arXiv subjects

Ziyang Xu

Publications and source records attributed to Ziyang Xu.

At least 37 records · Page 2Linked to original sources

arXiv2026

Establishing dermatopathology encyclopedia DermpathNet with Artificial Intelligence-Based Workflow

Accessing high-quality, open-access dermatopathology image datasets for learning and cross-referencing is a common challenge for clinicians and dermatopathology trainees. To establish a comprehensive open-access dermatopathology dataset for educational, cross-referencing, and machine-learning purposes, we employed a hybrid workflow to curate and categorize images from the PubMed Central (PMC) repository. We used specific keywords to extract relevant images, and classified them using a novel hybrid method that combined deep learning-based image modality classification with figure caption analyses. Validation on 651 manually annotated images demonstrated the robustness of our workflow, with an F-score of 89.6% for the deep learning approach, 61.0% for the keyword-based retrieval method, and 90.4% for the hybrid approach. We retrieved over 7,772 images across 166 diagnoses and released this fully annotated dataset, reviewed by board-certified dermatopathologists. Using our dataset as a challenging task, we found the current image analysis algorithm from OpenAI inadequate for analyzing dermatopathology images. In conclusion, we have developed a large, peer-reviewed, open-access dermatopathology image dataset, DermpathNet, which features a semi-automated curation workflow.

cs.CV↗

arXiv2026

All That Glisters Is Not Gold: A Benchmark for Reference-Free Counterfactual Financial Misinformation Detection

We introduce RFC Bench, a benchmark for evaluating large language models on financial misinformation under realistic news. RFC Bench operates at the paragraph level and captures the contextual complexity of financial news where meaning emerges from dispersed cues. The benchmark defines two complementary tasks: reference free misinformation detection and comparison based diagnosis using paired original perturbed inputs. Experiments reveal a consistent pattern: performance is substantially stronger when comparative context is available, while reference free settings expose significant weaknesses, including unstable predictions and elevated invalid outputs. These results indicate that current models struggle to maintain coherent belief states without external grounding. By highlighting this gap, RFC Bench provides a structured testbed for studying reference free reasoning and advancing more reliable financial misinformation detection in real world settings.

cs.CL↗

arXiv2025

A general language model for peptide function identification

Accurate identification of bioactive peptides (BPs) and protein post-translational modifications (PTMs) is essential for understanding protein function and advancing therapeutic discovery. However, most computational methods remain limited in their generalizability across diverse peptide functions. Here, we present PDeepPP, a unified deep learning framework that integrates pretrained protein language models with a hybrid transformer-CNN architecture, enabling robust identification across diverse peptide classes and PTM sites. We curated comprehensive benchmark datasets and implemented strategies to address data imbalance, allowing PDeepPP to systematically extract both global and local sequence features. Through extensive analyses including dimensionality reduction and comparison studies, PDeepPP demonstrates strong, interpretable peptide representations and achieves state-of-the-art performance in 25 of the 33 biological identification tasks. Notably, PDeepPP attains high accuracy in antimicrobial (0.9726) and phosphorylation site (0.9984) identification, with 99.5% specificity in glycosylation site prediction and substantial reduction in false negatives in antimalarial tasks. By enabling large-scale, accurate peptide analysis, PDeepPP supports biomedical research and the discovery of novel therapeutic targets for disease treatment. All code, datasets, and pretrained models are publicly available via GitHub (https://github.com/fondress/PDeepPP) and Hugging Face (https://huggingface.co/fondress/PDeppPP)

cs.LG↗

arXiv2025

From Propagation to Prediction: Point-level Uncertainty Evaluation of MLS Point Clouds under Limited Ground Truth

Evaluating uncertainty is critical for reliable use of Mobile Laser Scanning (MLS) point clouds in many high-precision applications such as Scan-to-BIM, deformation analysis, and 3D modeling. However, obtaining the ground truth (GT) for evaluation is often costly and infeasible in many real-world applications. To reduce this long-standing reliance on GT in uncertainty evaluation research, this study presents a learning-based framework for MLS point clouds that integrates optimal neighborhood estimation with geometric feature extraction. Experiments on a real-world dataset show that the proposed framework is feasible and the XGBoost model delivers fully comparable accuracy to Random Forest while achieving substantially higher efficiency (about 3 times faster), providing initial evidence that geometric features can be used to predict point-level uncertainty quantified by the C2C distance. In summary, this study shows that MLS point clouds' uncertainty is learnable, offering a novel learning-based viewpoint towards uncertainty evaluation research.

