Coarse-grained (CG) molecular dynamics enables the study of biological processes at temporal and spatial scales that would be intractable at an atomistic resolution. However, accurately learning a CG force field remains a challenge. In this work, we leverage connections between score-based generative models, force fields and molecular dynamics to learn a CG force field without requiring any force inputs during training. Specifically, we train a diffusion generative model on protein structures from molecular dynamics simulations, and we show that its score function approximates a force field that can directly be used to simulate CG molecular dynamics. While having a vastly simplified training setup compared to previous work, we demonstrate that our approach leads to improved performance across several small- to medium-sized protein simulations, reproducing the CG equilibrium distribution, and preserving dynamics of all-atom simulations such as protein folding events.

Partial differential equations (PDEs) see widespread use in sciences and engineering to describe simulation of physical processes as scalar and vector fields interacting and coevolving over time. Due to the computationally expensive nature of their standard solution methods, neural PDE surrogates have become an active research topic to accelerate these simulations. However, current methods do not explicitly take into account the relationship between different fields and their internal components, which are often correlated. Viewing the time evolution of such correlated fields through the lens of multivector fields allows us to overcome these limitations. Multivector fields consist of scalar, vector, as well as higher-order components, such as bivectors and trivectors. Their algebraic properties, such as multiplication, addition and other arithmetic operations can be described by Clifford algebras. To our knowledge, this paper presents the first usage of such multivector representations together with Clifford convolutions and Clifford Fourier transforms in the context of deep learning. The resulting Clifford neural layers are universally applicable and will find direct use in the areas of fluid dynamics, weather forecasting, and the modeling of physical systems in general. We empirically evaluate the benefit of Clifford neural layers by replacing convolution and Fourier operations in common neural PDE surrogates by their Clifford counterparts on 2D Navier-Stokes and weather modeling tasks, as well as 3D Maxwell equations. For similar parameter count, Clifford neural layers consistently improve generalization capabilities of the tested neural PDE surrogates. Source code for our PyTorch implementation is available at https://microsoft.github.io/cliffordlayers/.

The ability to computationally generate novel yet physically foldable protein structures could lead to new biological discoveries and new treatments targeting yet incurable diseases. Despite recent advances in protein structure prediction, directly generating diverse, novel protein structures from neural networks remains difficult. In this work, we present a new diffusion-based generative model that designs protein backbone structures via a procedure that mirrors the native folding process. We describe protein backbone structure as a series of consecutive angles capturing the relative orientation of the constituent amino acid residues, and generate new structures by denoising from a random, unfolded state towards a stable folded structure. Not only does this mirror how proteins biologically twist into energetically favorable conformations, the inherent shift and rotational invariance of this representation crucially alleviates the need for complex equivariant networks. We train a denoising diffusion probabilistic model with a simple transformer backbone and demonstrate that our resulting model unconditionally generates highly realistic protein structures with complexity and structural patterns akin to those of naturally-occurring proteins. As a useful resource, we release the first open-source codebase and trained models for protein structure diffusion.

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Denoising diffusion probabilistic models (DDPMs) (Ho et al. 2020) have shown impressive results on image and waveform generation in continuous state spaces. Here, we introduce Discrete Denoising Diffusion Probabilistic Models (D3PMs), diffusion-like generative models for discrete data that generalize the multinomial diffusion model of Hoogeboom et al. 2021, by going beyond corruption processes with uniform transition probabilities. This includes corruption with transition matrices that mimic Gaussian kernels in continuous space, matrices based on nearest neighbors in embedding space, and matrices that introduce absorbing states. The third allows us to draw a connection between diffusion models and autoregressive and mask-based generative models. We show that the choice of transition matrix is an important design decision that leads to improved results in image and text domains. We also introduce a new loss function that combines the variational lower bound with an auxiliary cross entropy loss. For text, this model class achieves strong results on character-level text generation while scaling to large vocabularies on LM1B. On the image dataset CIFAR-10, our models approach the sample quality and exceed the log-likelihood of the continuous-space DDPM model.

