Improving word embeddings in Portuguese: increasing accuracy while reducing the size of the corpus.
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ABSTRACT:
SUBMITTER: Pinto JP
PROVIDER: S-EPMC9301597 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Distributed word representations have become an essential foundation for biomedical natural language processing (BioNLP), text mining and information retrieval. Word embeddings are traditionally computed at the word level from a large corpus of unlabeled text, ignoring the information present in the internal structure of words or any information available in domain specific structured resources such as ontologies. However, such information holds potentials for greatly improving the quality of the word representation, as suggested in some recent studies in the general domain. Here we present BioWordVec: an open set of biomedical word vectors/embeddings that combines subword information from unlabeled biomedical text with a widely-used biomedical controlled vocabulary called Medical Subject Headings (MeSH). We assess both the validity and utility of our generated word embeddings over multiple NLP tasks in the biomedical domain. Our benchmarking results demonstrate that our word embeddings can result in significantly improved performance over the previous state of the art in those challenging tasks.
| S-EPMC6510737 | biostudies-literature
Project description:In Western societies, the stereotype prevails that pink is for girls and blue is for boys. A third possible gendered colour is red. While liked by women, it represents power, stereotypically a masculine characteristic. Empirical studies confirmed such gendered connotations when testing colour-emotion associations or colour preferences in males and females. Furthermore, empirical studies demonstrated that pink is a positive colour, blue is mainly a positive colour, and red is both a positive and a negative colour. Here, we assessed if the same valence and gender connotations appear in widely available written texts (Wikipedia and newswire articles). Using a word embedding method (GloVe), we extracted gender and valence biases for blue, pink, and red, as well as for the remaining basic colour terms from a large English-language corpus containing six billion words. We found and confirmed that pink was biased towards femininity and positivity, and blue was biased towards positivity. We found no strong gender bias for blue, and no strong gender or valence biases for red. For the remaining colour terms, we only found that green, white, and brown were positively biased. Our finding on pink shows that writers of widely available English texts use this colour term to convey femininity. This gendered communication reinforces the notion that results from research studies find their analogue in real word phenomena. Other findings were either consistent or inconsistent with results from research studies. We argue that widely available written texts have biases on their own, because they have been filtered according to context, time, and what is appropriate to be reported.
| S-EPMC8168888 | biostudies-literature
Project description:Machine learning has emerged as a powerful approach in materials discovery. Its major challenge is selecting features that create interpretable representations of materials, useful across multiple prediction tasks. We introduce an end-to-end machine learning model that automatically generates descriptors that capture a complex representation of a material's structure and chemistry. This approach builds on computational topology techniques (namely, persistent homology) and word embeddings from natural language processing. It automatically encapsulates geometric and chemical information directly from the material system. We demonstrate our approach on multiple nanoporous metal-organic framework datasets by predicting methane and carbon dioxide adsorption across different conditions. Our results show considerable improvement in both accuracy and transferability across targets compared to models constructed from the commonly-used, manually-curated features, consistently achieving an average 25-30% decrease in root-mean-squared-deviation and an average increase of 40-50% in R2 scores. A key advantage of our approach is interpretability: Our model identifies the pores that correlate best to adsorption at different pressures, which contributes to understanding atomic-level structure-property relationships for materials design.
| S-EPMC8076181 | biostudies-literature
Project description:OBJECTIVE:In this work, we introduce a privacy technique for anonymizing clinical notes that guarantees all private health information is secured (including sensitive data, such as family history, that are not adequately covered by current techniques). MATERIALS AND METHODS:We employ a new "random replacement" paradigm (replacing each token in clinical notes with neighboring word vectors from the embedding space) to achieve 100% recall on the removal of sensitive information, unachievable with current "search-and-secure" paradigms. We demonstrate the utility of this paradigm on multiple corpora in a diverse set of classification tasks. RESULTS:We empirically evaluate the effect of our anonymization technique both on upstream and downstream natural language processing tasks to show that our perturbations, while increasing security (ie, achieving 100% recall on any dataset), do not greatly impact the results of end-to-end machine learning approaches. DISCUSSION:As long as current approaches utilize precision and recall to evaluate deidentification algorithms, there will remain a risk of overlooking sensitive information. Inspired by differential privacy, we sought to make it statistically infeasible to recreate the original data, although at the cost of readability. We hope that the work will serve as a catalyst to further research into alternative deidentification methods that can address current weaknesses. CONCLUSION:Our proposed technique can secure clinical texts at a low cost and extremely high recall with a readability trade-off while remaining useful for natural language processing classification tasks. We hope that our work can be used by risk-averse data holders to release clinical texts to researchers.
