new

Get trending papers in your email inbox!

Subscribe

Daily Papers

byAK and the research community

Nov 11

DRAP: Dynamics-Risk Adaptive Plasticity for Continual Learning in Physical AI

Continual learning in physical AI differs from conventional continual learning because small per-step policy errors can accumulate over a trajectory. Each deviation may move the agent outside the training distribution, increase subsequent prediction errors, and ultimately cause closed-loop task failure. This work introduces Dynamics-Risk Adaptive Plasticity (DRAP), a replay-free method that estimates the historical importance of adaptable model tensors from sample-level action gradients weighted by local trajectory-amplification risk. A ridge-regularized local linear model is fitted to expert state-action transitions, and the largest singular value of its state-transition matrix provides a policy-independent, Lyapunov-inspired estimate of one-step perturbation amplification. After each task, risk-weighted squared gradients are accumulated in a tensor-level importance memory. During subsequent tasks, DRAP uses normalized cumulative importance to scale the effective AdamW learning rate of each tensor, immediately reducing the plasticity of components that supported previous behavior at dynamically sensitive trajectory points. We instantiate DRAP on a fixed KappaTune-selected subnetwork of OpenVLA and evaluate replay-free sequential adaptation across the LIBERO Spatial, Object, and Goal suites. Compared with standard AdamW fine-tuning and EWC, the results show substantially improved retention of previously learned behaviors while preserving strong new-suite acquisition.

  • 1 authors
·
Nov 3 2

MintFlow: Minimal Trajectory Intervention for Constrained Flow Matching

Flow matching models excel at generative modeling, and many downstream applications require their samples to satisfy prescribed constraints, such as observed measurements and physical laws. However, existing constrained samplers often face a trade-off: enforcing constraints can substantially displace samples from the pretrained data distribution. To address this trade-off, we introduce MintFlow, a training-free constrained sampling framework that formulates constraint enforcement as a minimal intervention on the pretrained flow trajectory. MintFlow seeks the minimal perturbation of an intermediate flow state such that its subsequent evolution under the pretrained flow field satisfies the target constraint. By minimally perturbing the flow state while keeping the pretrained flow field unchanged, MintFlow enforces the constraint while minimizing unnecessary deviation from the pretrained distribution. An adjoint formulation yields a closed-form expression for this perturbation, eliminating expensive iterative optimization. Furthermore, MintFlow adaptively selects the intervention time to balance the required perturbation magnitude with its amplification by the remaining flow. Across a range of tasks in generative vision and physical system modeling, MintFlow achieves competitive constraint satisfaction while preserving the pretrained generative distribution substantially better than state-of-the-art constrained methods.

  • 5 authors
·
Sep 29

SNIC bifurcation and its Application to MEMS

This project focuses on a method to extract a frequency comb in mechanical means, for general interest and numerous practical applications in MEMS. The method of execution is the implementation of a beam that is exhibiting non-linear dynamics that is perturbed and analyzed for its transverse vibrations. The perturbation is an external harmonic driver with a chosen small amplitude and frequency (which is slightly detuned from the beam eigenfrequency), that when engaged with the unperturbed beam oscillations, causes it reach a state of "injection pulling" - an effect that occurs when one harmonic oscillator is coupled with a second one and causes it to oscillate in a frequency near its own. This causes the beam to reach SNIC bifurcation, rendering a frequency comb as desired. Theoretical analysis showed that the problem can be modelled using a non-linear equation of the beam, that translates to a form of the non-linear Duffing equation. While a solution to the dynamics function of the beam is hard to obtain in practice due to mathematical difficulties, a slow evolution model is suggested that is composed of functions of a amplitude and phase. Using several additional mathematical assumptions, the amplitude is seen to be related to the phase, while the phase equation solution is seen to be of the form of Adler's equation. These assumptions ultimately reduce the entire behaviour of the beam to a relatively simple solution to the Adler equation, which has a known analytical solution. Computerized numerical simulations are run on it to check the results and compare them to the theory and desired outcome. The results agreed with the theory and produce the expected frequency comb, showing the assumptions to be valid in extracting the comb.

