Ontology Population via NLP Techniques in Risk Management

In this paper we propose an NLP-based method for Ontology Population from texts and apply it to semi automatic instantiate a Generic Knowledge Base (Generic Domain Ontology) in the risk management domain. The approach is semi-automatic and uses a domain expert intervention for validation. The proposed approach relies on a set of Instances Recognition Rules based on syntactic structures, and on the predicative power of verbs in the instantiation process. It is not domain dependent since it heavily relies on linguistic knowledge. A description of an experiment performed on a part of the ontology of the PRIMA project (supported by the European community) is given. A first validation of the method is done by populating this ontology with Chemical Fact Sheets from Environmental Protection Agency . The results of this experiment complete the paper and support the hypothesis that relying on the predicative power of verbs in the instantiation process improves the performance.Information Extraction, Instance Recognition Rules, Ontology Population, Risk Management, Semantic Analysis

Using Neural Networks for Relation Extraction from Biomedical Literature

Using different sources of information to support automated extracting of relations between biomedical concepts contributes to the development of our understanding of biological systems. The primary comprehensive source of these relations is biomedical literature. Several relation extraction approaches have been proposed to identify relations between concepts in biomedical literature, namely, using neural networks algorithms. The use of multichannel architectures composed of multiple data representations, as in deep neural networks, is leading to state-of-the-art results. The right combination of data representations can eventually lead us to even higher evaluation scores in relation extraction tasks. Thus, biomedical ontologies play a fundamental role by providing semantic and ancestry information about an entity. The incorporation of biomedical ontologies has already been proved to enhance previous state-of-the-art results.Comment: Artificial Neural Networks book (Springer) - Chapter 1

Corporate Smart Content Evaluation

Nowadays, a wide range of information sources are available due to the evolution of web and collection of data. Plenty of these information are consumable and usable by humans but not understandable and processable by machines. Some data may be directly accessible in web pages or via data feeds, but most of the meaningful existing data is hidden within deep web databases and enterprise information systems. Besides the inability to access a wide range of data, manual processing by humans is effortful, error-prone and not contemporary any more. Semantic web technologies deliver capabilities for machine-readable, exchangeable content and metadata for automatic processing of content. The enrichment of heterogeneous data with background knowledge described in ontologies induces re-usability and supports automatic processing of data. The establishment of “Corporate Smart Content” (CSC) - semantically enriched data with high information content with sufficient benefits in economic areas - is the main focus of this study. We describe three actual research areas in the field of CSC concerning scenarios and datasets applicable for corporate applications, algorithms and research. Aspect- oriented Ontology Development advances modular ontology development and partial reuse of existing ontological knowledge. Complex Entity Recognition enhances traditional entity recognition techniques to recognize clusters of related textual information about entities. Semantic Pattern Mining combines semantic web technologies with pattern learning to mine for complex models by attaching background knowledge. This study introduces the afore-mentioned topics by analyzing applicable scenarios with economic and industrial focus, as well as research emphasis. Furthermore, a collection of existing datasets for the given areas of interest is presented and evaluated. The target audience includes researchers and developers of CSC technologies - people interested in semantic web features, ontology development, automation, extracting and mining valuable information in corporate environments. The aim of this study is to provide a comprehensive and broad overview over the three topics, give assistance for decision making in interesting scenarios and choosing practical datasets for evaluating custom problem statements. Detailed descriptions about attributes and metadata of the datasets should serve as starting point for individual ideas and approaches

