arXiv subjects

Bo Fang

Publications and source records attributed to Bo Fang.

At least 19 recordsLinked to original sources

arXiv2026

Quantum Sampling Architecture for Protein Structure Reconstruction on Utility-Scale Hardware

Predicting the structure of short peptides in protein binding pockets remains difficult because this regime requires physics-based conformational search, yet existing methods do not provide a practical way to carry out that search on current hardware. We present QSAD, a quantum-classical framework that reformulates peptide structure prediction as amino-acid-level Hamiltonian sampling and replaces iterative optimization with non-iterative Hamiltonian evolution. Executed entirely on IBM Heron R2 across 101 binding-pocket peptides (5-18 residues), QSAD improves prediction accuracy by 27-71% over all evaluated AI and quantum baselines while maintaining the lowest variance across tested lengths. QSAD also tolerates noise levels 3-5x beyond typical hardware error rates, where iterative methods fail, and reduces mean quantum execution time by 27x relative to VQE. The sampled ensemble further supports approximate reconstruction of protein energy landscapes. These results establish coarse-grained quantum sampling as a practical computational path for structure prediction in regimes where data-driven methods lack sufficient signal.

cs.ET↗

arXiv2026

Graph-VQE: A CUDA-Q Multi-QPU Simulation Framework for Hamiltonian-Aware Protein-Folding VQE

The Variational Quantum Eigensolver (VQE) is essential for molecular simulation in drug discovery, but hardware noise and algorithmic limits restrict its precision. While the NVIDIA CUDA-Q platform mitigates some hardware issues via exact simulation, it lacks Qiskit support and restricts parallelization. To solve this, we introduce Graph-VQE, a novel framework that extends CUDA-Q with optimization-level parallelism. Graph-VQE leverages amino acid sequence structures by partitioning Hamiltonian interaction graphs into weakly coupled clusters using Louvain community detection. These clusters undergo restricted updates on the full-Hamiltonian objective, followed by a global refinement stage utilizing Hamiltonian batching. Furthermore, a custom Qiskit-CUDA-Q integration layer enables standard workflows with GPU acceleration. Evaluations on protein folding tasks prove that Graph-VQE outperforms baselines, achieving lower final energies. It delivers competitive RMSD and binding affinity compared to AlphaFold3 and IBM quantum processors while maintaining stable quality across multi-GPU environments, thereby providing a highly practical path toward high-fidelity biomolecular simulations.

cs.ET↗

arXiv2026

Splaxel: Efficient Distributed Training of 3D Gaussian Splatting for Large-scale Scene Reconstruction via Pixel-level Communication

3D Gaussian Splatting (3DGS) enables high-fidelity and real-time 3D scene reconstruction, but scaling training to large-scale scenes requires optimizing hundreds of millions of Gaussians across multiple GPUs. Existing distributed approaches either partition scenes into isolated regions, causing global inconsistency, or rely on global Gaussian-level exchanges, which lead to substantial growth in inter-GPU communication and quickly dominate iteration time. We propose Splaxel, a communication-efficient distributed 3DGS training framework based on pixel-level local rendering and global composition. Instead of synchronizing Gaussians, each GPU renders its local subset and exchanges only partial pixel values, maintaining mathematical consistency while keeping communication cost stable as the scene size increases. Splaxel further reduces pixel-level redundancy through geometric and transmittance visibility prediction and improves GPU utilization via conflict-free camera-view consolidation. Evaluated on large-scale datasets with up to 120M Gaussians, Splaxel achieves up to 7.6$\times$ speedup over the state-of-the-art distributed 3DGS framework while preserving high reconstruction quality.

cs.DC↗

arXiv2026

Power Reinforcement Post-Training of Text-to-Image Models with Super-Linear Advantage Shaping

