scholarly journals Automated Confirmation of Protein Annotation Using NLP and the UniProtKB Database

2020 ◽  
Vol 11 (1) ◽  
pp. 24
Author(s):  
Jin Tao ◽  
Kelly Brayton ◽  
Shira Broschat
Keyword(s):  
Language Processing ◽  
Fine Tuning ◽  
Support Vector ◽  
Protein Annotation ◽  
Computing Power ◽  
Journal Publication ◽  
Novel Approach ◽  
Uniprotkb Database ◽  
Public Repositories ◽  
Annotation Errors

Advances in genome sequencing technology and computing power have brought about the explosive growth of sequenced genomes in public repositories with a concomitant increase in annotation errors. Many protein sequences are annotated using computational analysis rather than experimental verification, leading to inaccuracies in annotation. Confirmation of existing protein annotations is urgently needed before misannotation becomes even more prevalent due to error propagation. In this work we present a novel approach for automatically confirming the existence of manually curated information with experimental evidence of protein annotation. Our ensemble learning method uses a combination of recurrent convolutional neural network, logistic regression, and support vector machine models. Natural language processing in the form of word embeddings is used with journal publication titles retrieved from the UniProtKB database. Importantly, we use recall as our most significant metric to ensure the maximum number of verifications possible; results are reported to a human curator for confirmation. Our ensemble model achieves 91.25% recall, 71.26% accuracy, 65.19% precision, and an F1 score of 76.05% and outperforms the Bidirectional Encoder Representations from Transformers for Biomedical Text Mining (BioBERT) model with fine-tuning using the same data.

scholarly journals EventEpi–A Natural Language Processing Framework for Event-Based Surveillance

2019 ◽  
Author(s):  
Auss Abbood ◽  
Alexander Ullrich ◽  
Rüdiger Busche ◽  
Stéphane Ghozzi
Keyword(s):  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Web Application ◽  
Fine Tuning ◽  
Entity Recognition ◽  
World Health ◽  
Support Vector ◽  
Event Based ◽  
Processing Framework

AbstractAccording to the World Health Organization (WHO), around 60% of all outbreaks are detected using informal sources. In many public health institutes, including the WHO and the Robert Koch Institute (RKI), dedicated groups of epidemiologists sift through numerous articles and newsletters to detect relevant events. This media screening is one important part of event-based surveillance (EBS). Reading the articles, discussing their relevance, and putting key information into a database is a time-consuming process. To support EBS, but also to gain insights into what makes an article and the event it describes relevant, we developed a natural-language-processing framework for automated information extraction and relevance scoring. First, we scraped relevant sources for EBS as done at RKI (WHO Disease Outbreak News and ProMED) and automatically extracted the articles’ key data: disease, country, date, and confirmed-case count. For this, we performed named entity recognition in two steps: EpiTator, an open-source epidemiological annotation tool, suggested many different possibilities for each. We trained a naive Bayes classifier to find the single most likely one using RKI’s EBS database as labels. Then, for relevance scoring, we defined two classes to which any article might belong: The article is relevant if it is in the EBS database and irrelevant otherwise. We compared the performance of different classifiers, using document and word embeddings. Two of the tested algorithms stood out: The multilayer perceptron performed best overall, with a precision of 0.19, recall of 0.50, specificity of 0.89, F1 of 0.28, and the highest tested index balanced accuracy of 0.46. The support-vector machine, on the other hand, had the highest recall (0.88) which can be of higher interest for epidemiologists. Finally, we integrated these functionalities into a web application called EventEpi where relevant sources are automatically analyzed and put into a database. The user can also provide any URL or text, that will be analyzed in the same way and added to the database. Each of these steps could be improved, in particular with larger labeled datasets and fine-tuning of the learning algorithms. The overall framework, however, works already well and can be used in production, promising improvements in EBS. The source code is publicly available at https://github.com/aauss/EventEpi.

