We formulate an algorithm to lower bound the fidelity between quantum many-body states only from partial information, such as the one accessible by few-body observables. Our method is especially tailored to permutationally invariant states, but it gives nontrivial results in all situations where this symmetry is even partial. This property makes it particularly useful for experiments with atomic ensembles, where relevant many-body states can be certified from collective measurements. As an example, we show that a $xi^2approx-6;text{dB}$ spin squeezed state of $N=100$ particles can be certified with a fidelity up to $F=0.999$, only from the measurement of its polarization and of its squeezed quadrature. Moreover, we show how to quantitatively account for both measurement noise and partial symmetry in the states, which makes our method useful in realistic experimental situations.
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