Wilson G. Gregory

Nabeel Sarwar, Wilson Gregory, George A Kevrekidis et al.

Single-cell RNA-seq data allow the quantification of cell type differences across a growing set of biological contexts. However, pinpointing a small subset of genomic features explaining this variability can be ill-defined and computationally intractable. Here we introduce MarkerMap, a generative model for selecting minimal gene sets which are maximally informative of cell type origin and enable whole transcriptome reconstruction. MarkerMap provides a scalable framework for both supervised marker selection, aimed at identifying specific cell type populations, and unsupervised marker selection, aimed at gene expression imputation and reconstruction. We benchmark MarkerMap's competitive performance against previously published approaches on real single cell gene expression data sets. MarkerMap is available as a pip installable package, as a community resource aimed at developing explainable machine learning techniques for enhancing interpretability in single-cell studies.

Wilson G. Gregory, Josué Tonelli-Cueto, Nicholas F. Marshall et al.

Tensors are a fundamental data structure for many scientific contexts, such as time series analysis, materials science, and physics, among many others. Improving our ability to produce and handle tensors is essential to efficiently address problems in these domains. In this paper, we show how to exploit the underlying symmetries of functions that map tensors to tensors. More concretely, we develop universally expressive equivariant machine learning architectures on tensors that exploit that, in many cases, these tensor functions are equivariant with respect to the diagonal action of the orthogonal, Lorentz, and/or symplectic groups. We showcase our results on three problems coming from material science, theoretical computer science, and time series analysis. For time series, we combine our method with the increasingly popular path signatures approach, which is also invariant with respect to reparameterizations. Our numerical experiments show that our equivariant models perform better than corresponding non-equivariant baselines.

Wilson G. Gregory, David W. Hogg, Ben Blum-Smith et al.

Machine learning methods are increasingly being employed as surrogate models in place of computationally expensive and slow numerical integrators for a bevy of applications in the natural sciences. However, while the laws of physics are relationships between scalars, vectors, and tensors that hold regardless of the frame of reference or chosen coordinate system, surrogate machine learning models are not coordinate-free by default. We enforce coordinate freedom by using geometric convolutions in three model architectures: a ResNet, a Dilated ResNet, and a UNet. In numerical experiments emulating 2D compressible Navier-Stokes, we see better accuracy and improved stability compared to baseline surrogate models in almost all cases. The ease of enforcing coordinate freedom without making major changes to the model architecture provides an exciting recipe for any CNN-based method applied to an appropriate class of problems