Biodata Mining最新文献

{"title":"Comparing new tools of artificial intelligence to the authentic intelligence of our global health students.","authors":"Shilpa R Thandla, Grace Q Armstrong, Adil Menon, Aashna Shah, David L Gueye, Clara Harb, Estefania Hernandez, Yasaswini Iyer, Abigail R Hotchner, Riddhi Modi, Anusha Mudigonda, Maria A Prokos, Tharun M Rao, Olivia R Thomas, Camilo A Beltran, Taylor Guerrieri, Sydney LeBlanc, Skanda Moorthy, Sara G Yacoub, Jacob E Gardner, Benjamin M Greenberg, Alyssa Hubal, Yuliana P Lapina, Jacqueline Moran, Joseph P O'Brien, Anna C Winnicki, Christina Yoka, Junwei Zhang, Peter A Zimmerman","doi":"10.1186/s13040-024-00408-7","DOIUrl":"10.1186/s13040-024-00408-7","url":null,"abstract":"<p><strong>Introduction: </strong>The transformative feature of Artificial Intelligence (AI) is the massive capacity for interpreting and transforming unstructured data into a coherent and meaningful context. In general, the potential that AI will alter traditional approaches to student research and its evaluation appears to be significant. With regard to research in global health, it is important for students and research experts to assess strengths and limitations of GenAI within this space. Thus, the goal of our research was to evaluate the information literacy of GenAI compared to expectations that graduate students meet in writing research papers.</p><p><strong>Methods: </strong>After completing the course, Fundamentals of Global Health (INTH 401) at Case Western Reserve University (CWRU), Graduate students who successfully completed their required research paper were recruited to compare their original papers with a paper they generated by ChatGPT-4o using the original assignment prompt. Students also completed a Google Forms survey to evaluate different sections of the AI-generated paper (e.g., Adherence to Introduction guidelines, Presentation of three perspectives, Conclusion) and their original papers and their overall satisfaction with the AI work. The original student to ChatGPT-4o comparison also enabled evaluation of narrative elements and references.</p><p><strong>Results: </strong>Of the 54 students who completed the required research paper, 28 (51.8%) agreed to collaborate in the comparison project. A summary of the survey responses suggested that students evaluated the AI-generated paper as inferior or similar to their own paper (overall satisfaction average = 2.39 (1.61-3.17); Likert scale: 1 to 5 with lower scores indicating inferiority). Evaluating the average individual student responses for 5 Likert item queries showed that 17 scores were < 2.9; 7 scores were between 3.0 to 3.9; 4 scores were ≥ 4.0, consistent with inferiority of the AI-generated paper. Evaluation of reference selection by ChatGPT-4o (n = 729 total references) showed that 54% (n = 396) were authentic, 46% (n = 333) did not exist. Of the authentic references, 26.5% (105/396) were relevant to the paper narrative; 14.4% of the 729 total references.</p><p><strong>Discussion: </strong>Our findings reveal strengths and limitations on the potential of AI tools to assist in understanding the complexities of global health topics. Strengths mentioned by students included the ability of ChatGPT-4o to produce content very quickly and to suggest topics that they had not considered in the 3-perspective sections of their papers. Consistently presenting up-to-date facts and references, as well as further examining or summarizing the complexities of global health topics, appears to be a current limitation of ChatGPT-4o. Because ChatGPT-4o generated references from highly credible biomedical research journals that did not exist, our findings conclude that ChatGPT-4o failed a","PeriodicalId":48947,"journal":{"name":"Biodata Mining","volume":"17 1","pages":"58"},"PeriodicalIF":4.0,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11656723/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142856210","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Detection and classification of long terminal repeat sequences in plant LTR-retrotransposons and their analysis using explainable machine learning.","authors":"Jakub Horvath, Pavel Jedlicka, Marie Kratka, Zdenek Kubat, Eduard Kejnovsky, Matej Lexa","doi":"10.1186/s13040-024-00410-z","DOIUrl":"10.1186/s13040-024-00410-z","url":null,"abstract":"<p><strong>Background: </strong>Long terminal repeats (LTRs) represent important parts of LTR retrotransposons and retroviruses found in high copy numbers in a majority of eukaryotic genomes. LTRs contain regulatory sequences essential for the life cycle of the retrotransposon. Previous experimental and sequence studies have provided only limited information about LTR structure and composition, mostly from model systems. To enhance our understanding of these key sequence modules, we focused on the contrasts between LTRs of various retrotransposon families and other genomic regions. Furthermore, this approach can be utilized for the classification and prediction of LTRs.