Recently, post-training methods based on reinforcement learning, with a particular focus on Group Relative Policy Optimization (GRPO), have emerged as the robust paradigm for further advancement of text-to-image (T2I) models. However, these methods are often prone to reward hacking, wherein models exploit biases in imperfect reward functions rather than yielding genuine performance gains. In this work, we identify that normalization could lead to miscalibration and directly removing the prompt-level standard deviation term yields an optimal policy ascent direction that is linear in the advantage but still limits the separation of genuine signals from noise. To mitigate the above issues, we propose Super-Linear Advantage Shaping (SLAS) by revisiting the functional update from an information geometry perspective. By extending the Fisher-Rao information metric with advantage-dependent weighting, SLAS introduces a non-linear geometric structure that reshapes the local policy space. This design relaxes constraints along high-advantage directions to amplify informative updates, while tightening those in low-advantage regions to suppress illusory gradients. In addition, batch-level normalization is applied to stabilize training under varying reward scales. Extensive evaluations demonstrate that SLAS consistently surpasses the DanceGRPO baseline across multiple backbones and benchmarks. In particular, it yields faster training dynamics, improved out-of-domain performance on GenEval and UniGenBench++, and enhanced robustness to model scaling, while mitigating reward hacking and preserving semantic and compositional fidelity in generations.

cs.CV↗

arXiv2026

SAMA: Factorized Semantic Anchoring and Motion Alignment for Instruction-Guided Video Editing

Current instruction-guided video editing models struggle to simultaneously balance precise semantic modifications with faithful motion preservation. While existing approaches rely on injecting explicit external priors (e.g., VLM features or structural conditions) to mitigate these issues, this reliance severely bottlenecks model robustness and generalization. To overcome this limitation, we present SAMA (factorized Semantic Anchoring and Motion Alignment), a framework that factorizes video editing into semantic anchoring and motion modeling. First, we introduce Semantic Anchoring, which establishes a reliable visual anchor by jointly predicting semantic tokens and video latents at sparse anchor frames, enabling purely instruction-aware structural planning. Second, Motion Alignment pre-trains the same backbone on motion-centric video restoration pretext tasks (cube inpainting, speed perturbation, and tube shuffle), enabling the model to internalize temporal dynamics directly from raw videos. SAMA is optimized with a two-stage pipeline: a factorized pre-training stage that learns inherent semantic-motion representations without paired video-instruction editing data, followed by supervised fine-tuning on paired editing data. Remarkably, the factorized pre-training alone already yields strong zero-shot video editing ability, validating the proposed factorization. SAMA achieves state-of-the-art performance among open-source models and is competitive with leading commercial systems (e.g., Kling-Omni). Code, models, and datasets will be released.

cs.CV↗

arXiv2026

M2P: Improving Visual Foundation Models with Mask-to-Point Weakly-Supervised Learning for Dense Point Tracking

Tracking Any Point (TAP) has emerged as a fundamental tool for video understanding. Current approaches adapt Vision Foundation Models (VFMs) like DINOv2 via offline finetuning or test-time optimization. However, these VFMs rely on static image pre-training, which is inherently sub-optimal for capturing dense temporal correspondence in videos. To address this, we propose Mask-to-Point (M2P) learning, which leverages rich video object segmentation (VOS) mask annotations to improve VFMs for dense point tracking. Our M2P introduces three new mask-based constraints for weakly-supervised representation learning. First, we propose a local structure consistency loss, which leverages Procrustes analysis to model the cohesive motion of points lying within a local structure, achieving more reliable point-to-point matching learning. Second, we propose a mask label consistency (MLC) loss, which enforces that sampled foreground points strictly match foreground regions across frames. The proposed MLC loss can be regarded as a regularization, which stabilizes training and prevents convergence to trivial solutions. Finally, mask boundary constrain is applied to explicitly supervise boundary points. We show that our weaklysupervised M2P models significantly outperform baseline VFMs with efficient training by using only 3.6K VOS training videos. Notably, M2P achieves 12.8% and 14.6% performance gains over DINOv2-B/14 and DINOv3-B/16 on the TAP-Vid-DAVIS benchmark, respectively. Moreover, the proposed M2P models are used as pre-trained backbones for both test-time optimized and offline fine-tuned TAP tasks, demonstrating its potential to serve as general pre-trained models for point tracking. Code will be made publicly available upon acceptance.

cs.CV↗

arXiv2026

VeriHGN: Heterogeneous Graph-Based Congestion Prediction for Chip Layout Verification

