DeepLncPro: an interpretable convolutional neural network model for identifying long non-coding RNA promoters.

Long non-coding RNA (lncRNA) plays important roles in a series of biological processes. The transcription of lncRNA is regulated by its promoter. Hence, accurate identification of lncRNA promoter will be helpful to understand its regulatory mechanisms. Since experimental techniques remain time consuming for gnome-wide promoter identification, developing computational tools to identify promoters are necessary. However, only few computational methods have been proposed for lncRNA promoter prediction and their performances still have room to be improved. In the present work, a convolutional neural network based model, called DeepLncPro, was proposed to identify lncRNA promoters in human and mouse. Comparative results demonstrated that DeepLncPro was superior to both state-of-the-art machine learning methods and existing models for identifying lncRNA promoters. Furthermore, DeepLncPro has the ability to extract and analyze transcription factor binding motifs from lncRNAs, which made it become an interpretable model. These results indicate that the DeepLncPro can server as a powerful tool for identifying lncRNA promoters. An open-source tool for DeepLncPro was provided at https://github.com/zhangtian-yang/DeepLncPro.

Arrhythmia detection by the graph convolution network and a proposed structure for communication between cardiac leads.

One of the most common causes of death worldwide is heart disease, including arrhythmia. Today, sciences such as artificial intelligence and medical statistics are looking for methods and models for correct and automatic diagnosis of cardiac arrhythmia. In pursuit of increasing the accuracy of automated methods, many studies have been conducted. However, in none of the previous articles, the relationship and structure between the heart leads have not been included in the model. It seems that the structure of ECG data can help develop the accuracy of arrhythmia detection. Therefore, in this study, a new structure of Electrocardiogram (ECG) data was introduced, and the Graph Convolution Network (GCN), which has the possibility of learning the structure, was used to develop the accuracy of cardiac arrhythmia diagnosis. Considering the relationship between the heart leads and clusters based on different ECG poles, a new structure was introduced. In this structure, the Mutual Information(MI) index was used to evaluate the relationship between the leads, and weight was given based on the poles of the leads. Weighted Mutual Information (WMI) matrices (new structure) were formed by R software. Finally, the 15-layer GCN network was adjusted by this structure and the arrhythmia of people was detected and classified by it. To evaluate the performance of the proposed new network, sensitivity, precision, specificity, accuracy, and confusion matrix indices were used. Also, the accuracy of GCN networks was compared by three different structures, including WMI, MI, and Identity. Chapman's 12-lead ECG Dataset was used in this study. The results showed that the values of sensitivity, precision, specificity, and accuracy of the GCN-WMI network with 15 intermediate layers were equal to 98.74%, 99.08%, 99.97% & 99.82%, respectively. This new proposed network was more accurate than the Graph Convolution Network-Mutual Information (GCN-MI) with an accuracy equal to 99.71% and GCN-Id with an accuracy equal to 92.68%. Therefore, utilizing this network, the types of arrhythmia were recognized and classified. Also, the new network proposed by the Graph Convolution Network-Weighted Mutual Information (GCN-WMI) was more accurate than those conducted in other studies on the same data set (Chapman). Based on the obtained results, the structure proposed in this study increased the accuracy of cardiac arrhythmia diagnosis and classification on the Chapman data set. Achieving such accuracy for arrhythmia diagnosis is a great achievement in clinical sciences.

Attention-based deep convolutional neural network for classification of generalized and focal epileptic seizures.

Epilepsy affects over 50 million people globally. Electroencephalography is critical for epilepsy diagnosis, but manual seizure classification is time-consuming and requires extensive expertise. This paper presents an automated multi-class seizure classification model using EEG signals from the Temple University Hospital Seizure Corpus ver. 1.5.2. 11 features including time-based correlation, time-based eigenvalues, power spectral density, frequency-based correlation, frequency-based eigenvalues, sample entropy, spectral entropy, logarithmic sum, standard deviation, absolute mean, and ratio of Daubechies D4 wavelet transformed coefficients were extracted from 10-second sliding windows across channels. The model combines multi-head self-attention mechanism with a deep convolutional neural network (CNN) to classify seven subtypes of generalized and focal epileptic seizures. The model achieved 0.921 weighted accuracy and 0.902 weighted F1 score in classifying focal onset non-motor, generalized onset non-motor, simple partial, complex partial, absence, tonic, and tonic-clonic seizures. In comparison, a CNN model without multi-head attention achieved 0.767 weighted accuracy. Ablation studies were conducted to validate the importance of transformer encoders and attention. The promising classification results demonstrate the potential of deep learning for handling EEG complexity and improving epilepsy diagnosis. This seizure classification model could enable timely interventions when translated into clinical practice.

