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JAMIA at 30: looking back and forward

Journal of the American Medical informatics Association 2024年第1期31卷 1-9页

作者： Stead, William W. Miller, Randolph A. Ohno-Machado, Lucila Bakken, Suzanne Department of Biomedical Informatics Department of Medicine Vanderbilt University Medical Center Nashville United States Department of Biomedical Informatics Vanderbilt University School of Medicine Alexandria United States Section of Biomedical Informatics & Data Science Yale University School of Medicine New Haven CT 06520 United States School of Nursing Department of Biomedical Informatics Data Science Institute Columbia University NY 10032 NY United States

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data Quality in Medical Real-World data - An Oncological Use Case

Data Quality in Medical Real-World Data - An Oncological Use...

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34th Medical informatics Europe Conference, MIE 2024

作者： Gehrmann, Julia Beyan, Oya Institute for Biomedical Informatics Cologne Germany Department of Data Science and Artificial Intelligence Fraunhofer FIT Sankt Augustin Germany

ISBN: (纸本)9781643685335

data quality deficiencies significantly limit the applicability of real-world data in data-driven medical research. In this study, using an oncological use case, we report and discuss common quality deficiencies in real-world medical datasets, such as missing data, class imbalances, and timeliness issues. We compiled a multidepartmental real-world dataset comprising 13861 cancer cases diagnosed at University Hospital Cologne and examined data quality throughout the data integration process. © 2024 The Authors.

关键词： data Quality Germany Medical data Oncology Real-World data

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A comprehensive evaluation of large language models in mining gene relations and pathway knowledge

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Quantitative Biology 2024年第4期12卷 360-374页

作者： Muhammad Azam Yibo Chen Micheal Olaolu Arowolo Haowang Liu Mihail Popescu Dong Xu Department of Electrical Engineering and Computer Science University of MissouriColumbiaMissouriUSA Bond Life Sciences Center University of MissouriColumbiaMissouriUSA Institute for Data Science and Informatics University of MissouriColumbiaMissouriUSA Department of Biomedical Informatics Biostatistics and Medical EpidemiologyUniversity of MissouriColumbiaMissouriUSA

Understanding complex biological pathways,including gene–gene interactions and gene regulatory networks,is critical for exploring disease mechanisms and drug *** literature curation of biological pathways cannot keep up with the exponential growth of new discoveries in the ***-scale language models(LLMs)trained on extensive text corpora contain rich biological information,and they can be mined as a biological knowledge *** study assesses 21 LLMs,including both application programming interface(API)-based models and open-source models in their capacities of retrieving biological *** evaluation focuses on predicting gene regulatory relations(activation,inhibition,and phosphorylation)and the Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway *** indicated a significant disparity in model ***-based models GPT-4 and Claude-Pro showed superior performance,with an F1 score of 0.4448 and 0.4386 for the gene regulatory relation prediction,and a Jaccard similarity index of 0.2778 and 0.2657 for the KEGG pathway prediction,***-source models lagged behind their API-based counterparts,whereas Falcon-180b and llama2-7b had the highest F1 scores of 0.2787 and 0.1923 in gene regulatory relations,*** KEGG pathway recognition had a Jaccard similarity index of 0.2237 for Falcon-180b and 0.2207 for *** study suggests that LLMs are informative in gene network analysis and pathway mapping,but their effectiveness varies,necessitating careful model *** work also provides a case study and insight into using LLMs das knowledge *** code is publicly available at the website of GitHub(Muh-aza).

关键词： biomedical text mining gene-gene interaction KEGG pathway large language model

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Refining Dimensions for Improving Clustering-based Cross-lingual Topic Models 18

Refining Dimensions for Improving Clustering-based Cross-lin...

