University of Amsterdam

Flow-matching framework that translates omics signatures across biological domains, such as mouse to human transcriptomics, without paired samples.

mRNA language model with a hyperbolic prediction head encoding the codon-amino-acid hierarchy, beating Euclidean baselines on 9 of 10 property tasks.

MSA design model generating alignments from protein language model embeddings to improve folding accuracy on orphan and low-homology proteins.

Peptide-MHC structure prediction by SE(3)-equivariant diffusion, sampling 10 Cα conformations in under 6 seconds at 0.45 Å best-of-10 RMSD.

Computational tumour-infiltrating lymphocyte scoring for breast cancer, regressing the stromal TIL percentage from H&E slide features in one step.

Peptide-MHC binding affinity and all-atom 3D structure in one attention network pass, reaching 1.19 Å median C-RMSD at 0.009 s per affinity call.