We propose a new approach for fine-grained uncertainty quantification (UQ) using a collision matrix. For a classification problem involving $K$ classes, the $K\times K$ collision matrix $S$ measures the inherent (aleatoric) difficulty in distinguishing between each pair of classes. In contrast to existing UQ methods, the collision matrix gives a much more detailed picture of the difficulty of classification. We discuss several possible downstream applications of the collision matrix, establish its fundamental mathematical properties, as well as show its relationship with existing UQ methods, including the Bayes error rate. We also address the new problem of estimating the collision matrix using one-hot labeled data. We propose a series of innovative techniques to estimate $S$. First, we learn a contrastive binary classifier which takes two inputs and determines if they belong to the same class. We then show that this contrastive classifier (which is PAC learnable) can be used to reliably estimate the Gramian matrix of $S$, defined as $G=S^TS$. Finally, we show that under very mild assumptions, $G$ can be used to uniquely recover $S$, a new result on stochastic matrices which could be of independent interest. Experimental results are also presented to validate our methods on several datasets.

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