Emile Mathieu

Jason Yim, Brian L. Trippe, Valentin De Bortoli et al. · oxford

The design of novel protein structures remains a challenge in protein engineering for applications across biomedicine and chemistry. In this line of work, a diffusion model over rigid bodies in 3D (referred to as frames) has shown success in generating novel, functional protein backbones that have not been observed in nature. However, there exists no principled methodological framework for diffusion on SE(3), the space of orientation preserving rigid motions in R3, that operates on frames and confers the group invariance. We address these shortcomings by developing theoretical foundations of SE(3) invariant diffusion models on multiple frames followed by a novel framework, FrameDiff, for learning the SE(3) equivariant score over multiple frames. We apply FrameDiff on monomer backbone generation and find it can generate designable monomers up to 500 amino acids without relying on a pretrained protein structure prediction network that has been integral to previous methods. We find our samples are capable of generalizing beyond any known protein structure.

Ning Miao, Tom Rainforth, Emile Mathieu et al. · microsoft-research, oxford

We introduce InstaAug, a method for automatically learning input-specific augmentations from data. Previous methods for learning augmentations have typically assumed independence between the original input and the transformation applied to that input. This can be highly restrictive, as the invariances we hope our augmentation will capture are themselves often highly input dependent. InstaAug instead introduces a learnable invariance module that maps from inputs to tailored transformation parameters, allowing local invariances to be captured. This can be simultaneously trained alongside the downstream model in a fully end-to-end manner, or separately learned for a pre-trained model. We empirically demonstrate that InstaAug learns meaningful input-dependent augmentations for a wide range of transformation classes, which in turn provides better performance on both supervised and self-supervised tasks.

Laurence I. Midgley, Vincent Stimper, Javier Antorán et al. · cambridge, oxford

Coupling normalizing flows allow for fast sampling and density evaluation, making them the tool of choice for probabilistic modeling of physical systems. However, the standard coupling architecture precludes endowing flows that operate on the Cartesian coordinates of atoms with the SE(3) and permutation invariances of physical systems. This work proposes a coupling flow that preserves SE(3) and permutation equivariance by performing coordinate splits along additional augmented dimensions. At each layer, the flow maps atoms' positions into learned SE(3) invariant bases, where we apply standard flow transformations, such as monotonic rational-quadratic splines, before returning to the original basis. Crucially, our flow preserves fast sampling and density evaluation, and may be used to produce unbiased estimates of expectations with respect to the target distribution via importance sampling. When trained on the DW4, LJ13, and QM9-positional datasets, our flow is competitive with equivariant continuous normalizing flows and diffusion models, while allowing sampling more than an order of magnitude faster. Moreover, to the best of our knowledge, we are the first to learn the full Boltzmann distribution of alanine dipeptide by only modeling the Cartesian positions of its atoms. Lastly, we demonstrate that our flow can be trained to approximately sample from the Boltzmann distribution of the DW4 and LJ13 particle systems using only their energy functions.

Angus Phillips, Thomas Seror, Michael Hutchinson et al. · oxford

Score-based generative modelling (SGM) has proven to be a very effective method for modelling densities on finite-dimensional spaces. In this work we propose to extend this methodology to learn generative models over functional spaces. To do so, we represent functional data in spectral space to dissociate the stochastic part of the processes from their space-time part. Using dimensionality reduction techniques we then sample from their stochastic component using finite dimensional SGM. We demonstrate our method's effectiveness for modelling various multimodal datasets.

James Thornton, Michael Hutchinson, Emile Mathieu et al. · oxford

Score-based generative models exhibit state of the art performance on density estimation and generative modeling tasks. These models typically assume that the data geometry is flat, yet recent extensions have been developed to synthesize data living on Riemannian manifolds. Existing methods to accelerate sampling of diffusion models are typically not applicable in the Riemannian setting and Riemannian score-based methods have not yet been adapted to the important task of interpolation of datasets. To overcome these issues, we introduce \emph{Riemannian Diffusion Schrödinger Bridge}. Our proposed method generalizes Diffusion Schrödinger Bridge introduced in \cite{debortoli2021neurips} to the non-Euclidean setting and extends Riemannian score-based models beyond the first time reversal. We validate our proposed method on synthetic data and real Earth and climate data.

