Editorial for the First Workshop on Mining Scientific Papers: Computational Linguistics and Bibliometrics

The workshop "Mining Scientific Papers: Computational Linguistics and Bibliometrics" (CLBib 2015), co-located with the 15th International Society of Scientometrics and Informetrics Conference (ISSI 2015), brought together researchers in Bibliometrics and Computational Linguistics in order to study the ways Bibliometrics can benefit from large-scale text analytics and sense mining of scientific papers, thus exploring the interdisciplinarity of Bibliometrics and Natural Language Processing (NLP). The goals of the workshop were to answer questions like: How can we enhance author network analysis and Bibliometrics using data obtained by text analytics? What insights can NLP provide on the structure of scientific writing, on citation networks, and on in-text citation analysis? This workshop is the first step to foster the reflection on the interdisciplinarity and the benefits that the two disciplines Bibliometrics and Natural Language Processing can drive from it.Comment: 4 pages, Workshop on Mining Scientific Papers: Computational Linguistics and Bibliometrics at ISSI 201

On the composition of scientific abstracts

Purpose Scientific abstracts reproduce only part of the information and the complexity of argumentation in a scientific article. The purpose of this paper provides a first analysis of the similarity between the text of scientific abstracts and the body of articles, using sentences as the basic textual unit. It contributes to the understanding of the structure of abstracts. Design/methodology/approach Using sentence-based similarity metrics, the authors quantify the phenomenon of text re-use in abstracts and examine the positions of the sentences that are similar to sentences in abstracts in the introduction, methods, results and discussion structure, using a corpus of over 85,000 research articles published in the seven Public Library of Science journals. Findings The authors provide evidence that 84 percent of abstract have at least one sentence in common with the body of the paper. Studying the distributions of sentences in the body of the articles that are re-used in abstracts, the authors show that there exists a strong relation between the rhetorical structure of articles and the zones that authors re-use when writing abstracts, with sentences mainly coming from the beginning of the introduction and the end of the conclusion. Originality/value Scientific abstracts contain what is considered by the author(s) as information that best describe documents’ content. This is a first study that examines the relation between the contents of abstracts and the rhetorical structure of scientific articles. The work might provide new insight for improving automatic abstracting tools as well as information retrieval approaches, in which text organization and structure are important features

Mining Scientific Papers for Bibliometrics: a (very) Brief Survey of Methods and Tools

The Open Access movement in scientific publishing and search engines like Google Scholar have made scientific articles more broadly accessible. During the last decade, the availability of scientific papers in full text has become more and more widespread thanks to the growing number of publications on online platforms such as ArXiv and CiteSeer. The efforts to provide articles in machine-readable formats and the rise of Open Access publishing have resulted in a number of standardized formats for scientific papers (such as NLM-JATS, TEI, DocBook). Our aim is to stimulate research at the intersection of Bibliometrics and Computational Linguistics in order to study the ways Bibliometrics can benefit from large-scale text analytics and sense mining of scientific papers, thus exploring the interdisciplinarity of Bibliometrics and Natural Language Processing.Comment: 2 pages, paper accepted for the 15th International Society of Scientometrics and Informetrics Conference (ISSI

The linguistic patterns and rhetorical structure of citation context : an approach using n-grams

Using the full-text corpus of more than 75,000 research articles published by seven PLOS journals, this paper proposes a natural language processing approach for identifying the function of citations. Citation contexts are assigned based on the frequency of n-gram co-occurrences located near the citations. Results show that the most frequent linguistic patterns found in the citation contexts of papers vary according to their location in the IMRaD structure of scientific articles. The presence of negative citations is also dependent on this structure. This methodology offers new perspectives to locate these discursive forms according to the rhetorical structure of scientific articles, and will lead to a better understanding of the use of citations in scientific articles

