Low-fidelity data is typically inexpensive to generate but inaccurate, whereas high-fidelity data is accurate but expensive. To address this, multi-fidelity methods use a small set of high-fidelity data to enhance the accuracy of a large set of low-fidelity data. In the approach described in this paper, this is accomplished by constructing a graph Laplacian from the low-fidelity data and computing its low-lying spectrum. This is used to cluster the data and identify points closest to the cluster centroids, where high-fidelity data is acquired. Thereafter, a transformation that maps every low-fidelity data point to a multi-fidelity counterpart is determined by minimizing the discrepancy between the multi- and high-fidelity data while preserving the underlying structure of the low-fidelity data distribution. The method is tested with problems in solid and fluid mechanics. By utilizing only a small fraction of high-fidelity data, the accuracy of a large set of low-fidelity data is significantly improved.