Compressed Sensing MRI reconstructs images of the body’s internal anatomy from undersampled measurements, thereby reducing scan time—the time subjects need to remain still. Recently, deep learning has shown great potential for reconstructing high-fidelity images from highly undersampled measurements. However, one needs to train multiple models for different undersampling patterns and desired output image resolutions, since most networks operate on a fixed discretization. Such approaches are highly impractical in clinical settings, where undersampling patterns and image resolutions are frequently changed to accommodate different real-time imaging and diagnostic requirements.We propose a unified MRI reconstruction model robust to various measurement undersampling patterns and image resolutions. Our approach uses neural operators—a discretization-agnostic architecture applied in both image and measurement spaces—to capture local and global features. Empirically, our model improves SSIM by 11% and PSNR by 4 dB over a state-of-the-art CNN (End-to-End VarNet), with 600× faster inference than diffusion methods. The resolution-agnostic design also enables zero-shot super-resolution and extended field-of-view reconstruction, offering a versatile and efficient solution for clinical MR imaging. Our unified model offers a versatile solution for MRI, adapting seamlessly to various measurement undersampling and imaging resolutions, making it highly effective for flexible and reliable clinical imaging. Our code is available at https://armeet.ca/nomri.

Recent advancements in diffusion models have been effective in learning data priors for solving inverse problems. They leverage diffusion sampling steps for inducing a data prior while using a measurement guidance gradient at each step to impose data consistency. For general inverse problems, approximations are needed when an unconditionally trained diffusion model is used since the measurement likelihood is intractable, leading to inaccurate posterior sampling. In other words, due to their approximations, these methods fail to preserve the generation process on the data manifold defined by the diffusion prior, leading to artifacts in applications such as image restoration. To enhance the performance and robustness of diffusion models in solving inverse problems, we propose Diffusion State-Guided Projected Gradient (DiffStateGrad), which projects the measurement gradient onto a subspace that is a low-rank approximation of an intermediate state of the diffusion process. DiffStateGrad, as a module, can be added to a wide range of diffusion-based inverse solvers to improve the preservation of the diffusion process on the prior manifold and filter out artifact-inducing components. We highlight that DiffStateGrad improves the robustness of diffusion models in terms of the choice of measurement guidance step size and noise while improving the worst-case performance. Finally, we demonstrate that DiffStateGrad improves upon the state-of-the-art on linear and nonlinear image restoration inverse problems. Our code is available at https://github.com/Anima-Lab/DiffStateGrad.

Motivated by the hypothesis that neural network representations encode abstract, interpretable features as linearly accessible, approximately orthogonal directions, sparse autoencoders (SAEs) have become a popular tool in interpretability literature. However, recent work has demonstrated phenomenology of model representations that lies outside the scope of this hypothesis, showing signatures of hierarchical, nonlinear, and multi-dimensional features. This raises the question: do SAEs represent features that possess structure at odds with their motivating hypothesis? If not, does avoiding this mismatch help identify said features and gain further insights into neural network representations? To answer these questions, we take a construction-based approach and re-contextualize the popular matching pursuit (MP) algorithm from sparse coding to design MP-SAE—an SAE that unrolls its encoder into a sequence of residual-guided steps, allowing it to capture hierarchical and nonlinearly accessible features. Comparing this architecture with existing SAEs on a mixture of synthetic and natural data settings, we show: (i) hierarchical concepts induce conditionally orthogonal features, which existing SAEs are unable to faithfully capture, and (ii) the nonlinear encoding step of MP-SAE recovers highly meaningful features, helping us unravel shared structure in the seemingly dichotomous representation spaces of different modalities in a vision-language model, hence demonstrating the assumption that useful features are solely linearly accessible is insufficient. We also show that the sequential encoder principle of MP-SAE affords an additional benefit of adaptive sparsity at inference time, which may be of independent interest. Overall, we argue our results provide credence to the idea that interpretability should begin with the phenomenology of representations, with methods emerging from assumptions that fit it.

