Ge Wang

Zicheng Liu, Siyuan Li, Ge Wang et al.

Mixup is an efficient data augmentation approach that improves the generalization of neural networks by smoothing the decision boundary with mixed data. Recently, dynamic mixup methods have improved previous static policies effectively (e.g., linear interpolation) by maximizing target-related salient regions in mixed samples, but excessive additional time costs are not acceptable. These additional computational overheads mainly come from optimizing the mixed samples according to the mixed labels. However, we found that the extra optimizing step may be redundant because label-mismatched mixed samples are informative hard mixed samples for deep models to localize discriminative features. In this paper, we thus are not trying to propose a more complicated dynamic mixup policy but rather an efficient mixup objective function with a decoupled regularizer named Decoupled Mixup (DM). The primary effect is that DM can adaptively utilize those hard mixed samples to mine discriminative features without losing the original smoothness of mixup. As a result, DM enables static mixup methods to achieve comparable or even exceed the performance of dynamic methods without any extra computation. This also leads to an interesting objective design problem for mixup training that we need to focus on both smoothing the decision boundaries and identifying discriminative features. Extensive experiments on supervised and semi-supervised learning benchmarks across seven datasets validate the effectiveness of DM as a plug-and-play module. Source code and models are available at https://github.com/Westlake-AI/openmixup

Zhihao Chen, Chuang Niu, Qi Gao et al.

This paper studies 3D low-dose computed tomography (CT) imaging. Although various deep learning methods were developed in this context, typically they focus on 2D images and perform denoising due to low-dose and deblurring for super-resolution separately. Up to date, little work was done for simultaneous in-plane denoising and through-plane deblurring, which is important to obtain high-quality 3D CT images with lower radiation and faster imaging speed. For this task, a straightforward method is to directly train an end-to-end 3D network. However, it demands much more training data and expensive computational costs. Here, we propose to link in-plane and through-plane transformers for simultaneous in-plane denoising and through-plane deblurring, termed as LIT-Former, which can efficiently synergize in-plane and through-plane sub-tasks for 3D CT imaging and enjoy the advantages of both convolution and transformer networks. LIT-Former has two novel designs: efficient multi-head self-attention modules (eMSM) and efficient convolutional feedforward networks (eCFN). First, eMSM integrates in-plane 2D self-attention and through-plane 1D self-attention to efficiently capture global interactions of 3D self-attention, the core unit of transformer networks. Second, eCFN integrates 2D convolution and 1D convolution to extract local information of 3D convolution in the same fashion. As a result, the proposed LIT-Former synergize these two subtasks, significantly reducing the computational complexity as compared to 3D counterparts and enabling rapid convergence. Extensive experimental results on simulated and clinical datasets demonstrate superior performance over state-of-the-art models. The source code is made available at https://github.com/hao1635/LIT-Former.

Zilong Li, Qi Gao, Yaping Wu et al.

Metal implants and other high-density objects in patients introduce severe streaking artifacts in CT images, compromising image quality and diagnostic performance. Although various methods were developed for CT metal artifact reduction over the past decades, including the latest dual-domain deep networks, remaining metal artifacts are still clinically challenging in many cases. Here we extend the state-of-the-art dual-domain deep network approach into a quad-domain counterpart so that all the features in the sinogram, image, and their corresponding Fourier domains are synergized to eliminate metal artifacts optimally without compromising structural subtleties. Our proposed quad-domain network for MAR, referred to as Quad-Net, takes little additional computational cost since the Fourier transform is highly efficient, and works across the four receptive fields to learn both global and local features as well as their relations. Specifically, we first design a Sinogram-Fourier Restoration Network (SFR-Net) in the sinogram domain and its Fourier space to faithfully inpaint metal-corrupted traces. Then, we couple SFR-Net with an Image-Fourier Refinement Network (IFR-Net) which takes both an image and its Fourier spectrum to improve a CT image reconstructed from the SFR-Net output using cross-domain contextual information. Quad-Net is trained on clinical datasets to minimize a composite loss function. Quad-Net does not require precise metal masks, which is of great importance in clinical practice. Our experimental results demonstrate the superiority of Quad-Net over the state-of-the-art MAR methods quantitatively, visually, and statistically. The Quad-Net code is publicly available at https://github.com/longzilicart/Quad-Net.

Zelin Zang, Siyuan Li, Di Wu et al. · tsinghua

Manifold learning (ML) aims to seek low-dimensional embedding from high-dimensional data. The problem is challenging on real-world datasets, especially with under-sampling data, and we find that previous methods perform poorly in this case. Generally, ML methods first transform input data into a low-dimensional embedding space to maintain the data's geometric structure and subsequently perform downstream tasks therein. The poor local connectivity of under-sampling data in the former step and inappropriate optimization objectives in the latter step leads to two problems: structural distortion and underconstrained embedding. This paper proposes a novel ML framework named Deep Local-flatness Manifold Embedding (DLME) to solve these problems. The proposed DLME constructs semantic manifolds by data augmentation and overcomes the structural distortion problem using a smoothness constrained based on a local flatness assumption about the manifold. To overcome the underconstrained embedding problem, we design a loss and theoretically demonstrate that it leads to a more suitable embedding based on the local flatness. Experiments on three types of datasets (toy, biological, and image) for various downstream tasks (classification, clustering, and visualization) show that our proposed DLME outperforms state-of-the-art ML and contrastive learning methods.

Chuang Niu, Md Sayed Tanveer, Md Zabirul Islam et al.

Current LLMs for creating fully-structured reports face the challenges of formatting errors, content hallucinations, and privacy leakage issues when uploading data to external servers.We aim to develop an open-source, accurate LLM for creating fully-structured and standardized LCS reports from varying free-text reports across institutions and demonstrate its utility in automatic statistical analysis and individual lung nodule retrieval. With IRB approvals, our retrospective study included 5,442 de-identified LDCT LCS radiology reports from two institutions. We constructed two evaluation datasets by labeling 500 pairs of free-text and fully-structured radiology reports and one large-scale consecutive dataset from January 2021 to December 2023. Two radiologists created a standardized template for recording 27 lung nodule features on LCS. We designed a dynamic-template-constrained decoding method to enhance existing LLMs for creating fully-structured reports from free-text radiology reports. Using consecutive structured reports, we automated descriptive statistical analyses and a nodule retrieval prototype. Our best LLM for creating fully-structured reports achieved high performance on cross-institutional datasets with an F1 score of about 97%, with neither formatting errors nor content hallucinations. Our method consistently improved the best open-source LLMs by up to 10.42%, and outperformed GPT-4o by 17.19%. The automatically derived statistical distributions were consistent with prior findings regarding attenuation, location, size, stability, and Lung-RADS. The retrieval system with structured reports allowed flexible nodule-level search and complex statistical analysis. Our developed software is publicly available for local deployment and further research.

Yuhui Ruan, Qiao Yuan, Chuang Niu et al.

