10 citations · 16 across the 14 of their papers we have counts for
15 papers
LLM-to-Flow Distillation: Teaching Natural Language Goals to Scientific Generators
Riccardo De Santi, Federico Di Gennaro, Angelo Gnazzo +6
Generative discovery in science requires coupling high-level scientific reasoning with the ability to generate samples respecting the structure of a design space. Yet these capabil…
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…
Foundations of Schrödinger Bridges for Generative Modeling
Sophia Tang
At the core of modern generative modeling frameworks, including diffusion models, score-based models, and flow matching, is the task of transforming a simple prior distribution int…
A Complete Guide to Spherical Equivariant Graph Transformers
Sophia Tang
Spherical equivariant graph neural networks (EGNNs) provide a principled framework for learning on three-dimensional molecular and biomolecular systems, where predictions must resp…
Entangled Schrödinger Bridge Matching
Sophia Tang, Yinuo Zhang, Pranam Chatterjee
Simulating trajectories of multi-particle systems on complex energy landscapes is a central task in molecular dynamics (MD) and drug discovery, but remains challenging at scale due…
TR2-D2: Tree Search Guided Trajectory-Aware Fine-Tuning for Discrete Diffusion
Sophia Tang, Yuchen Zhu, Molei Tao +1
Reinforcement learning with stochastic optimal control offers a promising framework for diffusion fine-tuning, where a pre-trained diffusion model is optimized to generate paths th…
Branched Schrödinger Bridge Matching
Sophia Tang, Yinuo Zhang, Alexander Tong +1
Predicting the intermediate trajectories between an initial and target distribution is a central problem in generative modeling. Existing approaches, such as flow matching and Schr…
Multi-Objective-Guided Discrete Flow Matching for Controllable Biological Sequence Design
Tong Chen, Yinuo Zhang, Sophia Tang +1
Designing biological sequences that satisfy multiple, often conflicting, functional and biophysical criteria remains a central challenge in biomolecule engineering. While discrete…
Gumbel-Softmax Flow Matching with Straight-Through Guidance for Controllable Biological Sequence Generation
Sophia Tang, Yinuo Zhang, Alexander Tong +1
Flow matching in the continuous simplex has emerged as a promising strategy for DNA sequence design, but struggles to scale to higher simplex dimensions required for peptide and pr…
PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion
Sophia Tang, Yinuo Zhang, Pranam Chatterjee
We present PepTune, a multi-objective discrete diffusion model for simultaneous generation and optimization of therapeutic peptide SMILES. Built on the Masked Discrete Language Mod…