Lei Xing

Rui Yan, Liangqiong Qu, Qingyue Wei et al.

The collection and curation of large-scale medical datasets from multiple institutions is essential for training accurate deep learning models, but privacy concerns often hinder data sharing. Federated learning (FL) is a promising solution that enables privacy-preserving collaborative learning among different institutions, but it generally suffers from performance deterioration due to heterogeneous data distributions and a lack of quality labeled data. In this paper, we present a robust and label-efficient self-supervised FL framework for medical image analysis. Our method introduces a novel Transformer-based self-supervised pre-training paradigm that pre-trains models directly on decentralized target task datasets using masked image modeling, to facilitate more robust representation learning on heterogeneous data and effective knowledge transfer to downstream models. Extensive empirical results on simulated and real-world medical imaging non-IID federated datasets show that masked image modeling with Transformers significantly improves the robustness of models against various degrees of data heterogeneity. Notably, under severe data heterogeneity, our method, without relying on any additional pre-training data, achieves an improvement of 5.06%, 1.53% and 4.58% in test accuracy on retinal, dermatology and chest X-ray classification compared to the supervised baseline with ImageNet pre-training. In addition, we show that our federated self-supervised pre-training methods yield models that generalize better to out-of-distribution data and perform more effectively when fine-tuning with limited labeled data, compared to existing FL algorithms. The code is available at https://github.com/rui-yan/SSL-FL.

Qingyue Wei, Lequan Yu, Xianhang Li et al.

Medical imaging has witnessed remarkable progress but usually requires a large amount of high-quality annotated data which is time-consuming and costly to obtain. To alleviate this burden, semi-supervised learning has garnered attention as a potential solution. In this paper, we present Meta-Learning for Bootstrapping Medical Image Segmentation (MLB-Seg), a novel method for tackling the challenge of semi-supervised medical image segmentation. Specifically, our approach first involves training a segmentation model on a small set of clean labeled images to generate initial labels for unlabeled data. To further optimize this bootstrapping process, we introduce a per-pixel weight mapping system that dynamically assigns weights to both the initialized labels and the model's own predictions. These weights are determined using a meta-process that prioritizes pixels with loss gradient directions closer to those of clean data, which is based on a small set of precisely annotated images. To facilitate the meta-learning process, we additionally introduce a consistency-based Pseudo Label Enhancement (PLE) scheme that improves the quality of the model's own predictions by ensembling predictions from various augmented versions of the same input. In order to improve the quality of the weight maps obtained through multiple augmentations of a single input, we introduce a mean teacher into the PLE scheme. This method helps to reduce noise in the weight maps and stabilize its generation process. Our extensive experimental results on public atrial and prostate segmentation datasets demonstrate that our proposed method achieves state-of-the-art results under semi-supervision. Our code is available at https://github.com/aijinrjinr/MLB-Seg.

Jieneng Chen, Jieru Mei, Xianhang Li et al.

Medical image segmentation plays a crucial role in advancing healthcare systems for disease diagnosis and treatment planning. The u-shaped architecture, popularly known as U-Net, has proven highly successful for various medical image segmentation tasks. However, U-Net's convolution-based operations inherently limit its ability to model long-range dependencies effectively. To address these limitations, researchers have turned to Transformers, renowned for their global self-attention mechanisms, as alternative architectures. One popular network is our previous TransUNet, which leverages Transformers' self-attention to complement U-Net's localized information with the global context. In this paper, we extend the 2D TransUNet architecture to a 3D network by building upon the state-of-the-art nnU-Net architecture, and fully exploring Transformers' potential in both the encoder and decoder design. We introduce two key components: 1) A Transformer encoder that tokenizes image patches from a convolution neural network (CNN) feature map, enabling the extraction of global contexts, and 2) A Transformer decoder that adaptively refines candidate regions by utilizing cross-attention between candidate proposals and U-Net features. Our investigations reveal that different medical tasks benefit from distinct architectural designs. The Transformer encoder excels in multi-organ segmentation, where the relationship among organs is crucial. On the other hand, the Transformer decoder proves more beneficial for dealing with small and challenging segmented targets such as tumor segmentation. Extensive experiments showcase the significant potential of integrating a Transformer-based encoder and decoder into the u-shaped medical image segmentation architecture. TransUNet outperforms competitors in various medical applications.

Rui Xu, Lei Xing, Shuai Shao et al.

Few-shot learning (FSL), purposing to resolve the problem of data-scarce, has attracted considerable attention in recent years. A popular FSL framework contains two phases: (i) the pre-train phase employs the base data to train a CNN-based feature extractor. (ii) the meta-test phase applies the frozen feature extractor to novel data (novel data has different categories from base data) and designs a classifier for recognition. To correct few-shot data distribution, researchers propose Semi-Supervised Few-Shot Learning (SSFSL) by introducing unlabeled data. Although SSFSL has been proved to achieve outstanding performances in the FSL community, there still exists a fundamental problem: the pre-trained feature extractor can not adapt to the novel data flawlessly due to the cross-category setting. Usually, large amounts of noises are introduced to the novel feature. We dub it as Feature-Extractor-Maladaptive (FEM) problem. To tackle FEM, we make two efforts in this paper. First, we propose a novel label prediction method, Isolated Graph Learning (IGL). IGL introduces the Laplacian operator to encode the raw data to graph space, which helps reduce the dependence on features when classifying, and then project graph representation to label space for prediction. The key point is that: IGL can weaken the negative influence of noise from the feature representation perspective, and is also flexible to independently complete training and testing procedures, which is suitable for SSFSL. Second, we propose Graph Co-Training (GCT) to tackle this challenge from a multi-modal fusion perspective by extending the proposed IGL to the co-training framework. GCT is a semi-supervised method that exploits the unlabeled samples with two modal features to crossly strengthen the IGL classifier.

Bingqian Lin, Zicong Chen, Mingjie Li et al.

Medical artificial general intelligence (MAGI) enables one foundation model to solve different medical tasks, which is very practical in the medical domain. It can significantly reduce the requirement of large amounts of task-specific data by sufficiently sharing medical knowledge among different tasks. However, due to the challenges of designing strongly generalizable models with limited and complex medical data, most existing approaches tend to develop task-specific models. To take a step towards MAGI, we propose a new paradigm called Medical-knOwledge-enhanced mulTimOdal pretRaining (MOTOR). In MOTOR, we combine two kinds of basic medical knowledge, i.e., general and specific knowledge, in a complementary manner to boost the general pretraining process. As a result, the foundation model with comprehensive basic knowledge can learn compact representations from pretraining radiographic data for better cross-modal alignment. MOTOR unifies the understanding and generation, which are two kinds of core intelligence of an AI system, into a single medical foundation model, to flexibly handle more diverse medical tasks. To enable a comprehensive evaluation and facilitate further research, we construct a medical multimodal benchmark including a wide range of downstream tasks, such as chest x-ray report generation and medical visual question answering. Extensive experiments on our benchmark show that MOTOR obtains promising results through simple task-oriented adaptation. The visualization shows that the injected knowledge successfully highlights key information in the medical data, demonstrating the excellent interpretability of MOTOR. Our MOTOR successfully mimics the human practice of fulfilling a "medical student" to accelerate the process of becoming a "specialist". We believe that our work makes a significant stride in realizing MAGI.

Yunfei Xie, Ce Zhou, Lang Gao et al.

