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Nov 3

Vision Matters: Simple Visual Perturbations Can Boost Multimodal Math Reasoning

Despite the rapid progress of multimodal large language models (MLLMs), they have largely overlooked the importance of visual processing. In a simple yet revealing experiment, we interestingly find that language-only models, when provided with image captions, can achieve comparable or even better performance than MLLMs that consume raw visual inputs. This suggests that current MLLMs may generate accurate visual descriptions but fail to effectively integrate them during reasoning. Motivated by this, we propose a simple visual perturbation framework that enhances perceptual robustness without requiring algorithmic modifications or additional training data. Our approach introduces three targeted perturbations: distractor concatenation, dominance-preserving mixup, and random rotation, that can be easily integrated into existing post-training pipelines including SFT, DPO, and GRPO. Through extensive experiments across multiple datasets, we demonstrate consistent improvements in mathematical reasoning performance, with gains comparable to those achieved through algorithmic changes. Additionally, we achieve competitive performance among open-source 7B RL-tuned models by training Qwen2.5-VL-7B with visual perturbation. Through comprehensive ablation studies, we analyze the effectiveness of different perturbation strategies, revealing that each perturbation type contributes uniquely to different aspects of visual reasoning. Our findings highlight the critical role of visual perturbation in multimodal mathematical reasoning: better reasoning begins with better seeing. Our code is available at https://github.com/YutingLi0606/Vision-Matters.

  • 7 authors
·
Jun 11, 2025 2

LoRA-GGPO: Mitigating Double Descent in LoRA Fine-Tuning via Gradient-Guided Perturbation Optimization

Large Language Models (LLMs) have achieved remarkable success in natural language processing, but their full fine-tuning remains resource-intensive. Parameter-Efficient Fine-Tuning (PEFT) methods, such as Low-Rank Adaptation (LoRA), have emerged as a practical solution by approximating parameter updates with low-rank matrices. However, LoRA often exhibits a "double descent" phenomenon during fine-tuning, where model performance degrades due to overfitting and limited expressiveness caused by low-rank constraints. To address this issue, we propose LoRA-GGPO (Gradient-Guided Perturbation Optimization), a novel method that leverages gradient and weight norms to generate targeted perturbations. By optimizing the sharpness of the loss landscape, LoRA-GGPO guides the model toward flatter minima, mitigating the double descent problem and improving generalization. Extensive experiments on natural language understanding (NLU) and generation (NLG) tasks demonstrate that LoRA-GGPO outperforms LoRA and its state-of-the-art variants. Furthermore, extended experiments specifically designed to analyze the double descent phenomenon confirm that LoRA-GGPO effectively alleviates this issue, producing more robust and generalizable models. Our work provides a robust and efficient solution for fine-tuning LLMs, with broad applicability in real-world scenarios. The code is available at https://github.com/llm172/LoRA-GGPO.

  • 4 authors
·
Feb 20, 2025

Finding Blind Spots in Evaluator LLMs with Interpretable Checklists

Large Language Models (LLMs) are increasingly relied upon to evaluate text outputs of other LLMs, thereby influencing leaderboards and development decisions. However, concerns persist over the accuracy of these assessments and the potential for misleading conclusions. In this work, we investigate the effectiveness of LLMs as evaluators for text generation tasks. We propose FBI, a novel framework designed to examine the proficiency of Evaluator LLMs in assessing four critical abilities in other LLMs: factual accuracy, instruction following, coherence in long-form writing, and reasoning proficiency. By introducing targeted perturbations in answers generated by LLMs, that clearly impact one of these key capabilities, we test whether an Evaluator LLM can detect these quality drops. By creating a total of 2400 perturbed answers covering 22 perturbation categories, we conduct a comprehensive study using different evaluation strategies on five prominent LLMs commonly used as evaluators in the literature. Our findings reveal significant shortcomings in current Evaluator LLMs, which failed to identify quality drops in over 50\% of cases on average. Single-answer and pairwise evaluations demonstrated notable limitations, whereas reference-based evaluations showed comparatively better performance. These results underscore the unreliable nature of current Evaluator LLMs and advocate for cautious implementation in practical applications. Code and data are available at https://github.com/AI4Bharat/FBI.

  • 4 authors
·
Jun 19, 2024

Seeing Isn't Believing: Uncovering Blind Spots in Evaluator Vision-Language Models

Large Vision-Language Models (VLMs) are increasingly used to evaluate outputs of other models, for image-to-text (I2T) tasks such as visual question answering, and text-to-image (T2I) generation tasks. Despite this growing reliance, the reliability of these Evaluator VLMs remains under explored. In this work, we systematically evaluate the reliability of Evaluator VLMs across both I2T and T2I tasks. We introduce targeted perturbations that degrade output quality along key error dimensions, including object hallucinations, spatial reasoning, factual grounding, and visual fidelity. These perturbations test whether Evaluator VLMs can reliably account for these quality degrading errors in their evaluations. Using a comprehensive benchmark of over 4000 perturbed instances spanning 40 perturbation dimensions, we evaluate 4 prominent VLMs using single-answer scoring, pairwise comparison, and reference-guided paradigms. Our findings reveal that current VLM evaluators exhibit substantial blind spots: they often fail to detect perturbed outputs - in some cases exceeding 50%, struggle particularly with fine-grained compositional and spatial errors, and are often insensitive to hallucinated content that contradicts the input image. Pairwise comparison proves more reliable, though failure rates persist. These results highlight the unreliable nature of current Evaluator VLMs and urge caution in their deployment for benchmarking and development decisions. Code and data have been made publicly available.

ai4bharat AI4Bharat
·
Apr 22 2

DeContext as Defense: Safe Image Editing in Diffusion Transformers

In-context diffusion models allow users to modify images with remarkable ease and realism. However, the same power raises serious privacy concerns: personal images can be easily manipulated for identity impersonation, misinformation, or other malicious uses, all without the owner's consent. While prior work has explored input perturbations to protect against misuse in personalized text-to-image generation, the robustness of modern, large-scale in-context DiT-based models remains largely unexamined. In this paper, we propose DeContext, a new method to safeguard input images from unauthorized in-context editing. Our key insight is that contextual information from the source image propagates to the output primarily through multimodal attention layers. By injecting small, targeted perturbations that weaken these cross-attention pathways, DeContext breaks this flow, effectively decouples the link between input and output. This simple defense is both efficient and robust. We further show that early denoising steps and specific transformer blocks dominate context propagation, which allows us to concentrate perturbations where they matter most. Experiments on Flux Kontext and Step1X-Edit show that DeContext consistently blocks unwanted image edits while preserving visual quality. These results highlight the effectiveness of attention-based perturbations as a powerful defense against image manipulation.

Weather Jiu-Jitsu: Exploring the Feasibility of Control Paradigms in Weather Foundation Models

Weather Jiu-Jitsu is a control paradigm for extreme climatological events, inspired by chaos theory. As a proposition, small, precise, targeted, and cost-inexpensive perturbations can redirect trajectories of a large dynamical system. This strategy has been demonstrated analytically in the Lorenz-63 system, where a naturally chaotic trajectory switching between two attractors can be confined to a single attractor, indefinitely, via arbitrarily small perturbations. This paper examines the feasibility of Microsoft's Aurora -- a 1.3 billion parameter global atmospheric model -- as a test bed for this strategy. This paper explores three questions: (1) Is Aurora a reliable enough simulation environment to serve as a meaningful testbed? (2) Are the perturbations required to redirect its trajectories small enough to be physically plausible? (3) Does Aurora's learned latent space (the parametric estimators on climatological attributes) yield any apparent, structured, and/or perhaps interpretable features that can convey a geo/atmospheric response to initial conditions? We find evidence consistent with all three: Aurora's modeled trajectories respond to perturbations beyond measurement drift, the perturbation magnitudes required are small relative to the model's own forecast uncertainty, and its latent representations exhibit directional structure that responds to Jiu-Jitsu-type interventions, even though that structure does not separate extreme from normal states outright. These results should be read as feasibility diagnostics rather than a demonstration of control: we do not implement or test an actual steering intervention on Aurora, and several of our findings, particularly around the model's latent-space geometry, are exploratory.

  • 3 authors
·
Sep 29

INTACT: Inducing Noise Tolerance through Adversarial Curriculum Training for LiDAR-based Safety-Critical Perception and Autonomy

In this work, we present INTACT, a novel two-phase framework designed to enhance the robustness of deep neural networks (DNNs) against noisy LiDAR data in safety-critical perception tasks. INTACT combines meta-learning with adversarial curriculum training (ACT) to systematically address challenges posed by data corruption and sparsity in 3D point clouds. The meta-learning phase equips a teacher network with task-agnostic priors, enabling it to generate robust saliency maps that identify critical data regions. The ACT phase leverages these saliency maps to progressively expose a student network to increasingly complex noise patterns, ensuring targeted perturbation and improved noise resilience. INTACT's effectiveness is demonstrated through comprehensive evaluations on object detection, tracking, and classification benchmarks using diverse datasets, including KITTI, Argoverse, and ModelNet40. Results indicate that INTACT improves model robustness by up to 20% across all tasks, outperforming standard adversarial and curriculum training methods. This framework not only addresses the limitations of conventional training strategies but also offers a scalable and efficient solution for real-world deployment in resource-constrained safety-critical systems. INTACT's principled integration of meta-learning and adversarial training establishes a new paradigm for noise-tolerant 3D perception in safety-critical applications. INTACT improved KITTI Multiple Object Tracking Accuracy (MOTA) by 9.6% (64.1% -> 75.1%) and by 12.4% under Gaussian noise (52.5% -> 73.7%). Similarly, KITTI mean Average Precision (mAP) rose from 59.8% to 69.8% (50% point drop) and 49.3% to 70.9% (Gaussian noise), highlighting the framework's ability to enhance deep learning model resilience in safety-critical object tracking scenarios.

  • 4 authors
·
Feb 3, 2025

FineTec: Fine-Grained Action Recognition Under Temporal Corruption via Skeleton Decomposition and Sequence Completion

Recognizing fine-grained actions from temporally corrupted skeleton sequences remains a significant challenge, particularly in real-world scenarios where online pose estimation often yields substantial missing data. Existing methods often struggle to accurately recover temporal dynamics and fine-grained spatial structures, resulting in the loss of subtle motion cues crucial for distinguishing similar actions. To address this, we propose FineTec, a unified framework for Fine-grained action recognition under Temporal Corruption. FineTec first restores a base skeleton sequence from corrupted input using context-aware completion with diverse temporal masking. Next, a skeleton-based spatial decomposition module partitions the skeleton into five semantic regions, further divides them into dynamic and static subgroups based on motion variance, and generates two augmented skeleton sequences via targeted perturbation. These, along with the base sequence, are then processed by a physics-driven estimation module, which utilizes Lagrangian dynamics to estimate joint accelerations. Finally, both the fused skeleton position sequence and the fused acceleration sequence are jointly fed into a GCN-based action recognition head. Extensive experiments on both coarse-grained (NTU-60, NTU-120) and fine-grained (Gym99, Gym288) benchmarks show that FineTec significantly outperforms previous methods under various levels of temporal corruption. Specifically, FineTec achieves top-1 accuracies of 89.1% and 78.1% on the challenging Gym99-severe and Gym288-severe settings, respectively, demonstrating its robustness and generalizability. Code and datasets could be found at https://smartdianlab.github.io/projects-FineTec/.