scholarly journals Automatic Incident Triage in Radiation Oncology Incident Learning System

Healthcare ◽  
2020 ◽  
Vol 8 (3) ◽  
pp. 272
Author(s):  
Khajamoinuddin Syed ◽  
William Sleeman ◽  
Michael Hagan ◽  
Jatinder Palta ◽  
Rishabh Kapoor ◽  
...  
Keyword(s):  
Machine Learning ◽  
Transfer Learning ◽  
Language Processing ◽  
Radiation Oncology ◽  
Learning System ◽  
Fine Tuning ◽  
Support Vector ◽  
Learning Approach ◽  
Veterans Health ◽  
Incident Reports

The Radiotherapy Incident Reporting and Analysis System (RIRAS) receives incident reports from Radiation Oncology facilities across the US Veterans Health Affairs (VHA) enterprise and Virginia Commonwealth University (VCU). In this work, we propose a computational pipeline for analysis of radiation oncology incident reports. Our pipeline uses machine learning (ML) and natural language processing (NLP) based methods to predict the severity of the incidents reported in the RIRAS platform using the textual description of the reported incidents. These incidents in RIRAS are reviewed by a radiation oncology subject matter expert (SME), who initially triages some incidents based on the salient elements in the incident report. To automate the triage process, we used the data from the VHA treatment centers and the VCU radiation oncology department. We used NLP combined with traditional ML algorithms, including support vector machine (SVM) with linear kernel, and compared it against the transfer learning approach with the universal language model fine-tuning (ULMFiT) algorithm. In RIRAS, severities are divided into four categories; A, B, C, and D, with A being the most severe to D being the least. In this work, we built models to predict High (A & B) vs. Low (C & D) severity instead of all the four categories. Models were evaluated with macro-averaged precision, recall, and F1-Score. The Traditional ML machine learning (SVM-linear) approach did well on the VHA dataset with 0.78 F1-Score but performed poorly on the VCU dataset with 0.5 F1-Score. The transfer learning approach did well on both datasets with 0.81 F1-Score on VHA dataset and 0.68 F1-Score on the VCU dataset. Overall, our methods show promise in automating the triage and severity determination process from radiotherapy incident reports.

scholarly journals A Novel Approach for Protein-Named Entity Recognition and Protein-Protein Interaction Extraction

2015 ◽  
Vol 2015 ◽  
pp. 1-10 ◽  
Author(s):  
Meijing Li ◽  
Tsendsuren Munkhdalai ◽  
Xiuming Yu ◽  
Keun Ho Ryu
Keyword(s):  
Language Processing ◽  
Protein Interaction ◽  
Named Entity Recognition ◽  
Entity Recognition ◽  
Support Vector ◽  
Protein Protein Interaction ◽  
Named Entity ◽  
Novel Approach ◽  
Interaction Extraction ◽  
Parsing Tree

Many researchers focus on developing protein-named entity recognition (Protein-NER) or PPI extraction systems. However, the studies about these two topics cannot be merged well; then existing PPI extraction systems’ Protein-NER still needs to improve. In this paper, we developed the protein-protein interaction extraction system named PPIMiner based on Support Vector Machine (SVM) and parsing tree. PPIMiner consists of three main models: natural language processing (NLP) model, Protein-NER model, and PPI discovery model. The Protein-NER model, which is named ProNER, identifies the protein names based on two methods: dictionary-based method and machine learning-based method. ProNER is capable of identifying more proteins than dictionary-based Protein-NER model in other existing systems. The final discovered PPIs extracted via PPI discovery model are represented in detail because we showed the protein interaction types and the occurrence frequency through two different methods. In the experiments, the result shows that the performances achieved by our ProNER and PPI discovery model are better than other existing tools. PPIMiner applied this protein-named entity recognition approach and parsing tree based PPI extraction method to improve the performance of PPI extraction. We also provide an easy-to-use interface to access PPIs database and an online system for PPIs extraction and Protein-NER.

