Leveraging Deep Learning Techniques and Integrated Omics Data for Tailored Treatment of Breast Cancer

An Innovative Multi-Omics Model Integrating Latent Alignment and Attention Mechanism for Drug Response Prediction

By using omics, we can now examine all components of biological systems simultaneously. Deep learning-based drug prediction methods have shown promise by integrating cancer-related multi-omics data. However, the complex interaction between genes poses challenges in accurately projecting multi-omics data. In this research, we present a predictive model for drug response that incorporates diverse types of omics data, comprising genetic mutation, copy number variation, methylation, and gene expression data. This study proposes latent alignment for information mismatch in integration, which is achieved through an attention module capturing interactions among diverse types of omics data. The latent alignment and attention modules significantly improve predictions, outperforming the baseline model, with MSE = 1.1333, F1-score = 0.5342, and AUROC = 0.5776. High accuracy was achieved in predicting drug responses for piplartine and tenovin-6, while the accuracy was comparatively lower for mitomycin-C and obatoclax. The latent alignment module exclusively outperforms the baseline model, enhancing the MSE by 0.2375, the F1-score by 4.84%, and the AUROC by 6.1%. Similarly, the attention module only improves these metrics by 0.1899, 2.88%, and 2.84%, respectively. In the interpretability case study, panobinostat exhibited the most effective predicted response, with a value of -4.895. We provide reliable insights for drug selection in personalized medicine by identifying crucial genetic factors influencing drug response.

A survey on multi-omics-based cancer diagnosis using machine learning with the potential application in gastrointestinal cancer

Gastrointestinal cancer is becoming increasingly common, which leads to over 3 million deaths every year. No typical symptoms appear in the early stage of gastrointestinal cancer, posing a significant challenge in the diagnosis and treatment of patients with gastrointestinal cancer. Many patients are in the middle and late stages of gastrointestinal cancer when they feel uncomfortable, unfortunately, most of them will die of gastrointestinal cancer. Recently, various artificial intelligence techniques like machine learning based on multi-omics have been presented for cancer diagnosis and treatment in the era of precision medicine. This paper provides a survey on multi-omics-based cancer diagnosis using machine learning with potential application in gastrointestinal cancer. Particularly, we make a comprehensive summary and analysis from the perspective of multi-omics datasets, task types, and multi-omics-based integration methods. Furthermore, this paper points out the remaining challenges of multi-omics-based cancer diagnosis using machine learning and discusses future topics.

Artificial intelligence assists precision medicine in cancer treatment

Cancer is a major medical problem worldwide. Due to its high heterogeneity, the use of the same drugs or surgical methods in patients with the same tumor may have different curative effects, leading to the need for more accurate treatment methods for tumors and personalized treatments for patients. The precise treatment of tumors is essential, which renders obtaining an in-depth understanding of the changes that tumors undergo urgent, including changes in their genes, proteins and cancer cell phenotypes, in order to develop targeted treatment strategies for patients. Artificial intelligence (AI) based on big data can extract the hidden patterns, important information, and corresponding knowledge behind the enormous amount of data. For example, the ML and deep learning of subsets of AI can be used to mine the deep-level information in genomics, transcriptomics, proteomics, radiomics, digital pathological images, and other data, which can make clinicians synthetically and comprehensively understand tumors. In addition, AI can find new biomarkers from data to assist tumor screening, detection, diagnosis, treatment and prognosis prediction, so as to providing the best treatment for individual patients and improving their clinical outcomes.

Multiclass Cancer Prediction Based on Copy Number Variation Using Deep Learning

DNA copy number variation (CNV) is the type of DNA variation which is associated with various human diseases. CNV ranges in size from 1 kilobase to several megabases on a chromosome. Most of the computational research for cancer classification is traditional machine learning based, which relies on handcrafted extraction and selection of features. To the best of our knowledge, the deep learning-based research also uses the step of feature extraction and selection. To understand the difference between multiple human cancers, we developed three end-to-end deep learning models, i.e., DNN (fully connected), CNN (convolution neural network), and RNN (recurrent neural network), to classify six cancer types using the CNV data of 24,174 genes. The strength of an end-to-end deep learning model lies in representation learning (automatic feature extraction). The purpose of proposing more than one model is to find which architecture among them performs better for CNV data. Our best model achieved 92% accuracy with an ROC of 0.99, and we compared the performances of our proposed models with state-of-the-art techniques. Our models have outperformed the state-of-the-art techniques in terms of accuracy, precision, and ROC. In the future, we aim to work on other types of cancers as well.

Three-Dimensional Postoperative Results Prediction for Orthognathic Surgery through Deep Learning-Based Alignment Network

To date, for the diagnosis of dentofacial dysmorphosis, we have relied almost entirely on reference points, planes, and angles. This is time consuming, and it is also greatly influenced by the skill level of the practitioner. To solve this problem, we wanted to know if deep neural networks could predict postoperative results of orthognathic surgery without relying on reference points, planes, and angles. We use three-dimensional point cloud data of the skull of 269 patients. The proposed method has two main stages for prediction. In step 1, the skull is divided into six parts through the segmentation network. In step 2, three-dimensional transformation parameters are predicted through the alignment network. The ground truth values of transformation parameters are calculated through the iterative closest points (ICP), which align the preoperative part of skull to the corresponding postoperative part of skull. We compare pointnet, pointnet++ and pointconv for the feature extractor of the alignment network. Moreover, we design a new loss function, which considers the distance error of transformed points for a better accuracy. The accuracy, mean intersection over union (mIoU), and dice coefficient (DC) of the first segmentation network, which divides the upper and lower part of skull, are 0.9998, 0.9994, and 0.9998, respectively. For the second segmentation network, which divides the lower part of skull into 5 parts, they were 0.9949, 0.9900, 0.9949, respectively. The mean absolute error of transverse, anterior-posterior, and vertical distance of part 2 (maxilla) are 0.765 mm, 1.455 mm, and 1.392 mm, respectively. For part 3 (mandible), they were 1.069 mm, 1.831 mm, and 1.375 mm, respectively, and for part 4 (chin), they were 1.913 mm, 2.340 mm, and 1.257 mm, respectively. From this study, postoperative results can now be easily predicted by simply entering the point cloud data of computed tomography.