  • 3 authors
·
Dec 31, 2025

One Surrogate to Fool Them All: Universal, Transferable, and Targeted Adversarial Attacks with CLIP

Deep Neural Networks (DNNs) have achieved widespread success yet remain prone to adversarial attacks. Typically, such attacks either involve frequent queries to the target model or rely on surrogate models closely mirroring the target model -- often trained with subsets of the target model's training data -- to achieve high attack success rates through transferability. However, in realistic scenarios where training data is inaccessible and excessive queries can raise alarms, crafting adversarial examples becomes more challenging. In this paper, we present UnivIntruder, a novel attack framework that relies solely on a single, publicly available CLIP model and publicly available datasets. By using textual concepts, UnivIntruder generates universal, transferable, and targeted adversarial perturbations that mislead DNNs into misclassifying inputs into adversary-specified classes defined by textual concepts. Our extensive experiments show that our approach achieves an Attack Success Rate (ASR) of up to 85% on ImageNet and over 99% on CIFAR-10, significantly outperforming existing transfer-based methods. Additionally, we reveal real-world vulnerabilities, showing that even without querying target models, UnivIntruder compromises image search engines like Google and Baidu with ASR rates up to 84%, and vision language models like GPT-4 and Claude-3.5 with ASR rates up to 80%. These findings underscore the practicality of our attack in scenarios where traditional avenues are blocked, highlighting the need to reevaluate security paradigms in AI applications.

  • 4 authors
·
May 26, 2025

Corrupted but Correct: Why Vision-Language Models Lie to Themselves Internally

A targeted adversarial perturbation can drive a vision-language model's (VLM's) teacher-forced training loss for a fixed target caption to near zero, yet the same model, allowed to generate freely, produces the original, correct description with no trace of the target. We call this dissociation the train/inference gap, and give it a precise mechanistic account on Qwen2.5-VL-7B-Instruct using a controlled two-stage PGD attack on 200 held-out COCO images. First, we show that image-level pixel statistics, including a correctly re-implemented, texture-based attackability measure from the CNN robustness literature, have essentially no predictive power over which images are corrupted (best predictor r=-0.050, p=0.484; ridge regression R^2=0.069). Second, using the logit lens, we localise the gap to a single autoregressive step: the rank of the target token, conditioned on the correct first token already being generated, is fixed at exactly 3,488 out of 152,064 vocabulary entries for every image and every condition, with zero variance. Third, tracking target-token rank across all 28 LLM decoder layers reveals that the visual encoder corrupts every image's representation by a comparable margin regardless of eventual outcome, but the language model decoder then differentially arbitrates: amplifying the corrupted signal for susceptible images and actively suppressing it, past its clean-image baseline, for resistant ones (p<0.001, rank-biserial r=0.579). A linear probe on the merger hidden state separates these two outcomes with AUC=0.858, though we flag a circularity concern in this estimate. Together these results argue that adversarial robustness in autoregressive VLMs is substantially a property of the language decoder's prior, not the visual encoder, with direct implications for where faithfulness evaluations and defenses for deployed VLM systems should be targeted.

  • 3 authors
·
Oct 1

PerturBot: Breaking Shortcut Priors in Vision-Language-Action Models with Perturbative Training

A vision--language--action (VLA) policy can complete complex tasks while ignoring the evidence that should determine its actions. An object held near the wrist camera can displace the instructed target. Language and action show the same pattern: a familiar noun can trigger the operation it was paired with in training even after the verb changes, and a gripper that closed on nothing may lift anyway. We call these dependencies modality shortcuts: regularities in successful demonstrations make visual, lexical, or motor cues sufficient to predict expert actions without the task evidence needed for the underlying decision. More demonstrations of the same kind can raise task success while leaving these shortcuts intact. We propose Perturbot which makes task-relevant evidence easier to use and shortcuts insufficient on their own: it applies task-preserving wrist-view perturbations, enriches instructions with decision-relevant captions, and adds random and failed trajectory segments relabeled with the behavior they contain. It complements scaling by changing what is scaled, and leaves inference unchanged. Moreover, we propose GroundingFscore, an offline score that diagnoses how severely a policy relies on modality shortcuts. Task success rate shows whether a policy improves, while GroundingFscore reveals whether the policy scales healthily, relying on task evidence rather than shortcuts. Together, Perturbot and GroundingFscore provide a training-and-evaluation framework for disentangling VLA decisions from shortcut priors while preserving responsiveness to task-relevant evidence.

  • 7 authors
·
Oct 2 2

ICA Lens: Interpreting Language Models Without Training Another Dictionary

Finding interpretable directions in language-model representations is critical for understanding and controlling model behavior. Sparse autoencoders (SAEs) have become the standard tool for this purpose, but using them as the default first lens often requires training, storing, and evaluating large overcomplete dictionaries. This bottleneck limits rapid exploration and raises a fundamental question: how much interpretable structure is already visible from activation geometry before training another neural dictionary? Our intuition is simple: many interpretable directions are selective on tokens, and these directions should look less Gaussian than random directions. We therefore revisit independent component analysis (ICA), a classical method for finding non-Gaussian directions, as a compact lens for language-model interpretability. We find that ICA has been underestimated for LLM interpretability, because prior uses often relied on off-the-shelf ICA implementations that are brittle on LLM activations and lacked systematic tools for inspecting and evaluating the recovered directions. To bridge these gaps, we introduce ICALens, the first practical workflow for stable, efficient, and auditable ICA analysis of LLM representations. It combines an optimized GPU-parallel FastICA pipeline with LLM-specific stability recipes and better fitting diagnostics, enabling efficient and reliable layer-wise analysis. Across GPT-2 Small, Gemma 2 2B, and Qwen 3.5 2B Base, ICALens efficiently recovers compact, human-interpretable directions without per-layer gradient-based dictionary training. On SAEBench, ICA is competitive with public SAEs in sparse probing and outperforms them in targeted probe perturbation under small-to-medium budgets. These results suggest that ICA should not be viewed as a weak baseline, but as an efficient and complementary first lens for exploring language-model representations.

ClasSAE: Class-Aligned Sparse Autoencoders via Differentiable Feature-Class Affinity

Sparse Autoencoders (SAEs) began as an unsupervised tool for decomposing neural representations into sparse, interpretable features, and are increasingly used not only for passive analysis but also for active interventions such as unlearning, bias mitigation, and concept editing. A central challenge for these editing and steering methods is reliably matching features to target concepts; most current approaches address this by computing post-hoc scores over an already-trained, frozen dictionary. We instead introduce ClasSAE, a novel method that both automatically assigns classes to features and guides the encoder toward class-separable representations during training. Specifically, we apply a differentiable top-k operator to a trainable feature--class affinity matrix with per-feature budgets, coupling the features selected for each sample to the classes they are trained to represent. Because gradients flow through the selection of active features rather than only through their magnitudes, the encoder and the affinity matrix co-adapt rather than being fit in separate stages. The result is a dictionary that is both class-separable and class-annotated, with no need for post-hoc probing. We propose three variants for enforcing sparsity within this framework, which achieve comparable overall performance with slightly different trade-offs. Using CLIP ViT-L/14 embeddings on ImageNet, we show that the learned affinity matrix agrees closely with an independently estimated post-hoc feature-class matrix computed on held-out data. The model also supports direct class prediction from the encoder and affinity matrix alone, without a separately fitted classifier, and its more class-aligned encoder yields improved separation in Targeted Probe Perturbation evaluations. https://github.com/St0pien/ClasSAE.

  • 4 authors
·
Oct 1

A Novel Bifurcation Method for Observation Perturbation Attacks on Reinforcement Learning Agents: Load Altering Attacks on a Cyber Physical Power System

Components of cyber physical systems, which affect real-world processes, are often exposed to the internet. Replacing conventional control methods with Deep Reinforcement Learning (DRL) in energy systems is an active area of research, as these systems become increasingly complex with the advent of renewable energy sources and the desire to improve their efficiency. Artificial Neural Networks (ANN) are vulnerable to specific perturbations of their inputs or features, called adversarial examples. These perturbations are difficult to detect when properly regularized, but have significant effects on the ANN's output. Because DRL uses ANN to map optimal actions to observations, they are similarly vulnerable to adversarial examples. This work proposes a novel attack technique for continuous control using Group Difference Logits loss with a bifurcation layer. By combining aspects of targeted and untargeted attacks, the attack significantly increases the impact compared to an untargeted attack, with drastically smaller distortions than an optimally targeted attack. We demonstrate the impacts of powerful gradient-based attacks in a realistic smart energy environment, show how the impacts change with different DRL agents and training procedures, and use statistical and time-series analysis to evaluate attacks' stealth. The results show that adversarial attacks can have significant impacts on DRL controllers, and constraining an attack's perturbations makes it difficult to detect. However, certain DRL architectures are far more robust, and robust training methods can further reduce the impact.

  • 3 authors
·
Jul 6, 2024

Towards Cross-Domain Multi-Targeted Adversarial Attacks

Multi-targeted adversarial attacks aim to mislead classifiers toward specific target classes using a single perturbation generator with a conditional input specifying the desired target class. Existing methods face two key limitations: (1) a single generator supports only a limited number of predefined target classes, and (2) it requires access to the victim model's training data to learn target class semantics. This dependency raises data leakage concerns in practical black-box scenarios where the training data is typically private. To address these limitations, we propose a novel Cross-Domain Multi-Targeted Attack (CD-MTA) that can generate perturbations toward arbitrary target classes, even those that do not exist in the attacker's training data. CD-MTA is trained on a single public dataset but can perform targeted attacks on black-box models trained on different datasets with disjoint and unknown class sets. Our method requires only a single example image that visually represents the desired target class, without relying its label, class distribution or pretrained embeddings. We achieve this through a Feature Injection Module (FIM) and class-agnostic objectives which guide the generator to extract transferable, fine-grained features from the target image without inferring class semantics. Experiments on ImageNet and seven additional datasets show that CD-MTA outperforms existing multi-targeted attack methods on unseen target classes in black-box and cross-domain scenarios. The code is available at https://github.com/tgoncalv/CD-MTA.