Deep learning has been successfully applied to low-dose CT (LDCT) image denoising for reducing potential radiation risk. However, the widely reported supervised LDCT denoising networks require a training set of paired images, which is expensive to obtain and cannot be perfectly simulated. Unsupervised learning utilizes unpaired data and is highly desirable for LDCT denoising. As an example, an artifact disentanglement network (ADN) relies on unparied images and obviates the need for supervision but the results of artifact reduction are not as good as those through supervised learning.An important observation is that there is often hidden similarity among unpaired data that can be utilized. This paper introduces a new learning mode, called quasi-supervised learning, to empower the ADN for LDCT image denoising.For every LDCT image, the best matched image is first found from an unpaired normal-dose CT (NDCT) dataset. Then, the matched pairs and the corresponding matching degree as prior information are used to construct and train our ADN-type network for LDCT denoising.The proposed method is different from (but compatible with) supervised and semi-supervised learning modes and can be easily implemented by modifying existing networks. The experimental results show that the method is competitive with state-of-the-art methods in terms of noise suppression and contextual fidelity. The code and working dataset are publicly available at https://github.com/ruanyuhui/ADN-QSDL.git.

Razi Mahmood, Diego Machado Reyes, Ge Wang et al. · berkeley

With advances in generative artificial intelligence (AI), it is now possible to produce realistic-looking automated reports for preliminary reads of radiology images. This can expedite clinical workflows, improve accuracy and reduce overall costs. However, it is also well-known that such models often hallucinate, leading to false findings in the generated reports. In this paper, we propose a new method of fact-checking of AI-generated reports using their associated images. Specifically, the developed examiner differentiates real and fake sentences in reports by learning the association between an image and sentences describing real or potentially fake findings. To train such an examiner, we first created a new dataset of fake reports by perturbing the findings in the original ground truth radiology reports associated with images. Text encodings of real and fake sentences drawn from these reports are then paired with image encodings to learn the mapping to real/fake labels. The utility of such an examiner is demonstrated for verifying automatically generated reports by detecting and removing fake sentences. Future generative AI approaches can use the resulting tool to validate their reports leading to a more responsible use of AI in expediting clinical workflows.

Jiangbin Zheng, Yile Wang, Cheng Tan et al.

Sign language recognition (SLR) is a weakly supervised task that annotates sign videos as textual glosses. Recent studies show that insufficient training caused by the lack of large-scale available sign datasets becomes the main bottleneck for SLR. Most SLR works thereby adopt pretrained visual modules and develop two mainstream solutions. The multi-stream architectures extend multi-cue visual features, yielding the current SOTA performances but requiring complex designs and might introduce potential noise. Alternatively, the advanced single-cue SLR frameworks using explicit cross-modal alignment between visual and textual modalities are simple and effective, potentially competitive with the multi-cue framework. In this work, we propose a novel contrastive visual-textual transformation for SLR, CVT-SLR, to fully explore the pretrained knowledge of both the visual and language modalities. Based on the single-cue cross-modal alignment framework, we propose a variational autoencoder (VAE) for pretrained contextual knowledge while introducing the complete pretrained language module. The VAE implicitly aligns visual and textual modalities while benefiting from pretrained contextual knowledge as the traditional contextual module. Meanwhile, a contrastive cross-modal alignment algorithm is designed to explicitly enhance the consistency constraints. Extensive experiments on public datasets (PHOENIX-2014 and PHOENIX-2014T) demonstrate that our proposed CVT-SLR consistently outperforms existing single-cue methods and even outperforms SOTA multi-cue methods.

Cheng Tan, Zhangyang Gao, Hanqun Cao et al.

The secondary structure of ribonucleic acid (RNA) is more stable and accessible in the cell than its tertiary structure, making it essential for functional prediction. Although deep learning has shown promising results in this field, current methods suffer from poor generalization and high complexity. In this work, we reformulate the RNA secondary structure prediction as a K-Rook problem, thereby simplifying the prediction process into probabilistic matching within a finite solution space. Building on this innovative perspective, we introduce RFold, a simple yet effective method that learns to predict the most matching K-Rook solution from the given sequence. RFold employs a bi-dimensional optimization strategy that decomposes the probabilistic matching problem into row-wise and column-wise components to reduce the matching complexity, simplifying the solving process while guaranteeing the validity of the output. Extensive experiments demonstrate that RFold achieves competitive performance and about eight times faster inference efficiency than the state-of-the-art approaches. The code and Colab demo are available in (http://github.com/A4Bio/RFold).

Jiangbin Zheng, Yile Wang, Ge Wang et al.

Although contextualized embeddings generated from large-scale pre-trained models perform well in many tasks, traditional static embeddings (e.g., Skip-gram, Word2Vec) still play an important role in low-resource and lightweight settings due to their low computational cost, ease of deployment, and stability. In this paper, we aim to improve word embeddings by 1) incorporating more contextual information from existing pre-trained models into the Skip-gram framework, which we call Context-to-Vec; 2) proposing a post-processing retrofitting method for static embeddings independent of training by employing priori synonym knowledge and weighted vector distribution. Through extrinsic and intrinsic tasks, our methods are well proven to outperform the baselines by a large margin.

Qing Lyu, Josh Tan, Michael E. Zapadka et al.

The large language model called ChatGPT has drawn extensively attention because of its human-like expression and reasoning abilities. In this study, we investigate the feasibility of using ChatGPT in experiments on using ChatGPT to translate radiology reports into plain language for patients and healthcare providers so that they are educated for improved healthcare. Radiology reports from 62 low-dose chest CT lung cancer screening scans and 76 brain MRI metastases screening scans were collected in the first half of February for this study. According to the evaluation by radiologists, ChatGPT can successfully translate radiology reports into plain language with an average score of 4.27 in the five-point system with 0.08 places of information missing and 0.07 places of misinformation. In terms of the suggestions provided by ChatGPT, they are general relevant such as keeping following-up with doctors and closely monitoring any symptoms, and for about 37% of 138 cases in total ChatGPT offers specific suggestions based on findings in the report. ChatGPT also presents some randomness in its responses with occasionally over-simplified or neglected information, which can be mitigated using a more detailed prompt. Furthermore, ChatGPT results are compared with a newly released large model GPT-4, showing that GPT-4 can significantly improve the quality of translated reports. Our results show that it is feasible to utilize large language models in clinical education, and further efforts are needed to address limitations and maximize their potential.

Md Selim, Jie Zhang, Michael A. Brooks et al.

Computed tomography (CT) is one of the modalities for effective lung cancer screening, diagnosis, treatment, and prognosis. The features extracted from CT images are now used to quantify spatial and temporal variations in tumors. However, CT images obtained from various scanners with customized acquisition protocols may introduce considerable variations in texture features, even for the same patient. This presents a fundamental challenge to downstream studies that require consistent and reliable feature analysis. Existing CT image harmonization models rely on GAN-based supervised or semi-supervised learning, with limited performance. This work addresses the issue of CT image harmonization using a new diffusion-based model, named DiffusionCT, to standardize CT images acquired from different vendors and protocols. DiffusionCT operates in the latent space by mapping a latent non-standard distribution into a standard one. DiffusionCT incorporates an Unet-based encoder-decoder, augmented by a diffusion model integrated into the bottleneck part. The model is designed in two training phases. The encoder-decoder is first trained, without embedding the diffusion model, to learn the latent representation of the input data. The latent diffusion model is then trained in the next training phase while fixing the encoder-decoder. Finally, the decoder synthesizes a standardized image with the transformed latent representation. The experimental results demonstrate a significant improvement in the performance of the standardization task using DiffusionCT.