  • 1 authors
·
Aug 24, 2025

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
·
Oct 11

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
·
Oct 12

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
·
Oct 7

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

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
·
Oct 17

Robust Latent Matters: Boosting Image Generation with Sampling Error

Recent image generation schemes typically capture image distribution in a pre-constructed latent space relying on a frozen image tokenizer. Though the performance of tokenizer plays an essential role to the successful generation, its current evaluation metrics (e.g. rFID) fail to precisely assess the tokenizer and correlate its performance to the generation quality (e.g. gFID). In this paper, we comprehensively analyze the reason for the discrepancy of reconstruction and generation qualities in a discrete latent space, and, from which, we propose a novel plug-and-play tokenizer training scheme to facilitate latent space construction. Specifically, a latent perturbation approach is proposed to simulate sampling noises, i.e., the unexpected tokens sampled, from the generative process. With the latent perturbation, we further propose (1) a novel tokenizer evaluation metric, i.e., pFID, which successfully correlates the tokenizer performance to generation quality and (2) a plug-and-play tokenizer training scheme, which significantly enhances the robustness of tokenizer thus boosting the generation quality and convergence speed. Extensive benchmarking are conducted with 11 advanced discrete image tokenizers with 2 autoregressive generation models to validate our approach. The tokenizer trained with our proposed latent perturbation achieve a notable 1.60 gFID with classifier-free guidance (CFG) and 3.45 gFID without CFG with a sim400M generator. Code: https://github.com/lxa9867/ImageFolder.

  • 10 authors
·
Mar 11, 2025

Dominant Shuffle: A Simple Yet Powerful Data Augmentation for Time-series Prediction

Recent studies have suggested frequency-domain Data augmentation (DA) is effec tive for time series prediction. Existing frequency-domain augmentations disturb the original data with various full-spectrum noises, leading to excess domain gap between augmented and original data. Although impressive performance has been achieved in certain cases, frequency-domain DA has yet to be generalized to time series prediction datasets. In this paper, we found that frequency-domain augmentations can be significantly improved by two modifications that limit the perturbations. First, we found that limiting the perturbation to only dominant frequencies significantly outperforms full-spectrum perturbations. Dominant fre quencies represent the main periodicity and trends of the signal and are more important than other frequencies. Second, we found that simply shuffling the dominant frequency components is superior over sophisticated designed random perturbations. Shuffle rearranges the original components (magnitudes and phases) and limits the external noise. With these two modifications, we proposed dominant shuffle, a simple yet effective data augmentation for time series prediction. Our method is very simple yet powerful and can be implemented with just a few lines of code. Extensive experiments with eight datasets and six popular time series models demonstrate that our method consistently improves the baseline performance under various settings and significantly outperforms other DA methods. Code can be accessed at https://kaizhao.net/time-series.

  • 4 authors
·
May 25, 2024

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
·
Feb 22

Experimental Demonstration of a Balanced Travelling Wave Parametric Amplifier

Superconducting travelling-wave parametric amplifiers (TWPAs) provide broadband gain, low added noise, and high dynamic range, making them attractive for applications requiring wide instantaneous bandwidth. This is crucial for amplifying multiplexed narrow band signals spread over a wide frequency range, such as qubit resonator arrays, or amplifying inherently wide band signals, such as in spectrometers or radiometers. In many cases, however, the useful bandwidth of a TWPA is limited by the production of the idler tone at an image frequency. For three-wave-mixing (3WM) TWPAs, for example, an input signal at f_s is indistinguishable from one at f_p - f_s, which can produce spectral ambiguity when the input spectrum is broadband or not known in advance. We experimentally demonstrate a balanced architecture that doubles the instantaneous image-rejected bandwidth available to a 3WM TWPA by spatially separating the amplified signal from the output pump and generated idler, which resolves the sideband degeneracy. The architecture consists of two amplifiers connected between a pair of 180^{circ} hybrid couplers, with the signal and pump injected and output through the sum and difference ports, respectively. Using two kinetic-inductance TWPAs, we demonstrate approximately 20 dB of signal gain across nearly an octave of bandwidth, together with pump rejection below --20 dB and an average image rejection of approximately --15 dB over the operating band. These results establish balanced TWPAs as a practical approach to broadband parametric amplification, enabling improved contamination free bandwidth and eliminating the need for complex filtering.

