Author name cluster

Neel Dey

Possible papers associated with this exact author name in Arrow. This page groups case-insensitive exact name matches and is not a full identity disambiguation profile.

5 papers

2 author rows

ICLR Conference 2025 Conference Paper

Learning General-purpose Biomedical Volume Representations using Randomized Synthesis

Neel Dey
Benjamin Billot
Hallee E. Wong
Clinton J. Wang
Mengwei Ren
Ellen Grant
Adrian V. Dalca
Polina Golland

Current volumetric biomedical foundation models struggle to generalize as public 3D datasets are small and do not cover the broad diversity of medical procedures, conditions, anatomical regions, and imaging protocols. We address this by creating a representation learning method that instead anticipates strong domain shifts at training time itself. We first propose a data engine that synthesizes highly variable training samples that would enable generalization to new biomedical contexts. To then train a single 3D network for any voxel-level task, we develop a contrastive learning method that pretrains the network to be stable against nuisance imaging variation simulated by the data engine, a key inductive bias for generalization. This network's features can be used as robust representations of input images for downstream tasks and its weights provide a strong, _dataset-agnostic_ initialization for finetuning on new datasets. As a result, we set new standards across _both_ multimodality registration and few-shot segmentation, a first for any 3D biomedical vision model, all without (pre-)training on any existing dataset of real images.

Details

NeurIPS Conference 2025 Conference Paper

PolyPose: Deformable 2D/3D Registration via Polyrigid Transformations

Vivek Gopalakrishnan
Neel Dey
Polina Golland

Determining the 3D pose of a patient from a limited set of 2D X-ray images is a critical task in interventional settings. While preoperative volumetric imaging (e. g. , CT and MRI) provides precise 3D localization and visualization of anatomical targets, these modalities cannot be acquired during procedures, where fast 2D imaging (X-ray) is used instead. To integrate volumetric guidance into intraoperative procedures, we present PolyPose, a simple and robust method for deformable 2D/3D registration. PolyPose parameterizes complex 3D deformation fields as a composition of rigid transforms, leveraging the biological constraint that individual bones do not bend in typical motion. Unlike existing methods that either assume no inter-joint movement or fail outright in this under-determined setting, our polyrigid formulation enforces anatomically plausible priors that respect the piecewise-rigid nature of human movement. This approach eliminates the need for expensive deformation regularizers that require patient- and procedure-specific hyperparameter optimization. Across extensive experiments on diverse datasets from orthopedic surgery and radiotherapy, we show that this strong inductive bias enables PolyPose to successfully align the patient's preoperative volume to as few as two X-rays, thereby providing crucial 3D guidance in challenging sparse-view and limited-angle settings where current registration methods fail. Additional visualizations, tutorials, and code are available at https: //polypose. csail. mit. edu.

PDF Details

NeurIPS Conference 2024 Conference Paper

Equivariant spatio-hemispherical networks for diffusion MRI deconvolution

Axel Elaldi
Guido Gerig
Neel Dey

Each voxel in a diffusion MRI (dMRI) image contains a spherical signal corresponding to the direction and strength of water diffusion in the brain. This paper advances the analysis of such spatio-spherical data by developing convolutional network layers that are equivariant to the $\mathbf{E(3) \times SO(3)}$ group and account for the physical symmetries of dMRI including rotations, translations, and reflections of space alongside voxel-wise rotations. Further, neuronal fibers are typically antipodally symmetric, a fact we leverage to construct highly efficient spatio-*hemispherical* graph convolutions to accelerate the analysis of high-dimensional dMRI data. In the context of sparse spherical fiber deconvolution to recover white matter microstructure, our proposed equivariant network layers yield substantial performance and efficiency gains, leading to better and more practical resolution of crossing neuronal fibers and fiber tractography. These gains are experimentally consistent across both simulation and in vivo human datasets.

PDF Details DOI

NeurIPS Conference 2022 Conference Paper

Local Spatiotemporal Representation Learning for Longitudinally-consistent Neuroimage Analysis

Mengwei Ren
Neel Dey
Martin Styner
Kelly Botteron
Guido Gerig

Recent self-supervised advances in medical computer vision exploit the global and local anatomical self-similarity for pretraining prior to downstream tasks such as segmentation. However, current methods assume i. i. d. image acquisition, which is invalid in clinical study designs where follow-up longitudinal scans track subject-specific temporal changes. Further, existing self-supervised methods for medically-relevant image-to-image architectures exploit only spatial or temporal self-similarity and do so via a loss applied only at a single image-scale, with naive multi-scale spatiotemporal extensions collapsing to degenerate solutions. To these ends, this paper makes two contributions: (1) It presents a local and multi-scale spatiotemporal representation learning method for image-to-image architectures trained on longitudinal images. It exploits the spatiotemporal self-similarity of learned multi-scale intra-subject image features for pretraining and develops several feature-wise regularizations that avoid degenerate representations; (2) During finetuning, it proposes a surprisingly simple self-supervised segmentation consistency regularization to exploit intra-subject correlation. Benchmarked across various segmentation tasks, the proposed framework outperforms both well-tuned randomly-initialized baselines and current self-supervised techniques designed for both i. i. d. and longitudinal datasets. These improvements are demonstrated across both longitudinal neurodegenerative adult MRI and developing infant brain MRI and yield both higher performance and longitudinal consistency.

PDF Details

ICLR Conference 2021 Conference Paper

Group Equivariant Generative Adversarial Networks

Neel Dey
Antong Chen
Soheil Ghafurian

Recent improvements in generative adversarial visual synthesis incorporate real and fake image transformation in a self-supervised setting, leading to increased stability and perceptual fidelity. However, these approaches typically involve image augmentations via additional regularizers in the GAN objective and thus spend valuable network capacity towards approximating transformation equivariance instead of their desired task. In this work, we explicitly incorporate inductive symmetry priors into the network architectures via group-equivariant convolutional networks. Group-convolutions have higher expressive power with fewer samples and lead to better gradient feedback between generator and discriminator. We show that group-equivariance integrates seamlessly with recent techniques for GAN training across regularizers, architectures, and loss functions. We demonstrate the utility of our methods for conditional synthesis by improving generation in the limited data regime across symmetric imaging datasets and even find benefits for natural images with preferred orientation.

Details