arXiv subjects

Dan Huang

Publications and source records attributed to Dan Huang.

At least 19 recordsLinked to original sources

arXiv2026

Towards Reliable Stain Transfer: An Iterative Data-Model Co-Optimization Framework Based on Multimodal Expert-Guided Assessment

Histopathological examination primarily relies on hematoxylin and eosin (H&E) and immunohistochemistry (IHC) staining. Although IHC provides critical molecular information, it is costly and requires specialized expertise. Stain transfer provides an efficient alternative by computationally generating IHC from H&E images, but remains challenged by unified and interpretable modeling for heterogeneous biomarkers under pixel-unaligned supervision. We propose DMCoStain, a novel Data-Model Co-optimization framework for Stain transfer. It iteratively co-refines training data and model capability, improving staining accuracy and interpretability in both pathological and structural consistency. To refine training data in a clinically meaningful manner, it incorporates the Multimodal Expert-Guided Finer Selection (MEGFS) strategy, built upon a pioneering IHC-positive-expression (IPE) vision-language model (VLM) that emulates pathologist reasoning. To support MEGFS, we construct ImmunoInstruction, the first large-scale IPE instruction-following dataset with 150K VQA samples. Extensive experiments on multiple tissues and biomarkers demonstrate that DMCoStain achieves state-of-the-art (SOTA) accuracy. This paradigm offers strong practical value, and MEGFS also functions as a specialized evaluation tool for future model development. Dataset, code, and more details are in https://github.com/SikangSHU/DMCoStain.

cs.CV↗

arXiv2026

ICAE-Bench: Evaluating Coding Agents as Interactive Project Builders

The recent emergence of vibe-coding workflows is changing what coding agents are expected to do. Instead of merely completing code under fully specified instructions, agents are increasingly expected to transform incomplete product intent into working software by combining various abilities including planning, requirement clarification, tool use, debugging, and repository-level construction. Yet existing benchmarks have not fully caught up with this shift, evaluating agents on static, fully specified tasks. In this paper, we introduce ICAE-Bench, a benchmark for evaluating coding agents under interactive project-building settings. The basic idea is to start from a fuzzy product requirement, simulating the dynamic paradigm with an automated User Agent. To make this setting both realistic and evaluable, ICAE-Bench introduces three key designs. First, to avoid the ambiguity of unconstrained fuzzy requirements, each task derives ambiguity from a precise real open-source repository with executable behavior. Second, to ensure high-quality and reproducible user simulation, ICAE-Bench grounds interaction through User Agent Data, allowing the User Agent to reveal hidden constraints without inventing new requirements or leaking implementation artifacts. Third, to evaluate open-ended repositories fairly, ICAE-Bench uses standardized black-box tests together with multi-dimensional diagnostics, including functional correctness, semantic and API similarity, structural fidelity, design quality, and interaction quality.

cs.AI↗

arXiv2026

Extreme-Scale Atomistic Simulation of Real-Temperature Magnetic Skyrmion Dynamics by Coupled Spin-Lattice Modeling

Real-temperature topological magnetic dynamics in functional materials is governed by coupled lattice and spin evolution, yet remains inaccessible to predictive simulation at device-relevant scales. As a flagship example, thermally driven helix-to-skyrmion transformation in FeGe requires atomistic resolution, explicit lattice motion, and micrometer-scale domains to resolve device-scale topological texture formation. We combine a spin-constrained density-functional-theory-trained neuro-evolution potential with a structure-preserving spin-lattice integrator within one machine-learned framework. Architecture-specific optimizations, kernel fusion, SVE2 vectorization, and NUMA-aware data layout deliver a seven orders-of-magnitude speedup over prior spin-aware methods. Deployed on LineShine exascale supercomputer, the full application scales to 12.45 million CPU cores with 89.7% weak-scaling efficiency, enabling simulations of 1.34 trillion atoms and an equal number of spins while reaching 48.5 PFLOPS in double precision. The simulations directly resolve real-temperature skyrmion nucleation and reorganization at previously inaccessible scales, establishing a new regime for predictive simulation of coupled spin-lattice topological magnetic dynamics.