Arabic Biomedical Community Question Answering Based on Contextualized Embeddings

2021 ◽  
Vol 17 (3) ◽  
pp. 13-29
Author(s):  
Yassine El Adlouni ◽  
Noureddine En Nahnahi ◽  
Said Ouatik El Alaoui ◽  
Mohammed Meknassi ◽  
Horacio Rodríguez ◽  
...  
Keyword(s):  
Language Processing ◽  
Question Answering ◽  
State Of The Art ◽  
Fine Tuning ◽  
Neural Models ◽  
Community Question Answering ◽  
Novel Approach ◽  
Language Representation ◽  
Textual Entailment ◽  
Scarcity Of Resources

Community question answering has become increasingly important as they are practical for seeking and sharing information. Applying deep learning models often leads to good performance, but it requires an extensive amount of annotated data, a problem exacerbated for languages suffering a scarcity of resources. Contextualized language representation models have gained success due to promising results obtained on a wide array of downstream natural language processing tasks such as text classification, textual entailment, and paraphrase identification. This paper presents a novel approach by fine-tuning contextualized embeddings for a medical domain community question answering task. The authors propose an architecture combining two neural models powered by pre-trained contextual embeddings to learn a sentence representation and thereafter fine-tuned on the task to compute a score used for both ranking and classification. The experimental results on SemEval Task 3 CQA show that the model significantly outperforms the state-of-the-art models by almost 2% for the '16 edition and 1% for the '17 edition.

Similarity detection of English text and teaching evaluation based on improved TCUSS clustering algorithm

2020 ◽  
pp. 1-11
Author(s):  
Yu Wang
Keyword(s):  
Language Processing ◽  
Calculation Method ◽  
Clustering Algorithm ◽  
Research Result ◽  
Structural Features ◽  
English Text ◽  
Support Vector ◽  
Similarity Calculation ◽  
Other Information ◽  
Calculation Task

The semantic similarity calculation task of English text has important influence on other fields of natural language processing and has high research value and application prospect. At present, research on the similarity calculation of short texts has achieved good results, but the research result on long text sets is still poor. This paper proposes a similarity calculation method that combines planar features with structured features and uses support vector regression models. Moreover, this paper uses PST and PDT to represent the syntax, semantics and other information of the text. In addition, through the two structural features suitable for text similarity calculation, this paper proposes a similarity calculation method combining structural features with Tree-LSTM model. Experiments show that this method provides a new idea for interest network extraction.

scholarly journals Synthesis of 4-Substituted-1,2-Dihydroquinolines by Means of Gold-Catalyzed Intramolecular Hydroarylation Reaction of N-Ethoxycarbonyl-N-Propargylanilines

Molecules ◽  
2021 ◽  
Vol 26 (11) ◽  
pp. 3366
Author(s):  
Antonio Arcadi ◽  
Andrea Calcaterra ◽  
Giancarlo Fabrizi ◽  
Andrea Fochetti ◽  
Antonella Goggiamani ◽  
...  
Keyword(s):  
Building Blocks ◽  
Fine Tuning ◽  
Para Position ◽  
Cyclization Product ◽  
Synthetic Route ◽  
Substituted Anilines ◽  
Novel Approach ◽  
High Yields

An alternative Au(I)-catalyzed synthetic route to functionalized 1,2-dihydroquinolines is reported. This novel approach is based on the use of N-ethoxycarbonyl protected-N-propargylanilines as building blocks that rapidly undergo the IMHA reaction affording the 6-endo cyclization product in good to high yields. In the presence of N-ethoxycarbonyl-N-propargyl-meta-substituted anilines, the regiodivergent cyclization at the ortho-/para-position is achieved by the means of catalyst fine tuning.

scholarly journals Interpretable deep learning for the remote characterisation of ambulation in multiple sclerosis using smartphones

