We present a physics-informed machine learning framework based on Neural Ordinary Differential Equations that solves the holographic inverse problem: reconstructing the bulk spacetime and gauge field of a charged AdS black hole directly from boundary fermionic spectral functions. Encoding the UV asymptotics, horizon regularity, and zero temperature extremality as hard constraints in the neural network architecture, our framework reliably reconstructs the extremal Reissner-Nordström AdS geometry across three quantum critical regimes set by the
U(1) probe charge---non-Fermi liquid, marginal Fermi liquid (strange metal), and Fermi-liquid-like states---and can jointly infer the probe charge itself to sub-percent accuracy. Relaxing the near-AdS boundary constraint uncovers a geometrical degeneracy: bulk profiles that differ throughout the radial direction but share the same near-horizon
AdS2×R2 data reproduce identical spectral functions near the Fermi surface. This isospectral non-uniqueness is precisely the bulk degeneracy expected on general holographic grounds at zero temperature, and its spontaneous emergence across independent training runs shows that the network isolates the IR CFT universality rather than overfitting a single UV completion.