Abstract:Visual Language Models (VLMs) have gained significant popularity due to their remarkable ability. While various methods exist to enhance privacy in text-based applications, privacy risks associated with visual inputs remain largely overlooked such as Protected Health Information (PHI) in medical images. To tackle this problem, two key tasks: accurately localizing sensitive text and processing it to ensure privacy protection should be performed. To address this issue, we introduce VisShield (Vision Privacy Shield), an end-to-end framework designed to enhance the privacy awareness of VLMs. Our framework consists of two key components: a specialized instruction-tuning dataset OPTIC (Optical Privacy Text Instruction Collection) and a tailored training methodology. The dataset provides diverse privacy-oriented prompts that guide VLMs to perform targeted Optical Character Recognition (OCR) for precise localization of sensitive text, while the training strategy ensures effective adaptation of VLMs to privacy-preserving tasks. Specifically, our approach ensures that VLMs recognize privacy-sensitive text and output precise bounding boxes for detected entities, allowing for effective masking of sensitive information. Extensive experiments demonstrate that our framework significantly outperforms existing approaches in handling private information, paving the way for privacy-preserving applications in vision-language models. Our dataset and code can be found here.
Abstract:Privacy risks in text-only Large Language Models (LLMs) are well studied, particularly their tendency to memorize and leak sensitive information. However, Multi-modal Large Language Models (MLLMs), which process both text and images, introduce unique privacy challenges that remain underexplored. Compared to text-only models, MLLMs can extract and expose sensitive information embedded in images, posing new privacy risks. We reveal that some MLLMs are susceptible to privacy breaches, leaking sensitive data embedded in images or stored in memory. Specifically, in this paper, we (1) introduce MM-Privacy, a comprehensive dataset designed to assess privacy risks across various multi-modal tasks and scenarios, where we define Disclosure Risks and Retention Risks. (2) systematically evaluate different MLLMs using MM-Privacy and demonstrate how models leak sensitive data across various tasks, and (3) provide additional insights into the role of task inconsistency in privacy risks, emphasizing the urgent need for mitigation strategies. Our findings highlight privacy concerns in MLLMs, underscoring the necessity of safeguards to prevent data exposure. Our dataset and code can be found here.
Abstract:In healthcare, multimodal time series tasks often operate on incomplete observations in practice, for example when ECG segments are lost because electrodes detach or an entire respiratory channel is unavailable during overnight monitoring. Such missingness typically appears in two structurally distinct patterns: within-modality missing, where values are absent within an otherwise observed modality, and modality-level missing, where an entire modality is unavailable. Existing methods typically represent unobserved data implicitly through masks or missing embeddings, without learning instance-specific missing information, and most are designed for only one missingness pattern. A natural approach is to explicitly estimate the missing data; however, existing imputation methods treat missingness uniformly despite their different structural priors, and the imputation process is often isolated from downstream tasks, preventing downstream tasks from guiding imputation toward more informative representations. To address these limitations, we present PAMF, a multimodal time-series framework that explicitly handles different missingness patterns while coupling imputation with downstream prediction through prior-aware flow matching and weight sharing. Specifically, the method initializes the flow-matching source state with type-specific priors to distinguish two missing types. It further connects imputation and classification through architecturally matched encoders with weight sharing, transferring task-relevant representations into the imputation process. Experiments on multiple multimodal healthcare time-series benchmarks show that the proposed method achieves the strongest overall downstream performance across diverse datasets and missing settings compared with existing baselines.
Abstract:Time series foundation models (TS-FMs) aim to learn generalizable temporal representations that can be adapted to a wide range of downstream tasks. In real-world multimodal settings, time series are frequently affected by temporal misalignment and partial modality missingness, where different modalities are observed at heterogeneous time scales or are partially absent. Existing approaches typically rely on naive imputation or masking strategies, which fail to account for cross-modal dependencies and often lead to misaligned or degraded representations. We propose TRACE, a conditional estimation paradigm for multimodal time series foundation model pipelines under missingness and irregular sampling, allowing incomplete target modalities to be systematically inferred from available auxiliary modalities. We evaluate TRACE on diverse multimodal benchmarks spanning healthcare and affective computing, including the MIMIC-IV clinical dataset and the CMU-MOSI and CMU-MOSEI benchmarks for multimodal sentiment analysis. Across a range of downstream prediction tasks and missing-modality settings, TRACE consistently outperforms prior multimodal fusion approaches, demonstrating improved robustness to severe modality missingness and more reliable cross-modal representations.