Characterizing the cellular properties of neurons is fundamental to understanding their function in the brain. In this quest, the generation of bio-realistic models is central towards integrating multimodal cellular data sets and establishing causal relationships. However, current modeling approaches remain constrained by the limited availability and intrinsic variability of experimental neuronal data. The deterministic formalism of bio-realistic models currently precludes accounting for the natural variability observed experimentally. While deep learning is becoming increasingly relevant in this space, it fails to capture the full biophysical complexity of neurons, their nonlinear voltage dynamics, and variability. To address these shortcomings, we introduce $\texttt{NOBLE}$, a neural operator framework that learns a mapping from a continuous frequency-modulated embedding of interpretable neuron features to the somatic voltage response induced by current injection. Trained on synthetic data generated from bio-realistic neuron models, $\texttt{NOBLE}$ predicts distributions of neural dynamics accounting for the intrinsic experimental variability. Unlike conventional bio-realistic neuron models, interpolating within the embedding space offers models whose dynamics are consistent with experimentally observed responses. $\texttt{NOBLE}$ enables the efficient generation of synthetic neurons that closely resemble experimental data and exhibit trial-to-trial variability, offering a $4200$× speedup over the numerical solver. $\texttt{NOBLE}$ is the first scaled-up deep learning framework that validates its generalization with real experimental data. To this end, $\texttt{NOBLE}$ captures fundamental neural properties in a unique and emergent manner that opens the door to a better understanding of cellular composition and computations, neuromorphic architectures, large-scale brain circuits, and general neuroAI applications.

Latent Gaussian models have a rich history in statistics and machine learning, with applications ranging from factor analysis to compressed sensing to time series analysis. The classical method for maximizing the likelihood of these models is the expectation-maximization (EM) algorithm. For problems with high-dimensional latent variables and large datasets, EM scales poorly because it needs to invert as many large covariance matrices as the number of data points. We introduce probabilistic unrolling, a method that combines Monte Carlo sampling with iterative linear solvers to circumvent matrix inversion. Our theoretical analyses reveal that unrolling and backpropagation through the iterations of the solver can accelerate gradient estimation for maximum likelihood estimation. In experiments on simulated and real data, we demonstrate that probabilistic unrolling learns latent Gaussian models up to an order of magnitude faster than gradient EM, with minimal losses in model performance.

Deep learning-based speech enhancement has shown unprecedented performance in recent years. The most popular mono speech enhancement frameworks are end-to-end networks mapping the noisy mixture into an estimate of the clean speech. With growing computational power and availability of multichannel microphone recordings, prior work has aimed to incorporate spatial statistics along with spectral information to boost up performance. Despite an improvement in enhancement performance of mono output, the spatial image preservation and subjective evaluations have not gained much attention in the literature. This paper proposes a novel stereo-aware framework for speech enhancement, i.e., a training loss for deep learning-based speech enhancement to preserve the spatial image while enhancing the stereo mixture. The proposed framework is model independent, hence it can be applied to any deep learning based architecture. We provide an extensive objective and subjective evaluation of the trained models through a listening test. We show that by regularizing for an image preservation loss, the overall performance is improved, and the stereo aspect of the speech is better preserved.

Convolutional dictionary learning (CDL), the problem of estimating shift-invariant templates from data, is typically conducted in the absence of a prior/structure on the templates. In data-scarce or low signal-to-noise ratio (SNR) regimes, learned templates overfit the data and lack smoothness, which can affect the predictive performance of downstream tasks. To address this limitation, we propose GPCDL, a convolutional dictionary learning framework that enforces priors on templates using Gaussian Processes (GPs). With the focus on smoothness, we show theoretically that imposing a GP prior is equivalent to Wiener filtering the learned templates, thereby suppressing high-frequency components and promoting smoothness. We show that the algorithm is a simple extension of the classical iteratively reweighted least squares algorithm, independent of the choice of GP kernels. This property allows one to experiment flexibly with different smoothness assumptions. Through simulation, we show that GPCDL learns smooth dictionaries with better accuracy than the unregularized alternative across a range of SNRs. Through an application to neural spiking data, we show that GPCDL learns a more accurate and visually-interpretable smooth dictionary, leading to superior predictive performance compared to non-regularized CDL, as well as parametric alternatives.