cs.CV↗

arXiv2025

Point-level Uncertainty Evaluation of Mobile Laser Scanning Point Clouds

Reliable quantification of uncertainty in Mobile Laser Scanning (MLS) point clouds is essential for ensuring the accuracy and credibility of downstream applications such as 3D mapping, modeling, and change analysis. Traditional backward uncertainty modeling heavily rely on high-precision reference data, which are often costly or infeasible to obtain at large scales. To address this issue, this study proposes a machine learning-based framework for point-level uncertainty evaluation that learns the relationship between local geometric features and point-level errors. The framework is implemented using two ensemble learning models, Random Forest (RF) and XGBoost, which are trained and validated on a spatially partitioned real-world dataset to avoid data leakage. Experimental results demonstrate that both models can effectively capture the nonlinear relationships between geometric characteristics and uncertainty, achieving mean ROC-AUC values above 0.87. The analysis further reveals that geometric features describing elevation variation, point density, and local structural complexity play a dominant role in predicting uncertainty. The proposed framework offers a data-driven perspective of uncertainty evaluation, providing a scalable and adaptable foundation for future quality control and error analysis of large-scale point clouds.

cs.CV↗

arXiv2025

Biology-Instructions: A Dataset and Benchmark for Multi-Omics Sequence Understanding Capability of Large Language Models

Large language models (LLMs) have shown remarkable capabilities in general domains, but their application to multi-omics biology remains underexplored. To address this gap, we introduce Biology-Instructions, the first large-scale instruction-tuning dataset for multi-omics biological sequences, including DNA, RNA, proteins, and multi-molecules. This dataset bridges LLMs and complex biological sequence-related tasks, enhancing their versatility and reasoning while maintaining conversational fluency. We also highlight significant limitations of current state-of-the-art LLMs on multi-omics tasks without specialized training. To overcome this, we propose ChatMultiOmics, a strong baseline with a novel three-stage training pipeline, demonstrating superior biological understanding through Biology-Instructions. Both resources are publicly available, paving the way for better integration of LLMs in multi-omics analysis. The Biology-Instructions is publicly available at: https://github.com/hhnqqq/Biology-Instructions.

q-bio.BM↗

arXiv2025

Model-free High Dimensional Mediator Selection with False Discovery Rate Control

There is a challenge in selecting high-dimensional mediators when the mediators have complex correlation structures and interactions. In this work, we frame the high-dimensional mediator selection problem into a series of hypothesis tests with composite nulls, and develop a method to control the false discovery rate (FDR) which has mild assumptions on the mediation model. We show the theoretical guarantee that the proposed method and algorithm achieve FDR control. We present extensive simulation results to demonstrate the power and finite sample performance compared with existing methods. Lastly, we demonstrate the method for analyzing the Alzheimer's Disease Neuroimaging Initiative (ADNI) data, in which the proposed method selects the volume of the hippocampus and amygdala, as well as some other important MRI-derived measures as mediators for the relationship between gender and dementia progression.

stat.ME↗

arXiv2025

Experimental and numerical study on current distribution in parallel co-wound no-insulation coils

No-insulation (NI) coils are known for their high thermal stability and self-protection features due to turn-to-turn contacts. Parallel co-winding is a promising method to reduce the charging delay of NI coils while maintaining thermal stability, demonstrating significant potential for applications in fusion and other large-scale or high-field magnets. The non-uniform current distribution among parallel superconducting tapes in parallel co-wound NI coils may lead to thermal and mechanical stability issues. In this work, we conducted current measurement experiments on small parallel co-wound NI REBCO coils to investigate the non-uniform current distribution and its influencing factors. The parallel tapes in the input and output sections of the test coils were separated and a series of Rogowski coils was used to measure the current in each tape during ramping charging process. We combined a field-circuit coupled model based on the T-A formulation with an equivalent circuit model to calculate the current distribution in co-wound coils. Both the measured and calculated results indicated that the current distribution during ramping was highly non-uniform, with some tapes carrying reverse currents. We calculated the current distribution in co-wound coils with different insulation methods and analyzed the influencing factors of the reverse current. The influence of the terminal resistance on current distribution was also discussed. This work could contribute to a deeper understanding of current distribution behavior in co-wound coils and provide insights for their application in large-scale or high-field magnet systems.