</p><p><strong>Results: </strong>We used machine learning methods suitable for DNA sequence classification and applied them to a large dataset of plant LTR retrotransposon sequences. We trained three machine learning models using (i) traditional model ensembles (Gradient Boosting), (ii) hybrid convolutional/long and short memory network models, and (iii) a DNA pre-trained transformer-based model using k-mer sequence representation. All three approaches were successful in classifying and isolating LTRs in this data, as well as providing valuable insights into LTR sequence composition. The best classification (expressed as F1 score) achieved for LTR detection was 0.85 using the hybrid network model. The most accurate classification task was superfamily classification (F1=0.89) while the least accurate was family classification (F1=0.74). The trained models were subjected to explainability analysis. Positional analysis identified a mixture of interesting features, many of which had a preferred absolute position within the LTR and/or were biologically relevant, such as a centrally positioned TATA-box regulatory sequence, and TG..CA nucleotide patterns around both LTR edges.</p><p><strong>Conclusions: </strong>Our results show that the models used here recognized biologically relevant motifs, such as core promoter elements in the LTR detection task, and a development and stress-related subclass of transcription factor binding sites in the family classification task. Explainability analysis also highlighted the importance of 5'- and 3'- edges in LTR identity and revealed need to analyze more than just dinucleotides at these ends. Our work shows the applicability of machine learning models to regulatory sequence analysis and classification, and demonstrates the important role of the identified motifs in LTR detection.</p>","PeriodicalId":48947,"journal":{"name":"Biodata Mining","volume":"17 1","pages":"57"},"PeriodicalIF":4.0,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11656987/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142856213","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"TGNet: tensor-based graph convolutional networks for multimodal brain network analysis.","authors":"Zhaoming Kong, Rong Zhou, Xinwei Luo, Songlin Zhao, Ann B Ragin, Alex D Leow, Lifang He","doi":"10.1186/s13040-024-00409-6","DOIUrl":"10.1186/s13040-024-00409-6","url":null,"abstract":"<p><p>Multimodal brain network analysis enables a comprehensive understanding of neurological disorders by integrating information from multiple neuroimaging modalities. However, existing methods often struggle to effectively model the complex structures of multimodal brain networks. In this paper, we propose a novel tensor-based graph convolutional network (TGNet) framework that combines tensor decomposition with multi-layer GCNs to capture both the homogeneity and intricate graph structures of multimodal brain networks. We evaluate TGNet on four datasets-HIV, Bipolar Disorder (BP), and Parkinson's Disease (PPMI), Alzheimer's Disease (ADNI)-demonstrating that it significantly outperforms existing methods for disease classification tasks, particularly in scenarios with limited sample sizes. The robustness and effectiveness of TGNet highlight its potential for advancing multimodal brain network analysis. The code is available at  https://github.com/rongzhou7/TGNet .</p>","PeriodicalId":48947,"journal":{"name":"Biodata Mining","volume":"17 1","pages":"55"},"PeriodicalIF":4.0,"publicationDate":"2024-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11622555/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142787246","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Predictive modeling of ALS progression: an XGBoost approach using clinical features.","authors":"Richa Gupta, Mansi Bhandari, Anhad Grover, Taher Al-Shehari, Mohammed Kadrie, Taha Alfakih, Hussain Alsalman","doi":"10.1186/s13040-024-00399-5","DOIUrl":"10.1186/s13040-024-00399-5","url":null,"abstract":"<p><p>This research presents a predictive model aimed at estimating the progression of Amyotrophic Lateral Sclerosis (ALS) based on clinical features collected from a dataset of 50 patients. Important features included evaluations of speech, mobility, and respiratory function. We utilized an XGBoost regression model to forecast scores on the ALS Functional Rating Scale (ALSFRS-R), achieving a training mean squared error (MSE) of 0.1651 and a testing MSE of 0.0073, with R² values of 0.9800 for training and 0.9993 for testing. The model demonstrates high accuracy, providing a useful tool for clinicians to track disease progression and enhance patient management and treatment strategies.