arXiv subjects

Polina Golland

Publications and source records attributed to Polina Golland.

At least 55 records · Page 3Linked to original sources

arXiv2023

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.

cs.CV↗

arXiv2023

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.

cs.CV↗

arXiv2023

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.

eess.IV↗

arXiv2023

RadTex: Learning Efficient Radiograph Representations from Text Reports

Automated analysis of chest radiography using deep learning has tremendous potential to enhance the clinical diagnosis of diseases in patients. However, deep learning models typically require large amounts of annotated data to achieve high performance -- often an obstacle to medical domain adaptation. In this paper, we build a data-efficient learning framework that utilizes radiology reports to improve medical image classification performance with limited labeled data (fewer than 1000 examples). Specifically, we examine image-captioning pretraining to learn high-quality medical image representations that train on fewer examples. Following joint pretraining of a convolutional encoder and transformer decoder, we transfer the learned encoder to various classification tasks. Averaged over 9 pathologies, we find that our model achieves higher classification performance than ImageNet-supervised and in-domain supervised pretraining when labeled training data is limited.

cs.CV↗

arXiv2023

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 in several downstream tasks.

cs.CV↗

arXiv2022

Symmetric Volume Maps: Order-Invariant Volumetric Mesh Correspondence with Free Boundary

Although shape correspondence is a central problem in geometry processing, most methods for this task apply only to two-dimensional surfaces. The neglected task of volumetric correspondence--a natural extension relevant to shapes extracted from simulation, medical imaging, and volume rendering--presents unique challenges that do not appear in the two-dimensional case. In this work, we propose a method for mapping between volumes represented as tetrahedral meshes. Our formulation minimizes a distortion energy designed to extract maps symmetrically, i.e., without dependence on the ordering of the source and target domains. We accompany our method with theoretical discussion describing the consequences of this symmetry assumption, leading us to select a symmetrized ARAP energy that favors isometric correspondences. Our final formulation optimizes for near-isometry while matching the boundary. We demonstrate our method on a diverse geometric dataset, producing low-distortion matchings that align closely to the boundary.

cs.GR↗

arXiv2022

Segmentation of Anatomical Layers and Artifacts in Intravascular Polarization Sensitive Optical Coherence Tomography Using Attending Physician and Boundary Cardinality Losses

Intravascular ultrasound and optical coherence tomography are widely available for characterizing coronary stenoses and provide critical vessel parameters to optimize percutaneous intervention. Intravascular polarization-sensitive optical coherence tomography (PS-OCT) simultaneously provides high-resolution cross-sectional images of vascular structures while also revealing preponderant tissue components such as collagen and smooth muscle and thereby enhances plaque characterization. Automated interpretation of these features promises to facilitate the objective clinical investigation of the natural history and significance of coronary atheromas. Here, we propose a convolutional neural network model, optimized using a new multi-term loss function, to classify the lumen, intima, and media layers in addition to the guidewire and plaque shadows. We demonstrate that our multi-class classification model outperforms state-of-the-art methods in detecting the coronary anatomical layers. Furthermore, the proposed model segments two classes of common imaging artifacts and detects the anatomical layers within the thickened vessel wall regions that were excluded from analysis by other studies. The source code and the trained model are publicly available at https://github.com/mhaft/OCTseg

eess.IV↗

arXiv2022

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.

cs.CV↗

arXiv2022

Automatic Segmentation of the Placenta in BOLD MRI Time Series

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.

eess.IV↗

arXiv2022

SVoRT: Iterative Transformer for Slice-to-Volume Registration in Fetal Brain MRI

Volumetric reconstruction of fetal brains from multiple stacks of MR slices, acquired in the presence of almost unpredictable and often severe subject motion, is a challenging task that is highly sensitive to the initialization of slice-to-volume transformations. We propose a novel slice-to-volume registration method using Transformers trained on synthetically transformed data, which model multiple stacks of MR slices as a sequence. With the attention mechanism, our model automatically detects the relevance between slices and predicts the transformation of one slice using information from other slices. We also estimate the underlying 3D volume to assist slice-to-volume registration and update the volume and transformations alternately to improve accuracy. Results on synthetic data show that our method achieves lower registration error and better reconstruction quality compared with existing state-of-the-art methods. Experiments with real-world MRI data are also performed to demonstrate the ability of the proposed model to improve the quality of 3D reconstruction under severe fetal motion.

