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A Graph Neural Network Approach for Predicting the Lung Carcinogenicity of Single Molecular Compounds
http://doi.org/10.5626/JOK.2025.52.6.482
Cancer is one of the major diseases causing millions of deaths worldwide every year, and lung cancer has been recorded as the leading cause of cancer-related deaths in Korea in 2022. Therefore, research on lung cancer-causing compounds is essential, and this study proposes and evaluates a novel approach to predict lung cancer-causing potential using graph neural networks to overcome the limitations of existing machine learning and deep learning methods. Based on SMILES(Simplified Molecular Input Line Entry System) information from the compound carcinogenicity databases CPDB, CCRIS, IRIS and T3DB, the structure and chemical properties of molecules were converted into graph data for training, and the proposed model showed superior prediction performance compared to other models. This demonstrates the potential of graph neural networks as an effective tool for lung cancer prediction and suggests that they can make important contributions to future cancer research and treatment development.
Prediction of Cancer Prognosis Using Patient-Specific Cancer Driver Gene Information
http://doi.org/10.5626/JOK.2024.51.6.574
Accurate prediction of cancer prognosis is crucial for effective treatment. Consequently, numerous studies on cancer prognosis have been conducted, with recent research leveraging various machine learning techniques such as deep learning. In this paper, we first constructed patient-specific gene networks for each patient, then selected patient-specific cancer driver genes, considering the heterogeneity of cancer. We propose a deep neural architecture that can predict the prognosis more accurately using patient-specific cancer driver gene information. When our method was applied to gene expression data for 11 types of cancer, it demonstrated a significantly higher prediction accuracy compared to the existing methods.
Improvement of Prostate Cancer Aggressiveness Prediction Based on the Deep Learning Model Using Size Normalization and Multiple Loss Functions on Multi-parametric MR Images
Yoon Jo Kim, Julip Jung, Sung Il Hwang, Helen Hong
http://doi.org/10.5626/JOK.2023.50.10.866
Prostate cancer is the second most common cancer in men worldwide, and it is essential to predict the aggressiveness of prostate cancer because the recurrence rate and the effectiveness of treatment vary depending on the aggressiveness. This study enhances the information on small tumors by applying size normalization to predict the aggressiveness of prostate cancer in multi-parametric MR imaging. Additionally, we propose the use of multiple loss functions to distinguish tumors with different aggressiveness while having a similar visual appearance. Experimental results show that the proposed model trained with size-normalized ADC maps achieves an accuracy of 76.28%, sensitivity of 76.81%, specificity of 75.86%, and an AUC of 0.77. Moreover, compared to the tumor-centered ADC maps, size-normalized ADC maps demonstrate improved performance in tumors smaller than 1.5 cm, with an accuracy of 76.47%, sensitivity of 90.91%, and specificity of 69.57%, corresponding to a significant improvement of 17.65%, 27.27%, and 13.05% respectively.
Automatic Segmentation of Lung Cancer in Chest CT Images through Capsule Network-based Dual-Window Ensemble Learning
Jumin Lee, Julip Jung, Helen Hong, Bong-Seog Kim
http://doi.org/10.5626/JOK.2021.48.8.905
It is difficult to accurately segment lung cancer in chest CT images when it has an irregular shape or nearby structures have a similar intensity as lung cancer. In this study, we proposed a dual window ensemble network that uses a capsule network to learn the relationship between lung cancer and nearby structures and additionally considers the mediastinal window image with the lung window image to distinguish lung cancer from the nearby structures. First, intensity and spacing normalization was performed on the input images of the lung window setting and mediastinal window setting. Second, two types of 2D capsule network were performed with the lung and mediastinal setting images. Third, the final segmentation mask was generated by ensemble the probability maps of the lung and mediastinal window images through average voting by reflecting the weight based on the characteristics of each image. The proposed method showed a Dice similarity coefficient(DSC) of 75.98% which was 0.53% higher than the method not considering the weight of each window setting. Furthermore, segmentation accuracy was improved even when lung cancer was surrounded by nearby structures.