Deep learning framework for peak detection at the intact level of therapeutic proteins.

While automated peak detection functionalities are available in commercially accessible software, achieving optimal true positive rates frequently necessitates visual inspection and manual adjustments. In the initial phase of this study, hetero-variants (glycoforms) of a monoclonal antibody were distinguished using liquid chromatography-mass spectrometry, revealing discernible peaks at the intact level. To comprehensively identify each peak (hetero-variant) in the intact-level analysis, a deep learning approach utilizing convolutional neural networks (CNNs) was employed in the subsequent phase of the study. In the current case study, utilizing conventional software for peak identification, five peaks were detected using a 0.5 threshold, whereas seven peaks were identified using the CNN model. The model exhibited strong performance with a probability area under the curve (AUC) of 0.9949, surpassing that of partial least squares discriminant analysis (PLS-DA) (probability AUC of 0.8041), and locally weighted regression (LWR) (probability AUC of 0.6885) on the data acquired during experimentation in real-time. The AUC of the receiver operating characteristic curve also illustrated the superior performance of the CNN over PLS-DA and LWR.

Deep transfer learning with fuzzy ensemble approach for the early detection of breast cancer.

Breast Cancer is a significant global health challenge, particularly affecting women with higher mortality compared with other cancer types. Timely detection of such cancer types is crucial, and recent research, employing deep learning techniques, shows promise in earlier detection. The research focuses on the early detection of such tumors using mammogram images with deep-learning models. The paper utilized four public databases where a similar amount of 986 mammograms each for three classes (normal, benign, malignant) are taken for evaluation. Herein, three deep CNN models such as VGG-11, Inception v3, and ResNet50 are employed as base classifiers. The research adopts an ensemble method where the proposed approach makes use of the modified Gompertz function for building a fuzzy ranking of the base classification models and their decision scores are integrated in an adaptive manner for constructing the final prediction of results. The classification results of the proposed fuzzy ensemble approach outperform transfer learning models and other ensemble approaches such as weighted average and Sugeno integral techniques. The proposed ResNet50 ensemble network using the modified Gompertz function-based fuzzy ranking approach provides a superior classification accuracy of 98.986%.

Explainable deep-neural-network supported scheme for tuberculosis detection from chest radiographs.

Chest radiographs are examined in typical clinical settings by competent physicians for tuberculosis diagnosis. However, this procedure is time consuming and subjective. Due to the growing usage of machine learning techniques in applied sciences, researchers have begun applying comparable concepts to medical diagnostics, such as tuberculosis screening. In the period of extremely deep neural nets which comprised of hundreds of convolution layers for feature extraction, we create a shallow-CNN for screening of TB condition from Chest X-rays so that the model is able to offer appropriate interpretation for right diagnosis. The suggested model consists of four convolution-maxpooling layers with various hyperparameters that were optimized for optimal performance using a Bayesian optimization technique. The model was reported with a peak classification accuracy, F1-score, sensitivity and specificity of 0.95. In addition, the receiver operating characteristic (ROC) curve for the proposed shallow-CNN showed a peak area under the curve value of 0.976. Moreover, we have employed class activation maps (CAM) and Local Interpretable Model-agnostic Explanations (LIME), explainer systems for assessing the transparency and explainability of the model in comparison to a state-of-the-art pre-trained neural net such as the DenseNet.

Computer-based facial recognition as an assisting diagnostic tool to identify children with Noonan syndrome.