physics.app-ph↗

arXiv2025

Genesis: Multimodal Driving Scene Generation with Spatio-Temporal and Cross-Modal Consistency

We present Genesis, a unified framework for joint generation of multi-view driving videos and LiDAR sequences with spatio-temporal and cross-modal consistency. Genesis employs a two-stage architecture that integrates a DiT-based video diffusion model with 3D-VAE encoding, and a BEV-aware LiDAR generator with NeRF-based rendering and adaptive sampling. Both modalities are directly coupled through a shared latent space, enabling coherent evolution across visual and geometric domains. To guide the generation with structured semantics, we introduce DataCrafter, a captioning module built on vision-language models that provides scene-level and instance-level supervision. Extensive experiments on the nuScenes benchmark demonstrate that Genesis achieves state-of-the-art performance across video and LiDAR metrics (FVD 16.95, FID 4.24, Chamfer 0.611), and benefits downstream tasks including segmentation and 3D detection, validating the semantic fidelity and practical utility of the generated data.

cs.CV↗

arXiv2025

REACT: Representation Extraction And Controllable Tuning to Overcome Overfitting in LLM Knowledge Editing

Large language model editing methods frequently suffer from overfitting, wherein factual updates can propagate beyond their intended scope, overemphasizing the edited target even when it's contextually inappropriate. To address this challenge, we introduce REACT (Representation Extraction And Controllable Tuning), a unified two-phase framework designed for precise and controllable knowledge editing. In the initial phase, we utilize tailored stimuli to extract latent factual representations and apply Principal Component Analysis with a simple learnbale linear transformation to compute a directional "belief shift" vector for each instance. In the second phase, we apply controllable perturbations to hidden states using the obtained vector with a magnitude scalar, gated by a pre-trained classifier that permits edits only when contextually necessary. Relevant experiments on EVOKE benchmarks demonstrate that REACT significantly reduces overfitting across nearly all evaluation metrics, and experiments on COUNTERFACT and MQuAKE shows that our method preserves balanced basic editing performance (reliability, locality, and generality) under diverse editing scenarios.

cs.AI↗

arXiv2025

TUM2TWIN: Introducing the Large-Scale Multimodal Urban Digital Twin Benchmark Dataset

Urban Digital Twins (UDTs) have become essential for managing cities and integrating complex, heterogeneous data from diverse sources. Creating UDTs involves challenges at multiple process stages, including acquiring accurate 3D source data, reconstructing high-fidelity 3D models, maintaining models' updates, and ensuring seamless interoperability to downstream tasks. Current datasets are usually limited to one part of the processing chain, hampering comprehensive UDTs validation. To address these challenges, we introduce the first comprehensive multimodal Urban Digital Twin benchmark dataset: TUM2TWIN. This dataset includes georeferenced, semantically aligned 3D models and networks along with various terrestrial, mobile, aerial, and satellite observations boasting 32 data subsets over roughly 100,000 $m^2$ and currently 767 GB of data. By ensuring georeferenced indoor-outdoor acquisition, high accuracy, and multimodal data integration, the benchmark supports robust analysis of sensors and the development of advanced reconstruction methods. Additionally, we explore downstream tasks demonstrating the potential of TUM2TWIN, including novel view synthesis of NeRF and Gaussian Splatting, solar potential analysis, point cloud semantic segmentation, and LoD3 building reconstruction. We are convinced this contribution lays a foundation for overcoming current limitations in UDT creation, fostering new research directions and practical solutions for smarter, data-driven urban environments. The project is available under: https://tum2t.win

cs.CV↗

arXiv2025

PixelHacker: Image Inpainting with Structural and Semantic Consistency

Image inpainting is a fundamental research area between image editing and image generation. Recent state-of-the-art (SOTA) methods have explored novel attention mechanisms, lightweight architectures, and context-aware modeling, demonstrating impressive performance. However, they often struggle with complex structure (e.g., texture, shape, spatial relations) and semantics (e.g., color consistency, object restoration, and logical correctness), leading to artifacts and inappropriate generation. To address this challenge, we design a simple yet effective inpainting paradigm called latent categories guidance, and further propose a diffusion-based model named PixelHacker. Specifically, we first construct a large dataset containing 14 million image-mask pairs by annotating foreground and background (potential 116 and 21 categories, respectively). Then, we encode potential foreground and background representations separately through two fixed-size embeddings, and intermittently inject these features into the denoising process via linear attention. Finally, by pre-training on our dataset and fine-tuning on open-source benchmarks, we obtain PixelHacker. Extensive experiments show that PixelHacker comprehensively outperforms the SOTA on a wide range of datasets (Places2, CelebA-HQ, and FFHQ) and exhibits remarkable consistency in both structure and semantics. Project page at https://hustvl.github.io/PixelHacker.