  • 4 authors
·
Oct 15

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
·
Feb 5

Excitation of non-modal perturbations in hypersonic boundary layers by free stream forcing. Part III: effects of wall temperature and nose bluntness

This paper constitutes Part III of a series investigating the excitation of non-modal perturbations in hypersonic blunt-nose boundary layers. Based on the numerical shock-fitting harmonic linearised Navier-Stokes (SF-HLNS) approach presented in Part I (Zhao & Dong, J. Fluid Mech. 2025, vol. 1013: A44) and the asymptotic analysis developed in Part II (Dong et al., J. Fluid Mech., under review), the present work focuses specifically on the influence of nose bluntness (Reynolds number R) and wall temperature T_w on receptivity efficiency through seven detailed case studies. Analysed via the three-step asymptotic model, the downstream perturbation amplitude is governed by two distinct factors: the stagnation vorticity perturbation, determined through shock-perturbation interaction and the slow-down convection mechanism, and the parabolic evolution of non-modal perturbations driven by the lift-up mechanism. Increasing R strongly amplifies the stagnation vorticity response, with only mild enhancement of the lift-up effect. In contrast, decreasing T_w strengthens the stagnation vorticity perturbation, but slightly weakens the lift-up effect; the net result is an overall intensification of the downstream perturbation amplitude with decreasing T_w. Furthermore, explicit scaling laws for receptivity efficiency with respect to R and T_w are established. This study completes the theoretical foundation for non-modal receptivity in hypersonic blunt boundary layers, and serves as a key step toward a physics-based transition prediction framework.

  • 4 authors
·
Oct 2

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
·
Apr 29

Parallel Successive Cancellation Perturbation-Enhanced Decoding of Polar Codes via Offline Variance Design

Successive cancellation perturbation-enhanced (SCP) decoding improves the performance of finite-length polar codes by performing multiple SC decoding attempts with receiver-side perturbations. However, many existing perturbation schemes generate or update subsequent perturbations according to the outcomes of previous decoding attempts, resulting in additional decoding latency. In this paper, we propose an offline variance design (OVD) method for parallel SCP (PSCP) decoding of short- and medium-length polar codes. First, we formulate the exact recovery objective conditioned on ordinary SC failure and classify failed frames by the position of the first genie-aided intrinsic error and the number of subsequent intrinsic errors. We also derive a consistent Gaussian representation of the perturbed channel that preserves min-sum SC hard decisions. Second, we construct a class-based approximation of the recovery objective using Gaussian approximation and backward recursions, accounting for both error correction and new errors introduced by perturbations. We prove that both the exact and analytical objectives are nondecreasing and exhibit diminishing marginal gains as independent branches are added. Third, we develop a greedy algorithm to select variances from a finite candidate set for a given code, signal-to-noise ratio (SNR), and number of perturbation branches. All variances are determined offline, allowing the original SC branch and all perturbation branches to start simultaneously. Simulations for rate-1/2 polar codes of lengths 64, 128, 256, and 512 show that OVD-PSCP achieves lower block error rates (BLERs) than conventional SCP with the same number of perturbation branches. The gains are larger for shorter codes and increase as the number of perturbation branches grows.

  • 3 authors
·
Sep 27

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
·
Aug 23

Where Does the Audio Jailbreak Live? A Controlled Frequency-Depth Audit of AdvWave-P on Qwen2-Audio

We audit frequency and decoder-depth claims for AdvWave-P, an additive audio jailbreak, on Qwen2-Audio. The protocol masks frequency components of the perturbation in the short-time Fourier transform (STFT) domain and measures attack success and audio-span representations. On 520 AdvBench prompts, the primary judge labels 76.7% of adversarial inputs as jailbreaks. A condition-blind, single-annotator validation yields a Rogan-Gladen sensitivity estimate of 0.87 for this condition (about 0.83-0.95 with validation-rate uncertainty); this correction is not applied to masked conditions. The apparent frequency ranking depends on the partition: energy share alone predicts the standard eight-band ranking (Spearman's rho = 0.95), and equal-Hz and equal-energy partitions show that masking any tested band can sharply reduce attack success. At a finer 16-band equal-energy resolution, however, masking the narrow 7520-7960 Hz band leaves ASR at 0.10, which remains unresolved without a matched control. Matched-energy scattered-removal tests show that contiguous removal is more damaging in lower bands, while both forms approach the floor in upper bands. Global rescaling leaves ASR near baseline but tests amplitude sensitivity rather than frequency location. In a re-optimization pilot (n = 20), tested single- and two-band supports reach ASRs of 0.00, 0.25, and 0.40, while random supports covering about half the STFT bins reach a mean of 0.86. In a prompt- and energy-adjusted model, audio-span divergence is associated with band necessity, with the coefficient rising from +0.63 at the projector output to +0.93 at layer 30 (contrast +0.293, 95% CI [0.11, 0.51]). This association is not a causal localization, and single-layer patching does not establish a causal layer. The results support partition-aware auditing of frequency claims, leaving the fine-resolution top-band result and broader generality open.