  • 3 authors
·
May 27, 2025

Fine-Grained Perturbation Guidance via Attention Head Selection

Recent guidance methods in diffusion models steer reverse sampling by perturbing the model to construct an implicit weak model and guide generation away from it. Among these approaches, attention perturbation has demonstrated strong empirical performance in unconditional scenarios where classifier-free guidance is not applicable. However, existing attention perturbation methods lack principled approaches for determining where perturbations should be applied, particularly in Diffusion Transformer (DiT) architectures where quality-relevant computations are distributed across layers. In this paper, we investigate the granularity of attention perturbations, ranging from the layer level down to individual attention heads, and discover that specific heads govern distinct visual concepts such as structure, style, and texture quality. Building on this insight, we propose "HeadHunter", a systematic framework for iteratively selecting attention heads that align with user-centric objectives, enabling fine-grained control over generation quality and visual attributes. In addition, we introduce SoftPAG, which linearly interpolates each selected head's attention map toward an identity matrix, providing a continuous knob to tune perturbation strength and suppress artifacts. Our approach not only mitigates the oversmoothing issues of existing layer-level perturbation but also enables targeted manipulation of specific visual styles through compositional head selection. We validate our method on modern large-scale DiT-based text-to-image models including Stable Diffusion 3 and FLUX.1, demonstrating superior performance in both general quality enhancement and style-specific guidance. Our work provides the first head-level analysis of attention perturbation in diffusion models, uncovering interpretable specialization within attention layers and enabling practical design of effective perturbation strategies.

  • 10 authors
·
Jun 12, 2025 3

Towards generalizable single-cell perturbation modeling via the Conditional Monge Gap

Learning the response of single-cells to various treatments offers great potential to enable targeted therapies. In this context, neural optimal transport (OT) has emerged as a principled methodological framework because it inherently accommodates the challenges of unpaired data induced by cell destruction during data acquisition. However, most existing OT approaches are incapable of conditioning on different treatment contexts (e.g., time, drug treatment, drug dosage, or cell type) and we still lack methods that unanimously show promising generalization performance to unseen treatments. Here, we propose the Conditional Monge Gap which learns OT maps conditionally on arbitrary covariates. We demonstrate its value in predicting single-cell perturbation responses conditional to one or multiple drugs, a drug dosage, or combinations thereof. We find that our conditional models achieve results comparable and sometimes even superior to the condition-specific state-of-the-art on scRNA-seq as well as multiplexed protein imaging data. Notably, by aggregating data across conditions we perform cross-task learning which unlocks remarkable generalization abilities to unseen drugs or drug dosages, widely outperforming other conditional models in capturing heterogeneity (i.e., higher moments) in the perturbed population. Finally, by scaling to hundreds of conditions and testing on unseen drugs, we narrow the gap between structure-based and effect-based drug representations, suggesting a promising path to the successful prediction of perturbation effects for unseen treatments.

  • 4 authors
·
Apr 11, 2025

XAI-CLIP: ROI-Guided Perturbation Framework for Explainable Medical Image Segmentation in Multimodal Vision-Language Models

Medical image segmentation is a critical component of clinical workflows, enabling accurate diagnosis, treatment planning, and disease monitoring. However, despite the superior performance of transformer-based models over convolutional architectures, their limited interpretability remains a major obstacle to clinical trust and deployment. Existing explainable artificial intelligence (XAI) techniques, including gradient-based saliency methods and perturbation-based approaches, are often computationally expensive, require numerous forward passes, and frequently produce noisy or anatomically irrelevant explanations. To address these limitations, we propose XAI-CLIP, an ROI-guided perturbation framework that leverages multimodal vision-language model embeddings to localize clinically meaningful anatomical regions and guide the explanation process. By integrating language-informed region localization with medical image segmentation and applying targeted, region-aware perturbations, the proposed method generates clearer, boundary-aware saliency maps while substantially reducing computational overhead. Experiments conducted on the FLARE22 and CHAOS datasets demonstrate that XAI-CLIP achieves up to a 60\% reduction in runtime, a 44.6\% improvement in dice score, and a 96.7\% increase in Intersection-over-Union for occlusion-based explanations compared to conventional perturbation methods. Qualitative results further confirm cleaner and more anatomically consistent attribution maps with fewer artifacts, highlighting that the incorporation of multimodal vision-language representations into perturbation-based XAI frameworks significantly enhances both interpretability and efficiency, thereby enabling transparent and clinically deployable medical image segmentation systems.

  • 5 authors
·
Jan 31

A Local Perturbation Theory for Cross-Domain Interference and Recovery in Multi-Domain RL

Reinforcement learning (RL) post-training improves large language models (LLMs) on individual domains such as mathematical reasoning, code generation, question answering, and creative writing (CW), but training on one domain often degrades performance on others. Existing explanations based on catastrophic forgetting or global gradient conflict are incomplete: substantial interference can occur even when full-model gradients are nearly orthogonal. We show that single-domain RL produces sparse, small-magnitude parameter edits with weak overlap among top-changed neurons, while different domains still share substantial active computation routes on which update directions determine whether they act synergistically or conflict. Guided by this observation, we prove under a local perturbation model of multi-domain RL that later-domain training harms an earlier domain mainly through a second-order damage term, which under the observed sparse route structure concentrates in a low-dimensional shared conflict subspace. Moreover, a short domain refresh contracts the harmful component on this subspace, enabling selective recovery with limited collateral damage. Consistent with the theory, a brief Re-Math refresh after Code rightarrow Math rightarrow QA rightarrow CW recovers Math from 57.66 to 66.04 while largely preserving performance on the other domains, yielding the best average score of 66.39. Beyond refresh, a training-free rollback on a sparse proxy conflict coordinate set for the Math-QA pair partially restores Math, providing direct proxy-level evidence for localized damage. These results provide a localized mechanistic account of interference and recovery in multi-domain RL.

  • 3 authors
·
May 31 1

DART-ES: Difficulty-Aware Reweighting and Targeted Replay for Fine-Tuning LLMs with Evolution Strategies

Evolution Strategies (ES) enable memory efficient full parameter fine-tuning of large language models (LLMs) using only forward computation. However, standard ES uniformly averages rewards across problems and compresses problem level population feedback into a single scalar, making it difficult to capture how the learning value of each problem changes with model capability. To address this limitation, we propose Difficulty-Aware Reweighting and Targeted Replay for Evolution Strategies (DART-ES). DART-ES estimates the local solvability of each problem from its pass rate across the perturbation population and aggregates historical observations to construct a dynamic difficulty state. This shared state jointly guides continuous difficulty reweighting and rare solvable sample replay, thereby improving perturbation direction evaluation and training data allocation without introducing an additional difficulty model or backpropagation. Extensive experiments show that DART-ES achieves good fine-tuning performance. DART-ES outperforms ES on all five base models and improves the average accuracy from 72.07\% to 73.53\%, exceeding the 73.26\% achieved by GRPO on GSM8K. Across five challenging mathematical reasoning benchmarks, DART-ES achieves an average accuracy of 49.20\%, compared with 48.34\% for ES and remains competitive with strong 7B models trained with RL. Further experiments show consistent gains in instruction tuning, code generation and the Countdown task with a 14B model, demonstrating strong generalization across tasks and scalability to larger models. Beyond performance gains, DART-ES also shows clear advantages in system efficiency. It reduces runtime per step by 15.2\%--50.2\% and peak memory usage per GPU by 21.1\%--51.1\% compared with GRPO. Despite performing full parameter fine-tuning, DART-ES also requires less runtime and GPU memory than GRPO+LoRA.

  • 5 authors
·
Oct 3

MENTOR: Mixture-of-Experts Network with Task-Oriented Perturbation for Visual Reinforcement Learning

Visual deep reinforcement learning (RL) enables robots to acquire skills from visual input for unstructured tasks. However, current algorithms suffer from low sample efficiency, limiting their practical applicability. In this work, we present MENTOR, a method that improves both the architecture and optimization of RL agents. Specifically, MENTOR replaces the standard multi-layer perceptron (MLP) with a mixture-of-experts (MoE) backbone, enhancing the agent's ability to handle complex tasks by leveraging modular expert learning to avoid gradient conflicts. Furthermore, MENTOR introduces a task-oriented perturbation mechanism, which heuristically samples perturbation candidates containing task-relevant information, leading to more targeted and effective optimization. MENTOR outperforms state-of-the-art methods across three simulation domains -- DeepMind Control Suite, Meta-World, and Adroit. Additionally, MENTOR achieves an average of 83% success rate on three challenging real-world robotic manipulation tasks including peg insertion, cable routing, and tabletop golf, which significantly surpasses the success rate of 32% from the current strongest model-free visual RL algorithm. These results underscore the importance of sample efficiency in advancing visual RL for real-world robotics. Experimental videos are available at https://suninghuang19.github.io/mentor_page.

  • 9 authors
·
Oct 19, 2024

Audio Jailbreak: An Open Comprehensive Benchmark for Jailbreaking Large Audio-Language Models

The rise of Large Audio Language Models (LAMs) brings both potential and risks, as their audio outputs may contain harmful or unethical content. However, current research lacks a systematic, quantitative evaluation of LAM safety especially against jailbreak attacks, which are challenging due to the temporal and semantic nature of speech. To bridge this gap, we introduce AJailBench, the first benchmark specifically designed to evaluate jailbreak vulnerabilities in LAMs. We begin by constructing AJailBench-Base, a dataset of 1,495 adversarial audio prompts spanning 10 policy-violating categories, converted from textual jailbreak attacks using realistic text to speech synthesis. Using this dataset, we evaluate several state-of-the-art LAMs and reveal that none exhibit consistent robustness across attacks. To further strengthen jailbreak testing and simulate more realistic attack conditions, we propose a method to generate dynamic adversarial variants. Our Audio Perturbation Toolkit (APT) applies targeted distortions across time, frequency, and amplitude domains. To preserve the original jailbreak intent, we enforce a semantic consistency constraint and employ Bayesian optimization to efficiently search for perturbations that are both subtle and highly effective. This results in AJailBench-APT, an extended dataset of optimized adversarial audio samples. Our findings demonstrate that even small, semantically preserved perturbations can significantly reduce the safety performance of leading LAMs, underscoring the need for more robust and semantically aware defense mechanisms.

