Xinyue Hu

Xinyue Hu, Lin Gu, Qiyuan An et al.

To contribute to automating the medical vision-language model, we propose a novel Chest-Xray Difference Visual Question Answering (VQA) task. Given a pair of main and reference images, this task attempts to answer several questions on both diseases and, more importantly, the differences between them. This is consistent with the radiologist's diagnosis practice that compares the current image with the reference before concluding the report. We collect a new dataset, namely MIMIC-Diff-VQA, including 700,703 QA pairs from 164,324 pairs of main and reference images. Compared to existing medical VQA datasets, our questions are tailored to the Assessment-Diagnosis-Intervention-Evaluation treatment procedure used by clinical professionals. Meanwhile, we also propose a novel expert knowledge-aware graph representation learning model to address this task. The proposed baseline model leverages expert knowledge such as anatomical structure prior, semantic, and spatial knowledge to construct a multi-relationship graph, representing the image differences between two images for the image difference VQA task. The dataset and code can be found at https://github.com/Holipori/MIMIC-Diff-VQA. We believe this work would further push forward the medical vision language model.

Zhoujin Tian, Chaozhuo Li, Shuo Ren et al.

Bilingual lexicon induction induces the word translations by aligning independently trained word embeddings in two languages. Existing approaches generally focus on minimizing the distances between words in the aligned pairs, while suffering from low discriminative capability to distinguish the relative orders between positive and negative candidates. In addition, the mapping function is globally shared by all words, whose performance might be hindered by the deviations in the distributions of different languages. In this work, we propose a novel ranking-oriented induction model RAPO to learn personalized mapping function for each word. RAPO is capable of enjoying the merits from the unique characteristics of a single word and the cross-language isomorphism simultaneously. Extensive experimental results on public datasets including both rich-resource and low-resource languages demonstrate the superiority of our proposal. Our code is publicly available in \url{https://github.com/Jlfj345wf/RAPO}.

Xinyue Hu, Lin Gu, Kazuma Kobayashi et al.

Medical visual question answering (VQA) aims to answer clinically relevant questions regarding input medical images. This technique has the potential to improve the efficiency of medical professionals while relieving the burden on the public health system, particularly in resource-poor countries. Existing medical VQA methods tend to encode medical images and learn the correspondence between visual features and questions without exploiting the spatial, semantic, or medical knowledge behind them. This is partially because of the small size of the current medical VQA dataset, which often includes simple questions. Therefore, we first collected a comprehensive and large-scale medical VQA dataset, focusing on chest X-ray images. The questions involved detailed relationships, such as disease names, locations, levels, and types in our dataset. Based on this dataset, we also propose a novel baseline method by constructing three different relationship graphs: spatial relationship, semantic relationship, and implicit relationship graphs on the image regions, questions, and semantic labels. The answer and graph reasoning paths are learned for different questions.

Mengliang Zhang, Xinyue Hu, Lin Gu et al.

Patients undergoing chest X-rays (CXR) often endure multiple lung diseases. When evaluating a patient's condition, due to the complex pathologies, subtle texture changes of different lung lesions in images, and patient condition differences, radiologists may make uncertain even when they have experienced long-term clinical training and professional guidance, which makes much noise in extracting disease labels based on CXR reports. In this paper, we re-extract disease labels from CXR reports to make them more realistic by considering disease severity and uncertainty in classification. Our contributions are as follows: 1. We re-extracted the disease labels with severity and uncertainty by a rule-based approach with keywords discussed with clinical experts. 2. To further improve the explainability of chest X-ray diagnosis, we designed a multi-relationship graph learning method with an expert uncertainty-aware loss function. 3. Our multi-relationship graph learning method can also interpret the disease classification results. Our experimental results show that models considering disease severity and uncertainty outperform previous state-of-the-art methods.

Xujia Chen, Xinyue Hu, Letian Chen et al.

Physics-Informed Neural Networks (PINNs) combine deep learning with physical constraints for solving partial differential equations (PDEs), and are widely applied in fluid mechanics, heat transfer, and solid mechanics. However, PINN training still suffers from high-dimensional non-convex loss landscapes, imbalanced multiobjective constraints, and ineffective information propagation. Existing curriculum learning and causality-guided strategies improve training stability, but mainly focus on temporal or parametric progression, lacking explicit treatment of spatial information propagation and inter-region consistency. Moreover, they are not directly applicable to boundary value problems (BVPs) with strong spatial coupling. To address this issue, we propose a spatially correlated curriculum learning framework for PINNs. To the best of our knowledge, this is the first work to address PINN training difficulties from the perspective of spatial coupling among subregions. First, spatial causal weights guide information from near-boundary regions inward, reducing optimization failures and spurious convergence. Second, a low-frequency information bridge enforces pseudo-label-based consistency across spatially separated regions, suppressing global low-frequency drift. Third, a region-adaptive reweighting strategy adjusts subregion losses to reduce local residuals and recover high-frequency details. Experiments on PDE benchmarks show that, under comparable computational cost, the proposed method alleviates training failures and improves solution accuracy. The code is available at https://github.com/pigofmomo/CurriculumLearningPINN.