cs.DC↗

arXiv2025

Equivariant Diffusion for Crystal Structure Prediction

In addressing the challenge of Crystal Structure Prediction (CSP), symmetry-aware deep learning models, particularly diffusion models, have been extensively studied, which treat CSP as a conditional generation task. However, ensuring permutation, rotation, and periodic translation equivariance during diffusion process remains incompletely addressed. In this work, we propose EquiCSP, a novel equivariant diffusion-based generative model. We not only address the overlooked issue of lattice permutation equivariance in existing models, but also develop a unique noising algorithm that rigorously maintains periodic translation equivariance throughout both training and inference processes. Our experiments indicate that EquiCSP significantly surpasses existing models in terms of generating accurate structures and demonstrates faster convergence during the training process.

cond-mat.mtrl-sci↗

arXiv2025

PolyKAN: Efficient Fused GPU Operators for Polynomial Kolmogorov-Arnold Network Variants

Kolmogorov-Arnold Networks (KANs) promise higher expressive capability and stronger interpretability than Multi-Layer Perceptron, particularly in the domain of AI for Science. However, practical adoption has been hindered by low GPU utilization of existing parallel implementations. To address this challenge, we present a GPU-accelerated operator library, named PolyKAN which is the first general open-source implementation of KAN and its variants. PolyKAN fuses the forward and backward passes of polynomial KAN layers into a concise set of optimized CUDA kernels. Four orthogonal techniques underpin the design: (i) \emph{lookup-table} with linear interpolation that replaces runtime expensive math-library functions; (ii) \emph{2D tiling} to expose thread-level parallelism with preserving memory locality; (iii) a \emph{two-stage reduction} scheme converting scattered atomic updates into a single controllable merge step; and (iv) \emph{coefficient-layout reordering} yielding unit-stride reads under the tiled schedule. Using a KAN variant, Chebyshev KAN, as a case-study, PolyKAN delivers $1.2$--$10\times$ faster inference and $1.4$--$12\times$ faster training than a Triton + cuBLAS baseline, with identical accuracy on speech, audio-enhancement, and tabular-regression workloads on both highend GPU and consumer-grade GPU.

cs.DC↗

arXiv2025

HPC-AI Coupling Methodology for Scientific Applications

Artificial intelligence (AI) technologies have fundamentally transformed numerical-based high-performance computing (HPC) applications with data-driven approaches and endeavored to address existing challenges, e.g. high computational intensity, in various scientific domains. In this study, we explore the scenarios of coupling HPC and AI (HPC-AI) in the context of emerging scientific applications, presenting a novel methodology that incorporates three patterns of coupling: surrogate, directive, and coordinate. Each pattern exemplifies a distinct coupling strategy, AI-driven prerequisite, and typical HPC-AI ensembles. Through case studies in materials science, we demonstrate the application and effectiveness of these patterns. The study highlights technical challenges, performance improvements, and implementation details, providing insight into promising perspectives of HPC-AI coupling. The proposed coupling patterns are applicable not only to materials science but also to other scientific domains, offering valuable guidance for future HPC-AI ensembles in scientific discovery.

cs.CE↗

arXiv2025

Selective profiling of non-canonical nucleic acid structures via size-discriminative supramolecular probes

Nucleic acids can form diverse non-canonical structures, such as G-quadruplexes (G4s) and i-motifs (iMs), which are critical in biological processes and disease pathways. This study presents an innovative probe design strategy based on groove size differences, leading to the development of BT-Cy-1, a supramolecular cyanine probe optimized by fine-tuning dimer "thickness". BT-Cy-1 demonstrated high sensitivity in detecting structural transitions and variations in G4s and iMs, even in complex environments with excess dsDNA. Applied to clinical blood samples, it revealed significant differences in RNA G4 and iM levels between liver cancer patients and healthy individuals, marking the first report of altered iM levels in clinical samples. This work highlights a novel approach for precise nucleic acid structural profiling, offering insights into their biological significance and potential in disease diagnostics.