This paper introduces MedTrinity-25M, a comprehensive, large-scale multimodal dataset for medicine, covering over 25 million images across 10 modalities with multigranular annotations for more than 65 diseases. These multigranular annotations encompass both global information, such as modality and organ detection, and local information like ROI analysis, lesion texture, and region-wise correlations. Unlike the existing multimodal datasets, which are limited by the availability of image-text pairs, we have developed the first automated pipeline that scales up multimodal data by generating multigranular visual and textual annotations in the form of image-ROI-description triplets without the need for any paired text descriptions. Specifically, data from over 30 different sources have been collected, preprocessed, and grounded using domain-specific expert models to identify ROIs related to abnormal regions. We then build a comprehensive knowledge base and prompt multimodal large language models to perform retrieval-augmented generation with the identified ROIs as guidance, resulting in multigranular textual descriptions. Compared to existing datasets, MedTrinity-25M provides the most enriched annotations, supporting a comprehensive range of multimodal tasks such as captioning and report generation, as well as vision-centric tasks like classification and segmentation. We propose LLaVA-Tri by pretraining LLaVA on MedTrinity-25M, achieving state-of-the-art performance on VQA-RAD, SLAKE, and PathVQA, surpassing representative SOTA multimodal large language models. Furthermore, MedTrinity-25M can also be utilized to support large-scale pre-training of multimodal medical AI models, contributing to the development of future foundation models in the medical domain. We will make our dataset available.

Guiyao Tie, Jiawen Shi, Dingjie Song et al.

Scientific research is being reshaped by AI systems that move beyond isolated assistance toward longer-horizon workflows spanning literature grounding, hypothesis generation, experimentation, validation, reporting, and revision. This shift marks a transition from task-level AI for science to workflow-level research automation. Yet current systems remain fragmented, differing in autonomy, domain scope, execution environment, validation mechanism, and human oversight, while still struggling with evidence preservation, reproducibility, weak-direction rejection, provenance tracking, cross-domain robustness, and accountable scientific closure. This survey examines these developments through AutoResearch, defined as the developmental spectrum of AI-powered scientific workflow automation. Within it, Vibe Research denotes the human-steered region of prompt-based assistance and human-verified execution, whereas emerging AI-led systems coordinate larger portions of the discovery loop without achieving robust autonomy. We analyze how research systems redistribute control, evidence, execution, validation, and accountability across workflows and organize the field around five workflow conditions: literature and research grounding; hypothesis formation and planning; experimentation and tool use; feedback, validation, and review; and reporting and knowledge communication. We further synthesize AI scientist systems, mixed-initiative co-research frameworks, benchmarks, domain deployments, and open-source infrastructures. Finally, we propose five evaluation dimensions--novelty, validity, impact, reliability, and provenance--and show that AutoResearch autonomy is domain-conditioned, being more credible in structured, executable, and rapidly verifiable settings but limited in embodied, delayed, heterogeneous, ethical, or institutionally accountable contexts.

Shuanghao Bai, Jing Lyu, Wanqi Zhou et al.

Vision-Language-Action (VLA) models benefit from chain-of-thought (CoT) reasoning, but existing approaches incur high inference overhead and rely on discrete reasoning representations that mismatch continuous perception and control. We propose Latent Reasoning VLA (LaRA-VLA), a unified VLA framework that internalizes multi-modal CoT reasoning into continuous latent representations for embodied action. LaRA-VLA performs unified reasoning and prediction in latent space, eliminating explicit CoT generation at inference time and enabling efficient, action-oriented control. To realize latent embodied reasoning, we introduce a curriculum-based training paradigm that progressively transitions from explicit textual and visual CoT supervision to latent reasoning, and finally adapts latent reasoning dynamics to condition action generation. We construct two structured CoT datasets and evaluate LaRA-VLA on both simulation benchmarks and long-horizon real-robot manipulation tasks. Experimental results show that LaRA-VLA consistently outperforms state-of-the-art VLA methods while reducing inference latency by up to 90\% compared to explicit CoT-based approaches, demonstrating latent reasoning as an effective and efficient paradigm for real-time embodied control. Project Page: https://loveju1y.github.io/Latent-Reasoning-VLA/

Sheng Liu, Haotian Ye, Lei Xing et al.

Large language models (LLMs) demonstrate emergent in-context learning capabilities, where they adapt to new tasks based on example demonstrations. However, in-context learning has seen limited effectiveness in many settings, is difficult to quantitatively control and takes up context window space. To overcome these limitations, we propose an alternative approach that recasts in-context learning as in-context vectors (ICV). Using ICV has two steps. We first use a forward pass on demonstration examples to create the in-context vector from the latent embedding of the LLM. This vector captures essential information about the intended task. On a new query, instead of adding demonstrations to the prompt, we shift the latent states of the LLM using the ICV. The ICV approach has several benefits: 1) it enables the LLM to more effectively follow the demonstration examples; 2) it's easy to control by adjusting the magnitude of the ICV; 3) it reduces the length of the prompt by removing the in-context demonstrations; 4) ICV is computationally much more efficient than fine-tuning. We demonstrate that ICV achieves better performance compared to standard in-context learning and fine-tuning on diverse tasks including safety, style transfer, role-playing and formatting. Moreover, we show that we can flexibly teach LLM to simultaneously follow different types of instructions by simple vector arithmetics on the corresponding ICVs.

Charles Huang, Varun Vasudevan, Oscar Pastor-Serrano et al.

Objective: Knowledge based planning (KBP) typically involves training an end-to-end deep learning model to predict dose distributions. However, training end-to-end methods may be associated with practical limitations due to the limited size of medical datasets that are often used. To address these limitations, we propose a content based image retrieval (CBIR) method for retrieving dose distributions of previously planned patients based on anatomical similarity. Approach: Our proposed CBIR method trains a representation model that produces latent space embeddings of a patient's anatomical information. The latent space embeddings of new patients are then compared against those of previous patients in a database for image retrieval of dose distributions. All source code for this project is available on github. Main Results: The retrieval performance of various CBIR methods is evaluated on a dataset consisting of both publicly available plans and clinical plans from our institution. This study compares various encoding methods, ranging from simple autoencoders to more recent Siamese networks like SimSiam, and the best performance was observed for the multitask Siamese network. Significance: Applying CBIR to inform subsequent treatment planning potentially addresses many limitations associated with end-to-end KBP. Our current results demonstrate that excellent image retrieval performance can be obtained through slight changes to previously developed Siamese networks. We hope to integrate CBIR into automated planning workflow in future works, potentially through methods like the MetaPlanner framework.

Sakib Mostafa, Tarik Massoud, Maximilian Diehn et al.

Tabular data are central to biomedical research, from liquid biopsy and bulk and single-cell transcriptomics to electronic health records and phenotypic profiling. Unlike images or sequences, however, tabular datasets lack intrinsic spatial organization: features are treated as unordered dimensions, and their relationships must be inferred implicitly by the model. This limits the ability of vision architectures to exploit local structure and higher-order feature interactions in non-spatial biomedical data. Here we introduce Dynamic Feature Mapping (Dynomap), an end-to-end deep learning framework that learns a task-optimized spatial topology of features directly from data. Dynomap jointly optimizes feature placement and prediction through a fully differentiable rendering mechanism, without relying on heuristics, predefined groupings, or external priors. By transforming high-dimensional tabular vectors into learned feature maps, Dynomap enables vision-based models to operate effectively on unordered biomedical inputs. Across multiple clinical and biological datasets, Dynomap consistently outperformed classical machine learning, modern deep tabular models, and existing vector-to-image approaches. In liquid biopsy data, Dynomap organized clinically relevant gene signatures into coherent spatial patterns and improved multiclass cancer subtype prediction accuracy by up to 18%. In a Parkinson disease voice dataset, it clustered disease-associated acoustic descriptors and improved accuracy by up to 8%. Similar gains and interpretable feature organization were observed in additional biomedical datasets. These results establish Dynomap as a general strategy for bridging tabular and vision-based deep learning and for uncovering structured, clinically relevant patterns in high-dimensional biomedical data.

Yuwei Xue, Sakib Mostafa, James Zou et al.

