Consistency Regularization Improves Placenta Segmentation in Fetal EPI MRI Time Series

The placenta plays a crucial role in fetal development. Automated 3D placenta segmentation from fetal EPI MRI holds promise for advancing prenatal care. This paper proposes an effective semi-supervised learning method for improving placenta segmentation in fetal EPI MRI time series. We employ consistency regularization loss that promotes consistency under spatial transformation of the same image and temporal consistency across nearby images in a time series. The experimental results show that the method improves the overall segmentation accuracy and provides better performance for outliers and hard samples. The evaluation also indicates that our method improves the temporal coherency of the prediction, which could lead to more accurate computation of temporal placental biomarkers. This work contributes to the study of the placenta and prenatal clinical decision-making. Code is available at https://github.com/firstmover/cr-seg.

Interpolating between Images with Diffusion Models

One little-explored frontier of image generation and editing is the task of interpolating between two input images, a feature missing from all currently deployed image generation pipelines. We argue that such a feature can expand the creative applications of such models, and propose a method for zero-shot interpolation using latent diffusion models. We apply interpolation in the latent space at a sequence of decreasing noise levels, then perform denoising conditioned on interpolated text embeddings derived from textual inversion and (optionally) subject poses. For greater consistency, or to specify additional criteria, we can generate several candidates and use CLIP to select the highest quality image. We obtain convincing interpolations across diverse subject poses, image styles, and image content, and show that standard quantitative metrics such as FID are insufficient to measure the quality of an interpolation. Code and data are available at https://clintonjwang.github.io/interpolation.

Boundary-weighted logit consistency improves calibration of segmentation networks

Neural network prediction probabilities and accuracy are often only weakly-correlated. Inherent label ambiguity in training data for image segmentation aggravates such miscalibration. We show that logit consistency across stochastic transformations acts as a spatially varying regularizer that prevents overconfident predictions at pixels with ambiguous labels. Our boundary-weighted extension of this regularizer provides state-of-the-art calibration for prostate and heart MRI segmentation.

AnyStar: Domain randomized universal star-convex 3D instance segmentation

Star-convex shapes arise across bio-microscopy and radiology in the form of nuclei, nodules, metastases, and other units. Existing instance segmentation networks for such structures train on densely labeled instances for each dataset, which requires substantial and often impractical manual annotation effort. Further, significant reengineering or finetuning is needed when presented with new datasets and imaging modalities due to changes in contrast, shape, orientation, resolution, and density. We present AnyStar, a domain-randomized generative model that simulates synthetic training data of blob-like objects with randomized appearance, environments, and imaging physics to train general-purpose star-convex instance segmentation networks. As a result, networks trained using our generative model do not require annotated images from unseen datasets. A single network trained on our synthesized data accurately 3D segments C. elegans and P. dumerilii nuclei in fluorescence microscopy, mouse cortical nuclei in micro-CT, zebrafish brain nuclei in EM, and placental cotyledons in human fetal MRI, all without any retraining, finetuning, transfer learning, or domain adaptation. Code is available at https://github.com/neel-dey/AnyStar.

Domain-agnostic segmentation of thalamic nuclei from joint structural and diffusion MRI

The human thalamus is a highly connected subcortical grey-matter structure within the brain. It comprises dozens of nuclei with different function and connectivity, which are affected differently by disease. For this reason, there is growing interest in studying the thalamic nuclei in vivo with MRI. Tools are available to segment the thalamus from 1 mm T1 scans, but the contrast of the lateral and internal boundaries is too faint to produce reliable segmentations. Some tools have attempted to incorporate information from diffusion MRI in the segmentation to refine these boundaries, but do not generalise well across diffusion MRI acquisitions. Here we present the first CNN that can segment thalamic nuclei from T1 and diffusion data of any resolution without retraining or fine tuning. Our method builds on a public histological atlas of the thalamic nuclei and silver standard segmentations on high-quality diffusion data obtained with a recent Bayesian adaptive segmentation tool. We combine these with an approximate degradation model for fast domain randomisation during training. Our CNN produces a segmentation at 0.7 mm isotropic resolution, irrespective of the resolution of the input. Moreover, it uses a parsimonious model of the diffusion signal at each voxel (fractional anisotropy and principal eigenvector) that is compatible with virtually any set of directions and b-values, including huge amounts of legacy data. We show results of our proposed method on three heterogeneous datasets acquired on dozens of different scanners. An implementation of the method is publicly available at https://freesurfer.net/fswiki/ThalamicNucleiDTI.