A Method for Cancer Prognosis Prediction Using Gene Embedding
http://doi.org/10.5626/JOK.2021.48.7.842
Identifying prognostic genes and using them to predict the prognosis of cancer patients can help provide them with more effective treatments. Many methods have been proposed to identify prognostic genes and predict cancer prognosis, and recent studies have focused on machine learning methods including deep learning. However, applying gene expression data to machine learning methods has the limitations of a small number of samples and a large number of genes. In this study, we additionally use a gene network to generate many random gene paths, which we used for training the model, thereby compensating for the small sample problem. We identified the prognostic genes and predicted the prognosis of patients using the gene expression data and gene networks for five cancer types and confirmed that the proposed method showed better predictive accuracy compared to other existing methods, and good performance on small sample data.
AttDRP: Attention Mechanism-based Model for Anti-Cancer Drug Response Prediction
Jonghwan Choi, Sangmin Seo, Sanghyun Park
http://doi.org/10.5626/JOK.2021.48.6.713
Resistance to anti-cancer drugs makes chemotherapy ineffective for cancer patients. Drug resistance is caused by genetic alterations in cancer cells. Many studies have investigated drug responses of diverse cancer cell lines to various anti-cancer drugs to understand drug response mechanisms. Existing studies have proposed machine learning models for drug response prediction to find effective anti-cancer drugs. However, currently there are no models to learn the relationship between anticancer drugs and genes to improve the prediction accuracy. In this paper, we proposed a predictive model AttDRP that could identify important genes associated with anti-cancer drugs and predict drug responses based on identified genes. AttDRP exhibited better predictive accuracy than existing models and we found that the attention scores of AttDRP could be effective tools to analyze molecular structures of anticancer drugs. We hope that our proposed method would contribute to the development of precision medicine for effective chemotherapy. Resistance to anti-cancer drugs makes chemotherapy ineffective for cancer patients. Drug resistance is caused by genetic alterations in cancer cells. Many studies have investigated drug responses of diverse cancer cell lines to various anti-cancer drugs to understand drug response mechanisms. Existing studies have proposed machine learning models for drug response prediction to find effective anti-cancer drugs. However, currently there are no models to learn the relationship between anticancer drugs and genes to improve the prediction accuracy. In this paper, we proposed a predictive model AttDRP that could identify important genes associated with anti-cancer drugs and predict drug responses based on identified genes. AttDRP exhibited better predictive accuracy than existing models and we found that the attention scores of AttDRP could be effective tools to analyze molecular structures of anticancer drugs.
Breast Cancer Subtype Classification Using Multi-omics Data Integration Based on Neural Network
Joungmin Choi, Jiyoung Lee, Jieun Kim, Jihyun Kim, Heejoon Chae
http://doi.org/10.5626/JOK.2020.47.9.835
Breast cancer is one of the highly heterogeneous diseases comprising multiple biological factors, causing multiple subtypes. Early diagnosis and accurate subtype prediction of breast cancer play a critical role in the prognosis of cancer and are crucial to providing appropriate treatment for each patient with different subtypes. To identify significant patterns from enormous volumes of genetic and epigenetic data, machine learning-based methods have been adopted to the breast cancer subtype classification. Recently, multi-omics data integration has attracted much attention as a promising approach in recognizing complex molecular mechanisms and providing a comprehensive view of patients. However, because of the characteristics of high dimensionality, multi-omics based approaches are limited in prediction accuracy. In this paper, we propose a neural network-based breast cancer subtype classification model using multi-omics data integration. The gene expression, DNA methylation, and miRNA omics dataset were integrated after preprocessing and the classification model was trained based on the neural network using the dataset. Our performance evaluation results showed that the proposed model outperforms all other methods, providing the highest classification accuracy of 90.45%. We expect this model to be useful in predicting the subtypes of breast cancer and improving patients’ prognosis.
Identification of Heterogeneous Prognostic Genes and Prediction of Cancer Outcome using PageRank
http://doi.org/10.5626/JOK.2018.45.1.61
The identification of genes that contribute to the prediction of prognosis in patients with cancer is one of the challenges in providing appropriate therapies. To find the prognostic genes, several classification models using gene expression data have been proposed. However, the prediction accuracy of cancer prognosis is limited due to the heterogeneity of cancer. In this paper, we integrate microarray data with biological network data using a modified PageRank algorithm to identify prognostic genes. We also predict the prognosis of patients with 6 cancer types (including breast carcinoma) using the K-Nearest Neighbor algorithm. Before we apply the modified PageRank, we separate samples by K-Means clustering to address the heterogeneity of cancer. The proposed algorithm showed better performance than traditional algorithms for prognosis. We were also able to identify cluster-specific biological processes using GO enrichment analysis.
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