  • 12 authors
·
May 21, 2025 2

Robust Physical-World Attacks on Deep Learning Models

Recent studies show that the state-of-the-art deep neural networks (DNNs) are vulnerable to adversarial examples, resulting from small-magnitude perturbations added to the input. Given that that emerging physical systems are using DNNs in safety-critical situations, adversarial examples could mislead these systems and cause dangerous situations.Therefore, understanding adversarial examples in the physical world is an important step towards developing resilient learning algorithms. We propose a general attack algorithm,Robust Physical Perturbations (RP2), to generate robust visual adversarial perturbations under different physical conditions. Using the real-world case of road sign classification, we show that adversarial examples generated using RP2 achieve high targeted misclassification rates against standard-architecture road sign classifiers in the physical world under various environmental conditions, including viewpoints. Due to the current lack of a standardized testing method, we propose a two-stage evaluation methodology for robust physical adversarial examples consisting of lab and field tests. Using this methodology, we evaluate the efficacy of physical adversarial manipulations on real objects. Witha perturbation in the form of only black and white stickers,we attack a real stop sign, causing targeted misclassification in 100% of the images obtained in lab settings, and in 84.8%of the captured video frames obtained on a moving vehicle(field test) for the target classifier.

  • 9 authors
·
Apr 9, 2018

Breaking the Shot-Noise Barrier: Cached Recycled Variance-Reduced Gradients for Quantum Optimization

Variational Quantum Algorithms (VQAs) rely heavily on classical optimization routines to navigate high-dimensional, noisy parameter landscapes. However, the evaluation of analytical gradients via the parameter-shift rule requires O(p) circuit executions, rendering this approach computationally prohibitive for deep circuits. While simultaneous perturbation methods provide an O(1) alternative, their gradient estimates suffer from severe O(p) spatial variance, which impedes convergence. To resolve this tension, we introduce the Cached Recycled Variance-Reduced Gradient (CRVG) by leveraging variance reduction techniques. We formulate two variants: a 3-Circuit (1-Sided) Non-Recursive CRVG and a Recursive CRVG. By introducing a center-point caching mechanism, the 3-Circuit CRVG mathematically recycles quantum measurements to reduce the inner-loop circuit complexity by 25\% across both variants. We establish a theoretical separation between the two routing paths to achieve an ε^2-stationary point: the non-recursive variant reaches a sample complexity of O(max{p/ε^2, p^{2/3}/ε^{10/3}}), while the recursive variant achieves an improved complexity of O(max{p/ε^2, p/ε^3}). Empirically, extensive evaluations on MaxCut and Maximum Independent Set (MIS) benchmarks validate these findings. While standard simultaneous perturbation remains a robust baseline across varying depths, CRVG demonstrates targeted advantages in specific amortizable regimes, such as the non-recursive variant on EfficientSU2 circuits and both variants on depth-three QAOA, yielding superior energy minimums and tighter output variances. Ultimately, CRVG establishes a principled bias-throughput trade-off for scaling near-term quantum optimization.

  • 3 authors
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Sep 29

Persistent Depth Ordering amid Shifting Block-Bypass Responses in Language Model Pretraining

Layer interventions are widely used to probe the internal organization of language models, yet most analyses examine a single training checkpoint even though model representations and computations evolve throughout pretraining. This leaves open which depth-dependent intervention responses reflect persistent organization and which are transient consequences of training. We study this question using single-block identity bypass on fixed teacher-forced contexts across five released trajectories and 11 model-domain combinations. We find that block-bypass responses retain recognizable depth ordering while their magnitudes redistribute: nearby checkpoints preserve stronger rank correspondence than distant ones, and large changes concentrate at positions that recur across text samples and transfer across evaluation domains. Controlled experiments further show that changes in the natural bypass effect cannot be reduced to a single downstream sensitivity: in replicated Pythia runs, local missing-update magnitude grows while the pooled matched downstream response decreases, whereas OLMo-2 7B exhibits a different balance. These matched responses also depend on perturbation strength and direction, without identifying targeted compensation. Together, our results show that longitudinal layer sensitivity is structured but not static, and that single-checkpoint intervention responses should be interpreted in the context of how the underlying perturbation pathway evolves during training.

  • 3 authors
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Sep 30

Using Mechanistic Interpretability to Craft Adversarial Attacks against Large Language Models

Traditional white-box methods for creating adversarial perturbations against LLMs typically rely only on gradient computation from the targeted model, ignoring the internal mechanisms responsible for attack success or failure. Conversely, interpretability studies that analyze these internal mechanisms lack practical applications beyond runtime interventions. We bridge this gap by introducing a novel white-box approach that leverages mechanistic interpretability techniques to craft practical adversarial inputs. Specifically, we first identify acceptance subspaces - sets of feature vectors that do not trigger the model's refusal mechanisms - then use gradient-based optimization to reroute embeddings from refusal subspaces to acceptance subspaces, effectively achieving jailbreaks. This targeted approach significantly reduces computation cost, achieving attack success rates of 80-95\% on state-of-the-art models including Gemma2, Llama3.2, and Qwen2.5 within minutes or even seconds, compared to existing techniques that often fail or require hours of computation. We believe this approach opens a new direction for both attack research and defense development. Furthermore, it showcases a practical application of mechanistic interpretability where other methods are less efficient, which highlights its utility. The code and generated datasets are available at https://github.com/Sckathach/subspace-rerouting.

  • 3 authors
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Mar 8, 2025 2

Escaping cells dilute CRISPR screen responses unequally across cell types

Single-cell CRISPR screens run in many cell types are used to compare how cell types respond to perturbation, to train models that transfer effects between them and to score such models. These uses assume that cells carrying a guide RNA had their target knocked down. Yet cells grow for days before sequencing: when an essential gene is knocked down, knocked-down cells are depleted or stop dividing while cells that escaped knockdown keep growing, and the measured response, an average over all cells carrying the guide, is diluted. We define the escape fraction of a perturbation as the share of its measured cells whose target was not effectively knocked down, and estimate it from each cell's counts of the targeted gene with a two-group mixture that recovers known fractions in simulated mixtures. In most cell types the escape fraction rises with how essential the gene is, it is higher in a later screen of the same cells, and it reaches about half of the measured cells in human embryonic stem cells (hESCs). It predicts how much each response is diluted: the response size falls to (1 - e)^2 of that of the knocked-down cells. Because the escape fraction differs between cell types, it changes all three uses: hESCs respond like K562 cells unless knockdown depletes them, the coefficient a simple transfer model learns is lowered by the dilution of the cell type it predicts, and a benchmark scored on all cells rewards predictions shrunk towards no change, partly because that ground truth is itself diluted. Where cells stop dividing instead, the response also contains expression differences between cell-cycle stages. Response sizes should be compared on knocked-down cells or corrected for the escape fraction.

  • 1 authors
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Oct 25

Measuring the Robustness of Audio Deepfake Detectors

Deepfakes have become a universal and rapidly intensifying concern of generative AI across various media types such as images, audio, and videos. Among these, audio deepfakes have been of particular concern due to the ease of high-quality voice synthesis and distribution via platforms such as social media and robocalls. Consequently, detecting audio deepfakes plays a critical role in combating the growing misuse of AI-synthesized speech. However, real-world scenarios often introduce various audio corruptions, such as noise, modification, and compression, that may significantly impact detection performance. This work systematically evaluates the robustness of 10 audio deepfake detection models against 16 common corruptions, categorized into noise perturbation, audio modification, and compression. Using both traditional deep learning models and state-of-the-art foundation models, we make four unique observations. First, our findings show that while most models demonstrate strong robustness to noise, they are notably more vulnerable to modifications and compression, especially when neural codecs are applied. Second, speech foundation models generally outperform traditional models across most scenarios, likely due to their self-supervised learning paradigm and large-scale pre-training. Third, our results show that increasing model size improves robustness, albeit with diminishing returns. Fourth, we demonstrate how targeted data augmentation during training can enhance model resilience to unseen perturbations. A case study on political speech deepfakes highlights the effectiveness of foundation models in achieving high accuracy under real-world conditions. These findings emphasize the importance of developing more robust detection frameworks to ensure reliability in practical deployment settings.

  • 3 authors
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Mar 21, 2025

IF-MAP: Influence-Function-Inspired Agent Prioritization in Multi-Agent Systems

Improving every agent in an LLM-based multi-agent system can be prohibitively costly, making it important to identify which agent should be prioritized to achieve the greatest system-level gain with limited resources. Failure attribution can inform this decision, but an agent's responsibility for failures does not directly reveal the system-level gains achievable by improving it. We therefore introduce IF-MAP, an influence-function-inspired method for identifying agents with high potential for system-level improvement. For each agent, IF-MAP measures end-to-end loss changes under controlled semantic prompt perturbations, fits a regularized local response model in a low-dimensional prompt-embedding subspace, and uses the estimated response norm as a priority score. This black-box procedure requires no access to model parameters or gradients and produces agent priorities that can guide subsequent improvement effort. We evaluate IF-MAP across six multi-agent workflows spanning code generation, question answering, and mathematical reasoning, using the same priorities for prompt optimization and model upgrades. Optimizing the selected agents' prompts achieves a macro-average gain of 3.81 percentage points, compared with 1.85 for uniform agent selection. Across five target models, upgrading the selected agents yields macro-average gains of 7.62-16.42 percentage points, compared with 3.81-8.62 for uniform agent selection. Despite its probing overhead, IF-MAP reduces Qwen3-8B and DeepSeek-V3.2 token use by 74.2% and 35.2%, respectively, relative to optimizing every agent, and reduces target-model tokens by 63.6-64.9% relative to upgrading every agent. These results support the use of IF-MAP to identify promising agents and direct improvement effort toward greater end-to-end performance gains.

  • 9 authors
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Oct 16 2

SAE Interventions are Unreliable: Post-Intervention Recovery of Suppressed Behavior

Sparse Autoencoders (SAEs) decompose residual-stream activations into interpretable features. Recent latent-space defenses increasingly rely on these decompositions, assuming that identified "unsafe" SAE features serve as actionable handles for monitoring and intervention. In this paradigm, clamping a specific harmful feature is expected to reliably prevent model misbehavior. However, we show that this success may hide a recoverable failure mode: the clamp may block one visible route to a behavior without eliminating the behavior itself. We formulate this vulnerability as post-intervention recovery, a constrained residual-space optimization problem. Starting from the post-intervention residual state, we optimize residual perturbations to recover the pre-intervention behavior while preserving the post-intervention values of the targeted SAE features. Even under a strong threat model where the intervention remains active throughout optimization and generation, recovery remains possible. To rule out that recovery simply undoes the intervention, we use encoder-orthogonal updates for single-layer interventions and the corresponding feature-map Jacobian in the cross-layer setting. Across TPP, unlearning, IOI, and refusal steering experiments, this stress test reveals recoverable behavior despite successful feature-level intervention. Especially in the safety-critical refusal-steering setting, we achieve a 95.8% recovery rate on valid samples while keeping defended-feature relative drift to 0.131, substantially below suffix-based baselines. A recovery-path attribution analysis further localizes this recovery to the SAE reconstruction residual, the component left unexplained by the SAE. These results expose a gap between feature-level control and behavioral completeness: SAE features can support causal intervention, but controlling them does not guarantee control over the underlying behavior.

