoBERTa, e XLNet, pode ajudar a detetar e classificar eventos perigosos de forma eficiente. Tem sido evidente que a utilização de modelos de aprendizagem profunda, tais como BERT, RoBERTa, e XLNet, pode ajudar a detetar e classificar eventos perigosos de forma eficiente. Em geral, o BERT tem um desempenho superior ao do RoBERTa e XLNet na detecção de eventos perigosos. É igualmente importante rastrear os eventos após a sua detecção. Por conseguinte, para trabalhos futuros, propõe-se a implementação das técnicas que lidam com o espaço e o tempo, a fim de monitorizar a sua emergência com o tempo

Health systems data interoperability and implementation

Objective The objective of this study was to use machine learning and health standards to address the problem of clinical data interoperability across healthcare institutions. Addressing this problem has the potential to make clinical data comparable, searchable and exchangeable between healthcare providers. Data sources Structured and unstructured data has been used to conduct the experiments in this study. The data was collected from two disparate data sources namely MIMIC-III and NHanes. The MIMIC-III database stored data from two electronic health record systems which are CareVue and MetaVision. The data stored in these systems was not recorded with the same standards; therefore, it was not comparable because some values were conflicting, while one system would store an abbreviation of a clinical concept, the other would store the full concept name and some of the attributes contained missing information. These few issues that have been identified make this form of data a good candidate for this study. From the identified data sources, laboratory, physical examination, vital signs, and behavioural data were used for this study. Methods This research employed a CRISP-DM framework as a guideline for all the stages of data mining. Two sets of classification experiments were conducted, one for the classification of structured data, and the other for unstructured data. For the first experiment, Edit distance, TFIDF and JaroWinkler were used to calculate the similarity weights between two datasets, one coded with the LOINC terminology standard and another not coded. Similar sets of data were classified as matches while dissimilar sets were classified as non-matching. Then soundex indexing method was used to reduce the number of potential comparisons. Thereafter, three classification algorithms were trained and tested, and the performance of each was evaluated through the ROC curve. Alternatively the second experiment was aimed at extracting patient’s smoking status information from a clinical corpus. A sequence-oriented classification algorithm called CRF was used for learning related concepts from the given clinical corpus. Hence, word embedding, random indexing, and word shape features were used for understanding the meaning in the corpus. Results Having optimized all the model’s parameters through the v-fold cross validation on a sampled training set of structured data ( ), out of 24 features, only ( 8) were selected for a classification task. RapidMiner was used to train and test all the classification algorithms. On the final run of classification process, the last contenders were SVM and the decision tree classifier. SVM yielded an accuracy of 92.5% when the and parameters were set to and . These results were obtained after more relevant features were identified, having observed that the classifiers were biased on the initial data. On the other side, unstructured data was annotated via the UIMA Ruta scripting language, then trained through the CRFSuite which comes with the CLAMP toolkit. The CRF classifier obtained an F-measure of 94.8% for “nonsmoker” class, 83.0% for “currentsmoker”, and 65.7% for “pastsmoker”. It was observed that as more relevant data was added, the performance of the classifier improved. The results show that there is a need for the use of FHIR resources for exchanging clinical data between healthcare institutions. FHIR is free, it uses: profiles to extend coding standards; RESTFul API to exchange messages; and JSON, XML and turtle for representing messages. Data could be stored as JSON format on a NoSQL database such as CouchDB, which makes it available for further post extraction exploration. Conclusion This study has provided a method for learning a clinical coding standard by a computer algorithm, then applying that learned standard to unstandardized data so that unstandardized data could be easily exchangeable, comparable and searchable and ultimately achieve data interoperability. Even though this study was applied on a limited scale, in future, the study would explore the standardization of patient’s long-lived data from multiple sources using the SHARPn open-sourced tools and data scaling platformsInformation ScienceM. Sc. (Computing