arXiv subjects

Siqi Lu

Publications and source records attributed to Siqi Lu.

At least 19 recordsLinked to original sources

arXiv2026

Decision-Level Hijacking: Injecting Cognitive Bias into Large Language Models via Bit-Flip Attacks

Large Language Models (LLMs) have been widely applied in high-stakes decision-making scenarios such as corporate strategy, and users are increasingly relying on their outputs. However, the deep integration of open-source model sharing ecosystems with LLM-powered critical decision-making applications also introduces critical risks: if an attacker can manipulate the model's cognitive stance, they can indirectly influence the judgments and actions of downstream decision-makers. This paper defines such threats as decision-level hijacking. Existing attacks fail to achieve targeted cognitive manipulation without triggering prohibited content or degrading model functionality. To fill this gap, this paper reveals that Bit-Flip Attacks (BFAs) can serve as an attack vector for inducing decision-level hijacking, requiring no real-time interaction or control over the training process, and only a minimal number of weight bits need to be flipped after deployment to achieve stealthy, low-cost, and persistent cognitive manipulation. Therefore, we propose CogBias, a cognitive bias injection framework for LLMs. CogBias converts subjective preferences into optimization signals via a differentiable sentiment evaluator, uses a multi-objective loss to jointly constrain multiple dimensions, and constructs BitScout to locate critical bits, achieving targeted cognitive intervention under an ultra-sparse flip budget. Experiments on Llama-3.2-3B, Mistral-7B, and Qwen2.5-14B, as well as on the commercial recommendation and controversial factual topic scenarios, demonstrate that flipping only a small number of bits stably induces significant stance shifts on target topics, while the impact on non-target tasks and overall output distribution is limited. This work demonstrates that minute perturbations to low-level weight data suffice to undermine the high-level value alignment of LLMs.

cs.CR↗

arXiv2026

Toward Template-Free Explainability for Monte Carlo Tree Search

Probabilistic search algorithms, such as Monte Carlo Tree Search (MCTS), have proven very effective in solving sequential decision-making tasks under uncertainty. However, interpreting asymmetric search trees that incorporate bandit-based tree traversal and simulation-based value estimation is difficult for end users based solely on raw tree statistics. While prior work requires hand-crafted formal logic constraints that must be updated when the problem changes, we present a framework that enables large language models (LLMs) to generate evidence-grounded explanations of MCTS decisions from recorded search traces in an end-to-end manner. Our framework maps natural-language questions to a structured set of intent categories, determines whether the existing tree contains sufficient evidence, triggers targeted expansion when needed, and generates explanations using tree statistics such as visit counts, value estimates, and risk information. Experimental results provide the first evidence that LLMs can serve as end-to-end explainers for probabilistic search, without requiring intermediate formal representations.

cs.HC↗

arXiv2026

Plug, Play, and Fortify: A Low-Cost Module for Robust Multimodal Image Understanding Models

Missing modalities present a fundamental challenge in multimodal models, often causing catastrophic performance degradation. Our observations suggest that this fragility stems from an imbalanced learning process, where the model develops an implicit preference for certain modalities, leading to the under-optimization of others. We propose a simple yet efficient method to address this challenge. The central insight of our work is that the dominance relationship between modalities can be effectively discerned and quantified in the frequency domain. To leverage this principle, we first introduce a Frequency Ratio Metric (FRM) to quantify modality preference by analyzing features in the frequency domain. Guided by FRM, we then propose a Multimodal Weight Allocation Module, a plug-and-play component that dynamically re-balances the contribution of each branch during training, promoting a more holistic learning paradigm. Extensive experiments demonstrate that MWAM can be seamlessly integrated into diverse architectural backbones, such as those based on CNNs and ViTs. Furthermore, MWAM delivers consistent performance gains across a wide range of tasks and modality combinations. This advancement extends beyond merely optimizing the performance of the base model; it also manifests as further performance improvements to state-of-the-art methods addressing the missing modality problem.

cs.CV↗

arXiv2025

SCR2-ST: Combine Single Cell with Spatial Transcriptomics for Efficient Active Sampling via Reinforcement Learning