Prompt2Perturb (P2P): Text-Guided Diffusion-Based Adversarial Attacks on Breast Ultrasound Images

Deep neural networks (DNNs) offer significant promise for improving breast cancer diagnosis in medical imaging. However, these models are highly susceptible to adversarial attacks--small, imperceptible changes that can mislead classifiers--raising critical concerns about their reliability and security. Traditional attacks rely on fixed-norm perturbations, misaligning with human perception. In contrast, diffusion-based attacks require pre-trained models, demanding substantial data when these models are unavailable, limiting practical use in data-scarce scenarios. In medical imaging, however, this is often unfeasible due to the limited availability of datasets. Building on recent advancements in learnable prompts, we propose Prompt2Perturb (P2P), a novel language-guided attack method capable of generating meaningful attack examples driven by text instructions. During the prompt learning phase, our approach leverages learnable prompts within the text encoder to create subtle, yet impactful, perturbations that remain imperceptible while guiding the model towards targeted outcomes. In contrast to current prompt learning-based approaches, our P2P stands out by directly updating text embeddings, avoiding the need for retraining diffusion models. Further, we leverage the finding that optimizing only the early reverse diffusion steps boosts efficiency while ensuring that the generated adversarial examples incorporate subtle noise, thus preserving ultrasound image quality without introducing noticeable artifacts. We show that our method outperforms state-of-the-art attack techniques across three breast ultrasound datasets in FID and LPIPS. Moreover, the generated images are both more natural in appearance and more effective compared to existing adversarial attacks. Our code will be publicly available https://github.com/yasamin-med/P2P.

  • 5 authors
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Dec 13, 2024 2

Breaking the weakest link to evade vision language models

Vision Language Models (VLMs) have recently emerged as a critical component of multimodal AI systems, enabling joint reasoning over visual and textual inputs in real-world and safety-critical applications. Despite their growing deployment, the robustness of VLMs against adversarial threats remains insufficiently explored, particularly in the context of evasion attacks targeting multimodal alignment. In this work, we investigate the vulnerability of VLMs to adversarial perturbations applied to visual inputs and study two attack settings: untargeted attacks, where the goal is to disrupt the model's interpretation of the original image, and targeted attacks, where the adversary aims to force the model to generate a specific semantic description unrelated to the original image. To efficiently generate adversarial examples, we propose a gradient-based attack method that performs optimization exclusively on the vision encoder of the VLM rather than on the entire multimodal architecture. This design significantly reduces the computational cost and resource requirements of the attack while maintaining strong effectiveness. We evaluate our approach on several open-source VLMs, including Qwen2.5-VL, Granite-Vision, FastVLM, and Phi-3.5-Vision, and show that small, human-imperceptible perturbations can substantially alter the textual interpretation produced by the models. Our findings highlight the vulnerability of modern VLMs to adversarial manipulation and emphasize the need for improved robustness and security mechanisms in multimodal AI systems.

  • 3 authors
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Aug 18

Synergy-Aware Residual Flow Matching for Single-Cell Perturbation Prediction

Predicting single-cell responses to genetic and chemical perturbations is important for understanding regulatory mechanisms and prioritizing therapeutic interventions. Existing methods have made progress by modeling perturbation-conditioned expression shifts with neural networks, graph priors, foundation-model representations, or distributional generative models. However, combinatorial perturbation prediction remains challenging because much of the response can be explained by additive single-perturbation effects, while the biologically informative signal often lies in a smaller non-additive residual induced by perturbation interactions. Directly generating the full post-perturbation expression profile may therefore allocate substantial capacity to the dominant additive component and underemphasize synergy-specific structure. To address this issue, we propose SynGeneFlow, a synergy-aware flow matching framework that anchors the source distribution at an additive prior and learns a residual flow toward the true perturbed state. SynGeneFlow further incorporates perturbation-conditioned gene interaction modeling, where a static gene-gene mask provides biological structure and a perturbation-dependent deformation bias dynamically modulates gene-gene coupling. To preserve population-level response structure, we align both endpoint distributions and biological residual distributions with MMD-based regularization. We evaluate SynGeneFlow on genetic and drug perturbation benchmarks under observed-single, held-out, and cross-modality settings. The results demonstrate that residualizing flow matching around additive perturbation effects provides a biologically grounded and robust framework for single-cell perturbation response prediction.

  • 2 authors
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Oct 17

PerturbDiff: Functional Diffusion for Single-Cell Perturbation Modeling

Building Virtual Cells that can accurately simulate cellular responses to perturbations is a long-standing goal in systems biology. A fundamental challenge is that high-throughput single-cell sequencing is destructive: the same cell cannot be observed both before and after a perturbation. Thus, perturbation prediction requires mapping unpaired control and perturbed populations. Existing models address this by learning maps between distributions, but typically assume a single fixed response distribution when conditioned on observed cellular context (e.g., cell type) and the perturbation type. In reality, responses vary systematically due to unobservable latent factors such as microenvironmental fluctuations and complex batch effects, forming a manifold of possible distributions for the same observed conditions. To account for this variability, we introduce PerturbDiff, which shifts modeling from individual cells to entire distributions. By embedding distributions as points in a Hilbert space, we define a diffusion-based generative process operating directly over probability distributions. This allows PerturbDiff to capture population-level response shifts across hidden factors. Benchmarks on established datasets show that PerturbDiff achieves state-of-the-art performance in single-cell response prediction and generalizes substantially better to unseen perturbations. See our project page (https://katarinayuan.github.io/PerturbDiff-ProjectPage/), where code and data will be made publicly available (https://github.com/DeepGraphLearning/PerturbDiff).

  • 6 authors
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Feb 22

Learning Perturbation-Specific Representations through Conditional Energy Prior for Cellular Response Prediction

AI-based cellular perturbation prediction is essential to accelerate drug discovery and therapeutic identification. However, perturbation-specific signals are generally obscured by cellular complexity, making it difficult for existing methods to correctly capture perturbation effects. To address this problem, we propose PerturbEnergy, which introduces a conditional energy-based prior over perturbation representations. It assigns lower energy (higher probability) to representations compatible with the given perturbation and higher energy to others, thereby explicitly tilting the latent space toward perturbation-preferred regions. Besides, PerturbEnergy can be integrated into autoencoder architectures as we find its Evidence Lower Bound (ELBO) is equivalent to the ELBO of the complete autoencoder. We further prove that optimizing PerturbEnergy increases the lower bound on the conditional mutual information between representation and perturbation. Extensive experiments on four benchmark datasets demonstrate the effectiveness of our PerturbEnergy: it improves perturbation recognition especially in latent space with improvement of up to 83.2\%; It also achieves state-of-the-art performance for predicting top-50/100/200 differentially expressed gene(DEG) response and remaining competitive on highly variable gene(HVG) prediction. The code is provided: https://github.com/BlueWhaleLab/PerturbEnergy

  • 2 authors
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Oct 12

scDFM: Distributional Flow Matching Model for Robust Single-Cell Perturbation Prediction

A central goal in systems biology and drug discovery is to predict the transcriptional response of cells to perturbations. This task is challenging due to the noisy and sparse nature of single-cell measurements, as well as the fact that perturbations often induce population-level shifts rather than changes in individual cells. Existing deep learning methods typically assume cell-level correspondences, limiting their ability to capture such global effects. We present scDFM, a generative framework based on conditional flow matching that models the full distribution of perturbed cells conditioned on control states. By incorporating a maximum mean discrepancy (MMD) objective, our method aligns perturbed and control populations beyond cell-level correspondences. To further improve robustness to sparsity and noise, we introduce the Perturbation-Aware Differential Transformer (PAD-Transformer), a backbone architecture that leverages gene interaction graphs and differential attention to capture context-specific expression changes. Across multiple genetic and drug perturbation benchmarks, scDFM consistently outperforms prior methods, demonstrating strong generalization in both unseen and combinatorial settings. In the combinatorial setting, it reduces mean squared error by 19.6% relative to the strongest baseline. These results highlight the importance of distribution-level generative modeling for robust in silico perturbation prediction. The code is available at https://github.com/AI4Science-WestlakeU/scDFM

  • 4 authors
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Feb 5

Compared to What? Baselines and Metrics for Counterfactual Prompting

Counterfactual prompting (i.e., perturbing a single factor and measuring output change) is widely used to evaluate things like LLM bias and CoT faithfulness. But in this work we argue that observed effects cannot be attributed to the targeted factor without accounting for baseline ``meaning-preserving'' modifications to text that establish general model sensitivity. This is because every counterfactual edit is a compound treatment that bundles the variable of interest with incidental surface-form variation; this violates treatment variation irrelevance. We observe prediction flip rates on MedQA of 14.9% when we surgically change patient gender. However, this is statistically indistinguishable from the flip rates induced by simply paraphrasing inputs (14.1%). In this case, it would therefore be unwarranted to conclude that the LLM is especially sensitive to patient gender. To account for this and robustly measure the effects of targeted interventions, we propose a framework in which we compare (via statistical testing) differences observed under target interventions to those induced by paraphrasing inputs. We then use this framework to revisit a analysis done on the MedPerturb dataset, which reported evidence of model sensitivity to patient demographics and stylistic cues. We find that these effects largely dissipate when we account for general model sensitivity, with only 5 of 120 tests reaching statistical significance. Applying the same framework to occupational biography classification, we detect clearly significant directional gender bias, showing that the framework identifies real directional effects even when they are small. We evaluate a range of metrics -- aggregate, per-sample distributional, and regression -- and find that per-sample metrics are dramatically more powerful than aggregate metrics and regression powerfully and uniquely characterizes effect direction and magnitude.