BACKGROUND: Noonan syndrome (NS) is a rare genetic disease, and patients who suffer from it exhibit a facial morphology that is characterized by a high forehead, hypertelorism, ptosis, inner epicanthal folds, down-slanting palpebral fissures, a highly arched palate, a round nasal tip, and posteriorly rotated ears. Facial analysis technology has recently been applied to identify many genetic syndromes (GSs). However, few studies have investigated the identification of NS based on the facial features of the subjects. OBJECTIVES: This study develops advanced models to enhance the accuracy of diagnosis of NS. METHODS: A total of 1,892 people were enrolled in this study, including 233 patients with NS, 863 patients with other GSs, and 796 healthy children. We took one to 10 frontal photos of each subject to build a dataset, and then applied the multi-task convolutional neural network (MTCNN) for data pre-processing to generate standardized outputs with five crucial facial landmarks. The ImageNet dataset was used to pre-train the network so that it could capture generalizable features and minimize data wastage. We subsequently constructed seven models for facial identification based on the VGG16, VGG19, VGG16-BN, VGG19-BN, ResNet50, MobileNet-V2, and squeeze-and-excitation network (SENet) architectures. The identification performance of seven models was evaluated and compared with that of six physicians. RESULTS: All models exhibited a high accuracy, precision, and specificity in recognizing NS patients. The VGG19-BN model delivered the best overall performance, with an accuracy of 93.76%, precision of 91.40%, specificity of 98.73%, and F1 score of 78.34%. The VGG16-BN model achieved the highest AUC value of 0.9787, while all models based on VGG architectures were superior to the others on the whole. The highest scores of six physicians in terms of accuracy, precision, specificity, and the F1 score were 74.00%, 75.00%, 88.33%, and 61.76%, respectively. The performance of each model of facial recognition was superior to that of the best physician on all metrics. CONCLUSION: Models of computer-assisted facial recognition can improve the rate of diagnosis of NS. The models based on VGG19-BN and VGG16-BN can play an important role in diagnosing NS in clinical practice.

Improved prostate cancer diagnosis using a modified ResNet50-based deep learning architecture.

Prostate cancer, the most common cancer in men, is influenced by age, family history, genetics, and lifestyle factors. Early detection of prostate cancer using screening methods improves outcomes, but the balance between overdiagnosis and early detection remains debated. Using Deep Learning (DL) algorithms for prostate cancer detection offers a promising solution for accurate and efficient diagnosis, particularly in cases where prostate imaging is challenging. In this paper, we propose a Prostate Cancer Detection Model (PCDM) model for the automatic diagnosis of prostate cancer. It proves its clinical applicability to aid in the early detection and management of prostate cancer in real-world healthcare environments. The PCDM model is a modified ResNet50-based architecture that integrates faster R-CNN and dual optimizers to improve the performance of the detection process. The model is trained on a large dataset of annotated medical images, and the experimental results show that the proposed model outperforms both ResNet50 and VGG19 architectures. Specifically, the proposed model achieves high sensitivity, specificity, precision, and accuracy rates of 97.40%, 97.09%, 97.56%, and 95.24%, respectively.

Efficiency-Accuracy Trade-Off in Light Field Estimation with Cost Volume Construction and Aggregation.

The Rich spatial and angular information in light field images enables accurate depth estimation, which is a crucial aspect of environmental perception. However, the abundance of light field information also leads to high computational costs and memory pressure. Typically, selectively pruning some light field information can significantly improve computational efficiency but at the expense of reduced depth estimation accuracy in the pruned model, especially in low-texture regions and occluded areas where angular diversity is reduced. In this study, we propose a lightweight disparity estimation model that balances speed and accuracy and enhances depth estimation accuracy in textureless regions. We combined cost matching methods based on absolute difference and correlation to construct cost volumes, improving both accuracy and robustness. Additionally, we developed a multi-scale disparity cost fusion architecture, employing 3D convolutions and a UNet-like structure to handle matching costs at different depth scales. This method effectively integrates information across scales, utilizing the UNet structure for efficient fusion and completion of cost volumes, thus yielding more precise depth maps. Extensive testing shows that our method achieves computational efficiency on par with the most efficient existing methods, yet with double the accuracy. Moreover, our approach achieves comparable accuracy to the current highest-accuracy methods but with an order of magnitude improvement in computational performance.

Action Recognition of Taekwondo Unit Actions Using Action Images Constructed with Time-Warped Motion Profiles.

Taekwondo has evolved from a traditional martial art into an official Olympic sport. This study introduces a novel action recognition model tailored for Taekwondo unit actions, utilizing joint-motion data acquired via wearable inertial measurement unit (IMU) sensors. The utilization of IMU sensor-measured motion data facilitates the capture of the intricate and rapid movements characteristic of Taekwondo techniques. The model, underpinned by a conventional convolutional neural network (CNN)-based image classification framework, synthesizes action images to represent individual Taekwondo unit actions. These action images are generated by mapping joint-motion profiles onto the RGB color space, thus encapsulating the motion dynamics of a single unit action within a solitary image. To further refine the representation of rapid movements within these images, a time-warping technique was applied, adjusting motion profiles in relation to the velocity of the action. The effectiveness of the proposed model was assessed using a dataset compiled from 40 Taekwondo experts, yielding remarkable outcomes: an accuracy of 0.998, a precision of 0.983, a recall of 0.982, and an F1 score of 0.982. These results underscore this time-warping technique's contribution to enhancing feature representation, as well as the proposed method's scalability and effectiveness in recognizing Taekwondo unit actions.