Xinyue Hu, Lin Gu, Liangchen Liu et al.

Existing video domain adaption (DA) methods need to store all temporal combinations of video frames or pair the source and target videos, which are memory cost expensive and can't scale up to long videos. To address these limitations, we propose a memory-efficient graph-based video DA approach as follows. At first our method models each source or target video by a graph: nodes represent video frames and edges represent the temporal or visual similarity relationship between frames. We use a graph attention network to learn the weight of individual frames and simultaneously align the source and target video into a domain-invariant graph feature space. Instead of storing a large number of sub-videos, our method only constructs one graph with a graph attention mechanism for one video, reducing the memory cost substantially. The extensive experiments show that, compared with the state-of-art methods, we achieved superior performance while reducing the memory cost significantly.

Xinyue Hu, Zenan Sun, Yi Nian et al.

Background: Alzheimer's disease and related dementias (ADRD) ranks as the sixth leading cause of death in the US, underlining the importance of accurate ADRD risk prediction. While recent advancement in ADRD risk prediction have primarily relied on imaging analysis, yet not all patients undergo medical imaging before an ADRD diagnosis. Merging machine learning with claims data can reveal additional risk factors and uncover interconnections among diverse medical codes. Objective: Our goal is to utilize Graph Neural Networks (GNNs) with claims data for ADRD risk prediction. Addressing the lack of human-interpretable reasons behind these predictions, we introduce an innovative method to evaluate relationship importance and its influence on ADRD risk prediction, ensuring comprehensive interpretation. Methods: We employed Variationally Regularized Encoder-decoder Graph Neural Network (VGNN) for estimating ADRD likelihood. We created three scenarios to assess the model's efficiency, using Random Forest and Light Gradient Boost Machine as baselines. We further used our relation importance method to clarify the key relationships for ADRD risk prediction. Results: VGNN surpassed other baseline models by 10% in the area under the receiver operating characteristic. The integration of the GNN model and relation importance interpretation could potentially play an essential role in providing valuable insight into factors that may contribute to or delay ADRD progression. Conclusions: Employing a GNN approach with claims data enhances ADRD risk prediction and provides insights into the impact of interconnected medical code relationships. This methodology not only enables ADRD risk modeling but also shows potential for other image analysis predictions using claims data.

Xinyue Hu, Zhibin Duan, Xinyang Liu et al.

Recently, generative graph models have shown promising results in learning graph representations through self-supervised methods. However, most existing generative graph representation learning (GRL) approaches rely on random masking across the entire graph, which overlooks the entanglement of learned representations. This oversight results in non-robustness and a lack of explainability. Furthermore, disentangling the learned representations remains a significant challenge and has not been sufficiently explored in GRL research. Based on these insights, this paper introduces DiGGR (Disentangled Generative Graph Representation Learning), a self-supervised learning framework. DiGGR aims to learn latent disentangled factors and utilizes them to guide graph mask modeling, thereby enhancing the disentanglement of learned representations and enabling end-to-end joint learning. Extensive experiments on 11 public datasets for two different graph learning tasks demonstrate that DiGGR consistently outperforms many previous self-supervised methods, verifying the effectiveness of the proposed approach.

Yushan Jiang, Shuteng Niu, Dongjin Song et al.

Graft-versus-host disease (GVHD) is a rare but often fatal complication in liver transplantation, with a very high mortality rate. By harnessing multi-modal deep learning methods to integrate heterogeneous and imbalanced electronic health records (EHR), we aim to advance early prediction of GVHD, paving the way for timely intervention and improved patient outcomes. In this study, we analyzed pre-transplant electronic health records (EHR) spanning the period before surgery for 2,100 liver transplantation patients, including 42 cases of graft-versus-host disease (GVHD), from a cohort treated at Mayo Clinic between 1992 and 2025. The dataset comprised four major modalities: patient demographics, laboratory tests, diagnoses, and medications. We developed a multi-modal deep learning framework that dynamically fuses these modalities, handles irregular records with missing values, and addresses extreme class imbalance through AUC-based optimization. The developed framework outperforms all single-modal and multi-modal machine learning baselines, achieving an AUC of 0.836, an AUPRC of 0.157, a recall of 0.768, and a specificity of 0.803. It also demonstrates the effectiveness of our approach in capturing complementary information from different modalities, leading to improved performance. Our multi-modal deep learning framework substantially improves existing approaches for early GVHD prediction. By effectively addressing the challenges of heterogeneity and extreme class imbalance in real-world EHR, it achieves accurate early prediction. Our proposed multi-modal deep learning method demonstrates promising results for early prediction of a GVHD in liver transplantation, despite the challenge of extremely imbalanced EHR data.

