arXiv subjects

Yuqi Zhang

Publications and source records attributed to Yuqi Zhang.

At least 55 records · Page 3Linked to original sources

arXiv2025

QDockBank: A Dataset for Ligand Docking on Protein Fragments Predicted on Utility-Level Quantum Computers

Protein structure prediction is a core challenge in computational biology, particularly for fragments within ligand-binding regions, where accurate modeling is still difficult. Quantum computing offers a novel first-principles modeling paradigm, but its application is currently limited by hardware constraints, high computational cost, and the lack of a standardized benchmarking dataset. In this work, we present QDockBank-the first large-scale protein fragment structure dataset generated entirely using utility-level quantum computers, specifically designed for protein-ligand docking tasks. QDockBank comprises 55 protein fragments extracted from ligand-binding pockets. The dataset was generated through tens of hours of execution on superconducting quantum processors, making it the first quantum-based protein structure dataset with a total computational cost exceeding one million USD. Experimental evaluations demonstrate that structures predicted by QDockBank outperform those predicted by AlphaFold2 and AlphaFold3 in terms of both RMSD and docking affinity scores. QDockBank serves as a new benchmark for evaluating quantum-based protein structure prediction.

cs.ET↗

arXiv2025

Infinity: Scaling Bitwise AutoRegressive Modeling for High-Resolution Image Synthesis

We present Infinity, a Bitwise Visual AutoRegressive Modeling capable of generating high-resolution, photorealistic images following language instruction. Infinity redefines visual autoregressive model under a bitwise token prediction framework with an infinite-vocabulary tokenizer & classifier and bitwise self-correction mechanism, remarkably improving the generation capacity and details. By theoretically scaling the tokenizer vocabulary size to infinity and concurrently scaling the transformer size, our method significantly unleashes powerful scaling capabilities compared to vanilla VAR. Infinity sets a new record for autoregressive text-to-image models, outperforming top-tier diffusion models like SD3-Medium and SDXL. Notably, Infinity surpasses SD3-Medium by improving the GenEval benchmark score from 0.62 to 0.73 and the ImageReward benchmark score from 0.87 to 0.96, achieving a win rate of 66%. Without extra optimization, Infinity generates a high-quality 1024x1024 image in 0.8 seconds, making it 2.6x faster than SD3-Medium and establishing it as the fastest text-to-image model. Models and codes will be released to promote further exploration of Infinity for visual generation and unified tokenizer modeling.

cs.CV↗

arXiv2025

The Energy Loss Phenomenon in RLHF: A New Perspective on Mitigating Reward Hacking

This work identifies the Energy Loss Phenomenon in Reinforcement Learning from Human Feedback (RLHF) and its connection to reward hacking. Specifically, energy loss in the final layer of a Large Language Model (LLM) gradually increases during the RL process, with an excessive increase in energy loss characterizing reward hacking. Beyond empirical analysis, we further provide a theoretical foundation by proving that, under mild conditions, the increased energy loss reduces the upper bound of contextual relevance in LLMs, which is a critical aspect of reward hacking as the reduced contextual relevance typically indicates overfitting to reward model-favored patterns in RL. To address this issue, we propose an Energy loss-aware PPO algorithm (EPPO) which penalizes the increase in energy loss in the LLM's final layer during reward calculation to prevent excessive energy loss, thereby mitigating reward hacking. We theoretically show that EPPO can be conceptually interpreted as an entropy-regularized RL algorithm, which provides deeper insights into its effectiveness. Extensive experiments across various LLMs and tasks demonstrate the commonality of the energy loss phenomenon, as well as the effectiveness of EPPO in mitigating reward hacking and improving RLHF performance.

cs.LG↗

arXiv2025

Data-Efficient Machine Learning Potentials via Difference Vectors Based on Local Atomic Environments

Constructing efficient and diverse datasets is essential for the development of accurate machine learning potentials (MLPs) in atomistic simulations. However, existing approaches often suffer from data redundancy and high computational costs. Herein, we propose a new method--Difference Vectors based on Local Atomic Environments (DV-LAE)--that encodes structural differences via histogram-based descriptors and enables visual analysis through t-SNE dimensionality reduction. This approach facilitates redundancy detection and dataset optimization while preserving structural diversity. We demonstrate that DV-LAE significantly reduces dataset size and training time across various materials systems, including high-pressure hydrogen, iron-hydrogen binaries, magnesium hydrides, and carbon allotropes, with minimal compromise in prediction accuracy. For instance, in the $α$-Fe/H system, maintaining a highly similar MLP accuracy, the dataset size was reduced by 56%, and the training time per iteration dropped by over 50%. Moreover, we show how visualizing the DV-LAE representation aids in identifying out-of-distribution data by examining the spatial distribution of high-error prediction points, providing a robust reliability metric for new structures during simulations. Our results highlight the utility of local environment visualization not only as an interpretability tool but also as a practical means for accelerating MLP development and ensuring data efficiency in large-scale atomistic modeling.

