Yiyang Lu

Mengbo Wang, Shourya Verma, Aditya Malusare et al.

Spatial transcriptomics (ST) technologies can be used to align transcriptomes with histopathological morphology, presenting exciting new opportunities for biomolecular discovery. Using ST data, we construct a novel framework, GeneFlow, to map transcriptomics onto paired cellular images. By combining an attention-based RNA encoder with a conditional UNet guided by rectified flow, we generate high-resolution images with different staining methods (e.g. H&E, DAPI) to highlight various cellular/tissue structures. Rectified flow with high-order ODE solvers creates a continuous, bijective mapping between transcriptomics and image manifolds, addressing the many-to-one relationship inherent in this problem. Our method enables the generation of realistic cellular morphology features and spatially resolved intercellular interactions from observational gene expression profiles, provides potential to incorporate genetic/chemical perturbations, and enables disease diagnosis by revealing dysregulated patterns in imaging phenotypes. Our rectified flow-based method outperforms diffusion-based baseline method in all experiments. Code can be found at https://github.com/wangmengbo/GeneFlow.

Zhengyang Geng, Yiyang Lu, Zongze Wu et al.

MeanFlow (MF) has recently been established as a framework for one-step generative modeling. However, its ``fastforward'' nature introduces key challenges in both the training objective and the guidance mechanism. First, the original MF's training target depends not only on the underlying ground-truth fields but also on the network itself. To address this issue, we recast the objective as a loss on the instantaneous velocity $v$, re-parameterized by a network that predicts the average velocity $u$. Our reformulation yields a more standard regression problem and improves the training stability. Second, the original MF fixes the classifier-free guidance scale during training, which sacrifices flexibility. We tackle this issue by formulating guidance as explicit conditioning variables, thereby retaining flexibility at test time. The diverse conditions are processed through in-context conditioning, which reduces model size and benefits performance. Overall, our $\textbf{improved MeanFlow}$ ($\textbf{iMF}$) method, trained entirely from scratch, achieves $\textbf{1.72}$ FID with a single function evaluation (1-NFE) on ImageNet 256$\times$256. iMF substantially outperforms prior methods of this kind and closes the gap with multi-step methods while using no distillation. We hope our work will further advance fastforward generative modeling as a stand-alone paradigm.

Yiyang Lu, Mohammad Pedramfar, Vaneet Aggarwal

Projection-based algorithms for constrained Online Convex Optimization (COCO) face scalability challenges in high-dimensional settings due to the computational complexity of projecting iterates onto constraint sets. This paper introduces a projection-free algorithm for COCO that achieves state-of-the-art performance guarantees while eliminating the need for projections. By integrating a separation oracle with adaptive Online Gradient Descent (OGD) and employing a Lyapunov-driven surrogate function, while dynamically adjusting step sizes using gradient norms, our method jointly optimizes the regret and cumulative constraint violation (CCV). We also use a blocked version of OGD that helps achieve tradeoffs betweeen the regret and CCV with the number of calls to the separation oracle. For convex cost functions, our algorithm attains an optimal regret of $\mathcal{O}(\sqrt{T})$ and a CCV of $\mathcal{O}(\sqrt{T} \log T)$, matching the best-known projection-based results, while only using $\tilde{\mathcal{O}}({T})$ calls to the separation oracle. The results also demonstrate a tradeoff where lower calls to the separation oracle increase the regret and the CCV. In the strongly convex setting, we further achieve a regret of $\mathcal{O}(\log T)$ and a CCV of $\mathcal{O}(\sqrt{T\log T} )$, while requiring ${\mathcal{O}}({T}^2)$ calls to the separation oracle. Further, tradeoff with the decreasing oracle calls is studied. These results close the gap between projection-free and projection-based approaches, demonstrating that projection-free methods can achieve performance comparable to projection-based counterparts.

Yiyang Lu, Mohammad Pedramfar, Vaneet Aggarwal

We introduce a novel framework for decentralized projection-free optimization, extending projection-free methods to a broader class of upper-linearizable functions. Our approach leverages decentralized optimization techniques with the flexibility of upper-linearizable function frameworks, effectively generalizing traditional DR-submodular function optimization. We obtain the regret of $O(T^{1-θ/2})$ with communication complexity of $O(T^θ)$ and number of linear optimization oracle calls of $O(T^{2θ})$ for decentralized upper-linearizable function optimization, for any $0\le θ\le 1$. This approach allows for the first results for monotone up-concave optimization with general convex constraints and non-monotone up-concave optimization with general convex constraints. Further, the above results for first order feedback are extended to zeroth order, semi-bandit, and bandit feedback.