James Gee

Michael S. Yao, Allison Chae, Matthew T. MacLean et al.

Early diagnosis of Type 2 Diabetes Mellitus (T2DM) is crucial to enable timely therapeutic interventions and lifestyle modifications. As the time available for clinical office visits shortens and medical imaging data become more widely available, patient image data could be used to opportunistically identify patients for additional T2DM diagnostic workup by physicians. We investigated whether image-derived phenotypic data could be leveraged in tabular learning classifier models to predict T2DM risk in an automated fashion to flag high-risk patients without the need for additional blood laboratory measurements. In contrast to traditional binary classifiers, we leverage neural networks and decision tree models to represent patient data as 'SynthA1c' latent variables, which mimic blood hemoglobin A1c empirical lab measurements, that achieve sensitivities as high as 87.6%. To evaluate how SynthA1c models may generalize to other patient populations, we introduce a novel generalizable metric that uses vanilla data augmentation techniques to predict model performance on input out-of-domain covariates. We show that image-derived phenotypes and physical examination data together can accurately predict diabetes risk as a means of opportunistic risk stratification enabled by artificial intelligence and medical imaging. Our code is available at https://github.com/allisonjchae/DMT2RiskAssessment.

Rohit Jena, Lukas Zhornyak, Nehal Doiphode et al.

Correctness of instance segmentation constitutes counting the number of objects, correctly localizing all predictions and classifying each localized prediction. Average Precision is the de-facto metric used to measure all these constituents of segmentation. However, this metric does not penalize duplicate predictions in the high-recall range, and cannot distinguish instances that are localized correctly but categorized incorrectly. This weakness has inadvertently led to network designs that achieve significant gains in AP but also introduce a large number of false positives. We therefore cannot rely on AP to choose a model that provides an optimal tradeoff between false positives and high recall. To resolve this dilemma, we review alternative metrics in the literature and propose two new measures to explicitly measure the amount of both spatial and categorical duplicate predictions. We also propose a Semantic Sorting and NMS module to remove these duplicates based on a pixel occupancy matching scheme. Experiments show that modern segmentation networks have significant gains in AP, but also contain a considerable amount of duplicates. Our Semantic Sorting and NMS can be added as a plug-and-play module to mitigate hedged predictions and preserve AP.

Rohit Jena, Ganesh Subramanian Iyer, Siddharth Choudhary et al.

We propose SplatArmor, a novel approach for recovering detailed and animatable human models by `armoring' a parameterized body model with 3D Gaussians. Our approach represents the human as a set of 3D Gaussians within a canonical space, whose articulation is defined by extending the skinning of the underlying SMPL geometry to arbitrary locations in the canonical space. To account for pose-dependent effects, we introduce a SE(3) field, which allows us to capture both the location and anisotropy of the Gaussians. Furthermore, we propose the use of a neural color field to provide color regularization and 3D supervision for the precise positioning of these Gaussians. We show that Gaussian splatting provides an interesting alternative to neural rendering based methods by leverging a rasterization primitive without facing any of the non-differentiability and optimization challenges typically faced in such approaches. The rasterization paradigms allows us to leverage forward skinning, and does not suffer from the ambiguities associated with inverse skinning and warping. We show compelling results on the ZJU MoCap and People Snapshot datasets, which underscore the effectiveness of our method for controllable human synthesis.

Rohit Jena, Pratik Chaudhari, James Gee et al.

Human reconstruction and synthesis from monocular RGB videos is a challenging problem due to clothing, occlusion, texture discontinuities and sharpness, and framespecific pose changes. Many methods employ deferred rendering, NeRFs and implicit methods to represent clothed humans, on the premise that mesh-based representations cannot capture complex clothing and textures from RGB, silhouettes, and keypoints alone. We provide a counter viewpoint to this fundamental premise by optimizing a SMPL+D mesh and an efficient, multi-resolution texture representation using only RGB images, binary silhouettes and sparse 2D keypoints. Experimental results demonstrate that our approach is more capable of capturing geometric details compared to visual hull, mesh-based methods. We show competitive novel view synthesis and improvements in novel pose synthesis compared to NeRF-based methods, which introduce noticeable, unwanted artifacts. By restricting the solution space to the SMPL+D model combined with differentiable rendering, we obtain dramatic speedups in compute, training times (up to 24x) and inference times (up to 192x). Our method therefore can be used as is or as a fast initialization to NeRF-based methods.

Huzheng Yang, James Gee, Jianbo Shi

We explore a new class of brain encoding model by adding memory-related information as input. Memory is an essential brain mechanism that works alongside visual stimuli. During a vision-memory cognitive task, we found the non-visual brain is largely predictable using previously seen images. Our Memory Encoding Model (Mem) won the Algonauts 2023 visual brain competition even without model ensemble (single model score 66.8, ensemble score 70.8). Our ensemble model without memory input (61.4) can also stand a 3rd place. Furthermore, we observe periodic delayed brain response correlated to 6th-7th prior image, and hippocampus also showed correlated activity timed with this periodicity. We conjuncture that the periodic replay could be related to memory mechanism to enhance the working memory.

