Sean I. Young

Sean I. Young, Yaël Balbastre, Adrian V. Dalca et al. · harvard

In recent years, learning-based image registration methods have gradually moved away from direct supervision with target warps to instead use self-supervision, with excellent results in several registration benchmarks. These approaches utilize a loss function that penalizes the intensity differences between the fixed and moving images, along with a suitable regularizer on the deformation. In this paper, we argue that the relative failure of supervised registration approaches can in part be blamed on the use of regular U-Nets, which are jointly tasked with feature extraction, feature matching, and estimation of deformation. We introduce one simple but crucial modification to the U-Net that disentangles feature extraction and matching from deformation prediction, allowing the U-Net to warp the features, across levels, as the deformation field is evolved. With this modification, direct supervision using target warps begins to outperform self-supervision approaches that require segmentations, presenting new directions for registration when images do not have segmentations. We hope that our findings in this preliminary workshop paper will re-ignite research interest in supervised image registration techniques. Our code is publicly available from https://github.com/balbasty/superwarp.

S. Mazdak Abulnaga, Sean I. Young, Katherine Hobgood et al. · mit

Blood oxygen level dependent (BOLD) MRI with maternal hyperoxia can assess oxygen transport within the placenta and has emerged as a promising tool to study placental function. Measuring signal changes over time requires segmenting the placenta in each volume of the time series. Due to the large number of volumes in the BOLD time series, existing studies rely on registration to map all volumes to a manually segmented template. As the placenta can undergo large deformation due to fetal motion, maternal motion, and contractions, this approach often results in a large number of discarded volumes, where the registration approach fails. In this work, we propose a machine learning model based on a U-Net neural network architecture to automatically segment the placenta in BOLD MRI and apply it to segmenting each volume in a time series. We use a boundary-weighted loss function to accurately capture the placental shape. Our model is trained and tested on a cohort of 91 subjects containing healthy fetuses, fetuses with fetal growth restriction, and mothers with high BMI. We achieve a Dice score of 0.83+/-0.04 when matching with ground truth labels and our model performs reliably in segmenting volumes in both normoxic and hyperoxic points in the BOLD time series. Our code and trained model are available at https://github.com/mabulnaga/automatic-placenta-segmentation.

Alan Q. Wang, Batuhan K. Karaman, Heejong Kim et al.

Interpretability for machine learning models in medical imaging (MLMI) is an important direction of research. However, there is a general sense of murkiness in what interpretability means. Why does the need for interpretability in MLMI arise? What goals does one actually seek to address when interpretability is needed? To answer these questions, we identify a need to formalize the goals and elements of interpretability in MLMI. By reasoning about real-world tasks and goals common in both medical image analysis and its intersection with machine learning, we identify five core elements of interpretability: localization, visual recognizability, physical attribution, model transparency, and actionability. From this, we arrive at a framework for interpretability in MLMI, which serves as a step-by-step guide to approaching interpretability in this context. Overall, this paper formalizes interpretability needs in the context of medical imaging, and our applied perspective clarifies concrete MLMI-specific goals and considerations in order to guide method design and improve real-world usage. Our goal is to provide practical and didactic information for model designers and practitioners, inspire developers of models in the medical imaging field to reason more deeply about what interpretability is achieving, and suggest future directions of interpretability research.

Matthew G. French, Gonzalo D. Maso Talou, Thiranja P. Babarenda Gamage et al. · harvard

In breast surgical planning, accurate registration of MR images across patient positions has the potential to improve the localisation of tumours during breast cancer treatment. While learning-based registration methods have recently become the state-of-the-art approach for most medical image registration tasks, these methods have yet to make inroads into breast image registration due to certain difficulties-the lack of rich texture information in breast MR images and the need for the deformations to be diffeomophic. In this work, we propose learning strategies for breast MR image registration that are amenable to diffeomorphic constraints, together with early experimental results from in-silico and in-vivo experiments. One key contribution of this work is a registration network which produces superior registration outcomes for breast images in addition to providing diffeomorphic guarantees.

Margherita Firenze, Sean I. Young, Clinton J. Wang et al.

Fully convolutional networks have become the backbone of modern medical imaging due to their ability to learn multi-scale representations and perform end-to-end inference. Yet their potential for slice-to-volume reconstruction (SVR), the task of jointly estimating 3D anatomy and slice poses from misaligned 2D acquisitions, remains underexplored. We introduce a fast convolutional framework that fuses multiple orthogonal 2D slice stacks to recover coherent 3D structure and refines slice alignment through lightweight model-based optimization. Applied to fetal brain MRI, our approach reconstructs high-quality 3D volumes in under 10s, with 1s slice registration and accuracy on par with state-of-the-art iterative SVR pipelines, offering more than speedup. The framework uses non-rigid displacement fields to represent transformations, generalizing to other SVR problems like fetal body and placental MRI. Additionally, the fast inference time paves the way for real-time, scanner-side volumetric feedback during MRI acquisition.

