DeepInverse: A Python package for solving imaging inverse problems with deep learning

DeepInverse is an open-source PyTorch-based library for solving imaging inverse problems. The library covers all crucial steps in image reconstruction from the efficient implementation of forward operators (e.g., optics, MRI, tomography), to the definition and resolution of variational problems and the design and training of advanced neural network architectures. In this paper, we describe the main functionality of the library and discuss the main design choices.

On the Relation between Rectified Flows and Optimal Transport

This paper investigates the connections between rectified flows, flow matching, and optimal transport. Flow matching is a recent approach to learning generative models by estimating velocity fields that guide transformations from a source to a target distribution. Rectified flow matching aims to straighten the learned transport paths, yielding more direct flows between distributions. Our first contribution is a set of invariance properties of rectified flows and explicit velocity fields. In addition, we also provide explicit constructions and analysis in the Gaussian (not necessarily independent) and Gaussian mixture settings and study the relation to optimal transport. Our second contribution addresses recent claims suggesting that rectified flows, when constrained such that the learned velocity field is a gradient, can yield (asymptotically) solutions to optimal transport problems. We study the existence of solutions for this problem and demonstrate that they only relate to optimal transport under assumptions that are significantly stronger than those previously acknowledged. In particular, we present several counter-examples that invalidate earlier equivalence results in the literature, and we argue that enforcing a gradient constraint on rectified flows is, in general, not a reliable method for computing optimal transport maps.

Iterative Importance Fine-tuning of Diffusion Models

Diffusion models are an important tool for generative modelling, serving as effective priors in applications such as imaging and protein design. A key challenge in applying diffusion models for downstream tasks is efficiently sampling from resulting posterior distributions, which can be addressed using the $h$-transform. This work introduces a self-supervised algorithm for fine-tuning diffusion models by estimating the $h$-transform, enabling amortised conditional sampling. Our method iteratively refines the $h$-transform using a synthetic dataset resampled with path-based importance weights. We demonstrate the effectiveness of this framework on class-conditional sampling and reward fine-tuning for text-to-image diffusion models.

Plug-and-Play Half-Quadratic Splitting for Ptychography

Ptychography is a coherent diffraction imaging method that uses phase retrieval techniques to reconstruct complex-valued images. It achieves this by sequentially illuminating overlapping regions of a sample with a coherent beam and recording the diffraction pattern. Although this addresses traditional imaging system challenges, it is computationally intensive and highly sensitive to noise, especially with reduced illumination overlap. Data-driven regularisation techniques have been applied in phase retrieval to improve reconstruction quality. In particular, plug-and-play (PnP) offers flexibility by integrating data-driven denoisers as implicit priors. In this work, we propose a half-quadratic splitting framework for using PnP and other data-driven priors for ptychography. We evaluate our method both on natural images and real test objects to validate its effectiveness for ptychographic image reconstruction.

Generative Feature Training of Thin 2-Layer Networks

We consider the approximation of functions by 2-layer neural networks with a small number of hidden weights based on the squared loss and small datasets. Due to the highly non-convex energy landscape, gradient-based training often suffers from local minima. As a remedy, we initialize the hidden weights with samples from a learned proposal distribution, which we parameterize as a deep generative model. To train this model, we exploit the fact that with fixed hidden weights, the optimal output weights solve a linear equation. After learning the generative model, we refine the sampled weights with a gradient-based post-processing in the latent space. Here, we also include a regularization scheme to counteract potential noise. Finally, we demonstrate the effectiveness of our approach by numerical examples.

Fast Summation of Radial Kernels via QMC Slicing

The fast computation of large kernel sums is a challenging task, which arises as a subproblem in any kernel method. We approach the problem by slicing, which relies on random projections to one-dimensional subspaces and fast Fourier summation. We prove bounds for the slicing error and propose a quasi-Monte Carlo (QMC) approach for selecting the projections based on spherical quadrature rules. Numerical examples demonstrate that our QMC-slicing approach significantly outperforms existing methods like (QMC-)random Fourier features, orthogonal Fourier features or non-QMC slicing on standard test datasets.

