Construction of a scaffold structure that supports a desired motif, conferring protein function, shows promise for the design of vaccines and enzymes. But a general solution to this motif-scaffolding problem remains open. Current machine-learning techniques for scaffold design are either limited to unrealistically small scaffolds (up to length 20) or struggle to produce multiple diverse scaffolds. We propose to learn a distribution over diverse and longer protein backbone structures via an E(3)-equivariant graph neural network. We develop SMCDiff to efficiently sample scaffolds from this distribution conditioned on a given motif; our algorithm is the first to theoretically guarantee conditional samples from a diffusion model in the large-compute limit. We evaluate our designed backbones by how well they align with AlphaFold2-predicted structures. We show that our method can (1) sample scaffolds up to 80 residues and (2) achieve structurally diverse scaffolds for a fixed motif.

Molecular conformer generation is a fundamental task in computational chemistry. Several machine learning approaches have been developed, but none have outperformed state-of-the-art cheminformatics methods. We propose torsional diffusion, a novel diffusion framework that operates on the space of torsion angles via a diffusion process on the hypertorus and an extrinsic-to-intrinsic score model. On a standard benchmark of drug-like molecules, torsional diffusion generates superior conformer ensembles compared to machine learning and cheminformatics methods in terms of both RMSD and chemical properties, and is orders of magnitude faster than previous diffusion-based models. Moreover, our model provides exact likelihoods, which we employ to build the first generalizable Boltzmann generator.

Score-based models generate samples by mapping noise to data (and vice versa) via a high-dimensional diffusion process. We question whether it is necessary to run this entire process at high dimensionality and incur all the inconveniences thereof. Instead, we restrict the diffusion via projections onto subspaces as the data distribution evolves toward noise. When applied to state-of-the-art models, our framework simultaneously improves sample quality -- reaching an FID of 2.17 on unconditional CIFAR-10 -- and reduces the computational cost of inference for the same number of denoising steps. Our framework is fully compatible with continuous-time diffusion and retains its flexible capabilities, including exact log-likelihoods and controllable generation. Code is available at https://github.com/bjing2016/subspace-diffusion.

Diffusion models generate samples by reversing a fixed forward diffusion process. Despite already providing impressive empirical results, these diffusion models algorithms can be further improved by reducing the variance of the training targets in their denoising score-matching objective. We argue that the source of such variance lies in the handling of intermediate noise-variance scales, where multiple modes in the data affect the direction of reverse paths. We propose to remedy the problem by incorporating a reference batch which we use to calculate weighted conditional scores as more stable training targets. We show that the procedure indeed helps in the challenging intermediate regime by reducing (the trace of) the covariance of training targets. The new stable targets can be seen as trading bias for reduced variance, where the bias vanishes with increasing reference batch size. Empirically, we show that the new objective improves the image quality, stability, and training speed of various popular diffusion models across datasets with both general ODE and SDE solvers. When used in combination with EDM, our method yields a current SOTA FID of 1.90 with 35 network evaluations on the unconditional CIFAR-10 generation task. The code is available at https://github.com/Newbeeer/stf

Predicting the binding structure of a small molecule ligand to a protein--a task known as molecular docking--is critical to drug design. Recent deep learning methods that treat docking as a regression problem have decreased runtime compared to traditional search-based methods but have yet to offer substantial improvements in accuracy. To do so, we map this manifold to the product space of the degrees of freedom (translational, rotational, and torsional) involved in docking and develop an efficient diffusion process on this space. Moreover, while previous methods are not able to dock on computationally folded structures (maximum accuracy 10.4%), D The biological functions of proteins can be modulated by small molecule ligands (such as drugs) binding to them. Thus, a crucial task in computational drug design is molecular docking--predicting the position, orientation, and conformation of a ligand when bound to a target protein--from which the effect of the ligand (if any) might be ...

