Objective N6-methyladenosine(m6A),the most prevalent epigenetic modification in eukaryotic RNA,plays a pivotal role in regulating cellular differentiation and developmental processes,with its dysregulation implicated ...Objective N6-methyladenosine(m6A),the most prevalent epigenetic modification in eukaryotic RNA,plays a pivotal role in regulating cellular differentiation and developmental processes,with its dysregulation implicated in diverse pathological conditions.Accurate prediction of m6A sites is critical for elucidating their regulatory mechanisms and informing drug development.However,traditional experimental methods are time-consuming and costly.Although various computational approaches have been proposed,challenges remain in feature learning,predictive accuracy,and generalization.Here,we present m6A-PSRA,a dual-branch residual-network-based predictor that fully exploits RNA sequence information to enhance prediction performance and model generalization.Methods m6A-PSRA adopts a parallel dual-branch network architecture to comprehensively extract RNA sequence features via two independent pathways.The first branch applies one-hot encoding to transform the RNA sequence into a numerical matrix while strictly preserving positional information and sequence continuity.This ensures that the biological context conveyed by nucleotide order is retained.A bidirectional long short-term memory network(BiLSTM)then processes the encoded matrix,capturing both forward and backward dependencies between bases to resolve contextual correlations.The second branch employs a k-mer tokenization strategy(k=3),decomposing the sequence into overlapping 3-mer subsequences to capture local sequence patterns.A pre-trained Doc2vec model maps these subsequences into fixeddimensional vectors,reducing feature dimensionality while extracting latent global semantic information via context learning.Both branches integrate residual networks(ResNet)and a self-attention mechanism:ResNet mitigates vanishing gradients through skip connections,preserving feature integrity,while self-attention adaptively assigns weights to focus on sequence regions most relevant to methylation prediction.This synergy enhances both feature learning and generalization capability.Results Across 11 tissues from humans,mice,and rats,m6A-PSRA consistently outperformed existing methods in accuracy(ACC)and area under the curve(AUC),achieving>90%ACC and>95%AUC in every tissue tested,indicating strong cross-species and cross-tissue adaptability.Validation on independent datasets—including three human cell lines(MOLM1,HEK293,A549)and a long-sequence dataset(m6A_IND,1001 nt)—confirmed stable performance across varied biological contexts and sequence lengths.Ablation studies demonstrated that the dual-branch architecture,residual network,and self-attention mechanism each contribute critically to performance,with their combination reducing interference between pathways.Motif analysis revealed an enrichment of m6A sites in guanine(G)and cytosine(C),consistent with known regulatory patterns,supporting the model’s biological plausibility.Conclusion m6A-PSRA effectively captures RNA sequence features,achieving high prediction accuracy and robust generalization across tissues and species,providing an efficient computational tool for m6A methylation site prediction.展开更多
In low signal-to-noise ratio(SNR)environments,the traditional radar emitter recognition(RER)method struggles to recognize multiple radar emitter signals in parallel.This paper proposes a multi-label classification and...In low signal-to-noise ratio(SNR)environments,the traditional radar emitter recognition(RER)method struggles to recognize multiple radar emitter signals in parallel.This paper proposes a multi-label classification and recognition method for multiple radar-emitter modulation types based on a residual network.This method can quickly perform parallel classification and recognition of multi-modulation radar time-domain aliasing signals under low SNRs.First,we perform time-frequency analysis on the received signal to extract the normalized time-frequency image through the short-time Fourier transform(STFT).The time-frequency distribution image is then denoised using a deep normalized convolutional neural network(DNCNN).Secondly,the multi-label classification and recognition model for multi-modulation radar emitter time-domain aliasing signals is established,and learning the characteristics of radar signal time-frequency distribution image dataset to achieve the purpose of training model.Finally,time-frequency image is recognized and classified through the model,thus completing the automatic classification and recognition of the time-domain aliasing signal.Simulation results show that the proposed method can classify and recognize radar emitter signals of different modulation types in parallel under low SNRs.展开更多
