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Register a new userAligning Biomedical Metadata with Ontologies Using Clustering and Embeddings
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Added by
Rafael S. Gon\\c{c}alves
Publication date
2019
fields
Informatics Engineering
and research's language is
English
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The metadata about scientific experiments published in online repositories have been shown to suffer from a high degree of representational heterogeneity---there are often many ways to represent the same type of information, such as a geographical location via its latitude and longitude. To harness the potential that metadata have for discovering scientific data, it is crucial that they be represented in a uniform way that can be queried effectively. One step toward uniformly-represented metadata is to normalize the multiple, distinct field names used in metadata (e.g., lat lon, lat and long) to describe the same type of value. To that end, we present a new method based on clustering and embeddings (i.e., vector representations of words) to align metadata field names with ontology terms. We apply our method to biomedical metadata by generating embeddings for terms in biomedical ontologies from the BioPortal repository. We carried out a comparative study between our method and the NCBO Annotator, which revealed that our method yields more and substantially better alignments between metadata and ontology terms.
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Capturing the semantics of related biological concepts, such as genes and mutations, is of significant importance to many research tasks in computational biology such as protein-protein interaction detection, gene-drug association prediction, and biomedical literature-based discovery. Here, we propose to leverage state-of-the-art text mining tools and machine learning models to learn the semantics via vector representations (aka. embeddings) of over 400,000 biological concepts mentioned in the entire PubMed abstracts. Our learned embeddings, namely BioConceptVec, can capture related concepts based on their surrounding contextual information in the literature, which is beyond exact term match or co-occurrence-based methods. BioConceptVec has been thoroughly evaluated in multiple bioinformatics tasks consisting of over 25 million instances from nine different biological datasets. The evaluation results demonstrate that BioConceptVec has better performance than existing methods in all tasks. Finally, BioConceptVec is made freely available to the research community and general public via https://github.com/ncbi-nlp/BioConceptVec.
Document categorization, which aims to assign a topic label to each document, plays a fundamental role in a wide variety of applications. Despite the success of existing studies in conventional supervised document classification, they are less concerned with two real problems: (1) textit{the presence of metadata}: in many domains, text is accompanied by various additional information such as authors and tags. Such metadata serve as compelling topic indicators and should be leveraged into the categorization framework; (2) textit{label scarcity}: labeled training samples are expensive to obtain in some cases, where categorization needs to be performed using only a small set of annotated data. In recognition of these two challenges, we propose textsc{MetaCat}, a minimally supervised framework to categorize text with metadata. Specifically, we develop a generative process describing the relationships between words, documents, labels, and metadata. Guided by the generative model, we embed text and metadata into the same semantic space to encode heterogeneous signals. Then, based on the same generative process, we synthesize training samples to address the bottleneck of label scarcity. We conduct a thorough evaluation on a wide range of datasets. Experimental results prove the effectiveness of textsc{MetaCat} over many competitive baselines.
In this paper, we propose to align sentence representations from different languages into a unified embedding space, where semantic similarities (both cross-lingual and monolingual) can be computed with a simple dot product. Pre-trained language models are fine-tuned with the translation ranking task. Existing work (Feng et al., 2020) uses sentences within the same batch as negatives, which can suffer from the issue of easy negatives. We adapt MoCo (He et al., 2020) to further improve the quality of alignment. As the experimental results show, the sentence representations produced by our model achieve the new state-of-the-art on several tasks, including Tatoeba en-zh similarity search (Artetxe and Schwenk, 2019b), BUCC en-zh bitext mining, and semantic textual similarity on 7 datasets.
Growing polarization of the news media has been blamed for fanning disagreement, controversy and even violence. Early identification of polarized topics is thus an urgent matter that can help mitigate conflict. However, accurate measurement of topic-wise polarization is still an open research challenge. To address this gap, we propose Partisanship-aware Contextualized Topic Embeddings (PaCTE), a method to automatically detect polarized topics from partisan news sources. Specifically, utilizing a language model that has been finetuned on recognizing partisanship of the news articles, we represent the ideology of a news corpus on a topic by corpus-contextualized topic embedding and measure the polarization using cosine distance. We apply our method to a dataset of news articles about the COVID-19 pandemic. Extensive experiments on different news sources and topics demonstrate the efficacy of our method to capture topical polarization, as indicated by its effectiveness of retrieving the most polarized topics.
Sentence embeddings have become an essential part of todays natural language processing (NLP) systems, especially together advanced deep learning methods. Although pre-trained sentence encoders are available in the general domain, none exists for biomedical texts to date. In this work, we introduce BioSentVec: the first open set of sentence embeddings trained with over 30 million documents from both scholarly articles in PubMed and clinical notes in the MIMIC-III Clinical Database. We evaluate BioSentVec embeddings in two sentence pair similarity tasks in different text genres. Our benchmarking results demonstrate that the BioSentVec embeddings can better capture sentence semantics compared to the other competitive alternatives and achieve state-of-the-art performance in both tasks. We expect BioSentVec to facilitate the research and development in biomedical text mining and to complement the existing resources in biomedical word embeddings. BioSentVec is publicly available at https://github.com/ncbi-nlp/BioSentVec
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