Thomas Li

Kaiwen Xu, Thomas Li, Mirza S. Khan et al.

Field-of-view (FOV) tissue truncation beyond the lungs is common in routine lung screening computed tomography (CT). This poses limitations for opportunistic CT- based body composition (BC) assessment as key anatomical structures are missing. Traditionally, extending the FOV of CT is considered as a CT reconstruction problem using limited data. However, this approach relies on the projection domain data which might not be available in application. In this work, we formulate the problem from the semantic image extension perspective which only requires image data as inputs. The proposed two-stage method identifies a new FOV border based on the estimated extent of the complete body and imputes missing tissues in the truncated region. The training samples are simulated using CT slices with complete body in FOV, making the model development self-supervised. We evaluate the validity of the proposed method in automatic BC assessment using lung screening CT with limited FOV. The proposed method effectively restores the missing tissues and reduces BC assessment error introduced by FOV tissue truncation. In the BC assessment for a large-scale lung screening CT dataset, this correction improves both the intra-subject consistency and the correlation with anthropometric approximations. The developed method is available at https://github.com/MASILab/S-EFOV.

Ho Hin Lee, Quan Liu, Shunxing Bao et al.

With the inspiration of vision transformers, the concept of depth-wise convolution revisits to provide a large Effective Receptive Field (ERF) using Large Kernel (LK) sizes for medical image segmentation. However, the segmentation performance might be saturated and even degraded as the kernel sizes scaled up (e.g., $21\times 21\times 21$) in a Convolutional Neural Network (CNN). We hypothesize that convolution with LK sizes is limited to maintain an optimal convergence for locality learning. While Structural Re-parameterization (SR) enhances the local convergence with small kernels in parallel, optimal small kernel branches may hinder the computational efficiency for training. In this work, we propose RepUX-Net, a pure CNN architecture with a simple large kernel block design, which competes favorably with current network state-of-the-art (SOTA) (e.g., 3D UX-Net, SwinUNETR) using 6 challenging public datasets. We derive an equivalency between kernel re-parameterization and the branch-wise variation in kernel convergence. Inspired by the spatial frequency in the human visual system, we extend to vary the kernel convergence into element-wise setting and model the spatial frequency as a Bayesian prior to re-parameterize convolutional weights during training. Specifically, a reciprocal function is leveraged to estimate a frequency-weighted value, which rescales the corresponding kernel element for stochastic gradient descent. From the experimental results, RepUX-Net consistently outperforms 3D SOTA benchmarks with internal validation (FLARE: 0.929 to 0.944), external validation (MSD: 0.901 to 0.932, KiTS: 0.815 to 0.847, LiTS: 0.933 to 0.949, TCIA: 0.736 to 0.779) and transfer learning (AMOS: 0.880 to 0.911) scenarios in Dice Score.

Xin Yu, Yucheng Tang, Yinchi Zhou et al.

Efficiently quantifying renal structures can provide distinct spatial context and facilitate biomarker discovery for kidney morphology. However, the development and evaluation of the transformer model to segment the renal cortex, medulla, and collecting system remains challenging due to data inefficiency. Inspired by the hierarchical structures in vision transformer, we propose a novel method using a 3D block aggregation transformer for segmenting kidney components on contrast-enhanced CT scans. We construct the first cohort of renal substructures segmentation dataset with 116 subjects under institutional review board (IRB) approval. Our method yields the state-of-the-art performance (Dice of 0.8467) against the baseline approach of 0.8308 with the data-efficient design. The Pearson R achieves 0.9891 between the proposed method and manual standards and indicates the strong correlation and reproducibility for volumetric analysis. We extend the proposed method to the public KiTS dataset, the method leads to improved accuracy compared to transformer-based approaches. We show that the 3D block aggregation transformer can achieve local communication between sequence representations without modifying self-attention, and it can serve as an accurate and efficient quantification tool for characterizing renal structures.