Emile Mathieu, Vincent Dutordoir, Michael J. Hutchinson et al. · oxford

Denoising diffusion models have proven to be a flexible and effective paradigm for generative modelling. Their recent extension to infinite dimensional Euclidean spaces has allowed for the modelling of stochastic processes. However, many problems in the natural sciences incorporate symmetries and involve data living in non-Euclidean spaces. In this work, we extend the framework of diffusion models to incorporate a series of geometric priors in infinite-dimension modelling. We do so by a) constructing a noising process which admits, as limiting distribution, a geometric Gaussian process that transforms under the symmetry group of interest, and b) approximating the score with a neural network that is equivariant w.r.t. this group. We show that with these conditions, the generative functional model admits the same symmetry. We demonstrate scalability and capacity of the model, using a novel Langevin-based conditional sampler, to fit complex scalar and vector fields, with Euclidean and spherical codomain, on synthetic and real-world weather data.

Nic Fishman, Leo Klarner, Valentin De Bortoli et al. · oxford

Denoising diffusion models are a novel class of generative algorithms that achieve state-of-the-art performance across a range of domains, including image generation and text-to-image tasks. Building on this success, diffusion models have recently been extended to the Riemannian manifold setting, broadening their applicability to a range of problems from the natural and engineering sciences. However, these Riemannian diffusion models are built on the assumption that their forward and backward processes are well-defined for all times, preventing them from being applied to an important set of tasks that consider manifolds defined via a set of inequality constraints. In this work, we introduce a principled framework to bridge this gap. We present two distinct noising processes based on (i) the logarithmic barrier metric and (ii) the reflected Brownian motion induced by the constraints. As existing diffusion model techniques cannot be applied in this setting, we derive new tools to define such models in our framework. We then demonstrate the practical utility of our methods on a number of synthetic and real-world tasks, including applications from robotics and protein design.

Nic Fishman, Leo Klarner, Emile Mathieu et al. · oxford

Denoising diffusion models have recently emerged as the predominant paradigm for generative modelling on image domains. In addition, their extension to Riemannian manifolds has facilitated a range of applications across the natural sciences. While many of these problems stand to benefit from the ability to specify arbitrary, domain-informed constraints, this setting is not covered by the existing (Riemannian) diffusion model methodology. Recent work has attempted to address this issue by constructing novel noising processes based on the reflected Brownian motion and logarithmic barrier methods. However, the associated samplers are either computationally burdensome or only apply to convex subsets of Euclidean space. In this paper, we introduce an alternative, simple noising scheme based on Metropolis sampling that affords substantial gains in computational efficiency and empirical performance compared to the earlier samplers. Of independent interest, we prove that this new process corresponds to a valid discretisation of the reflected Brownian motion. We demonstrate the scalability and flexibility of our approach on a range of problem settings with convex and non-convex constraints, including applications from geospatial modelling, robotics and protein design.

Jason Yim, Andrew Campbell, Emile Mathieu et al.

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 for a range of motifs. However, generated scaffolds tend to lack structural diversity, which can hinder success in wet-lab validation. In this work, we extend FrameFlow, an SE(3) flow matching model for protein backbone generation, to perform motif-scaffolding with two complementary approaches. The first is motif amortization, in which FrameFlow is trained with the motif as input using a data augmentation strategy. The second is motif guidance, which performs scaffolding using an estimate of the conditional score from FrameFlow without additional training. On a benchmark of 24 biologically meaningful motifs, we show our method achieves 2.5 times more designable and unique motif-scaffolds compared to state-of-the-art. Code: https://github.com/microsoft/protein-frame-flow

Aliaksandra Shysheya, Cristiana Diaconu, Federico Bergamin et al.

