Affinity network fusion and semi-supervised learning for cancer patient clustering

Abstract

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% accuracy 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. .

Stratifying cellular metabolism during weight loss: an interplay of metabolism, metabolic flexibility and inflammation

“…For the clustering of the transcriptomics and proteomics expression data across time points, we utilise affinity network fusion (ANF) 27 . ANF itself is built on top of the similarity network fusion algorithm 28 .…”

Integrated Multi-Omics Analyses in Oncology: A Review of Machine Learning Methods and Tools

“…Affinity Network Fusion (AFN) ( 44 ) is both a clustering and classification technique that applies graph clustering to a patient affinity matrix incorporating information from multiple views. For each omic, after feature selection and/or transformation, AFN computes patient pair-wise distances.…”

Integrative Network Fusion: A Multi-Omics Approach in Molecular Profiling

“…Conversely, the INF method for omics data integration is an improvement of the popular Similarity Network Fusion (SNF) approach (5), which has inspired several studies in the scientific literature, specifically in cancer genomics (77,87,(102)(103)(104)(105)(106). SNF maximizes the shared or correlated information between multiple datasets by combining data through inference of a joint network-based model, accounting for how informative each data type is to the observed similarity between samples.…”