Riqiang Gao, Thomas Li, Yucheng Tang et al.

Although deep learning prediction models have been successful in the discrimination of different classes, they can often suffer from poor calibration across challenging domains including healthcare. Moreover, the long-tail distribution poses great challenges in deep learning classification problems including clinical disease prediction. There are approaches proposed recently to calibrate deep prediction in computer vision, but there are no studies found to demonstrate how the representative models work in different challenging contexts. In this paper, we bridge the confidence calibration from computer vision to medical imaging with a comparative study of four high-impact calibration models. Our studies are conducted in different contexts (natural image classification and lung cancer risk estimation) including in balanced vs. imbalanced training sets and in computer vision vs. medical imaging. Our results support key findings: (1) We achieve new conclusions which are not studied under different learning contexts, e.g., combining two calibration models that both mitigate the overconfident prediction can lead to under-confident prediction, and simpler calibration models from the computer vision domain tend to be more generalizable to medical imaging. (2) We highlight the gap between general computer vision tasks and medical imaging prediction, e.g., calibration methods ideal for general computer vision tasks may in fact damage the calibration of medical imaging prediction. (3) We also reinforce previous conclusions in natural image classification settings. We believe that this study has merits to guide readers to choose calibration models and understand gaps between general computer vision and medical imaging domains.

Aravind R. Krishnan, Kaiwen Xu, Thomas Li et al.

The reconstruction kernel in computed tomography (CT) generation determines the texture of the image. Consistency in reconstruction kernels is important as the underlying CT texture can impact measurements during quantitative image analysis. Harmonization (i.e., kernel conversion) minimizes differences in measurements due to inconsistent reconstruction kernels. Existing methods investigate harmonization of CT scans in single or multiple manufacturers. However, these methods require paired scans of hard and soft reconstruction kernels that are spatially and anatomically aligned. Additionally, a large number of models need to be trained across different kernel pairs within manufacturers. In this study, we adopt an unpaired image translation approach to investigate harmonization between and across reconstruction kernels from different manufacturers by constructing a multipath cycle generative adversarial network (GAN). We use hard and soft reconstruction kernels from the Siemens and GE vendors from the National Lung Screening Trial dataset. We use 50 scans from each reconstruction kernel and train a multipath cycle GAN. To evaluate the effect of harmonization on the reconstruction kernels, we harmonize 50 scans each from Siemens hard kernel, GE soft kernel and GE hard kernel to a reference Siemens soft kernel (B30f) and evaluate percent emphysema. We fit a linear model by considering the age, smoking status, sex and vendor and perform an analysis of variance (ANOVA) on the emphysema scores. Our approach minimizes differences in emphysema measurement and highlights the impact of age, sex, smoking status and vendor on emphysema quantification.

Xin Yu, Qi Yang, Yinchi Zhou et al.

Transformer-based models, capable of learning better global dependencies, have recently demonstrated exceptional representation learning capabilities in computer vision and medical image analysis. Transformer reformats the image into separate patches and realizes global communication via the self-attention mechanism. However, positional information between patches is hard to preserve in such 1D sequences, and loss of it can lead to sub-optimal performance when dealing with large amounts of heterogeneous tissues of various sizes in 3D medical image segmentation. Additionally, current methods are not robust and efficient for heavy-duty medical segmentation tasks such as predicting a large number of tissue classes or modeling globally inter-connected tissue structures. To address such challenges and inspired by the nested hierarchical structures in vision transformer, we proposed a novel 3D medical image segmentation method (UNesT), employing a simplified and faster-converging transformer encoder design that achieves local communication among spatially adjacent patch sequences by aggregating them hierarchically. We extensively validate our method on multiple challenging datasets, consisting of multiple modalities, anatomies, and a wide range of tissue classes, including 133 structures in the brain, 14 organs in the abdomen, 4 hierarchical components in the kidneys, inter-connected kidney tumors and brain tumors. We show that UNesT consistently achieves state-of-the-art performance and evaluate its generalizability and data efficiency. Particularly, the model achieves whole brain segmentation task complete ROI with 133 tissue classes in a single network, outperforming prior state-of-the-art method SLANT27 ensembled with 27 networks.

