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Bahareh Tolooshams

Publications and source records attributed to Bahareh Tolooshams.

At least 19 recordsLinked to original sources
arXiv2026

EquiReg: Equivariance Regularized Diffusion for Inverse Problems

Diffusion models represent the state-of-the-art for solving inverse problems such as image restoration tasks. Diffusion-based inverse solvers incorporate a likelihood term to guide prior sampling, generating data consistent with the posterior distribution. However, due to the intractability of the likelihood, most methods rely on isotropic Gaussian approximations, which can push estimates off the data manifold and produce inconsistent, poor reconstructions. We propose Equivariance Regularized (EquiReg) diffusion, a general plug-in framework that improves posterior sampling by penalizing trajectories that deviate from the data manifold. EquiReg formalizes manifold-preferential equivariant functions that exhibit low equivariance error for on-manifold samples and high error for off-manifold ones, thereby guiding sampling toward symmetry-preserving regions of the solution space. We highlight that such functions naturally emerge when training non-equivariant models with augmentation or on data with symmetries. EquiReg's largest gains are under reduced sampling and measurement consistency steps, where many methods suffer severe quality degradation. By regularizing trajectories toward the manifold, EquiReg implicitly accelerates convergence and enables high-quality reconstructions. EquiReg consistently improves performance in linear and nonlinear image restoration tasks and solving partial differential equations. Our code is available at https://github.com/Anima-Lab/EquiReg

cs.LG↗
arXiv2026

Beyond Uniform Local Isometry and Topology: FactoMap for Disentangled Representations

Many disentanglement methods represent generative factors using Euclidean product coordinates, although the underlying factor spaces may wrap, collapse, or have position-dependent geometry. We introduce factor-space structure, combining factor domains, generator-induced identifications, and position-dependent scales to distinguish topologically equivalent spaces with different factor geometries. We show that statistically independent factors need not be geometrically separable: hue and scale produce effects that grow at different rates, yielding anisotropy that no fixed rescaling removes. We propose the Factor-Space Topographic Map (FactoMap), which learns interpretable prototypes indexed by a factor-space lattice. Topographic learning transfers the lattice's periodicity, collapses, and non-uniform extent to the representation. Experiments show that matching this structure preserves factor continuity and enables disentanglement of the underlying factors.

cs.LG↗
arXiv2026

Mechanistic Interpretability with Sparse Autoencoder Neural Operators

We introduce sparse autoencoder neural operators (SAE-NOs), a new class of sparse autoencoders that operate in function spaces rather than fixed-dimensional Euclidean representations. We formalize the functional representation hypothesis, where data are explained through sparse compositions of structured functions. Unlike standard SAEs that represent concepts with scalar activations, SAE-NOs parameterize concepts as functions, enabling representations that capture not only a concept's presence, but also how and where it is expressed across the input domain. We achieve this through joint sparsity: concept sparsity selects active concepts, while domain sparsity governs where they are expressed. We instantiate this framework using Fourier neural operators (SAE-FNOs), parameterizing concepts as integral operators in the Fourier domain. This functional and spectral parameterization is particularly advantageous when data exhibit spatial structure across scales or when concepts are frequency-structured. We characterize SAE-FNO on vision data and demonstrate that it learns localized patterns, uses concepts more efficiently, and exhibits stable concept characteristics across sparsity levels. We further show that SAE-FNO adapts to changes in domain size and generalizes across discretizations, operating at resolutions beyond those seen during training, where standard SAEs fail. We also introduce lifting into SAEs and show theoretically and empirically that it acts as a preconditioner that accelerates optimization. Overall, our results show that moving from vector-valued to functional parameterizations, with concept and domain sparsity, extends SAEs from representing concept presence to modeling structured concept expression, highlighting the importance of parameterization.

cs.LG↗
arXiv2026

Discriminative reconstruction via simultaneous dense and sparse coding

Discriminative features extracted from the sparse coding model have been shown to perform well for classification. Recent deep learning architectures have further improved reconstruction in inverse problems by considering new dense priors learned from data. We propose a novel dense and sparse coding model that integrates both representation capability and discriminative features. The model studies the problem of recovering a dense vector $\mathbf{x}$ and a sparse vector $\mathbf{u}$ given measurements of the form $\mathbf{y} = \mathbf{A}\mathbf{x}+\mathbf{B}\mathbf{u}$. Our first analysis relies on a geometric condition, specifically the minimal angle between the spanning subspaces of matrices $\mathbf{A}$ and $\mathbf{B}$, which ensures a unique solution to the model. The second analysis shows that, under some conditions on $\mathbf{A}$ and $\mathbf{B}$, a convex program recovers the dense and sparse components. We validate the effectiveness of the model on simulated data and propose a dense and sparse autoencoder (DenSaE) tailored to learning the dictionaries from the dense and sparse model. We demonstrate that (i) DenSaE denoises natural images better than architectures derived from the sparse coding model ($\mathbf{B}\mathbf{u}$), (ii) in the presence of noise, training the biases in the latter amounts to implicitly learning the $\mathbf{A}\mathbf{x} + \mathbf{B}\mathbf{u}$ model, (iii) $\mathbf{A}$ and $\mathbf{B}$ capture low- and high-frequency contents, respectively, and (iv) compared to the sparse coding model, DenSaE offers a balance between discriminative power and representation.