Spatial transcriptomics (ST) is an emerging technology that enables researchers to investigate the molecular relationships underlying tissue morphology. However, acquiring ST data remains prohibitively expensive, and traditional fixed-grid sampling strategies lead to redundant measurements of morphologically similar or biologically uninformative regions, thus resulting in scarce data that constrain current methods. The well-established single-cell sequencing field, however, could provide rich biological data as an effective auxiliary source to mitigate this limitation. To bridge these gaps, we introduce SCR2-ST, a unified framework that leverages single-cell prior knowledge to guide efficient data acquisition and accurate expression prediction. SCR2-ST integrates a single-cell guided reinforcement learning-based (SCRL) active sampling and a hybrid regression-retrieval prediction network SCR2Net. SCRL combines single-cell foundation model embeddings with spatial density information to construct biologically grounded reward signals, enabling selective acquisition of informative tissue regions under constrained sequencing budgets. SCR2Net then leverages the actively sampled data through a hybrid architecture combining regression-based modeling with retrieval-augmented inference, where a majority cell-type filtering mechanism suppresses noisy matches and retrieved expression profiles serve as soft labels for auxiliary supervision. We evaluated SCR2-ST on three public ST datasets, demonstrating SOTA performance in both sampling efficiency and prediction accuracy, particularly under low-budget scenarios. Code is publicly available at: https://github.com/hrlblab/SCR2ST

cs.CV↗

arXiv2025

VK-Det: Visual Knowledge Guided Prototype Learning for Open-Vocabulary Aerial Object Detection

To identify objects beyond predefined categories, open-vocabulary aerial object detection (OVAD) leverages the zero-shot capabilities of visual-language models (VLMs) to generalize from base to novel categories. Existing approaches typically utilize self-learning mechanisms with weak text supervision to generate region-level pseudo-labels to align detectors with VLMs semantic spaces. However, text dependence induces semantic bias, restricting open-vocabulary expansion to text-specified concepts. We propose $\textbf{VK-Det}$, a $\textbf{V}$isual $\textbf{K}$nowledge-guided open-vocabulary object $\textbf{Det}$ection framework $\textit{without}$ extra supervision. First, we discover and leverage vision encoder's inherent informative region perception to attain fine-grained localization and adaptive distillation. Second, we introduce a novel prototype-aware pseudo-labeling strategy. It models inter-class decision boundaries through feature clustering and maps detection regions to latent categories via prototype matching. This enhances attention to novel objects while compensating for missing supervision. Extensive experiments show state-of-the-art performance, achieving 30.1 $\mathrm{mAP}^{N}$ on DIOR and 23.3 $\mathrm{mAP}^{N}$ on DOTA, outperforming even extra supervised methods.

cs.CV↗

arXiv2025

Has the Two-Decade-Old Prophecy Come True? Artificial Bad Intelligence Triggered by Merely a Single-Bit Flip in Large Language Models

Recently, Bit-Flip Attack (BFA) has garnered widespread attention for its ability to compromise software system integrity remotely through hardware fault injection. With the widespread distillation and deployment of large language models (LLMs) into single file .gguf formats, their weight spaces have become exposed to an unprecedented hardware attack surface. This paper is the first to systematically discover and validate the existence of single-bit vulnerabilities in LLM weight files: in mainstream open-source models (e.g., DeepSeek and QWEN) using .gguf quantized formats, flipping just single bit can induce three types of targeted semantic level failures Artificial Flawed Intelligence (outputting factual errors), Artificial Weak Intelligence (degradation of logical reasoning capability), and Artificial Bad Intelligence (generating harmful content). By building an information theoretic weight sensitivity entropy model and a probabilistic heuristic scanning framework called BitSifter, we achieved efficient localization of critical vulnerable bits in models with hundreds of millions of parameters. Experiments show that vulnerabilities are significantly concentrated in the tensor data region, particularly in areas related to the attention mechanism and output layers, which are the most sensitive. A negative correlation was observed between model size and robustness, with smaller models being more susceptible to attacks. Furthermore, a remote BFA chain was designed, enabling semantic-level attacks in real-world environments: At an attack frequency of 464.3 times per second, a single bit can be flipped with 100% success in as little as 31.7 seconds. This causes the accuracy of LLM to plummet from 73.5% to 0%, without requiring high-cost equipment or complex prompt engineering.