| S-EPMC7309261 | biostudies-literature
Project description:Word embeddings are a powerful machine-learning framework that represents each English word by a vector. The geometric relationship between these vectors captures meaningful semantic relationships between the corresponding words. In this paper, we develop a framework to demonstrate how the temporal dynamics of the embedding helps to quantify changes in stereotypes and attitudes toward women and ethnic minorities in the 20th and 21st centuries in the United States. We integrate word embeddings trained on 100 y of text data with the US Census to show that changes in the embedding track closely with demographic and occupation shifts over time. The embedding captures societal shifts-e.g., the women's movement in the 1960s and Asian immigration into the United States-and also illuminates how specific adjectives and occupations became more closely associated with certain populations over time. Our framework for temporal analysis of word embedding opens up a fruitful intersection between machine learning and quantitative social science.
| S-EPMC5910851 | biostudies-literature
Project description:BackgroundThere has been increasing interest in machine learning based natural language processing (NLP) methods in radiology; however, models have often used word embeddings trained on general web corpora due to lack of a radiology-specific corpus.PurposeWe examined the potential of Radiopaedia to serve as a general radiology corpus to produce radiology specific word embeddings that could be used to enhance performance on a NLP task on radiological text.Materials and methodsEmbeddings of dimension 50, 100, 200, and 300 were trained on articles collected from Radiopaedia using a GloVe algorithm and evaluated on analogy completion. A shallow neural network using input from either our trained embeddings or pre-trained Wikipedia 2014 + Gigaword 5 (WG) embeddings was used to label the Radiopaedia articles. Labeling performance was evaluated based on exact match accuracy and Hamming loss. The McNemar's test with continuity and the Benjamini-Hochberg correction and a 5×2 cross validation paired two-tailed t-test were used to assess statistical significance.ResultsFor accuracy in the analogy task, 50-dimensional (50-D) Radiopaedia embeddings outperformed WG embeddings on tumor origin analogies (p < 0.05) and organ adjectives (p < 0.01) whereas WG embeddings tended to outperform on inflammation location and bone vs. muscle analogies (p < 0.01). The two embeddings had comparable performance on other subcategories. In the labeling task, the Radiopaedia-based model outperformed the WG based model at 50, 100, 200, and 300-D for exact match accuracy (p < 0.001, p < 0.001, p < 0.01, and p < 0.05, respectively) and Hamming loss (p < 0.001, p < 0.001, p < 0.01, and p < 0.05, respectively).ConclusionWe have developed a set of word embeddings from Radiopaedia and shown that they can preserve relevant medical semantics and augment performance on a radiology NLP task. Our results suggest that the cultivation of a radiology-specific corpus can benefit radiology NLP models in the future.
| S-EPMC7856086 | biostudies-literature
Project description:MotivationInter-organ/inter-tissue communication is central to multi-cellular organisms including humans, and mapping inter-tissue interactions can advance system-level whole-body modeling efforts. Large volumes of biomedical literature have fostered studies that map within-tissue or tissue-agnostic interactions, but literature-mining studies that infer inter-tissue relations, such as between hormones and genes are solely missing.ResultsWe present a first study to predict from biomedical literature the hormone-gene associations mediating inter-tissue signaling in the human body. Our BioEmbedS* models use neural network-based Biomedical word Embeddings with a Support Vector Machine classifier to predict if a hormone-gene pair is associated or not, and whether an associated gene is involved in the hormone's production or response. Model training relies on our unified dataset Hormone-Gene version 1 of ground-truth associations between genes and endocrine hormones, which we compiled and carefully balanced in the embedded space to handle data disparities, such as between poorly- versus well-studied hormones. Our BioEmbedS model recapitulates known gene mediators of tissue-tissue signaling with 70.4% accuracy; predicts novel inter-tissue communication genes in humans, which are enriched for hormone-related disorders; and generalizes well to mouse, thereby holding promise for its extension to other multi-cellular organisms as well.Availability and implementationFreely available at https://cross-tissue-signaling.herokuapp.com are our model predictions & datasets; https://github.com/BIRDSgroup/BioEmbedS has all relevant code.Supplementary informationSupplementary data are available at Bioinformatics online.
