Chaoyang Zhang

Lei Huang, Hui Shen, Kuan-Jui Su et al.

Genotype-based cis-expression prediction depends on accurately modeling local regulatory architecture. We present block-sparse Bayesian sparse linear mixed model (bsBSLMM), an extension of Bayesian sparse linear mixed model (BSLMM) that incorporates linkage disequilibrium (LD)-block spike-and-slab sparsity and a transcription start site (TSS)-informed SNP inclusion prior. Across 23,098 genes from GEUVADIS European-ancestry lymphoblastoid cell lines, bsBSLMM retained more predictable genes than BSLMM, LASSO, BLUP, TIGAR elastic net, and TIGAR Dirichlet-process regression under matched evaluation criteria. Compared with BSLMM, bsBSLMM improved held-out prediction performance for most shared genes, with gains driven primarily by LD-block sparsity and further enhanced by the TSS-informed prior. Variants selected by bsBSLMM showed stronger enrichment in GM12878 DNase and H3K27ac regulatory regions than variants selected by BSLMM. In transcriptome-wide association study (TWAS) analysis, bsBSLMM recovered established inflammatory bowel disease signals, including IL23R, and identified additional genome-wide significant genes not detected by BSLMM. Independent validation in the Louisiana Osteoporosis Study reproduced the increased prediction yield across ancestries and recovered biologically relevant bone mineral density pathways in downstream TWAS and gene set enrichment analyses. These results demonstrate that incorporating LD-block structure and biologically informed SNP priors improves cis-expression prediction and enhances downstream TWAS discovery.

Zhongying Deng, Cheng Tang, Ziyan Huang et al. · pku

Foundation models have demonstrated remarkable success across diverse domains and tasks, primarily due to the thrive of large-scale, diverse, and high-quality datasets. However, in the field of medical imaging, the curation and assembling of such medical datasets are highly challenging due to the reliance on clinical expertise and strict ethical and privacy constraints, resulting in a scarcity of large-scale unified medical datasets and hindering the development of powerful medical foundation models. In this work, we present the largest survey to date of medical image datasets, covering over 1,000 open-access datasets with a systematic catalog of their modalities, tasks, anatomies, annotations, limitations, and potential for integration. Our analysis exposes a landscape that is modest in scale, fragmented across narrowly scoped tasks, and unevenly distributed across organs and modalities, which in turn limits the utility of existing medical image datasets for developing versatile and robust medical foundation models. To turn fragmentation into scale, we propose a metadata-driven fusion paradigm (MDFP) that integrates public datasets with shared modalities or tasks, thereby transforming multiple small data silos into larger, more coherent resources. Building on MDFP, we release an interactive discovery portal that enables end-to-end, automated medical image dataset integration, and compile all surveyed datasets into a unified, structured table that clearly summarizes their key characteristics and provides reference links, offering the community an accessible and comprehensive repository. By charting the current terrain and offering a principled path to dataset consolidation, our survey provides a practical roadmap for scaling medical imaging corpora, supporting faster data discovery, more principled dataset creation, and more capable medical foundation models.

Telang Xu, Chaoyang Zhang, Guangtao Zhai et al.

Single image reflection removal (SIRR) is challenging in real scenes, where reflection strength varies spatially and reflection patterns are tightly entangled with transmission structures. This paper presents a diffusion model with prior modulation framework (FUMO) that introduces explicit guidance signals to improve spatial controllability and structural faithfulness. Two priors are extracted directly from the mixed image, an intensity prior that estimates spatial reflection severity and a high-frequency prior that captures detail-sensitive responses via multi-scale residual aggregation. We propose a coarse-to-fine training paradigm. In the first stage, these cues are combined to gate the conditional residual injections, focusing the conditioning on regions that are both reflection-dominant and structure-sensitive. In the second stage, a fine-grained refinement network corrects local misalignment and sharpens fine details in the image space. Experiments conducted on both standard benchmarks and challenging images in the wild demonstrate competitive quantitative results and consistently improved perceptual quality. The code is released at https://github.com/Lucious-Desmon/FUMO.

Mahid Ahmed, Ali Dogru, Chaoyang Zhang et al.