Modelling partial differential equations (PDEs) is of crucial importance in science and engineering, and it includes tasks ranging from forecasting to inverse problems, such as data assimilation. However, most previous numerical and machine learning approaches that target forecasting cannot be applied out-of-the-box for data assimilation. Recently, diffusion models have emerged as a powerful tool for conditional generation, being able to flexibly incorporate observations without retraining. In this work, we perform a comparative study of score-based diffusion models for forecasting and assimilation of sparse observations. In particular, we focus on diffusion models that are either trained in a conditional manner, or conditioned after unconditional training. We address the shortcomings of existing models by proposing 1) an autoregressive sampling approach that significantly improves performance in forecasting, 2) a new training strategy for conditional score-based models that achieves stable performance over a range of history lengths, and 3) a hybrid model which employs flexible pre-training conditioning on initial conditions and flexible post-training conditioning to handle data assimilation. We empirically show that these modifications are crucial for successfully tackling the combination of forecasting and data assimilation, a task commonly encountered in real-world scenarios.

Kieran Didi, Francisco Vargas, Simon V Mathis et al. · cambridge

Many protein design applications, such as binder or enzyme design, require scaffolding a structural motif with high precision. Generative modelling paradigms based on denoising diffusion processes emerged as a leading candidate to address this motif scaffolding problem and have shown early experimental success in some cases. In the diffusion paradigm, motif scaffolding is treated as a conditional generation task, and several conditional generation protocols were proposed or imported from the Computer Vision literature. However, most of these protocols are motivated heuristically, e.g. via analogies to Langevin dynamics, and lack a unifying framework, obscuring connections between the different approaches. In this work, we unify conditional training and conditional sampling procedures under one common framework based on the mathematically well-understood Doob's h-transform. This new perspective allows us to draw connections between existing methods and propose a new variation on existing conditional training protocols. We illustrate the effectiveness of this new protocol in both, image outpainting and motif scaffolding and find that it outperforms standard methods.

Alexander Denker, Francisco Vargas, Shreyas Padhy et al.

Generative modelling paradigms based on denoising diffusion processes have emerged as a leading candidate for conditional sampling in inverse problems. In many real-world applications, we often have access to large, expensively trained unconditional diffusion models, which we aim to exploit for improving conditional sampling. Most recent approaches are motivated heuristically and lack a unifying framework, obscuring connections between them. Further, they often suffer from issues such as being very sensitive to hyperparameters, being expensive to train or needing access to weights hidden behind a closed API. In this work, we unify conditional training and sampling using the mathematically well-understood Doob's h-transform. This new perspective allows us to unify many existing methods under a common umbrella. Under this framework, we propose DEFT (Doob's h-transform Efficient FineTuning), a new approach for conditional generation that simply fine-tunes a very small network to quickly learn the conditional $h$-transform, while keeping the larger unconditional network unchanged. DEFT is much faster than existing baselines while achieving state-of-the-art performance across a variety of linear and non-linear benchmarks. On image reconstruction tasks, we achieve speedups of up to 1.6$\times$, while having the best perceptual quality on natural images and reconstruction performance on medical images. Further, we also provide initial experiments on protein motif scaffolding and outperform reconstruction guidance methods.

Valentin De Bortoli, Emile Mathieu, Michael Hutchinson et al.

Score-based generative models (SGMs) are a powerful class of generative models that exhibit remarkable empirical performance. Score-based generative modelling (SGM) consists of a ``noising'' stage, whereby a diffusion is used to gradually add Gaussian noise to data, and a generative model, which entails a ``denoising'' process defined by approximating the time-reversal of the diffusion. Existing SGMs assume that data is supported on a Euclidean space, i.e. a manifold with flat geometry. In many domains such as robotics, geoscience or protein modelling, data is often naturally described by distributions living on Riemannian manifolds and current SGM techniques are not appropriate. We introduce here Riemannian Score-based Generative Models (RSGMs), a class of generative models extending SGMs to Riemannian manifolds. We demonstrate our approach on a variety of manifolds, and in particular with earth and climate science spherical data.

Ning Miao, Emile Mathieu, N. Siddharth et al.

We explain why directly changing the prior can be a surprisingly ineffective mechanism for incorporating inductive biases into VAEs, and introduce a simple and effective alternative approach: Intermediary Latent Space VAEs(InteL-VAEs). InteL-VAEs use an intermediary set of latent variables to control the stochasticity of the encoding process, before mapping these in turn to the latent representation using a parametric function that encapsulates our desired inductive bias(es). This allows us to impose properties like sparsity or clustering on learned representations, and incorporate human knowledge into the generative model. Whereas changing the prior only indirectly encourages behavior through regularizing the encoder, InteL-VAEs are able to directly enforce desired characteristics. Moreover, they bypass the computation and encoder design issues caused by non-Gaussian priors, while allowing for additional flexibility through training of the parametric mapping function. We show that these advantages, in turn, lead to both better generative models and better representations being learned.