cs.CV↗

arXiv2025

MedReason: Eliciting Factual Medical Reasoning Steps in LLMs via Knowledge Graphs

Medical tasks such as diagnosis and treatment planning require precise and complex reasoning, particularly in life-critical domains. Unlike mathematical reasoning, medical reasoning demands meticulous, verifiable thought processes to ensure reliability and accuracy. However, there is a notable lack of datasets that provide transparent, step-by-step reasoning to validate and enhance the medical reasoning ability of AI models. To bridge this gap, we introduce MedReason, a large-scale high-quality medical reasoning dataset designed to enable faithful and explainable medical problem-solving in large language models (LLMs). We utilize a structured medical knowledge graph (KG) to convert clinical QA pairs into logical chains of reasoning, or ``thinking paths'', which trace connections from question elements to answers via relevant KG entities. Each path is validated for consistency with clinical logic and evidence-based medicine. Our pipeline generates detailed reasoning for various medical questions from 7 medical datasets, resulting in a dataset of 32,682 question-answer pairs, each with detailed, step-by-step explanations. Experiments demonstrate that fine-tuning with our dataset consistently boosts medical problem-solving capabilities, achieving significant gains of up to 7.7% for DeepSeek-Ditill-8B. Our top-performing model, MedReason-8B, outperforms the Huatuo-o1-8B, a state-of-the-art medical reasoning model, by up to 4.2% on the clinical benchmark MedBullets. We also engage medical professionals from diverse specialties to assess our dataset's quality, ensuring MedReason offers accurate and coherent medical reasoning. Our data, models, and code is available at https://github.com/UCSC-VLAA/MedReason.

cs.CL↗

arXiv2025

Achieving >97% on GSM8K: Deeply Understanding the Problems Makes LLMs Better Solvers for Math Word Problems

Chain-of-Thought (CoT) prompting has enhanced the performance of Large Language Models (LLMs) across various reasoning tasks. However, CoT still falls short in dealing with complex math word problems, as it usually suffers from three pitfalls: semantic misunderstanding errors, calculation errors, and step-missing errors. Prior studies involve addressing the calculation errors and step-missing errors, but neglect the semantic misunderstanding errors, which is the major factor limiting the reasoning performance of LLMs. To this end, we propose a simple-yet-effective method, namely Deeply Understanding the Problems (DUP), to improve the LLMs' math problem-solving ability by addressing semantic misunderstanding errors. The core of our method is to encourage the LLMs to deeply understand the problems and extract the key problem-solving information used for better reasoning. Extensive experiments on 10 diverse reasoning benchmarks show that our DUP method consistently outperforms the other counterparts by a large margin. More encouragingly, DUP achieves a new SOTA result on the GSM8K benchmark, with an accuracy of 97.1% under the zero-shot setting.

cs.CL↗

arXiv2025

A foundation model for human-AI collaboration in medical literature mining

Systematic literature review is essential for evidence-based medicine, requiring comprehensive analysis of clinical trial publications. However, the application of artificial intelligence (AI) models for medical literature mining has been limited by insufficient training and evaluation across broad therapeutic areas and diverse tasks. Here, we present LEADS, an AI foundation model for study search, screening, and data extraction from medical literature. The model is trained on 633,759 instruction data points in LEADSInstruct, curated from 21,335 systematic reviews, 453,625 clinical trial publications, and 27,015 clinical trial registries. We showed that LEADS demonstrates consistent improvements over four cutting-edge generic large language models (LLMs) on six tasks. Furthermore, LEADS enhances expert workflows by providing supportive references following expert requests, streamlining processes while maintaining high-quality results. A study with 16 clinicians and medical researchers from 14 different institutions revealed that experts collaborating with LEADS achieved a recall of 0.81 compared to 0.77 experts working alone in study selection, with a time savings of 22.6%. In data extraction tasks, experts using LEADS achieved an accuracy of 0.85 versus 0.80 without using LEADS, alongside a 26.9% time savings. These findings highlight the potential of specialized medical literature foundation models to outperform generic models, delivering significant quality and efficiency benefits when integrated into expert workflows for medical literature mining.