cs.CR↗

arXiv2025

Evaluating New AI Cell Foundation Models on Challenging Kidney Pathology Cases Unaddressed by Previous Foundation Models

Accurate cell nuclei segmentation is critical for downstream tasks in kidney pathology and remains a major challenge due to the morphological diversity and imaging variability of renal tissues. While our prior work has evaluated early-generation AI cell foundation models in this domain, the effectiveness of recent cell foundation models remains unclear. In this study, we benchmark advanced AI cell foundation models (2025), including CellViT++ variants and Cellpose-SAM, against three widely used cell foundation models developed prior to 2024, using a diverse large-scale set of kidney image patches within a human-in-the-loop rating framework. We further performed fusion-based ensemble evaluation and model agreement analysis to assess the segmentation capabilities of the different models. Our results show that CellViT++ [Virchow] yields the highest standalone performance with 40.3% of predictions rated as "Good" on a curated set of 2,091 challenging samples, outperforming all prior models. In addition, our fused model achieves 62.2% "Good" predictions and only 0.4% "Bad", substantially reducing segmentation errors. Notably, the fusion model (2025) successfully resolved the majority of challenging cases that remained unaddressed in our previous study. These findings demonstrate the potential of AI cell foundation model development in renal pathology and provide a curated dataset of challenging samples to support future kidney-specific model refinement.

q-bio.QM↗

arXiv2025

Understanding the atomically precise evolution of the miscibility of newly prepared face-centered cubic W-Cu nanoalloys and its asymmetry

According to classical Miedema theory, reducing crystals to the order of nanometer sizes might greatly modulate the mixing enthalpy of elements, thus enabling the invention of a lot of new bulk-immiscible alloys. Although numerous alloys with higher mixing enthalpies remain unexplored, this strategy is approaching its limit, as reflected by the critical diameter of recent alloys of 1.8 nm, which corresponds to ~150 atoms and hardly provides a crystalline order. Future development requires not only even smaller atomic-scale control but also a new surface energy-saving mechanism. Here, we report the formation of W-Cu nanoalloys with a very large miscibility gap in the bulk via the use of an atomically size-selected cluster beam source as an example. The face-centered cubic (FCC) structure was demonstrated through electron diffraction, which indicated a lattice constant of 3.88{\AA} for W0.85Cu0.15 nanoalloys (~2280 atoms). In this comprehensive study that covers a large parameter space of W/Cu compositions and numbers of atoms, an asymmetric miscibility nanophase diagram in which W-rich compositions favor mixing and the critical size is approximately 6000 atoms, which far exceeds the approximately tens of atoms predicted via classical theory, was obtained for the first time. Density functional theory (DFT) calculations revealed a mutual strain-induced mechanism that simultaneously lowers the surface energies while reducing the size to the atomic scale. This approach paves the way for the development of new high-performance nonequilibrium phase alloys.

cond-mat.mtrl-sci↗

arXiv2025

ZeroReg3D: A Zero-shot Registration Pipeline for 3D Consecutive Histopathology Image Reconstruction

Histological analysis plays a crucial role in understanding tissue structure and pathology. While recent advancements in registration methods have improved 2D histological analysis, they often struggle to preserve critical 3D spatial relationships, limiting their utility in both clinical and research applications. Specifically, constructing accurate 3D models from 2D slices remains challenging due to tissue deformation, sectioning artifacts, variability in imaging techniques, and inconsistent illumination. Deep learning-based registration methods have demonstrated improved performance but suffer from limited generalizability and require large-scale training data. In contrast, non-deep-learning approaches offer better generalizability but often compromise on accuracy. In this study, we introduced ZeroReg3D, a novel zero-shot registration pipeline tailored for accurate 3D reconstruction from serial histological sections. By combining zero-shot deep learning-based keypoint matching with optimization-based affine and non-rigid registration techniques, ZeroReg3D effectively addresses critical challenges such as tissue deformation, sectioning artifacts, staining variability, and inconsistent illumination without requiring retraining or fine-tuning. The code has been made publicly available at https://github.com/hrlblab/ZeroReg3D