Qiuhui Chen, Xuancheng Yao, Zhenglei Zhou et al.

Deep learning models for medical image analysis often act as black boxes, seldom aligning with clinical guidelines or explicitly linking decisions to supporting evidence. This is especially critical in Alzheimer's disease (AD), where predictions should be grounded in both anatomical and clinical findings. We present EMAD, a vision-language framework that generates structured AD diagnostic reports in which each claim is explicitly grounded in multimodal evidence. EMAD uses a hierarchical Sentence-Evidence-Anatomy (SEA) grounding mechanism: (i) sentence-to-evidence grounding links generated sentences to clinical evidence phrases, and (ii) evidence-to-anatomy grounding localizes corresponding structures on 3D brain MRI. To reduce dense annotation requirements, we propose GTX-Distill, which transfers grounding behavior from a teacher trained with limited supervision to a student operating on model-generated reports. We further introduce Executable-Rule GRPO, a reinforcement fine-tuning scheme with verifiable rewards that enforces clinical consistency, protocol adherence, and reasoning-diagnosis coherence. On the AD-MultiSense dataset, EMAD achieves state-of-the-art diagnostic accuracy and produces more transparent, anatomically faithful reports than existing methods. We will release code and grounding annotations to support future research in trustworthy medical vision-language models.

Qiuhui Chen, Xinyue Hu, Zirui Wang et al.

Vision-language pre-training (VLP) models have been demonstrated to be effective in many computer vision applications. In this paper, we consider developing a VLP model in the medical domain for making computer-aided diagnoses (CAD) based on image scans and text descriptions in electronic health records, as done in practice. To achieve our goal, we present a lightweight CAD system MedBLIP, a new paradigm for bootstrapping VLP from off-the-shelf frozen pre-trained image encoders and frozen large language models. We design a MedQFormer module to bridge the gap between 3D medical images and 2D pre-trained image encoders and language models as well. To evaluate the effectiveness of our MedBLIP, we collect more than 30,000 image volumes from five public Alzheimer's disease (AD) datasets, i.e., ADNI, NACC, OASIS, AIBL, and MIRIAD. On this largest AD dataset we know, our model achieves the SOTA performance on the zero-shot classification of healthy, mild cognitive impairment (MCI), and AD subjects, and shows its capability of making medical visual question answering (VQA). The code and pre-trained models is available online: https://github.com/Qybc/MedBLIP.

Qiuhui Chen, Haiying Lyu, Xinyue Hu et al.

Recently, weakly-supervised image segmentation using weak annotations like scribbles has gained great attention in computer vision and medical image analysis, since such annotations are much easier to obtain compared to time-consuming and labor-intensive labeling at the pixel/voxel level. However, due to a lack of structure supervision on regions of interest (ROIs), existing scribble-based methods suffer from poor boundary localization. Furthermore, most current methods are designed for 2D image segmentation, which do not fully leverage the volumetric information if directly applied to each image slice. In this paper, we propose a scribble-based volumetric image segmentation, Scribble2D5, which tackles 3D anisotropic image segmentation and aims to its improve boundary prediction. To achieve this, we augment a 2.5D attention UNet with a proposed label propagation module to extend semantic information from scribbles and use a combination of static and active boundary prediction to learn ROI's boundary and regularize its shape. Also, we propose an optional add-on component, which incorporates the shape prior information from unpaired segmentation masks to further improve model accuracy. Extensive experiments on three public datasets and one private dataset demonstrate our Scribble2D5 achieves state-of-the-art performance on volumetric image segmentation using scribbles and shape prior if available.

Ragini Gupta, Shinan Liu, Ruixiao Zhang et al.