Strategically locating a sawmill is vital for enhancing the efficiency, profitability, and sustainability of timber supply chains. Our study proposes a Learning-Based Multi-Criteria Decision-Making (LB-MCDM) framework that integrates machine learning (ML) with GIS-based spatial location analysis via MCDM. The proposed framework provides a data-driven, unbiased, and replicable approach to assessing site suitability. We demonstrate the utility of the proposed model through a case study in Mississippi (MS). We apply five ML algorithms (Random Forest Classifier, Support Vector Classifier, XGBoost Classifier, Logistic Regression, and K-Nearest Neighbors Classifier) to identify the most suitable sawmill locations in Mississippi. Among these models, the Random Forest Classifier achieved the highest performance. We use the SHAP (SHapley Additive exPlanations) technique to determine the relative importance of each criterion, revealing the Supply-Demand Ratio, a composite feature that reflects local market competition dynamics, as the most influential factor, followed by Road, Rail Line and Urban Area Distance. The validation of suitability maps generated by our LB-MCDM model suggests that 10-11% of the MS landscape is highly suitable for sawmill location.

Zelu Qi, Ping Shi, Chaoyang Zhang et al.

The development of AI-Generated Video (AIGV) technology has been remarkable in recent years, significantly transforming the paradigm of video content production. However, AIGVs still suffer from noticeable visual quality defects, such as noise, blurriness, frame jitter and low dynamic degree, which severely impact the user's viewing experience. Therefore, an effective automatic visual quality assessment is of great importance for AIGV content regulation and generative model improvement. In this work, we decompose the visual quality of AIGVs into three dimensions: technical quality, motion quality, and video semantics. For each dimension, we design corresponding encoder to achieve effective feature representation. Moreover, considering the outstanding performance of large language models (LLMs) in various vision and language tasks, we introduce a LLM as the quality regression module. To better enable the LLM to establish reasoning associations between multi-dimensional features and visual quality, we propose a specially designed multi-modal prompt engineering framework. Additionally, we incorporate LoRA fine-tuning technology during the training phase, allowing the LLM to better adapt to specific tasks. Our proposed method achieved \textbf{second place} in the NTIRE 2025 Quality Assessment of AI-Generated Content Challenge: Track 2 AI Generated video, demonstrating its effectiveness. Codes can be obtained at https://github.com/QiZelu/AIGVEval.

Junzhi Ning, Wei Li, Cheng Tang et al.

Medical diagnostic applications require models that can process multimodal medical inputs (images, patient histories, lab results) and generate diverse outputs including both textual reports and visual content (annotations, segmentation masks, and images). Despite this need, existing medical AI systems disrupt this unified process: medical image understanding models interpret images but cannot generate visual outputs, while medical image generation models synthesize images but cannot provide textual explanations. This leads to gaps in data representation, feature integration, and task-level multimodal capabilities. To this end, we propose a multi-level framework that draws inspiration from diagnostic workflows through the Observation-Knowledge-Analysis (OKA) paradigm. Specifically, at the observation level, we construct UniMed-5M, a dataset comprising over 5.6M samples that reformat diverse unimodal data into multimodal pairs for foundational observation. At the knowledge level, we propose Progressive Curriculum Learning that systematically introduces medical multimodal knowledge. At the analysis level, we introduce UniMedVL, the first medical unified multimodal model for the simultaneous analysis of image understanding and generation tasks within a single architecture. UniMedVL achieves superior performance on five medical image understanding benchmarks, while matching specialized models in generation quality across eight medical imaging modalities. Crucially, our unified architecture enables bidirectional knowledge sharing: generation tasks enhance visual understanding features, demonstrating that integrating traditionally separate capabilities within a single medical framework unlocks improvements across diverse medical vision-language tasks. Code is available at https://github.com/uni-medical/UniMedVL.

Xiaohong Liu, Xiongkuo Min, Qiang Hu et al.