We introduce a new family of physics-inspired generative models termed PFGM++ that unifies diffusion models and Poisson Flow Generative Models (PFGM). These models realize generative trajectories for $N$ dimensional data by embedding paths in $N{+}D$ dimensional space while still controlling the progression with a simple scalar norm of the $D$ additional variables. The new models reduce to PFGM when $D{=}1$ and to diffusion models when $D{\to}\infty$. The flexibility of choosing $D$ allows us to trade off robustness against rigidity as increasing $D$ results in more concentrated coupling between the data and the additional variable norms. We dispense with the biased large batch field targets used in PFGM and instead provide an unbiased perturbation-based objective similar to diffusion models. To explore different choices of $D$, we provide a direct alignment method for transferring well-tuned hyperparameters from diffusion models ($D{\to} \infty$) to any finite $D$ values. Our experiments show that models with finite $D$ can be superior to previous state-of-the-art diffusion models on CIFAR-10/FFHQ $64{\times}64$ datasets, with FID scores of $1.91/2.43$ when $D{=}2048/128$. In class-conditional setting, $D{=}2048$ yields current state-of-the-art FID of $1.74$ on CIFAR-10. In addition, we demonstrate that models with smaller $D$ exhibit improved robustness against modeling errors. Code is available at https://github.com/Newbeeer/pfgmpp

Protein complex formation is a central problem in biology, being involved in most of the cell's processes, and essential for applications, e.g. drug design or protein engineering. We tackle rigid body protein-protein docking, i.e., computationally predicting the 3D structure of a protein-protein complex from the individual unbound structures, assuming no conformational change within the proteins happens during binding. We design a novel pairwise-independent SE(3)-equivariant graph matching network to predict the rotation and translation to place one of the proteins at the right docked position relative to the second protein. We mathematically guarantee a basic principle: the predicted complex is always identical regardless of the initial locations and orientations of the two structures. Our model, named EquiDock, approximates the binding pockets and predicts the docking poses using keypoint matching and alignment, achieved through optimal transport and a differentiable Kabsch algorithm. Empirically, we achieve significant running time improvements and often outperform existing docking software despite not relying on heavy candidate sampling, structure refinement, or templates.

Current model-based reinforcement learning methods struggle when operating from complex visual scenes due to their inability to prioritize task-relevant features. To mitigate this problem, we propose learning Task Informed Abstractions (TIA) that explicitly separates reward-correlated visual features from distractors. For learning TIA, we introduce the formalism of Task Informed MDP (TiMDP) that is realized by training two models that learn visual features via cooperative reconstruction, but one model is adversarially dissociated from the reward signal. Empirical evaluation shows that TIA leads to significant performance gains over state-of-the-art methods on many visual control tasks where natural and unconstrained visual distractions pose a formidable challenge.

We develop a novel approach for confidently accelerating inference in the large and expensive multilayer Transformers that are now ubiquitous in natural language processing (NLP). Amortized or approximate computational methods increase efficiency, but can come with unpredictable performance costs. In this work, we present CATs -- Confident Adaptive Transformers -- in which we simultaneously increase computational efficiency, while guaranteeing a specifiable degree of consistency with the original model with high confidence. Our method trains additional prediction heads on top of intermediate layers, and dynamically decides when to stop allocating computational effort to each input using a meta consistency classifier. To calibrate our early prediction stopping rule, we formulate a unique extension of conformal prediction. We demonstrate the effectiveness of this approach on four classification and regression tasks.

We develop a novel approach to conformal prediction when the target task has limited data available for training. Conformal prediction identifies a small set of promising output candidates in place of a single prediction, with guarantees that the set contains the correct answer with high probability. When training data is limited, however, the predicted set can easily become unusably large. In this work, we obtain substantially tighter prediction sets while maintaining desirable marginal guarantees by casting conformal prediction as a meta-learning paradigm over exchangeable collections of auxiliary tasks. Our conformalization algorithm is simple, fast, and agnostic to the choice of underlying model, learning algorithm, or dataset. We demonstrate the effectiveness of this approach across a number of few-shot classification and regression tasks in natural language processing, computer vision, and computational chemistry for drug discovery.