In this study, deep learning is used to estimate kinetic parameters for modeling itaconic acid production based on real batch experiments conducted at different agitation speeds and reactor scales. Two deep learning strategies, namely direct deep learning (DDL) and generative conditional flow matching (CFM) are compared and benchmarked against nonlinear regression as a reference method. Compared with DDL, CFM consistently yields more accurate results. The concentration profiles predicted by CFM closely match those obtained from nonlinear regression, whereas DDL results in larger deviations. Similar behavior is observed in the scale-up experiments, where the CFM model again generalizes better and is more robust than the direct approach. These findings demonstrate that CFM can reliably predict system behavior across different operating conditions and scales, offering a flexible and data-efficient framework for parameter estimation in dynamic bioprocess models.
Performance of deep learning models is strongly governed by architectural capacity, with width and depth as primary controls. However, in physical-science applications, models are often compared at a single fixed size or by separating accuracy and computational cost, which can be misleading since architectures exhibit different accuracy-cost scaling as width and depth vary. This issue is particularly relevant for U-Net-type encoder-decoder models, widely used for multi-scale gas, fluid, and plasma dynamics due to their ability to represent features across spatial scales. A U-Net constructs a multi-resolution representation via an encoder that progressively reduces spatial resolution, followed by a decoder that restores it for prediction. Skip connections link corresponding encoder and decoder features, preserving fine-scale information and improving optimization. In practice, U-Net width is routinely tuned, while depth is typically kept fixed (a set number of down/up-sampling stages with few convolutions per stage), limiting systematic exploration of depth for improving the accuracy-cost trade-off. We address this limitation by increasing effective depth through stacking multiple encoder-decoder "waves" in series, with skip connections both within and across waves to enable progressive cross-scale refinement. We call this architecture a Deep Wave Network (DW-Net). Training data, optimization, and schedules are kept identical across models. Instead of evaluating single configurations, we train multiple width variants of each architecture and compare accuracy vs. GPU time Pareto fronts. Across several 2D and 3D flow benchmarks, DW-Net models consistently improve the Pareto frontier over single-wave U-Nets, achieving higher accuracy at matched cost or similar accuracy at reduced cost, and reaching low-error regimes with up to 3x less training time under identical training settings.
Alexander I. Khrabry, Edward A. Startsev, Andrew T. Powis +1
Estimating free energy differences quantifies thermodynamic preferences in molecular interactions, which is central to chemistry and drug discovery. Despite fruitful progress, existing methods still face key limitations: classical computational approaches remain prohibitively expensive due to their reliance on extensive molecular dynamics simulations, while deep learning-based methods are constrained by either less-expressive generative models or input dimensions tied to a specific system, resulting in negligible generalization. To address these challenges, we propose CARD, a generative framework that employs a novel radix-based decomposition to bijectively convert 3D coordinates into mixed discrete-continuous sequences, enabling coarse-to-fine autoregressive modeling with enhanced expressiveness. Notably, the model corresponds to a distribution with zero free energy, serving as a proposal for absolute free energy computation of arbitrary systems without relying on alchemical pathways. Experiments across diverse tasks demonstrate that CARD matches the accuracy of classical computational methods on unseen systems with diverse topologies, while achieving an approximately 40-fold speedup in inference.
Inertial confinement fusion (ICF) is a leading pathway toward clean energy, but each shot at the National Ignition Facility costs on the order of one million dollars, making accurate AI surrogates a high-value target. We study exogenous-driven ICF waveform prediction, where a 512-step neutron-rate diagnostic must be inferred directly from a laser pulse and target design parameters, with no historical response observed. The regime stresses standard time-series predictors with temporal sparsity (picosecond peak in a nanosecond window), input-output scale mismatch (under 300 real shots), and peak sensitivity (picosecond timing). We propose ICF-DLM, to our knowledge the first LM-based ICF predictor, combining (i) a physics-typed decomposition into yield YDT, peak timing tpeak, and local waveform wlocal; (ii) bidirectional denoising that defers commitment to peak location; and (iii) a physics-driven PPO reward re-injecting metric structure across numeric tokens. On ICFBench (50K simulations + 232 experimental shots), ICF-DLM cuts peak-timing error from 11.6 to 9.2 steps over a matched autoregressive LLaMA-3-8B and outperforms classical sequence models and LLM-based time-series predictors. Beyond ICF, the recipe shows potential to address science domains with low data and sparse events.