Quan Liu

Tianyuan Yao, Chang Qu, Jun Long et al.

With the rapid development of self-supervised learning (e.g., contrastive learning), the importance of having large-scale images (even without annotations) for training a more generalizable AI model has been widely recognized in medical image analysis. However, collecting large-scale task-specific unannotated data at scale can be challenging for individual labs. Existing online resources, such as digital books, publications, and search engines, provide a new resource for obtaining large-scale images. However, published images in healthcare (e.g., radiology and pathology) consist of a considerable amount of compound figures with subplots. In order to extract and separate compound figures into usable individual images for downstream learning, we propose a simple compound figure separation (SimCFS) framework without using the traditionally required detection bounding box annotations, with a new loss function and a hard case simulation. Our technical contribution is four-fold: (1) we introduce a simulation-based training framework that minimizes the need for resource extensive bounding box annotations; (2) we propose a new side loss that is optimized for compound figure separation; (3) we propose an intra-class image augmentation method to simulate hard cases; and (4) to the best of our knowledge, this is the first study that evaluates the efficacy of leveraging self-supervised learning with compound image separation. From the results, the proposed SimCFS achieved state-of-the-art performance on the ImageCLEF 2016 Compound Figure Separation Database. The pretrained self-supervised learning model using large-scale mined figures improved the accuracy of downstream image classification tasks with a contrastive learning algorithm. The source code of SimCFS is made publicly available at https://github.com/hrlblab/ImageSeperation.

Yunsong Zhou, Hongzi Zhu, Quan Liu et al.

Mobile monocular 3D object detection (Mono3D) (e.g., on a vehicle, a drone, or a robot) is an important yet challenging task. Existing transformer-based offline Mono3D models adopt grid-based vision tokens, which is suboptimal when using coarse tokens due to the limited available computational power. In this paper, we propose an online Mono3D framework, called MonoATT, which leverages a novel vision transformer with heterogeneous tokens of varying shapes and sizes to facilitate mobile Mono3D. The core idea of MonoATT is to adaptively assign finer tokens to areas of more significance before utilizing a transformer to enhance Mono3D. To this end, we first use prior knowledge to design a scoring network for selecting the most important areas of the image, and then propose a token clustering and merging network with an attention mechanism to gradually merge tokens around the selected areas in multiple stages. Finally, a pixel-level feature map is reconstructed from heterogeneous tokens before employing a SOTA Mono3D detector as the underlying detection core. Experiment results on the real-world KITTI dataset demonstrate that MonoATT can effectively improve the Mono3D accuracy for both near and far objects and guarantee low latency. MonoATT yields the best performance compared with the state-of-the-art methods by a large margin and is ranked number one on the KITTI 3D benchmark.

Can Cui, Ruining Deng, Quan Liu et al.

The Segment Anything Model (SAM) is a recently proposed prompt-based segmentation model in a generic zero-shot segmentation approach. With the zero-shot segmentation capacity, SAM achieved impressive flexibility and precision on various segmentation tasks. However, the current pipeline requires manual prompts during the inference stage, which is still resource intensive for biomedical image segmentation. In this paper, instead of using prompts during the inference stage, we introduce a pipeline that utilizes the SAM, called all-in-SAM, through the entire AI development workflow (from annotation generation to model finetuning) without requiring manual prompts during the inference stage. Specifically, SAM is first employed to generate pixel-level annotations from weak prompts (e.g., points, bounding box). Then, the pixel-level annotations are used to finetune the SAM segmentation model rather than training from scratch. Our experimental results reveal two key findings: 1) the proposed pipeline surpasses the state-of-the-art (SOTA) methods in a nuclei segmentation task on the public Monuseg dataset, and 2) the utilization of weak and few annotations for SAM finetuning achieves competitive performance compared to using strong pixel-wise annotated data.

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.

Ho Hin Lee, Quan Liu, Qi Yang et al.

The application of 3D ViTs to medical image segmentation has seen remarkable strides, somewhat overshadowing the budding advancements in Convolutional Neural Network (CNN)-based models. Large kernel depthwise convolution has emerged as a promising technique, showcasing capabilities akin to hierarchical transformers and facilitating an expansive effective receptive field (ERF) vital for dense predictions. Despite this, existing core operators, ranging from global-local attention to large kernel convolution, exhibit inherent trade-offs and limitations (e.g., global-local range trade-off, aggregating attentional features). We hypothesize that deformable convolution can be an exploratory alternative to combine all advantages from the previous operators, providing long-range dependency, adaptive spatial aggregation and computational efficiency as a foundation backbone. In this work, we introduce 3D DeformUX-Net, a pioneering volumetric CNN model that adeptly navigates the shortcomings traditionally associated with ViTs and large kernel convolution. Specifically, we revisit volumetric deformable convolution in depth-wise setting to adapt long-range dependency with computational efficiency. Inspired by the concepts of structural re-parameterization for convolution kernel weights, we further generate the deformable tri-planar offsets by adapting a parallel branch (starting from $1\times1\times1$ convolution), providing adaptive spatial aggregation across all channels. Our empirical evaluations reveal that the 3D DeformUX-Net consistently outperforms existing state-of-the-art ViTs and large kernel convolution models across four challenging public datasets, spanning various scales from organs (KiTS: 0.680 to 0.720, MSD Pancreas: 0.676 to 0.717, AMOS: 0.871 to 0.902) to vessels (e.g., MSD hepatic vessels: 0.635 to 0.671) in mean Dice.