Biological systems are governed by structured molecular interactions, where pathways, regulatory circuits, and functional gene relationships shape cellular behavior and disease progression. Much of this knowledge is naturally represented as graphs. However, most biomedical AI models cannot directly use graph-encoded biological knowledge and instead require compressed low-dimensional representations, which can lose important structure and reduce performance, especially in limited-sample clinical studies. Here, we introduce Graph-in-Graph (GiG), a knowledge graph-modulated deep learning framework for data-efficient clinical prediction. GiG represents each patient as a standalone modular graph, in which curated biological knowledge graphs define edges and patient-specific measurements, such as gene expression, define node features. This design allows multiple biological knowledge graphs to be integrated while preserving gene-gene interactions and pathway topology during patient-level representation learning. Across cohorts comprising nearly 9,700 patients and five clinical tasks, including liquid biopsy cancer detection, prostate cancer diagnosis, and 32-class pan-cancer classification, GiG consistently outperforms traditional and state-of-the-art methods, with the largest gains in limited-sample settings. On the challenging prostate cancer diagnosis task, GiG improves macro-F1 by up to 49 percentage points relative to competing methods. Control experiments replacing real pathway graphs with random topologies confirm that these gains arise from biologically grounded knowledge graph structure rather than graph modeling alone. These findings show that knowledge graph-modulated deep learning can improve robustness, interpretability, and sample efficiency in clinical data analysis, and provide a principled framework for integrating biological knowledge graphs into predictive modeling.

Praveenbalaji Rajendran, Yong Yang, Thomas R. Niedermayr et al.

Radiation therapy (RT) is one of the most effective treatments for cancer, and its success relies on the accurate delineation of targets. However, target delineation is a comprehensive medical decision that currently relies purely on manual processes by human experts. Manual delineation is time-consuming, laborious, and subject to interobserver variations. Although the advancements in artificial intelligence (AI) techniques have significantly enhanced the auto-contouring of normal tissues, accurate delineation of RT target volumes remains a challenge. In this study, we propose a visual language model-based RT target volume auto-delineation network termed Radformer. The Radformer utilizes a hierarichal vision transformer as the backbone and incorporates large language models to extract text-rich features from clinical data. We introduce a visual language attention module (VLAM) for integrating visual and linguistic features for language-aware visual encoding (LAVE). The Radformer has been evaluated on a dataset comprising 2985 patients with head-and-neck cancer who underwent RT. Metrics, including the Dice similarity coefficient (DSC), intersection over union (IOU), and 95th percentile Hausdorff distance (HD95), were used to evaluate the performance of the model quantitatively. Our results demonstrate that the Radformer has superior segmentation performance compared to other state-of-the-art models, validating its potential for adoption in RT practice.

Shuaishuai Guo, Jianheng Guo, KaiFan Ji et al.

With the release of a large amount of astronomical data, an increasing number of close-in hot Jupiters have been discovered. Calculating their evolutionary curves using star-planet interaction models presents a challenge. To expedite the generation of evolutionary curves for these close-in hot Jupiter systems, we utilized tidal interaction models established on MESA to create 15,745 samples of star-planet systems and 7,500 samples of stars. Additionally, we employed a neural network (Multi-Layer Perceptron - MLP) to predict the evolutionary curves of the systems, including stellar effective temperature, radius, stellar rotation period, and planetary orbital period. The median relative errors of the predicted evolutionary curves were found to be 0.15%, 0.43%, 2.61%, and 0.57%, respectively. Furthermore, the speed at which we generate evolutionary curves exceeds that of model-generated curves by more than four orders of magnitude. We also extracted features of planetary migration states and utilized lightGBM to classify the samples into 6 categories for prediction. We found that by combining three types that undergo long-term double synchronization into one label, the classifier effectively recognized these features. Apart from systems experiencing long-term double synchronization, the median relative errors of the predicted evolutionary curves were all below 4%. Our work provides an efficient method to save significant computational resources and time with minimal loss in accuracy. This research also lays the foundation for analyzing the evolutionary characteristics of systems under different migration states, aiding in the understanding of the underlying physical mechanisms of such systems. Finally, to a large extent, our approach could replace the calculations of theoretical models.

Lingting Zhu, Yizheng Chen, Lianli Liu et al.

Multi-modality imaging is widely used in clinical practice and biomedical research to gain a comprehensive understanding of an imaging subject. Currently, multi-modality imaging is accomplished by post hoc fusion of independently reconstructed images under the guidance of mutual information or spatially registered hardware, which limits the accuracy and utility of multi-modality imaging. Here, we investigate a data-driven multi-modality imaging (DMI) strategy for synergetic imaging of CT and MRI. We reveal two distinct types of features in multi-modality imaging, namely intra- and inter-modality features, and present a multi-sensor learning (MSL) framework to utilize the crossover inter-modality features for augmented multi-modality imaging. The MSL imaging approach breaks down the boundaries of traditional imaging modalities and allows for optimal hybridization of CT and MRI, which maximizes the use of sensory data. We showcase the effectiveness of our DMI strategy through synergetic CT-MRI brain imaging. The principle of DMI is quite general and holds enormous potential for various DMI applications across disciplines.

Chuanqing Tang, Yifei Shi, Guanghao Lin et al.

Class imbalance has been extensively studied in single-view scenarios; however, addressing this challenge in multi-view contexts remains an open problem, with even scarcer research focusing on trustworthy solutions. In this paper, we tackle a particularly challenging class imbalance problem in multi-view scenarios: long-tailed classification. We propose TMLC, a Trusted Multi-view Long-tailed Classification framework, which makes contributions on two critical aspects: opinion aggregation and pseudo-data generation. Specifically, inspired by Social Identity Theory, we design a group consensus opinion aggregation mechanism that guides decision making toward the direction favored by the majority of the group. In terms of pseudo-data generation, we introduce a novel distance metric to adapt SMOTE for multi-view scenarios and develop an uncertainty-guided data generation module that produces high-quality pseudo-data, effectively mitigating the adverse effects of class imbalance. Extensive experiments on long-tailed multi-view datasets demonstrate that our model is capable of achieving superior performance. The code is released at https://github.com/cncq-tang/TMLC.

Hongtao Wu, Boyun Zheng, Dingjie Song et al.

Autonomous systems that generate scientific hypotheses, conduct experiments, and draft manuscripts have recently emerged as a promising paradigm for accelerating discovery. However, existing AI Scientists remain largely domain-agnostic, limiting their applicability to clinical medicine, where research is required to be grounded in medical evidence with specialized data modalities. In this work, we introduce Medical AI Scientist, the first autonomous research framework tailored to clinical autonomous research. It enables clinically grounded ideation by transforming extensively surveyed literature into actionable evidence through clinician-engineer co-reasoning mechanism, which improves the traceability of generated research ideas. It further facilitates evidence-grounded manuscript drafting guided by structured medical compositional conventions and ethical policies. The framework operates under 3 research modes, namely paper-based reproduction, literature-inspired innovation, and task-driven exploration, each corresponding to a distinct level of automated scientific inquiry with progressively increasing autonomy. Comprehensive evaluations by both large language models and human experts demonstrate that the ideas generated by the Medical AI Scientist are of substantially higher quality than those produced by commercial LLMs across 171 cases, 19 clinical tasks, and 6 data modalities. Meanwhile, our system achieves strong alignment between the proposed method and its implementation, while also demonstrating significantly higher success rates in executable experiments. Double-blind evaluations by human experts and the Stanford Agentic Reviewer suggest that the generated manuscripts approach MICCAI-level quality, while consistently surpassing those from ISBI and BIBM. The proposed Medical AI Scientist highlights the potential of leveraging AI for autonomous scientific discovery in healthcare.

Sakib Mostafa, Lei Xing, Md. Tauhidul Islam

Graphs are a central representation in biomedical research, capturing molecular interaction networks, gene regulatory circuits, cell--cell communication maps, and knowledge graphs. Despite their importance, currently there is not a broadly reusable foundation model available for graph analysis comparable to those that have transformed language and vision. Existing graph neural networks are typically trained on a single dataset and learn representations specific only to that graph's node features, topology, and label space, limiting their ability to transfer across domains. This lack of generalization is particularly problematic in biology and medicine, where networks vary substantially across cohorts, assays, and institutions. Here we introduce a graph foundation model designed to learn transferable structural representations that are not specific to specific node identities or feature schemes. Our approach leverages feature-agnostic graph properties, including degree statistics, centrality measures, community structure indicators, and diffusion-based signatures, and encodes them as structural prompts. These prompts are integrated with a message-passing backbone to embed diverse graphs into a shared representation space. The model is pretrained once on heterogeneous graphs and subsequently reused on unseen datasets with minimal adaptation. Across multiple benchmarks, our pretrained model matches or exceeds strong supervised baselines while demonstrating superior zero-shot and few-shot generalization on held-out graphs. On the SagePPI benchmark, supervised fine-tuning of the pretrained backbone achieves a mean ROC-AUC of 95.5%, a gain of 21.8% over the best supervised message-passing baseline. The proposed technique thus provides a unique approach toward reusable, foundation-scale models for graph-structured data in biomedical and network science applications.

