Resolution-Robust 3D MRI Reconstruction with 2D Diffusion Priors: Diverse-Resolution Training Outperforms Interpolation

Deep learning-based 3D imaging, in particular magnetic resonance imaging (MRI), is challenging because of limited availability of 3D training data. Therefore, 2D diffusion models trained on 2D slices are starting to be leveraged for 3D MRI reconstruction. However, as we show in this paper, existing methods pertain to a fixed voxel size, and performance degrades when the voxel size is varied, as it is often the case in clinical practice. In this paper, we propose and study several approaches for resolution-robust 3D MRI reconstruction with 2D diffusion priors. As a result of this investigation, we obtain a simple resolution-robust variational 3D reconstruction approach based on diffusion-guided regularization of randomly sampled 2D slices. This method provides competitive reconstruction quality compared to posterior sampling baselines. Towards resolving the sensitivity to resolution-shifts, we investigate state-of-the-art model-based approaches including Gaussian splatting, neural representations, and infinite-dimensional diffusion models, as well as a simple data-centric approach of training the diffusion model on several resolutions. Our experiments demonstrate that the model-based approaches fail to close the performance gap in 3D MRI. In contrast, the data-centric approach of training the diffusion model on various resolutions effectively provides a resolution-robust method without compromising accuracy.

Measuring Bias of Web-filtered Text Datasets and Bias Propagation Through Training

We investigate biases in pretraining datasets for large language models (LLMs) through dataset classification experiments. Building on prior work demonstrating the existence of biases in popular computer vision datasets, we analyze popular open-source pretraining datasets for LLMs derived from CommonCrawl including C4, RefinedWeb, DolmaCC, RedPajama-V2, FineWeb, and DCLM-Baseline. Despite those datasets being obtained with similar filtering and deduplication steps, neural networks can classify surprisingly well which dataset a single text sequence belongs to, significantly better than a human can. This indicates that popular pretraining datasets have their own unique biases or fingerprints. Those biases remain even when the text is rewritten with LLMs. Moreover, these biases propagate through training: Random sequences generated by models trained on those datasets can be classified well by a classifier trained on the original datasets.

MotionTTT: 2D Test-Time-Training Motion Estimation for 3D Motion Corrected MRI

A major challenge of the long measurement times in magnetic resonance imaging (MRI), an important medical imaging technology, is that patients may move during data acquisition. This leads to severe motion artifacts in the reconstructed images and volumes. In this paper, we propose a deep learning-based test-time-training method for accurate motion estimation. The key idea is that a neural network trained for motion-free reconstruction has a small loss if there is no motion, thus optimizing over motion parameters passed through the reconstruction network enables accurate estimation of motion. The estimated motion parameters enable to correct for the motion and to reconstruct accurate motion-corrected images. Our method uses 2D reconstruction networks to estimate rigid motion in 3D, and constitutes the first deep learning based method for 3D rigid motion estimation towards 3D-motion-corrected MRI. We show that our method can provably reconstruct motion parameters for a simple signal and neural network model. We demonstrate the effectiveness of our method for both retrospectively simulated motion and prospectively collected real motion-corrupted data.

DataComp-LM: In search of the next generation of training sets for language models

We introduce DataComp for Language Models (DCLM), a testbed for controlled dataset experiments with the goal of improving language models. As part of DCLM, we provide a standardized corpus of 240T tokens extracted from Common Crawl, effective pretraining recipes based on the OpenLM framework, and a broad suite of 53 downstream evaluations. Participants in the DCLM benchmark can experiment with data curation strategies such as deduplication, filtering, and data mixing at model scales ranging from 412M to 7B parameters. As a baseline for DCLM, we conduct extensive experiments and find that model-based filtering is key to assembling a high-quality training set. The resulting dataset, DCLM-Baseline enables training a 7B parameter language model from scratch to 64% 5-shot accuracy on MMLU with 2.6T training tokens. Compared to MAP-Neo, the previous state-of-the-art in open-data language models, DCLM-Baseline represents a 6.6 percentage point improvement on MMLU while being trained with 40% less compute. Our baseline model is also comparable to Mistral-7B-v0.3 and Llama 3 8B on MMLU (63% & 66%), and performs similarly on an average of 53 natural language understanding tasks while being trained with 6.6x less compute than Llama 3 8B. Our results highlight the importance of dataset design for training language models and offer a starting point for further research on data curation.

Deep Learning for Accelerated and Robust MRI Reconstruction: a Review

Deep learning (DL) has recently emerged as a pivotal technology for enhancing magnetic resonance imaging (MRI), a critical tool in diagnostic radiology. This review paper provides a comprehensive overview of recent advances in DL for MRI reconstruction. It focuses on DL approaches and architectures designed to improve image quality, accelerate scans, and address data-related challenges. These include end-to-end neural networks, pre-trained networks, generative models, and self-supervised methods. The paper also discusses the role of DL in optimizing acquisition protocols, enhancing robustness against distribution shifts, and tackling subtle bias. Drawing on the extensive literature and practical insights, it outlines current successes, limitations, and future directions for leveraging DL in MRI reconstruction, while emphasizing the potential of DL to significantly impact clinical imaging practices.

