Geneformer

Broad Institute

Structures found in this family (3)

Persistent-homology / Betti profile across depth, Platonic Representation Hypothesis, Linear Direction

Hypotheses argued for by this family (1)

Platonic Representation Hypothesis

By model (1)

Geneformer

Persistent-homology / Betti profile across depth, Platonic Representation Hypothesis, Linear Direction

Observations (2)

A 141-hypothesis automated topology/geometry audit of scGPT and Geneformer gene-embedding representations finds statistically significant persistent homology in nearly every transformer layer and a canonical-correlation cross-model alignment of 0.80 between the two independently-trained models

Late-layer SAE feature directions in Geneformer steer cell differentiation

Papers

What Topological and Geometric Structure Do Biological Foundation Models Learn? Evidence from 141 Hypotheses (2026), Exhaustive Circuit Mapping of a Single-Cell Foundation Model Reveals Massive Redundancy, Heavy-Tailed Hub Architecture, and Layer-Dependent Differentiation Control (2026)