Using a quantum processor to embed and process classical data enables the generation of correlations between variables that are inefficient to represent through classical computation. A fundamental question is whether these correlations could be harnessed to enhance learning performances on real datasets. Here, we report the use of a neutral atom quantum processor comprising up to $32$ qubits to implement machine learning tasks on graph-structured data. To that end, we introduce a quantum feature map to encode the information about graphs in the parameters of a tunable Hamiltonian acting on an array of qubits. Using this tool, we first show that interactions in the quantum system can be used to distinguish non-isomorphic graphs that are locally equivalent. We then realize a toxicity screening experiment, consisting of a binary classification protocol on a biochemistry dataset comprising $286$ molecules of sizes ranging from $2$ to $32$ nodes, and obtain results which are comparable to those using the best classical kernels. Using techniques to compare the geometry of the feature spaces associated with kernel methods, we then show evidence that the quantum feature map perceives data in an original way, which is hard to replicate using classical kernels.