Machine learning has shown promise in network intrusion detection systems, yet its performance often degrades due to concept drift and imbalanced data. These challenges are compounded by the labor-intensive process of labeling network traffic, especially when dealing with evolving and rare attack types, which makes preparing the right data for adaptation difficult. To address these issues, we propose a generative active adaptation framework that minimizes labeling effort while enhancing model robustness. Our approach employs density-aware dataset prior selection to identify the most informative samples for annotation, and leverages deep generative models to conditionally synthesize diverse samples, thereby augmenting the training set and mitigating the effects of concept drift. We evaluate our end-to-end framework \NetGuard on both simulated IDS data and a real-world ISP dataset, demonstrating significant improvements in intrusion detection performance. Our method boosts the overall F1-score from 0.60 (without adaptation) to 0.86. Rare attacks such as Infiltration, Web Attack, and FTP-BruteForce, which originally achieved F1 scores of 0.001, 0.04, and 0.00, improve to 0.30, 0.50, and 0.71, respectively, with generative active adaptation in the CIC-IDS 2018 dataset. Our framework effectively enhances rare attack detection while reducing labeling costs, making it a scalable and practical solution for intrusion detection.

Xinyue Hu, Zhibin Duan, Bo Chen et al.

Although deep neural networks have demonstrated significant success due to their powerful expressiveness, most models struggle to meet practical requirements for uncertainty estimation. Concurrently, the entangled nature of deep neural networks leads to a multifaceted problem, where various localized explanation techniques reveal that multiple unrelated features influence the decisions, thereby undermining interpretability. To address these challenges, we develop a Bayesian Non-negative Decision Layer (BNDL), which reformulates deep neural networks as a conditional Bayesian non-negative factor analysis. By leveraging stochastic latent variables, the BNDL can model complex dependencies and provide robust uncertainty estimation. Moreover, the sparsity and non-negativity of the latent variables encourage the model to learn disentangled representations and decision layers, thereby improving interpretability. We also offer theoretical guarantees that BNDL can achieve effective disentangled learning. In addition, we developed a corresponding variational inference method utilizing a Weibull variational inference network to approximate the posterior distribution of the latent variables. Our experimental results demonstrate that with enhanced disentanglement capabilities, BNDL not only improves the model's accuracy but also provides reliable uncertainty estimation and improved interpretability.

Xinyue Hu, Wei Ye, Jiaxiang Tang et al.

Multiple Description Coding (MDC) is a promising error-resilient source coding method that is particularly suitable for dynamic networks with multiple (yet noisy and unreliable) paths. However, conventional MDC video codecs suffer from cumbersome architectures, poor scalability, limited loss resilience, and lower compression efficiency. As a result, MDC has never been widely adopted. Inspired by the potential of neural video codecs, this paper rethinks MDC design. We propose a novel MDC video codec, NeuralMDC, demonstrating how bidirectional transformers trained for masked token prediction can vastly simplify the design of MDC video codec. To compress a video, NeuralMDC starts by tokenizing each frame into its latent representation and then splits the latent tokens to create multiple descriptions containing correlated information. Instead of using motion prediction and warping operations, NeuralMDC trains a bidirectional masked transformer to model the spatial-temporal dependencies of latent representations and predict the distribution of the current representation based on the past. The predicted distribution is used to independently entropy code each description and infer any potentially lost tokens. Extensive experiments demonstrate NeuralMDC achieves state-of-the-art loss resilience with minimal sacrifices in compression efficiency, significantly outperforming the best existing residual-coding-based error-resilient neural video codec.

Shuo Xu, Sai Wang, Xinyue Hu et al.

Compositional Zero-Shot Learning (CZSL) aims to learn semantic primitives (attributes and objects) from seen compositions and recognize unseen attribute-object compositions. Existing CZSL datasets focus on single attributes, neglecting the fact that objects naturally exhibit multiple interrelated attributes. Their narrow attribute scope and single attribute labeling introduce annotation biases, misleading the learning of attributes and causing inaccurate evaluation. To address these issues, we introduce the Multi-Attribute Composition (MAC) dataset, encompassing 22,838 images and 17,627 compositions with comprehensive and representative attribute annotations. MAC shows complex relationship between attributes and objects, with each attribute type linked to an average of 82.2 object types, and each object type associated with 31.4 attribute types. Based on MAC, we propose multi-attribute compositional zero-shot learning that requires deeper semantic understanding and advanced attribute associations, establishing a more realistic and challenging benchmark for CZSL. We also propose Multi-attribute Visual-Primitive Integrator (MVP-Integrator), a robust baseline for multi-attribute CZSL, which disentangles semantic primitives and performs effective visual-primitive association. Experimental results demonstrate that MVP-Integrator significantly outperforms existing CZSL methods on MAC with improved inference efficiency.

Mark Steyvers, Heliodoro Tejeda, Aakriti Kumar et al.