eess.IV↗

arXiv2022

Joint Frequency and Image Space Learning for MRI Reconstruction and Analysis

We propose neural network layers that explicitly combine frequency and image feature representations and show that they can be used as a versatile building block for reconstruction from frequency space data. Our work is motivated by the challenges arising in MRI acquisition where the signal is a corrupted Fourier transform of the desired image. The proposed joint learning schemes enable both correction of artifacts native to the frequency space and manipulation of image space representations to reconstruct coherent image structures at every layer of the network. This is in contrast to most current deep learning approaches for image reconstruction that treat frequency and image space features separately and often operate exclusively in one of the two spaces. We demonstrate the advantages of joint convolutional learning for a variety of tasks, including motion correction, denoising, reconstruction from undersampled acquisitions, and combined undersampling and motion correction on simulated and real world multicoil MRI data. The joint models produce consistently high quality output images across all tasks and datasets. When integrated into a state of the art unrolled optimization network with physics-inspired data consistency constraints for undersampled reconstruction, the proposed architectures significantly improve the optimization landscape, which yields an order of magnitude reduction of training time. This result suggests that joint representations are particularly well suited for MRI signals in deep learning networks. Our code and pretrained models are publicly available at https://github.com/nalinimsingh/interlacer.

cs.CV↗

arXiv2021

The Alzheimer's Disease Prediction Of Longitudinal Evolution (TADPOLE) Challenge: Results after 1 Year Follow-up

We present the findings of "The Alzheimer's Disease Prediction Of Longitudinal Evolution" (TADPOLE) Challenge, which compared the performance of 92 algorithms from 33 international teams at predicting the future trajectory of 219 individuals at risk of Alzheimer's disease. Challenge participants were required to make a prediction, for each month of a 5-year future time period, of three key outcomes: clinical diagnosis, Alzheimer's Disease Assessment Scale Cognitive Subdomain (ADAS-Cog13), and total volume of the ventricles. The methods used by challenge participants included multivariate linear regression, machine learning methods such as support vector machines and deep neural networks, as well as disease progression models. No single submission was best at predicting all three outcomes. For clinical diagnosis and ventricle volume prediction, the best algorithms strongly outperform simple baselines in predictive ability. However, for ADAS-Cog13 no single submitted prediction method was significantly better than random guesswork. Two ensemble methods based on taking the mean and median over all predictions, obtained top scores on almost all tasks. Better than average performance at diagnosis prediction was generally associated with the additional inclusion of features from cerebrospinal fluid (CSF) samples and diffusion tensor imaging (DTI). On the other hand, better performance at ventricle volume prediction was associated with inclusion of summary statistics, such as the slope or maxima/minima of biomarkers. TADPOLE's unique results suggest that current prediction algorithms provide sufficient accuracy to exploit biomarkers related to clinical diagnosis and ventricle volume, for cohort refinement in clinical trials for Alzheimer's disease. However, results call into question the usage of cognitive test scores for patient selection and as a primary endpoint in clinical trials.

q-bio.PE↗

arXiv2021

Multimodal Representation Learning via Maximization of Local Mutual Information

We propose and demonstrate a representation learning approach by maximizing the mutual information between local features of images and text. The goal of this approach is to learn useful image representations by taking advantage of the rich information contained in the free text that describes the findings in the image. Our method trains image and text encoders by encouraging the resulting representations to exhibit high local mutual information. We make use of recent advances in mutual information estimation with neural network discriminators. We argue that the sum of local mutual information is typically a lower bound on the global mutual information. Our experimental results in the downstream image classification tasks demonstrate the advantages of using local features for image-text representation learning.

eess.IV↗

arXiv2021

Hypernet-Ensemble Learning of Segmentation Probability for Medical Image Segmentation with Ambiguous Labels

Despite the superior performance of Deep Learning (DL) on numerous segmentation tasks, the DL-based approaches are notoriously overconfident about their prediction with highly polarized label probability. This is often not desirable for many applications with the inherent label ambiguity even in human annotations. This challenge has been addressed by leveraging multiple annotations per image and the segmentation uncertainty. However, multiple per-image annotations are often not available in a real-world application and the uncertainty does not provide full control on segmentation results to users. In this paper, we propose novel methods to improve the segmentation probability estimation without sacrificing performance in a real-world scenario that we have only one ambiguous annotation per image. We marginalize the estimated segmentation probability maps of networks that are encouraged to under-/over-segment with the varying Tversky loss without penalizing balanced segmentation. Moreover, we propose a unified hypernetwork ensemble method to alleviate the computational burden of training multiple networks. Our approaches successfully estimated the segmentation probability maps that reflected the underlying structures and provided the intuitive control on segmentation for the challenging 3D medical image segmentation. Although the main focus of our proposed methods is not to improve the binary segmentation performance, our approaches marginally outperformed the state-of-the-arts. The codes are available at \url{https://github.com/sh4174/HypernetEnsemble}.