cs.LG↗

arXiv2025

AMIA: Automatic Masking and Joint Intention Analysis Makes LVLMs Robust Jailbreak Defenders

We introduce AMIA, a lightweight, inference-only defense for Large Vision-Language Models (LVLMs) that (1) Automatically Masks a small set of text-irrelevant image patches to disrupt adversarial perturbations, and (2) conducts joint Intention Analysis to uncover and mitigate hidden harmful intents before response generation. Without any retraining, AMIA improves defense success rates across diverse LVLMs and jailbreak benchmarks from an average of 52.4% to 81.7%, preserves general utility with only a 2% average accuracy drop, and incurs only modest inference overhead. Ablation confirms both masking and intention analysis are essential for a robust safety-utility trade-off.

cs.CV↗

arXiv2025

Transformer representation learning is necessary for dynamic multi-modal physiological data on small-cohort patients

Postoperative delirium (POD), a severe neuropsychiatric complication affecting nearly 50% of high-risk surgical patients, is defined as an acute disorder of attention and cognition, It remains significantly underdiagnosed in the intensive care units (ICUs) due to subjective monitoring methods. Early and accurate diagnosis of POD is critical and achievable. Here, we propose a POD prediction framework comprising a Transformer representation model followed by traditional machine learning algorithms. Our approaches utilizes multi-modal physiological data, including amplitude-integrated electroencephalography (aEEG), vital signs, electrocardiographic monitor data as well as hemodynamic parameters. We curated the first multi-modal POD dataset encompassing two patient types and evaluated the various Transformer architectures for representation learning. Empirical results indicate a consistent improvements of sensitivity and Youden index in patient TYPE I using Transformer representations, particularly our fusion adaptation of Pathformer. By enabling effective delirium diagnosis from postoperative day 1 to 3, our extensive experimental findings emphasize the potential of multi-modal physiological data and highlight the necessity of representation learning via multi-modal Transformer architecture in clinical diagnosis.

cs.LG↗

arXiv2025

On-demand longitudinal transformations of light beams via an amplitude-phase-decoupled Pancharatnam-Berry phase element

Overcoming the inherent phase-only modulation limitation of conventional Pancharatnam-Berry (PB) elements, we propose a checkerboard-encoded PB element that enables simultaneous amplitude and phase modulation through PB phase engineering. This single-element platform directly generates polarization-rotating beams with continuously varying polarization angles along the propagation axis, eliminating traditional dynamic phase requirements. By strategically combining the proposed element with a liquid crystal q-plate and waveplates, we demonstrate on-demand longitudinal transformations of polarization states and high-order Poincaré sphere beams. Significantly, we achieve, for the first time to our knowledge, the propagation-transformed optical skyrmions, whose topological textures evolve with propagation distance. This amplitude-phase decoupling mechanism and the integration solution for various longitudinal transformations open new avenues in structured light manipulation, particularly benefiting quantum optics and topological photonics applications requiring longitudinal mode control.

physics.optics↗

arXiv2025

Goku: Flow Based Video Generative Foundation Models

This paper introduces Goku, a state-of-the-art family of joint image-and-video generation models leveraging rectified flow Transformers to achieve industry-leading performance. We detail the foundational elements enabling high-quality visual generation, including the data curation pipeline, model architecture design, flow formulation, and advanced infrastructure for efficient and robust large-scale training. The Goku models demonstrate superior performance in both qualitative and quantitative evaluations, setting new benchmarks across major tasks. Specifically, Goku achieves 0.76 on GenEval and 83.65 on DPG-Bench for text-to-image generation, and 84.85 on VBench for text-to-video tasks. We believe that this work provides valuable insights and practical advancements for the research community in developing joint image-and-video generation models.

cs.CV↗

arXiv2025

ILETIA: An AI-enhanced method for individualized trigger-oocyte pickup interval estimation of progestin-primed ovarian stimulation protocol