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18th Workshop on Building and Using Comparable Corpora, BUCC 2025 at 31st International Conference on Computational Linguistics, COLING 2025

作者： Chang, Chia-Hsuan Huang, Tien-Yuan Tsai, Yi-Hang Chang, Chia-Ming Hwang, San-Yih Department of Biomedical Informatics & Data Science Yale University New HavenCT06510 United States Department of Information Management National Sun Yat-sen University Kaohsiung80424 Taiwan

ISBN: (纸本)9798891762114

Recent works in clustering-based topic models perform well in monolingual topic identification by introducing a pipeline to cluster the contextualized representations. However, the pipeline is suboptimal in identifying topics across languages due to the presence of language-dependent dimensions (LDDs) generated by multilingual language models. To address this issue, we introduce a novel, SVD-based dimension refinement component into the pipeline of the clustering-based topic model. This component effectively neutralizes the negative impact of LDDs, enabling the model to accurately identify topics across languages. Our experiments on three datasets demonstrate that the updated pipeline with the dimension refinement component generally outperforms other state-of-the-art cross-lingual topic models. © 2025 Association for Computational Linguistics

关键词： Computational linguistics

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Evaluating and Improvi g the Performance and Racial Fairness of Algori ims for GFR Estimation 1

Evaluating and Improvi g the Performance and Racial Fairness...

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1st IEEE International Conference on Artificial Intelligence for Medicine, Health and Care, AIMHC 2024

作者： Zhang, Linying Kim, Tevin Richter, Lauren R. Hripcsak, George Department of Biomedical Informatics Columbia University New YorkNY United States Institutefor Informatics Data Science and Biostatistics Washington University in St. Louis St. LouisMO United States

ISBN: (纸本)9798350371987

data-driven clinical prediction algorithms are used widely by clinicians. Understanding what factors can impact the performance and fairness of data-driven algorithms is an important step towards achieving equitable healthcare. To investigate the impact of modeling choices on the algorithmic performance and fairness, we make use of a case study to build a prediction algorithm for estimating glomerular filtration rate (GFR) based on the patient's electronic health record (EHR). We compare three distinct approaches for estimating GFR: CKD-EPI equations, epidemiological models, and EHR-based models. For epidemiological models and EHR-based models, four machine learning models of varying computational complexity (i.e., linear regression, support vector machine, random forest regression, and neural network) were compared. Performance metrics included root mean squared error (RMSE), median difference, and the proportion of GFR estimates within 30% of the measured GFR value (P30). Differential performance between non-African American and African American group was used to assess algorithmic fairness with respect to race. Our study showed that the variable race had a negligible effect on error, accuracy, and differential performance. Furthermore, including more relevant clinical features (e.g., common comorbidities of chronic kidney disease) and using more complex machine learning models, namely random forest regression, significantly lowered the estimation error of GFR. However, the difference in performance between African American and non-African American patients did not decrease, where the estimation error for African American patients remained consistently higher than non-African American patients, indicating that more objective patient characteristics should be discovered and included to improve algorithm performance. ©2024 IEEE.

关键词： Mean square error

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HAM: Hybrid Associations Models for Sequential Recommendation (Extended abstract) 39

HAM: Hybrid Associations Models for Sequential Recommendatio...

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39th IEEE International Conference on data Engineering, ICDE 2023

作者： Peng, Bo Ren, Zhiyun Parthasarathy, Srinivasan Ning, Xia The Ohio State University Department of Computer Science and Engineering United States The Ohio State University Department of Biomedical Informatics United States The Ohio State University Translational Data Analytics Institute Department of Computer Science and Engineering United States The Ohio State University Translational Data Analytics Institute Department of Biomedical Informatics Department of Computer Science and Engineering United States

ISBN: (纸本)9798350322279

Sequential recommendation aims to identify and recommend the next few items of users' interest. It becomes an effective tool to help users select their favorite items from a variety of options. A key challenge in sequential recommendation is to learn the patterns and dynamics, which are most pertinent to inform future interactions of users. With the prosperity of deep learning, many deep models, particularly based on recurrent neural networks [1] and with attention mechanisms [2] , [3] , have been developed for sequential recommendation purposes. However, our analysis demonstrates that, these deep models, particularly those with attention mechanisms, may not always learn meaningful attention weights from the extremely sparse recommendation data, and thus, could degrade the recommendation performance. Therefore, in this study, instead of deep models, we develop novel, effective and efficient hybrid associations models (HAM) to better learn from the sparse and limited recommendation data. This study has been published in IEEE Transactions on Knowledge and data Engineering. Please refer to the full manuscript [4] for more details. © 2023 IEEE.

