Daily Papers

Dynamic Mode Decomposition (DMD) is an equation-free method that aims at reconstructing the best linear fit from temporal datasets. In this paper, we show that DMD does not provide accurate approximation for datasets describing oscillatory dynamics, like spiral waves and relaxation oscillations, or spatio-temporal Turing instability. Inspired from the classical "divide and conquer" approach, we propose a piecewise version of DMD (pDMD) to overcome this problem. The main idea is to split the original dataset in N submatrices and then apply the exact (randomized) DMD method in each subset of the obtained partition. We describe the pDMD algorithm in detail and we introduce some error indicators to evaluate its performance when N is increased. Numerical experiments show that very accurate reconstructions are obtained by pDMD for datasets arising from time snapshots of some reaction-diffusion PDE systems, like the FitzHugh-Nagumo model, the lambda-omega system and the DIB morpho-chemical system for battery modeling.

Designing biological sequences that satisfy multiple, often conflicting, functional and biophysical criteria remains a central challenge in biomolecule engineering. While discrete flow matching models have recently shown promise for efficient sampling in high-dimensional sequence spaces, existing approaches address only single objectives or require continuous embeddings that can distort discrete distributions. We present Multi-Objective-Guided Discrete Flow Matching (MOG-DFM), a general framework to steer any pretrained discrete-time flow matching generator toward Pareto-efficient trade-offs across multiple scalar objectives. At each sampling step, MOG-DFM computes a hybrid rank-directional score for candidate transitions and applies an adaptive hypercone filter to enforce consistent multi-objective progression. We also trained two unconditional discrete flow matching models, PepDFM for diverse peptide generation and EnhancerDFM for functional enhancer DNA generation, as base generation models for MOG-DFM. We demonstrate MOG-DFM's effectiveness in generating peptide binders optimized across five properties (hemolysis, non-fouling, solubility, half-life, and binding affinity), and in designing DNA sequences with specific enhancer classes and DNA shapes. In total, MOG-DFM proves to be a powerful tool for multi-property-guided biomolecule sequence design.

Practitioners frequently aim to infer an unobserved population trajectory using sample snapshots at multiple time points. For instance, in single-cell sequencing, scientists would like to learn how gene expression evolves over time. But sequencing any cell destroys that cell. So we cannot access any cell's full trajectory, but we can access snapshot samples from many cells. Stochastic differential equations are commonly used to analyze systems with full individual-trajectory access; since here we have only sample snapshots, these methods are inapplicable. The deep learning community has recently explored using Schr\"odinger bridges (SBs) and their extensions to estimate these dynamics. However, these methods either (1) interpolate between just two time points or (2) require a single fixed reference dynamic within the SB, which is often just set to be Brownian motion. But learning piecewise from adjacent time points can fail to capture long-term dependencies. And practitioners are typically able to specify a model class for the reference dynamic but not the exact values of the parameters within it. So we propose a new method that (1) learns the unobserved trajectories from sample snapshots across multiple time points and (2) requires specification only of a class of reference dynamics, not a single fixed one. In particular, we suggest an iterative projection method inspired by Schr\"odinger bridges; we alternate between learning a piecewise SB on the unobserved trajectories and using the learned SB to refine our best guess for the dynamics within the reference class. We demonstrate the advantages of our method via a well-known simulated parametric model from ecology, simulated and real data from systems biology, and real motion-capture data.

Recent approaches have shown promises distilling diffusion models into efficient one-step generators. Among them, Distribution Matching Distillation (DMD) produces one-step generators that match their teacher in distribution, without enforcing a one-to-one correspondence with the sampling trajectories of their teachers. However, to ensure stable training, DMD requires an additional regression loss computed using a large set of noise-image pairs generated by the teacher with many steps of a deterministic sampler. This is costly for large-scale text-to-image synthesis and limits the student's quality, tying it too closely to the teacher's original sampling paths. We introduce DMD2, a set of techniques that lift this limitation and improve DMD training. First, we eliminate the regression loss and the need for expensive dataset construction. We show that the resulting instability is due to the fake critic not estimating the distribution of generated samples accurately and propose a two time-scale update rule as a remedy. Second, we integrate a GAN loss into the distillation procedure, discriminating between generated samples and real images. This lets us train the student model on real data, mitigating the imperfect real score estimation from the teacher model, and enhancing quality. Lastly, we modify the training procedure to enable multi-step sampling. We identify and address the training-inference input mismatch problem in this setting, by simulating inference-time generator samples during training time. Taken together, our improvements set new benchmarks in one-step image generation, with FID scores of 1.28 on ImageNet-64x64 and 8.35 on zero-shot COCO 2014, surpassing the original teacher despite a 500X reduction in inference cost. Further, we show our approach can generate megapixel images by distilling SDXL, demonstrating exceptional visual quality among few-step methods.