Quan Liu, Kehao Wang, Lin Chen

In this paper,we consider the restless bandit problem, which is one of the most well-studied generalizations of the celebrated stochastic multi-armed bandit problem in decision theory. However, it is known be PSPACE-Hard to approximate to any non-trivial factor. Thus the optimality is very difficult to obtain due to its high complexity. A natural method is to obtain the greedy policy considering its stability and simplicity. However, the greedy policy will result in the optimality loss for its intrinsic myopic behavior generally. In this paper, by analyzing one class of so-called standard reward function, we establish the closed-form condition about the discounted factor βsuch that the optimality of the greedy policy is guaranteed under the discounted expected reward criterion, especially, the condition β= 1 indicating the optimality of the greedy policy under the average accumulative reward criterion. Thus, the standard form of reward function can easily be used to judge the optimality of the greedy policy without any complicated calculation. Some examples in cognitive radio networks are presented to verify the effectiveness of the mathematical result in judging the optimality of the greedy policy.

Jialin Yue, Tianyuan Yao, Ruining Deng et al.

Recently, the use of circle representation has emerged as a method to improve the identification of spherical objects (such as glomeruli, cells, and nuclei) in medical imaging studies. In traditional bounding box-based object detection, combining results from multiple models improves accuracy, especially when real-time processing isn't crucial. Unfortunately, this widely adopted strategy is not readily available for combining circle representations. In this paper, we propose Weighted Circle Fusion (WCF), a simple approach for merging predictions from various circle detection models. Our method leverages confidence scores associated with each proposed bounding circle to generate averaged circles. We evaluate our method on a proprietary dataset for glomerular detection in whole slide imaging (WSI) and find a performance gain of 5% compared to existing ensemble methods. Additionally, we assess the efficiency of two annotation methods, fully manual annotation and a human-in-the-loop (HITL) approach, in labeling 200,000 glomeruli. The HITL approach, which integrates machine learning detection with human verification, demonstrated remarkable improvements in annotation efficiency. The Weighted Circle Fusion technique not only enhances object detection precision but also notably reduces false detections, presenting a promising direction for future research and application in pathological image analysis. The source code has been made publicly available at https://github.com/hrlblab/WeightedCircleFusion

Tianyuan Yao, Chang Qu, Quan Liu et al.

Unsupervised learning algorithms (e.g., self-supervised learning, auto-encoder, contrastive learning) allow deep learning models to learn effective image representations from large-scale unlabeled data. In medical image analysis, even unannotated data can be difficult to obtain for individual labs. Fortunately, national-level efforts have been made to provide efficient access to obtain biomedical image data from previous scientific publications. For instance, NIH has launched the Open-i search engine that provides a large-scale image database with free access. However, the images in scientific publications consist of a considerable amount of compound figures with subplots. To extract and curate individual subplots, many different compound figure separation approaches have been developed, especially with the recent advances in deep learning. However, previous approaches typically required resource extensive bounding box annotation to train detection models. In this paper, we propose a simple compound figure separation (SimCFS) framework that uses weak classification annotations from individual images. Our technical contribution is three-fold: (1) we introduce a new side loss that is designed for compound figure separation; (2) we introduce an intra-class image augmentation method to simulate hard cases; (3) the proposed framework enables an efficient deployment to new classes of images, without requiring resource extensive bounding box annotations. From the results, the SimCFS achieved a new state-of-the-art performance on the ImageCLEF 2016 Compound Figure Separation Database. The source code of SimCFS is made publicly available at https://github.com/hrlblab/ImageSeperation.

Yunzhe Li, Facheng Hu, Hongzi Zhu et al.

A wide range of user perception applications leverage inertial measurement unit (IMU) data for online prediction. However, restricted by the non-i.i.d. nature of IMU data collected from mobile devices, most systems work well only in a controlled setting (e.g., for a specific user in particular postures), limiting application scenarios. To achieve uncontrolled online prediction on mobile devices, referred to as the flexible user perception (FUP) problem, is attractive but hard. In this paper, we propose a novel scheme, called Prism, which can obtain high FUP accuracy on mobile devices. The core of Prism is to discover task-aware domains embedded in IMU dataset, and to train a domain-aware model on each identified domain. To this end, we design an expectation-maximization (EM) algorithm to estimate latent domains with respect to the specific downstream perception task. Finally, the best-fit model can be automatically selected for use by comparing the test sample and all identified domains in the feature space. We implement Prism on various mobile devices and conduct extensive experiments. Results demonstrate that Prism can achieve the best FUP performance with a low latency.

Yu-Ping Ruan, Xiaodan Zhu, Zhen-Hua Ling et al.

Winograd Schema Challenge (WSC) was proposed as an AI-hard problem in testing computers' intelligence on common sense representation and reasoning. This paper presents the new state-of-theart on WSC, achieving an accuracy of 71.1%. We demonstrate that the leading performance benefits from jointly modelling sentence structures, utilizing knowledge learned from cutting-edge pretraining models, and performing fine-tuning. We conduct detailed analyses, showing that fine-tuning is critical for achieving the performance, but it helps more on the simpler associative problems. Modelling sentence dependency structures, however, consistently helps on the harder non-associative subset of WSC. Analysis also shows that larger fine-tuning datasets yield better performances, suggesting the potential benefit of future work on annotating more Winograd schema sentences.