cs.IT↗
arXiv2026

NOBLE -- Neural Operator with Biologically-informed Latent Embeddings to Capture Experimental Variability in Biological Neuron Models

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 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, 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. NOBLE enables the efficient generation of synthetic neurons that closely resemble experimental data and exhibit trial-to-trial variability, offering a $4200\times$ speedup over the numerical solver. NOBLE is the first scaled-up deep learning framework that validates its generalization with real experimental data. To this end, 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.

cs.LG↗
arXiv2026

Fourier Neural Operators for Learning Dynamics in Quantum Spin Systems

Fourier Neural Operators (FNOs) excel on tasks using functional data, such as those originating from partial differential equations. Such characteristics render them an effective approach for simulating the time evolution of quantum wavefunctions, which is a computationally challenging, yet coveted task for studying quantum systems. In this manuscript, we use FNOs to model the evolution of quantum spin systems, so chosen due to their representative quantum dynamics. We explore two distinct FNO architectures, examining their performance for learning and predicting time evolution on both random and low-energy input states. We find that standard neural networks in fixed dimensions, such as U-Net, exhibit limited ability to extrapolate beyond the training time interval, whereas FNOs reliably capture the underlying time-evolution operator, generalizing effectively to unseen times. Additionally, we apply FNOs to a compact set of Hamiltonian observables ($\sim\text{poly}(n)$) instead of the entire $2^n$ quantum wavefunction, which greatly reduces the size of our FNO inputs, outputs and model dimensions. Moreover, this Hamiltonian observable-based method demonstrates that FNOs can effectively distill information from high-dimensional spaces into lower-dimensional spaces. Using this approach, we perform numerical experiments on a 20-qubit system and extrapolate Hamiltonian observables to twice the training time with a relative error of $5.8\%$. Relative to numerical time-evolution methods, FNO achieves an inference speedup of approximately $10^{4}\times$ for 20-qubit systems. The extrapolation of Hamiltonian observables to times later than those used in training is of particular interest, as this stands to fundamentally increase the simulatability of quantum systems past both the coherence times of contemporary quantum architectures and the circuit-depths of tractable tensor networks.

quant-ph↗
arXiv2025

From Flat to Hierarchical: Extracting Sparse Representations with Matching Pursuit

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. 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 pursuits (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.

cs.LG↗
arXiv2025

Evaluating Sparse Autoencoders: From Shallow Design to Matching Pursuit

Sparse autoencoders (SAEs) have recently become central tools for interpretability, leveraging dictionary learning principles to extract sparse, interpretable features from neural representations whose underlying structure is typically unknown. This paper evaluates SAEs in a controlled setting using MNIST, which reveals that current shallow architectures implicitly rely on a quasi-orthogonality assumption that limits the ability to extract correlated features. To move beyond this, we compare them with an iterative SAE that unrolls Matching Pursuit (MP-SAE), enabling the residual-guided extraction of correlated features that arise in hierarchical settings such as handwritten digit generation while guaranteeing monotonic improvement of the reconstruction as more atoms are selected.

cs.LG↗
arXiv2025

A Unified Model for Compressed Sensing MRI Across Undersampling Patterns

Compressed Sensing MRI reconstructs images of the body's internal anatomy from undersampled measurements, thereby reducing scan time. 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$\times$ 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.

eess.IV↗
arXiv2025

Diffusion State-Guided Projected Gradient for Inverse Problems

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.

cs.LG↗
arXiv2025

Ultrasound Lung Aeration Map via Physics-Aware Neural Operators

Lung ultrasound is a growing modality in clinics for diagnosing and monitoring acute and chronic lung diseases due to its low cost and accessibility. Lung ultrasound works by emitting diagnostic pulses, receiving pressure waves and converting them into radio frequency (RF) data, which are then processed into B-mode images with beamformers for radiologists to interpret. However, unlike conventional ultrasound for soft tissue anatomical imaging, lung ultrasound interpretation is complicated by complex reverberations from the pleural interface caused by the inability of ultrasound to penetrate air. The indirect B-mode images make interpretation highly dependent on reader expertise, requiring years of training, which limits its widespread use despite its potential for high accuracy in skilled hands. To address these challenges and democratize ultrasound lung imaging as a reliable diagnostic tool, we propose LUNA, an AI model that directly reconstructs lung aeration maps from RF data, bypassing the need for traditional beamformers and indirect interpretation of B-mode images. LUNA uses a Fourier neural operator, which processes RF data efficiently in Fourier space, enabling accurate reconstruction of lung aeration maps. LUNA offers a quantitative, reader-independent alternative to traditional semi-quantitative lung ultrasound scoring methods. The development of LUNA involves synthetic and real data: We simulate synthetic data with an experimentally validated approach and scan ex vivo swine lungs as real data. Trained on abundant simulated data and fine-tuned with a small amount of real-world data, LUNA achieves robust performance, demonstrated by an aeration estimation error of 9% in ex-vivo lung scans. We demonstrate the potential of reconstructing lung aeration maps from RF data, providing a foundation for improving lung ultrasound reproducibility and diagnostic utility.