Matthew A. Chan, Sean I. Young, Christopher A. Metzler

Many imaging inverse problems$\unicode{x2014}$such as image-dependent in-painting and dehazing$\unicode{x2014}$are challenging because their forward models are unknown or depend on unknown latent parameters. While one can solve such problems by training a neural network with vast quantities of paired training data, such paired training data is often unavailable. In this paper, we propose a generalized framework for training image reconstruction networks when paired training data is scarce. In particular, we demonstrate the ability of image denoising algorithms and, by extension, denoising diffusion models to supervise network training in the absence of paired training data.

Sean I. Young

In recent years, compression of large language models (LLMs) has emerged as an important problem to enable language model deployment on resource-constrained devices, reduce computational costs, and mitigate the environmental footprint of large-scale AI infrastructure. In this paper, we lay down the foundation for LLM quantization from a convex optimization perspective and propose a quantization technique that builds on this foundation for optimum quantization outcomes. Our quantization framework, CVXQ, scales to models containing hundreds of billions of weight parameters and provides users with the flexibility to compress models to any specified model size, post-training. A reference implementation of CVXQ can be obtained from github.com/seannz/cvxq.

Sean I. Young, Yaël Balbastre, Bruce Fischl et al. · harvard

In magnetic resonance imaging (MRI), slice-to-volume reconstruction (SVR) refers to computational reconstruction of an unknown 3D magnetic resonance volume from stacks of 2D slices corrupted by motion. While promising, current SVR methods require multiple slice stacks for accurate 3D reconstruction, leading to long scans and limiting their use in time-sensitive applications such as fetal fMRI. Here, we propose a SVR method that overcomes the shortcomings of previous work and produces state-of-the-art reconstructions in the presence of extreme inter-slice motion. Inspired by the recent success of single-view depth estimation methods, we formulate SVR as a single-stack motion estimation task and train a fully convolutional network to predict a motion stack for a given slice stack, producing a 3D reconstruction as a byproduct of the predicted motion. Extensive experiments on the SVR of adult and fetal brains demonstrate that our fully convolutional method is twice as accurate as previous SVR methods. Our code is available at github.com/seannz/svr.

S. Mazdak Abulnaga, Neel Dey, Sean I. Young et al. · mit

Blood oxygen level dependent (BOLD) MRI time series with maternal hyperoxia can assess placental oxygenation and function. Measuring precise BOLD changes in the placenta requires accurate temporal placental segmentation and is confounded by fetal and maternal motion, contractions, and hyperoxia-induced intensity changes. Current BOLD placenta segmentation methods warp a manually annotated subject-specific template to the entire time series. However, as the placenta is a thin, elongated, and highly non-rigid organ subject to large deformations and obfuscated edges, existing work cannot accurately segment the placental shape, especially near boundaries. In this work, we propose a machine learning segmentation framework for placental BOLD MRI and apply it to segmenting each volume in a time series. We use a placental-boundary weighted loss formulation and perform a comprehensive evaluation across several popular segmentation objectives. Our model is trained and tested on a cohort of 91 subjects containing healthy fetuses, fetuses with fetal growth restriction, and mothers with high BMI. Biomedically, our model performs reliably in segmenting volumes in both normoxic and hyperoxic points in the BOLD time series. We further find that boundary-weighting increases placental segmentation performance by 8.3% and 6.0% Dice coefficient for the cross-entropy and signed distance transform objectives, respectively. Our code and trained model is available at https://github.com/mabulnaga/automatic-placenta-segmentation.

Lin Tian, Sean I. Young, Jonathan Williams Ramirez et al. · harvard

Correlation of neuropathology with MRI has the potential to transfer microscopic signatures of pathology to invivo scans. Recently, a classical registration method has been proposed, to build these correlations from 3D reconstructed stacks of dissection photographs, which are routinely taken at brain banks. These photographs bypass the need for exvivo MRI, which is not widely accessible. However, this method requires a full stack of brain slabs and a reference mask (e.g., acquired with a surface scanner), which severely limits the applicability of the technique. Here we propose RefFree, a dissection photograph reconstruction method without external reference. RefFree is a learning approach that estimates the 3D coordinates in the atlas space for every pixel in every photograph; simple least-squares fitting can then be used to compute the 3D reconstruction. As a by-product, RefFree also produces an atlas-based segmentation of the reconstructed stack. RefFree is trained on synthetic photographs generated from digitally sliced 3D MRI data, with randomized appearance for enhanced generalization ability. Experiments on simulated and real data show that RefFree achieves performance comparable to the baseline method without an explicit reference while also enabling reconstruction of partial stacks. Our code is available at https://github.com/lintian-a/reffree.