Huidong Xie, Zhao Liu, Luyao Shi et al.

In nuclear imaging, limited resolution causes partial volume effects (PVEs) that affect image sharpness and quantitative accuracy. Partial volume correction (PVC) methods incorporating high-resolution anatomical information from CT or MRI have been demonstrated to be effective. However, such anatomical-guided methods typically require tedious image registration and segmentation steps. Accurately segmented organ templates are also hard to obtain, particularly in cardiac SPECT imaging, due to the lack of hybrid SPECT/CT scanners with high-end CT and associated motion artifacts. Slight mis-registration/mis-segmentation would result in severe degradation in image quality after PVC. In this work, we develop a deep-learning-based method for fast cardiac SPECT PVC without anatomical information and associated organ segmentation. The proposed network involves a densely-connected multi-dimensional dynamic mechanism, allowing the convolutional kernels to be adapted based on the input images, even after the network is fully trained. Intramyocardial blood volume (IMBV) is introduced as an additional clinical-relevant loss function for network optimization. The proposed network demonstrated promising performance on 28 canine studies acquired on a GE Discovery NM/CT 570c dedicated cardiac SPECT scanner with a 64-slice CT using Technetium-99m-labeled red blood cells. This work showed that the proposed network with densely-connected dynamic mechanism produced superior results compared with the same network without such mechanism. Results also showed that the proposed network without anatomical information could produce images with statistically comparable IMBV measurements to the images generated by anatomical-guided PVC methods, which could be helpful in clinical translation.

Md Motaleb Hossen Manik, Ge Wang

Biomedical question answering with large language models is commonly evaluated using answer accuracy, but answer accuracy alone does not indicate whether a model can produce parseable outputs, follow structured reliability instructions, recognize weak answer spaces, or avoid confident incorrect commitments. This paper presents HypothesisMed, an inference-time reliability pipeline for biomedical multiple-choice question answering. It combines direct, chain-of-thought, HypothesisMed-v3 prompting, and answer fusion. The final answer is selected by fusion, while HypothesisMed-v3 supplies SPACE labels and confidence information. SPACE labels mark the answer space as VALID, INCOMPLETE, or CONTRADICTED. We evaluate Qwen2.5-7B, Phi-4-mini, DeepSeek-R1-32B, and BioMistral-7B on MedQA, MedMCQA, and PubMedQA using 1,000 examples per dataset. The pipeline improves weighted accuracy over each model's best direct or chain-of-thought baseline while increasing parse and SPACE coverage. We also scale evaluation to Qwen2.5-7B and Phi-4-mini using 10,183 examples per model. Fusion improves Phi-4-mini accuracy from 0.4296 to 0.5192, while Qwen2.5-7B chain-of-thought remains slightly higher in answer accuracy. However, Qwen2.5-7B fusion achieves complete parse and SPACE coverage with much lower false commitment. A 12,000-example SPACE stress test shows answer-space diagnosis remains difficult, with SPACE accuracy of 0.3074 for Qwen2.5-7B and 0.4168 for Phi-4-mini. These results show that answer accuracy, parseability, structured reliability reporting, calibration behavior, and false-commitment behavior are separable capabilities. The main contribution is not a universal state-of-the-art claim, but a reproducible inference-time framework for evaluating biomedical question answering models as auditable workflow components under structured reliability constraints.

Wenjun Xia, Hongming Shan, Ge Wang et al.

Since 2016, deep learning (DL) has advanced tomographic imaging with remarkable successes, especially in low-dose computed tomography (LDCT) imaging. Despite being driven by big data, the LDCT denoising and pure end-to-end reconstruction networks often suffer from the black box nature and major issues such as instabilities, which is a major barrier to apply deep learning methods in low-dose CT applications. An emerging trend is to integrate imaging physics and model into deep networks, enabling a hybridization of physics/model-based and data-driven elements. %This type of hybrid methods has become increasingly influential. In this paper, we systematically review the physics/model-based data-driven methods for LDCT, summarize the loss functions and training strategies, evaluate the performance of different methods, and discuss relevant issues and future directions.

Ge Wang, Li Tan, Tianbao Song et al.

Social media has been rapidly developing in the public sphere due to its ease of spreading new information, which leads to the circulation of rumors. However, detecting rumors from such a massive amount of information is becoming an increasingly arduous challenge. Previous work generally obtained valuable features from propagation information. It should be noted that most methods only target the propagation structure while ignoring the rumor transmission pattern. This limited focus severely restricts the collection of spread data. To solve this problem, the authors of the present study are motivated to explore the regionalized propagation patterns of rumors. Specifically, a novel region-enhanced deep graph convolutional network (RDGCN) that enhances the propagation features of rumors by learning regionalized propagation patterns and trains to learn the propagation patterns by unsupervised learning is proposed. In addition, a source-enhanced residual graph convolution layer (SRGCL) is designed to improve the graph neural network (GNN) oversmoothness and increase the depth limit of the rumor detection methods-based GNN. Experiments on Twitter15 and Twitter16 show that the proposed model performs better than the baseline approach on rumor detection and early rumor detection.

Yufei Huang, Lirong Wu, Haitao Lin et al.

Learning meaningful protein representation is important for a variety of biological downstream tasks such as structure-based drug design. Having witnessed the success of protein sequence pretraining, pretraining for structural data which is more informative has become a promising research topic. However, there are three major challenges facing protein structure pretraining: insufficient sample diversity, physically unrealistic modeling, and the lack of protein-specific pretext tasks. To try to address these challenges, we present the 3D Geometric Pretraining. In this paper, we propose a unified framework for protein pretraining and a 3D geometric-based, data-efficient, and protein-specific pretext task: RefineDiff (Refine the Diffused Protein Structure Decoy). After pretraining our geometric-aware model with this task on limited data(less than 1% of SOTA models), we obtained informative protein representations that can achieve comparable performance for various downstream tasks.

Ge Wang, Jie Zhang, Hao Gao et al.

Current tomographic imaging systems need major improvements, especially when multi-dimensional, multi-scale, multi-temporal and multi-parametric phenomena are under investigation. Both preclinical and clinical imaging now depend on in vivo tomography, often requiring separate evaluations by different imaging modalities to define morphologic details, delineate interval changes due to disease or interventions, and study physiological functions that have interconnected aspects. Over the past decade, fusion of multimodality images has emerged with two different approaches: post-hoc image registration and combined acquisition on PET-CT, PET-MRI and other hybrid scanners. There are intrinsic limitations for both the post-hoc image analysis and dual/triple modality approaches defined by registration errors and physical constraints in the acquisition chain. We envision that tomography will evolve beyond current modality fusion and towards grand fusion, a large scale fusion of all or many imaging modalities, which may be referred to as omni-tomography or multi-tomography. Unlike modality fusion, grand fusion is here proposed for truly simultaneous but often localized reconstruction in terms of all or many relevant imaging mechanisms such as CT, MRI, PET, SPECT, US, optical, and possibly more. In this paper, the technical basis for omni-tomography is introduced and illustrated with a top-level design of a next generation scanner, interior tomographic reconstructions of representative modalities, and anticipated applications of omni-tomography.

Chuang Niu, Qing Lyu, Christopher D. Carothers et al.

