We introduce Probabilistic Ball Mapper, a formulation of Ball Mapper in which each data point is assigned a probability distribution supported only on the metric balls that contain it. This assignment defines both a partition subordinate to the Ball Mapper cover and a Markov kernel from the finite data space to the cover. We study two assignment schemes: a uniform-on-support rule and a localized radial-basis rule that incorporates distance to landmarks while preserving the underlying cover. Pushing the empirical data distribution through the kernel produces a probability distribution over vertices. Drawing twice, conditionally and independently, from each pointwise distribution produces a soft-overlap matrix. This matrix is symmetric, nonnegative, positive semidefinite, and has the vertex distribution as both marginals. It therefore provides a mass-normalized refinement of classical Ball Mapper overlap rather than another unnormalized edge count. For graphs constructed on a common cover, the vertex and overlap distributions can be compared directly. For independently fitted covers, we formulate Wasserstein and fused Gromov--Wasserstein-type discrepancies that account for vertex mass, landmark geometry when a common ambient metric is available, and intrinsic graph relations. For a fixed cover, we derive explicit perturbation bounds controlled by the sensitivity of the assignment rule, the magnitude of the data perturbation, and the data mass near cover boundaries. When the cover is recomputed, landmark motion creates an additional source of variation, for which we state a transport-based stability principle rather than an unconditional theorem. The resulting framework turns Ball Mapper into a probability-valued representation suitable for quantitative comparison while retaining its geometric interpretability and computational simplicity.

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