检索结果-内蒙古大学图书馆

International Conference on Computing and Networking Technology (ICCNT)

作者： I. R. Oviya N Shanmukha Sravya Kalpana Raja Department of Computer Science Engineering Amrita School Of Computing Amrita Vishwa Vidyapeetham Chennai India Section for Biomedical Informatics and Data Science School of Medicine Yale University New Haven Connecticut USA

ISBN: (数字)9798350370249

ISBN: (纸本)9798350370270

Predicting Protein-protein interactions are central to understanding the intricate mechanisms governing cellular functions, as proteins seldom act in isolation. While current machine learning and deep learning models focus on encoding protein sequences based on residue composition or physicochemical properties, they often overlook the complex relationships between amino acid segments within lengthy sequences. To address these limitations, we propose a novel hybrid model that combines a self-attention to enhance Deep neural network feature extraction with an with FastText Protein embeddings for predicting PPI. Utilizing transfer learning via the unsupervised FastText embedding technique to derive statistical representations of protein sequences, offers advantages over traditional protein encoding techniques in the context of analysing k-Mer sequences. Our model’s performance is assessed through $\mathbf{5 - f o l d}$ cross-validation on datasets of *** and Human-Bacillus Anthracis protein interactions, resulting in accuracies of $\mathbf{9 2. 2 8 \%}$ and $\mathbf{9 4. 0 8 \%}$, respectively. Compared to existing machine learning models, our model demonstrates superior performance on both datasets.

关键词： Proteins Accuracy Transfer learning Pathogenesis Artificial neural networks Organizations Predictive models Feature extraction Encoding Vectors

来源：评论

学校读者我要写书评

暂无评论

From Survey to Ontology, the challenges and opportunities in ontologizing questions and answers 13

From Survey to Ontology, the challenges and opportunities in...

引用

13th International Conference on biomedical Ontology, ICBO 2022

作者： Chan, Lauren Phuong, Jimmy Thessen, Anne Hong, Stephanie Essaid, Shahim Haendel, Melissa College of Public Health and Human Sciences Oregon State University CorvallisOR97331 United States Division of Biomedical Health and Informatics University of Washington Medicine SeattleWA98195 United States Department of Biomedical Informatics University of Colorado Anschutz Medical Campus AuroraCO80054 United States Section of Biomedical Informatics and Data Science Johns Hopkins University School of Medicine BaltimoreMD21218 United States

Surveys are an essential tool for gathering data from individuals in a wide variety of fields. Common data Elements (CDEs) are routinely used in surveys to streamline frequently asked questions and support question reuse. While CDEs are a widespread method for collecting survey data, they face a variety of problems including inconsistent file formats, lack of computational encoding, little to no community development standards, and frequent duplication of CDEs across various registries. Alternative approaches such as ontologies can serve as meaningful translation tools to not only support interoperability between similar/duplicate CDEs, but also to coordinate survey data with other ontology aligned data from heterogeneous methodologies including wet lab, clinical, or field research. To capitalize on the extensive data collected using CDEs, we propose a two-step approach of 1) aligning CDEs with ontology terminology to coordinate similar questions based on primary topic and 2) using standardized enumerations for CDE responses that can support data harmonization for meta analytics. Using this approach, greater data integration can support higher powered analytics and coordination of heterogeneous data types which are often difficult to study in tandem. © 2022 Copyright for this paper by its authors.

关键词： Ontology

来源：评论

学校读者我要写书评

暂无评论

Suicide Phenotyping from Clinical Notes in Safety-Net Psychiatric Hospital Using Multi-Label Classification with Pre-Trained Language Models

arXiv

引用

arXiv 2024年

作者： Li, Zehan Hu, Yan Lane, Scott Selek, Salih Shahani, Lokesh Machado-Vieira, Rodrigo Soares, Jair Xu, Hua Liu, Hongfang Huang, Ming MacWilliam School of Biomedical Informatics The University of Texas Health Science Center HoustonTX United States Department of Psychiatry & Behavioral Sciences McGovern Medical School The University of Texas Health Science at Houston HoustonTX United States Section of Biomedical Informatics and Data Science School of Medicine Yale University New HavenCT United States

Accurate identification and categorization of suicidal events can yield better suicide precautions, reducing operational burden, and improving care quality in high-acuity psychiatric settings. Pre-trained language models offer promise for identifying suicidality from unstructured clinical narratives. We evaluated the performance of four BERT-based models using two fine-tuning strategies (multiple single-label and single multi-label) for detecting coexisting suicidal events from 500 annotated psychiatric evaluation notes. The notes were labeled for suicidal ideation (SI), suicide attempts (SA), exposure to suicide (ES), and non-suicidal self-injury (NSSI). RoBERTa outperformed other models using binary relevance (acc=0.86, F1=0.78). MentalBERT (F1=0.74) also exceeded BioClinicalBERT (F1=0.72). RoBERTa fine-tuned with a single multi-label classifier further improved performance (acc=0.88, F1=0.81), highlighting that models pre-trained on domain-relevant data and the single multi-label classification strategy enhance efficiency and performance. © 2024, CC BY.

