Background:In the field of genetic diagnostics,DNA sequencing is an important tool because the depth and complexity of this field have major implications in light of the genetic architectures of diseases and the ident...Background:In the field of genetic diagnostics,DNA sequencing is an important tool because the depth and complexity of this field have major implications in light of the genetic architectures of diseases and the identification of risk factors associated with genetic disorders.Methods:Our study introduces a novel two-tiered analytical framework to raise the precision and reliability of genetic data interpretation.It is initiated by extracting and analyzing salient features from DNA sequences through a CNN-based feature analysis,taking advantage of the power inherent in Convolutional neural networks(CNNs)to attain complex patterns and minute mutations in genetic data.This study embraces an elite collection of machine learning classifiers interweaved through a stern voting mechanism,which synergistically joins the predictions made from multiple classifiers to generate comprehensive and well-balanced interpretations of the genetic data.Results:This state-of-the-art method was further tested by carrying out an empirical analysis on a variants'dataset of DNA sequences taken from patients affected by breast cancer,juxtaposed with a control group composed of healthy people.Thus,the integration of CNNs with a voting-based ensemble of classifiers returned outstanding outcomes,with performance metrics accuracy,precision,recall,and F1-scorereaching the outstanding rate of 0.88,outperforming previous models.Conclusions:This dual accomplishment underlines the transformative potential that integrating deep learning techniques with ensemble machine learning might provide in real added value for further genetic diagnostics and prognostics.These results from this study set a new benchmark in the accuracy of disease diagnosis through DNA sequencing and promise future studies on improved personalized medicine and healthcare approaches with precise genetic information.展开更多
Existing weakly supervised semantic segmentation(WSSS)methods based on image-level labels always rely on class activation maps(CAMs),which measure the relationships between features and classifiers.However,CAMs only f...Existing weakly supervised semantic segmentation(WSSS)methods based on image-level labels always rely on class activation maps(CAMs),which measure the relationships between features and classifiers.However,CAMs only focus on the most discriminative regions of images,resulting in their poor coverage performance.We attribute this to the deficiency in the recognition ability of a single classifier and the negative impacts caused by magnitudes during the CAMs normalisation process.To address the aforementioned issues,we propose to construct selective multiple classifiers(SMC).During the training process,we extract multiple prototypes for each class and store them in the corresponding memory bank.These prototypes are divided into foreground and background prototypes,with the former used to identify foreground objects and the latter aimed at preventing the false activation of background pixels.As for the inference stage,multiple prototypes are adaptively selected from the memory bank for each image as SMC.Subsequently,CAMs are generated by measuring the angle between SMC and features.We enhance the recognition ability of classifiers by adaptively constructing multiple classifiers for each image,while only relying on angle measurement to generate CAMs can alleviate the suppression phenomenon caused by magnitudes.Furthermore,SMC can be integrated into other WSSS approaches to help generate better CAMs.Extensive experiments conducted on standard WSSS benchmarks such as PASCAL VOC 2012 and MS COCO 2014 demonstrate the superiority of our proposed method.展开更多
To improve the performance of the multiple classifier system, a new method of feature-decision level fusion is proposed based on knowledge discovery. In the new method, the base classifiers operate on different featur...To improve the performance of the multiple classifier system, a new method of feature-decision level fusion is proposed based on knowledge discovery. In the new method, the base classifiers operate on different feature spaces and their types depend on different measures of between-class separability. The uncertainty measures corresponding to each output of each base classifier are induced from the established decision tables （DTs） in the form of mass function in the Dempster-Shafer theory （DST）. Furthermore, an effective fusion framework is built at the feature-decision level on the basis of a generalized rough set model and the DST. The experiment for the classification of hyperspectral remote sensing images shows that the performance of the classification can be improved by the proposed method compared with that of plurality voting （PV）.展开更多
Domain adaptation aims to reduce the distribution gap between the training data(source domain)and the target data.This enables effective predictions even for domains not seen during training.However,most conventional ...Domain adaptation aims to reduce the distribution gap between the training data(source domain)and the target data.This enables effective predictions even for domains not seen during training.However,most conventional domain adaptation methods assume a single source domain,making them less suitable for modern deep learning settings that rely on diverse and large-scale datasets.To address this limitation,recent research has focused on Multi-Source Domain Adaptation(MSDA),which aims to learn effectively from multiple source domains.In this paper,we propose Efficient Domain Transition for Multi-source(EDTM),a novel and efficient framework designed to tackle two major challenges in existing MSDA approaches:(1)integrating knowledge across different source domains and(2)aligning label distributions between source and target domains.EDTM leverages an ensemble-based classifier expert mechanism to enhance the contribution of source domains that are more similar to the target domain.To further stabilize the learning process and improve performance,we incorporate imitation learning into the training of the target model.In addition,Maximum Classifier Discrepancy(MCD)is employed to align class-wise label distributions between the source and target domains.Experiments were conducted using Digits-Five,one of the most representative benchmark datasets for MSDA.The results show that EDTM consistently outperforms existing methods in terms of average classification accuracy.Notably,EDTM achieved significantly higher performance on target domains such as Modified National Institute of Standards and Technolog with blended background images(MNIST-M)and Street View House Numbers(SVHN)datasets,demonstrating enhanced generalization compared to baseline approaches.Furthermore,an ablation study analyzing the contribution of each loss component validated the effectiveness of the framework,highlighting the importance of each module in achieving optimal performance.展开更多