  • 7 authors
·
Oct 3

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
·
Sep 27

Femtosecond laser-induced cavitation seeds liquid-jet breakup beyond the Rayleigh-Plateau stability limit

The Rayleigh-Plateau instability predicts that infinitesimal perturbations of a liquid jet grow only for kR < 1, with kR = 1 marking the classical stability boundary. Here, we show that femtosecond-laser-induced cavitation generates a localized, impulsive recoil perturbation on a flowing liquid jet, enabling a two-dimensional map of jet breakup across the (kR, epsilon/R) plane. The perturbation's spacing (wavelength) and strength (amplitude) are set independently by the laser repetition rate and pulse energy, respectively. At low amplitudes, tuning the repetition rate recovers the classical Rayleigh-Plateau dispersion relation and its kR = 1 cutoff, while increasing the wavelength enables controlled generation of monodisperse droplet trains, bidisperse droplet populations, and ultimately isolated single droplets. Along the amplitude axis, low pulse energies produce a seed that amplifies only the imposed wavenumber, whereas above a critical energy Ec, the seed broadens to excite many wavenumbers simultaneously. At still higher amplitudes, we demonstrate deterministic breakup for kR > 1, extending to kR = 1.9, with laser-synchronized droplet production rates up to 0.2 MHz. These results establish localized femtosecond-laser-induced cavitation as a route to controlled Rayleigh-Plateau breakup both within and beyond the classical linear-stability boundary.

  • 4 authors
·
Sep 30

Revisit Input Perturbation Problems for LLMs: A Unified Robustness Evaluation Framework for Noisy Slot Filling Task

With the increasing capabilities of large language models (LLMs), these high-performance models have achieved state-of-the-art results on a wide range of natural language processing (NLP) tasks. However, the models' performance on commonly-used benchmark datasets often fails to accurately reflect their reliability and robustness when applied to real-world noisy data. To address these challenges, we propose a unified robustness evaluation framework based on the slot-filling task to systematically evaluate the dialogue understanding capability of LLMs in diverse input perturbation scenarios. Specifically, we construct a input perturbation evaluation dataset, Noise-LLM, which contains five types of single perturbation and four types of mixed perturbation data. Furthermore, we utilize a multi-level data augmentation method (character, word, and sentence levels) to construct a candidate data pool, and carefully design two ways of automatic task demonstration construction strategies (instance-level and entity-level) with various prompt templates. Our aim is to assess how well various robustness methods of LLMs perform in real-world noisy scenarios. The experiments have demonstrated that the current open-source LLMs generally achieve limited perturbation robustness performance. Based on these experimental observations, we make some forward-looking suggestions to fuel the research in this direction.

  • 11 authors
·
Oct 10, 2023

Hallucinations in Neural Automatic Speech Recognition: Identifying Errors and Hallucinatory Models

Hallucinations are a type of output error produced by deep neural networks. While this has been studied in natural language processing, they have not been researched previously in automatic speech recognition. Here, we define hallucinations in ASR as transcriptions generated by a model that are semantically unrelated to the source utterance, yet still fluent and coherent. The similarity of hallucinations to probable natural language outputs of the model creates a danger of deception and impacts the credibility of the system. We show that commonly used metrics, such as word error rates, cannot differentiate between hallucinatory and non-hallucinatory models. To address this, we propose a perturbation-based method for assessing the susceptibility of an automatic speech recognition (ASR) model to hallucination at test time, which does not require access to the training dataset. We demonstrate that this method helps to distinguish between hallucinatory and non-hallucinatory models that have similar baseline word error rates. We further explore the relationship between the types of ASR errors and the types of dataset noise to determine what types of noise are most likely to create hallucinatory outputs. We devise a framework for identifying hallucinations by analysing their semantic connection with the ground truth and their fluency. Finally, we discover how to induce hallucinations with a random noise injection to the utterance.