Justin B. Hart, Awwab A. Azam, Thomas Li et al.

We develop a representability-aware and interpolable neural network (NN) framework for predicting two-particle reduced density matrices (2-RDMs). The NN incorporates a subset of representability conditions through its architecture and loss function, and can operate on different momentum meshes, enabling evaluating the representability conditions across multiple meshes, which we call interpolated representability condition. The framework can be used either to predict 2-RDMs on large momentum meshes by interpolating exact results from small meshes, or as a variational 2-RDM ansatz optimized by energy minimization on arbitrary meshes. We apply this approach to the fractional Chern insulator in the one-band projected model of twisted bilayer MoTe$_2$ at twist angle $3.89^\circ$ and hole filling $2/3$. Trained on exact-diagonalization (ED) 2-RDMs from meshes with $12$ or $18$ momentum points using six different NN architectures, the best NN is the residual multilayer perceptron, which predicts the $6\times6$ 2-RDM with $97.07\%-98.18\%$ accuracy relative to the ED 2-RDM but predicts an energy $77.353$ meV above ED ground-state energy. We then variationally optimize the NN on several meshes including $6\times6$, predicting a $6\times 6$ energy of just $0.104$ meV below ED while maintaining $98.94\%-98.96\%$ accuracy. Compared with the conventional boundary-point semidefinite programming, which gives an energy $5.560$ meV below ED with $96.40\%-98.94\%$ accuracy, the NN achieves a more accurate energy and similar accuracy while using only less than 1/20 as many parameters. Eventually, we add a symmetric mesh of $48$ momentum points to the variational optimization of the NN, and provide a prediction of the many-body ground-state energy and the many-body quantum metric on that mesh.

Yuanqi Chen, Ge Li, Cece Jin et al.

This paper observes that there is an issue of high frequencies missing in the discriminator of standard GAN, and we reveal it stems from downsampling layers employed in the network architecture. This issue makes the generator lack the incentive from the discriminator to learn high-frequency content of data, resulting in a significant spectrum discrepancy between generated images and real images. Since the Fourier transform is a bijective mapping, we argue that reducing this spectrum discrepancy would boost the performance of GANs. To this end, we introduce SSD-GAN, an enhancement of GANs to alleviate the spectral information loss in the discriminator. Specifically, we propose to embed a frequency-aware classifier into the discriminator to measure the realness of the input in both the spatial and spectral domains. With the enhanced discriminator, the generator of SSD-GAN is encouraged to learn high-frequency content of real data and generate exact details. The proposed method is general and can be easily integrated into most existing GANs framework without excessive cost. The effectiveness of SSD-GAN is validated on various network architectures, objective functions, and datasets. Code will be available at https://github.com/cyq373/SSD-GAN.

Zhangheng Li, Jia-Xing Zhong, Jingjia Huang et al.

In recent years, memory-augmented neural networks(MANNs) have shown promising power to enhance the memory ability of neural networks for sequential processing tasks. However, previous MANNs suffer from complex memory addressing mechanism, making them relatively hard to train and causing computational overheads. Moreover, many of them reuse the classical RNN structure such as LSTM for memory processing, causing inefficient exploitations of memory information. In this paper, we introduce a novel MANN, the Auto-addressing and Recurrent Memory Integrating Network (ARMIN) to address these issues. The ARMIN only utilizes hidden state ht for automatic memory addressing, and uses a novel RNN cell for refined integration of memory information. Empirical results on a variety of experiments demonstrate that the ARMIN is more light-weight and efficient compared to existing memory networks. Moreover, we demonstrate that the ARMIN can achieve much lower computational overhead than vanilla LSTM while keeping similar performances. Codes are available on github.com/zoharli/armin.

