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arXiv 2024年

作者： Li, Rongbin Chen, Wenbo Li, Jinbo Xing, Hanwen Xu, Hua Li, Zhao Zheng, W. Jim McWilliams School of Biomedical Informatics University of Texas Health Science Center at Houston HoustonTX77030 United States Section of Biomedical Informatics and Data Science School of Medicine Yale University New HavenCT06510 United States

By leveraging GPT-4 for ontology narration, we developed GPTON to infuse structured knowledge into LLMs through verbalized ontology terms, achieving accurate text and ontology annotations for over 68% of gene sets in the top five predictions. Manual evaluations confirm GPTON's robustness, highlighting its potential to harness LLMs and structured knowledge to significantly advance biomedical research beyond gene set annotation. Copyright © 2024, The Authors. All rights reserved.

关键词： Gene Ontology

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Identifying and Extracting Rare Disease Phenotypes with Large Language Models

arXiv

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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

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

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

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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.

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Stroke Prediction Using Machine Learning

Stroke Prediction Using Machine Learning

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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

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ML Based Phenotype Analysis Using Differential Gene Expression data in Schizophrenia

ML Based Phenotype Analysis Using Differential Gene Expressi...

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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

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Elevating Ocular Diagnosis: Harnessing the Power of EfficientNet for Eye Disease Classification

Elevating Ocular Diagnosis: Harnessing the Power of Efficien...

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Artificial Intelligence For Internet of Things (AIIoT), International Conference on

作者： Vankadari Mohith Kalpana Raja I. R. Oviya Department of Computer Science and Engineering 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)9798350372120

ISBN: (纸本)9798350372137

In response to the evolving landscape of healthcare technology this study addresses the need for automated diagnostic tools in the field of ophthalmology. By utilizing deep learning methods specifically leveraging the EfficientNetV2S framework we achieve an overall accuracy rate of 94.6% in classifying images depicting common eye conditions like cataract, diabetic retinopathy, glaucoma, and normal cases. Our model exhibits capabilities across a diverse spectrum of medical conditions due to meticulous preprocessing and fine-tuning procedures. The results highlight the potential for automated technology integration in healthcare settings, which might improve patient care and treatment plans. This paper highlights the use of advanced neural network designs in the diagnosis of ocular illnesses, offering insights at the nexus of learning and medical image processing.

关键词： Glaucoma Deep learning Diabetic retinopathy Accuracy Computational modeling Neural networks Medical treatment

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EMPATHIC: Emulating Human-Like Multimodal Personality Architecture Through Thoughtful Human-AI Conversation

EMPATHIC: Emulating Human-Like Multimodal Personality Archit...

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International Conference on Confluence The Next Generation Information Technology Summit (Confluence)

作者： Varshini Devi I I. R. Oviya Kalpana Raja Department of Computer Science and 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

In the evolving landscape of human-computer interaction, this paper introduces an innovative framework poised to revolutionize chatbot systems. Our framework, meticulously designed for emotionally aware multimodal chatbots, seamlessly integrates real-time face and emotion recognition with natural language processing. Currently in the developmental phase, the framework exhibits a distinctive proficiency in executing a diverse array of human instructions. These instructions span tasks such as generating detailed captions, object counting, and responding to general queries. Leveraging parameter-efficient fine-tuning from OpenFlamingo, augmented by the inclusion of the Low-rank Adapter (LoRA), our framework strategically prioritizes versatility and operational efficiency. The core of our approach lies in the establishment of instruction templates that intricately merge both vision and language data. This strategic integration forms the backbone of our multi-modality instruction tuning methodology, enhancing the adaptability of the chatbot. Recognizing the pivotal role of high-quality training data, we emphasize its significance in shaping the dialogue performance of the chatbot. As the framework progresses through its developmental stages, this research lays a robust foundation for the creation of a versatile conversational agent. The envisioned applications of this agent range from enhancing customer service experiences to providing valuable support in mental health scenarios.

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R2V-PPI: Enhancing Prediction of Protein-Protein Interactions Using Word2Vec Embeddings and Deep Neural Networks

R2V-PPI: Enhancing Prediction of Protein-Protein Interaction...

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Advances in Electrical, Computing, Communication and Sustainable Technologies (ICAECT), International Conference on

作者： I. R. Oviya Shanmukha Sravya N 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

Proteins play a crucial role in living organisms, and understanding protein-protein interactions is vital for comprehending their functions and aiding drug discovery. In recent years, advanced deep learning models have been developed to predict protein-protein interactions from sequences. However, these large-scale approaches often suffer from deficiencies, resulting in both false positive and false negative predictions. Traditional encoding methods struggle to effectively represent the semantic meaning of individual residues in protein sequences and their impact on neighbouring residues. To overcome these deficiencies, we propose a novel method named R2V-PPI (Residue-to-Vector embeddings based Protein-Protein Interaction Framework) that effectively represents protein sequences and predicts protein-protein interactions. Inspired by Word2Vec, R2V-PPI learns informative representations of individual amino acid residues, capturing the context and relationships between them in raw protein sequences. These representations provide valuable input features for a downstream deep learning model. Our methodology offers a robust and versatile approach for predicting protein-protein interactions, especially when structural information is limited or unavailable. Evaluation on the S. cerevisiae dataset demonstrates that R2V-PPI outperforms existing state-of-the-art machine learning models.

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Predicting Protein-Protein Interactions Using Self-Attention-Based Deep Neural Networks and FastText Embeddings

Predicting Protein-Protein Interactions Using Self-Attention...

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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

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Enhancing Diabetic Retinopathy Screening with Sequential Deep Learning Models

Enhancing Diabetic Retinopathy Screening with Sequential Dee...

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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

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