Related papers: AffinityFlow: Guided Flows for Antibody Affinity M…

Protein structure prediction has reached revolutionary levels of accuracy on single structures, yet distributional modeling paradigms are needed to capture the conformational ensembles and flexibility that underlie biological function.…

Predicting accurate protein-ligand binding affinity is important in drug discovery but remains a challenge even with computationally expensive biophysics-based energy scoring methods and state-of-the-art deep learning approaches. Despite…

Identifying drug-target interactions is essential for developing effective therapeutics. Binding affinity quantifies these interactions, and traditional approaches rely on computationally intensive 3D structural data. In contrast, language…

Consistency models imitate the multi-step sampling of score-based diffusion in a single forward pass of a neural network. They can be learned in two ways: consistency distillation and consistency training. The former relies on the true…

Flow matching has emerged as a promising framework for training generative models, demonstrating impressive empirical performance while offering relative ease of training compared to diffusion-based models. However, this method still…

Motivation: Drug discovery demands rapid quantification of compound-protein interaction (CPI). However, there is a lack of methods that can predict compound-protein affinity from sequences alone with high applicability, accuracy, and…

A Flow is a collection of component models ("Agents") which constructs the solution to a complex problem via iterative communication. Flows have emerged as state of the art architectures for code generation, and are the raison d'etre for…

Predicting low-energy molecular conformations given a molecular graph is an important but challenging task in computational drug discovery. Existing state-of-the-art approaches either resort to large scale transformer-based models that…

We present FrameFlow, a method for fast protein backbone generation using SE(3) flow matching. Specifically, we adapt FrameDiff, a state-of-the-art diffusion model, to the flow-matching generative modeling paradigm. We show how flow…

Recent advances in large multi-modal generative models have demonstrated impressive capabilities in multi-modal generation, including image and video generation. These models are typically built upon multi-step frameworks like diffusion and…

Accurate prediction of antibody-antigen (Ab-Ag) binding affinity is essential for therapeutic design and vaccine development, yet the performance of current models is limited by noisy experimental labels, heterogeneous assay conditions, and…

To perform recognition, molecules must locate and specifically bind their targets within a noisy biochemical environment with many look-alikes. Molecular recognition processes, especially the induced-fit mechanism, are known to involve…

Adversarial learning of probabilistic models has recently emerged as a promising alternative to maximum likelihood. Implicit models such as generative adversarial networks (GAN) often generate better samples compared to explicit models…

The accurate prediction of antigen-antibody structures is essential for advancing immunology and therapeutic development, as it helps elucidate molecular interactions that underlie immune responses. Despite recent progress with deep…

Protein design often begins with the knowledge of a desired function from a motif which motif-scaffolding aims to construct a functional protein around. Recently, generative models have achieved breakthrough success in designing scaffolds…

Normalizing Flows (NFs) are a class of generative models distinguished by a mathematically invertible architecture, where the forward pass transforms data into a latent space for density estimation, and the reverse pass generates new…

We present JanusFlow, a powerful framework that unifies image understanding and generation in a single model. JanusFlow introduces a minimalist architecture that integrates autoregressive language models with rectified flow, a…

We propose an algorithm for learning a conditional generative model of a molecule given a target. Specifically, given a receptor molecule that one wishes to bind to, the conditional model generates candidate ligand molecules that may bind…

Diffusion models achieve strong generative performance but often rely on large datasets that may include sensitive content. This challenge is compounded by the models' tendency to memorize training data, raising privacy concerns. SFBD (Lu…

Conditional flow matching (CFM) stands out as an efficient, simulation-free approach for training flow-based generative models, achieving remarkable performance for data generation. However, CFM is insufficient to ensure accuracy in…