  • 4 authors
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Apr 30

The Butterfly Effect in LLM Social Simulations: From Architecture Sensitivity to Robustness Audits

A butterfly effect occurs when a local perturbation propagates through a system and produces divergence in its collective outcome. In LLM social simulations, this creates a particular challenge for scientific inference: sensitivity to implementation choices can enter agent interactions and alter the collective outcomes on which scientific claims are based. We study this problem through a repeated Prisoner's Dilemma and a social-media echo chamber, spanning representation- and design-level perturbations across four LLM families. We find that controlled perturbations can substantially alter collective outcomes, with sensitivity varying across both perturbations and models. In the Prisoner's Dilemma, changing only the representation of a matched persona shifts two-agent cooperation by 75.2 percentage points for GPT-5.2, while game framing and memory representation produce smaller or less consistent effects. Multi-agent interaction further reshapes representation sensitivity, producing amplification or attenuation depending on the model and perturbation. In the echo-chamber simulation, persona representation changes interaction targeting and is accompanied by divergence in collective interaction structure, extending representation sensitivity from agent behavior to network-level outcomes. These results show that robustness cannot be inferred from a single simulation configuration and that local sensitivity can change as it propagates through interaction. We introduce TRAILS (Taxonomy for Robustness Audits In LLM Simulations) and the Social Simulation Audit Card as a framework for systematically auditing these dependencies and calibrating the scope of scientific claims to the robustness evidence that supports them.

  • 4 authors
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Oct 19

PerturbBridge: Direct Phenotypic Supervision for Cellular Perturbation Generation

Virtual cell models should capture phenotypes induced by specific perturbations. However, image-based models are typically trained and evaluated to match real-image distributions, which alone does not explicitly prioritize perturbation-specific biological responses. Recent approaches add biological signals through reinforcement-learning post-training or inference-time steering, raising a central question: where should biological response information enter the generative pipeline? We introduce PerturbBridge, a stochastic data-to-data bridge model that directly supervises perturbation-specific phenotypes in predicted perturbed images during training. PerturbBridge jointly optimizes bridge regression and differentiable biological response losses, with biological gradients passing through a frozen image encoder. We further introduce perturbation-response evaluations based on downstream classification and retrieval. Across three microscopy benchmarks for perturbation profiling and subcellular imaging, PerturbBridge surpasses CellFlux in biological fidelity, image quality, and sampling efficiency. On BBBC021, mechanism-of-action classification improves by 5.66 and 7.5 percentage points with morphological and learned visual features, respectively. On JUMP and AllenCell, retrieval Hit@10 and Hit@1 improve by 1.77 and 7.15 percentage points, respectively. On BBBC021 and JUMP, PerturbBridge achieves lower FID with 80% fewer model evaluations than CellFlux. Overall, these results show that directly supervising perturbation responses during training improves phenotypic fidelity while enabling efficient cellular image generation. Code is available at https://github.com/yyc1215lll-creator/PerturbBridge.

  • 6 authors
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Oct 11

Perturbation Probing: A Two-Pass-per-Prompt Diagnostic for FFN Behavioral Circuits in Aligned LLMs

Perturbation probing generates task-specific causal hypotheses for FFN neurons in large language models using two forward passes per prompt and no backpropagation, followed by a one-time intervention sweep of about 150 passes amortized across all identified neurons. Across eight behavioral circuits, 13 models, and four architecture families, we identify two circuit structures that organize LLM behavior. Opposition circuits appear when RLHF suppresses a pre-training tendency. In safety refusal, about 50 neurons, or 0.014 percent of all neurons, control the refusal template; ablating them changes 80 percent of response formats on 520 AdvBench prompts while producing near-zero harmful compliance, 3 of 520 cases, all with disclaimers. Routing circuits appear for pre-training behaviors distributed through attention. For language selection, residual-stream direction injection switches English to Chinese output on 99.1 percent of 580 benchmark prompts in the 3 of 19 tested models that satisfy three observed conditions: bilingual training, FFN-to-skip signal ratio between 0.3 and 1.1, and linear representability. The same intervention fails on the other 16 models and on math, code, and factual circuits, defining the limits of directional steering. The FFN-to-skip signal ratio, computed from the same two forward passes, distinguishes the two structures and predicts the appropriate intervention. Circuit topology varies by architecture, from Qwen's concentrated FFN bottleneck to Gemma's normalization-shielded circuit. In Qwen3.5-2B, ablating 20 neurons eliminates multi-turn sycophantic capitulation, while amplifying 10 related neurons improves factual correction from 52 percent to 88 percent on 200 TruthfulQA prompts. These results show that perturbation probing offers mechanistic insight into RLHF-organized behavior and a practical toolkit for precision template-layer editing.

  • 3 authors
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Apr 29

STRAND: Sequence-Conditioned Transport for Single-Cell Perturbations

Predicting how genetic perturbations change cellular state is a core problem for building controllable models of gene regulation. Perturbations targeting the same gene can produce different transcriptional responses depending on their genomic locus, including different transcription start sites and regulatory elements. Gene-level perturbation models collapse these distinct interventions into the same representation. We introduce STRAND, a generative model that predicts single-cell transcriptional responses by conditioning on regulatory DNA sequence. STRAND represents a perturbation by encoding the sequence at its genomic locus and uses this representation to parameterize a conditional transport process from control to perturbed cell states. Representing perturbations by sequence, rather than by a fixed set of gene identifiers, supports zero-shot inference at loci not seen during training and expands inference-time genomic coverage from ~1.5% for gene-level single-cell foundation models to ~95% of the genome. We evaluate STRAND on CRISPR perturbation datasets in K562, Jurkat, and RPE1 cells. STRAND improves discrimination scores by up to 33% in low-sample regimes, achieves the best average rank on unseen gene perturbation benchmarks, and improves transfer to novel cell lines by up to 0.14 in Pearson correlation. Ablations isolate the gains to sequence conditioning and transport, and case studies show that STRAND resolves functionally alternative transcription start sites missed by gene-level models.

  • 8 authors
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Feb 9

Don't Waste the Noise: Importance-Guided Perturbation Allocation under Joint Global and Local Constraints

Adversarial optimization under a shared ell_1 budget requires deciding not only how much perturbation to use, but also where that limited budget should be spent. This allocation problem becomes particularly important when individual input coordinates are subject to local magnitude constraints, which restrict the extent to which perturbation can be concentrated on a small number of locations. We introduce an importance-guided allocation mechanism that uses a fixed clean-gradient prior to steer perturbation toward model-sensitive regions while leaving the feasible perturbation set unchanged. A centered allocation objective encourages perturbation at above-average importance locations and discourages unnecessary expenditure elsewhere, thereby redistributing rather than enlarging the available budget. Across ten robust model--dataset configurations under a common capacity-limited threat setting, the proposed method improves attack success over matched APGD- and PMA-based baselines by 2.52 to 17.70 percentage points. Allocation analysis shows that these gains are accompanied by substantially greater perturbation mass in high-importance regions without increased global ell_1 consumption. Mechanism ablations further show that centered non-uniform redistribution provides part of the benefit, while model-derived importance yields an additional improvement. These results identify perturbation allocation as a distinct and practically relevant dimension of adversarial optimization under shared-budget, locally constrained threat models.

  • 2 authors
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Sep 30

GIST: Targeted Data Selection for Instruction Tuning via Coupled Optimization Geometry

Targeted data selection has emerged as a crucial paradigm for efficient instruction tuning, aiming to identify a small yet influential subset of training examples for a specific target task. In practice, influence is often measured through the effect of an example on parameter updates. To make selection scalable, many approaches leverage optimizer statistics (e.g., Adam states) as an axis-aligned surrogate for update geometry (i.e., diagonal precondition), implicitly treating parameters as coordinate-wise independent. We show that this assumption breaks down in parameter-efficient fine-tuning (PEFT) methods such as LoRA. In this setting, the induced optimization geometry exhibits strong cross-parameter coupling with non-trivial off-diagonal interactions, while the task-relevant update directions are confined to a low-dimensional subspace. Motivated by this mismatch, we propose GIST (Gradient Isometric Subspace Transformation), a simple yet principled alternative that replaces axis-aligned scaling with robust subspace alignment. GIST recovers a task-specific subspace from validation gradients via spectral filtering (SVD), projects training gradients into this coupled subspace, and scores examples by their alignment with target directions.Extensive experiments have demonstrated that GIST matches or outperforms the state-of-the-art baseline with only 0.29% of the storage and 25% of the computational time under the same selection budget.

Equal Path Cost, Unequal Output Effects: Understanding Perturbation Propagation in Diffusion Models

Diffusion models have achieved remarkable success in generative modeling, with their sampling procedures routinely modified to control generation and improve efficiency. These modifications introduce perturbations along the sampling trajectory, raising a central question: how do such perturbations affect generated output? To address this question, we develop a theoretical framework to investigate perturbation propagation, combining dynamical analysis of the sampling process with an information-theoretic characterization of output responses. Within this framework, we quantify perturbation strength using the Kullback--Leibler (KL) divergence between perturbed and reference trajectory distributions, termed as path cost, which is shown to bound, but do not determine, changes in the output distribution. Building on this analysis, we derive a response identity that connects the propagation and accumulation of local perturbations with the information captured by a selected feature mean, explaining why changes in the output distribution can remain undetected by its first-order response. We test our theoretical analysis through controlled interventions at equal path cost in pretrained diffusion models, revealing distinct patterns of output sensitivity across sampling stages and spatial frequencies. To assess whether our framework can diagnose perturbations arising from practical approximations, we apply it to cache-based acceleration and show that our propagation analysis reliably identifies sampling intervals where caching causes larger image errors.

  • 4 authors
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Oct 7

When Normalization Selects the Sign: Auditing Robustness Ablations in Quantum Attention

Removing an input-scaling module changes both a classifier and the perturbations reaching its encoder. A robustness difference can therefore reflect the comparison rule as well as the module. We demonstrate this problem in a four-qubit quantum-attention detector on generated power-grid trajectories. A learned scaling module appears beneficial at a fixed physical attack budget, but matching an upper bound on perturbations at the encoder reverses the ordering. Neither comparison alone establishes a robustness benefit caused by the module. The initial test also perturbs clean examples into attacked examples while retaining their original labels; tests restricted to already attacked examples do not establish a benefit. Replacing a trained model's input scales disrupts detection. Retraining its linear classification layer restores the detection rate, but changes individual predictions, leaving the comparison descriptive rather than causal. Two further design checks explain why the input quantum Fisher information regularizer cannot train this model's query parameters, and why removing confidence bounds does not establish a larger certified radius. The evidence is limited to ten seeds, exact simulation, synthetic data, and a restricted set of attacks; classical baselines achieve better clean prediction. The practical lesson is to specify which perturbation budget is fixed, check that attacks preserve labels and interventions preserve predictions, and distinguish exploratory controls from confirmatory evidence.