关键词： Recurrent neural networks

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Elevating Ocular Diagnosis: Harnessing the Power of EfficientNet for Eye Disease Classification 3

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

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3rd International Conference on Artificial Intelligence For Internet of Things, AIIoT 2024

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

ISBN: (纸本)9798350372120

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. © 2024 IEEE.

关键词： Ophthalmology

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Early Multimodal data Integration for data-Driven Medical Research - A Scoping Review

Early Multimodal Data Integration for Data-Driven Medical Re...

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69th Annual Meeting of the German Association of Medical informatics, Biometry and Epidemiology, GMDS 2024

作者： Gehrmann, Julia Beyan, Oya Institute for Biomedical Informatics University of Cologne Faculty of Medicine University Hospital Cologne Cologne Germany Department of Data Science and Artificial Intelligence Fraunhofer FIT Sankt Augustin Germany

ISBN: (纸本)9781643685366

Introduction data-driven medical research (DDMR) needs multimodal data (MMD) to sufficiently capture the complexity of clinical cases. Methods for early multimodal data integration (MMDI), i.e. integration of the data before performing a data analysis, vary from basic concatenation to applying Deep Learning, each with distinct characteristics and challenges. Besides early MMDI, there exists late MMDI which performs modality-specific data analyses and then combines the analysis results. Methods We conducted a scoping review, following PRISMA guidelines, to find and analyze 21 reviews on methods for early MMDI between 2019 and 2024. Results Our analysis categorized these methods into four groups and summarized group-specific characteristics that are relevant for choosing the optimal method combination for MMDI pipelines in DDMR projects. Moreover, we found that early MMDI is often performed by executing several methods subsequently in a pipeline. This early MMDI pipeline is usually subject to manual *** Our focus was on structural integration in DDMR. The choice of MMDI method depends on the research setting, complexity, and the researcher team's expertise. Future research could focus on comparing early and late MMDI approaches as well as automating the optimization of MMDI pipelines to integrate vast amounts of real-world medical data effectively, facilitating holistic DDMR. © 2024 The Authors.

关键词： data-Driven Medicine Early Integration Multimodal data Integration Multimodality Scoping Review

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EMPATHIC: Emulating Human-Like Multimodal Personality Architecture Through Thoughtful Human-AI Conversation 14

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

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14th International Conference on Cloud Computing, data science and Engineering, Confluence 2024

作者： Varshini Devi, I. Oviya, I.R. Raja, Kalpana Amrita School of Computing Amrita Vishwa Vidyapeetham Department of Computer Science and Engineering Chennai India School of Medicine Yale University Section for Biomedical Informatics and Data Science New HavenCT United States

ISBN: (纸本)9798350344837

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. © 2024 IEEE.

关键词： Emotion Recognition

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Predicting Protein-Protein Interactions Using Self-Attention-Based Deep Neural Networks and FastText Embeddings 15

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

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15th International Conference on Computing Communication and Networking Technologies, ICCCNT 2024

作者： Oviya, I.R. Shanmukha Sravya, N. Raja, Kalpana Amrita Vishwa Vidyapeetham Amrita School Of Computing Department of Computer Science Engineering Chennai601103 India Yale University Section for Biomedical Informatics and Data Science School of Medicine New HavenCT United States

ISBN: (纸本)9798350370249

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 5-fold cross-validation on datasets of *** and Human-Bacillus Anthracis protein interactions, resulting in accuracies of 92.28% and 94.08%, respectively. Compared to existing machine learning models, our model demonstrates superior performance on both datasets. © 2024 IEEE.

关键词： Adversarial machine learning

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