</p>","PeriodicalId":48947,"journal":{"name":"Biodata Mining","volume":"17 1","pages":"54"},"PeriodicalIF":4.0,"publicationDate":"2024-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11610297/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142774029","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deep learning-based Emergency Department In-hospital Cardiac Arrest Score (Deep EDICAS) for early prediction of cardiac arrest and cardiopulmonary resuscitation in the emergency department.","authors":"Yuan-Xiang Deng, Jyun-Yi Wang, Chia-Hsin Ko, Chien-Hua Huang, Chu-Lin Tsai, Li-Chen Fu","doi":"10.1186/s13040-024-00407-8","DOIUrl":"10.1186/s13040-024-00407-8","url":null,"abstract":"<p><strong>Background: </strong>Timely identification of deteriorating patients is crucial to prevent the progression to cardiac arrest. However, current methods predicting emergency department cardiac arrest are primarily static, rule-based with limited precision and cannot accommodate time-series data. Deep learning has the potential to continuously update data and provide more precise predictions throughout the emergency department stay.</p><p><strong>Methods: </strong>We developed and internally validated a deep learning-based scoring system, the Deep EDICAS for early prediction of cardiac arrest and a subset of arrest, cardiopulmonary resuscitation (CPR), in the emergency department. Our proposed model effectively integrates tabular and time series data to enhance predictive accuracy. To address data imbalance and bolster early prediction capabilities, we implemented data augmentation techniques.</p><p><strong>Results: </strong>Our system achieved an AUPRC of 0.5178 and an AUROC of 0.9388 on on data from the National Taiwan University Hospital. For early prediction, our system achieved an AUPRC of 0.2798 and an AUROC of 0.9046, demonstrating superiority over other early warning scores. Moerover, Deep EDICAS offers interpretability through feature importance analysis.</p><p><strong>Conclusion: </strong>Our study demonstrates the effectiveness of deep learning in predicting cardiac arrest in emergency department. Despite the higher clinical value associated with detecting patients requiring CPR, there is a scarcity of literature utilizing deep learning in CPR detection tasks. Therefore, this study embarks on an initial exploration into the task of CPR detection.</p>","PeriodicalId":48947,"journal":{"name":"Biodata Mining","volume":"17 1","pages":"52"},"PeriodicalIF":4.0,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11585162/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142695993","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Supervised multiple kernel learning approaches for multi-omics data integration.","authors":"Mitja Briscik, Gabriele Tazza, László Vidács, Marie-Agnès Dillies, Sébastien Déjean","doi":"10.1186/s13040-024-00406-9","DOIUrl":"10.1186/s13040-024-00406-9","url":null,"abstract":"<p><strong>Background: </strong>Advances in high-throughput technologies have originated an ever-increasing availability of omics datasets. The integration of multiple heterogeneous data sources is currently an issue for biology and bioinformatics. Multiple kernel learning (MKL) has shown to be a flexible and valid approach to consider the diverse nature of multi-omics inputs, despite being an underused tool in genomic data mining.</p><p><strong>Results: </strong>We provide novel MKL approaches based on different kernel fusion strategies. To learn from the meta-kernel of input kernels, we adapted unsupervised integration algorithms for supervised tasks with support vector machines. We also tested deep learning architectures for kernel fusion and classification. The results show that MKL-based models can outperform more complex, state-of-the-art, supervised multi-omics integrative approaches.</p><p><strong>Conclusion: </strong>Multiple kernel learning offers a natural framework for predictive models in multi-omics data. It proved to provide a fast and reliable solution that can compete with and outperform more complex architectures. Our results offer a direction for bio-data mining research, biomarker discovery and further development of methods for heterogeneous data integration.