14 papers
Beckmann Transport Models: From Autonomous Flows to One-Step Maps
Lee Cheuk-Kit, Florentin Coeurdoux, Yuyuan Chen +5
We propose an instantiation of flow matching that relies on a time-independent velocity field (an \emph{autonomous flow}) to exactly map between two distributions, so long as the t…
Expanding Flow Maps
Sophia Tang, Pranam Chatterjee
Flow-based generative models have enabled remarkable progress in fast and controllable generation across continuous and discrete state spaces, yet existing parameterizations are co…
A2D2: Fine-Tuning Any-Length Discrete Diffusion for Adaptive Decoding
Sophia Tang, Yuchen Zhu, Molei Tao +1
Discrete diffusion models offer a simple and stable likelihood-based framework for sequence generation, recently extended to any-length settings via token insertion. Principled rew…
Active Flow Expansion for Out-of-Distribution Discovery: from Theory to Molecules
Riccardo De Santi, Bruce Lee, Cristian Perez Jensen +6
Standard flow and diffusion pre-training matches the distribution of available data (e.g., molecules), which often covers only a small fraction of the valid design space. In genera…
mRNAutilus: Multi-Objective-Guided Discrete Generation of mRNA with Optimized Therapeutic Properties
Sawan Patel, Sophia Tang, Yesol Kim +8
Therapeutic mRNA design requires coordinating multiple interacting sequence features across the full transcript, where codon usage, untranslated regions (UTRs), and their coupling…
TD3B: Transition-Directed Discrete Diffusion for Allosteric Binder Generation
Hanqun Cao, Aastha Pal, Sophia Tang +4
Protein function is often controlled by ligands that bias the direction of state transitions, such as agonists and antagonists, rather than stabilizing a single conformation. This…