Hallee E. Wong

Hallee E. Wong, Marianne Rakic, John Guttag et al.

Biomedical image segmentation is a crucial part of both scientific research and clinical care. With enough labelled data, deep learning models can be trained to accurately automate specific biomedical image segmentation tasks. However, manually segmenting images to create training data is highly labor intensive and requires domain expertise. We present \emph{ScribblePrompt}, a flexible neural network based interactive segmentation tool for biomedical imaging that enables human annotators to segment previously unseen structures using scribbles, clicks, and bounding boxes. Through rigorous quantitative experiments, we demonstrate that given comparable amounts of interaction, ScribblePrompt produces more accurate segmentations than previous methods on datasets unseen during training. In a user study with domain experts, ScribblePrompt reduced annotation time by 28% while improving Dice by 15% compared to the next best method. ScribblePrompt's success rests on a set of careful design decisions. These include a training strategy that incorporates both a highly diverse set of images and tasks, novel algorithms for simulated user interactions and labels, and a network that enables fast inference. We showcase ScribblePrompt in an interactive demo, provide code, and release a dataset of scribble annotations at https://scribbleprompt.csail.mit.edu

Neel Dey, Benjamin Billot, Hallee E. Wong et al. · mit

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.

Hallee E. Wong, Jose Javier Gonzalez Ortiz, John Guttag et al.

Medical researchers and clinicians often need to perform novel segmentation tasks on a set of related images. Existing methods for segmenting a new dataset are either interactive, requiring substantial human effort for each image, or require an existing set of previously labeled images. We introduce a system, MultiverSeg, that enables practitioners to rapidly segment an entire new dataset without requiring access to any existing labeled data from that task or domain. Along with the image to segment, the model takes user interactions such as clicks, bounding boxes or scribbles as input, and predicts a segmentation. As the user segments more images, those images and segmentations become additional inputs to the model, providing context. As the context set of labeled images grows, the number of interactions required to segment each new image decreases. We demonstrate that MultiverSeg enables users to interactively segment new datasets efficiently, by amortizing the number of interactions per image to achieve an accurate segmentation. Compared to using a state-of-the-art interactive segmentation method, MultiverSeg reduced the total number of clicks by 36% and scribble steps by 25% to achieve 90% Dice on sets of images from unseen tasks. We release code and model weights at https://multiverseg.csail.mit.edu

Marianne Rakic, Hallee E. Wong, Jose Javier Gonzalez Ortiz et al.

Existing learning-based solutions to medical image segmentation have two important shortcomings. First, for most new segmentation task, a new model has to be trained or fine-tuned. This requires extensive resources and machine learning expertise, and is therefore often infeasible for medical researchers and clinicians. Second, most existing segmentation methods produce a single deterministic segmentation mask for a given image. In practice however, there is often considerable uncertainty about what constitutes the correct segmentation, and different expert annotators will often segment the same image differently. We tackle both of these problems with Tyche, a model that uses a context set to generate stochastic predictions for previously unseen tasks without the need to retrain. Tyche differs from other in-context segmentation methods in two important ways. (1) We introduce a novel convolution block architecture that enables interactions among predictions. (2) We introduce in-context test-time augmentation, a new mechanism to provide prediction stochasticity. When combined with appropriate model design and loss functions, Tyche can predict a set of plausible diverse segmentation candidates for new or unseen medical images and segmentation tasks without the need to retrain.

Hallee E. Wong, Brianna C. Heggeseth, Steven J. Miller

Accurately predicting patients' risk of 30-day hospital readmission would enable hospitals to efficiently allocate resource-intensive interventions. We develop a new method, Categorical Co-Frequency Analysis (CoFA), for clustering diagnosis codes from the International Classification of Diseases (ICD) according to the similarity in relationships between covariates and readmission risk. CoFA measures the similarity between diagnoses by the frequency with which two diagnoses are split in the same direction versus split apart in random forests to predict readmission risk. Applying CoFA to de-identified data from Berkshire Medical Center, we identified three groups of diagnoses that vary in readmission risk. To evaluate CoFA, we compared readmission risk models using ICD majors and CoFA groups to a baseline model without diagnosis variables. We found substituting ICD majors for the CoFA-identified clusters simplified the model without compromising the accuracy of predictions. Fitting separate models for each ICD major and CoFA group did not improve predictions, suggesting that readmission risk may be more homogeneous that heterogeneous across diagnosis groups.

Hallee E. Wong, Osman Akar, Emmanuel Antonio Cuevas et al.

Markerless augmented reality can be a challenging computer vision task, especially in live broadcast settings and in the absence of information related to the video capture such as the intrinsic camera parameters. This typically requires the assistance of a skilled artist, along with the use of advanced video editing tools in a post-production environment. We present an automated video augmentation pipeline that identifies textures of interest and overlays an advertisement onto these regions. We constrain the advertisement to be placed in a way that is aesthetic and natural. The aim is to augment the scene such that there is no longer a need for commercial breaks. In order to achieve seamless integration of the advertisement with the original video we build a 3D representation of the scene, place the advertisement in 3D, and then project it back onto the image plane. After successful placement in a single frame, we use homography-based, shape-preserving tracking such that the advertisement appears perspective correct for the duration of a video clip. The tracker is designed to handle smooth camera motion and shot boundaries.