This paper reports on the NTIRE 2025 XGC Quality Assessment Challenge, which will be held in conjunction with the New Trends in Image Restoration and Enhancement Workshop (NTIRE) at CVPR 2025. This challenge is to address a major challenge in the field of video and talking head processing. The challenge is divided into three tracks, including user generated video, AI generated video and talking head. The user-generated video track uses the FineVD-GC, which contains 6,284 user generated videos. The user-generated video track has a total of 125 registered participants. A total of 242 submissions are received in the development phase, and 136 submissions are received in the test phase. Finally, 5 participating teams submitted their models and fact sheets. The AI generated video track uses the Q-Eval-Video, which contains 34,029 AI-Generated Videos (AIGVs) generated by 11 popular Text-to-Video (T2V) models. A total of 133 participants have registered in this track. A total of 396 submissions are received in the development phase, and 226 submissions are received in the test phase. Finally, 6 participating teams submitted their models and fact sheets. The talking head track uses the THQA-NTIRE, which contains 12,247 2D and 3D talking heads. A total of 89 participants have registered in this track. A total of 225 submissions are received in the development phase, and 118 submissions are received in the test phase. Finally, 8 participating teams submitted their models and fact sheets. Each participating team in every track has proposed a method that outperforms the baseline, which has contributed to the development of fields in three tracks.

Ming Hu, Chenglong Ma, Wei Li et al. · pku

Scientific Large Language Models (Sci-LLMs) are transforming how knowledge is represented, integrated, and applied in scientific research, yet their progress is shaped by the complex nature of scientific data. This survey presents a comprehensive, data-centric synthesis that reframes the development of Sci-LLMs as a co-evolution between models and their underlying data substrate. We formulate a unified taxonomy of scientific data and a hierarchical model of scientific knowledge, emphasizing the multimodal, cross-scale, and domain-specific challenges that differentiate scientific corpora from general natural language processing datasets. We systematically review recent Sci-LLMs, from general-purpose foundations to specialized models across diverse scientific disciplines, alongside an extensive analysis of over 270 pre-/post-training datasets, showing why Sci-LLMs pose distinct demands -- heterogeneous, multi-scale, uncertainty-laden corpora that require representations preserving domain invariance and enabling cross-modal reasoning. On evaluation, we examine over 190 benchmark datasets and trace a shift from static exams toward process- and discovery-oriented assessments with advanced evaluation protocols. These data-centric analyses highlight persistent issues in scientific data development and discuss emerging solutions involving semi-automated annotation pipelines and expert validation. Finally, we outline a paradigm shift toward closed-loop systems where autonomous agents based on Sci-LLMs actively experiment, validate, and contribute to a living, evolving knowledge base. Collectively, this work provides a roadmap for building trustworthy, continually evolving artificial intelligence (AI) systems that function as a true partner in accelerating scientific discovery.

Zelu Qi, Ping Shi, Shuqi Wang et al.

Recent advances in text-to-video (T2V) technology, as demonstrated by models such as Runway Gen-3, Pika, Sora, and Kling, have significantly broadened the applicability and popularity of the technology. This progress has created a growing demand for accurate quality assessment metrics to evaluate the perceptual quality of T2V-generated videos and optimize video generation models. However, assessing the quality of text-to-video outputs remain challenging due to the presence of highly complex distortions, such as unnatural actions and phenomena that defy human cognition. To address these challenges, we constructed T2VEval-Bench, a multi-dimensional benchmark dataset for text-to-video quality evaluation, which contains 148 textual prompts and 1,783 videos generated by 13 T2V models. To ensure a comprehensive evaluation, we scored each video on four dimensions in the subjective experiment, which are overall impression, text-video consistency, realness, and technical quality. Based on T2VEval-Bench, we developed T2VEval, a multi-branch fusion scheme for T2V quality evaluation. T2VEval assesses videos across three branches: text-video consistency, realness, and technical quality. Using an attention-based fusion module, T2VEval effectively integrates features from each branch and predicts scores with the aid of a large language model. Additionally, we implemented a divide-and-conquer training strategy, enabling each branch to learn targeted knowledge while maintaining synergy with the others. Experimental results demonstrate that T2VEval achieves state-of-the-art performance across multiple metrics.

Lei Huang, Chuan Qiu, Kuan-Jui Su et al.

