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Interacting particle or agent systems that exhibit diverse swarming behaviors are prevalent in science and engineering. Developing effective differential equation models to understand the connection between individual interaction rules and swarming is a fundamental and challenging goal. In this paper, we study the data-driven discovery of a second-order particle swarming model that describes the evolution of $N$particles in ${\mathbb{R}}^d$under radial interactions. We propose a learning approach that models the latent radial interaction function as Gaussian processes, which can simultaneously fulfill two inference goals: one is the nonparametric inference of the interaction function with pointwise uncertainty quantification, and the other is the inference of unknown scalar parameters in the noncollective friction forces of the system. We formulate the learning problem as a statistical inverse learning problem and introduce an operator-theoretic framework that provides a detailed analysis of recoverability conditions, establishing that a coercivity condition is sufficient for recoverability. Given data collected from $M$i.i.d trajectories with independent Gaussian observational noise, we provide a finite-sample analysis, showing that our posterior mean estimator converges in a Reproducing Kernel Hilbert Space norm, at an optimal rate in $M$equal to the one in the classical 1-dimensional Kernel Ridge regression. As a byproduct, we show we can obtain a parametric learning rate in $M$for the posterior marginal variance using $L^{\mathrm{\infty <\#comment/>}}$norm and that the rate could also involve $N$and $L$(the number of observation time instances for each trajectory) depending on the condition number of the inverse problem. We provide numerical results on systems exhibiting different swarming behaviors, highlighting the effectiveness of our approach in the scarce, noisy trajectory data regime.