Defining subtypes of complex diseases such as cancer and stratifying patient groups with the same disease but different subtypes for targeted treatments is important for personalized and precision medicine. Approaches that incorporate multi-omic data are more advantageous to those using only one data type for patient clustering and disease subtype discovery. However, it is challenging to integrate multi-omic data as they are heterogeneous and noisy. In this paper, we present Affinity Network Fusion (ANF) to integrate multi-omic data for patient clustering. ANF first constructs patient affinity networks for each omic data type, and then calculates a fused network for spectral clustering. We applied ANF to a processed harmonized cancer dataset downloaded from GDC data portal consisting of 2193 patients, and generated promising results on clustering patients into correct disease types. Moreover, we developed a semi-supervised model combining ANF and neural network for few-shot learning. In several cases, the model can achieve greater than 90 acccuracy on test set with training less than 1 of the data. This demonstrates the power of ANF in learning a good representation of patients, and shows the great potential of semi-supervised learning in cancer patient clustering.
Based on the main idea of SNF @cite_8 , we developed a simpler and more general framework, Affinity Network Fusion (ANF), to combine multiple networks into a fused consensus network. The fused network captures complementary information from multiple views and is much more robust to noise than individual networks learned from each view.
@cite_8
1987219048 2885205930 2788475065 2963144883
Similarity network fusion (SNF) is an approach to integrate multiple data types on the basis of similarity between biological samples rather than individual measurements. The authors demonstrate SNF by constructing patient networks to identify disease subtypes with differential survival profiles. Abstract Similarity networks contain important topological features and patterns critical to understanding interactions among samples in a large dataset. To create a comprehensive view of the interactions within a dataset, the Similarity Network Fusion (SNF) technique has been proposed to fuse the similarity networks based on different data types into one similarity network that represents the full spectrum of underlying data. In this paper, a modified version of SNF, which is named as Contextual Information based SNF (CI-SNF), is proposed. In CI-SNF, first, modified Jaccard distance is performed on the SNF fused similarity to utilize the contextual information contained in the fused similarity network. Second, the local consistency of samples from the same category is enhanced by speculating that the samples which are located high in the Jaccard distance based ranking list of a specific query are from the same category as the query. Third, the inverted index technique is introduced to utilize the sparsity property of the locally consistent similarity network to enhance the computational efficiency. To verify the effectiveness and efficiency of CI-SNF model, it is applied in four different tasks, Cover Song Identification (CSI), image classification, cancer subtype identification, and drug taxonomy, respectively. Extensive experiments on thirteen challenging datasets demonstrate that CI-SNF scheme outperforms state-of-the-art similarity fusion algorithms including SNF in all four tasks. It is also verified that utilizing the contextual information contained in the SNF-based similarity network helps to enhance the performance of the SNF-based scheme, further. We propose a retrieval-augmented convolutional network and propose to train it with local mixup, a novel variant of the recently proposed mixup algorithm. The proposed hybrid architecture combining a convolutional network and an off-the-shelf retrieval engine was designed to mitigate the adverse effect of off-manifold adversarial examples, while the proposed local mixup addresses on-manifold ones by explicitly encouraging the classifier to locally behave linearly on the data manifold. Our evaluation of the proposed approach against five readily-available adversarial attacks on three datasets--CIFAR-10, SVHN and ImageNet--demonstrate the improved robustness compared to the vanilla convolutional network. Clustering cancer patients into subgroups and identifying cancer subtypes is an important task in cancer genomics. Clustering based on comprehensive multi-omic molecular profiling can often achieve better results than those using a single data type, since each omic data type may contain complementary information. However, it is challenging to integrate heterogeneous omic data directly. Based on one popular method – Similarity Network Fusion (SNF), we presented Affinity Network Fusion (ANF), an “upgrade” of SNF with several advantages. Similar to SNF, ANF treats each omic data type as one view of patients and learns a fused affinity matrix for clustering. We applied ANF to a harmonized TCGA dataset consisting of 2193 patients, and generated promising results on clustering patients into correct disease types. Our experimental results also demonstrated the power of feature selection and transformation combined with using ANF in patient clustering. Moreover, eigengap analysis suggests that the learned affinity matrices of four cancer types using our proposed framework may have successfully captured patient group structure and can be used for discovering unknown cancer subtypes.