Genotype imputation enables dense variant coverage for genome-wide association and risk-prediction studies, yet conventional reference-panel methods remain limited by ancestry bias and reduced rare-variant accuracy. We present Genotype Bidirectional Encoder Representations from Transformers (GenoBERT), a transformer-based, reference-free framework that tokenizes phased genotypes and uses a self-attention mechanism to capture both short- and long-range linkage disequilibrium (LD) dependencies. Benchmarking on two independent datasets including the Louisiana Osteoporosis Study (LOS) and the 1000 Genomes Project (1KGP) across ancestry groups and multiple genotype missingness levels (5-50%) shows that GenoBERT achieves the highest overall accuracy compared to four baseline methods (Beagle5.4, SCDA, BiU-Net, and STICI). At practical sparsity levels (up to 25% missing), GenoBERT attains high overall imputation accuracy ($r^2 approx 0.98$) across datasets, and maintains robust performance ($r^2 > 0.90$) even at 50% missingness. Experimental results across different ancestries confirm consistent gains across datasets, with resilience to small sample sizes and weak LD. A 128-SNP (single-nucleotide polymorphism) context window (approximately 100 Kb) is validated through LD-decay analyses as sufficient to capture local correlation structures. By eliminating reference-panel dependence while preserving high accuracy, GenoBERT provides a scalable and robust solution for genotype imputation and a foundation for downstream genomic modeling.

Junhao Xia, Chaoyang Zhang, Yecheng Zhang et al.

Video generation based on diffusion models presents a challenging multimodal task, with video editing emerging as a pivotal direction in this field. Recent video editing approaches primarily fall into two categories: training-required and training-free methods. While training-based methods incur high computational costs, training-free alternatives often yield suboptimal performance. To address these limitations, we propose DAPE, a high-quality yet cost-effective two-stage parameter-efficient fine-tuning (PEFT) framework for video editing. In the first stage, we design an efficient norm-tuning method to enhance temporal consistency in generated videos. The second stage introduces a vision-friendly adapter to improve visual quality. Additionally, we identify critical shortcomings in existing benchmarks, including limited category diversity, imbalanced object distribution, and inconsistent frame counts. To mitigate these issues, we curate a large dataset benchmark comprising 232 videos with rich annotations and 6 editing prompts, enabling objective and comprehensive evaluation of advanced methods. Extensive experiments on existing datasets (BalanceCC, LOVEU-TGVE, RAVE) and our proposed benchmark demonstrate that DAPE significantly improves temporal coherence and text-video alignment while outperforming previous state-of-the-art approaches.

Mahid Ahmed, Ali Dogru, Chaoyang Zhang et al.

Strategically locating sawmills is critical for the efficiency, profitability, and sustainability of timber supply chains, yet it involves a series of complex decision-making affected by various factors, such as proximity to resources and markets, proximity to roads and rail lines, distance from the urban area, slope, labor market, and existing sawmill data. Although conventional Multi-Criteria Decision-Making (MCDM) approaches utilize these factors while locating facilities, they are susceptible to bias since they rely heavily on expert opinions to determine the relative factor weights. Machine learning (ML) models provide an objective, data-driven alternative for site selection that derives these weights directly from the patterns in large datasets without requiring subjective weighting. Additionally, ML models autonomously identify critical features, eliminating the need for subjective feature selection. In this study, we propose integrated ML and MCDM methods and showcase the utility of this integrated model to improve sawmill location decisions via a case study in Mississippi. This integrated model is flexible and applicable to site selection problems across various industries.

Chaoyang Zhang, Shaojie Chang, Ti Bai et al.

Photon counting spectral CT (PCCT) can produce reconstructed attenuation maps in different energy channels, reflecting energy properties of the scanned object. Due to the limited photon numbers and the non-ideal detector response of each energy channel, the reconstructed images usually contain much noise. With the development of Deep Learning (DL) technique, different kinds of DL-based models have been proposed for noise reduction. However, most of the models require clean data set as the training labels, which are not always available in medical imaging field. Inspiring by the similarities of each channel's reconstructed image, we proposed a self-supervised learning based PCCT image enhancement framework via multi-spectral channels (S2MS). In S2MS framework, both the input and output labels are noisy images. Specifically, one single channel image was used as output while images of other single channels and channel-sum image were used as input to train the network, which can fully use the spectral data information without extra cost. The simulation results based on the AAPM Low-dose CT Challenge database showed that the proposed S2MS model can suppress the noise and preserve details more effectively in comparison with the traditional DL models, which has potential to improve the image quality of PCCT in clinical applications.