In vitro fertilization-embryo transfer (IVF-ET) stands as one of the most prevalent treatments for infertility. During an IVF-ET cycle, the time interval between trigger shot and oocyte pickup (OPU) is a pivotal period for follicular maturation, which determines mature oocytes yields and impacts the success of subsequent procedures. However, accurately predicting this interval is severely hindered by the variability of clinicians'experience that often leads to suboptimal oocyte retrieval rate. To address this challenge, we propose ILETIA, the first machine learning-based method that could predict the optimal trigger-OPU interval for patients receiving progestin-primed ovarian stimulation (PPOS) protocol. Specifically, ILETIA leverages a Transformer to learn representations from clinical tabular data, and then employs gradient-boosted trees for interval prediction. For model training and evaluating, we compiled a dataset PPOS-DS of nearly ten thousand patients receiving PPOS protocol, the largest such dataset to our knowledge. Experimental results demonstrate that our method achieves strong performance (AUROC = 0.889), outperforming both clinicians and other widely used computational models. Moreover, ILETIA also supports premature ovulation risk prediction in a specific OPU time (AUROC = 0.838). Collectively, by enabling more precise and individualized decisions, ILETIA has the potential to improve clinical outcomes and lay the foundation for future IVF-ET research.

q-bio.QM↗

arXiv2025

Universal Catalyst Design Framework for Electrochemical Hydrogen Peroxide Synthesis Facilitated by Local Atomic Environment Descriptors

Developing a universal and precise design framework is crucial to search high-performance catalysts, but it remains a giant challenge due to the diverse structures and sites across various types of catalysts. To address this challenge, herein, we developed a novel framework by the refined local atomic environment descriptors (i.e., weighted Atomic Center Symmetry Function, wACSF) combined with machine learning (ML), microkinetic modeling, and computational high-throughput screening. This framework is successfully integrated into the Digital Catalysis Database (DigCat), enabling efficient screening for 2e- water oxidation reaction (2e- WOR) catalysts across four material categories (i.e., metal alloys, metal oxides and perovskites, and single-atom catalysts) within a ML model. The proposed wACSF descriptors integrating both geometric and chemical features are proven effective in predicting the adsorption free energies with ML. Excitingly, based on the wACSF descriptors, the ML models accurately predict the adsorption free energies of hydroxyl (ΔGOH*) and oxygen (ΔGO*) for such a wide range of catalysts, achieving R2 values of 0.84 and 0.91, respectively. Through density functional theory calculations and microkinetic modeling, a universal 2e- WOR microkinetic volcano model was derived with excellent agreement with experimental observations reported to date, which was further used to rapidly screen high-performance catalysts with the input of ML-predicted ΔGOH*. Most importantly, this universal framework can significantly improve the efficiency of catalyst design by considering multiple types of materials at the same time, which can dramatically accelerate the screening of high-performance catalysts.

cond-mat.mtrl-sci↗

arXiv2024

Intention Analysis Makes LLMs A Good Jailbreak Defender

Aligning large language models (LLMs) with human values, particularly when facing complex and stealthy jailbreak attacks, presents a formidable challenge. Unfortunately, existing methods often overlook this intrinsic nature of jailbreaks, which limits their effectiveness in such complex scenarios. In this study, we present a simple yet highly effective defense strategy, i.e., Intention Analysis ($\mathbb{IA}$). $\mathbb{IA}$ works by triggering LLMs' inherent self-correct and improve ability through a two-stage process: 1) analyzing the essential intention of the user input, and 2) providing final policy-aligned responses based on the first round conversation. Notably, $\mathbb{IA}$ is an inference-only method, thus could enhance LLM safety without compromising their helpfulness. Extensive experiments on varying jailbreak benchmarks across a wide range of LLMs show that $\mathbb{IA}$ could consistently and significantly reduce the harmfulness in responses (averagely -48.2% attack success rate). Encouragingly, with our $\mathbb{IA}$, Vicuna-7B even outperforms GPT-3.5 regarding attack success rate. We empirically demonstrate that, to some extent, $\mathbb{IA}$ is robust to errors in generated intentions. Further analyses reveal the underlying principle of $\mathbb{IA}$: suppressing LLM's tendency to follow jailbreak prompts, thereby enhancing safety.

cs.CL↗

arXiv2024

A Semi-Supervised Approach with Error Reflection for Echocardiography Segmentation

