Yiwen Li

M. Jorge Cardoso, Wenqi Li, Richard Brown et al.

Artificial Intelligence (AI) is having a tremendous impact across most areas of science. Applications of AI in healthcare have the potential to improve our ability to detect, diagnose, prognose, and intervene on human disease. For AI models to be used clinically, they need to be made safe, reproducible and robust, and the underlying software framework must be aware of the particularities (e.g. geometry, physiology, physics) of medical data being processed. This work introduces MONAI, a freely available, community-supported, and consortium-led PyTorch-based framework for deep learning in healthcare. MONAI extends PyTorch to support medical data, with a particular focus on imaging, and provide purpose-specific AI model architectures, transformations and utilities that streamline the development and deployment of medical AI models. MONAI follows best practices for software-development, providing an easy-to-use, robust, well-documented, and well-tested software framework. MONAI preserves the simple, additive, and compositional approach of its underlying PyTorch libraries. MONAI is being used by and receiving contributions from research, clinical and industrial teams from around the world, who are pursuing applications spanning nearly every aspect of healthcare.

Yunguan Fu, Yiwen Li, Shaheer U Saeed et al.

Denoising diffusion models have found applications in image segmentation by generating segmented masks conditioned on images. Existing studies predominantly focus on adjusting model architecture or improving inference, such as test-time sampling strategies. In this work, we focus on improving the training strategy and propose a novel recycling method. During each training step, a segmentation mask is first predicted given an image and a random noise. This predicted mask, which replaces the conventional ground truth mask, is used for denoising task during training. This approach can be interpreted as aligning the training strategy with inference by eliminating the dependence on ground truth masks for generating noisy samples. Our proposed method significantly outperforms standard diffusion training, self-conditioning, and existing recycling strategies across multiple medical imaging data sets: muscle ultrasound, abdominal CT, prostate MR, and brain MR. This holds for two widely adopted sampling strategies: denoising diffusion probabilistic model and denoising diffusion implicit model. Importantly, existing diffusion models often display a declining or unstable performance during inference, whereas our novel recycling consistently enhances or maintains performance. We show that, under a fair comparison with the same network architectures and computing budget, the proposed recycling-based diffusion models achieved on-par performance with non-diffusion-based supervised training. By ensembling the proposed diffusion and the non-diffusion models, significant improvements to the non-diffusion models have been observed across all applications, demonstrating the value of this novel training method. This paper summarizes these quantitative results and discusses their values, with a fully reproducible JAX-based implementation, released at https://github.com/mathpluscode/ImgX-DiffSeg.

Yunguan Fu, Yiwen Li, Shaheer U. Saeed et al.

Recently, denoising diffusion probabilistic models (DDPM) have been applied to image segmentation by generating segmentation masks conditioned on images, while the applications were mainly limited to 2D networks without exploiting potential benefits from the 3D formulation. In this work, we studied the DDPM-based segmentation model for 3D multiclass segmentation on two large multiclass data sets (prostate MR and abdominal CT). We observed that the difference between training and test methods led to inferior performance for existing DDPM methods. To mitigate the inconsistency, we proposed a recycling method which generated corrupted masks based on the model's prediction at a previous time step instead of using ground truth. The proposed method achieved statistically significantly improved performance compared to existing DDPMs, independent of a number of other techniques for reducing train-test discrepancy, including performing mask prediction, using Dice loss, and reducing the number of diffusion time steps during training. The performance of diffusion models was also competitive and visually similar to non-diffusion-based U-net, within the same compute budget. The JAX-based diffusion framework has been released at https://github.com/mathpluscode/ImgX-DiffSeg.

Yiwen Li, Yunguan Fu, Iani Gayo et al.

The prowess that makes few-shot learning desirable in medical image analysis is the efficient use of the support image data, which are labelled to classify or segment new classes, a task that otherwise requires substantially more training images and expert annotations. This work describes a fully 3D prototypical few-shot segmentation algorithm, such that the trained networks can be effectively adapted to clinically interesting structures that are absent in training, using only a few labelled images from a different institute. First, to compensate for the widely recognised spatial variability between institutions in episodic adaptation of novel classes, a novel spatial registration mechanism is integrated into prototypical learning, consisting of a segmentation head and an spatial alignment module. Second, to assist the training with observed imperfect alignment, support mask conditioning module is proposed to further utilise the annotation available from the support images. Extensive experiments are presented in an application of segmenting eight anatomical structures important for interventional planning, using a data set of 589 pelvic T2-weighted MR images, acquired at seven institutes. The results demonstrate the efficacy in each of the 3D formulation, the spatial registration, and the support mask conditioning, all of which made positive contributions independently or collectively. Compared with the previously proposed 2D alternatives, the few-shot segmentation performance was improved with statistical significance, regardless whether the support data come from the same or different institutes.

