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Biomedical and Clinical Language Models for Spanish: On the Benefits of Domain-Specific Pretraining in a Mid-Resource Scenario [article]

Casimiro Pio Carrino, Jordi Armengol-Estapé, Asier Gutiérrez-Fandiño, Joan Llop-Palao, Marc Pàmies, Aitor Gonzalez-Agirre, Marta Villegas
2021 arXiv   pre-print
We evaluated our models on Named Entity Recognition (NER) tasks for biomedical documents and challenging hospital discharge reports.  ...  To the best of our knowledge, we provide the first biomedical and clinical transformer-based pretrained language models for Spanish, intending to boost native Spanish NLP applications in biomedicine.  ...  We assess the effectiveness of these models in different settings, two biomedical scenarios and a demanding clinical scenario with real hospital reports. 3.  ... 
arXiv:2109.03570v2 fatcat:kxnedqd43ng7hnedtjfdmrgpmm

Neural Natural Language Processing for Unstructured Data in Electronic Health Records: a Review [article]

Irene Li, Jessica Pan, Jeremy Goldwasser, Neha Verma, Wai Pan Wong, Muhammed Yavuz Nuzumlalı, Benjamin Rosand, Yixin Li, Matthew Zhang, David Chang, R. Andrew Taylor, Harlan M. Krumholz (+1 others)
2021 arXiv   pre-print
In this survey paper, we summarize current neural NLP methods for EHR applications.  ...  We focus on a broad scope of tasks, namely, classification and prediction, word embeddings, extraction, generation, and other topics such as question answering, phenotyping, knowledge graphs, medical dialogue  ...  Named Entity Recognition Named Entity Recognition (NER) is the task of determining whether tokens or spans in a text correspond to certain "named entities" of interest, such as medications and diseases  ... 
arXiv:2107.02975v1 fatcat:nayhw7gadfdzrovycdkvzy75pi

Pre-trained Language Models in Biomedical Domain: A Systematic Survey [article]

Benyou Wang, Qianqian Xie, Jiahuan Pei, Prayag Tiwari, Zhao Li, Jie fu
2021 arXiv   pre-print
In this paper, we summarize the recent progress of pre-trained language models in the biomedical domain and their applications in biomedical downstream tasks.  ...  Pre-trained language models (PLMs) have been the de facto paradigm for most natural language processing (NLP) tasks.  ...  full-text articles) for biomedical named entity recognition.  ... 
arXiv:2110.05006v2 fatcat:aykwfhgi4jgmfovissgdvknny4

Transformers for Clinical Coding in Spanish

Guillermo Lopez-Garcia, Jose M. Jerez, Nuria Ribelles, Emilio Alba, Francisco J. Veredas
2021 IEEE Access  
codesthat is, this last subtask became a named-entity-recognition and normalization (NER-N) task.  ...  In fact, as a result of fine-tuning 5 distinct instances of each model, 5 different probability matrices, namely, M 1 A , M 2 A , ..., M 5 A , were obtained for model A.  ... 
doi:10.1109/access.2021.3080085 fatcat:y3qh3udqjrfxdfa7xdi2olmzjm

Pragmatic medicine in solid cancer: a translational alternative to precision medicine

Jan Brabek, Daniel Rosel, Michael Fernandes
2016 OncoTargets and Therapy  
In solid cancer, drug induced tumor shrinkage, is a drug effect and not a disease response; tumor shrinkage does not reflect nor predict interruption of the disease.  ...  A revised initiative that prioritizes metastasis research could replicate the successful HIV/AIDS model in solid cancer.  ...  Acknowledgment We thank Roberto Fiorentini, MD, Washington, DC, for his comments on pharma and regulatory strategy.  ... 
doi:10.2147/ott.s103832 pmid:27103822 pmcid:PMC4827419 fatcat:azcgltnbkjezrahtniwnlzts5y

Findings of the WMT 2019 Biomedical Translation Shared Task: Evaluation for MEDLINE Abstracts and Biomedical Terminologies

Rachel Bawden, Kevin Bretonnel Cohen, Cristian Grozea, Antonio Jimeno Yepes, Madeleine Kittner, Martin Krallinger, Nancy Mah, Aurelie Neveol, Mariana Neves, Felipe Soares, Amy Siu, Karin Verspoor (+1 others)
2019 Proceedings of the Fourth Conference on Machine Translation (Volume 3: Shared Task Papers, Day 2)  
In the fourth edition of the WMT Biomedical Translation task, we considered a total of six languages, namely Chinese (zh), English (en), French (fr), German (de), Portuguese (pt), and Spanish (es).  ...  In addition to that, we offered a new sub-task for the translation of terms in biomedical terminologies for the en/es language direction.  ...  Acknowledgments We would like to thank all participants in the challenges, and especially those who supported us for the manual evaluation, including Melana Uceda (es/en).  ... 
doi:10.18653/v1/w19-5403 dblp:conf/wmt/BawdenCGJKKMNNS19 fatcat:ir5jjy2zgvf5josqkr42l4rikq

On the use of agent technology in intelligent, multisensory and distributed surveillance

José M. Gascueña, Antonio Fernández-Caballero
2011 Knowledge engineering review (Print)  
), suggest that the agency is a good choice for solving problems which appear and are dealt with in surveillance systems. 192  ...  Current surveillance systems are noted for using several devices, heterogeneous in many instances, distributed along the observed scenario, while incorporating a certain degree of intelligence to alert  ...  Acknowledgments This work was partially supported by the Spanish Ministerio de Ciencia e Innovacio´n under projects TIN2007-67586-C02-02 and TIN2010-20845-C03-01 and by the Spanish Junta de Comunidades  ... 
doi:10.1017/s0269888911000026 fatcat:72b3jx6wurb6daoylicir2el4a