eess.IV↗

arXiv2021

Bayesian Image Reconstruction using Deep Generative Models

Machine learning models are commonly trained end-to-end and in a supervised setting, using paired (input, output) data. Examples include recent super-resolution methods that train on pairs of (low-resolution, high-resolution) images. However, these end-to-end approaches require re-training every time there is a distribution shift in the inputs (e.g., night images vs daylight) or relevant latent variables (e.g., camera blur or hand motion). In this work, we leverage state-of-the-art (SOTA) generative models (here StyleGAN2) for building powerful image priors, which enable application of Bayes' theorem for many downstream reconstruction tasks. Our method, Bayesian Reconstruction through Generative Models (BRGM), uses a single pre-trained generator model to solve different image restoration tasks, i.e., super-resolution and in-painting, by combining it with different forward corruption models. We keep the weights of the generator model fixed, and reconstruct the image by estimating the Bayesian maximum a-posteriori (MAP) estimate over the input latent vector that generated the reconstructed image. We further use variational inference to approximate the posterior distribution over the latent vectors, from which we sample multiple solutions. We demonstrate BRGM on three large and diverse datasets: (i) 60,000 images from the Flick Faces High Quality dataset (ii) 240,000 chest X-rays from MIMIC III and (iii) a combined collection of 5 brain MRI datasets with 7,329 scans. Across all three datasets and without any dataset-specific hyperparameter tuning, our simple approach yields performance competitive with current task-specific state-of-the-art methods on super-resolution and in-painting, while being more generalisable and without requiring any training. Our source code and pre-trained models are available online: https://razvanmarinescu.github.io/brgm/.

cs.CV↗

arXiv2021

Volumetric Parameterization of the Placenta to a Flattened Template

We present a volumetric mesh-based algorithm for parameterizing the placenta to a flattened template to enable effective visualization of local anatomy and function. MRI shows potential as a research tool as it provides signals directly related to placental function. However, due to the curved and highly variable in vivo shape of the placenta, interpreting and visualizing these images is difficult. We address interpretation challenges by mapping the placenta so that it resembles the familiar ex vivo shape. We formulate the parameterization as an optimization problem for mapping the placental shape represented by a volumetric mesh to a flattened template. We employ the symmetric Dirichlet energy to control local distortion throughout the volume. Local injectivity in the mapping is enforced by a constrained line search during the gradient descent optimization. We validate our method using a research study of 111 placental shapes extracted from BOLD MRI images. Our mapping achieves sub-voxel accuracy in matching the template while maintaining low distortion throughout the volume. We demonstrate how the resulting flattening of the placenta improves visualization of anatomy and function. Our code is freely available at https://github.com/mabulnaga/placenta-flattening .

cs.CV↗

arXiv2021

Image Classification with Consistent Supporting Evidence

Adoption of machine learning models in healthcare requires end users' trust in the system. Models that provide additional supportive evidence for their predictions promise to facilitate adoption. We define consistent evidence to be both compatible and sufficient with respect to model predictions. We propose measures of model inconsistency and regularizers that promote more consistent evidence. We demonstrate our ideas in the context of edema severity grading from chest radiographs. We demonstrate empirically that consistent models provide competitive performance while supporting interpretation.

cs.CV↗

arXiv2021

Equivariant Filters for Efficient Tracking in 3D Imaging

We demonstrate an object tracking method for 3D images with fixed computational cost and state-of-the-art performance. Previous methods predicted transformation parameters from convolutional layers. We instead propose an architecture that does not include either flattening of convolutional features or fully connected layers, but instead relies on equivariant filters to preserve transformations between inputs and outputs (e.g. rot./trans. of inputs rotate/translate outputs). The transformation is then derived in closed form from the outputs of the filters. This method is useful for applications requiring low latency, such as real-time tracking. We demonstrate our model on synthetically augmented adult brain MRI, as well as fetal brain MRI, which is the intended use-case.

cs.CV↗