Indirectly Named Entity Recognition

[EN] We define here indirectly named entities, as a term to denote multiword expressions referring to known named entities by means of periphrasis.  While named entity recognition is a classical task in natural language processing, little attention has been paid to indirectly named entities and their treatment. In this paper, we try to address this gap, describing issues related to the detection and understanding of indirectly named entities in texts. We introduce a proof of concept for retrieving both lexicalised and non-lexicalised indirectly named entities in French texts. We also show example cases where this proof of concept is applied, and discuss future perspectives. We have initiated the creation of a first lexicon of 712 indirectly named entity entries that is available for future research.This research has been funded by the FEDER (Fonds européen de développement régional) and selected by the French-Swiss programme Interreg V. We would like to thank Claire Wuillemin for her preliminary work in the DecRIPT project about the State-of-the-Art in NER and SER in 2020. We would also like to thank for their advice Gilles Falquet, Luka Nerima, Eric Wehrli and Jean-Philippe Goldman at the University of Geneva.Kauffmann, A.; Rey, F.; Atanassova, I.; Gaudinat, A.; Greenfield, P.; Madinier, H.; Cardey, S. (2021). Indirectly Named Entity Recognition. Journal of Computer-Assisted Linguistic Research. 5(1):27-46. https://doi.org/10.4995/jclr.2021.15922OJS274651Abney, Steven. 1987. "The English Noun Phrase in its Sentential Aspect." PhD diss., Massachusetts Institute of Technology.Alsharaf, H., S. Cardey, P. Greenfield, D. Limame, and I. Skouratov. 2003. "Fixedness, the complexity and fragility of the phenomenon: some solutions for natural language processing." In Proceedings of ICL17. Prague, Czech Republic: Matfyzpress.Ananthanarayanan, Rema, Vijil Chenthamarakshan, Prasad M Deshpande, and Raghuram Krishnapuram. 2008. "Rule Based Synonyms for Entity Extraction from Noisy Text." In Proceedings of the Second Workshop on Analytics for Noisy Unstructured Text Data AND '08, 31-38. Singapore: Association for Computing Machinery. https://doi.org/10.1145/1390749.1390756Bachellier, Jean-Louis. 1972. "Sur-Nom." Le texte: de la théorie à la recherche, no. 19: 69-92. doi :10.3406/comm.1972.1283. https://doi.org/10.3406/comm.1972.1283Baldwin, Timothy, and Su Nam Kim. 2013. "Multiword Expressions." In Handbook of Natural Language Processing, Second Edition, edited by Nitin Indurkhya and Fred J. Damerau, 267-292. Boca Raton, USA: CRCPress.Bohn, C., and Kjeti Nørvag. 2010. "Extracting Named Entities and Synonyms from Wikipedia." In Proceedings of the 24th IEEE International Conference on Advanced Information Networking and Applications, 1300-1307. https://doi.org/10.1109/AINA.2010.50Cai, Desheng, and Gongqing Wu. 2019. "Content-aware attributed entity embedding for synonymous named entity discovery." Neurocomputing 329: 237-247. https://doi.org/10.1016/j.neucom.2018.10.055Chakrabarti, K., S. Chaudhuri, T. Cheng, and Dong Xin. 2012. "A framework for robust discovery of entity synonyms." In Proceedings of the 18th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 1384-1392, Beijing, China: Association for Computing Machinery. https://doi.org/10.1145/2339530.2339743Charton, Eric, Michel Gagnon, and Benoit Ozell. 2011. "Génération automatique de motifs de détection d'entités nommées en utilisant des contenus encyclopédiques (Automatic generation of named entity detection patterns using encyclopedic contents)" [in French]. In Actes de la 18e conférence sur le Traitement Automatique des Langues Naturelles. Articles longs, 13-24. Montpellier, France: ATALA.Cho, Hyejin, Wonjun Choi, and Hyunju Lee. 2017. "A method for named entity normalization in biomedical articles: application to diseases and plants." BMC bioinformatics 18, no. 1 ( 1-12. https://doi.org/10.1186/s12859-017-1857-8Devlin, Jacob, Ming-Wei Chang, Kenton Lee, and Kristina Toutanova. 2019. "BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding." In Proceedings of the 2019 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Volume 1 (Long and Short Papers), 4171-4186. Minneapolis, Minnesota: Association for Computational Linguistics.Friburger, Nathalie. 2006. "Linguistique et reconnaissance automatique des noms propres." Meta 51, no. 4: 637-650. doi:10.7202/014331ar. https://doi.org/10.7202/014331arGuenoune, Hani, Kevin Cousot, Mathieu Lafourcade, Melissa Mekaoui, and Cédric Lopez. 