Konik Kothari

AmirEhsan Khorashadizadeh, Konik Kothari, Leonardo Salsi et al.

Most deep learning models for computational imaging regress a single reconstructed image. In practice, however, ill-posedness, nonlinearity, model mismatch, and noise often conspire to make such point estimates misleading or insufficient. The Bayesian approach models images and (noisy) measurements as jointly distributed random vectors and aims to approximate the posterior distribution of unknowns. Recent variational inference methods based on conditional normalizing flows are a promising alternative to traditional MCMC methods, but they come with drawbacks: excessive memory and compute demands for moderate to high resolution images and underwhelming performance on hard nonlinear problems. In this work, we propose C-Trumpets -- conditional injective flows specifically designed for imaging problems, which greatly diminish these challenges. Injectivity reduces memory footprint and training time while low-dimensional latent space together with architectural innovations like fixed-volume-change layers and skip-connection revnet layers, C-Trumpets outperform regular conditional flow models on a variety of imaging and image restoration tasks, including limited-view CT and nonlinear inverse scattering, with a lower compute and memory budget. C-Trumpets enable fast approximation of point estimates like MMSE or MAP as well as physically-meaningful uncertainty quantification.

Zahra Shamsi, Isaac Reid, Drew Bryant et al.

We present a machine learning method capable of accurately detecting chromosome abnormalities that cause blood cancers directly from microscope images of the metaphase stage of cell division. The pipeline is built on a series of fine-tuned Vision Transformers. Current state of the art (and standard clinical practice) requires expensive, manual expert analysis, whereas our pipeline takes only 15 seconds per metaphase image. Using a novel pretraining-finetuning strategy to mitigate the challenge of data scarcity, we achieve a high precision-recall score of 94% AUC for the clinically significant del(5q) and t(9;22) anomalies. Our method also unlocks zero-shot detection of rare aberrations based on model latent embeddings. The ability to quickly, accurately, and scalably diagnose genetic abnormalities directly from metaphase images could transform karyotyping practice and improve patient outcomes. We will make code publicly available.

Sidharth Gupta, Konik Kothari, Valentin Debarnot et al.

We propose a differentiable imaging framework to address uncertainty in measurement coordinates such as sensor locations and projection angles. We formulate the problem as measurement interpolation at unknown nodes supervised through the forward operator. To solve it we apply implicit neural networks, also known as neural fields, which are naturally differentiable with respect to the input coordinates. We also develop differentiable spline interpolators which perform as well as neural networks, require less time to optimize and have well-understood properties. Differentiability is key as it allows us to jointly fit a measurement representation, optimize over the uncertain measurement coordinates, and perform image reconstruction which in turn ensures consistent calibration. We apply our approach to 2D and 3D computed tomography, and show that it produces improved reconstructions compared to baselines that do not account for the lack of calibration. The flexibility of the proposed framework makes it easy to extend to almost arbitrary imaging problems.

Konik Kothari, AmirEhsan Khorashadizadeh, Maarten de Hoop et al.

We propose injective generative models called Trumpets that generalize invertible normalizing flows. The proposed generators progressively increase dimension from a low-dimensional latent space. We demonstrate that Trumpets can be trained orders of magnitudes faster than standard flows while yielding samples of comparable or better quality. They retain many of the advantages of the standard flows such as training based on maximum likelihood and a fast, exact inverse of the generator. Since Trumpets are injective and have fast inverses, they can be effectively used for downstream Bayesian inference. To wit, we use Trumpet priors for maximum a posteriori estimation in the context of image reconstruction from compressive measurements, outperforming competitive baselines in terms of reconstruction quality and speed. We then propose an efficient method for posterior characterization and uncertainty quantification with Trumpets by taking advantage of the low-dimensional latent space.

Michael Puthawala, Konik Kothari, Matti Lassas et al.

Injectivity plays an important role in generative models where it enables inference; in inverse problems and compressed sensing with generative priors it is a precursor to well posedness. We establish sharp characterizations of injectivity of fully-connected and convolutional ReLU layers and networks. First, through a layerwise analysis, we show that an expansivity factor of two is necessary and sufficient for injectivity by constructing appropriate weight matrices. We show that global injectivity with iid Gaussian matrices, a commonly used tractable model, requires larger expansivity between 3.4 and 10.5. We also characterize the stability of inverting an injective network via worst-case Lipschitz constants of the inverse. We then use arguments from differential topology to study injectivity of deep networks and prove that any Lipschitz map can be approximated by an injective ReLU network. Finally, using an argument based on random projections, we show that an end-to-end -- rather than layerwise -- doubling of the dimension suffices for injectivity. Our results establish a theoretical basis for the study of nonlinear inverse and inference problems using neural networks.

Konik Kothari, Maarten de Hoop, Ivan Dokmanić

We propose a general physics-based deep learning architecture for wave-based imaging problems. A key difficulty in imaging problems with a varying background wave speed is that the medium "bends" the waves differently depending on their position and direction. This space-bending geometry makes the equivariance to translations of convolutional networks an undesired inductive bias. We build an interpretable neural architecture inspired by Fourier integral operators (FIOs) which approximate the wave physics. FIOs model a wide range of imaging modalities, from seismology and radar to Doppler and ultrasound. We focus on learning the geometry of wave propagation captured by FIOs, which is implicit in the data, via a loss based on optimal transport. The proposed FIONet performs significantly better than the usual baselines on a number of imaging inverse problems, especially in out-of-distribution tests.

Sidharth Gupta, Konik Kothari, Maarten V. de Hoop et al.

We propose a new learning-based approach to solve ill-posed inverse problems in imaging. We address the case where ground truth training samples are rare and the problem is severely ill-posed - both because of the underlying physics and because we can only get few measurements. This setting is common in geophysical imaging and remote sensing. We show that in this case the common approach to directly learn the mapping from the measured data to the reconstruction becomes unstable. Instead, we propose to first learn an ensemble of simpler mappings from the data to projections of the unknown image into random piecewise-constant subspaces. We then combine the projections to form a final reconstruction by solving a deconvolution-like problem. We show experimentally that the proposed method is more robust to measurement noise and corruptions not seen during training than a directly learned inverse.