Background:Stomach cancer(SC)is one of the most lethal malignancies worldwide due to late-stage diagnosis and limited treatment.The transcriptomic,epigenomic,and proteomic,etc.,omics datasets generated by high-through...Background:Stomach cancer(SC)is one of the most lethal malignancies worldwide due to late-stage diagnosis and limited treatment.The transcriptomic,epigenomic,and proteomic,etc.,omics datasets generated by high-throughput sequencing technology have become prominent in biomedical research,and they reveal molecular aspects of cancer diagnosis and therapy.Despite the development of advanced sequencing technology,the presence of high-dimensionality in multi-omics data makes it challenging to interpret the data.Methods:In this study,we introduce RankXLAN,an explainable ensemble-based multi-omics framework that integrates feature selection(FS),ensemble learning,bioinformatics,and in-silico validation for robust biomarker detection,potential therapeutic drug-repurposing candidates’identification,and classification of SC.To enhance the interpretability of the model,we incorporated explainable artificial intelligence(SHapley Additive exPlanations analysis),as well as accuracy,precision,F1-score,recall,cross-validation,specificity,likelihood ratio(LR)+,LR−,and Youden index results.Results:The experimental results showed that the top four FS algorithms achieved improved results when applied to the ensemble learning classification model.The proposed ensemble model produced an area under the curve(AUC)score of 0.994 for gene expression,0.97 for methylation,and 0.96 for miRNA expression data.Through the integration of bioinformatics and ML approach of the transcriptomic and epigenomic multi-omics dataset,we identified potential marker genes,namely,UBE2D2,HPCAL4,IGHA1,DPT,and FN3K.In-silico molecular docking revealed a strong binding affinity between ANKRD13C and the FDA-approved drug Everolimus(binding affinity−10.1 kcal/mol),identifying ANKRD13C as a potential therapeutic drug-repurposing target for SC.Conclusion:The proposed framework RankXLAN outperforms other existing frameworks for serum biomarker identification,therapeutic target identification,and SC classification with multi-omics datasets.展开更多
文摘Background:In the field of genetic diagnostics,DNA sequencing is an important tool because the depth and complexity of this field have major implications in light of the genetic architectures of diseases and the identification of risk factors associated with genetic disorders.Methods:Our study introduces a novel two-tiered analytical framework to raise the precision and reliability of genetic data interpretation.It is initiated by extracting and analyzing salient features from DNA sequences through a CNN-based feature analysis,taking advantage of the power inherent in Convolutional neural networks(CNNs)to attain complex patterns and minute mutations in genetic data.This study embraces an elite collection of machine learning classifiers interweaved through a stern voting mechanism,which synergistically joins the predictions made from multiple classifiers to generate comprehensive and well-balanced interpretations of the genetic data.Results:This state-of-the-art method was further tested by carrying out an empirical analysis on a variants'dataset of DNA sequences taken from patients affected by breast cancer,juxtaposed with a control group composed of healthy people.Thus,the integration of CNNs with a voting-based ensemble of classifiers returned outstanding outcomes,with performance metrics accuracy,precision,recall,and F1-scorereaching the outstanding rate of 0.88,outperforming previous models.Conclusions:This dual accomplishment underlines the transformative potential that integrating deep learning techniques with ensemble machine learning might provide in real added value for further genetic diagnostics and prognostics.These results from this study set a new benchmark in the accuracy of disease diagnosis through DNA sequencing and promise future studies on improved personalized medicine and healthcare approaches with precise genetic information.
基金supported by the National Natural Science Foundation of China(Grants 62176097,61433007)Fundamental Research Funds for the Central Universities(Grant 2019kfyXKJC024)the 111 Project on Computational Intelligence and Intelligent Control(Grant B18024).
文摘Existing weakly supervised semantic segmentation(WSSS)methods based on image-level labels always rely on class activation maps(CAMs),which measure the relationships between features and classifiers.However,CAMs only focus on the most discriminative regions of images,resulting in their poor coverage performance.We attribute this to the deficiency in the recognition ability of a single classifier and the negative impacts caused by magnitudes during the CAMs normalisation process.To address the aforementioned issues,we propose to construct selective multiple classifiers(SMC).During the training process,we extract multiple prototypes for each class and store them in the corresponding memory bank.These prototypes are divided into foreground and background prototypes,with the former used to identify foreground objects and the latter aimed at preventing the false activation of background pixels.As for the inference stage,multiple prototypes are adaptively selected from the memory bank for each image as SMC.Subsequently,CAMs are generated by measuring the angle between SMC and features.We enhance the recognition ability of classifiers by adaptively constructing multiple classifiers for each image,while only relying on angle measurement to generate CAMs can alleviate the suppression phenomenon caused by magnitudes.Furthermore,SMC can be integrated into other WSSS approaches to help generate better CAMs.Extensive experiments conducted on standard WSSS benchmarks such as PASCAL VOC 2012 and MS COCO 2014 demonstrate the superiority of our proposed method.