2020. "A Dataset for Anaphora Analysis in French Emails." In Proceedings of the Third Workshop on Computational Models of Reference, Anaphora and Coreference, 165-175. Barcelona, Spain (online): Association for Computational Linguistics.Honnibal, Matthew, and Ines Montani. 2017. "spaCy 2: Natural language understanding with Bloom embeddings, convolutional neural networks and incremental parsing."Kampeera, Wannachai, and Sylviane Cardey-Greenfield. 2012. "Building a Lexically and Semantically-Rich Resource for Paraphrase Processing." In Advances in Natural Language Processing, edited by Hitoshi Isahara and Kyoko Kanzaki, 138-143. Springer Berlin Heidelberg. https://doi.org/10.1007/978-3-642-33983-7_14Kauffmann, Alexis. 2013. "Structural Asymmetries in Machine Translation: The case of English-Japanese". PhD diss., Université de Genève. https://doi.org/10.13097/archive-ouverte/unige:34540.Lample, Guillaume, Miguel Ballesteros, Sandeep Subramanian, Kazuya Kawakami, and Chris Dyer. 2016. "Neural Architectures for Named Entity Recognition." In Proceedings of the 2016 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, 260-270. San Diego, California: Association for Computational Linguistics. https://doi.org/10.18653/v1/N16-1030Lin, Bill Yuchen, Dong-Ho Lee, M. Shen, Ryan Rene Moreno, X. Huang, Prashant Shiralkar, and X. Ren. 2020. "TriggerNER: Learning with Entity Triggers as Explanations for Named Entity Recognition." In Proceedings of the 58th Annual Meeting of the Association for Computational Linguistics, 8503-8511. Online: Association for Computational Linguistics. https://doi.org/10.18653/v1/2020.acl-main.752Lopez, C., Melissa Mekaoui, K. Aubry, Jean Bort, and Philippe Garnier. 2019. "Reconnaissance d'entités nommées itérative sur une structure en dépendances syntaxiques avec l'ontologie NERD." Revue des Nouvelles Technologies de l'Information, Extraction et Gestion des connaissances, RNTI-E-35, 81-92.Ma, Jie, Jun Liu, Y. Li, X. Hu, Yudai Pan, S. Sun, and Qika Lin. 2020. "Jointly Optimized Neural Coreference Resolution with Mutual Attention." In Proceedings of the 13th International Conference on Web Search and Data Mining. Houston, Texas, USA: Association for Computing Machinery. https://doi.org/10.1145/3336191.3371787Manning, Christopher D., Mihai Surdeanu, John Bauer, Jenny Finkel, Steven J. Bethard, and David McClosky. 2014. The Stanford CoreNLP Natural Language Processing Toolkit In Proceedings of the 52nd Annual Meeting of the Association for Computational Linguistics: System Demonstrations, pp. 55-60. Baltimore, Maryland: Association for Computational Linguistics. https://doi.org/10.3115/v1/P14-5010Martin, Louis, Benjamin Muller, Pedro Javier Ortiz Suarez, Yoann Dupont, Laurent Romary, Eric Villemonte de la Clergerie, Benoıt Sagot, and Djamé Seddah. 2020. "Les modèles de langue contextuels CamemBERT pour le français: impact de la taille et de l'hétérogénéité des données d'entrainement (CamemBERT Contextual Language Models for French: Impact of Training Data Size and Heterogeneity)" [in French]. In Actes de la 6e conférence conjointe Journées d'Etudes sur la Parole (JEP, 33e édition), Traitement Automatique des Langues Naturelles (TALN, 27e édition), Rencontre des Etudiants Chercheurs en Informatique pour le' Traitement Automatique des Langues (RECITAL, 22e édition). Volume 2: Traitement Automatique des Langues Naturelles, 54-65. Nancy, France: ATALA et AFCP.Mitkov, Ruslan. 2014. Anaphora resolution. Routledge. https://doi.org/10.4324/9781315840086Mohamed, Muhidin A., and Mourad Chabane Oussalah. 2020. "A hybrid approach for paraphrase identification based on knowledge-enriched semantic heuristics." Language Resources and Evaluation 54 : 457-485. https://doi.org/10.1007/s10579-019-09466-4Nadeau, David, and Satoshi Sekine. 2007. "A survey of named entity recognition and classification." Lingvisticae Investigationes 30: 3-26. https://doi.org/10.1075/li.30.1.03nadNayel, Hamada A., H. L. Shashirekha, Hiroyuki Shindo, and Yuji Matsumoto. 2019. "Improving Multi-Word Entity Recognition for Biomedical Texts." CoRRabs/1908.05691. arXiv:1908.05691.Nebhi, Kamel. 2013. "Named Entity Disambiguation using Freebase and Syntactic Parsing." In [email protected], Damien, Maud Ehrmann, and Sophie Rosset. 