Huzheng Yang, Jianbo Shi, James Gee

Brain encoding models aim to predict brain voxel-wise responses to stimuli images, replicating brain signals captured by neuroimaging techniques. There is a large volume of publicly available data, but training a comprehensive brain encoding model is challenging. The main difficulties stem from a) diversity within individual brain, with functional heterogeneous brain regions; b) diversity of brains from different subjects, due to genetic and developmental differences; c) diversity of imaging modalities and processing pipelines. We use this diversity to our advantage by introducing the All-for-One training recipe, which divides the challenging one-big-model problem into multiple small models, with the small models aggregating the knowledge while preserving the distinction between the different functional regions. Agnostic of the training recipe, we use biological knowledge of the brain, specifically retinotopy, to introduce inductive bias to learn a 3D brain-to-image mapping that ensures a) each neuron knows which image regions and semantic levels to gather information, and b) no neurons are left behind in the model. We pre-trained a brain encoding model using over one million data points from five public datasets spanning three imaging modalities. To the best of our knowledge, this is the most comprehensive brain encoding model to the date. We demonstrate the effectiveness of the pre-trained model as a drop-in replacement for commonly used vision backbone models. Furthermore, we demonstrate the application of the model to brain decoding. Code and the model checkpoint will be made available.

Huzheng Yang, James Gee, Jianbo Shi

We study the intriguing connection between visual data, deep networks, and the brain. Our method creates a universal channel alignment by using brain voxel fMRI response prediction as the training objective. We discover that deep networks, trained with different objectives, share common feature channels across various models. These channels can be clustered into recurring sets, corresponding to distinct brain regions, indicating the formation of visual concepts. Tracing the clusters of channel responses onto the images, we see semantically meaningful object segments emerge, even without any supervised decoder. Furthermore, the universal feature alignment and the clustering of channels produce a picture and quantification of how visual information is processed through the different network layers, which produces precise comparisons between the networks.

Huzheng Yang, James Gee, Jianbo Shi

We developed a tool for visualizing and analyzing large pre-trained vision models by mapping them onto the brain, thus exposing their hidden inside. Our innovation arises from a surprising usage of brain encoding: predicting brain fMRI measurements in response to images. We report two findings. First, explicit mapping between the brain and deep-network features across dimensions of space, layers, scales, and channels is crucial. This mapping method, FactorTopy, is plug-and-play for any deep-network; with it, one can paint a picture of the network onto the brain (literally!). Second, our visualization shows how different training methods matter: they lead to remarkable differences in hierarchical organization and scaling behavior, growing with more data or network capacity. It also provides insight into fine-tuning: how pre-trained models change when adapting to small datasets. We found brain-like hierarchically organized network suffer less from catastrophic forgetting after fine-tuned.

Jiancong Wang, Yuhua Chen, Yifan Wu et al.

Single image super-resolution (SISR) reconstruction for magnetic resonance imaging (MRI) has generated significant interest because of its potential to not only speed up imaging but to improve quantitative processing and analysis of available image data. Generative Adversarial Networks (GAN) have proven to perform well in recovering image texture detail, and many variants have therefore been proposed for SISR. In this work, we develop an enhancement to tackle GAN-based 3D SISR by introducing a new residual-in-residual dense block (RRDG) generator that is both memory efficient and achieves state-of-the-art performance in terms of PSNR (Peak Signal to Noise Ratio), SSIM (Structural Similarity) and NRMSE (Normalized Root Mean Squared Error) metrics. We also introduce a patch GAN discriminator with improved convergence behavior to better model brain image texture. We proposed a novel the anatomical fidelity evaluation of the results using a pre-trained brain parcellation network. Finally, these developments are combined through a simple and efficient method to balance etween image and texture quality in the final output.

Jiancong Wang, Long Xie, Paul Yushkevich et al.

Geodesic shooting has been successfully applied to diffeo-morphic registration of point sets. Exact computation of the geodesicshooting between point sets, however, requiresO(N2) calculations each time step on the number of points in the point set. We proposean approximation approach based on the Barnes-Hut algorithm to speedup point set geodesic shooting. This approximation can reduce the al-gorithm complexity toO(N b+N logN). The evaluation of the proposedmethod in both simulated images and the medial temporal lobe thick-ness analysis demonstrates a comparable accuracy to the exact point set geodesic shooting while offering up to 3-fold speed up. This improvementopens up a range of clinical research studies and practical problems towhich the method can be effectively applied.