A Snapshot Multi-Spectral Demosaicing Method for Multi-Spectral Filter Array Images Based on Channel Attention Network.

Multi-spectral imaging technologies have made great progress in the past few decades. The development of snapshot cameras equipped with a specific multi-spectral filter array (MSFA) allow dynamic scenes to be captured on a miniaturized platform across multiple spectral bands, opening up extensive applications in quantitative and visualized analysis. However, a snapshot camera based on MSFA captures a single band per pixel; thus, the other spectral band components of pixels are all missed. The raw images, which are captured by snapshot multi-spectral imaging systems, require a reconstruction procedure called demosaicing to estimate a fully defined multi-spectral image (MSI). With increasing spectral bands, the challenge of demosaicing becomes more difficult. Furthermore, the existing demosaicing methods will produce adverse artifacts and aliasing because of the adverse effects of spatial interpolation and the inadequacy of the number of layers in the network structure. In this paper, a novel multi-spectral demosaicing method based on a deep convolution neural network (CNN) is proposed for the reconstruction of full-resolution multi-spectral images from raw MSFA-based spectral mosaic images. The CNN is integrated with the channel attention mechanism to protect important channel features. We verify the merits of the proposed method using 5 × 5 raw mosaic images on synthetic as well as real-world data. The experimental results show that the proposed method outperforms the existing demosaicing methods in terms of spatial details and spectral fidelity.

A New Method for Traffic Participant Recognition Using Doppler Radar Signature and Convolutional Neural Networks.

The latest survey results show an increase in accidents on the roads involving pedestrians and cyclists. The reasons for such situations are many, the fault actually lies on both sides. Equipping vehicles, especially autonomous vehicles, with frequency-modulated continuous-wave (FMCW) radar and dedicated algorithms for analyzing signals in the time-frequency domain as well as algorithms for recognizing objects in radar imaging through deep neural networks can positively affect safety. This paper presents a method for recognizing and distinguishing a group of objects based on radar signatures of objects and a special convolutional neural network structure. The proposed approach is based on a database of radar signatures generated on pedestrian, cyclist, and car models in a Matlab environment. The obtained results of simulations and positive tests provide a basis for the application of the system in many sectors and areas of the economy. Innovative aspects of the work include the method of discriminating between multiple objects on a single radar signature, the dedicated architecture of the convolutional neural network, and the use of a method of generating a custom input database.

A Dual-Branch Fusion of a Graph Convolutional Network and a Convolutional Neural Network for Hyperspectral Image Classification.

Semi-supervised graph convolutional networks (SSGCNs) have been proven to be effective in hyperspectral image classification (HSIC). However, limited training data and spectral uncertainty restrict the classification performance, and the computational demands of a graph convolution network (GCN) present challenges for real-time applications. To overcome these issues, a dual-branch fusion of a GCN and convolutional neural network (DFGCN) is proposed for HSIC tasks. The GCN branch uses an adaptive multi-scale superpixel segmentation method to build fusion adjacency matrices at various scales, which improves the graph convolution efficiency and node representations. Additionally, a spectral feature enhancement module (SFEM) enhances the transmission of crucial channel information between the two graph convolutions. Meanwhile, the CNN branch uses a convolutional network with an attention mechanism to focus on detailed features of local areas. By combining the multi-scale superpixel features from the GCN branch and the local pixel features from the CNN branch, this method leverages complementary features to fully learn rich spatial-spectral information. Our experimental results demonstrate that the proposed method outperforms existing advanced approaches in terms of classification efficiency and accuracy across three benchmark data sets.

Autonomous Detection of Humans in Off-Limits Mountain Areas.