cs.CL↗

arXiv2024

GaraMoSt: Parallel Multi-Granularity Motion and Structural Modeling for Efficient Multi-Frame Interpolation in DSA Images

The rapid and accurate direct multi-frame interpolation method for Digital Subtraction Angiography (DSA) images is crucial for reducing radiation and providing real-time assistance to physicians for precise diagnostics and treatment. DSA images contain complex vascular structures and various motions. Applying natural scene Video Frame Interpolation (VFI) methods results in motion artifacts, structural dissipation, and blurriness. Recently, MoSt-DSA has specifically addressed these issues for the first time and achieved SOTA results. However, MoSt-DSA's focus on real-time performance leads to insufficient suppression of high-frequency noise and incomplete filtering of low-frequency noise in the generated images. To address these issues within the same computational time scale, we propose GaraMoSt. Specifically, we optimize the network pipeline with a parallel design and propose a module named MG-MSFE. MG-MSFE extracts frame-relative motion and structural features at various granularities in a fully convolutional parallel manner and supports independent, flexible adjustment of context-aware granularity at different scales, thus enhancing computational efficiency and accuracy. Extensive experiments demonstrate that GaraMoSt achieves the SOTA performance in accuracy, robustness, visual effects, and noise suppression, comprehensively surpassing MoSt-DSA and other natural scene VFI methods. The code and models are available at https://github.com/ZyoungXu/GaraMoSt.

cs.CV↗

arXiv2024

A MapReduce Approach to Effectively Utilize Long Context Information in Retrieval Augmented Language Models

While holding great promise for improving and facilitating healthcare, large language models (LLMs) struggle to produce up-to-date responses on evolving topics due to outdated knowledge or hallucination. Retrieval-augmented generation (RAG) is a pivotal innovation that improves the accuracy and relevance of LLM responses by integrating LLMs with a search engine and external sources of knowledge. However, the quality of RAG responses can be largely impacted by the rank and density of key information in the retrieval results, such as the "lost-in-the-middle" problem. In this work, we aim to improve the robustness and reliability of the RAG workflow in the medical domain. Specifically, we propose a map-reduce strategy, BriefContext, to combat the "lost-in-the-middle" issue without modifying the model weights. We demonstrated the advantage of the workflow with various LLM backbones and on multiple QA datasets. This method promises to improve the safety and reliability of LLMs deployed in healthcare domains.

cs.CL↗

arXiv2024

GSCo: Towards Generalizable AI in Medicine via Generalist-Specialist Collaboration

Generalist foundation models (GFMs) are renowned for their exceptional capability and flexibility in effectively generalizing across diverse tasks and modalities. In the field of medicine, while GFMs exhibit superior generalizability based on their extensive intrinsic knowledge as well as proficiency in instruction following and in-context learning, specialist models excel in precision due to their domain knowledge. In this work, for the first time, we explore the synergy between the GFM and specialist models, to enable precise medical image analysis on a broader scope. Specifically, we propose a cooperative framework, Generalist-Specialist Collaboration (GSCo), which consists of two stages, namely the construction of GFM and specialists, and collaborative inference on downstream tasks. In the construction stage, we develop MedDr, the largest open-source GFM tailored for medicine, showcasing exceptional instruction-following and in-context learning capabilities. Meanwhile, a series of lightweight specialists are crafted for downstream tasks with low computational cost. In the collaborative inference stage, we introduce two cooperative mechanisms, Mixture-of-Expert Diagnosis and Retrieval-Augmented Diagnosis, to harvest the generalist's in-context learning abilities alongside the specialists' domain expertise. For a comprehensive evaluation, we curate a large-scale benchmark featuring 28 datasets and about 250,000 images. Extensive results demonstrate that MedDr consistently outperforms state-of-the-art GFMs on downstream datasets. Furthermore, GSCo exceeds both GFMs and specialists across all out-of-domain disease diagnosis datasets. These findings indicate a significant paradigm shift in the application of GFMs, transitioning from separate models for specific tasks to a collaborative approach between GFMs and specialists, thereby advancing the frontiers of generalizable AI in medicine.

cs.CV↗