Modern medical records include a vast amount of multimodal free text clinical data and imaging data from radiology, cardiology, and digital pathology. Fully mining such big data requires multitasking; otherwise, occult but important aspects may be overlooked, adversely affecting clinical management and population healthcare. Despite remarkable successes of AI in individual tasks with single-modal data, the progress in developing generalist medical AI remains relatively slow to combine multimodal data for multitasks because of the dual challenges of data curation and model architecture. The data challenge involves querying and curating multimodal structured and unstructured text, alphanumeric, and especially 3D tomographic scans on an individual patient level for real-time decisions and on a scale to estimate population health statistics. The model challenge demands a scalable and adaptable network architecture to integrate multimodal datasets for diverse clinical tasks. Here we propose the first-of-its-kind medical multimodal-multitask foundation model (M3FM) with application in lung cancer screening and related tasks. After we curated a comprehensive multimodal multitask dataset consisting of 49 clinical data types including 163,725 chest CT series and 17 medical tasks involved in LCS, we develop a multimodal question-answering framework as a unified training and inference strategy to synergize multimodal information and perform multiple tasks via free-text prompting. M3FM consistently outperforms the state-of-the-art single-modal task-specific models, identifies multimodal data elements informative for clinical tasks and flexibly adapts to new tasks with a small out-of-distribution dataset. As a specialty-oriented generalist medical AI model, M3FM paves the way for similar breakthroughs in other areas of medicine, closing the gap between specialists and the generalist.

Wenjun Xia, Wenxiang Cong, Ge Wang

Sparse-view computed tomography (CT) can be used to reduce radiation dose greatly but is suffers from severe image artifacts. Recently, the deep learning based method for sparse-view CT reconstruction has attracted a major attention. However, neural networks often have a limited ability to remove the artifacts when they only work in the image domain. Deep learning-based sinogram processing can achieve a better anti-artifact performance, but it inevitably requires feature maps of the whole image in a video memory, which makes handling large-scale or three-dimensional (3D) images rather challenging. In this paper, we propose a patch-based denoising diffusion probabilistic model (DDPM) for sparse-view CT reconstruction. A DDPM network based on patches extracted from fully sampled projection data is trained and then used to inpaint down-sampled projection data. The network does not require paired full-sampled and down-sampled data, enabling unsupervised learning. Since the data processing is patch-based, the deep learning workflow can be distributed in parallel, overcoming the memory problem of large-scale data. Our experiments show that the proposed method can effectively suppress few-view artifacts while faithfully preserving textural details.

Dennis Hein, Afshin Bozorgpour, Dorit Merhof et al.

Physics-inspired Generative Models (GMs), in particular Diffusion Models (DMs) and Poisson Flow Models (PFMs), enhance Bayesian methods and promise great utility in medical imaging. This review examines the transformative role of such generative methods. First, a variety of physics-inspired GMs, including Denoising Diffusion Probabilistic Models (DDPMs), Score-based Diffusion Models (SDMs), and Poisson Flow Generative Models (PFGMs and PFGM++), are revisited, with an emphasis on their accuracy, robustness as well as acceleration. Then, major applications of physics-inspired GMs in medical imaging are presented, comprising image reconstruction, image generation, and image analysis. Finally, future research directions are brainstormed, including unification of physics-inspired GMs, integration with Vision-Language Models (VLMs), and potential novel applications of GMs. Since the development of generative methods has been rapid, this review will hopefully give peers and learners a timely snapshot of this new family of physics-driven generative models and help capitalize their enormous potential for medical imaging.

Zihan Liu, Ge Wang, Jiaqi Wang et al.

Peptides are formed by the dehydration condensation of multiple amino acids. The primary structure of a peptide can be represented either as an amino acid sequence or as a molecular graph consisting of atoms and chemical bonds. Previous studies have indicated that deep learning routes specific to sequential and graphical peptide forms exhibit comparable performance on downstream tasks. Despite the fact that these models learn representations of the same modality of peptides, we find that they explain their predictions differently. Considering sequential and graphical models as two experts making inferences from different perspectives, we work on fusing expert knowledge to enrich the learned representations for improving the discriminative performance. To achieve this, we propose a peptide co-modeling method, RepCon, which employs a contrastive learning-based framework to enhance the mutual information of representations from decoupled sequential and graphical end-to-end models. It considers representations from the sequential encoder and the graphical encoder for the same peptide sample as a positive pair and learns to enhance the consistency of representations between positive sample pairs and to repel representations between negative pairs. Empirical studies of RepCon and other co-modeling methods are conducted on open-source discriminative datasets, including aggregation propensity, retention time, antimicrobial peptide prediction, and family classification from Peptide Database. Our results demonstrate the superiority of the co-modeling approach over independent modeling, as well as the superiority of RepCon over other methods under the co-modeling framework. In addition, the attribution on RepCon further corroborates the validity of the approach at the level of model explanation.

Wenjun Xia, Yongyi Shi, Chuang Niu et al.

Computed tomography (CT) involves a patient's exposure to ionizing radiation. To reduce the radiation dose, we can either lower the X-ray photon count or down-sample projection views. However, either of the ways often compromises image quality. To address this challenge, here we introduce an iterative reconstruction algorithm regularized by a diffusion prior. Drawing on the exceptional imaging prowess of the denoising diffusion probabilistic model (DDPM), we merge it with a reconstruction procedure that prioritizes data fidelity. This fusion capitalizes on the merits of both techniques, delivering exceptional reconstruction results in an unsupervised framework. To further enhance the efficiency of the reconstruction process, we incorporate the Nesterov momentum acceleration technique. This enhancement facilitates superior diffusion sampling in fewer steps. As demonstrated in our experiments, our method offers a potential pathway to high-definition CT image reconstruction with minimized radiation.

Huidong Xie, Bo Zhou, Xiongchao Chen et al.

Cardiovascular disease (CVD) is the leading cause of death worldwide, and myocardial perfusion imaging using SPECT has been widely used in the diagnosis of CVDs. The GE 530/570c dedicated cardiac SPECT scanners adopt a stationary geometry to simultaneously acquire 19 projections to increase sensitivity and achieve dynamic imaging. However, the limited amount of angular sampling negatively affects image quality. Deep learning methods can be implemented to produce higher-quality images from stationary data. This is essentially a few-view imaging problem. In this work, we propose a novel 3D transformer-based dual-domain network, called TIP-Net, for high-quality 3D cardiac SPECT image reconstructions. Our method aims to first reconstruct 3D cardiac SPECT images directly from projection data without the iterative reconstruction process by proposing a customized projection-to-image domain transformer. Then, given its reconstruction output and the original few-view reconstruction, we further refine the reconstruction using an image-domain reconstruction network. Validated by cardiac catheterization images, diagnostic interpretations from nuclear cardiologists, and defect size quantified by an FDA 510(k)-cleared clinical software, our method produced images with higher cardiac defect contrast on human studies compared with previous baseline methods, potentially enabling high-quality defect visualization using stationary few-view dedicated cardiac SPECT scanners.