This paper is on the autonomous detection of humans in off-limits mountains. In off-limits mountains, a human rarely exists, thus human detection is an extremely rare event. Due to the advances in artificial intelligence, object detection-classification algorithms based on a Convolution Neural Network (CNN) can be used for this application. However, considering off-limits mountains, there should be no person in general. Thus, it is not desirable to run object detection-classification algorithms continuously, since they are computationally heavy. This paper addresses a time-efficient human detector system, based on both motion detection and object classification. The proposed scheme is to run a motion detection algorithm from time to time. In the camera image, we define a feasible human space where a human can appear. Once motion is detected inside the feasible human space, one enables the object classification, only inside the bounding box where motion is detected. Since motion detection inside the feasible human space runs much faster than an object detection-classification method, the proposed approach is suitable for real-time human detection with low computational loads. As far as we know, no paper in the literature used the feasible human space, as in our paper. The outperformance of our human detector system is verified by comparing it with other state-of-the-art object detection-classification algorithms (HOG detector, YOLOv7 and YOLOv7-tiny) under experiments. This paper demonstrates that the accuracy of the proposed human detector system is comparable to other state-of-the-art algorithms, while outperforming in computational speed. Our experiments show that in environments with no humans, the proposed human detector runs 62 times faster than YOLOv7 method, while showing comparable accuracy.

[Mental fatigue state recognition method based on convolution neural network and long short-term memory].

The pace of modern life is accelerating, the pressure of life is gradually increasing, and the long-term accumulation of mental fatigue poses a threat to health. By analyzing physiological signals and parameters, this paper proposes a method that can identify the state of mental fatigue, which helps to maintain a healthy life. The method proposed in this paper is a new recognition method of psychological fatigue state of electrocardiogram signals based on convolutional neural network and long short-term memory. Firstly, the convolution layer of one-dimensional convolutional neural network model is used to extract local features, the key information is extracted through pooling layer, and some redundant data is removed. Then, the extracted features are used as input to the long short-term memory model to further fuse the ECG features. Finally, by integrating the key information through the full connection layer, the accurate recognition of mental fatigue state is successfully realized. The results show that compared with traditional machine learning algorithms, the proposed method significantly improves the accuracy of mental fatigue recognition to 96.3%, which provides a reliable basis for the early warning and evaluation of mental fatigue.

RFPR-IDP: reduce the false positive rates for intrinsically disordered protein and region prediction by incorporating both fully ordered proteins and disordered proteins.

As an important type of proteins, intrinsically disordered proteins/regions (IDPs/IDRs) are related to many crucial biological functions. Accurate prediction of IDPs/IDRs is beneficial to the prediction of protein structures and functions. Most of the existing methods ignore the fully ordered proteins without IDRs during training and test processes. As a result, the corresponding predictors prefer to predict the fully ordered proteins as disordered proteins. Unfortunately, these methods were only evaluated on datasets consisting of disordered proteins without or with only a few fully ordered proteins, and therefore, this problem escapes the attention of the researchers. However, most of the newly sequenced proteins are fully ordered proteins in nature. These predictors fail to accurately predict the ordered and disordered proteins in real-world applications. In this regard, we propose a new method called RFPR-IDP trained with both fully ordered proteins and disordered proteins, which is constructed based on the combination of convolution neural network (CNN) and bidirectional long short-term memory (BiLSTM). The experimental results show that although the existing predictors perform well for predicting the disordered proteins, they tend to predict the fully ordered proteins as disordered proteins. In contrast, the RFPR-IDP predictor can correctly predict the fully ordered proteins and outperform the other 10 state-of-the-art methods when evaluated on a test dataset with both fully ordered proteins and disordered proteins. The web server and datasets of RFPR-IDP are freely available at http://bliulab.net/RFPR-IDP/server.

Learned spatiotemporal correlation priors for CEST image denoising using incorporated global-spectral convolution neural network.

