We study the task of agnostic tomography: given copies of an unknown $n$-qubit state $\rho$ which has fidelity $\tau$ with some state in a given class $C$, find a state which has fidelity $\ge \tau - \epsilon$ with $\rho$. We give a new framework, stabilizer bootstrapping, for designing computationally efficient protocols for this task, and use this to get new agnostic tomography protocols for the following classes: Stabilizer states: We give a protocol that runs in time $\mathrm{poly}(n,1/\epsilon)\cdot (1/\tau)^{O(\log(1/\tau))}$, answering an open question posed by Grewal, Iyer, Kretschmer, Liang [43] and Anshu and Arunachalam [6]. Previous protocols ran in time $\mathrm{exp}(\Theta(n))$ or required $\tau>\cos^2(\pi/8)$. States with stabilizer dimension $n - t$: We give a protocol that runs in time $n^3\cdot(2^t/\tau)^{O(\log(1/\epsilon))}$, extending recent work on learning quantum states prepared by circuits with few non-Clifford gates, which only applied in the realizable setting where $\tau = 1$ [33, 40, 49, 66]. Discrete product states: If $C = K^{\otimes n}$ for some $\mu$-separated discrete set $K$ of single-qubit states, we give a protocol that runs in time $(n/\mu)^{O((1 + \log (1/\tau))/\mu)}/\epsilon^2$. This strictly generalizes a prior guarantee which applied to stabilizer product states [42]. For stabilizer product states, we give a further improved protocol that runs in time $(n^2/\epsilon^2)\cdot (1/\tau)^{O(\log(1/\tau))}$. As a corollary, we give the first protocol for estimating stabilizer fidelity, a standard measure of magic for quantum states, to error $\epsilon$ in $n^3 \mathrm{quasipoly}(1/\epsilon)$ time.

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