  • 2 authors
·
Jan 3, 2024

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
·
Sep 27

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
·
Jan 24, 2018

Exploring Quality and Generalizability in Parameterized Neural Audio Effects

Deep neural networks have shown promise for music audio signal processing applications, often surpassing prior approaches, particularly as end-to-end models in the waveform domain. Yet results to date have tended to be constrained by low sample rates, noise, narrow domains of signal types, and/or lack of parameterized controls (i.e. "knobs"), making their suitability for professional audio engineering workflows still lacking. This work expands on prior research published on modeling nonlinear time-dependent signal processing effects associated with music production by means of a deep neural network, one which includes the ability to emulate the parameterized settings you would see on an analog piece of equipment, with the goal of eventually producing commercially viable, high quality audio, i.e. 44.1 kHz sampling rate at 16-bit resolution. The results in this paper highlight progress in modeling these effects through architecture and optimization changes, towards increasing computational efficiency, lowering signal-to-noise ratio, and extending to a larger variety of nonlinear audio effects. Toward these ends, the strategies employed involved a three-pronged approach: model speed, model accuracy, and model generalizability. Most of the presented methods provide marginal or no increase in output accuracy over the original model, with the exception of dataset manipulation. We found that limiting the audio content of the dataset, for example using datasets of just a single instrument, provided a significant improvement in model accuracy over models trained on more general datasets.

  • 2 authors
·
Jun 9, 2020

When Good Sounds Go Adversarial: Jailbreaking Audio-Language Models with Benign Inputs

As large language models become increasingly integrated into daily life, audio has emerged as a key interface for human-AI interaction. However, this convenience also introduces new vulnerabilities, making audio a potential attack surface for adversaries. Our research introduces WhisperInject, a two-stage adversarial audio attack framework that can manipulate state-of-the-art audio language models to generate harmful content. Our method uses imperceptible perturbations in audio inputs that remain benign to human listeners. The first stage uses a novel reward-based optimization method, Reinforcement Learning with Projected Gradient Descent (RL-PGD), to guide the target model to circumvent its own safety protocols and generate harmful native responses. This native harmful response then serves as the target for Stage 2, Payload Injection, where we use Projected Gradient Descent (PGD) to optimize subtle perturbations that are embedded into benign audio carriers, such as weather queries or greeting messages. Validated under the rigorous StrongREJECT, LlamaGuard, as well as Human Evaluation safety evaluation framework, our experiments demonstrate a success rate exceeding 86% across Qwen2.5-Omni-3B, Qwen2.5-Omni-7B, and Phi-4-Multimodal. Our work demonstrates a new class of practical, audio-native threats, moving beyond theoretical exploits to reveal a feasible and covert method for manipulating AI behavior.

AIM-Intelligence AIM Intelligence
·
Aug 5, 2025 2

Adversarial Style Augmentation for Domain Generalization

It is well-known that the performance of well-trained deep neural networks may degrade significantly when they are applied to data with even slightly shifted distributions. Recent studies have shown that introducing certain perturbation on feature statistics (\eg, mean and standard deviation) during training can enhance the cross-domain generalization ability. Existing methods typically conduct such perturbation by utilizing the feature statistics within a mini-batch, limiting their representation capability. Inspired by the domain generalization objective, we introduce a novel Adversarial Style Augmentation (ASA) method, which explores broader style spaces by generating more effective statistics perturbation via adversarial training. Specifically, we first search for the most sensitive direction and intensity for statistics perturbation by maximizing the task loss. By updating the model against the adversarial statistics perturbation during training, we allow the model to explore the worst-case domain and hence improve its generalization performance. To facilitate the application of ASA, we design a simple yet effective module, namely AdvStyle, which instantiates the ASA method in a plug-and-play manner. We justify the efficacy of AdvStyle on tasks of cross-domain classification and instance retrieval. It achieves higher mean accuracy and lower performance fluctuation. Especially, our method significantly outperforms its competitors on the PACS dataset under the single source generalization setting, \eg, boosting the classification accuracy from 61.2\% to 67.1\% with a ResNet50 backbone. Our code will be available at https://github.com/YBZh/AdvStyle.