Lucas W. Remedios, Shunxing Bao, Samuel W. Remedios et al.

Understanding the way cells communicate, co-locate, and interrelate is essential to understanding human physiology. Hematoxylin and eosin (H&E) staining is ubiquitously available both for clinical studies and research. The Colon Nucleus Identification and Classification (CoNIC) Challenge has recently innovated on robust artificial intelligence labeling of six cell types on H&E stains of the colon. However, this is a very small fraction of the number of potential cell classification types. Specifically, the CoNIC Challenge is unable to classify epithelial subtypes (progenitor, endocrine, goblet), lymphocyte subtypes (B, helper T, cytotoxic T), or connective subtypes (fibroblasts, stromal). In this paper, we propose to use inter-modality learning to label previously un-labelable cell types on virtual H&E. We leveraged multiplexed immunofluorescence (MxIF) histology imaging to identify 14 subclasses of cell types. We performed style transfer to synthesize virtual H&E from MxIF and transferred the higher density labels from MxIF to these virtual H&E images. We then evaluated the efficacy of learning in this approach. We identified helper T and progenitor nuclei with positive predictive values of $0.34 \pm 0.15$ (prevalence $0.03 \pm 0.01$) and $0.47 \pm 0.1$ (prevalence $0.07 \pm 0.02$) respectively on virtual H&E. This approach represents a promising step towards automating annotation in digital pathology.

Youngseung Jeon, Ziwen Li, Thomas Li et al.

Retrieving the biological impacts of protein-protein interactions (PPIs) is essential for target identification (Target ID) in drug development. Given the vast number of proteins involved, this process remains time-consuming and challenging. Large Language Models (LLMs) and Retrieval-Augmented Generation (RAG) frameworks have supported Target ID; however, no benchmark currently exists for identifying the biological impacts of PPIs. To bridge this gap, we introduce the RAG Benchmark for PPIs (RAGPPI), a factual question-answer benchmark of 4,420 question-answer pairs that focus on the potential biological impacts of PPIs. Through interviews with experts, we identified criteria for a benchmark dataset, such as a type of QA and source. We built a gold-standard dataset (500 QA pairs) through expert-driven data annotation. We developed an ensemble auto-evaluation LLM that reflected expert labeling characteristics, which facilitates the construction of a silver-standard dataset (3,720 QA pairs). We are committed to maintaining RAGPPI as a resource to support the research community in advancing RAG systems for drug discovery QA solutions.

Lucas W. Remedios, Shunxing Bao, Samuel W. Remedios et al.

Understanding the way cells communicate, co-locate, and interrelate is essential to furthering our understanding of how the body functions. H&E is widely available, however, cell subtyping often requires expert knowledge and the use of specialized stains. To reduce the annotation burden, AI has been proposed for the classification of cells on H&E. For example, the recent Colon Nucleus Identification and Classification (CoNIC) Challenge focused on labeling 6 cell types on H&E of the colon. However, the CoNIC Challenge was unable to classify epithelial subtypes (progenitor, enteroendocrine, goblet), lymphocyte subtypes (B, helper T, cytotoxic T), and connective subtypes (fibroblasts). We use inter-modality learning to label previously un-labelable cell types on H&E. We take advantage of multiplexed immunofluorescence (MxIF) histology to label 14 cell subclasses. We performed style transfer on the same MxIF tissues to synthesize realistic virtual H&E which we paired with the MxIF-derived cell subclassification labels. We evaluated the efficacy of using a supervised learning scheme where the input was realistic-quality virtual H&E and the labels were MxIF-derived cell subclasses. We assessed our model on private virtual H&E and public real H&E. On virtual H&E, we were able to classify helper T cells and epithelial progenitors with positive predictive values of $0.34 \pm 0.15$ (prevalence $0.03 \pm 0.01$) and $0.47 \pm 0.1$ (prevalence $0.07 \pm 0.02$) respectively, when using ground truth centroid information. On real H&E we could classify helper T cells and epithelial progenitors with upper bound positive predictive values of $0.43 \pm 0.03$ (parent class prevalence 0.21) and $0.94 \pm 0.02$ (parent class prevalence 0.49) when using ground truth centroid information. This is the first work to provide cell type classification for helper T and epithelial progenitor nuclei on H&E.