Chengshuai Yang, Lei Xing, Gregory Entin et al.

Background. RGB-trained capsule-endoscopy classifiers underperform on small-vessel vascular findings by conflating hemoglobin contrast with bile and illumination falloff. Thus, here we test whether a Monte Carlo-inspired analytic model can compute hemoglobin from RGB signal built upon extracted classifier. Methods. On Kvasir-Capsule (47,238 frames, video-level 70/15/15 split, 11 evaluable classes) we evaluate two software-only configurations against RGB-only EfficientNet-B0 across 6 seeds: (i) a prior P_blood = sigma(alpha * (H_norm - 0.5)) * Phi(r) fused as 2 zero-init auxiliary channels; (ii) a distillation head training a 3-channel RGB backbone to predict P_blood. Significance: paired DeLong, McNemar, bootstrap CIs with Bonferroni correction. Results. Across 6 seeds (n=6,423), the analytic prior provides a small but direction-consistent macro-AUC improvement: RGB-only 0.760 +/- 0.027, input-fusion 0.783 +/- 0.024 (paired Delta = +0.023, sign-positive on 5/6 seeds), distillation 0.773 +/- 0.028. The largest robust per-class lift is on Lymphangiectasia, where AUC rises from RGB 0.238 +/- 0.057 to input-fusion 0.337 +/- 0.019, sign-consistent across all 6 seeds. On rare focal-vascular classes (Angiectasia, Blood - fresh) the prior's per-seed effects are bimodal: seed=42 reaches Angiectasia AUC 0.528 -> 0.916, but the cross-seed mean is 0.646 -> 0.608 with sigma_PI = 0.23 - reported as a high-variance per-seed exemplar. Conclusion. A Monte Carlo-inspired analytic prior provides a small, direction-consistent macro-AUC improvement on Kvasir-Capsule across 6 seeds with the largest robust per-class lift on Lymphangiectasia; the distillation variant runs on plain 3-channel RGB and yields a free interpretability heatmap.

Sheng Liu, Long Chen, Zeyun Zhao et al.

Modern clinical practice increasingly depends on reasoning over heterogeneous, evolving, and incomplete patient data. Although recent advances in multimodal foundation models have improved performance on various clinical tasks, most existing models remain static, opaque, and poorly aligned with real-world clinical workflows. We present Cerebra, an interactive multi-agent AI team that coordinates specialized agents for EHR, clinical notes, and medical imaging analysis. These outputs are synthesized into a clinician-facing dashboard that combines visual analytics with a conversational interface, enabling clinicians to interrogate predictions and contextualize risk at the point of care. Cerebra supports privacy-preserving deployment by operating on structured representations and remains robust when modalities are incomplete. We evaluated Cerebra using a massive multi-institutional dataset spanning 3 million patients from four independent healthcare systems. Cerebra consistently outperformed both state-of-the-art single-modality models and large multimodal language model baselines. In dementia risk prediction, it achieved AUROCs up to 0.80, compared with 0.74 for the strongest single-modality model and 0.68 for language model baselines. For dementia diagnosis, it achieved an AUROC of 0.86, and for survival prediction, a C-index of 0.81. In a reader study with experienced physicians, Cerebra significantly improved expert performance, increasing accuracy by 17.5 percentage points in prospective dementia risk estimation. These results demonstrate Cerebra's potential for interpretable, robust decision support in clinical care.

Long Shi, Chuanqing Tang, Huangyi Deng et al.

Recently, multi-view learning has witnessed a considerable interest on the research of trusted decision-making. Previous methods are mainly inspired from an important paper published by Han et al. in 2021, which formulates a Trusted Multi-view Classification (TMC) framework that aggregates evidence from different views based on Dempster's combination rule. All these methods only consider inter-view aggregation, yet lacking exploitation of intra-view information. In this paper, we propose a generalized trusted multi-view classification framework with hierarchical opinion aggregation. This hierarchical framework includes a two-phase aggregation process: the intra-view and inter-view aggregation hierarchies. In the intra aggregation, we assume that each view is comprised of common information shared with other views, as well as its specific information. We then aggregate both the common and specific information. This aggregation phase is useful to eliminate the feature noise inherent to view itself, thereby improving the view quality. In the inter-view aggregation, we design an attention mechanism at the evidence level to facilitate opinion aggregation from different views. To the best of our knowledge, this is one of the pioneering efforts to formulate a hierarchical aggregation framework in the trusted multi-view learning domain. Extensive experiments show that our model outperforms some state-of art trust-related baselines. One can access the source code on https://github.com/lshi91/GTMC-HOA.

Ziqi Gao, Wendi Yang, Yujia Li et al.

Non-semantic context information is crucial for visual recognition, as the human visual perception system first uses global statistics to process scenes rapidly before identifying specific objects. However, while semantic information is increasingly incorporated into computer vision tasks such as image reconstruction, non-semantic information, such as global spatial structures, is often overlooked. To bridge the gap, we propose a biologically informed non-semantic context descriptor, \textbf{MS-Glance}, along with the Glance Index Measure for comparing two images. A Global Glance vector is formulated by randomly retrieving pixels based on a perception-driven rule from an image to form a vector representing non-semantic global context, while a local Glance vector is a flattened local image window, mimicking a zoom-in observation. The Glance Index is defined as the inner product of two standardized sets of Glance vectors. We evaluate the effectiveness of incorporating Glance supervision in two reconstruction tasks: image fitting with implicit neural representation (INR) and undersampled MRI reconstruction. Extensive experimental results show that MS-Glance outperforms existing image restoration losses across both natural and medical images. The code is available at \url{https://github.com/Z7Gao/MSGlance}.

Yuyin Zhou, Xianhang Li, Fengze Liu et al.

Deep neural networks have shown great success in representation learning. However, when learning with noisy labels (LNL), they can easily overfit and fail to generalize to new data. This paper introduces a simple and effective method, named Learning to Bootstrap (L2B), which enables models to bootstrap themselves using their own predictions without being adversely affected by erroneous pseudo-labels. It achieves this by dynamically adjusting the importance weight between real observed and generated labels, as well as between different samples through meta-learning. Unlike existing instance reweighting methods, the key to our method lies in a new, versatile objective that enables implicit relabeling concurrently, leading to significant improvements without incurring additional costs. L2B offers several benefits over the baseline methods. It yields more robust models that are less susceptible to the impact of noisy labels by guiding the bootstrapping procedure more effectively. It better exploits the valuable information contained in corrupted instances by adapting the weights of both instances and labels. Furthermore, L2B is compatible with existing LNL methods and delivers competitive results spanning natural and medical imaging tasks including classification and segmentation under both synthetic and real-world noise. Extensive experiments demonstrate that our method effectively mitigates the challenges of noisy labels, often necessitating few to no validation samples, and is well generalized to other tasks such as image segmentation. This not only positions it as a robust complement to existing LNL techniques but also underscores its practical applicability. The code and models are available at https://github.com/yuyinzhou/l2b.

Junfei Xiao, Lequan Yu, Zongwei Zhou et al.