As Very Large Scale Integration (VLSI) designs continue to scale in size and complexity, layout verification has become a central challenge in modern Electronic Design Automation (EDA) workflows. In practice, congestion can only be accurately identified after detailed routing, making traditional verification both time-consuming and costly. Learning-based approaches have therefore been explored to enable early-stage congestion prediction and reduce routing iterations. However, although prior methods incorporate both netlist connectivity and layout features, they often model the two in a loosely coupled manner and primarily produce numerical congestion estimates. We propose VeriHGN, a verification framework built on an enhanced heterogeneous graph that unifies circuit components and spatial grids into a single relational representation, enabling more faithful modeling of the interaction between logical intent and physical realization. Experiments on industrial benchmarks, including ISPD2015, CircuitNet-N14, and CircuitNet-N28, demonstrate that VeriHGN achieves the best or near-best performance over state-of-the-art methods in prediction accuracy and correlation metrics.

cs.AR↗

arXiv2026

Asking Forever: Universal Activations Behind Turn Amplification in Conversational LLMs

Multi-turn interaction length is a dominant factor in the operational costs of conversational LLMs. In this work, we present a new failure mode in conversational LLMs: turn amplification, in which a model consistently prolongs multi-turn interactions without completing the underlying task. We show that an adversary can systematically exploit clarification-seeking behavior$-$commonly encouraged in multi-turn conversation settings$-$to scalably prolong interactions. Moving beyond prompt-level behaviors, we take a mechanistic perspective and identify a query-independent, universal activation subspace associated with clarification-seeking responses. Unlike prior cost-amplification attacks that rely on per-turn prompt optimization, our attack arises from conversational dynamics and persists across prompts and tasks. We show that this mechanism provides a scalable pathway to induce turn amplification: both supply-chain attacks via fine-tuning and runtime attacks through low-level parameter corruptions consistently shift models toward abstract, clarification-seeking behavior across prompts. Across multiple instruction-tuned LLMs and benchmarks, our attack substantially increases turn count while remaining compliant. We also show that existing defenses offer limited protection against this emerging class of failures.

cs.LG↗

arXiv2025

ViSS-R1: Self-Supervised Reinforcement Video Reasoning

Complex video reasoning remains a significant challenge for Multimodal Large Language Models (MLLMs), as current R1-based methodologies often prioritize text-centric reasoning derived from text-based and image-based developments. In video tasks, such strategies frequently underutilize rich visual information, leading to potential shortcut learning and increased susceptibility to hallucination. To foster a more robust, visual-centric video understanding, we start by introducing a novel self-supervised reinforcement learning GRPO algorithm (Pretext-GRPO) within the standard R1 pipeline, in which positive rewards are assigned for correctly solving pretext tasks on transformed visual inputs, which makes the model to non-trivially process the visual information. Building on the effectiveness of Pretext-GRPO, we further propose the ViSS-R1 framework, which streamlines and integrates pretext-task-based self-supervised learning directly into the MLLM's R1 post-training paradigm. Instead of relying solely on sparse visual cues, our framework compels models to reason about transformed visual input by simultaneously processing both pretext questions (concerning transformations) and true user queries. This necessitates identifying the applied transformation and reconstructing the original video to formulate accurate final answers. Comprehensive evaluations on six widely-used video reasoning and understanding benchmarks demonstrate the effectiveness and superiority of our Pretext-GRPO and ViSS-R1 for complex video reasoning. Our codes and models will be publicly available.