cs.CV↗

arXiv2025

IRS: Incremental Relationship-guided Segmentation for Digital Pathology

Continual learning is rapidly emerging as a key focus in computer vision, aiming to develop AI systems capable of continuous improvement, thereby enhancing their value and practicality in diverse real-world applications. In healthcare, continual learning holds great promise for continuously acquired digital pathology data, which is collected in hospitals on a daily basis. However, panoramic segmentation on digital whole slide images (WSIs) presents significant challenges, as it is often infeasible to obtain comprehensive annotations for all potential objects, spanning from coarse structures (e.g., regions and unit objects) to fine structures (e.g., cells). This results in temporally and partially annotated data, posing a major challenge in developing a holistic segmentation framework. Moreover, an ideal segmentation model should incorporate new phenotypes, unseen diseases, and diverse populations, making this task even more complex. In this paper, we introduce a novel and unified Incremental Relationship-guided Segmentation (IRS) learning scheme to address temporally acquired, partially annotated data while maintaining out-of-distribution (OOD) continual learning capacity in digital pathology. The key innovation of IRS lies in its ability to realize a new spatial-temporal OOD continual learning paradigm by mathematically modeling anatomical relationships between existing and newly introduced classes through a simple incremental universal proposition matrix. Experimental results demonstrate that the IRS method effectively handles the multi-scale nature of pathological segmentation, enabling precise kidney segmentation across various structures (regions, units, and cells) as well as OOD disease lesions at multiple magnifications. This capability significantly enhances domain generalization, making IRS a robust approach for real-world digital pathology applications.

eess.IV↗

arXiv2025

DeepAndes: A Self-Supervised Vision Foundation Model for Multi-Spectral Remote Sensing Imagery of the Andes

By mapping sites at large scales using remotely sensed data, archaeologists can generate unique insights into long-term demographic trends, inter-regional social networks, and past adaptations to climate change. Remote sensing surveys complement field-based approaches, and their reach can be especially great when combined with deep learning and computer vision techniques. However, conventional supervised deep learning methods face challenges in annotating fine-grained archaeological features at scale. While recent vision foundation models have shown remarkable success in learning large-scale remote sensing data with minimal annotations, most off-the-shelf solutions are designed for RGB images rather than multi-spectral satellite imagery, such as the 8-band data used in our study. In this paper, we introduce DeepAndes, a transformer-based vision foundation model trained on three million multi-spectral satellite images, specifically tailored for Andean archaeology. DeepAndes incorporates a customized DINOv2 self-supervised learning algorithm optimized for 8-band multi-spectral imagery, marking the first foundation model designed explicitly for the Andes region. We evaluate its image understanding performance through imbalanced image classification, image instance retrieval, and pixel-level semantic segmentation tasks. Our experiments show that DeepAndes achieves superior F1 scores, mean average precision, and Dice scores in few-shot learning scenarios, significantly outperforming models trained from scratch or pre-trained on smaller datasets. This underscores the effectiveness of large-scale self-supervised pre-training in archaeological remote sensing. Codes will be available on https://github.com/geopacha/DeepAndes.

cs.CV↗

arXiv2025

MagNet: Multi-Level Attention Graph Network for Predicting High-Resolution Spatial Transcriptomics

The rapid development of spatial transcriptomics (ST) offers new opportunities to explore the gene expression patterns within the spatial microenvironment. Current research integrates pathological images to infer gene expression, addressing the high costs and time-consuming processes to generate spatial transcriptomics data. However, as spatial transcriptomics resolution continues to improve, existing methods remain primarily focused on gene expression prediction at low-resolution spot levels. These methods face significant challenges, especially the information bottleneck, when they are applied to high-resolution HD data. To bridge this gap, this paper introduces MagNet, a multi-level attention graph network designed for accurate prediction of high-resolution HD data. MagNet employs cross-attention layers to integrate features from multi-resolution image patches hierarchically and utilizes a GAT-Transformer module to aggregate neighborhood information. By integrating multilevel features, MagNet overcomes the limitations posed by low-resolution inputs in predicting high-resolution gene expression. We systematically evaluated MagNet and existing ST prediction models on both a private spatial transcriptomics dataset and a public dataset at three different resolution levels. The results demonstrate that MagNet achieves state-of-the-art performance at both spot level and high-resolution bin levels, providing a novel methodology and benchmark for future research and applications in high-resolution HD-level spatial transcriptomics. Code is available at https://github.com/Junchao-Zhu/MagNet.