We propose a learned-structured unfolding neural network for the problem of compressive sparse multichannel blind-deconvolution. In this problem, each channel’s measurements are given as convolution of a common source signal and sparse filter. Unlike prior works where the compression is achieved either through random projections or by applying a fixed structured compression matrix, this paper proposes to learn the compression matrix from data. Given the full measurements, the proposed network is trained in an unsupervised fashion to learn the source and estimate sparse filters. Then, given the estimated source, we learn a structured compression operator while optimizing for signal reconstruction and sparse filter recovery. The efficient structure of the compression allows its practical hardware implementation. The proposed neural network is an autoencoder constructed based on an unfolding approach: upon training, the encoder maps the compressed measurements into an estimate of sparse filters using the compression operator and the source, and the linear convolutional decoder reconstructs the full measurements. We demonstrate that our method is superior to classical structured compressive sparse multichannel blind-deconvolution methods in terms of accuracy and speed of sparse filter recovery.

We introduce a neural-network architecture, termed the constrained recurrent sparse autoencoder (CRsAE), that solves convolutional dictionary learning problems, thus establishing a link between dictionary learning and neural networks. Specifically, we leverage the interpretation of the alternating-minimization algorithm for dictionary learning as an approximate expectation-maximization algorithm to develop autoencoders that enable the simultaneous training of the dictionary and regularization parameter (ReLU bias). The forward pass of the encoder approximates the sufficient statistics of the E-step as the solution to a sparse coding problem, using an iterative proximal gradient algorithm called FISTA. The encoder can be interpreted either as a recurrent neural network or as a deep residual network, with two-sided ReLU nonlinearities in both cases. The M-step is implemented via a two-stage backpropagation. The first stage relies on a linear decoder applied to the encoder and a norm-squared loss. It parallels the dictionary update step in dictionary learning. The second stage updates the regularization parameter by applying a loss function to the encoder that includes a prior on the parameter motivated by Bayesian statistics. We demonstrate in an image-denoising task that CRsAE learns Gabor-like filters and that the EM-inspired approach for learning biases is superior to the conventional approach. In an application to recordings of electrical activity from the brain, we demonstrate that CRsAE learns realistic spike templates and speeds up the process of identifying spike times by 900× compared with algorithms based on convex optimization.

Supervised deep learning has gained significant attention for speech enhancement recently. The state-of-the-art deep learning methods perform the task by learning a ratio/binary mask that is applied to the mixture in the time-frequency domain to produce the clean speech. Despite the great performance in the single-channel setting, these frameworks lag in performance in the multichannel setting as the majority of these methods a) fail to exploit the available spatial information fully, and b) still treat the deep architecture as a black box which may not be well-suited for multichannel audio processing. This paper addresses these drawbacks, a) by utilizing complex ratio masking instead of masking on the magnitude of the spectrogram, and more importantly, b) by introducing a channel-attention mechanism inside the deep architecture to mimic beamforming. We propose Channel-Attention Dense U-Net, in which we apply the channel-attention unit recursively on feature maps at every layer of the network, enabling the network to perform non-linear beamforming. We demonstrate the superior performance of the network against the state-of-the-art approaches on the CHiME-3 dataset.

We introduce a class of auto-encoder neural networks tailored to data from the natural exponential family (e.g., count data). The architectures are inspired by the problem of learning the filters in a convolutional generative model with sparsity constraints, often referred to as convolutional dictionary learning (CDL). Our work is the first to combine ideas from convolutional generative models and deep learning for data that are naturally modeled with a non-Gaussian distribution (e.g., binomial and Poisson). This perspective provides us with a scalable and flexible framework that can be re-purposed for a wide range of tasks and assumptions on the generative model. Specifically, the iterative optimization procedure for solving CDL, an unsupervised task, is mapped to an unfolded and constrained neural network, with iterative adjustments to the inputs to account for the generative distribution. We also show that the framework can easily be extended for discriminative training, appropriate for a supervised task. We 1) demonstrate that fitting the generative model to learn, in an unsupervised fashion, the latent stimulus that underlies neural spiking data leads to better goodness-of-fit compared to other baselines, 2) show competitive performance compared to state-of-the-art algorithms for supervised Poisson image denoising, with significantly fewer parameters, and 3) characterize the gradient dynamics of the shallow binomial auto-encoder.