| S-EPMC9563690 | biostudies-literature
Project description:In terms of tillering potential, the aboveground portions of rice are significantly influenced by the nitrogen level (NL) and transplant density (TD). To obtain a suitable combination of NL and TD, five NLs (0, 90, 180, 270 and 360 kg ha-1) and two TDs [high density (HD), 32.5×104 hills ha-1; low density (LD), 25.5×104 hills ha-1] were used in the rice experiments during 2012 to 2014, in Jiangsu, China. The results showed the highest grain yield of rice obtained at HD and LD when N supply was 180 and 270 kg ha-1, respectively. That's because there are more tillers per unit area, a larger leaf biomass fraction of total aboveground biomass, a larger leaf area index (LAI) and a larger canopy photosynthesis potential (CPP) at HD. It can be concluded that, higher rice planting densities resulted in less N inputs, while more N is needed to improve single plant actual tiller ability under low density to offset the reduced planting density. When the NL was more than 180 kg ha-1, the actual tillering ability of a single plant at LD was 20% more than that at HD. Based on these results, the supply of 1 kg N can be replaced by adding approximately 1000 planting hills per hectare. Therefore, adjusting the transplant density could be an efficient method to reduce the amount of nitrogen fertilizer and increase the nitrogen fertilizer use efficiency, which is very conducive to the sustainable development of agriculture.
| S-EPMC5540556 | biostudies-literature
Project description:Increased interest in the use of word embeddings, such as word representation, for biomedical named entity recognition (BioNER) has highlighted the need for evaluations that aid in selecting the best word embedding to be used. One common criterion for selecting a word embedding is the type of source from which it is generated; that is, general (e.g., Wikipedia, Common Crawl), or specific (e.g., biomedical literature). Using specific word embeddings for the BioNER task has been strongly recommended, considering that they have provided better coverage and semantic relationships among medical entities. To the best of our knowledge, most studies have focused on improving BioNER task performance by, on the one hand, combining several features extracted from the text (for instance, linguistic, morphological, character embedding, and word embedding itself) and, on the other, testing several state-of-the-art named entity recognition algorithms. The latter, however, do not pay great attention to the influence of the word embeddings, and do not facilitate observing their real impact on the BioNER task. For this reason, the present study evaluates three well-known NER algorithms (CRF, BiLSTM, BiLSTM-CRF) with respect to two corpora (DrugBank and MedLine) using two classic word embeddings, GloVe Common Crawl (of the general type) and Pyysalo PM + PMC (specific), as unique features. Furthermore, three contextualized word embeddings (ELMo, Pooled Flair, and Transformer) are compared in their general and specific versions. The aim is to determine whether general embeddings can perform better than specialized ones on the BioNER task. To this end, four experiments were designed. In the first, we set out to identify the combination of classic word embedding, NER algorithm, and corpus that results in the best performance. The second evaluated the effect of the size of the corpus on performance. The third assessed the semantic cohesiveness of the classic word embeddings and their correlation with respect to several gold standards; while the fourth evaluates the performance of general and specific contextualized word embeddings on the BioNER task. Results show that the classic general word embedding GloVe Common Crawl performed better in the DrugBank corpus, despite having less word coverage and a lower internal semantic relationship than the classic specific word embedding, Pyysalo PM + PMC; while in the contextualized word embeddings the best results are presented in the specific ones. We conclude, therefore, when using classic word embeddings as features on the BioNER task, the general ones could be considered a good option. On the other hand, when using contextualized word embeddings, the specific ones are the best option.
| S-EPMC7959609 | biostudies-literature
Project description:BackgroundWord embeddings are dense numeric vectors used to represent language in neural networks. Until recently, there had been no publicly released embeddings trained on clinical data. Our work is the first to study the privacy implications of releasing these models.ObjectiveThis paper aims to demonstrate that traditional word embeddings created on clinical corpora that have been deidentified by removing personal health information (PHI) can nonetheless be exploited to reveal sensitive patient information.MethodsWe used embeddings created from 400,000 doctor-written consultation notes and experimented with 3 common word embedding methods to explore the privacy-preserving properties of each.ResultsWe found that if publicly released embeddings are trained from a corpus anonymized by PHI removal, it is possible to reconstruct up to 68.5% (n=411/600) of the full names that remain in the deidentified corpus and associated sensitive information to specific patients in the corpus from which the embeddings were created. We also found that the distance between the word vector representation of a patient's name and a diagnostic billing code is informative and differs significantly from the distance between the name and a code not billed for that patient.ConclusionsSpecial care must be taken when sharing word embeddings created from clinical texts, as current approaches may compromise patient privacy. If PHI removal is used for anonymization before traditional word embeddings are trained, it is possible to attribute sensitive information to patients who have not been fully deidentified by the (necessarily imperfect) removal algorithms. A promising alternative (ie, anonymization by PHI replacement) may avoid these flaws. Our results are timely and critical, as an increasing number of researchers are pushing for publicly available health data.
| S-EPMC7391163 | biostudies-literature