cs.CV↗

arXiv2025

A Survey on Agentic Multimodal Large Language Models

With the recent emergence of revolutionary autonomous agentic systems, research community is witnessing a significant shift from traditional static, passive, and domain-specific AI agents toward more dynamic, proactive, and generalizable agentic AI. Motivated by the growing interest in agentic AI and its potential trajectory toward AGI, we present a comprehensive survey on Agentic Multimodal Large Language Models (Agentic MLLMs). In this survey, we explore the emerging paradigm of agentic MLLMs, delineating their conceptual foundations and distinguishing characteristics from conventional MLLM-based agents. We establish a conceptual framework that organizes agentic MLLMs along three fundamental dimensions: (i) Agentic internal intelligence functions as the system's commander, enabling accurate long-horizon planning through reasoning, reflection, and memory; (ii) Agentic external tool invocation, whereby models proactively use various external tools to extend their problem-solving capabilities beyond their intrinsic knowledge; and (iii) Agentic environment interaction further situates models within virtual or physical environments, allowing them to take actions, adapt strategies, and sustain goal-directed behavior in dynamic real-world scenarios. To further accelerate research in this area for the community, we compile open-source training frameworks, training and evaluation datasets for developing agentic MLLMs. Finally, we review the downstream applications of agentic MLLMs and outline future research directions for this rapidly evolving field. To continuously track developments in this rapidly evolving field, we will also actively update a public repository at https://github.com/HJYao00/Awesome-Agentic-MLLMs.

cs.CV↗

arXiv2025

Understanding the Landscape of Ampere GPU Memory Errors

Graphics Processing Units (GPUs) have become a de facto solution for accelerating high-performance computing (HPC) applications. Understanding their memory error behavior is an essential step toward achieving efficient and reliable HPC systems. In this work, we present a large-scale cross-supercomputer study to characterize GPU memory reliability, covering three supercomputers - Delta, Polaris, and Perlmutter - all equipped with NVIDIA A100 GPUs. We examine error logs spanning 67.77 million GPU device-hours across 10,693 GPUs. We compare error rates and mean-time-between-errors (MTBE) and highlight both shared and distinct error characteristics among these three systems. Based on these observations and analyses, we discuss the implications and lessons learned, focusing on the reliable operation of supercomputers, the choice of checkpointing interval, and the comparison of reliability characteristics with those of previous-generation GPUs. Our characterization study provides valuable insights into fault-tolerant HPC system design and operation, enabling more efficient execution of HPC applications.

cs.DC↗

arXiv2025

ScSAM: Debiasing Morphology and Distributional Variability in Subcellular Semantic Segmentation

The significant morphological and distributional variability among subcellular components poses a long-standing challenge for learning-based organelle segmentation models, significantly increasing the risk of biased feature learning. Existing methods often rely on single mapping relationships, overlooking feature diversity and thereby inducing biased training. Although the Segment Anything Model (SAM) provides rich feature representations, its application to subcellular scenarios is hindered by two key challenges: (1) The variability in subcellular morphology and distribution creates gaps in the label space, leading the model to learn spurious or biased features. (2) SAM focuses on global contextual understanding and often ignores fine-grained spatial details, making it challenging to capture subtle structural alterations and cope with skewed data distributions. To address these challenges, we introduce ScSAM, a method that enhances feature robustness by fusing pre-trained SAM with Masked Autoencoder (MAE)-guided cellular prior knowledge to alleviate training bias from data imbalance. Specifically, we design a feature alignment and fusion module to align pre-trained embeddings to the same feature space and efficiently combine different representations. Moreover, we present a cosine similarity matrix-based class prompt encoder to activate class-specific features to recognize subcellular categories. Extensive experiments on diverse subcellular image datasets demonstrate that ScSAM outperforms state-of-the-art methods.

cs.CV↗

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

Threading Keyframe with Narratives: MLLMs as Strong Long Video Comprehenders

Employing Multimodal Large Language Models (MLLMs) for long video understanding remains a challenging problem due to the dilemma between the substantial number of video frames (i.e., visual tokens) versus the limited context length of language models. Traditional uniform sampling often leads to selection of irrelevant content, while post-training MLLMs on thousands of frames imposes a substantial computational burden. In this paper, we propose threading keyframes with narratives (Nar-KFC), a plug-and-play module to facilitate effective and efficient long video perception. Nar-KFC generally involves two collaborative steps. First, we formulate the keyframe selection process as an integer quadratic programming problem, jointly optimizing query-relevance and frame-diversity. To avoid its computational complexity, a customized greedy search strategy is designed as an efficient alternative. Second, to mitigate the temporal discontinuity caused by sparse keyframe sampling, we further introduce interleaved textual narratives generated from non-keyframes using off-the-shelf captioners. These narratives are inserted between keyframes based on their true temporal order, forming a coherent and compact representation. Nar-KFC thus serves as a temporal- and content-aware compression strategy that complements visual and textual modalities. Experimental results on multiple long-video benchmarks demonstrate that Nar-KFC significantly improves the performance of popular MLLMs. Code will be made publicly available.

cs.CV↗

arXiv2025

Can Large Language Models Understand Intermediate Representations in Compilers?