PURPOSE: To develop a deep learning-based method, dubbed Denoising CEST Network (DECENT), to fully exploit the spatiotemporal correlation prior to CEST image denoising. METHODS: DECENT is composed of two parallel pathways with different convolution kernel sizes aiming to extract the global and spectral features embedded in CEST images. Each pathway consists of a modified U-Net with residual Encoder-Decoder network and 3D convolution. Fusion pathway with 1 × 1 × 1 convolution kernel is utilized to concatenate two parallel pathways, and the output of DECENT is noise-reduced CEST images. The performance of DECENT was validated in numerical simulations, egg white phantom experiments, and ischemic mouse brain and human skeletal muscle experiments in comparison with existing state-of-the-art denoising methods. RESULTS: Rician noise was added to CEST images to mimic a low SNR situation for numerical simulation, egg white phantom experiment, and mouse brain experiments, while human skeletal muscle experiments were of inherently low SNR. From the denoising results evaluated by peak SNR (PSNR) and structural similarity index (SSIM), the proposed deep learning-based denoising method (DECENT) can achieve better performance compared to existing CEST denoising methods such as NLmCED, MLSVD, and BM4D, avoiding complicated parameter tuning or time-consuming iterative processes. CONCLUSIONS: DECENT can well exploit the prior spatiotemporal correlation knowledge of CEST images and restore the noise-free images from their noisy observations, outperforming state-of-the-art denoising methods.

Does Deep Learning Enhance the Estimation for Spatially Explicit Built Environment Stocks through Nighttime Light Data Set? Evidence from Japanese Metropolitans.

Built environment stocks have attracted much attention in recent decades because of their role in material and energy flows and environmental impacts. Spatially refined estimation of built environment stocks benefits city management, for example, in urban mining and resource circularity strategy making. Nighttime light (NTL) data sets are widely used and are regarded as high-resolution products in large-scale building stock research. However, some of their limitations, especially blooming/saturation effects, have hampered performance in estimating building stocks. In this study, we experimentally proposed and trained a convolution neural network (CNN)-based building stock estimation (CBuiSE) model and applied it to major Japanese metropolitan areas to estimate building stocks using NTL data. The results show that the CBuiSE model is capable of estimating building stocks at a relatively high resolution (approximately 830 m) and reflecting spatial distribution patterns, although the accuracy needs to be further improved to enhance the model performance. In addition, the CBuiSE model can effectively mitigate the overestimation of building stocks arising from the blooming effect of NTL. This study highlights the potential of NTL to provide a new research direction and serve as a cornerstone for future anthropogenic stock studies in the fields of sustainability and industrial ecology.

Prediction of the transcription factor binding sites with meta-learning.

With the accumulation of ChIP-seq data, convolution neural network (CNN)-based methods have been proposed for predicting transcription factor binding sites (TFBSs). However, biological experimental data are noisy, and are often treated as ground truth for both training and testing. Particularly, existing classification methods ignore the false positive and false negative which are caused by the error in the peak calling stage, and therefore, they can easily overfit to biased training data. It leads to inaccurate identification and inability to reveal the rules of governing protein-DNA binding. To address this issue, we proposed a meta learning-based CNN method (namely TFBS_MLCNN or MLCNN for short) for suppressing the influence of noisy labels data and accurately recognizing TFBSs from ChIP-seq data. Guided by a small amount of unbiased meta-data, MLCNN can adaptively learn an explicit weighting function from ChIP-seq data and update the parameter of classifier simultaneously. The weighting function overcomes the influence of biased training data on classifier by assigning a weight to each sample according to its training loss. The experimental results on 424 ChIP-seq datasets show that MLCNN not only outperforms other existing state-of-the-art CNN methods, but can also detect noisy samples which are given the small weights to suppress them. The suppression ability to the noisy samples can be revealed through the visualization of samples' weights. Several case studies demonstrate that MLCNN has superior performance to others.

GC6mA-Pred: A deep learning approach to identify DNA N6-methyladenine sites in the rice genome.

MOTIVATION: DNA N6-methyladenine (6mA) is a pivotal DNA modification for various biological processes. More accurate prediction of 6mA methylation sites plays an irreplaceable part in grasping the internal rationale of related biological activities. However, the existing prediction methods only extract information from a single dimension, which has some limitations. Therefore, it is very necessary to obtain the information of 6mA sites from different dimensions, so as to establish a reliable prediction method. RESULTS: In this study, a neural network based bioinformatics model named GC6mA-Pred is proposed to predict N6-methyladenine modifications in DNA sequences. GC6mA-Pred extracts significant information from both sequence level and graph level. In the sequence level, GC6mA-Pred uses a three-layer convolution neural network (CNN) model to represent the sequence. In the graph level, GC6mA-Pred employs graph neural network (GNN) method to integrate various information contained in the chemical molecular formula corresponding to DNA sequence. In our newly built dataset, GC6mA-Pred shows better performance than other existing models. The results of comparative experiments have illustrated that GC6mA-Pred is capable of producing a marked effect in accurately identifying DNA 6mA modifications.