Why Futhark?

A high-performance and high-level purely functional data-parallel array programming language that can execute on the GPU and CPU.

Better without U: Impact of Selective Hubbard U Correction on Foundational MLIPs

The training of foundational machine learning interatomic potentials (fMLIPs) relies on diverse databases with energies and forces calculated using ab initio methods. We show that fMLIPs trained on large datasets such as MPtrj, Alexandria, and OMat24 encode inconsistencies from the Materials Project's selective use of the Hubbard U correction, which is applied to certain transition metals only if O or F atoms are present in the simulation cell. This inconsistent use of +U creates two incompatible potential-energy surfaces (PES): a lower-energy GGA surface and a higher-energy GGA+U one. When trained on both, MLIPs interpolate between them, leading to systematic underbinding, or even spurious repulsion, between U-corrected metals and oxygen- or fluorine-containing species. Models such as MACE-OMAT and -MPA exhibit repulsion between U-corrected metals and their oxides, limiting their value for studying catalysis and oxidation. We link the severity of this pathology to the oxygen number density in U-corrected training configurations. This explains why OMAT-trained models are most affected and suggests the issue might worsen as expanding future datasets increasingly include configurations with low oxygen content, such as those generated through combinatorial exploration of multi-element or defect-containing systems. Our simple per-U-corrected-atom shift aligns PBE+U and PBE energies for identical structures, yielding a smoother PES compared to existing correction schemes, which target phase diagram accuracy. As a result, models trained on datasets with our shift applied exhibit smaller mean absolute errors for the adsorption energies of oxygen on U-corrected elemental slabs. Since datasets omitting +U entirely (e.g. MatPES, MP-ALOE) avoid these pathologies, we recommend excluding +U in future fMLIP datasets. For existing datasets, our post-hoc correction provides a low-cost improvement.

Introduction — Doing Things in Dyalog APL

Control systems for synthetic biology and a case-study in cell fate reprogramming

This paper gives an overview of the use of control systems engineering in synthetic biology, motivated by applications such as cell therapy and cell fate reprogramming for regenerative medicine. A ubiquitous problem in these and other applications is the ability to control the concentration of specific regulatory factors in the cell accurately despite environmental uncertainty and perturbations. The paper describes the origin of these perturbations and how they affect the dynamics of the biomolecular ``plant'' to be controlled. A variety of biomolecular control implementations are then introduced to achieve robustness of the plant's output to perturbations and are grouped into feedback and feedforward control architectures. Although sophisticated control laws can be implemented in a computer today, they cannot be necessarily implemented inside the cell via biomolecular processes. This fact constraints the set of feasible control laws to those realizable through biomolecular processes that can be engineered with synthetic biology. After reviewing biomolecular feedback and feedforward control implementations, mostly focusing on the author's own work, the paper illustrates the application of such control strategies to cell fate reprogramming. Within this context, a master regulatory factor needs to be controlled at a specific level inside the cell in order to reprogram skin cells to pluripotent stem cells. The article closes by highlighting on-going challenges and directions of future research for biomolecular control design.

WFR-MFM: One-Step Inference for Dynamic Unbalanced Optimal Transport

Reconstructing dynamical evolution from limited observations is a fundamental challenge in single-cell biology, where dynamic unbalanced optimal transport provides a principled framework for modeling coupled transport and mass variation. However, existing approaches rely on trajectory simulation at inference time, making inference a key bottleneck for scalable applications. In this work, we propose a mean-flow framework for unbalanced flow matching that summarizes both transport and mass-growth dynamics over arbitrary time intervals using mean velocity and mass-growth fields, enabling fast one-step generation without trajectory simulation. To solve dynamic unbalanced optimal transport under the Wasserstein-Fisher-Rao geometry, we further build on this framework to develop Wasserstein-Fisher-Rao Mean Flow Matching (WFR-MFM). Across synthetic and real single-cell RNA sequencing datasets, WFR-MFM achieves orders-of-magnitude faster inference than a range of existing baselines while maintaining high predictive accuracy, and enables efficient perturbation response prediction on large synthetic datasets with thousands of conditions.