Fold-CP: A Context Parallelism Framework for Biomolecular Modeling

Understanding cellular machinery requires atomic-scale reconstruction of large biomolecular assemblies. However, predicting the structures of these systems has been constrained by hardware memory requirements of models like AlphaFold 3, imposing a practical ceiling of a few thousand residues that can be processed on a single GPU. Here we present NVIDIA BioNeMo Fold-CP, a context parallelism framework that overcomes this barrier by distributing the inference and training pipelines of co-folding models across multiple GPUs. We use the Boltz models as open source reference architectures and implement custom multidimensional primitives that efficiently parallelize both the dense triangular updates and the irregular, data-dependent pattern of window-batched local attention. Our approach achieves efficient memory scaling; for an N-token input distributed across P GPUs, per-device memory scales as $O(N^2/P)$, enabling the structure prediction of assemblies exceeding 30,000 residues on 64 NVIDIA B300 GPUs. We demonstrate the scientific utility of this approach through successful developer use cases: Fold-CP enabled the scoring of over 90% of Comprehensive Resource of Mammalian protein complexes (CORUM) database, as well as folding of disease-relevant PI4KA lipid kinase complex bound to an intrinsically disordered region without cropping. By providing a scalable pathway for modeling massive systems with full global context, Fold-CP represents a significant step toward the realization of a virtual cell.

AdamD: Improved bias-correction in Adam

Here I present a small update to the bias-correction term in the Adam optimizer that has the advantage of making smaller gradient updates in the first several steps of training. With the default bias-correction, Adam may actually make larger than requested gradient updates early in training. By only including the well-justified bias-correction of the second moment gradient estimate, $v_t$, and excluding the bias-correction on the first-order estimate, $m_t$, we attain these more desirable gradient update properties in the first series of steps. The default implementation of Adam may be as sensitive as it is to the hyperparameters $\beta_1, \beta_2$ partially due to the originally proposed bias correction procedure, and its behavior in early steps.