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Andrew P. Creagh ◽  
Florian Lipsmeier ◽  
Michael Lindemann ◽  
Maarten De Vos
Keyword(s):  
Multiple Sclerosis ◽  
Deep Learning ◽  
Inertial Sensor ◽  
Heterogeneous Data ◽  
Fine Tuning ◽  
Sensor Data ◽  
Support Vector ◽  
Deep Convolutional Neural Networks ◽  
Healthcare Applications ◽  
Feature Based

AbstractThe emergence of digital technologies such as smartphones in healthcare applications have demonstrated the possibility of developing rich, continuous, and objective measures of multiple sclerosis (MS) disability that can be administered remotely and out-of-clinic. Deep Convolutional Neural Networks (DCNN) may capture a richer representation of healthy and MS-related ambulatory characteristics from the raw smartphone-based inertial sensor data than standard feature-based methodologies. To overcome the typical limitations associated with remotely generated health data, such as low subject numbers, sparsity, and heterogeneous data, a transfer learning (TL) model from similar large open-source datasets was proposed. Our TL framework leveraged the ambulatory information learned on human activity recognition (HAR) tasks collected from wearable smartphone sensor data. It was demonstrated that fine-tuning TL DCNN HAR models towards MS disease recognition tasks outperformed previous Support Vector Machine (SVM) feature-based methods, as well as DCNN models trained end-to-end, by upwards of 8–15%. A lack of transparency of “black-box” deep networks remains one of the largest stumbling blocks to the wider acceptance of deep learning for clinical applications. Ensuing work therefore aimed to visualise DCNN decisions attributed by relevance heatmaps using Layer-Wise Relevance Propagation (LRP). Through the LRP framework, the patterns captured from smartphone-based inertial sensor data that were reflective of those who are healthy versus people with MS (PwMS) could begin to be established and understood. Interpretations suggested that cadence-based measures, gait speed, and ambulation-related signal perturbations were distinct characteristics that distinguished MS disability from healthy participants. Robust and interpretable outcomes, generated from high-frequency out-of-clinic assessments, could greatly augment the current in-clinic assessment picture for PwMS, to inform better disease management techniques, and enable the development of better therapeutic interventions.

scholarly journals Transformers-sklearn: a toolkit for medical language understanding with transformer-based models

2021 ◽  
Vol 21 (S2) ◽  
Author(s):  
Feihong Yang ◽  
Xuwen Wang ◽  
Hetong Ma ◽  
Jiao Li
Keyword(s):  
Language Processing ◽  
Pearson Correlation ◽  
Fine Tuning ◽  
Entity Recognition ◽  
Training Dataset ◽  
Training Methods ◽  
Code Size ◽  
Model Framework ◽  
Language Understanding ◽  
Medical Language

Abstract Background Transformer is an attention-based architecture proven the state-of-the-art model in natural language processing (NLP). To reduce the difficulty of beginning to use transformer-based models in medical language understanding and expand the capability of the scikit-learn toolkit in deep learning, we proposed an easy to learn Python toolkit named transformers-sklearn. By wrapping the interfaces of transformers in only three functions (i.e., fit, score, and predict), transformers-sklearn combines the advantages of the transformers and scikit-learn toolkits. Methods In transformers-sklearn, three Python classes were implemented, namely, BERTologyClassifier for the classification task, BERTologyNERClassifier for the named entity recognition (NER) task, and BERTologyRegressor for the regression task. Each class contains three methods, i.e., fit for fine-tuning transformer-based models with the training dataset, score for evaluating the performance of the fine-tuned model, and predict for predicting the labels of the test dataset. transformers-sklearn is a user-friendly toolkit that (1) Is customizable via a few parameters (e.g., model_name_or_path and model_type), (2) Supports multilingual NLP tasks, and (3) Requires less coding. The input data format is automatically generated by transformers-sklearn with the annotated corpus. Newcomers only need to prepare the dataset. The model framework and training methods are predefined in transformers-sklearn. Results We collected four open-source medical language datasets, including TrialClassification for Chinese medical trial text multi label classification, BC5CDR for English biomedical text name entity recognition, DiabetesNER for Chinese diabetes entity recognition and BIOSSES for English biomedical sentence similarity estimation. In the four medical NLP tasks, the average code size of our script is 45 lines/task, which is one-sixth the size of transformers’ script. The experimental results show that transformers-sklearn based on pretrained BERT models achieved macro F1 scores of 0.8225, 0.8703 and 0.6908, respectively, on the TrialClassification, BC5CDR and DiabetesNER tasks and a Pearson correlation of 0.8260 on the BIOSSES task, which is consistent with the results of transformers. Conclusions The proposed toolkit could help newcomers address medical language understanding tasks using the scikit-learn coding style easily. The code and tutorials of transformers-sklearn are available at https://doi.org/10.5281/zenodo.4453803. In future, more medical language understanding tasks will be supported to improve the applications of transformers_sklearn.