Xiaoyu Ma, Yiwen Li, Haoyue Liu et al.

Automatic prompt optimization (APO) hinges on the quality of its evaluation signal, yet scoring every prompt candidate on the full training set is prohibitively expensive. Existing methods either fix a single evaluation subset before optimization begins (principled but prompt-agnostic) or adapt it heuristically during optimization (flexible but unstable and lacking formal guarantees). We observe that APO naturally maps to an online adaptive testing problem: prompts are examinees, training examples are test items, and the scheduler should select items that best discriminate among the strongest candidates. This insight motivates Prompt-Aware Online Evaluation Scheduling (POES), which integrates an IRT-based discrimination utility, a facility-location coverage term, and switching-cost-aware warm-start swaps into a unified objective that is provably monotone submodular, yielding a (1-1/e) greedy guarantee for cold starts and bounded drift for warm-start updates. An adaptive controller modulates the exploration-exploitation balance based on optimization progress. Across 36 tasks spanning three benchmark families, POES achieves the highest overall average accuracy (6.2 percent improvement over the best baseline) with negligible token overhead (approximately 4 percent) at the same evaluation budget. Moreover, principled selection at k = 20 examples matches or exceeds the performance of naive evaluation at k = 30-50, reducing token consumption by 35-60 percent, showing that selecting smarter is more effective than selecting more. Our results demonstrate that evaluation scheduling is a first-class component of APO, not an implementation detail.

Chengshuai Zhao, Fan Zhang, Kumar Satvik Chaudhary et al.

Open-ended grading is central to equitable and personalized education, yet manual grading remains time-consuming and costly, underscoring the need for automated grading systems. Although recent neural and large language model (LLM) based systems have demonstrated superior performance, they are typically black-box models whose scoring processes and rationales are difficult for educators to verify and trust. Concept bottleneck models (CBMs) have emerged as a promising approach by routing predictions through human-interpretable concepts, providing a mechanistic guarantee of transparency. However, standard CBMs are not tailored to open-ended grading: they do not explicitly model fine-grained rubric dimensions, inadequately capture the ordinal semantics of scoring scales, and neglect inherent reliability issues in human concept annotations. To address these limitations, we propose REC-CBM, a rubric-aware error-correction concept bottleneck model for trustworthy open-ended grading. REC-CBM introduces a rubric-aware concept encoder that learns concept-specific representations over responses and an ordinal pairwise calibration objective that preserves ranking structure among rubric dimensions. It further incorporates a latent concept error-correction module that denoises concept predictions before final grade prediction while preserving interpretability. Comprehensive experiments on publicly available datasets show that REC-CBM consistently improves grading performance and produces more faithful concept-level reasoning than both state-of-the-art baselines. Further analyses validate the contribution of each component and demonstrate the applicability in realistic educational settings. Overall, this work provides a practical, interpretable grading solution that enables educators to inspect, intervene in, and trust automated decisions, advancing more transparent and trustworthy education.

Yiwen Li, Yunguan Fu, Iani J. M. B. Gayo et al.

For training registration networks, weak supervision from segmented corresponding regions-of-interest (ROIs) have been proven effective for (a) supplementing unsupervised methods, and (b) being used independently in registration tasks in which unsupervised losses are unavailable or ineffective. This correspondence-informing supervision entails cost in annotation that requires significant specialised effort. This paper describes a semi-weakly-supervised registration pipeline that improves the model performance, when only a small corresponding-ROI-labelled dataset is available, by exploiting unlabelled image pairs. We examine two types of augmentation methods by perturbation on network weights and image resampling, such that consistency-based unsupervised losses can be applied on unlabelled data. The novel WarpDDF and RegCut approaches are proposed to allow commutative perturbation between an image pair and the predicted spatial transformation (i.e. respective input and output of registration networks), distinct from existing perturbation methods for classification or segmentation. Experiments using 589 male pelvic MR images, labelled with eight anatomical ROIs, show the improvement in registration performance and the ablated contributions from the individual strategies. Furthermore, this study attempts to construct one of the first computational atlases for pelvic structures, enabled by registering inter-subject MRs, and quantifies the significant differences due to the proposed semi-weak supervision with a discussion on the potential clinical use of example atlas-derived statistics.

Chengshuai Zhao, Riccardo De Maria, Tharindu Kumarage et al.