We focus on the problem of domain adaptation when the goal is shifting the model towards the target distribution, rather than learning domain invariant representations. It has been shown that under the following two assumptions: (a) access to samples from intermediate distributions, and (b) samples being annotated with the amount of change from the source distribution, self-training can be successfully applied on gradually shifted samples to adapt the model toward the target distribution. We hypothesize having (a) is enough to enable iterative self-training to slowly adapt the model to the target distribution, by making use of an implicit curriculum. In the case where (a) does not hold, we observe that iterative self-training falls short. We propose GIFT, a method that creates virtual samples from intermediate distributions by interpolating representations of examples from source and target domains. We evaluate an iterative-self-training method on datasets with natural distribution shifts, and show that when applied on top of other domain adaptation methods, it improves the performance of the model on the target dataset. We run an analysis on a synthetic dataset to show that in the presence of (a) iterative-self-training naturally forms a curriculum of samples. Furthermore, we show that when (a) does not hold, GIFT performs better than iterative self-training.

Speech synthesis is an important practical generative modeling problem that has seen great progress over the last few years, with likelihood-based autoregressive neural models now outperforming traditional concatenative systems. A downside of such autoregressive models is that they require executing tens of thousands of sequential operations per second of generated audio, making them ill-suited for deployment on specialized deep learning hardware. Here, we propose a new learning method that allows us to train highly parallel models of speech, without requiring access to an analytical likelihood function. Our approach is based on a generalized energy distance between the distributions of the generated and real audio. This spectral energy distance is a proper scoring rule with respect to the distribution over magnitude-spectrograms of the generated waveform audio and offers statistical consistency guarantees. The distance can be calculated from minibatches without bias, and does not involve adversarial learning, yielding a stable and consistent method for training implicit generative models. Empirically, we achieve state-of-the-art generation quality among implicit generative models, as judged by the recently-proposed cFDSD metric. When combining our method with adversarial techniques, we also improve upon the recently-proposed GAN-TTS model in terms of Mean Opinion Score as judged by trained human evaluators.

In this paper we analyse and improve integer discrete flows for lossless compression. Integer discrete flows are a recently proposed class of models that learn invertible transformations for integer-valued random variables. Due to its discrete nature, they can be combined in a straightforward manner with entropy coding schemes for lossless compression without the need for bits-back coding. We discuss the potential difference in flexibility between invertible flows for discrete random variables and flows for continuous random variables and show that (integer) discrete flows are more flexible than previously claimed. We furthermore investigate the influence of quantization operators on optimization and gradient bias in integer discrete flows. Finally, we introduce modifications to the architecture to improve the performance of this model class for lossless compression.

Scientific imaging techniques such as optical and electron microscopy and computed tomography (CT) scanning are used to study the 3D structure of an object through 2D observations. These observations are related to the original 3D object through orthogonal integral projections. For common 3D reconstruction algorithms, computational efficiency requires the modeling of the 3D structures to take place in Fourier space by applying the Fourier slice theorem. At present, it is unclear how to differentiate through the projection operator, and hence current learning algorithms can not rely on gradient based methods to optimize 3D structure models. In this paper we show how back-propagation through the projection operator in Fourier space can be achieved. We demonstrate the validity of the approach with experiments on 3D reconstruction of proteins. We further extend our approach to learning probabilistic models of 3D objects. This allows us to predict regions of low sampling rates or estimate noise. A higher sample efficiency can be reached by utilizing the learned uncertainties of the 3D structure as an unsupervised estimate of the model fit. Finally, we demonstrate how the reconstruction algorithm can be extended with an amortized inference scheme on unknown attributes such as object pose. Through empirical studies we show that joint inference of the 3D structure and the object pose becomes more difficult when the ground truth object contains more symmetries. Due to the presence of for instance (approximate) rotational symmetries, the pose estimation can easily get stuck in local optima, inhibiting a fine-grained high-quality estimate of the 3D structure.

Lossless compression methods shorten the expected representation size of data without loss of information, using a statistical model. Flow-based models are attractive in this setting because they admit exact likelihood optimization, which is equivalent to minimizing the expected number of bits per message. However, conventional flows assume continuous data, which may lead to reconstruction errors when quantized for compression. For that reason, we introduce a flow-based generative model for ordinal discrete data called Integer Discrete Flow (IDF): a bijective integer map that can learn rich transformations on high-dimensional data. As building blocks for IDFs, we introduce a flexible transformation layer called integer discrete coupling. Our experiments show that IDFs are competitive with other flow-based generative models. Furthermore, we demonstrate that IDF based compression achieves state-of-the-art lossless compression rates on CIFAR10, ImageNet32, and ImageNet64. To the best of our knowledge, this is the first lossless compression method that uses invertible neural networks.