Cliqueformer: Model-Based Optimization with Structured Transformers

Expressive large-scale neural networks enable training powerful models for prediction tasks. However, in many engineering and science domains, such models are intended to be used not just for prediction, but for design -- e.g., creating new proteins that serve as effective therapeutics, or creating new materials or chemicals that maximize a downstream performance measure. Thus, researchers have recently grown an interest in building deep learning methods that solve offline \emph{model-based optimization} (MBO) problems, in which design candidates are optimized with respect to surrogate models learned from offline data. However, straightforward application of predictive models that are effective at predicting in-distribution properties of a design are not necessarily the best suited for use in creating new designs. Thus, the most successful algorithms that tackle MBO draw inspiration from reinforcement learning and generative modeling to meet the in-distribution constraints. Meanwhile, recent theoretical works have observed that exploiting the structure of the target black-box function is an effective strategy for solving MBO from offline data. Unfortunately, discovering such structure remains an open problem. In this paper, following first principles, we develop a model that learns the structure of an MBO task and empirically leads to improved designs. To this end, we introduce \emph{Cliqueformer} -- a scalable transformer-based architecture that learns the black-box function's structure in the form of its \emph{functional graphical model} (FGM), thus bypassing the problem of distribution shift, previously tackled by conservative approaches. We evaluate Cliqueformer on various tasks, ranging from high-dimensional black-box functions from MBO literature to real-world tasks of chemical and genetic design, consistently demonstrating its state-of-the-art performance.