基金supported by grants from The National Natural Science Foundation of China(12361104)Yunnan Fundamental Research Projects(202301AT070016,202401AT070036)+2 种基金the Youth Talent Program of Xingdian Talent Support Plan(XDYC-QNRC-2022-0514)the Yunnan Province International Joint Laboratory for Intelligent Integration and Application of Ethnic Multilingualism(202403AP140014)the Open Research Fund of Yunnan Key Laboratory of Statistical Modeling and Data Analysis,Yunnan University(SMDAYB2023004)。
文摘Objective N6-methyladenosine(m6A),the most prevalent epigenetic modification in eukaryotic RNA,plays a pivotal role in regulating cellular differentiation and developmental processes,with its dysregulation implicated in diverse pathological conditions.Accurate prediction of m6A sites is critical for elucidating their regulatory mechanisms and informing drug development.However,traditional experimental methods are time-consuming and costly.Although various computational approaches have been proposed,challenges remain in feature learning,predictive accuracy,and generalization.Here,we present m6A-PSRA,a dual-branch residual-network-based predictor that fully exploits RNA sequence information to enhance prediction performance and model generalization.Methods m6A-PSRA adopts a parallel dual-branch network architecture to comprehensively extract RNA sequence features via two independent pathways.The first branch applies one-hot encoding to transform the RNA sequence into a numerical matrix while strictly preserving positional information and sequence continuity.This ensures that the biological context conveyed by nucleotide order is retained.A bidirectional long short-term memory network(BiLSTM)then processes the encoded matrix,capturing both forward and backward dependencies between bases to resolve contextual correlations.The second branch employs a k-mer tokenization strategy(k=3),decomposing the sequence into overlapping 3-mer subsequences to capture local sequence patterns.A pre-trained Doc2vec model maps these subsequences into fixeddimensional vectors,reducing feature dimensionality while extracting latent global semantic information via context learning.Both branches integrate residual networks(ResNet)and a self-attention mechanism:ResNet mitigates vanishing gradients through skip connections,preserving feature integrity,while self-attention adaptively assigns weights to focus on sequence regions most relevant to methylation prediction.This synergy enhances both feature learning and generalization capability.Results Across 11 tissues from humans,mice,and rats,m6A-PSRA consistently outperformed existing methods in accuracy(ACC)and area under the curve(AUC),achieving>90%ACC and>95%AUC in every tissue tested,indicating strong cross-species and cross-tissue adaptability.Validation on independent datasets—including three human cell lines(MOLM1,HEK293,A549)and a long-sequence dataset(m6A_IND,1001 nt)—confirmed stable performance across varied biological contexts and sequence lengths.Ablation studies demonstrated that the dual-branch architecture,residual network,and self-attention mechanism each contribute critically to performance,with their combination reducing interference between pathways.Motif analysis revealed an enrichment of m6A sites in guanine(G)and cytosine(C),consistent with known regulatory patterns,supporting the model’s biological plausibility.Conclusion m6A-PSRA effectively captures RNA sequence features,achieving high prediction accuracy and robust generalization across tissues and species,providing an efficient computational tool for m6A methylation site prediction.
基金The authors would like to acknowledge National Natural Science Foundation of China under Grant 61973037 and Grant 61673066 to provide fund for conducting experiments.
文摘In low signal-to-noise ratio(SNR)environments,the traditional radar emitter recognition(RER)method struggles to recognize multiple radar emitter signals in parallel.This paper proposes a multi-label classification and recognition method for multiple radar-emitter modulation types based on a residual network.This method can quickly perform parallel classification and recognition of multi-modulation radar time-domain aliasing signals under low SNRs.First,we perform time-frequency analysis on the received signal to extract the normalized time-frequency image through the short-time Fourier transform(STFT).The time-frequency distribution image is then denoised using a deep normalized convolutional neural network(DNCNN).Secondly,the multi-label classification and recognition model for multi-modulation radar emitter time-domain aliasing signals is established,and learning the characteristics of radar signal time-frequency distribution image dataset to achieve the purpose of training model.Finally,time-frequency image is recognized and classified through the model,thus completing the automatic classification and recognition of the time-domain aliasing signal.Simulation results show that the proposed method can classify and recognize radar emitter signals of different modulation types in parallel under low SNRs.