GAMA-IR: Global Additive Multidimensional Averaging for Fast Image Restoration

Deep learning-based methods have shown remarkable success for various image restoration tasks such as denoising and deblurring. The current state-of-the-art networks are relatively deep and utilize (variants of) self attention mechanisms. Those networks are significantly slower than shallow convolutional networks, which however perform worse. In this paper, we introduce an image restoration network that is both fast and yields excellent image quality. The network is designed to minimize the latency and memory consumption when executed on a standard GPU, while maintaining state-of-the-art performance. The network is a simple shallow network with an efficient block that implements global additive multidimensional averaging operations. This block can capture global information and enable a large receptive field even when used in shallow networks with minimal computational overhead. Through extensive experiments and evaluations on diverse tasks, we demonstrate that our network achieves comparable or even superior results to existing state-of-the-art image restoration networks with less latency. For instance, we exceed the state-of-the-art result on real-world SIDD denoising by 0.11dB, while being 2 to 10 times faster.

Language models scale reliably with over-training and on downstream tasks

Scaling laws are useful guides for developing language models, but there are still gaps between current scaling studies and how language models are ultimately trained and evaluated. For instance, scaling is usually studied in the compute-optimal training regime (i.e., "Chinchilla optimal" regime); however, in practice, models are often over-trained to reduce inference costs. Moreover, scaling laws mostly predict loss on next-token prediction, but ultimately models are compared based on downstream task performance. In this paper, we address both shortcomings. To do so, we create a testbed of 104 models with 0.011B to 6.9B parameters trained with various numbers of tokens on three data distributions. First, we investigate scaling in the over-trained regime. We fit scaling laws that extrapolate in both the number of model parameters and the ratio of training tokens to parameters. This enables us to predict the validation loss of a 1.4B parameter, 900B token run (i.e., 32$\times$ over-trained) and a 6.9B parameter, 138B token run$\unicode{x2014}$each from experiments that take 300$\times$ less compute. Second, we relate the perplexity of a language model to its downstream task performance via a power law. We use this law to predict top-1 error averaged over downstream tasks for the two aforementioned models using experiments that take 20$\times$ less compute. Our experiments are available at https://github.com/mlfoundations/scaling.

Robustness of Deep Learning for Accelerated MRI: Benefits of Diverse Training Data

Deep learning based methods for image reconstruction are state-of-the-art for a variety of imaging tasks. However, neural networks often perform worse if the training data differs significantly from the data they are applied to. For example, a network trained for accelerated magnetic resonance imaging (MRI) on one scanner performs worse on another scanner. In this work, we investigate the impact of the training data on the model's performance and robustness for accelerated MRI. We find that models trained on the combination of various data distributions, such as those obtained from different MRI scanners and anatomies, exhibit robustness equal or superior to models trained on the best single distribution for a specific target distribution. Thus training on diverse data tends to improve robustness. Furthermore, training on diverse data does not compromise in-distribution performance, i.e., a model trained on diverse data yields in-distribution performance at least as good as models trained on the more narrow individual distributions. Our results suggest that training a model for imaging on a variety of distributions tends to yield a more effective and robust model than maintaining separate models for individual distributions.

A Deep Learning Method for Simultaneous Denoising and Missing Wedge Reconstruction in Cryogenic Electron Tomography

Cryogenic electron tomography (cryo-ET) is a technique for imaging biological samples such as viruses, cells, and proteins in 3D. A microscope collects a series of 2D projections of the sample, and the goal is to reconstruct the 3D density of the sample called the tomogram. This is difficult as the 2D projections have a missing wedge of information and are noisy. Tomograms reconstructed with conventional methods, such as filtered back-projection, suffer from the noise, and from artifacts and anisotropic resolution due to the missing wedge of information. To improve the visual quality and resolution of such tomograms, we propose a deep-learning approach for simultaneous denoising and missing wedge reconstruction called DeepDeWedge. DeepDeWedge is based on fitting a neural network to the 2D projections with a self-supervised loss inspired by noise2noise-like methods. The algorithm requires no training or ground truth data. Experiments on synthetic and real cryo-ET data show that DeepDeWedge achieves competitive performance for deep learning-based denoising and missing wedge reconstruction of cryo-ET tomograms.

Approximating Positive Homogeneous Functions with Scale Invariant Neural Networks

We investigate to what extent it is possible to solve linear inverse problems with $ReLu$ networks. Due to the scaling invariance arising from the linearity, an optimal reconstruction function $f$ for such a problem is positive homogeneous, i.e., satisfies $f(\lambda x) = \lambda f(x)$ for all non-negative $\lambda$. In a $ReLu$ network, this condition translates to considering networks without bias terms. We first consider recovery of sparse vectors from few linear measurements. We prove that $ReLu$- networks with only one hidden layer cannot even recover $1$-sparse vectors, not even approximately, and regardless of the width of the network. However, with two hidden layers, approximate recovery with arbitrary precision and arbitrary sparsity level $s$ is possible in a stable way. We then extend our results to a wider class of recovery problems including low-rank matrix recovery and phase retrieval. Furthermore, we also consider the approximation of general positive homogeneous functions with neural networks. Extending previous work, we establish new results explaining under which conditions such functions can be approximated with neural networks. Our results also shed some light on the seeming contradiction between previous works showing that neural networks for inverse problems typically have very large Lipschitz constants, but still perform very well also for adversarial noise. Namely, the error bounds in our expressivity results include a combination of a small constant term and a term that is linear in the noise level, indicating that robustness issues may occur only for very small noise levels.