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Yuming Zeng

Publications and source records attributed to Yuming Zeng.

3 recordsLinked to original sources

Rethinking Diffusion Segmentation: When Does It Rely on Its Noisy State, and Does Diffusion Matter?

Diffusion models are increasingly adapted from generation to conditional prediction, where a conditioning signal is combined with an evolving noisy representation of the target. In fully supervised segmentation, however, the conditioning image can already support direct target prediction, so endpoint performance alone establishes neither reliance on the added diffusion state nor a deterministic advantage over image-only prediction. For state reliance, we disrupt target-derived state content or correct image-state pairing during retraining of twelve published methods across three datasets, with ten matched seeds per setting. All 40 original-method comparisons whose evaluated-mask routes remained downstream of noised-quantity reconstruction exhibited state reliance, whereas all 30 comparisons with a segmentation-supervised bypass preserved reference performance. Rerouting five originally bypass-capable methods by forcing segmentation supervision through noise-to-mask reconstruction converted all 30 corresponding comparisons from preserved performance to state reliance. For deterministic utility, matched image-only counterparts achieved similar or better performance in 28 of 35 settings overall, including 16 of 20 whose native methods relied on both audited state properties. These results identify supervision path as a determinant of state reliance in the audited methods. Separately, matched image-only counterparts show that diffusion-specific computation often provides no deterministic endpoint advantage, including in methods that rely on the audited state properties. More generally, when conditioning already supports strong target prediction, diffusion-specific claims require additional evidence that the added state is used and that diffusion-specific computation improves the claimed capability beyond a matched condition-only counterpart.

cs.CV↗

GlycoMAC: A Multiscale Metabolic-Glycosylation Framework for Predicting Glycosylation Across Conditions in Mammalian Cell Cultures

Antibody productivity and glycosylation quality in CHO cell cultures emerge from a dynamically evolving metabolic environment, yet existing models often work in isolation or at a single scale. Here, we present a multiscale mechanistic framework linking molecular, cellular, and process scales to predict how inputs shape bioprocess trajectories. The framework combines a single-cell kinetic model of metabolism and glycosylation with a stochastic population model that captures environment-dependent transitions among growth, production, and decline states. To characterize metabolic adaptation, we introduce the cumulative variation in oxygen uptake rate, a trajectory-based biomarker that quantifies the total metabolic adjustment experienced during culture. Unlike population-averaged approaches, the model propagates cell-resolved metabolic states (including ammonia-regulated Golgi pH, nucleotide sugar availability, manganese cofactors, and synthesis rates) into glycan processing. The framework was evaluated using CHO-K1 fed-batch cultures producing VRC01 IgG1 under targeted ammonia stress, matched control conditions, and a pyramid-feeding strategy with tighter control. It accurately reproduced trajectories of cell growth, metabolites, productivity, and harvest glycosylation, including increased G0F abundance and reduced galactosylation under ammonia stress. By mechanistically linking process conditions to cell-state dynamics and glycosylation outcomes, the framework provides a unified foundation for digital bioprocessing, predictive biomanufacturing, and advanced process control.

q-bio.CB↗

Adaptive Fast-Slow Operator Splitting for Multiscale Biochemical Stochastic Dynamics

Stochastic reaction networks governed by Chemical Langevin Equations (CLE) exhibit pronounced multiscale dynamics spanning fast molecular reactions, intermediate transport, and slow cellular regulation, posing significant challenges for efficient and accurate simulation. Although operator splitting naturally decouples fast and slow subsystems, a rigorous error characterization for CLE splitting schemes has been lacking. We propose a modular operator-splitting framework with adaptive discretization that enables reliable and efficient simulation across fast-slow dynamics with explicit control of discretization error. Using stochastic logarithmic representations, we present a complete error analysis of the fast-slow Lie-Trotter splitting method, decomposing the one-step error into stochastic flow truncation error, commutator errors due to subsystem noncommutativity, and numerical discretization errors from fast and slow integrations. Guided by this analysis, we develop a proportional-integral (PI) adaptive controller that jointly selects macro time steps and fast microsteps, achieving substantial efficiency gains while maintaining accuracy.

math.NA↗