</p>","PeriodicalId":48947,"journal":{"name":"Biodata Mining","volume":"17 1","pages":"53"},"PeriodicalIF":4.0,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11585117/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142695995","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptome-based network analysis related to regulatory T cells infiltration identified RCN1 as a potential biomarker for prognosis in clear cell renal cell carcinoma.","authors":"Yang Qixin, Huang Jing, He Jiang, Liu Xueyang, Yu Lu, Li Yuehua","doi":"10.1186/s13040-024-00404-x","DOIUrl":"10.1186/s13040-024-00404-x","url":null,"abstract":"<p><strong>Background: </strong>Regulatory T cells (Tregs) play a critical role in shaping the immunosuppressive microenvironment within tumors. Investigating the role of Tregs in Clear cell renal cell carcinoma (ccRCC) is crucial for identifying prognostic markers and therapeutic targets for ccRCC.</p><p><strong>Methods: </strong>Weighted gene co-expression network analysis (WGCNA) was utilized to pinpoint modules related to Treg infiltration in TCGA-KIRC samples. Following this, consensus clustering was employed to derive two clusters associated with Treg infiltration in ccRCC. A prognostic model was then developed using the gene module associated with Treg infiltration. We then evaluated the ability of the prognostic model to predict ccRCC overall survival and demonstrated that RCN1 can be used as a target to predict ccRCC prognosis.</p><p><strong>Results: </strong>We deduce that the two clusters associated with Treg infiltration exhibit distinct compositions of the immune microenvironment, pathway activations, prognosis, and drug sensitivities commonly utilized in ccRCC treatment. Furthermore, a 7-gene model risk score, developed based on ccRCC Treg infiltration, proved to be a reliable prognostic marker in both training and validation cohorts. Additionally, survival analysis indicated that RCN1 serves as a reliable prognostic factor for ccRCC. Single-cell sequencing analysis revealed that RCN1 is predominantly expressed in tumor cells. A pan-cancer analysis highlighted that RCN1 is linked with poor prognosis and the activation of inflammatory response pathways across various cancers.</p><p><strong>Conclusion: </strong>We developed a prognostic model associated with Treg infiltration, which facilitates the clinical categorization of ccRCC progression. Moreover, our findings underscore the significant potential of RCN1 as a ccRCC biomarker.</p>","PeriodicalId":48947,"journal":{"name":"Biodata Mining","volume":"17 1","pages":"51"},"PeriodicalIF":4.0,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11566375/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142631060","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deciphering the tissue-specific functional effect of Alzheimer risk SNPs with deep genome annotation.","authors":"Pradeep Varathan Pugalenthi, Bing He, Linhui Xie, Kwangsik Nho, Andrew J Saykin, Jingwen Yan","doi":"10.1186/s13040-024-00400-1","DOIUrl":"10.1186/s13040-024-00400-1","url":null,"abstract":"<p><p>Alzheimer's disease (AD) is a highly heritable brain dementia, along with substantial failure of cognitive function. Large-scale genome-wide association studies (GWASs) have led to a set of SNPs significantly associated with AD and related traits. GWAS hits usually emerge as clusters where a lead SNP with the highest significance is surrounded by other less significant neighboring SNPs. Although functionality is not guaranteed even with the strongest associations in GWASs, lead SNPs have historically been the focus of the field, with the remaining associations inferred to be redundant. Recent deep genome annotation tools enable the prediction of function from a segment of a DNA sequence with significantly improved precision, which allows in-silico mutagenesis to interrogate the functional effect of SNP alleles. In this project, we explored the impact of top AD GWAS hits around APOE region on chromatin functions and whether it will be altered by the genetic context (i.e., alleles of neighboring SNPs). Our results showed that highly correlated SNPs in the same LD block could have distinct impacts on downstream functions. Although some GWAS lead SNPs showed dominant functional effects regardless of the neighborhood SNP alleles, several other SNPs did exhibit enhanced loss or gain of function under certain genetic contexts, suggesting potential additional information hidden in the LD blocks.</p>","PeriodicalId":48947,"journal":{"name":"Biodata Mining","volume":"17 1","pages":"50"},"PeriodicalIF":4.0,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11558841/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142631056","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Investigating potential drug targets for IgA nephropathy and membranous nephropathy through multi-queue plasma protein analysis: a Mendelian randomization study based on SMR and co-localization analysis.","authors":"Xinyi Xu, Changhong Miao, Shirui Yang, Lu Xiao, Ying Gao, Fangying Wu, Jianbo Xu","doi":"10.1186/s13040-024-00405-w","DOIUrl":"10.1186/s13040-024-00405-w","url":null,"abstract":"<p><strong>Background: </strong>Membranous nephropathy (MN) and IgA nephropathy (IgAN) pose challenges in clinical treatment with existing therapies primarily focusing on symptom relief and often yielding unsatisfactory outcomes. The search for novel drug targets remains crucial to address the shortcomings in managing both kidney diseases.