Table 1.

Different approaches to the microbiome ML limitations discussed in the introduction.

Model	Completing missing data at higher level	Rare elements are taken into account	Smoothing over similar taxa CNN	Smoothing over similar taxa ordering
iMic	V	V	V	V
	Cladogram of averages	Log transform		Dendrogram ordering, such that similar sister taxa are closer in the image
gMic+v	X	V	V	X
		Log transform	GCN
gMic	X	X	V	X
	No use of values	No use of values	GCN
PopPhy-CNN	V	X	V	X
	Cladogram of sums	Relative abundances		No ordering
TopoPhy-CNN	V	X	V	X
	Cladogram of sums	Relative abundances Higher weight for hubs		No ordering
DeepEn-Phy	NN from each lower level to the higher level	X	V, GCN	X
CoDaCoRe	X	V	X	X
		Log transform
TaxoNN	X	X	V	X
			1-dimensional CNN
FCN	X	V	X	X
		If log transform is applied to the input
RF	X	V	X	X
		If log transform is applied to the input
LR	X	V	X	X
		If log transform is applied to the input
SVC	X	V	X	X
		If log transform is applied to the input