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Incorporating Figure Captions and Descriptive Text in MeSH Term Indexing
2019
Proceedings of the 18th BioNLP Workshop and Shared Task
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Beyond the normal use of the text from the abstract and title for model training, we also consider figure and table captions, as well as paragraphs associated with the figures and tables. ...
In this paper, we focus specifically on biomedical document classification using a deep learning approach. We present a novel multichannel TextCNN model for MeSH term indexing. ...
Acknowledgements This research is partially funded by The Natural Sciences and Engineering Research Council of Canada through a Discovery Grant to Robert E. Mercer. ...
doi:10.18653/v1/w19-5018
dblp:conf/bionlp/WangM19
fatcat:k2arbfqqq5b3nokdcy75nxiira
Automated Semantic Indexing of Figure Captions to Improve Radiology Image Retrieval
2009
JAMIA Journal of the American Medical Informatics Association
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Conclusion: Concept-based indexing of radiology journal figure captions achieved very high precision and recall, and significantly improved image retrieval. ...
Design: The MetaMap Transfer program (MMTx) was used to map the text of 84,846 figure captions from 9,004 peer-reviewed, English-language articles to concepts in three controlled vocabularies from the ...
Conceptual indexing differs from keyword indexing in that the text is labeled with descriptive terms, usually taken from a controlled terminology. ...
doi:10.1197/jamia.m2945
pmid:19261938
pmcid:PMC2732225
fatcat:jvo3am2fc5di7emgqomdrrsr5m
MeSHup: A Corpus for Full Text Biomedical Document Indexing
[article]
2022
arXiv
pre-print
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We release a large scale annotated MeSH indexing corpus, MeSHup, which contains 1,342,667 full text articles in English, together with the associated MeSH labels and metadata, authors, and publication ...
Medical Subject Heading (MeSH) indexing refers to the problem of assigning a given biomedical document with the most relevant labels from an extremely large set of MeSH terms. ...
Acknowledgements We thank all reviewers for their constructive comments and feedback. Resources used in preparing this research were provided, in part, by Compute Ontario ...
arXiv:2204.13604v1
fatcat:srvmuhrgjbb4nnysru2xhkzouy
Improving image retrieval effectiveness via query expansion using MeSH hierarchical structure
2013
JAMIA Journal of the American Medical Informatics Association
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In order to achieve greater effectiveness in the expansion, the search text was analyzed to identify which terms were most amenable to being expanded. ...
In the second strategy the text of the query was divided into n-grams, resulting in sequences corresponding to MeSH descriptors. ...
title text, figure captions, abstracts or full text. ...
doi:10.1136/amiajnl-2012-000943
pmid:22952301
pmcid:PMC3822102
fatcat:jq376vzfwzefrmzeqaodqv4wfu
Design and Development of a Multimodal Biomedical Information Retrieval System
2012
Journal of Computing Science and Engineering
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Biomedical information exists in different forms: as text and illustrations in journal articles and other documents, in images stored in databases, and as patients' cases in electronic health records. ...
This paper presents ways to move beyond conventional text-based searching of these resources, by combining text and visual features in search queries and document representation. ...
We thank Essie developers Russell Loane and Nicholas Ide for providing the search engine, and being wonderfully responsive and supportive in development of the OpenI systems. ...
doi:10.5626/jcse.2012.6.2.168
fatcat:am3nzm4djfft5g5ngklp6fjmae
Semedico: A Comprehensive Semantic Search Engine for the Life Sciences
2017
Proceedings of ACL 2017, System Demonstrations
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SEMEDICO excels with an ad-hoc search approach which directly reflects relevance in terms of information density of entities and relations among them (events) and, a truly unique feature, ranks interaction ...
SEMEDICO is a semantic search engine designed to support literature search in the life sciences by integrating the semantics of the domain at all stages of the search process-from query formulation via ...
captions and the complete document text, if applicable. ...
doi:10.18653/v1/p17-4016
dblp:conf/acl/FaesslerH17
fatcat:folqg7czdbdsdo5z6uqfnw2e5a
Multi-Attention and Incorporating Background Information Model for Chest X-Ray Image Report Generation
2019
IEEE Access
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INDEX TERMS Attention mechanism, deep learning, radiology report generation, word embedding. 154808 This work is licensed under a Creative Commons Attribution 4.0 License. ...
Chest X-ray images are widely used in clinical practice such as diagnosis and treatment. ...
IMAGE CAPTIONING Image Captioning is a task that automatically generates text descriptions for given images. ...
doi:10.1109/access.2019.2947134
fatcat:mynqvu4r5fdcrj5utuplhodxkq
ZeroCap: Zero-Shot Image-to-Text Generation for Visual-Semantic Arithmetic
[article]
2022
arXiv
pre-print
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2021 pre-print arXiv:2111.14447v1 fatcat:uhuh7ffgerf4pbd7jp3zsulcty
In this work, we repurpose such models to generate a descriptive text given an image at inference time, without any further training or tuning steps. ...