Chuang Niu, Ge Wang

Early detection of lung nodules with computed tomography (CT) is critical for the longer survival of lung cancer patients and better quality of life. Computer-aided detection/diagnosis (CAD) is proven valuable as a second or concurrent reader in this context. However, accurate detection of lung nodules remains a challenge for such CAD systems and even radiologists due to not only the variability in size, location, and appearance of lung nodules but also the complexity of lung structures. This leads to a high false-positive rate with CAD, compromising its clinical efficacy. Motivated by recent computer vision techniques, here we present a self-supervised region-based 3D transformer model to identify lung nodules among a set of candidate regions. Specifically, a 3D vision transformer (ViT) is developed that divides a CT image volume into a sequence of non-overlap cubes, extracts embedding features from each cube with an embedding layer, and analyzes all embedding features with a self-attention mechanism for the prediction. To effectively train the transformer model on a relatively small dataset, the region-based contrastive learning method is used to boost the performance by pre-training the 3D transformer with public CT images. Our experiments show that the proposed method can significantly improve the performance of lung nodule screening in comparison with the commonly used 3D convolutional neural networks.

Chi Ding, Qingchao Zhang, Ge Wang et al.

We propose a novel Learned Alternating Minimization Algorithm (LAMA) for dual-domain sparse-view CT image reconstruction. LAMA is naturally induced by a variational model for CT reconstruction with learnable nonsmooth nonconvex regularizers, which are parameterized as composite functions of deep networks in both image and sinogram domains. To minimize the objective of the model, we incorporate the smoothing technique and residual learning architecture into the design of LAMA. We show that LAMA substantially reduces network complexity, improves memory efficiency and reconstruction accuracy, and is provably convergent for reliable reconstructions. Extensive numerical experiments demonstrate that LAMA outperforms existing methods by a wide margin on multiple benchmark CT datasets.

Chuang Niu, Giridhar Dasegowda, Pingkun Yan et al.

Although radiographs are the most frequently used worldwide due to their cost-effectiveness and widespread accessibility, the structural superposition along the x-ray paths often renders suspicious or concerning lung nodules difficult to detect. In this study, we apply "X-ray dissectography" to dissect lungs digitally from a few radiographic projections, suppress the interference of irrelevant structures, and improve lung nodule detectability. For this purpose, a collaborative detection network is designed to localize lung nodules in 2D dissected projections and 3D physical space. Our experimental results show that our approach can significantly improve the average precision by 20+% in comparison with the common baseline that detects lung nodules from original projections using a popular detection network. Potentially, this approach could help re-design the current X-ray imaging protocols and workflows and improve the diagnostic performance of chest radiographs in lung diseases.

Soham Bhosale, Arjun Krishna, Ge Wang et al.

Medical Image Segmentation is a useful application for medical image analysis including detecting diseases and abnormalities in imaging modalities such as MRI, CT etc. Deep learning has proven to be promising for this task but usually has a low accuracy because of the lack of appropriate publicly available annotated or segmented medical datasets. In addition, the datasets that are available may have a different texture because of different dosage values or scanner properties than the images that need to be segmented. This paper presents a StyleGAN-driven approach for segmenting publicly available large medical datasets by using readily available extremely small annotated datasets in similar modalities. The approach involves augmenting the small segmented dataset and eliminating texture differences between the two datasets. The dataset is augmented by being passed through six different StyleGANs that are trained on six different style images taken from the large non-annotated dataset we want to segment. Specifically, style transfer is used to augment the training dataset. The annotations of the training dataset are hence combined with the textures of the non-annotated dataset to generate new anatomically sound images. The augmented dataset is then used to train a U-Net segmentation network which displays a significant improvement in the segmentation accuracy in segmenting the large non-annotated dataset.

Qing Lyu, Ge Wang

MRI and CT are most widely used medical imaging modalities. It is often necessary to acquire multi-modality images for diagnosis and treatment such as radiotherapy planning. However, multi-modality imaging is not only costly but also introduces misalignment between MRI and CT images. To address this challenge, computational conversion is a viable approach between MRI and CT images, especially from MRI to CT images. In this paper, we propose to use an emerging deep learning framework called diffusion and score-matching models in this context. Specifically, we adapt denoising diffusion probabilistic and score-matching models, use four different sampling strategies, and compare their performance metrics with that using a convolutional neural network and a generative adversarial network model. Our results show that the diffusion and score-matching models generate better synthetic CT images than the CNN and GAN models. Furthermore, we investigate the uncertainties associated with the diffusion and score-matching networks using the Monte-Carlo method, and improve the results by averaging their Monte-Carlo outputs. Our study suggests that diffusion and score-matching models are powerful to generate high quality images conditioned on an image obtained using a complementary imaging modality, analytically rigorous with clear explainability, and highly competitive with CNNs and GANs for image synthesis.

Yongyi Shi, Wenjun Xia, Ge Wang et al.

Lowering radiation dose per view and utilizing sparse views per scan are two common CT scan modes, albeit often leading to distorted images characterized by noise and streak artifacts. Blind image quality assessment (BIQA) strives to evaluate perceptual quality in alignment with what radiologists perceive, which plays an important role in advancing low-dose CT reconstruction techniques. An intriguing direction involves developing BIQA methods that mimic the operational characteristic of the human visual system (HVS). The internal generative mechanism (IGM) theory reveals that the HVS actively deduces primary content to enhance comprehension. In this study, we introduce an innovative BIQA metric that emulates the active inference process of IGM. Initially, an active inference module, implemented as a denoising diffusion probabilistic model (DDPM), is constructed to anticipate the primary content. Then, the dissimilarity map is derived by assessing the interrelation between the distorted image and its primary content. Subsequently, the distorted image and dissimilarity map are combined into a multi-channel image, which is inputted into a transformer-based image quality evaluator. Remarkably, by exclusively utilizing this transformer-based quality evaluator, we won the second place in the MICCAI 2023 low-dose computed tomography perceptual image quality assessment grand challenge. Leveraging the DDPM-derived primary content, our approach further improves the performance on the challenge dataset.

Zihan Liu, Ge Wang, Yun Luo et al.

Recent research has revealed that Graph Neural Networks (GNNs) are susceptible to adversarial attacks targeting the graph structure. A malicious attacker can manipulate a limited number of edges, given the training labels, to impair the victim model's performance. Previous empirical studies indicate that gradient-based attackers tend to add edges rather than remove them. In this paper, we present a theoretical demonstration revealing that attackers tend to increase inter-class edges due to the message passing mechanism of GNNs, which explains some previous empirical observations. By connecting dissimilar nodes, attackers can more effectively corrupt node features, making such attacks more advantageous. However, we demonstrate that the inherent smoothness of GNN's message passing tends to blur node dissimilarity in the feature space, leading to the loss of crucial information during the forward process. To address this issue, we propose a novel surrogate model with multi-level propagation that preserves the node dissimilarity information. This model parallelizes the propagation of unaggregated raw features and multi-hop aggregated features, while introducing batch normalization to enhance the dissimilarity in node representations and counteract the smoothness resulting from topological aggregation. Our experiments show significant improvement with our approach.Furthermore, both theoretical and experimental evidence suggest that adding inter-class edges constitutes an easily observable attack pattern. We propose an innovative attack loss that balances attack effectiveness and imperceptibility, sacrificing some attack effectiveness to attain greater imperceptibility. We also provide experiments to validate the compromise performance achieved through this attack loss.

Wenjun Xia, Hsin Wu Tseng, Chuang Niu et al.