scholarly journals Using NLP in openEHR archetypes retrieval to promote interoperability: a feasibility study in China

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Bo Sun ◽  
Fei Zhang ◽  
Jing Li ◽  
Yicheng Yang ◽  
Xiaolin Diao ◽  
...  
Keyword(s):  
Information Sharing ◽  
Language Processing ◽  
Medical Information ◽  
Medical Professional ◽  
Semantic Interoperability ◽  
Medical Information System ◽  
Search Term ◽  
Search Terms ◽  
Novel Approach ◽  
Test Sets

Abstract Background With the development and application of medical information system, semantic interoperability is essential for accurate and advanced health-related computing and electronic health record (EHR) information sharing. The openEHR approach can improve semantic interoperability. One key improvement of openEHR is that it allows for the use of existing archetypes. The crucial problem is how to improve the precision and resolve ambiguity in the archetype retrieval. Method Based on the query expansion technology and Word2Vec model in Nature Language Processing (NLP), we propose to find synonyms as substitutes for original search terms in archetype retrieval. Test sets in different medical professional level are used to verify the feasibility. Result Applying the approach to each original search term (n = 120) in test sets, a total of 69,348 substitutes were constructed. Precision at 5 (P@5) was improved by 0.767, on average. For the best result, the P@5 was up to 0.975. Conclusions We introduce a novel approach that using NLP technology and corpus to find synonyms as substitutes for original search terms. Compared to simply mapping the element contained in openEHR to an external dictionary, this approach could greatly improve precision and resolve ambiguity in retrieval tasks. This is helpful to promote the application of openEHR and advance EHR information sharing.

New Multi-View Classification Method with Uncertain Data

2021 ◽  
Vol 16 (1) ◽  
pp. 1-23
Author(s):  
Bo Liu ◽  
Haowen Zhong ◽  
Yanshan Xiao
Keyword(s):  
Learning Strategy ◽  
State Of The Art ◽  
Uncertain Data ◽  
Real Life ◽  
Support Vector ◽  
Classification Methods ◽  
Complementary Information ◽  
Novel Approach ◽  
Svm Model ◽  
Iterative Framework

Multi-view classification aims at designing a multi-view learning strategy to train a classifier from multi-view data, which are easily collected in practice. Most of the existing works focus on multi-view classification by assuming the multi-view data are collected with precise information. However, we always collect the uncertain multi-view data due to the collection process is corrupted with noise in real-life application. In this case, this article proposes a novel approach, called uncertain multi-view learning with support vector machine (UMV-SVM) to cope with the problem of multi-view learning with uncertain data. The method first enforces the agreement among all the views to seek complementary information of multi-view data and takes the uncertainty of the multi-view data into consideration by modeling reachability area of the noise. Then it proposes an iterative framework to solve the proposed UMV-SVM model such that we can obtain the multi-view classifier for prediction. Extensive experiments on real-life datasets have shown that the proposed UMV-SVM can achieve a better performance for uncertain multi-view classification in comparison to the state-of-the-art multi-view classification methods.

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