cs.CV↗

arXiv2025

KPIs 2024 Challenge: Advancing Glomerular Segmentation from Patch- to Slide-Level

Chronic kidney disease (CKD) is a major global health issue, affecting over 10% of the population and causing significant mortality. While kidney biopsy remains the gold standard for CKD diagnosis and treatment, the lack of comprehensive benchmarks for kidney pathology segmentation hinders progress in the field. To address this, we organized the Kidney Pathology Image Segmentation (KPIs) Challenge, introducing a dataset that incorporates preclinical rodent models of CKD with over 10,000 annotated glomeruli from 60+ Periodic Acid Schiff (PAS)-stained whole slide images. The challenge includes two tasks, patch-level segmentation and whole slide image segmentation and detection, evaluated using the Dice Similarity Coefficient (DSC) and F1-score. By encouraging innovative segmentation methods that adapt to diverse CKD models and tissue conditions, the KPIs Challenge aims to advance kidney pathology analysis, establish new benchmarks, and enable precise, large-scale quantification for disease research and diagnosis.

cs.CV↗

arXiv2024

ASIGN: An Anatomy-aware Spatial Imputation Graphic Network for 3D Spatial Transcriptomics

Spatial transcriptomics (ST) is an emerging technology that enables medical computer vision scientists to automatically interpret the molecular profiles underlying morphological features. Currently, however, most deep learning-based ST analyses are limited to two-dimensional (2D) sections, which can introduce diagnostic errors due to the heterogeneity of pathological tissues across 3D sections. Expanding ST to three-dimensional (3D) volumes is challenging due to the prohibitive costs; a 2D ST acquisition already costs over 50 times more than whole slide imaging (WSI), and a full 3D volume with 10 sections can be an order of magnitude more expensive. To reduce costs, scientists have attempted to predict ST data directly from WSI without performing actual ST acquisition. However, these methods typically yield unsatisfying results. To address this, we introduce a novel problem setting: 3D ST imputation using 3D WSI histology sections combined with a single 2D ST slide. To do so, we present the Anatomy-aware Spatial Imputation Graph Network (ASIGN) for more precise, yet affordable, 3D ST modeling. The ASIGN architecture extends existing 2D spatial relationships into 3D by leveraging cross-layer overlap and similarity-based expansion. Moreover, a multi-level spatial attention graph network integrates features comprehensively across different data sources. We evaluated ASIGN on three public spatial transcriptomics datasets, with experimental results demonstrating that ASIGN achieves state-of-the-art performance on both 2D and 3D scenarios. Code is available at https://github.com/hrlblab/ASIGN.

cs.CV↗

arXiv2024

GloFinder: AI-empowered QuPath Plugin for WSI-level Glomerular Detection, Visualization, and Curation

Artificial intelligence (AI) has demonstrated significant success in automating the detection of glomeruli, the key functional units of the kidney, from whole slide images (WSIs) in kidney pathology. However, existing open-source tools are often distributed as source code or Docker containers, requiring advanced programming skills that hinder accessibility for non-programmers, such as clinicians. Additionally, current models are typically trained on a single dataset and lack flexibility in adjusting confidence levels for predictions. To overcome these challenges, we introduce GloFinder, a QuPath plugin designed for single-click automated glomeruli detection across entire WSIs with online editing through the graphical user interface (GUI). GloFinder employs CircleNet, an anchor-free detection framework utilizing circle representations for precise object localization, with models trained on approximately 160,000 manually annotated glomeruli. To further enhance accuracy, the plugin incorporates Weighted Circle Fusion (WCF), an ensemble method that combines confidence scores from multiple CircleNet models to produce refined predictions, achieving superior performance in glomerular detection. GloFinder enables direct visualization and editing of results in QuPath, facilitating seamless interaction for clinicians and providing a powerful tool for nephropathology research and clinical practice. Code and the QuPath plugin are available at https://github.com/hrlblab/GloFinder

cs.CV↗

arXiv2024

Evaluating Cell AI Foundation Models in Kidney Pathology with Human-in-the-Loop Enrichment

