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Table 2 Comparison of PathME vs SNF and iCluster in terms of silhouette index. For PathME we report the silhouette index of the consensus clustering as well as the best individual one among 500 randomly initialized sNMF runs

From: PathME: pathway based multi-modal sparse autoencoders for clustering of patient-level multi-omics data

Cancer datasets

 

PathME

 

SNF

iCluster

Disease

Omics type

Cophenetic correlation

Consensus silhouette

Optimal silhouette

Silhouette

Silhouette

CRC

Number of clusters

 

(5)

 

(2)

(2)

Multi-omics

1

0.98

0.51

0.54

0.06

GBM

Number of clusters

 

(4)

 

(2)

(3)

Multi-omics

1

1

0.67

0.58

0.11

LSCC

Number of clusters

 

(4)

 

(4)

(2)

Multi-omics

1

1

0.82

0.71

0.35

BRCA

Number of clusters

 

(5)

 

(2)

(3)

Multi-omics

1

0.93

0.67

0.57

0.12

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