The discovery of cancer subtyping can help explore cancer pathogenesis, determine clinical actionability in treatment, and improve patients' survival rates. However, due to the diversity and complexity of multi-omics data, it is still challenging to develop integrated clustering algorithms for tumor molecular subtyping. We propose Subtype-GAN, a deep adversarial learning approach based on the multiple-input multiple-output neural network to model the complex omics data accurately. With the latent variables extracted from the neural network, Subtype-GAN uses consensus clustering and the Gaussian Mixture model to identify tumor samples' molecular subtypes. Compared with other state-of-the-art subtyping approaches, Subtype-GAN achieved outstanding performance on the benchmark datasets consisting of ∼4000 TCGA tumors from 10 types of cancer. We found that on the comparison dataset, the clustering scheme of Subtype-GAN is not always similar to that of the deep learning method AE but is identical to that of NEMO, MCCA, VAE and other excellent approaches. Finally, we applied Subtype-GAN to the BRCA dataset and automatically obtained the number of subtypes and the subtype labels of 1031 BRCA tumors. Through the detailed analysis, we found that the identified subtypes are clinically meaningful and show distinct patterns in the feature space, demonstrating the practicality of Subtype-GAN. The source codes, the clustering results of Subtype-GAN across the benchmark datasets are available at https://github.com/haiyang1986/Subtype-GAN. Supplementary data are available at Bioinformatics online.

The classification on imbalanced data sets is a great challenge in machine learning. In this paper, a geometric structural ensemble (GSE) learning framework is proposed to address the issue. It is known that the traditional ensemble methods train and combine a series of basic classifiers according to various weights, which might lack the geometric meaning. Oppositely, the GSE partitions and eliminates redundant majority samples by generating hyper-sphere through the Euclidean metric and learns basic classifiers to enclose the minority samples, which achieves higher efficiency in the training process and seems easier to understand. In detail, the current weak classifier builds boundaries between the majority and the minority samples and removes the former. Then, the remaining samples are used to train the next. When the training process is done, all of the majority samples could be cleaned and the combination of all basic classifiers is obtained. To further improve the generalization, two relaxation techniques are proposed. Theoretically, the computational complexity of GSE could approach O(ndłog(nmin)łog(n maj)). The comprehensive experiments validate both the effectiveness and efficiency of GSE.

In this article, we propose a novel entropy and confidence-based undersampling boosting (ECUBoost) framework to solve imbalanced problems. The boosting-based ensemble is combined with a new undersampling method to improve the generalization performance. To avoid losing informative samples during the data preprocessing of the boosting-based ensemble, both confidence and entropy are used in ECUBoost as benchmarks to ensure the validity and structural distribution of the majority samples during the undersampling. Furthermore, different from other iterative dynamic resampling methods, ECUBoost based on confidence can be applied to algorithms without iterations such as decision trees. Meanwhile, random forests are used as base classifiers in ECUBoost. Furthermore, experimental results on both artificial data sets and KEEL data sets prove the effectiveness of the proposed method.

Numerous studies have shown that in-depth mining of correlations between multi-modal features can help improve the accuracy of cross-modal data analysis tasks. However, the current image description methods based on the encoder-decoder framework only carry out the interaction and fusion of multi-modal features in the encoding stage or the decoding stage, which cannot effectively alleviate the semantic gap. In this paper, we propose a Deep Fusion Transformer (DFT) for image captioning to provide a deep multi-feature and multi-modal information fusion strategy throughout the encoding to decoding process. We propose a novel global cross encoder to align different types of visual features, which can effectively compensate for the differences between features and incorporate each other’s strengths. In the decoder, a novel cross on cross attention is proposed to realize hierarchical cross-modal data analysis, extending complex cross-modal reasoning capabilities through the multi-level interaction of visual and semantic features. Extensive experiments conducted on the MSCOCO dataset prove that our proposed DFT can achieve excellent performance and outperform state-of-the-art methods. The code is available at https://github.com/weimingboya/DFT.