Breast cancer is the most prevalent cancer among women worldwide, and early detection is crucial for reducing its mortality rate and improving quality of life. Dedicated breast computed tomography (CT) scanners offer better image quality than mammography and tomosynthesis in general but at higher radiation dose. To enable breast CT for cancer screening, the challenge is to minimize the radiation dose without compromising image quality, according to the ALARA principle (as low as reasonably achievable). Over the past years, deep learning has shown remarkable successes in various tasks, including low-dose CT especially few-view CT. Currently, the diffusion model presents the state of the art for CT reconstruction. To develop the first diffusion model-based breast CT reconstruction method, here we report innovations to address the large memory requirement for breast cone-beam CT reconstruction and high computational cost of the diffusion model. Specifically, in this study we transform the cutting-edge Denoising Diffusion Probabilistic Model (DDPM) into a parallel framework for sub-volume-based sparse-view breast CT image reconstruction in projection and image domains. This novel approach involves the concurrent training of two distinct DDPM models dedicated to processing projection and image data synergistically in the dual domains. Our experimental findings reveal that this method delivers competitive reconstruction performance at half to one-third of the standard radiation doses. This advancement demonstrates an exciting potential of diffusion-type models for volumetric breast reconstruction at high-resolution with much-reduced radiation dose and as such hopefully redefines breast cancer screening and diagnosis.

Xinrui Song, Jiajin Zhang, Pingkun Yan et al.

The integration of artificial intelligence (AI) chatbots into higher education marks a shift towards a new generation of pedagogical tools, mirroring the arrival of milestones like the internet. With the launch of ChatGPT-4 Turbo in November 2023, we developed a ChatGPT-based teaching application (https://chat.openai.com/g/g-1imx1py4K-chatge-medical-imaging) and integrated it into our undergraduate medical imaging course in the Spring 2024 semester. This study investigates the use of ChatGPT throughout a semester-long trial, providing insights into students' engagement, perception, and the overall educational effectiveness of the technology. We systematically collected and analyzed data concerning students' interaction with ChatGPT, focusing on their attitudes, concerns, and usage patterns. The findings indicate that ChatGPT offers significant advantages such as improved information access and increased interactivity, but its adoption is accompanied by concerns about the accuracy of the information provided and the necessity for well-defined guidelines to optimize its use.

Yuyuan Yang, Junkun Hong, Hongrong Wang et al.

Embodied task planning demands vision-language models to generate action sequences that are both visually grounded and causally coherent over time. However, existing training paradigms face a critical trade-off: joint end-to-end training often leads to premature temporal binding, while standard reinforcement learning methods suffer from optimization instability. To bridge this gap, we present Staged Vision-Language Learning (SVLL), a unified three-stage framework for robust, physically-grounded embodied planning. In the first two stages, SVLL decouples spatial grounding from temporal reasoning, establishing robust visual dependency before introducing sequential action history. In the final stage, we identify a key limitation of standard Direct Preference Optimization (DPO), its purely relative nature -- optimizing only the preference gap between winning and losing trajectories while neglecting absolute likelihood constraints on optimal path, often yields unsafe or hallucinated behaviors. To address this, we further introduce Bias-DPO, a novel alignment objective that injects an inductive bias toward expert trajectories by explicitly maximizing likelihood on ground-truth actions while penalizing overconfident hallucinations. By anchoring the policy to the expert manifold and mitigating causal misalignment, SVLL, powered by Bias-DPO, ensures strict adherence to environmental affordances and effectively suppresses physically impossible shortcuts. Finally, extensive experiments on the interactive AI2-THOR benchmark and real-world robotic deployments demonstrate that SVLL outperforms both state-of-the-art open-source (e.g., Qwen2.5-VL-7B) and closed-source models (e.g., GPT-4o, Gemini-2.0-flash) in task success rate, while significantly reducing physical constraint violations.

Rodrigo de Barros Vimieiro, Chuang Niu, Hongming Shan et al.

Digital breast tomosynthesis (DBT) exams should utilize the lowest possible radiation dose while maintaining sufficiently good image quality for accurate medical diagnosis. In this work, we propose a convolution neural network (CNN) to restore low-dose (LD) DBT projections to achieve an image quality equivalent to a standard full-dose (FD) acquisition. The proposed network architecture benefits from priors in terms of layers that were inspired by traditional model-based (MB) restoration methods, considering a model-based deep learning approach, where the network is trained to operate in the variance stabilization transformation (VST) domain. To accurately control the network operation point, in terms of noise and blur of the restored image, we propose a loss function that minimizes the bias and matches residual noise between the input and the output. The training dataset was composed of clinical data acquired at the standard FD and low-dose pairs obtained by the injection of quantum noise. The network was tested using real DBT projections acquired with a physical anthropomorphic breast phantom. The proposed network achieved superior results in terms of the mean normalized squared error (MNSE), training time and noise spatial correlation compared with networks trained with traditional data-driven methods. The proposed approach can be extended for other medical imaging application that requires LD acquisitions.

Ge Wang, Li Tan, Ziliang Shang et al.

In recent years, rumors have had a devastating impact on society, making rumor detection a significant challenge. However, the studies on rumor detection ignore the intense emotions of images in the rumor content. This paper verifies that the image emotion improves the rumor detection efficiency. A Multimodal Dual Emotion feature in rumor detection, which consists of visual and textual emotions, is proposed. To the best of our knowledge, this is the first study which uses visual emotion in rumor detection. The experiments on real datasets verify that the proposed features outperform the state-of-the-art sentiment features, and can be extended in rumor detectors while improving their performance.

Wenjun Xia, Qing Lyu, Ge Wang

Low-dose computed tomography (LDCT) is an important topic in the field of radiology over the past decades. LDCT reduces ionizing radiation-induced patient health risks but it also results in a low signal-to-noise ratio (SNR) and a potential compromise in the diagnostic performance. In this paper, to improve the LDCT denoising performance, we introduce the conditional denoising diffusion probabilistic model (DDPM) and show encouraging results with a high computational efficiency. Specifically, given the high sampling cost of the original DDPM model, we adapt the fast ordinary differential equation (ODE) solver for a much-improved sampling efficiency. The experiments show that the accelerated DDPM can achieve 20x speedup without compromising image quality.

Chuang Niu, Ge Wang

Self-supervised representation learning maps high-dimensional data into a meaningful embedding space, where samples of similar semantic contents are close to each other. Most of the recent representation learning methods maximize cosine similarity or minimize the distance between the embedding features of different views from the same sample usually on the $l2$ normalized unit hypersphere. To prevent the trivial solutions that all samples have the same embedding feature, various techniques have been developed, such as contrastive learning, stop gradient, variance and covariance regularization, etc. In this study, we propose MUlti-Segmental Informational Coding (MUSIC) for self-supervised representation learning. MUSIC divides the embedding feature into multiple segments that discriminatively partition samples into different semantic clusters and different segments focus on different partition principles. Information theory measurements are directly used to optimize MUSIC and theoretically guarantee trivial solutions are avoided. MUSIC does not depend on commonly used techniques, such as memory bank or large batches, asymmetry networks, gradient stopping, momentum weight updating, etc, making the training framework flexible. Our experiments demonstrate that MUSIC achieves better results than most related Barlow Twins and VICReg methods on ImageNet classification with linear probing, and requires neither deep projectors nor large feature dimensions. Code will be made available.