q-bio.BM↗

arXiv2025

Toward Generalizable Evaluation in the LLM Era: A Survey Beyond Benchmarks

Large Language Models (LLMs) are advancing at an amazing speed and have become indispensable across academia, industry, and daily applications. To keep pace with the status quo, this survey probes the core challenges that the rise of LLMs poses for evaluation. We identify and analyze two pivotal transitions: (i) from task-specific to capability-based evaluation, which reorganizes benchmarks around core competencies such as knowledge, reasoning, instruction following, multi-modal understanding, and safety; and (ii) from manual to automated evaluation, encompassing dynamic dataset curation and "LLM-as-a-judge" scoring. Yet, even with these transitions, a crucial obstacle persists: the evaluation generalization issue. Bounded test sets cannot scale alongside models whose abilities grow seemingly without limit. We will dissect this issue, along with the core challenges of the above two transitions, from the perspectives of methods, datasets, evaluators, and metrics. Due to the fast evolving of this field, we will maintain a living GitHub repository (links are in each section) to crowd-source updates and corrections, and warmly invite contributors and collaborators.

cs.CL↗

arXiv2025

Bizard: A Community-Driven Platform for Accelerating and Enhancing Biomedical Data Visualization

Biomedical research increasingly relies on heterogeneous, high-dimensional datasets, yet effective visualization remains hindered by fragmented code resources, steep programming barriers, and limited domain-specific guidance. Bizard is an open-source visualization code repository engineered to streamline data analysis in biomedical research. It aggregates a diverse array of executable visualization scripts, empowering researchers to select and tailor optimal graphical methods for their specific investigative demands. The platform features an intuitive interface equipped with sophisticated browsing and filtering capabilities, exhaustive tutorials, and interactive discussion forums that foster knowledge dissemination. Through its community-driven paradigm, Bizard promotes continual refinement and functional expansion, establishing itself as an essential resource for elevating biomedical data visualization and analytical standards. By harnessing Bizard's infrastructure, researchers can augment their visualization proficiency, propel methodological progress, and enhance interpretive rigor, ultimately accelerating precision medicine and personalized therapeutics. Bizard is freely accessible at https://openbiox.github.io/Bizard/.

q-bio.GN↗

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

LessLeak-Bench: A First Investigation of Data Leakage in LLMs Across 83 Software Engineering Benchmarks

Large Language Models (LLMs) are widely utilized in software engineering (SE) tasks, such as code generation and automated program repair. However, their reliance on extensive and often undisclosed pre-training datasets raises significant concerns about data leakage, where the evaluation benchmark data is unintentionally ``seen'' by LLMs during the model's construction phase. The data leakage issue could largely undermine the validity of LLM-based research and evaluations. Despite the increasing use of LLMs in the SE community, there is no comprehensive study that assesses the extent of data leakage in SE benchmarks for LLMs yet. To address this gap, this paper presents the first large-scale analysis of data leakage in 83 SE benchmarks concerning LLMs. Our results show that in general, data leakage in SE benchmarks is minimal, with average leakage ratios of only 4.8\%, 2.8\%, and 0.7\% for Python, Java, and C/C++ benchmarks, respectively. However, some benchmarks exhibit relatively higher leakage ratios, which raises concerns about their bias in evaluation. For instance, QuixBugs and BigCloneBench have leakage ratios of 100.0\% and 55.7\%, respectively. Furthermore, we observe that data leakage has a substantial impact on LLM evaluation. We also identify key causes of high data leakage, such as the direct inclusion of benchmark data in pre-training datasets and the use of coding platforms like LeetCode for benchmark construction. To address the data leakage, we introduce \textbf{LessLeak-Bench}, a new benchmark that removes leaked samples from the 83 SE benchmarks, enabling more reliable LLM evaluations in future research. Our study enhances the understanding of data leakage in SE benchmarks and provides valuable insights for future research involving LLMs in SE.

cs.SE↗

arXiv2024

Multi-modal Data Binding for Survival Analysis Modeling with Incomplete Data and Annotations