Moreover, as a zero-shot learning method, it is extremely flexible and we demonstrate its ability to perform image arithmetic in which the inputs can be either images or text, and the output is a sentence ...
Moreover, the semantic knowledge incorporated into CLIP and GPT-2 is manifested in the resulting caption, see Fig. 1 . ...
arXiv:2111.14447v2
fatcat:vfowvq2qofbt3aef4l5swdanum
Information Retrieval by Semantic Similarity
2006
International Journal on Semantic Web and Information Systems (IJSWIS)
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Typically, semantic similarity is computed by mapping terms to an ontology and by examining their relationships in that ontology. ...
The most popular semantic similarity methods are implemented and evaluated using WordNet and MeSH. ...
All OHSUMED documents are indexed by title, abstract and MeSH terms (MeSH Headings). ...
doi:10.4018/jswis.2006070104
fatcat:txa6cg4rwnejdgpkuw7giq3nf4
The Transcription Factor Encyclopedia
2012
Genome Biology
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TFe aims to rapidly educate scientists about the TFs they encounter through the delivery of succinct summaries written and vetted by experts in the field. TFe is available at ...
Notable features of the TFe website include a high-quality PDF generator and web API for programmatic data retrieval. ...
Computer hardware resources utilized in this project were supported by the Gene Regulation Bioinformatics Laboratory funded by the Canada Foundation for Innovation (CFI). ...
doi:10.1186/gb-2012-13-3-r24
pmid:22458515
pmcid:PMC3439975
fatcat:gxpf77o6urfddir5vw7igipj3a
Frontiers of biomedical text mining: current progress
2007
Briefings in Bioinformatics
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It is now almost 15 years since the publication of the first paper on text mining in the genomics domain, and decades since the first paper on text mining in the medical domain. ...
Some problems, such as abbreviationhandling, can essentially be considered solved problems, and others, such as identification of gene mentions in text, seem likely to be solved soon. ...
KBC was supported by NIH grants 'Construction of a Full Text Corpus for Biomedical Text Mining' (#1G08LM009639-01) and 'Technology Development for a Molecular Biology Knowledge-base' (#5R01 LM008111-03 ...
doi:10.1093/bib/bbm045
pmid:17977867
pmcid:PMC2516302
fatcat:4nfbokb7lfdjbnkijw2v6754qy
A Sparse Transformer-Based Approach for Image Captioning
2020
IEEE Access
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INDEX TERMS Image captioning, self-attention, explict sparse, local adaptive threshold. ...
Image Captioning is the task of providing a natural language description for an image. ...
ACKNOWLEDGMENT The authors would like to thank the High Performance Computing Center of Shanghai University for providing the computing resources and technical support. ...
doi:10.1109/access.2020.3024639
fatcat:j2wcwshcqrhe3oxzkiylq5wzcq
Geometry Attention Transformer with Position-aware LSTMs for Image Captioning
[article]
2021
arXiv
pre-print
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steps, and 2) a group of position-LSTMs, for precisely informing the decoder of relative word position in generating caption texts. ...
In recent years, transformer structures have been widely applied in image captioning with impressive performance. ...
Figure 3 : 3 The output comparison of captions generated respectively by our GAT and a base model, as well as three manual description captions of ground truth, GT1∼GT3. ...
arXiv:2110.00335v1
fatcat:emucqxpc3rdfpeu3xoewpwuj2i
GeneView: a comprehensive semantic search engine for PubMed
2012
Nucleic Acids Research
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Research results are primarily published in scientific literature and curation efforts cannot keep up with the rapid growth of published literature. ...
The plethora of knowledge remains hidden in large text repositories like MEDLINE. Consequently, life scientists have to spend a great amount of time searching for specific information. ...
ACKNOWLEDGEMENTS We thank the reviewers for their careful reading and helpful comments. ...
doi:10.1093/nar/gks563
pmid:22693219
pmcid:PMC3394277
fatcat:pdmdg5hdbvb4reroht5v6pzlsy
Figure-Associated Text Summarization and Evaluation
2015
PLoS ONE
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, and generate a text summary for every figure in an article. ...
Biomedical literature incorporates millions of figures, which are a rich and important knowledge resource for biomedical researchers. ...
[56] developed a method that computes similarities between the MeSH terms assigned to an article in addition to its word tokens and then returns the top N-ranked sentences as summary sentences. ...
doi:10.1371/journal.pone.0115671
pmid:25643357
pmcid:PMC4313946
fatcat:dbkj7zhyq5bmjkkhfdnef2wpne
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