Abstract:LLMs are vulnerable to prompt injection attacks. However, this vulnerability has been primarily demonstrated conceptually in academic studies or through a few anecdotal case studies. Its prevalence and impact in real-world LLM-based applications are largely unexplored. In this work, we present the first systematic study of prompt-injection attacks in a widely used application: LLM-based resume screening. Our analysis is based on approximately 200K real-world resumes collected over multiple years by hireEZ. We first design tailored methods to detect prompt injection in resumes. Manual validation on a small-scale dataset demonstrates that our detectors achieve high precision and outperform state-of-the-art general-purpose detectors. We then apply our detector to the full resume dataset and conduct a comprehensive measurement study of real-world prompt injection attacks. Our analysis reveals several intriguing findings: approximately 1% of resumes contain hidden prompt injections; the prevalence of such injected resumes has increased noticeably over the past one to two years; and more than 90% of injected prompts do not use explicit instructions. These results provide the first evidence of large-scale prompt injection in real-world LLM-based applications and lay the groundwork for future studies to understand and mitigate such attacks.
Abstract:Predicting how a cell will change its transcriptional state under a developmental signal or a genetic perturbation is the computational core of in-silico biology and the AI Virtual Cell program. Existing approaches either fit static control-to-treated maps that discard time, or solve multi-step ODE / Schrödinger-bridge problems on each dataset independently. We introduce Chreode, a one-step cell world model that predicts action-conditioned cell-state transitions through a structured residual transition operator. It shifts distributional evolution from inference time to training time, enabling single-pass generation while preserving a Waddington-inspired decomposition into downhill landscape flow, rotational in-tangent dynamics, and stochastic spread. The model is pretrained with a shared scVI encoder and a DiT-based dynamics backbone on a 2.4M-cell mouse embryonic atlas spanning 7 datasets. As a fine-tuning initialization, Chreode improves per-target Sinkhorn distance on Weinreb hematopoiesis and Veres islet differentiation over matched scratch models, PI-SDE, and PRESCIENT. As a transferable gene-state embedding for GEARS, the pretrained dynamics representation reduces shared-vocabulary DE20 mean squared error on Norman Perturb-seq from 0.2121 to 0.1858, a 12.4% relative improvement, without changing the GEARS training procedure. We interpret this transfer to perturbation prediction as evidence that pretrained developmental-trajectory dynamics encode differentiation primitives transferable to CRISPR-induced state shifts, since both involve cell-state transitions in a shared latent geometry. The pretrained backbone additionally produces zero-shot clonal fate scores on Weinreb that are competitive with strong dynamic-OT baselines.
Abstract:Healthcare models are transitioning from unimodal prediction toward multimodal reasoning over heterogeneous diagnostic inputs. In computational pathology, for complex tumor subtypes where morphology alone can be challenging to distinguish, pathology reports and molecular measurements may provide additional diagnostic evidence alongside whole-slide images, yet existing models often fail to clarify how diverse signals assemble into recognizable diagnostic concepts. We propose ConceptM$^3$oE (Concept Multimodal MoE), which embeds concept formation directly within interaction-aware mixture-of-experts (MoE) pathways. The architecture decomposes evidence into modality-specific, redundant, and synergistic experts, which are then projected into structured concept bottlenecks mapping latent features to a hierarchy of morphology and biomarker concepts. To prevent the information loss typical of interpretable bottlenecks, we utilize residual pathways within each expert to allow task-relevant signals to flow both through the concepts and directly to the final task prediction, so that high performance is maintained alongside interpretability. Across an institutional pediatric brain tumor cohort and a public glioma cohort, the framework delivers competitive performance to unconstrained models while producing reasoning traces validated by an independent neuropathologist. In data-limited regimes, ConceptM$^3$oE improves limited-data performance, increasing macro-F1 from 56.41% to 66.70% at small training sizes compared to non-concept-informed baselines, while also showing faster training convergence consistent with the regularizing effect of concept learning. This work offers a scalable path toward high-performance medical AI that is inherently verifiable and better aligned with the complex decision-making of clinical practice.