Batch normalization (BN) uniformly shifts and scales the activations based on the statistics of a batch of images. However, the intensity distribution of the background pixels often dominates the BN statistics because the background accounts for a large proportion of the entire image. This paper focuses on enhancing BN with the intensity distribution of foreground pixels, the one that really matters for image segmentation. We propose a new normalization strategy, named categorical normalization (CateNorm), to normalize the activations according to categorical statistics. The categorical statistics are obtained by dynamically modulating specific regions in an image that belong to the foreground. CateNorm demonstrates both precise and robust segmentation results across five public datasets obtained from different domains, covering complex and variable data distributions. It is attributable to the ability of CateNorm to capture domain-invariant information from multiple domains (institutions) of medical data. Code is available at https://github.com/lambert-x/CateNorm.

Rui Yan, Xiaohan Xing, Xun Wang et al.

Cellular identity and function are linked to both their intrinsic genomic makeup and extrinsic spatial context within the tissue microenvironment. Spatial transcriptomics (ST) offers an unprecedented opportunity to study this, providing in situ gene expression profiles at single-cell resolution and illuminating the spatial and functional organization of cells within tissues. However, a significant hurdle remains: ST data is inherently noisy, large, and structurally complex. This complexity makes it intractable for existing computational methods to effectively capture the interplay between spatial interactions and intrinsic genomic relationships, thus limiting our ability to discern critical biological patterns. Here, we present CellScape, a deep learning framework designed to overcome these limitations for high-performance ST data analysis and pattern discovery. CellScape jointly models cellular interactions in tissue space and genomic relationships among cells, producing comprehensive representations that seamlessly integrate spatial signals with underlying gene regulatory mechanisms. This technique uncovers biologically informative patterns that improve spatial domain segmentation and supports comprehensive spatial cellular analyses across diverse transcriptomics datasets, offering an accurate and versatile framework for deep analysis and interpretation of ST data.w

Mingjie Li, Yizheng Chen, Md Tauhidul Islam et al.

U-Net architectures have been instrumental in advancing biomedical image segmentation (BIS) but often struggle with capturing long-range information. One reason is the conventional down-sampling techniques that prioritize computational efficiency at the expense of information retention. This paper introduces a simple but effective strategy, we call it Stair Pooling, which moderates the pace of down-sampling and reduces information loss by leveraging a sequence of concatenated small and narrow pooling operations in varied orientations. Specifically, our method modifies the reduction in dimensionality within each 2D pooling step from $\frac{1}{4}$ to $\frac{1}{2}$. This approach can also be adapted for 3D pooling to preserve even more information. Such preservation aids the U-Net in more effectively reconstructing spatial details during the up-sampling phase, thereby enhancing its ability to capture long-range information and improving segmentation accuracy. Extensive experiments on three BIS benchmarks demonstrate that the proposed Stair Pooling can increase both 2D and 3D U-Net performance by an average of 3.8\% in Dice scores. Moreover, we leverage the transfer entropy to select the optimal down-sampling paths and quantitatively show how the proposed Stair Pooling reduces the information loss.

Sakib Mostafa, Lei Xing, Md. Tauhidul Islam

Complex biological networks are fundamental to biomedical science, capturing interactions among molecules, cells, genes, and tissues. Deciphering these networks is critical for understanding health and disease, yet their scale and complexity represent a daunting challenge for current computational methods. Traditional biological network analysis methods, including deep learning approaches, while powerful, face inherent challenges such as limited scalability, oversmoothing long-range dependencies, difficulty in multimodal integration, expressivity bounds, and poor interpretability. We present Graph2Image, a framework that transforms large biological networks into sets of two-dimensional images by spatially arranging representative network nodes on a 2D grid. This transformation decouples the nodes as images, enabling the use of convolutional neural networks (CNNs) with global receptive fields and multi-scale pyramids, thus overcoming limitations of existing biological network analysis methods in scalability, memory efficiency, and long-range context capture. Graph2Image also facilitates seamless integration with other imaging and omics modalities and enhances interpretability through direct visualization of node-associated images. When applied to several large-scale biological network datasets, Graph2Image improved classification accuracy by up to 67.2% over existing methods and provided interpretable visualizations that revealed biologically coherent patterns. It also allows analysis of very large biological networks (nodes > 1 billion) on a personal computer. Graph2Image thus provides a scalable, interpretable, and multimodal-ready approach for biological network analysis, offering new opportunities for disease diagnosis and the study of complex biological systems.

Sheng Liu, Haotian Ye, Lei Xing et al.

Hallucination poses a challenge to the deployment of large vision-language models (LVLMs) in applications. Unlike in large language models (LLMs), hallucination in LVLMs often arises from misalignments between visual inputs and textual outputs. This paper investigates the underlying mechanisms of hallucination, focusing on the unique structure of LVLMs that distinguishes them from large language models (LLMs). We identify that hallucinations often arise from the sensitivity of text decoders to vision inputs, a natural phenomenon when image encoders and text decoders are pre-trained separately. Inspired by this, we introduce Visual and Textual Intervention (VTI), a novel technique designed to reduce hallucinations by steering latent space representations during inference to enhance the stability of vision features. As a task-agnostic test-time intervention, VTI can be easily applied to any problem without additional cost. Extensive experiments demonstrate that it can effectively reduce hallucinations and outperform baseline methods across multiple metrics, highlighting the critical role of vision feature stability in LVLMs.

Sheng Liu, Tianlang Chen, Pan Lu et al.

Test-time compute has emerged as a powerful paradigm for improving the performance of large language models (LLMs), where generating multiple outputs or refining individual chains can significantly boost answer accuracy. However, existing methods like Best-of-N, majority voting, and self-reflection typically apply reasoning in a uniform way across inputs, overlooking the fact that different problems may require different levels of reasoning depth. In this work, we propose Fractional Reasoning, a training-free and model-agnostic framework that enables continuous control over reasoning intensity at inference time, going beyond the limitations of fixed instructional prompts. Our method operates by extracting the latent steering vector associated with deeper reasoning and reapplying it with a tunable scaling factor, allowing the model to tailor its reasoning process to the complexity of each input. This supports two key modes of test-time scaling: (1) improving output quality in breadth-based strategies (e.g., Best-of-N, majority voting), and (2) enhancing the correctness of individual reasoning chains in depth-based strategies (e.g., self-reflection). Experiments on GSM8K, MATH500, and GPQA demonstrate that Fractional Reasoning consistently improves performance across diverse reasoning tasks and models.

Liang Qiu, Liyue Shen, Lianli Liu et al.

During and after a course of therapy, imaging is routinely used to monitor the disease progression and assess the treatment responses. Despite of its significance, reliably capturing and predicting the spatial-temporal anatomic changes from a sequence of patient-specific image series presents a considerable challenge. Thus, the development of a computational framework becomes highly desirable for a multitude of practical applications. In this context, we propose a strategy of Spatial-Temporal Neural Representation learning with Prior embedding (ST-NeRP) for patient-specific imaging study. Our strategy involves leveraging an Implicit Neural Representation (INR) network to encode the image at the reference time point into a prior embedding. Subsequently, a spatial-temporally continuous deformation function is learned through another INR network. This network is trained using the whole patient-specific image sequence, enabling the prediction of deformation fields at various target time points. The efficacy of the ST-NeRP model is demonstrated through its application to diverse sequential image series, including 4D CT and longitudinal CT datasets within thoracic and abdominal imaging. The proposed ST-NeRP model exhibits substantial potential in enabling the monitoring of anatomical changes within a patient throughout the therapeutic journey.

Wasif Khan, Lin Gu, Noah Hammarlund et al.