As artificial intelligence (AI) systems, particularly large language models (LLMs), become increasingly integrated into decision-making processes, the ability to trust their outputs is crucial. To earn human trust, LLMs must be well calibrated such that they can accurately assess and communicate the likelihood of their predictions being correct. Whereas recent work has focused on LLMs' internal confidence, less is understood about how effectively they convey uncertainty to users. Here we explore the calibration gap, which refers to the difference between human confidence in LLM-generated answers and the models' actual confidence, and the discrimination gap, which reflects how well humans and models can distinguish between correct and incorrect answers. Our experiments with multiple-choice and short-answer questions reveal that users tend to overestimate the accuracy of LLM responses when provided with default explanations. Moreover, longer explanations increased user confidence, even when the extra length did not improve answer accuracy. By adjusting LLM explanations to better reflect the models' internal confidence, both the calibration gap and the discrimination gap narrowed, significantly improving user perception of LLM accuracy. These findings underscore the importance of accurate uncertainty communication and highlight the effect of explanation length in influencing user trust in AI-assisted decision-making environments. Code and Data can be found at https://osf.io/y7pr6/ . Journal publication can be found on Nature Machine Intelligence at https://www.nature.com/articles/s42256-024-00976-7 .

Yi Nian, Xinyue Hu, Rui Zhang et al.

To date, there are no effective treatments for most neurodegenerative diseases. Knowledge graphs can provide comprehensive and semantic representation for heterogeneous data, and have been successfully leveraged in many biomedical applications including drug repurposing. Our objective is to construct a knowledge graph from literature to study relations between Alzheimer's disease (AD) and chemicals, drugs and dietary supplements in order to identify opportunities to prevent or delay neurodegenerative progression. We collected biomedical annotations and extracted their relations using SemRep via SemMedDB. We used both a BERT-based classifier and rule-based methods during data preprocessing to exclude noise while preserving most AD-related semantic triples. The 1,672,110 filtered triples were used to train with knowledge graph completion algorithms (i.e., TransE, DistMult, and ComplEx) to predict candidates that might be helpful for AD treatment or prevention. Among three knowledge graph completion models, TransE outperformed the other two (MR = 13.45, Hits@1 = 0.306). We leveraged the time-slicing technique to further evaluate the prediction results. We found supporting evidence for most highly ranked candidates predicted by our model which indicates that our approach can inform reliable new knowledge. This paper shows that our graph mining model can predict reliable new relationships between AD and other entities (i.e., dietary supplements, chemicals, and drugs). The knowledge graph constructed can facilitate data-driven knowledge discoveries and the generation of novel hypotheses.

Yi Nian, Jingcheng Du, Larry Bu et al.

To date, there are no effective treatments for most neurodegenerative diseases. However, certain foods may be associated with these diseases and bring an opportunity to prevent or delay neurodegenerative progression. Our objective is to construct a knowledge graph for neurodegenerative diseases using literature mining to study their relations with diet. We collected biomedical annotations (Disease, Chemical, Gene, Species, SNP&Mutation) in the abstracts from 4,300 publications relevant to both neurodegenerative diseases and diet using PubTator, an NIH-supported tool that can extract biomedical concepts from literature. A knowledge graph was created from these annotations. Graph embeddings were then trained with the node2vec algorithm to support potential concept clustering and similar concept identification. We found several food-related species and chemicals that might come from diet and have an impact on neurodegenerative diseases.

Xinyue Hu, Haoji Hu, Saurabh Verma et al.

Solving power flow (PF) equations is the basis of power flow analysis, which is important in determining the best operation of existing systems, performing security analysis, etc. However, PF equations can be out-of-date or even unavailable due to system dynamics and uncertainties, making traditional numerical approaches infeasible. To address these concerns, researchers have proposed data-driven approaches to solve the PF problem by learning the mapping rules from historical system operation data. Nevertheless, prior data-driven approaches suffer from poor performance and generalizability, due to overly simplified assumptions of the PF problem or ignorance of physical laws governing power systems. In this paper, we propose a physics-guided neural network to solve the PF problem, with an auxiliary task to rebuild the PF model. By encoding different granularity of Kirchhoff's laws and system topology into the rebuilt PF model, our neural-network based PF solver is regularized by the auxiliary task and constrained by the physical laws. The simulation results show that our physics-guided neural network methods achieve better performance and generalizability compared to existing unconstrained data-driven approaches. Furthermore, we demonstrate that the weight matrices of our physics-guided neural networks embody power system physics by showing their similarities with the bus admittance matrices.