关键词： Classification (of information)

来源：评论

学校读者我要写书评

暂无评论

Identifying and Extracting Rare Disease Phenotypes with Large Language Models

arXiv

引用

arXiv 2023年

作者： Shyr, Cathy Hu, Yan Harris, Paul Xu, Hua Department of Biomedical Informatics Vanderbilt University Medical Center NashvilleTN United States School of Biomedical Informatics University of Texas Health Science HoustonTX United States Department of Biomedical Informatics Biostatistics and Biomedical Engineering Vanderbilt University Medical Center NashvilleTN United States Section of Biomedical Informatics and Data Science School of Medicine Yale University New HavenCT United States

Rare diseases (RDs) are collectively common and affect 300 million people worldwide. Accurate phenotyping is critical for informing diagnosis and treatment, but RD phenotypes are often embedded in unstructured text and time-consuming to extract manually. While natural language processing (NLP) models can perform named entity recognition (NER) to automate extraction, a major bottleneck is the development of a large, annotated corpus for model training. Recently, prompt learning emerged as an NLP paradigm that can lead to more generalizable results without any (zero-shot) or few labeled samples (few-shot). Despite growing interest in ChatGPT, a revolutionary large language model capable of following complex human prompts and generating high-quality responses, none have studied its NER performance for RDs in the zero- and few-shot settings. To this end, we engineered novel prompts aimed at extracting RD phenotypes and, to the best of our knowledge, are the first the establish a benchmark for evaluating ChatGPT’s performance in these settings. We compared its performance to the traditional fine-tuning approach and conducted an in-depth error analysis. Overall, fine-tuning BioClinicalBERT resulted in higher performance (F1 of 0.689) than ChatGPT (F1 of 0.472 and 0.591 in the zero- and few-shot settings, respectively). Despite this, ChatGPT achieved similar or higher accuracy for certain entities (i.e., rare diseases and signs) in the one-shot setting (F1 of 0.776 and 0.725). This suggests that with appropriate prompt engineering, ChatGPT has the potential to match or outperform fine-tuned language models for certain entity types with just one labeled sample. While the proliferation of large language models may provide opportunities for supporting RD diagnosis and treatment, researchers and clinicians should critically evaluate model outputs and be well-informed of their limitations. Copyright © 2023, The Authors. All rights reserved.

关键词： Diagnosis

来源：评论

学校读者我要写书评

暂无评论

Development of a Natural Language Processing Tool to Extract Acupuncture Point Location Terms

Development of a Natural Language Processing Tool to Extract...

引用

IEEE International Conference on Healthcare informatics (ICHI)

作者： Yiming Li Xueqing Peng Jianfu Li Suyuan Peng Donghong Pei Cui Tao Hua Xu Na Hong School of Biomedical Informatics The University of Texas Health Science Center at Houston Houston TX USA Section of Biomedical Informatics and Data Science School of Medicine Yale University New Haven CT USA National Institute of Health Data Science Peking University Beijing China The University of Texas MD Anderson Cancer Center Houston TX USA

Acupuncture point location information is significant to the effect of acupuncture therapy. A wealth of knowledge related to acupuncture point locations is typically dispersed across books or reports in free-text format, which can pose challenges for machines to understand and facilitate. In this study, our purpose is to develop a natural language processing (NLP) tool to extract acupuncture point location information. We adopted the World Health Organization (WHO) Standard Acupuncture Point Locations in the Western Pacific Region (WHO Standard) as our reference standard and corpus. Our proposed approach to develop and validate the NLP tool involves three key steps: 1) We leveraged pre-existing terminologies from the anatomy domain, specifically the International Anatomical Terminology (IAT) and Uber-anatomy Ontology (UBERON), to construct a baseline dictionary of acupoint locations. This dictionary was then used in conjunction with a dictionary lookup method to match terms in the acupuncture location descriptions outlined by the WHO Standard; 2) We employed NLP models based on machine learning and deep learning techniques, specifically utilizing Conditional Random Fields (CRFs) and Recurrent Neural Network (RNN) for training. The CRFs and RNN models achieved overall F1 scores of 0.955 and 0.945, respectively; 3) We encoded the extracted entities into standardized concepts and enriched the baseline dictionary using these entities. In this study, a customized NLP tool was developed and validated for extracting acupuncture point location terms. This tool can be used in various informatics applications to support acupuncture research, education, and practices.