Wasserstein Gradient Flows of MMD Functionals with Distance Kernel and Cauchy Problems on Quantile Functions

We give a comprehensive description of Wasserstein gradient flows of maximum mean discrepancy (MMD) functionals $\mathcal F_\nu := \text{MMD}_K^2(\cdot, \nu)$ towards given target measures $\nu$ on the real line, where we focus on the negative distance kernel $K(x,y) := -|x-y|$. In one dimension, the Wasserstein-2 space can be isometrically embedded into the cone $\mathcal C(0,1) \subset L_2(0,1)$ of quantile functions leading to a characterization of Wasserstein gradient flows via the solution of an associated Cauchy problem on $L_2(0,1)$. Based on the construction of an appropriate counterpart of $\mathcal F_\nu$ on $L_2(0,1)$ and its subdifferential, we provide a solution of the Cauchy problem. For discrete target measures $\nu$, this results in a piecewise linear solution formula. We prove invariance and smoothing properties of the flow on subsets of $\mathcal C(0,1)$. For certain $\mathcal F_\nu$-flows this implies that initial point measures instantly become absolutely continuous, and stay so over time. Finally, we illustrate the behavior of the flow by various numerical examples using an implicit Euler scheme and demonstrate differences to the explicit Euler scheme, which is easier to compute, but comes with limited convergence guarantees.

Importance Corrected Neural JKO Sampling

In order to sample from an unnormalized probability density function, we propose to combine continuous normalizing flows (CNFs) with rejection-resampling steps based on importance weights. We relate the iterative training of CNFs with regularized velocity fields to a JKO scheme and prove convergence of the involved velocity fields to the velocity field of the Wasserstein gradient flow (WGF). The alternation of local flow steps and non-local rejection-resampling steps allows to overcome local minima or slow convergence of the WGF for multimodal distributions. Since the proposal of the rejection step is generated by the model itself, they do not suffer from common drawbacks of classical rejection schemes. The arising model can be trained iteratively, reduces the reverse Kulback-Leibler (KL) loss function in each step, allows to generate iid samples and moreover allows for evaluations of the generated underlying density. Numerical examples show that our method yields accurate results on various test distributions including high-dimensional multimodal targets and outperforms the state of the art in almost all cases significantly.

Mixed Noise and Posterior Estimation with Conditional DeepGEM

Motivated by indirect measurements and applications from nanometrology with a mixed noise model, we develop a novel algorithm for jointly estimating the posterior and the noise parameters in Bayesian inverse problems. We propose to solve the problem by an expectation maximization (EM) algorithm. Based on the current noise parameters, we learn in the E-step a conditional normalizing flow that approximates the posterior. In the M-step, we propose to find the noise parameter updates again by an EM algorithm, which has analytical formulas. We compare the training of the conditional normalizing flow with the forward and reverse KL, and show that our model is able to incorporate information from many measurements, unlike previous approaches.

Fast Kernel Summation in High Dimensions via Slicing and Fourier Transforms

Kernel-based methods are heavily used in machine learning. However, they suffer from $O(N^2)$ complexity in the number $N$ of considered data points. In this paper, we propose an approximation procedure, which reduces this complexity to $O(N)$. Our approach is based on two ideas. First, we prove that any radial kernel with analytic basis function can be represented as sliced version of some one-dimensional kernel and derive an analytic formula for the one-dimensional counterpart. It turns out that the relation between one- and $d$-dimensional kernels is given by a generalized Riemann-Liouville fractional integral. Hence, we can reduce the $d$-dimensional kernel summation to a one-dimensional setting. Second, for solving these one-dimensional problems efficiently, we apply fast Fourier summations on non-equispaced data, a sorting algorithm or a combination of both. Due to its practical importance we pay special attention to the Gaussian kernel, where we show a dimension-independent error bound and represent its one-dimensional counterpart via a closed-form Fourier transform. We provide a run time comparison and error estimate of our fast kernel summations.