Physical activity is a modifiable lifestyle factor with potential to support cognitive resilience. However, the association of moderate-to-vigorous physical activity (MVPA) intensity, and timing, with cognitive function and region-specific brain structure remain poorly understood. We analyzed data from 45,892 UK Biobank participants aged 60 years and older with valid wrist-worn accelerometer data, cognitive testing, and structural brain MRI. MVPA was measured both continuously (mins per week) and categorically (thresholded using >=150 min/week based on WHO guidelines). Associations with cognitive performance and regional brain volumes were evaluated using multivariable linear models adjusted for demographic, socioeconomic, and health-related covariates. We conducted secondary analyses on MVPA timing and subgroup effects. Higher MVPA was associated with better performance across cognitive domains, including reasoning, memory, executive function, and processing speed. These associations persisted in fully adjusted models and were higher among participants meeting WHO guidelines. Greater MVPA was also associated with subcortical brain regions (caudate, putamen, pallidum, thalamus), as well as regional gray matter volumes involved in emotion, working memory, and perceptual processing. Secondary analyses showed that MVPA at any time of day was associated with cognitive functions and brain volume particularly in the midday-afternoon and evening. Sensitivity analysis shows consistent findings across subgroups, with evidence of dose-response relationships. Higher MVPA is associated with preserved brain structure and enhanced cognitive function in later life. Public health strategies to increase MVPA may support healthy cognitive aging and generate substantial economic benefits, with global gains projected to reach USD 760 billion annually by 2050.

Zixia Zhou, Junyan Liu, Wei Emma Wu et al.

Dynamic brain data, teeming with biological and functional insights, are becoming increasingly accessible through advanced measurements, providing a gateway to understanding the inner workings of the brain in living subjects. However, the vast size and intricate complexity of the data also pose a daunting challenge in reliably extracting meaningful information across various data sources. This paper introduces a generalizable unsupervised deep manifold learning for exploration of neurocognitive and behavioral patterns. Unlike existing methods that extract patterns directly from the input data as in the existing methods, the proposed Brain-dynamic Convolutional-Network-based Embedding (BCNE) seeks to capture the brain-state trajectories by deciphering the temporospatial correlations within the data and subsequently applying manifold learning to this correlative representation. The performance of BCNE is showcased through the analysis of several important dynamic brain datasets. The results, both visual and quantitative, reveal a diverse array of intriguing and interpretable patterns. BCNE effectively delineates scene transitions, underscores the involvement of different brain regions in memory and narrative processing, distinguishes various stages of dynamic learning processes, and identifies differences between active and passive behaviors. BCNE provides an effective tool for exploring general neuroscience inquiries or individual-specific patterns.

Md Tauhidul Islam, Lei Xing

Advancements in deep learning are revolutionizing science and engineering. The immense success of deep learning is largely due to its ability to extract essential high-dimensional (HD) features from input data and make inference decisions based on this information. However, current deep neural network (DNN) models face several challenges, such as the requirements of extensive amounts of data and computational resources. Here, we introduce a new learning scheme, referred to as deep-and-wide learning (DWL), to systematically capture features not only within individual input data (intra-data features) but also across the data (inter-data features). Furthermore, we propose a dual-interactive-channel network (D-Net) to realize the DWL, which leverages our Bayesian formulation of low-dimensional (LD) inter-data feature extraction and its synergistic interaction with the conventional HD representation of the dataset, for substantially enhanced computational efficiency and inference. The proposed technique has been applied to data across various disciplines for both classification and regression tasks. Our results demonstrate that DWL surpasses state-of-the-art DNNs in accuracy by a substantial margin with limited training data and improves the computational efficiency by order(s) of magnitude. The proposed DWL strategy dramatically alters the data-driven learning techniques, including emerging large foundation models, and sheds significant insights into the evolving field of AI.

Sheng Liu, Oscar Pastor-Serrano, Yizheng Chen et al.

Objective: Radiotherapy treatment planning is a time-consuming and potentially subjective process that requires the iterative adjustment of model parameters to balance multiple conflicting objectives. Recent advancements in frontier Artificial Intelligence (AI) models offer promising avenues for addressing the challenges in planning and clinical decision-making. This study introduces GPT-RadPlan, an automated treatment planning framework that integrates radiation oncology knowledge with the reasoning capabilities of large multi-modal models, such as GPT-4Vision (GPT-4V) from OpenAI. Approach: Via in-context learning, we incorporate clinical requirements and a few (3 in our experiments) approved clinical plans with their optimization settings, enabling GPT-4V to acquire treatment planning domain knowledge. The resulting GPT-RadPlan system is integrated into our in-house inverse treatment planning system through an application programming interface (API). For a given patient, GPT-RadPlan acts as both plan evaluator and planner, first assessing dose distributions and dose-volume histograms (DVHs), and then providing textual feedback on how to improve the plan to match the physician's requirements. In this manner, GPT-RadPlan iteratively refines the plan by adjusting planning parameters, such as weights and dose objectives, based on its suggestions. Main results: The efficacy of the automated planning system is showcased across 17 prostate cancer and 13 head and neck cancer VMAT plans with prescribed doses of 70.2 Gy and 72 Gy, respectively, where we compared GPT-RadPlan results to clinical plans produced by human experts. In all cases, GPT-RadPlan either outperformed or matched the clinical plans, demonstrating superior target coverage and reducing organ-at-risk doses by 5 Gy on average (15 percent for prostate and 10-15 percent for head and neck).

Pierre-Louis Benveniste, Julie Alberge, Lei Xing et al.

Lung cancer is a significant cause of mortality worldwide, emphasizing the importance of early detection for improved survival rates. In this study, we propose a machine learning (ML) tool trained on data from the PLCO Cancer Screening Trial and validated on the NLST to estimate the likelihood of lung cancer occurrence within five years. The study utilized two datasets, the PLCO (n=55,161) and NLST (n=48,595), consisting of comprehensive information on risk factors, clinical measurements, and outcomes related to lung cancer. Data preprocessing involved removing patients who were not current or former smokers and those who had died of causes unrelated to lung cancer. Additionally, a focus was placed on mitigating bias caused by censored data. Feature selection, hyper-parameter optimization, and model calibration were performed using XGBoost, an ensemble learning algorithm that combines gradient boosting and decision trees. The ML model was trained on the pre-processed PLCO dataset and tested on the NLST dataset. The model incorporated features such as age, gender, smoking history, medical diagnoses, and family history of lung cancer. The model was well-calibrated (Brier score=0.044). ROC-AUC was 82% on the PLCO dataset and 70% on the NLST dataset. PR-AUC was 29% and 11% respectively. When compared to the USPSTF guidelines for lung cancer screening, our model provided the same recall with a precision of 13.1% vs. 9.3% on the PLCO dataset and 3.2% vs. 3.1% on the NLST dataset. The developed ML tool provides a freely available web application for estimating the likelihood of developing lung cancer within five years. By utilizing risk factors and clinical data, individuals can assess their risk and make informed decisions regarding lung cancer screening. This research contributes to the efforts in early detection and prevention strategies, aiming to reduce lung cancer-related mortality rates.

Varun Vasudevan, Maxime Bassenne, Md Tauhidul Islam et al.

Prior studies using graph neural networks (GNNs) for image classification have focused on graphs generated from a regular grid of pixels or similar-sized superpixels. In the latter, a single target number of superpixels is defined for an entire dataset irrespective of differences across images and their intrinsic multiscale structure. On the contrary, this study investigates image classification using graphs generated from an image-specific number of multiscale superpixels. We propose WaveMesh, a new wavelet-based superpixeling algorithm, where the number and sizes of superpixels in an image are systematically computed based on its content. WaveMesh superpixel graphs are structurally different from similar-sized superpixel graphs. We use SplineCNN, a state-of-the-art network for image graph classification, to compare WaveMesh and similar-sized superpixels. Using SplineCNN, we perform extensive experiments on three benchmark datasets under three local-pooling settings: 1) no pooling, 2) GraclusPool, and 3) WavePool, a novel spatially heterogeneous pooling scheme tailored to WaveMesh superpixels. Our experiments demonstrate that SplineCNN learns from multiscale WaveMesh superpixels on-par with similar-sized superpixels. In all WaveMesh experiments, GraclusPool performs poorer than no pooling / WavePool, indicating that poor choice of pooling can result in inferior performance while learning from multiscale superpixels.

Shuai Shao, Lei Xing, Wei Yu et al.