Chuang Niu, Ge Wang

Minimum redundancy among different elements of an embedding in a latent space is a fundamental requirement or major preference in representation learning to capture intrinsic informational structures. Current self-supervised learning methods minimize a pair-wise covariance matrix to reduce the feature redundancy and produce promising results. However, such representation features of multiple variables may contain the redundancy among more than two feature variables that cannot be minimized via the pairwise regularization. Here we propose the High-Order Mixed-Moment-based Embedding (HOME) strategy to reduce the redundancy between any sets of feature variables, which is to our best knowledge the first attempt to utilize high-order statistics/information in this context. Multivariate mutual information is minimum if and only if multiple variables are mutually independent, which suggests the necessary conditions of factorized mixed moments among multiple variables. Based on these statistical and information theoretic principles, our general HOME framework is presented for self-supervised representation learning. Our initial experiments show that a simple version in the form of a three-order HOME scheme already significantly outperforms the current two-order baseline method (i.e., Barlow Twins) in terms of the linear evaluation on representation features.

Fenglei Fan, Juntong Fan, Dayang Wang et al.

The rapid growth of large models' size has far outpaced that of computing resources. To bridge this gap, encouraged by the parsimonious relationship between genotype and phenotype in the brain's growth and development, we propose the so-called Hyper-Compression that turns the model compression into the issue of parameter representation via a hyperfunction. Specifically, it is known that the trajectory of some low-dimensional dynamic systems can fill the high-dimensional space eventually. Thus, Hyper-Compression, using these dynamic systems as the hyperfunctions, represents the parameters of the target network by their corresponding composition number or trajectory length. This suggests a novel mechanism for model compression, substantially different from the existing pruning, quantization, distillation, and decomposition. Along this direction, we methodologically identify a suitable dynamic system with the irrational winding as the hyperfunction and theoretically derive its associated error bound. Next, guided by our theoretical insights, we propose several engineering twists to make the Hyper-Compression pragmatic and effective. Lastly, systematic and comprehensive experiments on \textcolor{black}{NLP models such as LLaMA and Qwen series and vision models} confirm that Hyper-Compression enjoys the following \textbf{PNAS} merits: 1) \textbf{P}referable compression ratio; 2) \textbf{N}o post-hoc retraining; 3) \textbf{A}ffordable inference time; and 4) \textbf{S}hort compression time. It compresses LLaMA2-7B in an hour and achieves close-to-int4-quantization performance, without retraining and with a performance drop of less than 1\%. We have open-sourced our code in https://github.com/Juntongkuki/Hyper-Compression.git for free download and evaluation.

Chuang Niu, Christopher Wiedeman, Mengzhou Li et al.

This study aims to improve photon counting CT (PCCT) image resolution using denoising diffusion probabilistic models (DDPM). Although DDPMs have shown superior performance when applied to various computer vision tasks, their effectiveness has yet to be translated to high dimensional CT super-resolution. To train DDPMs in a conditional sampling manner, we first leverage CatSim to simulate realistic lower resolution PCCT images from high-resolution CT scans. Since maximizing DDPM performance is time-consuming for both inference and training, especially on high-dimensional PCCT data, we explore both 2D and 3D networks for conditional DDPM and apply methods to accelerate training. In particular, we decompose the 3D task into efficient 2D DDPMs and design a joint 2D inference in the reverse diffusion process that synergizes 2D results of all three dimensions to make the final 3D prediction. Experimental results show that our DDPM achieves improved results versus baseline reference models in recovering high-frequency structures, suggesting that a framework based on realistic simulation and DDPM shows promise for improving PCCT resolution.

Qing Lyu, Jianxu Wang, Jeremy Hudson et al.

Accurate MRI-to-CT synthesis could enable MR-only pelvic workflows by providing CT-like images with bone details while avoiding additional ionizing radiation. In this work, we investigate recently proposed drifting models for synthesizing pelvis CT images from MRI and benchmark them against convolutional neural networks (UNet, VAE), a generative adversarial network (WGAN-GP), a physics-inspired probabilistic model (PPFM), and diffusion-based methods (FastDDPM, DDIM, DDPM). Experiments are performed on two complementary datasets: Gold Atlas Male Pelvis and the SynthRAD2023 pelvis subset. Image fidelity and structural consistency are evaluated with SSIM, PSNR, and RMSE, complemented by qualitative assessment of anatomically critical regions such as cortical bone and pelvic soft-tissue interfaces. Across both datasets, the proposed drifting model achieves high SSIM and PSNR and low RMSE, surpassing strong diffusion baselines and conventional CNN-, VAE-, GAN-, and PPFM-based methods. Visual inspection shows sharper cortical bone edges, improved depiction of sacral and femoral head geometry, and reduced artifacts or over-smoothing, particularly at bone-air-soft tissue boundaries. Moreover, the drifting model attains these gains with one-step inference and inference times on the order of milliseconds, yielding a more favorable accuracy-efficiency trade-off than iterative diffusion sampling while remaining competitive in image quality. These findings suggest that drifting models are a promising direction for fast, high-quality pelvic synthetic CT generation from MRI and warrant further investigation for downstream applications such as MRI-only radiotherapy planning and PET/MR attenuation correction.

Rongjun Ge, Yuxin Liu, Zhan Wu et al.

Non-ideal measurement computed tomography (NICT) employs suboptimal imaging protocols to expand CT applications. However, the resulting trade-offs degrade image quality, limiting clinical acceptability. Although deep learning methods have been used to enhance NICT images, their reliance on large training datasets and limited generalizability across diverse settings hinder practical use. We propose the multi-scale integrated Transformer AMPlifier (TAMP), the first imaging foundation model for universal NICT enhancement. Pre-trained on 10.8 million physics-driven simulated NICT images, TAMP generalizes effectively across various NICT settings, defect degrees, and body regions. Moreover, a parameter-efficient fine-tuning strategy enables TAMP to adapt to specific clinical scenarios using only few slices. Extensive experiments, including radiologists and real-world validations, demonstrate that TAMP consistently improves image quality and clinical acceptability, underscoring its significant potential to advance CT imaging and broaden NICT applications in clinical practice.

Md Selim, Jie Zhang, Faraneh Fathi et al.

Computed tomography (CT) serves as an effective tool for lung cancer screening, diagnosis, treatment, and prognosis, providing a rich source of features to quantify temporal and spatial tumor changes. Nonetheless, the diversity of CT scanners and customized acquisition protocols can introduce significant inconsistencies in texture features, even when assessing the same patient. This variability poses a fundamental challenge for subsequent research that relies on consistent image features. Existing CT image standardization models predominantly utilize GAN-based supervised or semi-supervised learning, but their performance remains limited. We present DiffusionCT, an innovative score-based DDPM model that operates in the latent space to transform disparate non-standard distributions into a standardized form. The architecture comprises a U-Net-based encoder-decoder, augmented by a DDPM model integrated at the bottleneck position. First, the encoder-decoder is trained independently, without embedding DDPM, to capture the latent representation of the input data. Second, the latent DDPM model is trained while keeping the encoder-decoder parameters fixed. Finally, the decoder uses the transformed latent representation to generate a standardized CT image, providing a more consistent basis for downstream analysis. Empirical tests on patient CT images indicate notable improvements in image standardization using DiffusionCT. Additionally, the model significantly reduces image noise in SPAD images, further validating the effectiveness of DiffusionCT for advanced imaging tasks.

