Stacked Autoencoder for classification of glioma grade III and grade IV

Uncovering the prognostic gene signatures for the improvement of risk stratification in cancers by using deep learning algorithm coupled with wavelet transform

Background

The aim of gene expression-based clinical modelling in tumorigenesis is not only to accurately predict the clinical endpoints, but also to reveal the genome characteristics for downstream analysis for the purpose of understanding the mechanisms of cancers. Most of the conventional machine learning methods involved a gene filtering step, in which tens of thousands of genes were firstly filtered based on the gene expression levels by a statistical method with an arbitrary cutoff. Although gene filtering procedure helps to reduce the feature dimension and avoid overfitting, there is a risk that some pathogenic genes important to the disease will be ignored.

Results

In this study, we proposed a novel deep learning approach by combining a convolutional neural network with stationary wavelet transform (SWT-CNN) for stratifying cancer patients and predicting their clinical outcomes without gene filtering based on tumor genomic profiles. The proposed SWT-CNN overperformed the state-of-art algorithms, including support vector machine (SVM) and logistic regression (LR), and produced comparable prediction performance to random forest (RF). Furthermore, for all the cancer types, we firstly proposed a method to weight the genes with the scores, which took advantage of the representative features in the hidden layer of convolutional neural network, and then selected the prognostic genes for the Cox proportional-hazards regression. The results showed that risk stratifications can be effectively improved by using the identified prognostic genes as feature, indicating that the representative features generated by SWT-CNN can well correlate the genes with prognostic risk in cancers and be helpful for selecting the prognostic gene signatures.

Conclusions

Our results indicated that gene expression-based SWT-CNN model can be an excellent tool for stratifying the prognostic risk for cancer patients. In addition, the representative features of SWT-CNN were validated to be useful for evaluating the importance of the genes in the risk stratification and can be further used to identify the prognostic gene signatures.

FDSR: A new fuzzy discriminative sparse representation method for medical image classification

Recent developments in medical image analysis techniques make them essential tools in medical diagnosis. Medical imaging is always involved with different kinds of uncertainties. Managing these uncertainties has motivated extensive research on medical image classification methods, particularly for the past decade. Despite being a powerful classification tool, the sparse representation suffers from the lack of sufficient discrimination and robustness, which are required to manage the uncertainty and noisiness in medical image classification issues. It is tried to overcome this deficiency by introducing a new fuzzy discriminative robust sparse representation classifier, which benefits from the fuzzy terms in its optimization function of the dictionary learning process. In this work, we present a new medical image classification approach, fuzzy discriminative sparse representation (FDSR). The proposed fuzzy terms increase the inter-class representation difference and the intra-class representation similarity. Also, an adaptive fuzzy dictionary learning approach is used to learn dictionary atoms. FDSR is applied on Magnetic Resonance Images (MRI) from three medical image databases. The comprehensive experimental results clearly show that our approach outperforms its series of rival techniques in terms of accuracy, sensitivity, specificity, and convergence speed.

DeePathology: Deep Multi-Task Learning for Inferring Molecular Pathology from Cancer Transcriptome

Despite great advances, molecular cancer pathology is often limited to the use of a small number of biomarkers rather than the whole transcriptome, partly due to computational challenges. Here, we introduce a novel architecture of Deep Neural Networks (DNNs) that is capable of simultaneous inference of various properties of biological samples, through multi-task and transfer learning. It encodes the whole transcription profile into a strikingly low-dimensional latent vector of size 8, and then recovers mRNA and miRNA expression profiles, tissue and disease type from this vector. This latent space is significantly better than the original gene expression profiles for discriminating samples based on their tissue and disease. We employed this architecture on mRNA transcription profiles of 10750 clinical samples from 34 classes (one healthy and 33 different types of cancer) from 27 tissues. Our method significantly outperforms prior works and classical machine learning approaches in predicting tissue-of-origin, normal or disease state and cancer type of each sample. For tissues with more than one type of cancer, it reaches 99.4% accuracy in identifying the correct cancer subtype. We also show this system is very robust against noise and missing values. Collectively, our results highlight applications of artificial intelligence in molecular cancer pathology and oncological research. DeePathology is freely available at https://github.com/SharifBioinf/DeePathology.