The label-embedded dictionary learning (DL) algorithms generate influential dictionaries by introducing discriminative information. However, there exists a limitation: All the label-embedded DL methods rely on the labels due that this way merely achieves ideal performances in supervised learning. While in semi-supervised and unsupervised learning, it is no longer sufficient to be effective. Inspired by the concept of self-supervised learning (e.g., setting the pretext task to generate a universal model for the downstream task), we propose a Self-Supervised Dictionary Learning (SSDL) framework to address this challenge. Specifically, we first design a $p$-Laplacian Attention Hypergraph Learning (pAHL) block as the pretext task to generate pseudo soft labels for DL. Then, we adopt the pseudo labels to train a dictionary from a primary label-embedded DL method. We evaluate our SSDL on two human activity recognition datasets. The comparison results with other state-of-the-art methods have demonstrated the efficiency of SSDL.

Shuai Shao, Lei Xing, Rui Xu et al.

In recent years, researchers pay growing attention to the few-shot learning (FSL) task to address the data-scarce problem. A standard FSL framework is composed of two components: i) Pre-train. Employ the base data to generate a CNN-based feature extraction model (FEM). ii) Meta-test. Apply the trained FEM to the novel data (category is different from base data) to acquire the feature embeddings and recognize them. Although researchers have made remarkable breakthroughs in FSL, there still exists a fundamental problem. Since the trained FEM with base data usually cannot adapt to the novel class flawlessly, the novel data's feature may lead to the distribution shift problem. To address this challenge, we hypothesize that even if most of the decisions based on different FEMs are viewed as weak decisions, which are not available for all classes, they still perform decently in some specific categories. Inspired by this assumption, we propose a novel method Multi-Decision Fusing Model (MDFM), which comprehensively considers the decisions based on multiple FEMs to enhance the efficacy and robustness of the model. MDFM is a simple, flexible, non-parametric method that can directly apply to the existing FEMs. Besides, we extend the proposed MDFM to two FSL settings (i.e., supervised and semi-supervised settings). We evaluate the proposed method on five benchmark datasets and achieve significant improvements of 3.4%-7.3% compared with state-of-the-arts.

Yuyin Zhou, Shih-Cheng Huang, Jason Alan Fries et al.

Despite the routine use of electronic health record (EHR) data by radiologists to contextualize clinical history and inform image interpretation, the majority of deep learning architectures for medical imaging are unimodal, i.e., they only learn features from pixel-level information. Recent research revealing how race can be recovered from pixel data alone highlights the potential for serious biases in models which fail to account for demographics and other key patient attributes. Yet the lack of imaging datasets which capture clinical context, inclusive of demographics and longitudinal medical history, has left multimodal medical imaging underexplored. To better assess these challenges, we present RadFusion, a multimodal, benchmark dataset of 1794 patients with corresponding EHR data and high-resolution computed tomography (CT) scans labeled for pulmonary embolism. We evaluate several representative multimodal fusion models and benchmark their fairness properties across protected subgroups, e.g., gender, race/ethnicity, age. Our results suggest that integrating imaging and EHR data can improve classification performance and robustness without introducing large disparities in the true positive rate between population groups.

Yang Song, Liyue Shen, Lei Xing et al.

Reconstructing medical images from partial measurements is an important inverse problem in Computed Tomography (CT) and Magnetic Resonance Imaging (MRI). Existing solutions based on machine learning typically train a model to directly map measurements to medical images, leveraging a training dataset of paired images and measurements. These measurements are typically synthesized from images using a fixed physical model of the measurement process, which hinders the generalization capability of models to unknown measurement processes. To address this issue, we propose a fully unsupervised technique for inverse problem solving, leveraging the recently introduced score-based generative models. Specifically, we first train a score-based generative model on medical images to capture their prior distribution. Given measurements and a physical model of the measurement process at test time, we introduce a sampling method to reconstruct an image consistent with both the prior and the observed measurements. Our method does not assume a fixed measurement process during training, and can thus be flexibly adapted to different measurement processes at test time. Empirically, we observe comparable or better performance to supervised learning techniques in several medical imaging tasks in CT and MRI, while demonstrating significantly better generalization to unknown measurement processes.

Lequan Yu, Zhicheng Zhang, Xiaomeng Li et al.

The presence of metallic implants often introduces severe metal artifacts in the X-ray CT images, which could adversely influence clinical diagnosis or dose calculation in radiation therapy. In this work, we present a novel deep-learning-based approach for metal artifact reduction (MAR). In order to alleviate the need for anatomically identical CT image pairs (i.e., metal artifact-corrupted CT image and metal artifact-free CT image) for network learning, we propose a self-supervised cross-domain learning framework. Specifically, we train a neural network to restore the metal trace region values in the given metal-free sinogram, where the metal trace is identified by the forward projection of metal masks. We then design a novel FBP reconstruction loss to encourage the network to generate more perfect completion results and a residual-learning-based image refinement module to reduce the secondary artifacts in the reconstructed CT images. To preserve the fine structure details and fidelity of the final MAR image, instead of directly adopting CNN-refined images as output, we incorporate the metal trace replacement into our framework and replace the metal-affected projections of the original sinogram with the prior sinogram generated by the forward projection of the CNN output. We then use the filtered backward projection (FBP) algorithms for final MAR image reconstruction. We conduct an extensive evaluation on simulated and real artifact data to show the effectiveness of our design. Our method produces superior MAR results and outperforms other compelling methods. We also demonstrate the potential of our framework for other organ sites.

Shuai Shao, Lei Xing, Yan Wang et al.

Few-shot learning (FSL) aims to address the data-scarce problem. A standard FSL framework is composed of two components: (1) Pre-train. Employ the base data to generate a CNN-based feature extraction model (FEM). (2) Meta-test. Apply the trained FEM to acquire the novel data's features and recognize them. FSL relies heavily on the design of the FEM. However, various FEMs have distinct emphases. For example, several may focus more attention on the contour information, whereas others may lay particular emphasis on the texture information. The single-head feature is only a one-sided representation of the sample. Besides the negative influence of cross-domain (e.g., the trained FEM can not adapt to the novel class flawlessly), the distribution of novel data may have a certain degree of deviation compared with the ground truth distribution, which is dubbed as distribution-shift-problem (DSP). To address the DSP, we propose Multi-Head Feature Collaboration (MHFC) algorithm, which attempts to project the multi-head features (e.g., multiple features extracted from a variety of FEMs) to a unified space and fuse them to capture more discriminative information. Typically, first, we introduce a subspace learning method to transform the multi-head features to aligned low-dimensional representations. It corrects the DSP via learning the feature with more powerful discrimination and overcomes the problem of inconsistent measurement scales from different head features. Then, we design an attention block to update combination weights for each head feature automatically. It comprehensively considers the contribution of various perspectives and further improves the discrimination of features. We evaluate the proposed method on five benchmark datasets (including cross-domain experiments) and achieve significant improvements of 2.1%-7.8% compared with state-of-the-arts.

Shuai Shao, Lei Xing, Yixin Chen et al.

Few-shot classification (FSC) is one of the most concerned hot issues in recent years. The general setting consists of two phases: (1) Pre-train a feature extraction model (FEM) with base data (has large amounts of labeled samples). (2) Use the FEM to extract the features of novel data (with few labeled samples and totally different categories from base data), then classify them with the to-be-designed classifier. The adaptability of pre-trained FEM to novel data determines the accuracy of novel features, thereby affecting the final classification performances. To this end, how to appraise the pre-trained FEM is the most crucial focus in the FSC community. It sounds like traditional Class Activate Mapping (CAM) based methods can achieve this by overlaying weighted feature maps. However, due to the particularity of FSC (e.g., there is no backpropagation when using the pre-trained FEM to extract novel features), we cannot activate the feature map with the novel classes. To address this challenge, we propose a simple, flexible method, dubbed as Class-Irrelevant Mapping (CIM). Specifically, first, we introduce dictionary learning theory and view the channels of the feature map as the bases in a dictionary. Then we utilize the feature map to fit the feature vector of an image to achieve the corresponding channel weights. Finally, we overlap the weighted feature map for visualization to appraise the ability of pre-trained FEM on novel data. For fair use of CIM in evaluating different models, we propose a new measurement index, called Feature Localization Accuracy (FLA). In experiments, we first compare our CIM with CAM in regular tasks and achieve outstanding performances. Next, we use our CIM to appraise several classical FSC frameworks without considering the classification results and discuss them.