Survival analysis stands as a pivotal process in cancer treatment research, crucial for predicting patient survival rates accurately. Recent advancements in data collection techniques have paved the way for enhancing survival predictions by integrating information from multiple modalities. However, real-world scenarios often present challenges with incomplete data, particularly when dealing with censored survival labels. Prior works have addressed missing modalities but have overlooked incomplete labels, which can introduce bias and limit model efficacy. To bridge this gap, we introduce a novel framework that simultaneously handles incomplete data across modalities and censored survival labels. Our approach employs advanced foundation models to encode individual modalities and align them into a universal representation space for seamless fusion. By generating pseudo labels and incorporating uncertainty, we significantly enhance predictive accuracy. The proposed method demonstrates outstanding prediction accuracy in two survival analysis tasks on both employed datasets. This innovative approach overcomes limitations associated with disparate modalities and improves the feasibility of comprehensive survival analysis using multiple large foundation models.

cs.LG↗

arXiv2024

Pathology-knowledge Enhanced Multi-instance Prompt Learning for Few-shot Whole Slide Image Classification

Current multi-instance learning algorithms for pathology image analysis often require a substantial number of Whole Slide Images for effective training but exhibit suboptimal performance in scenarios with limited learning data. In clinical settings, restricted access to pathology slides is inevitable due to patient privacy concerns and the prevalence of rare or emerging diseases. The emergence of the Few-shot Weakly Supervised WSI Classification accommodates the significant challenge of the limited slide data and sparse slide-level labels for diagnosis. Prompt learning based on the pre-trained models (\eg, CLIP) appears to be a promising scheme for this setting; however, current research in this area is limited, and existing algorithms often focus solely on patch-level prompts or confine themselves to language prompts. This paper proposes a multi-instance prompt learning framework enhanced with pathology knowledge, \ie, integrating visual and textual prior knowledge into prompts at both patch and slide levels. The training process employs a combination of static and learnable prompts, effectively guiding the activation of pre-trained models and further facilitating the diagnosis of key pathology patterns. Lightweight Messenger (self-attention) and Summary (attention-pooling) layers are introduced to model relationships between patches and slides within the same patient data. Additionally, alignment-wise contrastive losses ensure the feature-level alignment between visual and textual learnable prompts for both patches and slides. Our method demonstrates superior performance in three challenging clinical tasks, significantly outperforming comparative few-shot methods.

cs.CV↗

arXiv2024

Group Benefits Instances Selection for Data Purification

Manually annotating datasets for training deep models is very labor-intensive and time-consuming. To overcome such inferiority, directly leveraging web images to conduct training data becomes a natural choice. Nevertheless, the presence of label noise in web data usually degrades the model performance. Existing methods for combating label noise are typically designed and tested on synthetic noisy datasets. However, they tend to fail to achieve satisfying results on real-world noisy datasets. To this end, we propose a method named GRIP to alleviate the noisy label problem for both synthetic and real-world datasets. Specifically, GRIP utilizes a group regularization strategy that estimates class soft labels to improve noise robustness. Soft label supervision reduces overfitting on noisy labels and learns inter-class similarities to benefit classification. Furthermore, an instance purification operation globally identifies noisy labels by measuring the difference between each training sample and its class soft label. Through operations at both group and instance levels, our approach integrates the advantages of noise-robust and noise-cleaning methods and remarkably alleviates the performance degradation caused by noisy labels. Comprehensive experimental results on synthetic and real-world datasets demonstrate the superiority of GRIP over the existing state-of-the-art methods.

cs.LG↗

arXiv2023

AdaNAS: Adaptively Post-processing with Self-supervised Neural Architecture Search for Ensemble Rainfall Forecasts