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. "Multi-Task Learning for Chemical Named Entity Recognition with Chemical Compound Paraphrasing." 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), 6244-6249. Hong Kong, China: Association for Computational Linguistics. https://doi.org/10.18653/v1/D19-1648Wehrli, Eric, and Luka Nerima. 2018. "Anaphora resolution, collocations and translation." In Multiword units in machine translation and translation technology, edited by Johanna Monti, Violeta Seretan, Gloria Corpas Pastor, and Ruslan Mitkov, 244-256. John Benjamins. https://doi.org/10.1075/cilt.341.12wehWehrli, Eric, Violeta Seretan, and Luka Nerima. 2010. "Sentence Analysis and Collocation Identification." In Proceedings of the 2010 Workshop on Multiword Expressions: from Theory to Applications, 28-36. Beijing, China: Coling 2010 Organizing Committee.Weston, L., V. Tshitoyan, J. Dagdelen, O. Kononova, A. Trewartha, K. A. Persson, G. Ceder, and A. Jain. 2019. "Named Entity Recognition and Normalization Applied to Large-Scale Information Extraction from the Materials Science Literature." Journal of Chemical Information and Modeling 59, no. 9: 3692-3702. doi: 10.1021/acs.jcim.9b00470. https://doi.org/10.1021/acs.jcim.9b00470Wu, G., Y. He, and X. Hu. 2018. "Entity Linking: An Issue to Extract Corresponding Entity With Knowledge Base." IEEE Access 6: 6220-6231. doi:10.1109/ACCESS.2017.2787787. https://doi.org/10.1109/ACCESS.2017.2787787Yang, Yiying, Xi Yin, Haiqin Yang, Xingjian Fei, Hao Peng, Kaijie Zhou, Kunfeng Lai, and Jianping Shen. 2021. "KGSynNet: A Novel Entity Synonyms Discovery Framework with Knowledge Graph." In Database Systems for Advanced Applications, edited by Christian S. Jensen, Ee-Peng Lim, De-Nian Yang, Wang-Chien Lee, Vincent S. Tseng, Vana Kalogeraki, Jen-Wei Huang, and Chih-Ya Shen, 174-190. 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

Information retrieval and semantic annotation of scientific corpora (Keynote paper)

International audienc

Information Retrieval and Text Navigation through the Exploitation of the Automatic Semantic Annotation of the Excom Engine

À partir du moteur d’annotation sémantique Excom, nous avons élaboré un systèmede recherche d’informations qui repose sur des catégories sémantiques issues d’analyses linguistiquesautomatiques afin de proposer une approche de fouille textuelle innovante. Les annotationssont obtenues par la méthode d’Exploration Contextuelle faisant appel à une modélisationdes connaissances linguistiques sous forme de marqueurs et de règles. Le traitement des requêtesselon des points de vue de fouille se trouve au coeur de la stratégie de recherche d’informations.Pour cela, notre approche s’appuie sur des catégories d’annotation organisées en ontologies linguistiquessous forme de graphes. Afin d’offrir à l’utilisateur des résultats pertinents, nous avonsmis en place des algorithmes d’ordonnancement des réponses et de gestion de la redondance.Ces algorithmes reposent principalement sur la structure des ontologies linguistiques utiliséespour l’annotation. Nous avons proposé une évaluation de la pertinence des résultats en tenantcompte de la spécificité de l’approche. Les interfaces que nous avons développées permettent laconstruction de nouveaux produits documentaires tels que les fiches de synthèse offrant une extractiond’informations structurées selon des critères sémantiques. Cee approche a égalementpour vocation de proposer des outils dédiés à la veille stratégique et à l’intelligence économique.Using the Excom engine for semantic annotation, we have constructed an InformationRetrieval System based on semantic categories from automatic language analyses in order topropose a new approach to text search. e annotations are obtained by the Contextual Explorationmethod which is a knowledge based linguistic approach using markers and disambiguationrules. e queries are formulated according to search viewpoints which are at the heart of theInformation Retrieval strategy. Our approach uses the annotation categories which are organisedin linguistic ontologies structured as graphs. In order to provide relevant results to the user,we have designed algorithms for ranking and paraphrase identification. ese algorithms exploitprincipally the structure of the linguistic ontologies for the annotation. We have carriedout an evaluation of the relevance of the system results taking into account the specificity ofour approach. We have developed user interfaces allowing the construction of new informationproducts such as structured text syntheses using information extraction according to semanticcriteria. is approach also aims to offer tools in the field of economic intelligence

Beyond Metada: the New Challenges in Mining Scientific Papers

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De l’intuition scientifique au moment de l’illumination : étude de « Théorème vivant » par Cédric Villani

National audienc

Enjeux de l’étude des contextes citationnels dans le cadre des études bibliométriques : contextes de citation et blocs citationnels

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