Segmenting internal structure from echocardiography is essential for the diagnosis and treatment of various heart diseases. Semi-supervised learning shows its ability in alleviating annotations scarcity. While existing semi-supervised methods have been successful in image segmentation across various medical imaging modalities, few have attempted to design methods specifically addressing the challenges posed by the poor contrast, blurred edge details and noise of echocardiography. These characteristics pose challenges to the generation of high-quality pseudo-labels in semi-supervised segmentation based on Mean Teacher. Inspired by human reflection on erroneous practices, we devise an error reflection strategy for echocardiography semi-supervised segmentation architecture. The process triggers the model to reflect on inaccuracies in unlabeled image segmentation, thereby enhancing the robustness of pseudo-label generation. Specifically, the strategy is divided into two steps. The first step is called reconstruction reflection. The network is tasked with reconstructing authentic proxy images from the semantic masks of unlabeled images and their auxiliary sketches, while maximizing the structural similarity between the original inputs and the proxies. The second step is called guidance correction. Reconstruction error maps decouple unreliable segmentation regions. Then, reliable data that are more likely to occur near high-density areas are leveraged to guide the optimization of unreliable data potentially located around decision boundaries. Additionally, we introduce an effective data augmentation strategy, termed as multi-scale mixing up strategy, to minimize the empirical distribution gap between labeled and unlabeled images and perceive diverse scales of cardiac anatomical structures. Extensive experiments demonstrate the competitiveness of the proposed method.

eess.IV↗

arXiv2024

Shear-resistant topology in quasi one-dimensional van der Waals material Bi$_4$Br$_4$

Bi$_4$Br$_4$ is a prototypical quasi one-dimensional (1D) material in which covalently bonded bismuth bromide chains are arranged in parallel, side-by-side and layer-by-layer, with van der Waals (vdW) gaps in between. So far, two different structures have been reported for this compound, $α$-Bi$_4$Br$_4$ and $β$-Bi$_4$Br$_4$ , in both of which neighboring chains are shifted by $\mathbf{b}/2$, i.e., half a unit cell vector in the plane, but which differ in their vertical stacking. While the different layer arrangements are known to result in distinct electronic properties, the effect of possible in-plane shifts between the atomic chains remains an open question. Here, using scanning tunneling microscopy and spectroscopy (STM/STS), we report a new Bi$_4$Br$_4$(001) structure, with a shift of $\mathbf{b}/3$ between neighboring chains in the plane and AB layer stacking. We determine shear strain to be the origin of this new structure, which can readily result in shifts of neighboring atomic chains because of the weak inter-chain bonding. For the observed $b/3$ structure, the (residual) atomic chain shift corresponds to an in-plane shear strain of $γ\approx7.5\%$. STS reveals a bulk insulating gap and metallic edge states at surface steps, indicating that the new structure is also a higher-order topological insulator, just like $α$-Bi$_4$Br$_4$, in agreement with density functional theory (DFT) calculations.

cond-mat.mes-hall↗

arXiv2024

Guided Statistical Workflows with Interactive Explanations and Assumption Checking

Statistical practices such as building regression models or running hypothesis tests rely on following rigorous procedures of steps and verifying assumptions on data to produce valid results. However, common statistical tools do not verify users' decision choices and provide low-level statistical functions without instructions on the whole analysis practice. Users can easily misuse analysis methods, potentially decreasing the validity of results. To address this problem, we introduce GuidedStats, an interactive interface within computational notebooks that encapsulates guidance, models, visualization, and exportable results into interactive workflows. It breaks down typical analysis processes, such as linear regression and two-sample T-tests, into interactive steps supplemented with automatic visualizations and explanations for step-wise evaluation. Users can iterate on input choices to refine their models, while recommended actions and exports allow the user to continue their analysis in code. Case studies show how GuidedStats offers valuable instructions for conducting fluid statistical analyses while finding possible assumption violations in the underlying data, supporting flexible and accurate statistical analyses.

cs.HC↗

arXiv2024

Creating a Microstructure Latent Space with Rich Material Information for Multiphase Alloy Design