Training AI foundation models has emerged as a promising large-scale learning approach for addressing real-world healthcare challenges, including digital pathology. While many of these models have been developed for tasks like disease diagnosis and tissue quantification using extensive and diverse training datasets, their readiness for deployment on some arguably simplest tasks, such as nuclei segmentation within a single organ (e.g., the kidney), remains uncertain. This paper seeks to answer this key question, "How good are we?", by thoroughly evaluating the performance of recent cell foundation models on a curated multi-center, multi-disease, and multi-species external testing dataset. Additionally, we tackle a more challenging question, "How can we improve?", by developing and assessing human-in-the-loop data enrichment strategies aimed at enhancing model performance while minimizing the reliance on pixel-level human annotation. To address the first question, we curated a multicenter, multidisease, and multispecies dataset consisting of 2,542 kidney whole slide images (WSIs). Three state-of-the-art (SOTA) cell foundation models-Cellpose, StarDist, and CellViT-were selected for evaluation. To tackle the second question, we explored data enrichment algorithms by distilling predictions from the different foundation models with a human-in-the-loop framework, aiming to further enhance foundation model performance with minimal human efforts. Our experimental results showed that all three foundation models improved over their baselines with model fine-tuning with enriched data. Interestingly, the baseline model with the highest F1 score does not yield the best segmentation outcomes after fine-tuning. This study establishes a benchmark for the development and deployment of cell vision foundation models tailored for real-world data applications.

cs.CV↗

arXiv2024

Assessment of Cell Nuclei AI Foundation Models in Kidney Pathology

Cell nuclei instance segmentation is a crucial task in digital kidney pathology. Traditional automatic segmentation methods often lack generalizability when applied to unseen datasets. Recently, the success of foundation models (FMs) has provided a more generalizable solution, potentially enabling the segmentation of any cell type. In this study, we perform a large-scale evaluation of three widely used state-of-the-art (SOTA) cell nuclei foundation models (Cellpose, StarDist, and CellViT). Specifically, we created a highly diverse evaluation dataset consisting of 2,542 kidney whole slide images (WSIs) collected from both human and rodent sources, encompassing various tissue types, sizes, and staining methods. To our knowledge, this is the largest-scale evaluation of its kind to date. Our quantitative analysis of the prediction distribution reveals a persistent performance gap in kidney pathology. Among the evaluated models, CellViT demonstrated superior performance in segmenting nuclei in kidney pathology. However, none of the foundation models are perfect; a performance gap remains in general nuclei segmentation for kidney pathology.

eess.IV↗

arXiv2024

Vision Foundation Models in Remote Sensing: A Survey

Artificial Intelligence (AI) technologies have profoundly transformed the field of remote sensing, revolutionizing data collection, processing, and analysis. Traditionally reliant on manual interpretation and task-specific models, remote sensing research has been significantly enhanced by the advent of foundation models-large-scale, pre-trained AI models capable of performing a wide array of tasks with unprecedented accuracy and efficiency. This paper provides a comprehensive survey of foundation models in the remote sensing domain. We categorize these models based on their architectures, pre-training datasets, and methodologies. Through detailed performance comparisons, we highlight emerging trends and the significant advancements achieved by those foundation models. Additionally, we discuss technical challenges, practical implications, and future research directions, addressing the need for high-quality data, computational resources, and improved model generalization. Our research also finds that pre-training methods, particularly self-supervised learning techniques like contrastive learning and masked autoencoders, remarkably enhance the performance and robustness of foundation models. This survey aims to serve as a resource for researchers and practitioners by providing a panorama of advances and promising pathways for continued development and application of foundation models in remote sensing.

cs.CV↗