</p><p><strong>Methods: </strong>Utilizing GWAS data for MN (ncase = 2150, ncontrol = 5829) and IgAN (ncase = 15587, ncontrol = 462197), instrumental variables for plasma proteins were derived from recent GWAS. Sensitivity analysis involved bidirectional Mendelian randomization analysis, MR Steiger, Bayesian co-localization, and Phenotype scanning. The SMR analysis using eQTL data from the eQTLGen Consortium was conducted to assess the availability of selected protein targets. The PPI network was constructed to reveal potential associations with existing drug treatment targets.</p><p><strong>Results: </strong>The study, subjected to the stringent Bonferroni correction, revealed significant associations: four proteins with MN and three proteins with IgAN. In plasma protein cis-pQTL data from two cohorts, an increase in one standard deviation in PLA2R1 (OR = 2.01, 95%CI = 1.83-2.21), AIF1 (OR = 9.04, 95%CI = 4.69-17.41), MLN (OR = 3.79, 95%CI = 2.12-6.78), and NFKB1 (OR = 29.43, 95%CI = 7.73-112.0) was associated with an increased risk of MN. Additionally, in plasma protein cis-pQTL data, a standard deviation increase in FCGR3B (OR = 1.15, 95%CI = 1.09-1.22) and BTN3A1 (OR = 4.05, 95%CI = 2.65-6.19) correlated with elevated IgAN risk, while AIF1 (OR = 0.58, 95%CI = 0.46-0.73) exhibited IgAN protection. Bayesian co-localization indicated that PLA2R1 (coloc.abf-PPH4 = 0.695), NFKB1 (coloc.abf-PPH4 = 0.949), FCGR3B (coloc.abf-PPH4 = 0.909), and BTN3A1 (coloc.abf-PPH4 = 0.685) share the same variants associated with MN and IgAN. The SMR analysis indicated a causal link between NFKB1 and BTN3A1 plasma protein eQTL in both conditions, and BTN3A1 was validated externally.</p><p><strong>Conclusion: </strong>Genetically influenced plasma levels of PLA2R1 and NFKB1 impact MN risk, while FCGR3B and BTN3A1 levels are causally linked to IgAN risk, suggesting potential drug targets for further clinical exploration, notably BTN3A1 for IgAN.</p>","PeriodicalId":48947,"journal":{"name":"Biodata Mining","volume":"17 1","pages":"49"},"PeriodicalIF":4.0,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11545554/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142631058","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deep joint learning diagnosis of Alzheimer's disease based on multimodal feature fusion.","authors":"Jingru Wang, Shipeng Wen, Wenjie Liu, Xianglian Meng, Zhuqing Jiao","doi":"10.1186/s13040-024-00395-9","DOIUrl":"10.1186/s13040-024-00395-9","url":null,"abstract":"<p><p>Alzheimer's disease (AD) is an advanced and incurable neurodegenerative disease. Genetic variations are intrinsic etiological factors contributing to the abnormal expression of brain function and structure in AD patients. A new multimodal feature fusion called \"magnetic resonance imaging (MRI)-p value\" was proposed to construct 3D fusion images by introducing genes as a priori knowledge. Moreover, a new deep joint learning diagnostic model was constructed to fully learn images features. One branch trained a residual network (ResNet) to learn the features of local pathological regions. The other branch learned the position information of brain regions with different changes in the different categories of subjects' brains by introducing attention convolution, and then obtained the discriminative probability information from locations via convolution and global average pooling. The feature and position information of the two branches were linearly interacted to acquire the diagnostic basis for classifying the different categories of subjects. The diagnoses of AD and health control (HC), AD and mild cognitive impairment (MCI), HC and MCI were performed with data from the Alzheimer's Disease Neuroimaging Initiative (ADNI). The results showed that the proposed method achieved optimal results in AD-related diagnosis. The classification accuracy (ACC) and area under the curve (AUC) of the three experimental groups were 93.44% and 96.67%, 89.06% and 92%, and 84% and 81.84%, respectively. Moreover, a total of six novel genes were found to be significantly associated with AD, namely NTM, MAML2, NAALADL2, FHIT, TMEM132D and PCSK5, which provided new targets for the potential treatment of neurodegenerative diseases.</p>","PeriodicalId":48947,"journal":{"name":"Biodata Mining","volume":"17 1","pages":"48"},"PeriodicalIF":4.0,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11536794/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142584754","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}