Emile Mathieu, Adam Foster, Yee Whye Teh

Learning representations of stochastic processes is an emerging problem in machine learning with applications from meta-learning to physical object models to time series. Typical methods rely on exact reconstruction of observations, but this approach breaks down as observations become high-dimensional or noise distributions become complex. To address this, we propose a unifying framework for learning contrastive representations of stochastic processes (CReSP) that does away with exact reconstruction. We dissect potential use cases for stochastic process representations, and propose methods that accommodate each. Empirically, we show that our methods are effective for learning representations of periodic functions, 3D objects and dynamical processes. Our methods tolerate noisy high-dimensional observations better than traditional approaches, and the learned representations transfer to a range of downstream tasks.

Emile Mathieu, Maximilian Nickel

Normalizing flows have shown great promise for modelling flexible probability distributions in a computationally tractable way. However, whilst data is often naturally described on Riemannian manifolds such as spheres, torii, and hyperbolic spaces, most normalizing flows implicitly assume a flat geometry, making them either misspecified or ill-suited in these situations. To overcome this problem, we introduce Riemannian continuous normalizing flows, a model which admits the parametrization of flexible probability measures on smooth manifolds by defining flows as the solution to ordinary differential equations. We show that this approach can lead to substantial improvements on both synthetic and real-world data when compared to standard flows or previously introduced projected flows.

Emile Mathieu, Charline Le Lan, Chris J. Maddison et al.

The variational auto-encoder (VAE) is a popular method for learning a generative model and embeddings of the data. Many real datasets are hierarchically structured. However, traditional VAEs map data in a Euclidean latent space which cannot efficiently embed tree-like structures. Hyperbolic spaces with negative curvature can. We therefore endow VAEs with a Poincaré ball model of hyperbolic geometry as a latent space and rigorously derive the necessary methods to work with two main Gaussian generalisations on that space. We empirically show better generalisation to unseen data than the Euclidean counterpart, and can qualitatively and quantitatively better recover hierarchical structures.

Emile Mathieu, Tom Rainforth, N. Siddharth et al.

We develop a generalisation of disentanglement in VAEs---decomposition of the latent representation---characterising it as the fulfilment of two factors: a) the latent encodings of the data having an appropriate level of overlap, and b) the aggregate encoding of the data conforming to a desired structure, represented through the prior. Decomposition permits disentanglement, i.e. explicit independence between latents, as a special case, but also allows for a much richer class of properties to be imposed on the learnt representation, such as sparsity, clustering, independent subspaces, or even intricate hierarchical dependency relationships. We show that the $β$-VAE varies from the standard VAE predominantly in its control of latent overlap and that for the standard choice of an isotropic Gaussian prior, its objective is invariant to rotations of the latent representation. Viewed from the decomposition perspective, breaking this invariance with simple manipulations of the prior can yield better disentanglement with little or no detriment to reconstructions. We further demonstrate how other choices of prior can assist in producing different decompositions and introduce an alternative training objective that allows the control of both decomposition factors in a principled manner.

Benjamin Bloem-Reddy, Adam Foster, Emile Mathieu et al.

Empirical evidence suggests that heavy-tailed degree distributions occurring in many real networks are well-approximated by power laws with exponents $η$ that may take values either less than and greater than two. Models based on various forms of exchangeability are able to capture power laws with $η< 2$, and admit tractable inference algorithms; we draw on previous results to show that $η> 2$ cannot be generated by the forms of exchangeability used in existing random graph models. Preferential attachment models generate power law exponents greater than two, but have been of limited use as statistical models due to the inherent difficulty of performing inference in non-exchangeable models. Motivated by this gap, we design and implement inference algorithms for a recently proposed class of models that generates $η$ of all possible values. We show that although they are not exchangeable, these models have probabilistic structure amenable to inference. Our methods make a large class of previously intractable models useful for statistical inference.