Sample-Specific Debiasing for Better Image-Text Models

Self-supervised representation learning on image-text data facilitates crucial medical applications, such as image classification, visual grounding, and cross-modal retrieval. One common approach involves contrasting semantically similar (positive) and dissimilar (negative) pairs of data points. Drawing negative samples uniformly from the training data set introduces false negatives, i.e., samples that are treated as dissimilar but belong to the same class. In healthcare data, the underlying class distribution is nonuniform, implying that false negatives occur at a highly variable rate. To improve the quality of learned representations, we develop a novel approach that corrects for false negatives. Our method can be viewed as a variant of debiased constrastive learning that uses estimated sample-specific class probabilities. We provide theoretical analysis of the objective function and demonstrate the proposed approach on both image and paired image-text data sets. Our experiments demonstrate empirical advantages of sample-specific debiasing.

Data Consistent Deep Rigid MRI Motion Correction

Motion artifacts are a pervasive problem in MRI, leading to misdiagnosis or mischaracterization in population-level imaging studies. Current retrospective rigid intra-slice motion correction techniques jointly optimize estimates of the image and the motion parameters. In this paper, we use a deep network to reduce the joint image-motion parameter search to a search over rigid motion parameters alone. Our network produces a reconstruction as a function of two inputs: corrupted k-space data and motion parameters. We train the network using simulated, motion-corrupted k-space data generated from known motion parameters. At test-time, we estimate unknown motion parameters by minimizing a data consistency loss between the motion parameters, the network-based image reconstruction given those parameters, and the acquired measurements. Intra-slice motion correction experiments on simulated and realistic 2D fast spin echo brain MRI achieve high reconstruction fidelity while retaining the benefits of explicit data consistency-based optimization. Our code is publicly available at https://www.github.com/nalinimsingh/neuroMoCo.

Using Multiple Instance Learning to Build Multimodal Representations

Image-text multimodal representation learning aligns data across modalities and enables important medical applications, e.g., image classification, visual grounding, and cross-modal retrieval. In this work, we establish a connection between multimodal representation learning and multiple instance learning. Based on this connection, we propose a generic framework for constructing permutation-invariant score functions with many existing multimodal representation learning approaches as special cases. Furthermore, we use the framework to derive a novel contrastive learning approach and demonstrate that our method achieves state-of-the-art results on a number of downstream tasks.

Less is More: Rethinking Few-Shot Learning and Recurrent Neural Nets

The statistical supervised learning framework assumes an input-output set with a joint probability distribution that is reliably represented by the training dataset. The learner is then required to output a prediction rule learned from the training dataset's input-output pairs. In this work, we provide meaningful insights into the asymptotic equipartition property (AEP) \citep{Shannon:1948} in the context of machine learning, and illuminate some of its potential ramifications for few-shot learning. We provide theoretical guarantees for reliable learning under the information-theoretic AEP, and for the generalization error with respect to the sample size. We then focus on a highly efficient recurrent neural net (RNN) framework and propose a reduced-entropy algorithm for few-shot learning. We also propose a mathematical intuition for the RNN as an approximation of a sparse coding solver. We verify the applicability, robustness, and computational efficiency of the proposed approach with image deblurring and optical coherence tomography (OCT) speckle suppression. Our experimental results demonstrate significant potential for improving learning models' sample efficiency, generalization, and time complexity, that can therefore be leveraged for practical real-time applications.

Fast Auto-Differentiable Digitally Reconstructed Radiographs for Solving Inverse Problems in Intraoperative Imaging

The use of digitally reconstructed radiographs (DRRs) to solve inverse problems such as slice-to-volume registration and 3D reconstruction is well-studied in preoperative settings. In intraoperative imaging, the utility of DRRs is limited by the challenges in generating them in real-time and supporting optimization procedures that rely on repeated DRR synthesis. While immense progress has been made in accelerating the generation of DRRs through algorithmic refinements and GPU implementations, DRR-based optimization remains slow because most DRR generators do not offer a straightforward way to obtain gradients with respect to the imaging parameters. To make DRRs interoperable with gradient-based optimization and deep learning frameworks, we have reformulated Siddon's method, the most popular ray-tracing algorithm used in DRR generation, as a series of vectorized tensor operations. We implemented this vectorized version of Siddon's method in PyTorch, taking advantage of the library's strong automatic differentiation engine to make this DRR generator fully differentiable with respect to its parameters. Additionally, using GPU-accelerated tensor computation enables our vectorized implementation to achieve rendering speeds equivalent to state-of-the-art DRR generators implemented in CUDA and C++. We illustrate the resulting method in the context of slice-to-volume registration. Moreover, our simulations suggest that the loss landscapes for the slice-to-volume registration problem are convex in the neighborhood of the optimal solution, and gradient-based registration promises a much faster solution than prevailing gradient-free optimization strategies. The proposed DRR generator enables fast computer vision algorithms to support image guidance in minimally invasive procedures. Our implementation is publically available at https://github.com/v715/DiffDRR.