Abstract:Chain-of-thought (CoT) reasoning improves the problem-solving ability of large language models (LLMs), but generated reasoning traces may not faithfully reflect the model's actual decision process. Existing CoT unfaithfulness detectors mainly rely on external signals from generated rationales, such as textual plausibility or answer consistency, while overlooking evidence from the model's internal computation. Although recent circuit tracing methods provide a way to obtain model-internal evidence by tracing how information flows through model components during reasoning, constructing full reasoning circuits for long CoTs is costly and difficult to scale. To address these challenges, we propose Circuit-guided Internal-External Discrepancy Scorer (CIE-Scorer), a framework for instance-level CoT unfaithfulness detection. The key idea is that faithful reasoning traces should align with the model's computational process, whereas unfaithful traces may diverge from it. CIE-Scorer efficiently traces compact sentence-level circuits from informative reasoning tokens, constructs internal and external reasoning graphs, and measures their discrepancy using Fused Gromov--Wasserstein distance. Experiments on four datasets from FaithCoT-Bench show that CIE-Scorer achieves state-of-the-art performance while reducing the cost of circuit construction, demonstrating the effectiveness of combining mechanistic interpretability signals with external reasoning traces for CoT unfaithfulness detection.
Abstract:Mixture-of-Experts Large Language Models (MoE-LLMs) achieve strong performance but incur substantial memory overhead due to massive expert parameters. Mixed-precision quantization mitigates this cost by allocating expert-wise bit-widths based on their importance, approaching the accuracy-memory Pareto frontier and enabling extreme low-bit quantization. However, existing methods rely on layer-wise importance estimation and overlook router shifts induced by quantization, resulting in suboptimal allocation and routing. In this work, we propose Global Expert-level Mixed-precision Quantization (GEMQ) to overcome these limitations via (1) a global linear-programming formulation that captures model-wide expert importance based on quantization error analysis, and (2) efficient router fine-tuning to adapt routing to quantized experts. These components are integrated into a progressive quantization framework that iteratively refines importance estimation and allocation. Experiments demonstrate that GEMQ significantly reduces memory and accelerates inference with minimal accuracy degradation. Source code is available at https://github.com/jndeng/GEMQ .
Abstract:Accurate diagnosis of pediatric brain tumors, starting with histopathology, presents unique challenges for deep learning, including severe data scarcity, class imbalance, and fine-grained morphologic overlap across diagnostically distinct subtypes. While pathology foundation models have advanced patch-level representation learning, their effective adaptation to weakly supervised pediatric brain tumor classification under limited data remains underexplored. In this work, we introduce an expert-guided contrastive fine-tuning framework for pediatric brain tumor diagnosis from whole-slide images (WSI). Our approach integrates contrastive learning into slide-level multiple instance learning (MIL) to explicitly regularize the geometry of slide-level representations during downstream fine-tuning. We propose both a general supervised contrastive setting and an expert-guided variant that incorporates clinically informed hard negatives targeting diagnostically confusable subtypes. Through comprehensive experiments on pediatric brain tumor WSI classification under realistic low-sample and class-imbalanced conditions, we demonstrate that contrastive fine-tuning yields measurable improvements in fine-grained diagnostic distinctions. Our experimental analyses reveal complementary strengths across different contrastive strategies, with expert-guided hard negatives promoting more compact intra-class representations and improved inter-class separation. This work highlights the importance of explicitly shaping slide-level representations for robust fine-grained classification in data-scarce pediatric pathology settings.