The intricate microstructure serves as the cornerstone for the composition/processing-structure-property (CPSP) connection in multiphase alloys. Traditional alloy design methods often overlook microstructural details, which diminishes the reliability and effectiveness of the outcomes. This study introduces an improved alloy design algorithm that integrates authentic microstructural information to establish precise CPSP relationships. The approach utilizes a deep-learning framework based on a variational autoencoder to map real microstructural data to a latent space, enabling the prediction of composition, processing steps, and material properties from the latent space vector. By integrating this deep learning model with a specific sampling strategy in the latent space, a novel, microstructure-centered algorithm for multiphase alloy design is developed. This algorithm is demonstrated through the design of a unified dual-phase steel, and the results are assessed at three performance levels. Moreover, an exploration into the latent vector space of the model highlights its seamless interpolation ability and its rich material information content. Notably, the current configuration of the latent space is particularly advantageous for alloy design, offering an exhaustive representation of microstructure, composition, processing, and property variations essential for multiphase alloys.

cond-mat.mtrl-sci↗

arXiv2024

Mamba2MIL: State Space Duality Based Multiple Instance Learning for Computational Pathology

Computational pathology (CPath) has significantly advanced the clinical practice of pathology. Despite the progress made, Multiple Instance Learning (MIL), a promising paradigm within CPath, continues to face challenges, particularly related to incomplete information utilization. Existing frameworks, such as those based on Convolutional Neural Networks (CNNs), attention, and selective scan space state sequential model (SSM), lack sufficient flexibility and scalability in fusing diverse features, and cannot effectively fuse diverse features. Additionally, current approaches do not adequately exploit order-related and order-independent features, resulting in suboptimal utilization of sequence information. To address these limitations, we propose a novel MIL framework called Mamba2MIL. Our framework utilizes the state space duality model (SSD) to model long sequences of patches of whole slide images (WSIs), which, combined with weighted feature selection, supports the fusion processing of more branching features and can be extended according to specific application needs. Moreover, we introduce a sequence transformation method tailored to varying WSI sizes, which enhances sequence-independent features while preserving local sequence information, thereby improving sequence information utilization. Extensive experiments demonstrate that Mamba2MIL surpasses state-of-the-art MIL methods. We conducted extensive experiments across multiple datasets, achieving improvements in nearly all performance metrics. Specifically, on the NSCLC dataset, Mamba2MIL achieves a binary tumor classification AUC of 0.9533 and an accuracy of 0.8794. On the BRACS dataset, it achieves a multiclass classification AUC of 0.7986 and an accuracy of 0.4981. The code is available at https://github.com/YuqiZhang-Buaa/Mamba2MIL.

cs.CV↗

arXiv2024

Revolutionizing Alloy Microstructure Segmentation through SAM and Domain Knowledge without Extra Training

Fundamental models, trained on large-scale datasets and adapted to new data using innovative learning methods, have revolutionized various fields. In materials science, microstructure image segmentation plays a pivotal role in understanding alloy properties. However, conventional supervised modelling algorithms often necessitate extensive annotations and intricate optimization procedures. The segmentation anything model (SAM) introduces a fresh perspective. By combining SAM with domain knowledge, we propose a novel generalized algorithm for alloy image segmentation. This algorithm can process batches of images across diverse alloy systems without requiring training or annotations. Furthermore, it achieves segmentation accuracy comparable to that of supervised models and robustly handles complex phase distributions in various alloy images, regardless of data volume.

cond-mat.mtrl-sci↗

arXiv2024

Aerial Lifting: Neural Urban Semantic and Building Instance Lifting from Aerial Imagery

We present a neural radiance field method for urban-scale semantic and building-level instance segmentation from aerial images by lifting noisy 2D labels to 3D. This is a challenging problem due to two primary reasons. Firstly, objects in urban aerial images exhibit substantial variations in size, including buildings, cars, and roads, which pose a significant challenge for accurate 2D segmentation. Secondly, the 2D labels generated by existing segmentation methods suffer from the multi-view inconsistency problem, especially in the case of aerial images, where each image captures only a small portion of the entire scene. To overcome these limitations, we first introduce a scale-adaptive semantic label fusion strategy that enhances the segmentation of objects of varying sizes by combining labels predicted from different altitudes, harnessing the novel-view synthesis capabilities of NeRF. We then introduce a novel cross-view instance label grouping strategy based on the 3D scene representation to mitigate the multi-view inconsistency problem in the 2D instance labels. Furthermore, we exploit multi-view reconstructed depth priors to improve the geometric quality of the reconstructed radiance field, resulting in enhanced segmentation results. Experiments on multiple real-world urban-scale datasets demonstrate that our approach outperforms existing methods, highlighting its effectiveness.

cs.CV↗