文摘To improve the performance of the multiple classifier system, a new method of feature-decision level fusion is proposed based on knowledge discovery. In the new method, the base classifiers operate on different feature spaces and their types depend on different measures of between-class separability. The uncertainty measures corresponding to each output of each base classifier are induced from the established decision tables （DTs） in the form of mass function in the Dempster-Shafer theory （DST）. Furthermore, an effective fusion framework is built at the feature-decision level on the basis of a generalized rough set model and the DST. The experiment for the classification of hyperspectral remote sensing images shows that the performance of the classification can be improved by the proposed method compared with that of plurality voting （PV）.
基金supported by the National Research Foundation of Korea(NRF)grant funded by the Korea government(MSIT)(No.RS-2024-00406320)the Institute of Information&Communica-tions Technology Planning&Evaluation(IITP)-Innovative Human Resource Development for Local Intellectualization Program Grant funded by the Korea government(MSIT)(IITP-2026-RS-2023-00259678).
文摘Domain adaptation aims to reduce the distribution gap between the training data(source domain)and the target data.This enables effective predictions even for domains not seen during training.However,most conventional domain adaptation methods assume a single source domain,making them less suitable for modern deep learning settings that rely on diverse and large-scale datasets.To address this limitation,recent research has focused on Multi-Source Domain Adaptation(MSDA),which aims to learn effectively from multiple source domains.In this paper,we propose Efficient Domain Transition for Multi-source(EDTM),a novel and efficient framework designed to tackle two major challenges in existing MSDA approaches:(1)integrating knowledge across different source domains and(2)aligning label distributions between source and target domains.EDTM leverages an ensemble-based classifier expert mechanism to enhance the contribution of source domains that are more similar to the target domain.To further stabilize the learning process and improve performance,we incorporate imitation learning into the training of the target model.In addition,Maximum Classifier Discrepancy(MCD)is employed to align class-wise label distributions between the source and target domains.Experiments were conducted using Digits-Five,one of the most representative benchmark datasets for MSDA.The results show that EDTM consistently outperforms existing methods in terms of average classification accuracy.Notably,EDTM achieved significantly higher performance on target domains such as Modified National Institute of Standards and Technolog with blended background images(MNIST-M)and Street View House Numbers(SVHN)datasets,demonstrating enhanced generalization compared to baseline approaches.Furthermore,an ablation study analyzing the contribution of each loss component validated the effectiveness of the framework,highlighting the importance of each module in achieving optimal performance.
基金the Deanship of Research and Graduate Studies at King Khalid University,KSA,for funding this work through the Large Research Project under grant number RGP2/164/46.
文摘Background:Stomach cancer(SC)is one of the most lethal malignancies worldwide due to late-stage diagnosis and limited treatment.The transcriptomic,epigenomic,and proteomic,etc.,omics datasets generated by high-throughput sequencing technology have become prominent in biomedical research,and they reveal molecular aspects of cancer diagnosis and therapy.Despite the development of advanced sequencing technology,the presence of high-dimensionality in multi-omics data makes it challenging to interpret the data.Methods:In this study,we introduce RankXLAN,an explainable ensemble-based multi-omics framework that integrates feature selection(FS),ensemble learning,bioinformatics,and in-silico validation for robust biomarker detection,potential therapeutic drug-repurposing candidates’identification,and classification of SC.To enhance the interpretability of the model,we incorporated explainable artificial intelligence(SHapley Additive exPlanations analysis),as well as accuracy,precision,F1-score,recall,cross-validation,specificity,likelihood ratio(LR)+,LR−,and Youden index results.Results:The experimental results showed that the top four FS algorithms achieved improved results when applied to the ensemble learning classification model.The proposed ensemble model produced an area under the curve(AUC)score of 0.994 for gene expression,0.97 for methylation,and 0.96 for miRNA expression data.Through the integration of bioinformatics and ML approach of the transcriptomic and epigenomic multi-omics dataset,we identified potential marker genes,namely,UBE2D2,HPCAL4,IGHA1,DPT,and FN3K.In-silico molecular docking revealed a strong binding affinity between ANKRD13C and the FDA-approved drug Everolimus(binding affinity−10.1 kcal/mol),identifying ANKRD13C as a potential therapeutic drug-repurposing target for SC.Conclusion:The proposed framework RankXLAN outperforms other existing frameworks for serum biomarker identification,therapeutic target identification,and SC classification with multi-omics datasets.