Intermediate Representations (IRs) play a critical role in compiler design and program analysis, yet their comprehension by Large Language Models (LLMs) remains underexplored. In this paper, we present an explorative empirical study evaluating the capabilities of six state-of-the-art LLMs: GPT-4, GPT-3, DeepSeek, Gemma 2, Llama 3, and Code Llama, in understanding IRs. Specifically, we assess model performance across four core tasks: control flow graph reconstruction, decompilation, code summarization, and execution reasoning. While LLMs exhibit competence in parsing IR syntax and identifying high-level structures, they consistently struggle with instruction-level reasoning, especially in control flow reasoning, loop handling, and dynamic execution. Common failure modes include misinterpreting branching instructions, omitting critical operations, and relying on heuristic reasoning rather than precise instruction-level logic. Our findings highlight the need for IR-specific enhancements in LLM design. We recommend fine-tuning on structured IR datasets and integrating control-flow-sensitive architectures to improve model effectiveness. All experimental data and source code are publicly available at

cs.LG↗

arXiv2024

PrisonBreak: Jailbreaking Large Language Models with at Most Twenty-Five Targeted Bit-flips

We study a new vulnerability in commercial-scale safety-aligned large language models (LLMs): their refusal to generate harmful responses can be broken by flipping only a few bits in model parameters. Our attack jailbreaks billion-parameter language models with just 5 to 25 bit-flips, requiring up to 40$\times$ fewer bit flips than prior attacks on much smaller computer vision models. Unlike prompt-based jailbreaks, our method directly uncensors models in memory at runtime, enabling harmful outputs without requiring input-level modifications. Our key innovation is an efficient bit-selection algorithm that identifies critical bits for language model jailbreaks up to 20$\times$ faster than prior methods. We evaluate our attack on 10 open-source LLMs, achieving high attack success rates (ASRs) of 80-98% with minimal impact on model utility. We further demonstrate an end-to-end exploit via Rowhammer-based fault injection, reliably jailbreaking 5 models (69-91% ASR) on a GDDR6 GPU. Our analyses reveal that: (1) models with weaker post-training alignment require fewer bit-flips to jailbreak; (2) certain model components, e.g., value projection layers, are substantially more vulnerable; and (3) the attack is mechanistically different from existing jailbreak methods. We evaluate potential countermeasures and find that our attack remains effective against defenses at various stages of the LLM pipeline.

cs.CR↗

arXiv2024

DistinctAD: Distinctive Audio Description Generation in Contexts

Audio Descriptions (ADs) aim to provide a narration of a movie in text form, describing non-dialogue-related narratives, such as characters, actions, or scene establishment. Automatic generation of ADs remains challenging due to: i) the domain gap between movie-AD data and existing data used to train vision-language models, and ii) the issue of contextual redundancy arising from highly similar neighboring visual clips in a long movie. In this work, we propose DistinctAD, a novel two-stage framework for generating ADs that emphasize distinctiveness to produce better narratives. To address the domain gap, we introduce a CLIP-AD adaptation strategy that does not require additional AD corpora, enabling more effective alignment between movie and AD modalities at both global and fine-grained levels. In Stage-II, DistinctAD incorporates two key innovations: (i) a Contextual Expectation-Maximization Attention (EMA) module that reduces redundancy by extracting common bases from consecutive video clips, and (ii) an explicit distinctive word prediction loss that filters out repeated words in the context, ensuring the prediction of unique terms specific to the current AD. Comprehensive evaluations on MAD-Eval, CMD-AD, and TV-AD benchmarks demonstrate the superiority of DistinctAD, with the model consistently outperforming baselines, particularly in Recall@k/N, highlighting its effectiveness in producing high-quality, distinctive ADs.

cs.CV↗