Pablo Laso, Stefano Cerri, Annabel Sorby-Adams et al.

Brain atrophy and white matter hyperintensity (WMH) are critical neuroimaging features for ascertaining brain injury in cerebrovascular disease and multiple sclerosis. Automated segmentation and quantification is desirable but existing methods require high-resolution MRI with good signal-to-noise ratio (SNR). This precludes application to clinical and low-field portable MRI (pMRI) scans, thus hampering large-scale tracking of atrophy and WMH progression, especially in underserved areas where pMRI has huge potential. Here we present a method that segments white matter hyperintensity and 36 brain regions from scans of any resolution and contrast (including pMRI) without retraining. We show results on eight public datasets and on a private dataset with paired high- and low-field scans (3T and 64mT), where we attain strong correlation between the WMH ($ρ$=.85) and hippocampal volumes (r=.89) estimated at both fields. Our method is publicly available as part of FreeSurfer, at: http://surfer.nmr.mgh.harvard.edu/fswiki/WMH-SynthSeg.

Sean I. Young

In recent years, the compression of large language models (LLMs) has emerged as a key problem in facilitating LLM deployment on resource-limited devices, reducing compute costs, and mitigating the environmental footprint due to large-scale AI infrastructure. Here, we establish the foundations of LLM quantization from a rate-distortion theory perspective and propose a quantization technique based on simple rate-distortion optimization. Our technique scales to models containing hundreds of billions of weight parameters and offers users the flexibility to compress models, post-training, to a model size or accuracy specified by the user.

Sean I. Young, Adrian V. Dalca, Enzo Ferrante et al.

Learning-based image reconstruction models, such as those based on the U-Net, require a large set of labeled images if good generalization is to be guaranteed. In some imaging domains, however, labeled data with pixel- or voxel-level label accuracy are scarce due to the cost of acquiring them. This problem is exacerbated further in domains like medical imaging, where there is no single ground truth label, resulting in large amounts of repeat variability in the labels. Therefore, training reconstruction networks to generalize better by learning from both labeled and unlabeled examples (called semi-supervised learning) is problem of practical and theoretical interest. However, traditional semi-supervised learning methods for image reconstruction often necessitate handcrafting a differentiable regularizer specific to some given imaging problem, which can be extremely time-consuming. In this work, we propose "supervision by denoising" (SUD), a framework that enables us to supervise reconstruction models using their own denoised output as soft labels. SUD unifies stochastic averaging and spatial denoising techniques under a spatio-temporal denoising framework and alternates denoising and model weight update steps in an optimization framework for semi-supervision. As example applications, we apply SUD to two problems arising from biomedical imaging -- anatomical brain reconstruction (3D) and cortical parcellation (2D) -- to demonstrate a significant improvement in the image reconstructions over supervised-only and stochastic averaging baselines.

Sean I. Young, Wang Zhe, David Taubman et al.

In this paper, we compress convolutional neural network (CNN) weights post-training via transform quantization. Previous CNN quantization techniques tend to ignore the joint statistics of weights and activations, producing sub-optimal CNN performance at a given quantization bit-rate, or consider their joint statistics during training only and do not facilitate efficient compression of already trained CNN models. We optimally transform (decorrelate) and quantize the weights post-training using a rate-distortion framework to improve compression at any given quantization bit-rate. Transform quantization unifies quantization and dimensionality reduction (decorrelation) techniques in a single framework to facilitate low bit-rate compression of CNNs and efficient inference in the transform domain. We first introduce a theory of rate and distortion for CNN quantization, and pose optimum quantization as a rate-distortion optimization problem. We then show that this problem can be solved using optimal bit-depth allocation following decorrelation by the optimal End-to-end Learned Transform (ELT) we derive in this paper. Experiments demonstrate that transform quantization advances the state of the art in CNN compression in both retrained and non-retrained quantization scenarios. In particular, we find that transform quantization with retraining is able to compress CNN models such as AlexNet, ResNet and DenseNet to very low bit-rates (1-2 bits).