A central mechanism in machine learning is to identify, store, and recognize patterns. How to learn, access, and retrieve such patterns is crucial in Hopfield networks and the more recent transformer architectures. We show that the attention mechanism of transformer architectures is actually the update rule of modern Hopfield networks that can store exponentially many patterns. We exploit this high storage capacity of modern Hopfield networks to solve a challenging multiple instance learning (MIL) problem in computational biology: immune repertoire classification. In immune repertoire classification, a vast number of immune receptors are used to predict the immune status of an individual. This constitutes a MIL problem with an unprecedentedly massive number of instances, two orders of magnitude larger than currently considered problems, and with an extremely low witness rate. Accurate and interpretable machine learning methods solving this problem could pave the way towards new vaccines and therapies, which is currently a very relevant research topic intensified by the COVID-19 crisis.

Weaknesses: This manuscript contains a highly theoretical analysis of modern Hopfield networks and their relationship to the attention mechanism of a transformer model. It also contains a deep model that addresses the machine learning task of immune repertoire classification. The major issue with this submission is that the connection between the two topics addressed in this paper, (i) classification of immune repertoires, and (ii) equivalence of the update rule of modern Hopfield networks and the attention mechanism of the transformer, is at best unclear. It feels as though two distinct papers have been condensed into one. Overall, combining these two results into one paper results in a main text manuscript that does not provide sufficient detail about either.

The reviewers find the application compelling, to a timely topic, and with interesting theoretical connections that they now understand will primarily be presented elsewhere, and thus can now be cited in this NeurIPS paper, thereby enabling a cleaner exposition.

A central mechanism in machine learning is to identify, store, and recognize patterns. How to learn, access, and retrieve such patterns is crucial in Hopfield networks and the more recent transformer architectures. We show that the attention mechanism of transformer architectures is actually the update rule of modern Hopfield networks that can store exponentially many patterns. We exploit this high storage capacity of modern Hopfield networks to solve a challenging multiple instance learning (MIL) problem in computational biology: immune repertoire classification. In immune repertoire classification, a vast number of immune receptors are used to predict the immune status of an individual.