Previous post-processing studies on rainfall forecasts using numerical weather prediction (NWP) mainly focus on statistics-based aspects, while learning-based aspects are rarely investigated. Although some manually-designed models are proposed to raise accuracy, they are customized networks, which need to be repeatedly tried and verified, at a huge cost in time and labor. Therefore, a self-supervised neural architecture search (NAS) method without significant manual efforts called AdaNAS is proposed in this study to perform rainfall forecast post-processing and predict rainfall with high accuracy. In addition, we design a rainfall-aware search space to significantly improve forecasts for high-rainfall areas. Furthermore, we propose a rainfall-level regularization function to eliminate the effect of noise data during the training. Validation experiments have been performed under the cases of \emph{None}, \emph{Light}, \emph{Moderate}, \emph{Heavy} and \emph{Violent} on a large-scale precipitation benchmark named TIGGE. Finally, the average mean-absolute error (MAE) and average root-mean-square error (RMSE) of the proposed AdaNAS model are 0.98 and 2.04 mm/day, respectively. Additionally, the proposed AdaNAS model is compared with other neural architecture search methods and previous studies. Compared results reveal the satisfactory performance and superiority of the proposed AdaNAS model in terms of precipitation amount prediction and intensity classification. Concretely, the proposed AdaNAS model outperformed previous best-performing manual methods with MAE and RMSE improving by 80.5\% and 80.3\%, respectively.

cs.LG↗

arXiv2023

Co-attention Propagation Network for Zero-Shot Video Object Segmentation

Zero-shot video object segmentation (ZS-VOS) aims to segment foreground objects in a video sequence without prior knowledge of these objects. However, existing ZS-VOS methods often struggle to distinguish between foreground and background or to keep track of the foreground in complex scenarios. The common practice of introducing motion information, such as optical flow, can lead to overreliance on optical flow estimation. To address these challenges, we propose an encoder-decoder-based hierarchical co-attention propagation network (HCPN) capable of tracking and segmenting objects. Specifically, our model is built upon multiple collaborative evolutions of the parallel co-attention module (PCM) and the cross co-attention module (CCM). PCM captures common foreground regions among adjacent appearance and motion features, while CCM further exploits and fuses cross-modal motion features returned by PCM. Our method is progressively trained to achieve hierarchical spatio-temporal feature propagation across the entire video. Experimental results demonstrate that our HCPN outperforms all previous methods on public benchmarks, showcasing its effectiveness for ZS-VOS.

cs.CV↗

arXiv2023

Dynamics of a delayed population patch model with the dispersion matrix incorporating population loss

In this paper, we consider a general single population model with delay and patch structure, which could model the population loss during the dispersal. It is shown that the model admits a unique positive equilibrium when the dispersal rate is smaller than a critical value. The stability of the positive equilibrium and associated Hopf bifurcation are investigated when the dispersal rate is small or near the critical value. Moreover, we show the effect of network topology on Hopf bifurcation values for a delayed logistic population model.

math.DS↗

arXiv2022

Power of Continuous Triangular Norms with Application to Intuitionistic Fuzzy Information Aggregation

The power operation of continuous Archimedean triangular norms (t-norms) is fundamental for generalizing the multiplication and power operations of intuitionistic fuzzy sets (IFSs) within the framework of continuous Archimedean t-norms. However, due to the lack of systematic research on the power operation of general continuous t-norms in theory, it greatly limits the further generalization of the multiplication and power operations for IFSs via general continuous t-norms. This paper aims to investigate the power operation of continuous t-norms and develop some IF information aggregation methods. In theory, it is proved that a continuous t-norm is power stable if and only if every point is a power stable point, and if and only if it is the minimum t-norm, or it is strict, or it is an ordinal sum of strict t-norms. Moreover, the representation theorem of continuous t-norms is used to obtain the computational formula for the power of continuous t-norms. Based on the power operation of t-norms, four fundamental operations induced by a continuous t-norm for the IFSs are introduced. Furthermore, various IF aggregation operators based on these four fundamental operations, namely the IF weighted average (IFWA), IF weighted geometric (IFWG), and IF mean weighted average and geometric (IFMWAG) operators, are defined, and their properties are analyzed. In application, a new decision-making algorithm is designed based on the IFMWAG operator, which can remove the hindrance of indiscernibility on the boundaries of some classical aggregation operators. The practical applicability, comparative analysis, and advantages of the study with other decision-making methods are furnished to ascertain the efficacy of the designed method.

math.GM↗