  • 4 authors
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Oct 1

PertMind: Eliciting Emergent Biological Reasoning in LLM via Reinforcement Learning on Cellular Perturbation Data

Large language models can describe mechanisms, yet scalable post-training still depends on costly, manually curated biological reasoning traces. Here we show that cellular perturbation atlases can instead become reinforcement-learning environments, where measured gene responses provide computable rewards for biological reasoning. We introduce PertMind, which combines trusted-trajectory supervised initialization with gene-, pathway-, and format-level reinforcement signals. Although trained only on forward perturbation-response prediction, PertMind improves response inference in unseen cellular contexts while retaining general language capabilities. It also transfers, without task-specific post-training, to reverse perturbation identification, double-perturbation reasoning, phenotypic-screen prioritization, and biological-process interpretation. PertMind further generates biological profiles that support competitive gene, cell, and donor representations across multiscale downstream tasks. These results support the hypothesis that reinforcement on experimental endpoints can concentrate reusable biological strategies already accessible to pretrained models. More broadly, perturbation-derived reinforcement learning offers a scalable route for transforming expanding experimental atlases into training environments for general-purpose biological reasoning.

  • 19 authors
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Oct 5

DRIFT: Disentangled Responsive-Invariant Flow Transport for Single-Cell Perturbation Prediction

Predicting cellular responses to perturbations is a central problem in cellular biology, with broad applications in systems biology and drug discovery. This task is challenging because cellular responses can be complex and cell-state dependent, intrinsic cell-to-cell variability can be confounded with perturbation effects, and destructive single-cell RNA sequencing precludes paired measurements of the same cell before and after treatment. Flow matching transports control cells to perturbed states flexibly, but acting on the full cell state can confound perturbation effects with pre-existing cell-to-cell variability. Disentangled approaches separate responsive from invariant components, but model perturbations through prescribed mechanisms, such as latent shifts or graph edits, limiting their flexibility. We address both limitations in a unified framework. A variational encoder disentangles each cell into an invariant block, capturing state unaffected by the perturbation, and a responsive block, capturing state it changes, through conditional priors and an information-theoretic invariance constraint. Conditional flow matching transports only the responsive block, conditioned on the perturbation and invariant state, yielding a flexible, data-driven model of perturbation effects without confounding pre-existing variability. Across several benchmarks, our method outperforms the strongest published method in settings involving combinatorial and unseen perturbation prediction.

  • 3 authors
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Sep 27

A Pitfall in the Evaluation of Gene Perturbation Models

Gene perturbation models aim to predict transcriptional responses to unseen genetic interventions, but comparisons rely on heterogeneous evaluation metrics and differentially-expressed (DE) gene subsets. We investigate the consequences of these choices using eight methods across six single-gene perturbation datasets under a unified evaluation protocol. Varying the number of top DE genes reveals substantial instability in Precision-based rankings, with the winning method changing 86.7% of the time, while rankings based on the rest of the metrics remain comparatively stable. Investigating this discrepancy exposes that repeating a single predicted expression profile across cell-level rows, a standard practice for many methods, can inflate significance estimates and produce excessively large predicted significant-DE sets. Specifically we found that 67.1% of tested perturbation--gene pairs pass the significance threshold despite some of them having minuscule effects. We derive an inflation factor showing that replicated predictions can amplify the standardized Mann--Whitney statistic even after correction for tied ranks, without adding independent information. This artifact changes Precision mainly as the number of DE genes increases because for smaller cutoffs, most of the genes are already significant due to the effect-based ordering. Taking this pitfall into account in our benchmark comparison, we find that a random forest using Gene Ontology features achieves the best overall results.

  • 4 authors
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Oct 18

CellPrism: A Visual Analytics System for Exploring AI-Driven Virtual Cells in Drug Discovery

Gene perturbation analysis plays a critical role in drug discovery by enabling researchers to investigate how interventions on specific genes influence global gene expression patterns within cells. Recent advances in artificial intelligence-driven virtual cell models have made it possible to predict gene expression outcomes for a wide range of perturbation strategies in silico, substantially reducing reliance on costly and time-consuming biological experiments. However, effectively exploring and interpreting the high-dimensional perturbation spaces produced by these models remains challenging because of the combinatorial nature of perturbations and the complex cell-specific gene expression responses they generate. In this work, we present CellPrism, a visual analytics system designed to support the systematic exploration of gene perturbation strategies for drug discovery. Specifically, CellPrism integrates clustering-based overviews to summarize perturbation outcomes, a glyph-based representation to compactly encode gene expression patterns across cell types, and coordinated views that enable fine-grained comparison and interpretation of perturbation effects. We demonstrate the effectiveness of CellPrism through a real-world case study and expert interviews. This work highlights the value of visual analytics in bridging virtual cell modeling with expert-driven decision making in drug discovery.

  • 6 authors
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Aug 3

Control-Anchored Residual Flow Matching Conditioned on Gene Geometry for Virtual Cell Perturbation Modeling

A central task in virtual cell modeling is predicting single-cell transcriptional responses to unseen genetic perturbations and drug combinations, and biological networks provide valuable priors on gene relationships. Existing graph-based models commonly use the same network to structure gene representations and mediate intergene interactions, thereby implicitly treating stable associations as perturbation-response pathways. Gene Ontology and control-derived coexpression networks encode relatively stable relationships rather than intervention-specific response directions or magnitudes. We therefore propose GeneGeoFlow, which conditions a control-anchored residual flow on gene-wise geometry derived from biological networks to learn intervention-specific transcriptional responses. GeneGeoFlow derives multi-scale spectral coordinates from Gene Ontology and control-derived coexpression networks. A perturbation-conditioned, gene-wise gating module selects relevant structural scales and network sources, yielding intervention-specific gene geometry. The resulting geometry conditions a control-anchored residual flow without explicitly propagating target-derived signals along the graph. Condition-wise optimal transport couples unpaired control and perturbed populations for training, while a Delta-correlation objective aligns the predicted and observed condition-level expression-shift directions. GeneGeoFlow achieves Pearson Delta scores of 0.8979 on the Norman additive benchmark and 0.9088 on five held-out drug combinations in the fixed ComboSciPlex test split. These results support perturbation-conditioned gene geometry as an effective structural prior for intervention-specific response prediction, without conflating stable gene relationships with response propagation.

  • 13 authors
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Aug 6

Convex-Hull-Neighborhood Smooth Dual Generalization: Controlling Local Correction Propagation in Offline RL

Offline reinforcement learning (offline RL) can benefit from nearby out-of-distribution (OOD) actions, but estimation errors at these actions may be amplified by bootstrapping. Existing regularization and local-generalization methods control either the admissible OOD region or the influence of generalized targets, often through separate mechanisms. We propose Convex Hull Neighborhood Smooth Dual Generalization (CSDG), which expresses the Bellman backup as an in-sample value target plus a CHN-local correction. This formulation makes the generalized contribution explicit and separates it from the in-sample reference path. The correction is obtained by smoothing in-sample-oriented and OOD-oriented candidates sampled at different perturbation radii. A mixture coefficient lambda scales its contribution to each backup, while the recursive discount remains gamma. Under boundedness and fixed perturbation kernels, we derive an exact one-step correction identity, a time-varying iterate bound, and a fixed-point bound that depends only on the branch discrepancy at the fixed point. We further characterize the implicit policies induced by the idealized operators and give a conditional non-degradation criterion. The practical algorithm approximates these quantities using asymmetric bounded noise and expectile regression, without exact support classification or an additional pessimistic OOD penalty. Experiments on Gym-MuJoCo and AntMaze show strong aggregate performance and stable value estimation. Code is available at: https://github.com/YOUNG-fnxm/CSDG

  • 6 authors
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Aug 3

Self-Rectifying Diffusion Sampling with Perturbed-Attention Guidance

Recent studies have demonstrated that diffusion models are capable of generating high-quality samples, but their quality heavily depends on sampling guidance techniques, such as classifier guidance (CG) and classifier-free guidance (CFG). These techniques are often not applicable in unconditional generation or in various downstream tasks such as image restoration. In this paper, we propose a novel sampling guidance, called Perturbed-Attention Guidance (PAG), which improves diffusion sample quality across both unconditional and conditional settings, achieving this without requiring additional training or the integration of external modules. PAG is designed to progressively enhance the structure of samples throughout the denoising process. It involves generating intermediate samples with degraded structure by substituting selected self-attention maps in diffusion U-Net with an identity matrix, by considering the self-attention mechanisms' ability to capture structural information, and guiding the denoising process away from these degraded samples. In both ADM and Stable Diffusion, PAG surprisingly improves sample quality in conditional and even unconditional scenarios. Moreover, PAG significantly improves the baseline performance in various downstream tasks where existing guidances such as CG or CFG cannot be fully utilized, including ControlNet with empty prompts and image restoration such as inpainting and deblurring.

  • 9 authors
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Mar 26, 2024

PopPert: Population-level Joint-Distribution Modeling for Single-Cell Perturbation Prediction

Predicting transcriptional responses to specific perturbations is critical for understanding cellular regulatory mechanisms and accelerating drug discovery. Single-cell RNA sequencing destroys each measured cell, yielding only unpaired populations of control and perturbed cells. However, existing methods typically model perturbation prediction at the single-cell level and assume cell-to-cell correspondence, which conflicts with the unpaired nature of the observed data. To address this challenge, we propose PopPert, a framework that explicitly parameterizes population-level joint gene expression distributions for collective transcriptional state modeling. Given a control population distribution and a perturbation condition, PopPert predicts perturbation-induced changes in distribution parameters, eliminating the need for cell-level correspondence and reducing sensitivity to single-cell noise. To effectively capture gene co-expression patterns, PopPert leverages a low-rank Gaussian Copula to model cross-gene statistical dependencies and construct the joint gene expression distribution, additionally allowing sampling of synthetic perturbed single-cell profiles. Across multiple single-cell benchmarks spanning both genetic and chemical perturbations, PopPert achieves superior overall performance in differential expression recovery, perturbation effect estimation, and population-level distribution matching. These results establish population-level joint distribution learning as an effective paradigm for predicting transcriptional responses from unpaired single-cell populations. Code for PopPert is publicly available at https://github.com/whd1125/PopPert.

  • 4 authors
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Aug 31

Generalizable Data-free Objective for Crafting Universal Adversarial Perturbations

Machine learning models are susceptible to adversarial perturbations: small changes to input that can cause large changes in output. It is also demonstrated that there exist input-agnostic perturbations, called universal adversarial perturbations, which can change the inference of target model on most of the data samples. However, existing methods to craft universal perturbations are (i) task specific, (ii) require samples from the training data distribution, and (iii) perform complex optimizations. Additionally, because of the data dependence, fooling ability of the crafted perturbations is proportional to the available training data. In this paper, we present a novel, generalizable and data-free approaches for crafting universal adversarial perturbations. Independent of the underlying task, our objective achieves fooling via corrupting the extracted features at multiple layers. Therefore, the proposed objective is generalizable to craft image-agnostic perturbations across multiple vision tasks such as object recognition, semantic segmentation, and depth estimation. In the practical setting of black-box attack scenario (when the attacker does not have access to the target model and it's training data), we show that our objective outperforms the data dependent objectives to fool the learned models. Further, via exploiting simple priors related to the data distribution, our objective remarkably boosts the fooling ability of the crafted perturbations. Significant fooling rates achieved by our objective emphasize that the current deep learning models are now at an increased risk, since our objective generalizes across multiple tasks without the requirement of training data for crafting the perturbations. To encourage reproducible research, we have released the codes for our proposed algorithm.