Chen Zhao, Haipeng Tang, Daniel McGonigle et al.

In stable coronary artery disease (CAD), reduction in mortality and/or myocardial infarction with revascularization over medical therapy has not been reliably achieved. Coronary arteries are usually extracted to perform stenosis detection. We aim to develop an automatic algorithm by deep learning to extract coronary arteries from ICAs.In this study, a multi-input and multi-scale (MIMS) U-Net with a two-stage recurrent training strategy was proposed for the automatic vessel segmentation. Incorporating features such as the Inception residual module with depth-wise separable convolutional layers, the proposed model generated a refined prediction map with the following two training stages: (i) Stage I coarsely segmented the major coronary arteries from pre-processed single-channel ICAs and generated the probability map of vessels; (ii) during the Stage II, a three-channel image consisting of the original preprocessed image, a generated probability map, and an edge-enhanced image generated from the preprocessed image was fed to the proposed MIMS U-Net to produce the final segmentation probability map. During the training stage, the probability maps were iteratively and recurrently updated by feeding into the neural network. After segmentation, an arterial stenosis detection algorithm was developed to extract vascular centerlines and calculate arterial diameters to evaluate stenotic level. Experimental results demonstrated that the proposed method achieved an average Dice score of 0.8329, an average sensitivity of 0.8281, and an average specificity of 0.9979 in our dataset with 294 ICAs obtained from 73 patient. Moreover, our stenosis detection algorithm achieved a true positive rate of 0.6668 and a positive predictive value of 0.7043.

Chen Zhao, Joyce H. Keyak, Jinshan Tang et al.

Purpose: Proximal femur image analyses based on quantitative computed tomography (QCT) provide a method to quantify the bone density and evaluate osteoporosis and risk of fracture. We aim to develop a deep-learning-based method for automatic proximal femur segmentation. Methods and Materials: We developed a 3D image segmentation method based on V-Net, an end-to-end fully convolutional neural network (CNN), to extract the proximal femur QCT images automatically. The proposed V-net methodology adopts a compound loss function, which includes a Dice loss and a L2 regularizer. We performed experiments to evaluate the effectiveness of the proposed segmentation method. In the experiments, a QCT dataset which included 397 QCT subjects was used. For the QCT image of each subject, the ground truth for the proximal femur was delineated by a well-trained scientist. During the experiments for the entire cohort then for male and female subjects separately, 90% of the subjects were used in 10-fold cross-validation for training and internal validation, and to select the optimal parameters of the proposed models; the rest of the subjects were used to evaluate the performance of models. Results: Visual comparison demonstrated high agreement between the model prediction and ground truth contours of the proximal femur portion of the QCT images. In the entire cohort, the proposed model achieved a Dice score of 0.9815, a sensitivity of 0.9852 and a specificity of 0.9992. In addition, an R2 score of 0.9956 (p<0.001) was obtained when comparing the volumes measured by our model prediction with the ground truth. Conclusion: This method shows a great promise for clinical application to QCT and QCT-based finite element analysis of the proximal femur for evaluating osteoporosis and hip fracture risk.

ShiJie Sun, Naveed Akhtar, HuanSheng Song et al.

Vision-based automatic counting of people has widespread applications in intelligent transportation systems, security, and logistics. However, there is currently no large-scale public dataset for benchmarking approaches on this problem. This work fills this gap by introducing the first real-world RGB-D People Counting DataSet (PCDS) containing over 4,500 videos recorded at the entrance doors of buses in normal and cluttered conditions. It also proposes an efficient method for counting people in real-world cluttered scenes related to public transportations using depth videos. The proposed method computes a point cloud from the depth video frame and re-projects it onto the ground plane to normalize the depth information. The resulting depth image is analyzed for identifying potential human heads. The human head proposals are meticulously refined using a 3D human model. The proposals in each frame of the continuous video stream are tracked to trace their trajectories. The trajectories are again refined to ascertain reliable counting. People are eventually counted by accumulating the head trajectories leaving the scene. To enable effective head and trajectory identification, we also propose two different compound features. A thorough evaluation on PCDS demonstrates that our technique is able to count people in cluttered scenes with high accuracy at 45 fps on a 1.7 GHz processor, and hence it can be deployed for effective real-time people counting for intelligent transportation systems.