关键词：

来源：评论

学校读者我要写书评

暂无评论

Stroke Prediction Using Machine Learning

Stroke Prediction Using Machine Learning

引用

International Conference on Advances in Electronics, Computers and Communications (ICAECC)

作者： Abinandhini D M Aman Kumar Gudi Vishnu Teja Mandava Sukesh Divya S Naman Chauhan I R Oviya Kalpana Raja Department of Computer Science and Engineering (Artificial Intelligence) Amrita Vishwa Vidyapeetham Chennai India Section for Biomedical Informatics and Data Science School of Medicine Yale University New Haven Connecticut USA

ISBN: (数字)9798350305449

ISBN: (纸本)9798350305456

A stroke is a serious medical emergency that happens when bleeding or blood clots cut off the blood flow to a part of the brain. With a mortality rate of 5.5 million per year, it ranks as the second leading cause of death globally. Over 15 million individuals experience a stroke each year, and one person dies from one every four minutes. According to the World Health Organization, stroke is the main cause of death and disability worldwide (WHO). Identifying the many stroke warning signs helps lessen the severity of the stroke. A stroke can be avoided in up to 80% of instances because it is typically the result of a poor lifestyle. As a result, stroke prediction becomes important and should be employed to stop it from causing long-term harm. The current study uses a variety of machine learning models, including Gaussian Naive Bayes, Logistic Regression, Support Vector Machine (SVM), KNN and Random Forest to predict stroke. The paper presents the comparison among all machine learning algorithms. Analysis of results revealed that KNN had the least accuracy of 76.32% and Random Forest had the highest accuracy of 94.81%.

关键词： Support vector machines Accuracy Organizations Stroke (medical condition) Predictive models Vectors Physiology

来源：评论

学校读者我要写书评

暂无评论

ML Based Phenotype Analysis Using Differential Gene Expression data in Schizophrenia

ML Based Phenotype Analysis Using Differential Gene Expressi...

引用

Smart Technologies in Computing, Electrical and Electronics (ICSTCEE), International Conference on

作者： Aadhithyan D Shabarirajan KJ Varun Maniappan Shivanesh B Divya S Praghaadeesh R Kalpana Raja I R Oviya Department of Computer Science and Engineering (Artificial Intelligence) Amrita Vishwa Vidyapeetham Chennai India Section for Biomedical Informatics and Data Science School of Medicine Yale University New Haven Connecticut USA

ISBN: (数字)9798350384628

ISBN: (纸本)9798350384635

In this paper, differential gene expression (DGE) data in schizophrenia is analysed using machine learning approaches with the objective of predicting cell phenotypes related to the condition. The dataset contains information on cis eQTNs, gene orientation, probe information, gene expression profiles, and SNP information. When first investigating well-known machine learning methods, a hybrid model combining Random Forests and XGBoost is suggested, however it only offers a little increase. Increases in predicted accuracy of more than 99.12% are made possible by the H2O AutoML package. The results demonstrate the capability of ML-based analysis to unravel the underlying biological mechanisms of schizophrenia and contribute to the design of individualised therapeutic approaches. The paper represents the capability of machine learning to comprehend the relationship between gene expression patterns and complicated illnesses like schizophrenia.

关键词： Water Training Accuracy Phenotypes Mental disorders Predictive models data models

来源：评论

学校读者我要写书评

暂无评论

Enhancing Diabetic Retinopathy Screening with Sequential Deep Learning Models

Enhancing Diabetic Retinopathy Screening with Sequential Dee...

引用

International Conference on Image Information Processing

作者： Vankadari Mohith Kalpana Raja I. R. Oviya Department of Computer Science and Engineering (AIE) Amrita School of Computing Amrita Vishwa Vidyapeetham Chennai India Section for Biomedical Informatics and Data Science School of Medicine Yale University New Haven USA

ISBN: (数字)9798350371406

ISBN: (纸本)9798350371413

Diabetic retinopathy is a serious medical disorder that, if left untreated, can result in visual impairment or blindness. The precise and timely categorization of its severity is critical for appropriate medical management. This research describes an automated method for determining the severity of diabetic retinopathy using deep learning algorithms. The suggested methodology adopts a two-step process for identifying diabetic retinopathy and then categorizing its severity. In this technique, two pre-trained deep learning models, InceptionResNetV2 and DenseNet121, are used. For training and assessment purposes, the “APTOS 2019 Blindness Detection” dataset which consists of five severity classes is used as the foundation. To overcome class imbalance, data augmentation approaches are used to improve the model’s performance. The results of the experiment show that the strategy is effective, with an accuracy of 83.10 % and an F1 score of 82.77 %. This study contributes to the development of automated systems for assessing diabetic retinopathy, perhaps enhancing early detection and treatment.