2016. "Evaluating Named Entity Recognition." Chap. 6 in Named Entities for Computational Linguistics, 111-129. John Wiley & Sons, Ltd. https://doi.org/10.1002/9781119268567.ch6Ortiz Suarez, Pedro Javier, Yoann Dupont, Benjamin Muller, Laurent Romary, and Benoıt Sagot. 2020. "Establishing a New State-of-the-Art for French Named Entity Recognition" [in English]. In Proceedings of the 12th Language Resources and Evaluation Conference, 4631-4638. Marseille, France: European Language Resources Association.Petit, Gérard. 2006. "Le nom de marque déposée : nom propre, nom commun et terme." Meta 51, no. 4: 690-705. doi:10.7202/014335ar. https://doi.org/10.7202/014335arQu, Meng, Xiang Ren, and Jiawei Han. 2017. "Automatic Synonym Discovery with Knowledge Bases." In Proceedings of the 23rd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 997-1005. KDD '17. Halifax, NS, Canada: Association for Computing Machinery. https://doi.org/10.1145/3097983.3098185Racicot, André. 2009. "Traduire le monde: Venise du Nord et autres surnoms." L'Actualité langagière, vol. 6, n° 2, 23. Travaux publics et Services gouvernementaux Canada.Rey, François-Claude, and Kauffmann Alexis. 2021. "French indirectly named entities (version 1.3) [Data set]." Zenodo. https://doi.org/10.5281/zenodo.5158253.Rosales-Méndez, Henry, Aidan Hogan, and Barbara Poblete. 2019. "Fine-Grained Evaluation for Entity Linking." In Proceedings of the 2019 Conference on Empirical Methods in Natural Language Processing and the 9th International Joint Conference on Natural Language Processing (EMNLP-IJCNLP), 718-727. Hong Kong, China: Association for Computational Linguistics. https://doi.org/10.18653/v1/D19-1066Sales, Juliano Efson, André Freitas, Brian Davis, and Siegfried Handschuh. 2016. "A Compositional-Distributional Semantic Model for Searching Complex Entity Categories." In Proceedings of the Fifth Joint Conference on Lexical and Computational Semantics, 199-208. Berlin, Germany: Association for Computational Linguistics. https://doi.org/10.18653/v1/S16-2025Schmitt, X., S. Kubler, J. Robert, M. Papadakis, and Y. LeTraon. 2019. "A Replicable Comparison Study of NER Software: StanfordNLP, NLTK, OpenNLP, SpaCy, Gate." In Proceedings of the Sixth International Conference on Social Networks Analysis, Management and Security (SNAMS), 338-343. https://doi.org/10.1109/SNAMS.2019.8931850Shang, Jingbo, Liyuan Liu, Xiaotao Gu, Xiang Ren, Teng Ren, and Jiawei Han. 2018. "Learning Named Entity Tagger using Domain-Specific Dictionary." In Proceedings of the 2018 Conference on Empirical Methods in Natural Language Processing, 2054-2064. Brussels, Belgium: Association for Computational Linguistics. https://doi.org/10.18653/v1/D18-1230Shen, Jiaming, Ruiliang Lyu, Xiang Ren, Michelle Vanni, Brian Sadler, and Jiawei Han. 2019. "Mining entity synonyms with efficient neural set generation." In Proceedings of the AAAI Conference on Artificial Intelligence, 33:249-256. doi:10.1609/aaai.v33i01.3301249. https://doi.org/10.1609/aaai.v33i01.3301249Shinyama, Yusuke, Satoshi Sekine, and Kiyoshi Sudo. 2002. "Automatic Paraphrase Acquisition from News Articles." In Proceedings of the Second International Conference on Human Language Technology Research, 313-318. HLT '02. San Diego, California: Morgan Kaufmann Publishers Inc. https://doi.org/10.3115/1289189.1289218Sjöblom, Paula. 2016. "Commercial names." Chap. V.31 in The Oxford Handbook of Names and Naming, edited by Carole Hough, 453-464. Oxford, UK: Oxford University Press. https://doi.org/10.1093/oxfordhb/9780199656431.013.56Tenney, Ian, Dipanjan Das, and Ellie Pavlick. 2019. "BERT Rediscovers the Classical NLP Pipeline." In Proceedings of the 57th Annual Meeting of the Association for Computational Linguistics, 4593-4601. Florence, Italy: Association for Computational Linguistics. https://doi.org/10.18653/v1/P19-1452Treps, Marie. 2012. La rançon de la gloire - Les surnoms de nos politiques. Paris, France: Editions du Seuil.Watanabe, Taiki, Akihiro Tamura, Takashi Ninomiya, Takuya Makino, and Tomoya Iwakura. 2019. 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Cham: Springer International Publishing. https://doi.org/10.1007/978-3-030-73194-6_13Zhang, Ruoyu, Wenpeng Lu, Shoujin Wang, Xueping Peng, Rui Yu, and Yuan Gao. 2021. "Chinese clinical named entity recognition based on stacked neural network." Concurrency and Computation: Practice and Experience : 33:e5775. doi:10.1002/cpe.5775. https://doi.org/10.1002/cpe.577