Liyue Shen, John Pauly, Lei Xing

Image reconstruction is an inverse problem that solves for a computational image based on sampled sensor measurement. Sparsely sampled image reconstruction poses addition challenges due to limited measurements. In this work, we propose an implicit Neural Representation learning methodology with Prior embedding (NeRP) to reconstruct a computational image from sparsely sampled measurements. The method differs fundamentally from previous deep learning-based image reconstruction approaches in that NeRP exploits the internal information in an image prior, and the physics of the sparsely sampled measurements to produce a representation of the unknown subject. No large-scale data is required to train the NeRP except for a prior image and sparsely sampled measurements. In addition, we demonstrate that NeRP is a general methodology that generalizes to different imaging modalities such as CT and MRI. We also show that NeRP can robustly capture the subtle yet significant image changes required for assessing tumor progression.

Liyue Shen, Wei Zhao, Dante Capaldi et al.

Deep learning affords enormous opportunities to augment the armamentarium of biomedical imaging, albeit its design and implementation have potential flaws. Fundamentally, most deep learning models are driven entirely by data without consideration of any prior knowledge, which dramatically increases the complexity of neural networks and limits the application scope and model generalizability. Here we establish a geometry-informed deep learning framework for ultra-sparse 3D tomographic image reconstruction. We introduce a novel mechanism for integrating geometric priors of the imaging system. We demonstrate that the seamless inclusion of known priors is essential to enhance the performance of 3D volumetric computed tomography imaging with ultra-sparse sampling. The study opens new avenues for data-driven biomedical imaging and promises to provide substantially improved imaging tools for various clinical imaging and image-guided interventions.

Qiong Xu, Jeff Wang, Hiroki Shirato et al.

This paper presents a dictionary learning-based method with region-specific image patches to maximize the utility of the powerful sparse data processing technique for CT image reconstruction. Considering heterogeneous distributions of image features and noise in CT, region-specific customization of dictionaries is utilized in iterative reconstruction. Thoracic CT images are partitioned into several regions according to their structural and noise characteristics. Dictionaries specific to each region are then learned from the segmented thoracic CT images and applied to subsequent image reconstruction of the region. Parameters for dictionary learning and sparse representation are determined according to the structural and noise properties of each region. The proposed method results in better performance than the conventional reconstruction based on a single dictionary in recovering structures and suppressing noise in both simulation and human CT imaging. Quantitatively, the simulation study shows maximum improvement of image quality for the whole thorax can achieve 4.88% and 11.1% in terms of the Structure-SIMilarity (SSIM) and Root-Mean-Square Error (RMSE) indices, respectively. For human imaging data, it is found that the structures in the lungs and heart can be better recovered, while simultaneously decreasing noise around the vertebra effectively. The proposed strategy takes into account inherent regional differences inside of the reconstructed object and leads to improved images. The method can be readily extended to CT imaging of other anatomical regions and other applications.

Lequan Yu, Zhicheng Zhang, Xiaomeng Li et al.

Computed tomography (CT) has been widely used for medical diagnosis, assessment, and therapy planning and guidance. In reality, CT images may be affected adversely in the presence of metallic objects, which could lead to severe metal artifacts and influence clinical diagnosis or dose calculation in radiation therapy. In this paper, we propose a generalizable framework for metal artifact reduction (MAR) by simultaneously leveraging the advantages of image domain and sinogram domain-based MAR techniques. We formulate our framework as a sinogram completion problem and train a neural network (SinoNet) to restore the metal-affected projections. To improve the continuity of the completed projections at the boundary of metal trace and thus alleviate new artifacts in the reconstructed CT images, we train another neural network (PriorNet) to generate a good prior image to guide sinogram learning, and further design a novel residual sinogram learning strategy to effectively utilize the prior image information for better sinogram completion. The two networks are jointly trained in an end-to-end fashion with a differentiable forward projection (FP) operation so that the prior image generation and deep sinogram completion procedures can benefit from each other. Finally, the artifact-reduced CT images are reconstructed using the filtered backward projection (FBP) from the completed sinogram. Extensive experiments on simulated and real artifacts data demonstrate that our method produces superior artifact-reduced results while preserving the anatomical structures and outperforms other MAR methods.

Xiaomeng Li, Mengyu Jia, Md Tauhidul Islam et al.

The automatic diagnosis of various retinal diseases from fundus images is important to support clinical decision-making. However, developing such automatic solutions is challenging due to the requirement of a large amount of human-annotated data. Recently, unsupervised/self-supervised feature learning techniques receive a lot of attention, as they do not need massive annotations. Most of the current self-supervised methods are analyzed with single imaging modality and there is no method currently utilize multi-modal images for better results. Considering that the diagnostics of various vitreoretinal diseases can greatly benefit from another imaging modality, e.g., FFA, this paper presents a novel self-supervised feature learning method by effectively exploiting multi-modal data for retinal disease diagnosis. To achieve this, we first synthesize the corresponding FFA modality and then formulate a patient feature-based softmax embedding objective. Our objective learns both modality-invariant features and patient-similarity features. Through this mechanism, the neural network captures the semantically shared information across different modalities and the apparent visual similarity between patients. We evaluate our method on two public benchmark datasets for retinal disease diagnosis. The experimental results demonstrate that our method clearly outperforms other self-supervised feature learning methods and is comparable to the supervised baseline.

Liyue Shen, Wentao Zhu, Xiaosong Wang et al.

Multi-domain data are widely leveraged in vision applications taking advantage of complementary information from different modalities, e.g., brain tumor segmentation from multi-parametric magnetic resonance imaging (MRI). However, due to possible data corruption and different imaging protocols, the availability of images for each domain could vary amongst multiple data sources in practice, which makes it challenging to build a universal model with a varied set of input data. To tackle this problem, we propose a general approach to complete the random missing domain(s) data in real applications. Specifically, we develop a novel multi-domain image completion method that utilizes a generative adversarial network (GAN) with a representational disentanglement scheme to extract shared skeleton encoding and separate flesh encoding across multiple domains. We further illustrate that the learned representation in multi-domain image completion could be leveraged for high-level tasks, e.g., segmentation, by introducing a unified framework consisting of image completion and segmentation with a shared content encoder. The experiments demonstrate consistent performance improvement on three datasets for brain tumor segmentation, prostate segmentation, and facial expression image completion respectively.

Masoud Badiei Khuzani, Yinyu Ye, Sandy Napel et al.

We develop and analyze a projected particle Langevin optimization method to learn the distribution in the Schönberg integral representation of the radial basis functions from training samples. More specifically, we characterize a distributionally robust optimization method with respect to the Wasserstein distance to optimize the distribution in the Schönberg integral representation. To provide theoretical performance guarantees, we analyze the scaling limits of a projected particle online (stochastic) optimization method in the mean-field regime. In particular, we prove that in the scaling limits, the empirical measure of the Langevin particles converges to the law of a reflected Itô diffusion-drift process. Moreover, the drift is also a function of the law of the underlying process. Using Itô lemma for semi-martingales and Grisanov's change of measure for the Wiener processes, we then derive a Mckean-Vlasov type partial differential equation (PDE) with Robin boundary conditions that describes the evolution of the empirical measure of the projected Langevin particles in the mean-field regime. In addition, we establish the existence and uniqueness of the steady-state solutions of the derived PDE in the weak sense. We apply our learning approach to train radial kernels in the kernel locally sensitive hash (LSH) functions, where the training data-set is generated via a $k$-mean clustering method on a small subset of data-base. We subsequently apply our kernel LSH with a trained kernel for image retrieval task on MNIST data-set, and demonstrate the efficacy of our kernel learning approach. We also apply our kernel learning approach in conjunction with the kernel support vector machines (SVMs) for classification of benchmark data-sets.