eess.IV↗
arXiv2023

Probabilistic Unrolling: Scalable, Inverse-Free Maximum Likelihood Estimation for Latent Gaussian Models

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.

cs.LG↗
arXiv2023

Unrolled Compressed Blind-Deconvolution

The problem of sparse multichannel blind deconvolution (S-MBD) arises frequently in many engineering applications such as radar/sonar/ultrasound imaging. To reduce its computational and implementation cost, we propose a compression method that enables blind recovery from much fewer measurements with respect to the full received signal in time. The proposed compression measures the signal through a filter followed by a subsampling, allowing for a significant reduction in implementation cost. We derive theoretical guarantees for the identifiability and recovery of a sparse filter from compressed measurements. Our results allow for the design of a wide class of compression filters. We, then, propose a data-driven unrolled learning framework to learn the compression filter and solve the S-MBD problem. The encoder is a recurrent inference network that maps compressed measurements into an estimate of sparse filters. We demonstrate that our unrolled learning method is more robust to choices of source shapes and has better recovery performance compared to optimization-based methods. Finally, in data-limited applications (fewshot learning), we highlight the superior generalization capability of unrolled learning compared to conventional deep learning.

eess.SP↗
arXiv2022

Stable and Interpretable Unrolled Dictionary Learning

The dictionary learning problem, representing data as a combination of a few atoms, has long stood as a popular method for learning representations in statistics and signal processing. The most popular dictionary learning algorithm alternates between sparse coding and dictionary update steps, and a rich literature has studied its theoretical convergence. The success of dictionary learning relies on access to a "good" initial estimate of the dictionary and the ability of the sparse coding step to provide an unbiased estimate of the code. The growing popularity of unrolled sparse coding networks has led to the empirical finding that backpropagation through such networks performs dictionary learning. We offer the theoretical analysis of these empirical results through PUDLE, a Provable Unrolled Dictionary LEarning method. We provide conditions on the network initialization and data distribution sufficient to recover and preserve the support of the latent code. Additionally, we address two challenges; first, the vanilla unrolled sparse coding computes a biased code estimate, and second, gradients during backpropagated learning can become unstable. We show approaches to reduce the bias of the code estimate in the forward pass, and that of the dictionary estimate in the backward pass. We propose strategies to resolve the learning instability by tuning network parameters and modifying the loss function. Overall, we highlight the impact of loss, unrolling, and backpropagation on convergence. We complement our findings through synthetic and image denoising experiments. Finally, we demonstrate PUDLE's interpretability, a driving factor in designing deep networks based on iterative optimizations, by building a mathematical relation between network weights, its output, and the training set.

cs.LG↗
arXiv2022

A Training Framework for Stereo-Aware Speech Enhancement using Deep Neural Networks

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 works have 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.

eess.AS↗
arXiv2022

On the convergence of group-sparse autoencoders

Recent approaches in the theoretical analysis of model-based deep learning architectures have studied the convergence of gradient descent in shallow ReLU networks that arise from generative models whose hidden layers are sparse. Motivated by the success of architectures that impose structured forms of sparsity, we introduce and study a group-sparse autoencoder that accounts for a variety of generative models, and utilizes a group-sparse ReLU activation function to force the non-zero units at a given layer to occur in blocks. For clustering models, inputs that result in the same group of active units belong to the same cluster. We proceed to analyze the gradient dynamics of a shallow instance of the proposed autoencoder, trained with data adhering to a group-sparse generative model. In this setting, we theoretically prove the convergence of the network parameters to a neighborhood of the generating matrix. We validate our model through numerical analysis and highlight the superior performance of networks with a group-sparse ReLU compared to networks that utilize traditional ReLUs, both in sparse coding and in parameter recovery tasks. We also provide real data experiments to corroborate the simulated results, and emphasize the clustering capabilities of structured sparsity models.

cs.LG↗
arXiv2021

Gaussian Process Convolutional Dictionary Learning

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.

cs.LG↗
arXiv2021

Unfolding Neural Networks for Compressive Multichannel Blind Deconvolution

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.

eess.SP↗