关键词： Deep learning Training Diabetic retinopathy Visual impairment Transfer learning Blindness Information processing

来源：评论

学校读者我要写书评

暂无评论

Improving Large Language Models for Clinical Named Entity Recognition via Prompt Engineering

arXiv

引用

arXiv 2023年

作者： Hu, Yan Chen, Qingyu Du, Jingcheng Peng, Xueqing Keloth, Vipina Kuttichi Zuo, Xu Zhou, Yujia Li, Zehan Jiang, Xiaoqian Lu, Zhiyong Roberts, Kirk Xu, Hua School of Biomedical Informatics University of Texas Health Science at Houston Houston United States Section of Biomedical Informatics and Data Science School of Medicine Yale University New Haven United States National Center for Biotechnology Information National Library of Medicine National Institutes of Health MD United States

Objective: This study quantifies the capabilities of GPT-3.5 and GPT-4 for clinical named entity recognition (NER) tasks and proposes task-specific prompts to improve their performance. Materials and Methods: We evaluated these models on two clinical NER tasks: (1) to extract medical problems, treatments, and tests from clinical notes in the MTSamples corpus, following the 2010 i2b2 concept extraction shared task, and (2) identifying nervous system disorder-related adverse events from safety reports in the vaccine adverse event reporting system (VAERS). To improve the GPT models' performance, we developed a clinical task-specific prompt framework that includes (1) baseline prompts with task description and format specification, (2) annotation guideline-based prompts, (3) error analysis-based instructions, and (4) annotated samples for few-shot learning. We assessed each prompt's effectiveness and compared the models to BioClinicalBERT. Results: Using baseline prompts, GPT-3.5 and GPT-4 achieved relaxed F1 scores of 0.634, 0.804 for MTSamples, and 0.301, 0.593 for VAERS. Additional prompt components consistently improved model performance. When all four components were used, GPT-3.5 and GPT-4 achieved relaxed F1 socres of 0.794, 0.861 for MTSamples and 0.676, 0.736 for VAERS, demonstrating the effectiveness of our prompt framework. Although these results trail BioClinicalBERT (F1 of 0.901 for the MTSamples dataset and 0.802 for the VAERS), it is very promising considering few training samples are needed. Conclusion: While direct application of GPT models to clinical NER tasks falls short of optimal performance, our task-specific prompt framework, incorporating medical knowledge and training samples, significantly enhances GPT models' feasibility for potential clinical applications. Copyright © 2023, The Authors. All rights reserved.

关键词： Medical problems

来源：评论

学校读者我要写书评

暂无评论

A Variational Autoencoder-Feed Forward Networks (VAE-FNN) Model for Classifying DNA Barcodes

A Variational Autoencoder-Feed Forward Networks (VAE-FNN) Mo...

引用

Advances in Electrical, Electronics and Computational Intelligence (ICAEECI), International Conference on

作者： Abhivyakti Yadav Divya S I R Oviya Kalpana Raja Department of Computer Science and Engineering (Artificial Intelligence) Amrita School of Computing Amrita Vishwa Vidyapetham Chennai India Section for Biomedical Informatics and Data Science School of Medicine Yale University New Haven Connecticut USA

DNA Barcodes, which are particular fragments derived from brief sections of DNA (such as mitochondrial, nuclear, and plastid sequences), can be used to identify organisms from the major life kingdoms. In addition to supporting conventional taxonomic techniques, DNA barcoding is a potent tool that advances our knowledge of species diversity and their ecological functions. On a variety of organisms, the use of this approach for species categorization has been successful. In this paper, we examine how DNA barcoding has been used to classify species based on DNA barcodes as well as other related research that has been done over the years on the subject. After experimenting with a number of deep learning models, we have propose a Variational Auto Encoder + Feed Forward Neural Network workflow for classifiying species using DNA barcodes. The models have been assessed on the basis of performance factors including accuracy, recall, and precision. COI, rbcL, matK, and ITS are the specific gene sections that have been identified as barcodes. For both simulated and real datasets, the model can attain an average accuracy of greater than 95 percent. This DNA barcoding approach has the ability to simplify DNA barcode-based species identification and serve as a tool for species categorization.

关键词：

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：