Lei Shi, Zhimeng Liu, Yi Yang et al.

The extraction of Metal-Organic Frameworks (MOFs) synthesis route from literature has been crucial for the logical MOFs design with desirable functionality. The recent advent of large language models (LLMs) provides disruptively new solution to this long-standing problem. While the latest researches mostly stick to primitive zero-shot LLMs lacking specialized material knowledge, we introduce in this work the few-shot LLM in-context learning paradigm. First, a human-AI interactive data curation approach is proposed to secure high-quality demonstrations. Second, an information retrieval algorithm is applied to pick and quantify few-shot demonstrations for each extraction. Over three datasets randomly sampled from nearly 90,000 well-defined MOFs, we conduct triple evaluations to validate our method. The synthesis extraction, structure inference, and material design performance of the proposed few-shot LLMs all significantly outplay zero-shot LLM and baseline methods. The lab-synthesized material guided by LLM surpasses 91.1% high-quality MOFs of the same class reported in the literature, on the key physical property of specific surface area.

Zhihao Chen, Tao Chen, Chenhui Wang et al.

While various deep learning methods were proposed for low-dose computed tomography (CT) denoising, they often suffer from over-smoothing, blurring, and lack of explainability. To alleviate these issues, we propose a plug-and-play Language-Engaged Dual-space Alignment loss (LEDA) to optimize low-dose CT denoising models. Our idea is to leverage large language models (LLMs) to align denoised CT and normal dose CT images in both the continuous perceptual space and discrete semantic space, which is the first LLM-based scheme for low-dose CT denoising. LEDA involves two steps: the first is to pretrain an LLM-guided CT autoencoder, which can encode a CT image into continuous high-level features and quantize them into a token space to produce semantic tokens derived from the LLM's vocabulary; and the second is to minimize the discrepancy between the denoised CT images and normal dose CT in terms of both encoded high-level features and quantized token embeddings derived by the LLM-guided CT autoencoder. Extensive experimental results on two public LDCT denoising datasets demonstrate that our LEDA can enhance existing denoising models in terms of quantitative metrics and qualitative evaluation, and also provide explainability through language-level image understanding. Source code is available at https://github.com/hao1635/LEDA.

Christopher Wiedeman, Ge Wang

Artificial intelligence has made great progress in medical data analysis, but the lack of robustness and trustworthiness has kept these methods from being widely deployed. As it is not possible to train networks that are accurate in all scenarios, models must recognize situations where they cannot operate confidently. Bayesian deep learning methods sample the model parameter space to estimate uncertainty, but these parameters are often subject to the same vulnerabilities, which can be exploited by adversarial attacks. We propose a novel ensemble approach based on feature decorrelation and Fourier partitioning for teaching networks diverse complementary features, reducing the chance of perturbation-based fooling. We test our approach on single and multi-channel electrocardiogram classification, and adapt adversarial training and DVERGE into the Bayesian ensemble framework for comparison. Our results indicate that the combination of decorrelation and Fourier partitioning generally maintains performance on unperturbed data while demonstrating superior robustness and uncertainty estimation on projected gradient descent and smooth adversarial attacks of various magnitudes. Furthermore, our approach does not require expensive optimization with adversarial samples, adding much less compute to the training process than adversarial training or DVERGE. These methods can be applied to other tasks for more robust and trustworthy models.

Bo Lan, Pei Li, Jiaxi Yin et al.

Human Action Recognition (HAR) plays a crucial role in applications such as health monitoring, smart home automation, and human-computer interaction. While HAR has been extensively studied, action summarization using Wi-Fi and IMU signals in smart-home environments , which involves identifying and summarizing continuous actions, remains an emerging task. This paper introduces the novel XRF V2 dataset, designed for indoor daily activity Temporal Action Localization (TAL) and action summarization. XRF V2 integrates multimodal data from Wi-Fi signals, IMU sensors (smartphones, smartwatches, headphones, and smart glasses), and synchronized video recordings, offering a diverse collection of indoor activities from 16 volunteers across three distinct environments. To tackle TAL and action summarization, we propose the XRFMamba neural network, which excels at capturing long-term dependencies in untrimmed sensory sequences and achieves the best performance with an average mAP of 78.74, outperforming the recent WiFiTAD by 5.49 points in mAP@avg while using 35% fewer parameters. In action summarization, we introduce a new metric, Response Meaning Consistency (RMC), to evaluate action summarization performance. And it achieves an average Response Meaning Consistency (mRMC) of 0.802. We envision XRF V2 as a valuable resource for advancing research in human action localization, action forecasting, pose estimation, multimodal foundation models pre-training, synthetic data generation, and more. The data and code are available at https://github.com/aiotgroup/XRFV2.

Arjun Krishna, Ge Wang, Klaus Mueller

Medical imaging applications are highly specialized in terms of human anatomy, pathology, and imaging domains. Therefore, annotated training datasets for training deep learning applications in medical imaging not only need to be highly accurate but also diverse and large enough to encompass almost all plausible examples with respect to those specifications. We argue that achieving this goal can be facilitated through a controlled generation framework for synthetic images with annotations, requiring multiple conditional specifications as input to provide control. We employ a Denoising Diffusion Probabilistic Model (DDPM) to train a large-scale generative model in the lung CT domain and expand upon a classifier-free sampling strategy to showcase one such generation framework. We show that our approach can produce annotated lung CT images that can faithfully represent anatomy, convincingly fooling experts into perceiving them as real. Our experiments demonstrate that controlled generative frameworks of this nature can surpass nearly every state-of-the-art image generative model in achieving anatomical consistency in generated medical images when trained on comparable large medical datasets.

Zelin Liu, Xiangfu Yu, Jie Huang et al.

Pheochromocytomas and paragangliomas (PPGLs) are rare neuroendocrine tumors, of which 15-25% develop metastatic disease with 5-year survival rates reported as low as 34%. PPGL may indicate hereditary syndromes requiring stricter, syndrome-specific treatment and surveillance, but clinicians often fail to recognize these associations in routine care. Clinical practice uses GAPP score for PPGL grading, but several limitations remain for PPGL diagnosis: (1) GAPP scoring demands a high workload for clinician because it requires the manual evaluation of six independent components; (2) key components such as cellularity and Ki-67 are often evaluated with subjective criteria; (3) several clinically relevant metastatic risk factors are not captured by GAPP, such as SDHB mutations, which have been associated with reported metastatic rates of 35-75%. Agent-driven diagnostic systems appear promising, but most lack traceable reasoning for decision-making and do not incorporate domain-specific knowledge such as PPGL genotype information. To address these limitations, we present PPGL-Swarm, an agentic PPGL diagnostic system that generates a comprehensive report, including automated GAPP scoring (with quantified cellularity and Ki-67), genotype risk alerts, and multimodal report with integrated evidence. The system provides an auditable reasoning trail by decomposing diagnosis into micro-tasks, each assigned to a specialized agent. The gene and table agents use knowledge enhancement to better interpret genotype and laboratory findings, and during training we use reinforcement learning to refine tool selection and task assignment.