AI in drug discovery and its clinical relevance

The COVID-19 pandemic has emphasized the need for novel drug discovery process. However, the journey from conceptualizing a drug to its eventual implementation in clinical settings is a long, complex, and expensive process, with many potential points of failure. Over the past decade, a vast growth in medical information has coincided with advances in computational hardware (cloud computing, GPUs, and TPUs) and the rise of deep learning. Medical data generated from large molecular screening profiles, personal health or pathology records, and public health organizations could benefit from analysis by Artificial Intelligence (AI) approaches to speed up and prevent failures in the drug discovery pipeline. We present applications of AI at various stages of drug discovery pipelines, including the inherently computational approaches of de novo design and prediction of a drug's likely properties. Open-source databases and AI-based software tools that facilitate drug design are discussed along with their associated problems of molecule representation, data collection, complexity, labeling, and disparities among labels. How contemporary AI methods, such as graph neural networks, reinforcement learning, and generated models, along with structure-based methods, (i.e., molecular dynamics simulations and molecular docking) can contribute to drug discovery applications and analysis of drug responses is also explored. Finally, recent developments and investments in AI-based start-up companies for biotechnology, drug design and their current progress, hopes and promotions are discussed in this article.  Other InformationPublished in:HeliyonLicense: https://creativecommons.org/licenses/by/4.0/See article on publisher's website: https://doi.org/10.1016/j.heliyon.2023.e17575 </p

Application of Artificial Intelligence in Modern Healthcare System

Artificial intelligence (AI) has the potential of detecting significant interactions in a dataset and also it is widely used in several clinical conditions to expect the results, treat, and diagnose. Artificial intelligence (AI) is being used or trialed for a variety of healthcare and research purposes, including detection of disease, management of chronic conditions, delivery of health services, and drug discovery. In this chapter, we will discuss the application of artificial intelligence (AI) in modern healthcare system and the challenges of this system in detail. Different types of artificial intelligence devices are described in this chapter with the help of working mechanism discussion. Alginate, a naturally available polymer found in the cell wall of the brown algae, is used in tissue engineering because of its biocompatibility, low cost, and easy gelation. It is composed of α-L-guluronic and β-D-manuronic acid. To improve the cell-material interaction and erratic degradation, alginate is blended with other polymers. Here, we discuss the relationship of artificial intelligence with alginate in tissue engineering fields

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

A Series-Elastic Robot for Back-Pain Rehabilitation

Robotics research has been broadly expanding into various fields during the past decades. It is widely spread and best known for solving many technical necessities in different fields. With the rise of the industrial revolution, it upgraded many factories to use industrial robots to prevent the human operator from dangerous and hazardous tasks. The rapid development of application fields and their complexity have inspired researchers in the robotics community to find innovative solutions to meet the new desired requirements of the field. Currently, the creation of new needs outside the traditional industrial robots are demanding robots to attend to the new market and to assist humans in meeting their daily social needs (i.e., agriculture, construction, cleaning.). The future integration of robots into other types of production processes, added new requirements that require more safety, flexibility, and intelligence in robots. Areas of robotics has evolved into various fields. This dissertation addresses robotics research in four different areas: rehabilitation robots, biologically inspired robots, optimization techniques, and neural network implementation. Although these four areas may seem different from each other, they share some research topics and applications