Lianrui Zuo, Kaiwen Xu, Dingjie Su et al.

The interconnection between the human lungs and other organs, such as the liver and kidneys, is crucial for understanding the underlying risks and effects of lung diseases and improving patient care. However, most research chest CT imaging is focused solely on the lungs due to considerations of cost and radiation dose. This restricted field of view (FOV) in the acquired images poses challenges to comprehensive analysis and hinders the ability to gain insights into the impact of lung diseases on other organs. To address this, we propose SCOPE (Spatial Coverage Optimization with Prior Encoding), a novel approach to capture the inter-organ relationships from CT images and extend the FOV of chest CT images. Our approach first trains a variational autoencoder (VAE) to encode 2D axial CT slices individually, then stacks the latent representations of the VAE to form a 3D context for training a latent diffusion model. Once trained, our approach extends the FOV of CT images in the z-direction by generating new axial slices in a zero-shot manner. We evaluated our approach on the National Lung Screening Trial (NLST) dataset, and results suggest that it effectively extends the FOV to include the liver and kidneys, which are not completely covered in the original NLST data acquisition. Quantitative results on a held-out whole-body dataset demonstrate that the generated slices exhibit high fidelity with acquired data, achieving an SSIM of 0.81.

Sergio Casas, Ben Agro, Jiageng Mao et al.

The tasks of object detection and trajectory forecasting play a crucial role in understanding the scene for autonomous driving. These tasks are typically executed in a cascading manner, making them prone to compounding errors. Furthermore, there is usually a very thin interface between the two tasks, creating a lossy information bottleneck. To address these challenges, our approach formulates the union of the two tasks as a trajectory refinement problem, where the first pose is the detection (current time), and the subsequent poses are the waypoints of the multiple forecasts (future time). To tackle this unified task, we design a refinement transformer that infers the presence, pose, and multi-modal future behaviors of objects directly from LiDAR point clouds and high-definition maps. We call this model DeTra, short for object Detection and Trajectory forecasting. In our experiments, we observe that \ourmodel{} outperforms the state-of-the-art on Argoverse 2 Sensor and Waymo Open Dataset by a large margin, across a broad range of metrics. Last but not least, we perform extensive ablation studies that show the value of refinement for this task, that every proposed component contributes positively to its performance, and that key design choices were made.

Cece Jin, Yuanqi Chen, Ge Li et al.

In temporal action localization methods, temporal downsampling operations are widely used to extract proposal features, but they often lead to the aliasing problem, due to lacking consideration of sampling rates. This paper aims to verify the existence of aliasing in TAL methods and investigate utilizing low pass filters to solve this problem by inhibiting the high-frequency band. However, the high-frequency band usually contains large amounts of specific information, which is important for model inference. Therefore, it is necessary to make a tradeoff between anti-aliasing and reserving high-frequency information. To acquire optimal performance, this paper learns different cutoff frequencies for different instances dynamically. This design can be plugged into most existing temporal modeling programs requiring only one additional cutoff frequency parameter. Integrating low pass filters to the downsampling operations significantly improves the detection performance and achieves comparable results on THUMOS'14, ActivityNet~1.3, and Charades datasets. Experiments demonstrate that anti-aliasing with low pass filters in TAL is advantageous and efficient.

Wei-Hong Lin, Jia-Xing Zhong, Shan Liu et al.