Pragmatic medicine in solid cancer: a translational alternative to precision medicine

Brábek J, Rosel D, Fernandes M
2016 OncoTargets and Therapy  
In solid cancer, drug induced tumor shrinkage, is a drug effect and not a disease response; tumor shrinkage does not reflect nor predict interruption of the disease.  ...  A revised initiative that prioritizes metastasis research could replicate the successful HIV/AIDS model in solid cancer.  ...  For too long, drug approval in solid cancer has been based on the RECIST convention, namely, tumor shrinkage 45,46 (Figure 2).  ... 
doaj:ab6b8a281b684a63b5acc5efbe82e3c2 fatcat:xwiirmddejhknmkc6uj646veze

Adjectival vs. nominal categorization processes: The Rule vs. Similarity hypothesis

2011 Belgian Journal of Linguistics  
Classification of entities into categories can be determined based on a rule – a single criterion or relatively few criteria combined with logical operations like 'and' or 'or'.  ...  These links suggest that the rule vs. similarity (RS) hypothesis for the adjective-noun distinction should be studied more directly in the future.  ...  For example, recognition time is longer for adjectives than for nouns only in incomplete learners.  ... 
doi:10.1075/bjl.25.06sas fatcat:cwcdd7haffd55njxpltvmfkfhe

Orthographic variations and visual information processing

Daisy L. Hung, Ovid J. Tzeng
1981 Psychological bulletin  
Further analyses of segmentation in script as well as in speech reveal that every orthography transcribes sentences at the level of words and that the transcription is achieved in a morphemic way.  ...  This coincidence may imply that different cognitive processes are required for achieving reading proficiency in different writing systems.  ...  Actually, a VCG model would predict that word and nonword recognition accuracy should be the same and should be lower than for the single kana symbol.  ... 
doi:10.1037//0033-2909.90.3.377 fatcat:wyejx7qz45bxfpqfp3pfyowqdm

Orthographic variations and visual information processing

Daisy L. Hung, Ovid J. Tzeng
1981 Psychological bulletin  
Further analyses of segmentation in script as well as in speech reveal that every orthography transcribes sentences at the level of words and that the transcription is achieved in a morphemic way.  ...  This coincidence may imply that different cognitive processes are required for achieving reading proficiency in different writing systems.  ...  Actually, a VCG model would predict that word and nonword recognition accuracy should be the same and should be lower than for the single kana symbol.  ... 
doi:10.1037/0033-2909.90.3.377 fatcat:3ihq2gv4j5erjho5hyky35522a

Annotation and detection of drug effects in text for pharmacovigilance

Paul Thompson, Sophia Daikou, Kenju Ueno, Riza Batista-Navarro, Jun'ichi Tsujii, Sophia Ananiadou
2018 Journal of Cheminformatics  
guidelines and the demonstration of high levels of interannotator agreement (e.g., 92.6% F-Score for identifying named entities and 78.4% F-Score for identifying complex events, when relaxed matching  ...  Creating and maintaining such resources can be complex, since a particular medication may have divergent effects in different individuals, due to specific patient characteristics and/or interactions with  ...  We also thank Piotr Przybyła for his help with the visualisation of the annotations with the brat software.  ... 
doi:10.1186/s13321-018-0290-y pmid:30105604 fatcat:hqhfbgoyjzd3hcczvbcerpumwq

Microglia-Centered Combinatorial Strategies Against Glioblastoma

Tomás A. Martins, Philip Schmassmann, Tala Shekarian, Jean-Louis Boulay, Marie-Françoise Ritz, Steven Zanganeh, Johannes vom Berg, Gregor Hutter
2020 Frontiers in Immunology  
MG as a main factor for treatment failure.  ...  models and methods.  ...  Selina Ackermann for editorial support and critical revision of the manuscript.  ... 
doi:10.3389/fimmu.2020.571951 pmid:33117364 pmcid:PMC7552736 fatcat:cob3tsfblfhbffempkbhq3fmqa

Smart drug delivery systems: from fundamentals to the clinic

Carmen Alvarez-Lorenzo, Angel Concheiro
2014 Chemical Communications  
Acknowledgements Work supported by Spanish Ministerio de Economía y Competividad (SAF 2011-22771), Xunta de Galicia (CN 2012/045) and FEDER.  ...  In vivo studies carried out in a Bcap37 breast tumor xenograft model and a dimethylhydrazine (DMH)-induced autochthonous colon cancer model evidenced that the conjugate was better tolerated than the free  ...  model (e.g. red blood cells as encapsulating entities), the iterative scheme tries to answer a sequence of questions that may be useful for the design of new prototypes or further innovations (e.g. liposomes  ... 
doi:10.1039/c4cc01429d pmid:24805962 fatcat:76xignwlwvgv7dr2pv6cjm3oxe

Abstracts Presented at the Twenty-Third Annual Meeting of the International Neuropsychological Society February 8–11, 1995 Seattle, Washington

1995 Journal of the International Neuropsychological Society  
The attention measures loaded on factors for auditory' mental control, auditory sustained attention, and visual attention.  ...  the national model systems project.  ...  The deficit in face and name processing in DAT patients was at identification and naming, rather than recognition.  ... 
doi:10.1017/s1355617700001843 fatcat:kp53pe6bgfgwtgyncaxpe3vcca
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