Thus far, we viewed the cage molecules as rigid. But, often cages are flexible to some degree, and the shape of their cavity fluctuates, 9 which influences adsorption. To explore the effects of flexibility/ structural fluctuations of cages on their latent representations, we performed molecular dynamics (MD) simulations in the NVT ensemble (T = 298 K) on four empty, isolated cages (CC2, CC3, CC4 and CC5) using a polymer specific consistent force field (PCFF) as implemented by DL_FIELD v4.3 68 and a cage specific force field (CSFF). See Sec. S10 for details. We gathered snapshots of each cage while they were fluctuating in the MD simulation, computed their 3D porosity images, then projected them onto a ν = 2-dimensional latent space. Fig. .2 shows that flexible cages, on the basis of the MD snapshots, each occupy a region in latent space. The size of the region is determined by the degree of flexibility of the cage; for example, the larger cage CC5 explores a larger region of latent space than CC3. Moreover, the latent regions may overlap (as the case with CC3 and CC4), indicating that, a fraction of the time, the cages exhibit a very similar cavity shape. Analyzing the region in latent space explored by flexible cages could provide more information about fluctuations of cavity shape than simple descriptors such as pore diameter since our latent representation can capture more complex features. Still, considering a rigid cage-the average configuration of a cage-is valuable while requiring significantly less computational expense.