Advancements in large language models (LLMs) have enabled the development of intelligent educational tools that support inquiry-based learning across technical domains. In cybersecurity education, where accuracy and safety are paramount, systems must go beyond surface-level relevance to provide information that is both trustworthy and domain-appropriate. To address this challenge, we introduce CyberBOT, a question-answering chatbot that leverages a retrieval-augmented generation (RAG) pipeline to incorporate contextual information from course-specific materials and validate responses using a domain-specific cybersecurity ontology. The ontology serves as a structured reasoning layer that constrains and verifies LLM-generated answers, reducing the risk of misleading or unsafe guidance. CyberBOT has been deployed in a large graduate-level course at Arizona State University (ASU), where more than one hundred students actively engage with the system through a dedicated web-based platform. Computational evaluations in lab environments highlight the potential capacity of CyberBOT, and a forthcoming field study will evaluate its pedagogical impact. By integrating structured domain reasoning with modern generative capabilities, CyberBOT illustrates a promising direction for developing reliable and curriculum-aligned AI applications in specialized educational contexts.

Sixian Liu, Chen Xu, Qiang Wang et al.

Multimodal camera-LiDAR fusion technology has found extensive application in 3D object detection, demonstrating encouraging performance. However, existing methods exhibit significant performance degradation in challenging scenarios characterized by sensor degradation or environmental disturbances. We propose a novel Adaptive Gated Fusion (AG-Fusion) approach that selectively integrates cross-modal knowledge by identifying reliable patterns for robust detection in complex scenes. Specifically, we first project features from each modality into a unified BEV space and enhance them using a window-based attention mechanism. Subsequently, an adaptive gated fusion module based on cross-modal attention is designed to integrate these features into reliable BEV representations robust to challenging environments. Furthermore, we construct a new dataset named Excavator3D (E3D) focusing on challenging excavator operation scenarios to benchmark performance in complex conditions. Our method not only achieves competitive performance on the standard KITTI dataset with 93.92% accuracy, but also significantly outperforms the baseline by 24.88% on the challenging E3D dataset, demonstrating superior robustness to unreliable modal information in complex industrial scenes.

Yiwen Li, Yunguan Fu, Qianye Yang et al.

The ability to adapt medical image segmentation networks for a novel class such as an unseen anatomical or pathological structure, when only a few labelled examples of this class are available from local healthcare providers, is sought-after. This potentially addresses two widely recognised limitations in deploying modern deep learning models to clinical practice, expertise-and-labour-intensive labelling and cross-institution generalisation. This work presents the first 3D few-shot interclass segmentation network for medical images, using a labelled multi-institution dataset from prostate cancer patients with eight regions of interest. We propose an image alignment module registering the predicted segmentation of both query and support data, in a standard prototypical learning algorithm, to a reference atlas space. The built-in registration mechanism can effectively utilise the prior knowledge of consistent anatomy between subjects, regardless whether they are from the same institution or not. Experimental results demonstrated that the proposed registration-assisted prototypical learning significantly improved segmentation accuracy (p-values<0.01) on query data from a holdout institution, with varying availability of support data from multiple institutions. We also report the additional benefits of the proposed 3D networks with 75% fewer parameters and an arguably simpler implementation, compared with existing 2D few-shot approaches that segment 2D slices of volumetric medical images.

Yiwen Li, Gratianus Wesley Putra Data, Yunguan Fu et al.

Despite the success of deep learning methods for semantic segmentation, few-shot semantic segmentation remains a challenging task due to the limited training data and the generalisation requirement for unseen classes. While recent progress has been particularly encouraging, we discover that existing methods tend to have poor performance in terms of meanIoU when query images contain other semantic classes besides the target class. To address this issue, we propose a novel self-supervised task that generates random pseudo-classes in the background of the query images, providing extra training data that would otherwise be unavailable when predicting individual target classes. To that end, we adopted superpixel segmentation for generating the pseudo-classes. With this extra supervision, we improved the meanIoU performance of the state-of-the-art method by 2.5% and 5.1% on the one-shot tasks, as well as 6.7% and 4.4% on the five-shot tasks, on the PASCAL-5i and COCO benchmarks, respectively.

Henry Howard-Jenkins, Yiwen Li, Victor A. Prisacariu

We present a novel approach which is able to explore the configuration of grouped convolutions within neural networks. Group-size Series (GroSS) decomposition is a mathematical formulation of tensor factorisation into a series of approximations of increasing rank terms. GroSS allows for dynamic and differentiable selection of factorisation rank, which is analogous to a grouped convolution. Therefore, to the best of our knowledge, GroSS is the first method to enable simultaneous training of differing numbers of groups within a single layer, as well as all possible combinations between layers. In doing so, GroSS is able to train an entire grouped convolution architecture search-space concurrently. We demonstrate this through architecture searches with performance objectives on multiple datasets and networks. GroSS enables more effective and efficient search for grouped convolutional architectures.