  • 3 authors
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Jan 24, 2018

Integrating Biological Knowledge for Robust Microscopy Image Profiling on De Novo Cell Lines

High-throughput screening techniques, such as microscopy imaging of cellular responses to genetic and chemical perturbations, play a crucial role in drug discovery and biomedical research. However, robust perturbation screening for de novo cell lines remains challenging due to the significant morphological and biological heterogeneity across cell lines. To address this, we propose a novel framework that integrates external biological knowledge into existing pretraining strategies to enhance microscopy image profiling models. Our approach explicitly disentangles perturbation-specific and cell line-specific representations using external biological information. Specifically, we construct a knowledge graph leveraging protein interaction data from STRING and Hetionet databases to guide models toward perturbation-specific features during pretraining. Additionally, we incorporate transcriptomic features from single-cell foundation models to capture cell line-specific representations. By learning these disentangled features, our method improves the generalization of imaging models to de novo cell lines. We evaluate our framework on the RxRx database through one-shot fine-tuning on an RxRx1 cell line and few-shot fine-tuning on cell lines from the RxRx19a dataset. Experimental results demonstrate that our method enhances microscopy image profiling for de novo cell lines, highlighting its effectiveness in real-world phenotype-based drug discovery applications.

  • 4 authors
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Jul 14, 2025

P2P: Cross-View Population Denoising for Unpaired Single-Cell Perturbation Response Prediction

AIVC (AI Virtual Cell) is a learned simulator of cellular behavior across conditions. Predicting how a cell population responds transcriptionally to a genetic perturbation is a core task. Perturb-seq records that response by destructive sequencing, so a control cell and a perturbed cell are never observed as a pair, and cells under one condition remain heterogeneous and noisy. Regression on individual cells absorbs sampling variation into the estimated effect, whereas interpretation requires the reproducible population effect. P2P (Perturbation-to-Perturbation) takes a stochastic cell-set view as its supervision unit. Two views drawn from the same condition share a reproducible population effect and differ by view-specific variation. A permutation-invariant set encoder summarizes the control population, a structured encoder represents perturbation tokens, cellular context, dose, and combination interactions, and a gate blends empirical condition-effect memory with a neural residual. A heteroscedastic head predicts the population mean and gene-wise response variance. Under one protocol and five seeds, P2P attains the lowest expression RMSE and the highest Effect Pearson, DEG F1, and DEG average precision on each of Adamson, Norman, Replogle K562, and Replogle RPE1 relative to GenePert, LinearPert, SLIM, Scouter, and scPILOT. On Replogle K562, Effect Pearson rises from 0.643 to 0.702 and DEG F1 rises from 0.067 to 0.178 relative to Scouter, the strongest baseline on both metrics.

  • 2 authors
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Sep 27

Is Success All You Need? Investigating the Impact of Input Perturbations on VLA Behaviour in Tabletop Manipulation Tasks

Vision-Language-Action (VLA) models have achieved high task success rates on robot manipulation task benchmarks. More recently, there has been an emphasis on evaluating the robustness of VLA models to perturbations. However, this robustness is still predominantly measured through Task Success Rate (TSR). In this work, we propose a benchmark-agnostic evaluation framework to measure the behavioural robustness of models by characterising how successful trajectories are executed under perturbation. We implement this methodology by extending the widely-used LIBERO and LIBERO-Plus benchmarks. Across three state-of-the-art VLA models, four LIBERO task suites and seven perturbation conditions, we evaluate changes in both typical successful behaviour and its variability, including metrics of motion smoothness, efficiency and gripper behaviour. We find that perturbations can alter the behaviour of successful trajectories, a phenomenon which cannot necessarily be inferred from TSR alone. Across LIBERO suites, we identify cases where state-of-the-art VLA models achieve comparable TSR under the same perturbation condition, yet behaviour on successful trajectories diverges substantially. Therefore, to have a more robust assessment of task performance, we argue that suitable measures of robustness should capture not only whether a task is completed, but also how the robot behaves while completing it. When evaluating the robustness of VLA models, TSR may be complemented by behavioural evaluation metrics that characterise the nature and variability of successful task execution by robots.

  • 4 authors
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Sep 30

OCOO-T : A Simple and Scalable Virtual Cell Model for Transcriptional Perturbation Response Prediction

Predicting single-cell transcriptional responses to genetic, chemical and cytokine perturbations is a fundamental challenge in computational biology and AI Virtual Cell (AIVC) modeling, with direct implications for drug discovery and the elucidation of gene regulatory networks. Existing approaches often rely on auxiliary cell-state encoders, hierarchical variational autoencoders, dedicated Transformer encoder-decoder modules, or gene-interaction priors to compress high-dimensional expression profiles into latent representations. While effective, these designs increase architectural complexity and may limit scalability and generalizability. This paper introduces OCOO-T, a minimalist flow-matching-based AIVC model for transcriptional perturbation response prediction. OCOO-T utilizes a vanilla Transformer stack that operates directly on continuous gene expression profiles and formulates perturbation response prediction as a continuous-time denoising process. Perturbation embeddings, dosage information, and cell-line/cell-type specificity are integrated through adaptive layer normalization and in-context tokens. Comprehensive evaluations on Tahoe100M, Replogle, and PBMC benchmarks demonstrate that OCOO-T achieves state-of-the-art performance across diverse perturbations and cell types while effectively scaling to long transcriptional profiles through patching and depatching of cellular contexts. By leveraging the simplicity of Transformer-based denoising for single-cell omics, OCOO-T provides an effective and scalable framework for in-silico cellular simulation.

  • 6 authors
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Aug 13

Encoded but Not in Control: Revealing the Grounding Gap in Vision-Language Robot Policies

Instruction following is central to language-conditioned robot policies: language should determine what to do when the same scene permits multiple valid actions. Yet successful execution alone cannot establish whether a policy follows the instruction or infers the task from the scene. We study this ambiguity through scene-preserving instruction interventions, using valid target substitutions, arbitrary nouns, and unrelated sentences while holding the scene fixed. We evaluate vision-language-action (VLA) policies and world-action models (WAMs) in simulation and in real-world experiments. Our analysis addresses three questions: (a) Does task success imply instruction following? When instructions request a different visible object, all evaluated policies predominantly approach and pick up the incorrect original target associated with the scene. (b) Is this failure caused by language insensitivity? Instruction perturbations affect task performance. A layerwise action lens shows intermediate action predictions respond to these perturbations. Linear probes accurately recover instructed targets, indicating modified instructions are encoded despite rarely determining target selection. (c) Why does encoded language fail to control action? Attention analysis indicates weak instruction-token contributions to action generation. Target-token attention can remain focused on the original object, revealing a mismatch between target encoding and visual grounding. UMAP and shared non-negative matrix factorization show target information remains accessible within representations increasingly organized by scene identity. Our findings expose a grounding gap concealed by nominal success and provide a diagnostic framework. They further establish a concrete criterion for progress: policies should reliably follow valid changes in user intent, even when they conflict with scene-favored behavior.

  • 12 authors
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Oct 4

DeMixPert: Decomposed Response Modeling with Gaussian Mixtures for OOD Single-Cell Perturbation Prediction

Predicting transcriptome-wide responses to unseen genetic perturbations remains a major computational challenge because accurate prediction requires recovering both perturbation-specific transcriptional shifts and heterogeneous cellular responses. Existing methods often entangle deterministic response structure with stochastic population-level variation, causing dominant shared patterns to mask weaker perturbation-specific signals and impair distributional modeling. To address these challenges, we propose DeMixPert, an approach for Decomposed response Modeling with Gaussian Mixtures for Out-Of-Distribution (OOD) single-cell Perturbation prediction. DeMixPert decomposes perturbation-induced changes into a basal-state-dependent systematic response, a perturbation-specific response, and population-level variation. The systematic component is derived from the basal state encoded from control-cell expression, whereas the perturbation-specific component is inferred from pretrained target embeddings for unseen-target generalization. DeMixPert models population-level variation using a Gaussian prototype Invertible Network and adaptively combines reusable Gaussian prototypes according to the basal state and perturbation condition. The resulting mixture is mapped to a condition-specific variation distribution. Sampled variations are integrated with the systematic and perturbation-specific components, followed by joint decoding with the basal state to reconstruct perturbed-cell gene expression. Experimental results show that DeMixPert effectively captures heterogeneous single-cell perturbation responses and achieves superior performance across unseen-perturbation settings. The source code is made publicly available upon publication.

  • 8 authors
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Aug 23

It's the Thought that Counts: Evaluating the Attempts of Frontier LLMs to Persuade on Harmful Topics

Persuasion is a powerful capability of large language models (LLMs) that both enables beneficial applications (e.g. helping people quit smoking) and raises significant risks (e.g. large-scale, targeted political manipulation). Prior work has found models possess a significant and growing persuasive capability, measured by belief changes in simulated or real users. However, these benchmarks overlook a crucial risk factor: the propensity of a model to attempt to persuade in harmful contexts. Understanding whether a model will blindly ``follow orders'' to persuade on harmful topics (e.g. glorifying joining a terrorist group) is key to understanding the efficacy of safety guardrails. Moreover, understanding if and when a model will engage in persuasive behavior in pursuit of some goal is essential to understanding the risks from agentic AI systems. We propose the Attempt to Persuade Eval (APE) benchmark, that shifts the focus from persuasion success to persuasion attempts, operationalized as a model's willingness to generate content aimed at shaping beliefs or behavior. Our evaluation framework probes frontier LLMs using a multi-turn conversational setup between simulated persuader and persuadee agents. APE explores a diverse spectrum of topics including conspiracies, controversial issues, and non-controversially harmful content. We introduce an automated evaluator model to identify willingness to persuade and measure the frequency and context of persuasive attempts. We find that many open and closed-weight models are frequently willing to attempt persuasion on harmful topics and that jailbreaking can increase willingness to engage in such behavior. Our results highlight gaps in current safety guardrails and underscore the importance of evaluating willingness to persuade as a key dimension of LLM risk. APE is available at github.com/AlignmentResearch/AttemptPersuadeEval

  • 9 authors
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Feb 14