Generic object detection algorithms have proven their excellent performance in recent years. However, object detection on underwater datasets is still less explored. In contrast to generic datasets, underwater images usually have color shift and low contrast; sediment would cause blurring in underwater images. In addition, underwater creatures often appear closely to each other on images due to their living habits. To address these issues, our work investigates augmentation policies to simulate overlapping, occluded and blurred objects, and we construct a model capable of achieving better generalization. We propose an augmentation method called RoIMix, which characterizes interactions among images. Proposals extracted from different images are mixed together. Previous data augmentation methods operate on a single image while we apply RoIMix to multiple images to create enhanced samples as training data. Experiments show that our proposed method improves the performance of region-based object detectors on both Pascal VOC and URPC datasets.

Xiaoming Yu, Yuanqi Chen, Thomas Li et al.

Recent advances of image-to-image translation focus on learning the one-to-many mapping from two aspects: multi-modal translation and multi-domain translation. However, the existing methods only consider one of the two perspectives, which makes them unable to solve each other's problem. To address this issue, we propose a novel unified model, which bridges these two objectives. First, we disentangle the input images into the latent representations by an encoder-decoder architecture with a conditional adversarial training in the feature space. Then, we encourage the generator to learn multi-mappings by a random cross-domain translation. As a result, we can manipulate different parts of the latent representations to perform multi-modal and multi-domain translations simultaneously. Experiments demonstrate that our method outperforms state-of-the-art methods.

Weijie Kong, Nannan Li, Shan Liu et al.

Despite tremendous progress achieved in temporal action detection, state-of-the-art methods still suffer from the sharp performance deterioration when localizing the starting and ending temporal action boundaries. Although most methods apply boundary regression paradigm to tackle this problem, we argue that the direct regression lacks detailed enough information to yield accurate temporal boundaries. In this paper, we propose a novel Boundary Likelihood Pinpointing (BLP) network to alleviate this deficiency of boundary regression and improve the localization accuracy. Given a loosely localized search interval that contains an action instance, BLP casts the problem of localizing temporal boundaries as that of assigning probabilities on each equally divided unit of this interval. These generated probabilities provide useful information regarding the boundary location of the action inside this search interval. Based on these probabilities, we introduce a boundary pinpointing paradigm to pinpoint the accurate boundaries under a simple probabilistic framework. Compared with other C3D feature based detectors, extensive experiments demonstrate that BLP significantly improves the localization performance of recent state-of-the-art detectors, and achieves competitive detection mAP on both THUMOS' 14 and ActivityNet datasets, particularly when the evaluation tIoU is high.

Xiaoming Yu, Xing Cai, Zhenqiang Ying et al.

Image translation is a burgeoning field in computer vision where the goal is to learn the mapping between an input image and an output image. However, most recent methods require multiple generators for modeling different domain mappings, which are inefficient and ineffective on some multi-domain image translation tasks. In this paper, we propose a novel method, SingleGAN, to perform multi-domain image-to-image translations with a single generator. We introduce the domain code to explicitly control the different generative tasks and integrate multiple optimization goals to ensure the translation. Experimental results on several unpaired datasets show superior performance of our model in translation between two domains. Besides, we explore variants of SingleGAN for different tasks, including one-to-many domain translation, many-to-many domain translation and one-to-one domain translation with multimodality. The extended experiments show the universality and extensibility of our model.

Xiaoming Yu, Zhenqiang Ying, Thomas Li et al.

Recent advances in image-to-image translation have seen a rise in approaches generating diverse images through a single network. To indicate the target domain for a one-to-many mapping, the latent code is injected into the generator network. However, we found that the injection method leads to mode collapse because of normalization strategies. Existing normalization strategies might either cause the inconsistency of feature distribution or eliminate the effect of the latent code. To solve these problems, we propose the consistency within diversity criteria for designing the multi-mapping model. Based on the criteria, we propose central biasing normalization to inject the latent code information. Experiments show that our method can improve the quality and diversity of existing image-to-image translation models, such as StarGAN, BicycleGAN, and pix2pix.