  • 5 authors
·
Jan 29, 2023

Sample-Based Quantum Diagonalization with Amplitude Amplification

Recently, sample-based quantum diagonalization (SQD) has emerged as a promising approach to compute ground and excited states of problem Hamiltonians.This method classically diagonalizes a Hamiltonian in a subspace that is spanned by samples obtained from a quantum computer. However, by its nature, SQD suffers from a fundamental sampling problem, as some basis states that are required for a targeted accuracy may only be sampled extremely rarely. To alleviate this limitation, we introduce the SQD-AA algorithm that combines SQD with amplitude amplification (AA). SQD-AA uses AA to sequentially reduce probabilities of already measured bitstrings, thus making the observation of new ones more likely. We observe a reduction in the total query complexity of more than a factor 100 for algebraically and exponentially decaying model distributions, and analytically show a quadratic advantage for the latter. Moreover, we evaluate real molecules in an early fault-tolerant scenario and compare SQD-AA to SQD and iterative quantum phase estimation (iQPE). For all considered examples, we observe the lowest total number of T-gates for SQD-AA while only requiring circuits that are 3-4 orders of magnitude shallower than those needed for iQPE. Given this substantial reduction in circuit depth compared to iQPE while saving 2 orders of magnitude in total runtime compared to SQD, we expect a significant regime in early fault-tolerance where SQD-AA runs feasibly, but iQPE circuits are too deep to execute confidently.

  • 3 authors
·
May 3

Decodable but Not Detectable: A Leakage Fingerprint for Near-OOD Benchmarks

While auditing a perturbation-based OOD detector on a document benchmark, we recorded an AUROC of 0.326 -- well below the 0.5 chance level. The cause is a benchmark leak: the designated "OOD" class is one the model was trained on, so its examples sit inside the in-distribution fit set and the detector is penalized for correctly ranking them as familiar. Deleting the class and retraining 35 models across two domains raises the score to 0.911. We distill the contamination into a leak fingerprint -- near-perfect supervised decodability (AUROC approximately 1) coupled with unsupervised detection collapsed below 0.65 -- and validate it on a controlled battery of 52 settings (20 leaked, 32 clean) across ResNet-50 and ViT-B/16 on CIFAR-10/100, achieving sensitivity 18/20 and specificity 31/32 in embedding space; the matched fit-set-exclusion controls are perfect at 20/20. An in-the-wild audit of 24 standard near/far OOD benchmark pairs fires on exactly one (the intrinsically hard CIFAR-100 vs CIFAR-10 pair) and on no far-OOD pair, confirming specificity and that standard cross-dataset construction is clean. Under the corrected protocol, perturbation signals are decodable but not detectable: a supervised reader recovers the OOD signal (AUROC 0.87-1.00) while no unsupervised detector does, and the perturbation method does not improve on plain Mahalanobis distance. We provide a theoretical account of why and, for transparency, retract an earlier circular correlation. The contributions are a corrected protocol and a validated leak diagnostic, not a new OOD method.

  • 1 authors
·
Jul 1

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
·
Aug 13

When Non-Adversarial Noise Hurts Learning: Benchmarking Skill Self-Evolution in Agents

Large language model agents increasingly improve by distilling experience into reusable skills, but errors in that experience can persist in learned rules and affect later tasks. Existing evaluations largely examine clean learning or perturbations encountered after skills are frozen, leaving robustness during self-evolution insufficiently understood. We introduce RSE-Bench, to our knowledge the first benchmark for evaluating skill self-evolution under ordinary, non-adversarial noise. It spans four domains and six benchmarks, with controlled perturbations to instructions, environmental evidence, execution records, and outcome--record pairings that preserve the underlying tasks and native scoring rules. The protocol separates noise during learning from input-side noise at evaluation, testing frozen skill stores on held-out tasks. We also introduce RSEClaw, a method-agnostic framework supporting consistent noise injection and process diagnostics of actual exposure and skill updates. Across three methods and two backbones, noisy learning retains only 25.5%--42.1% of the aggregate gain achieved by clean self-evolution, depending on the noise type. Perturbations confined to execution records and outcome--record pairings cause average losses comparable to input-side noise, despite leaving the original executions and evaluations intact. Diagnostics further identify differences in candidate skill text that coexist with small changes in mean held-out performance.

  • 22 authors
·
Oct 13

Robust Learnability of Sample-Compressible Distributions under Noisy or Adversarial Perturbations

Learning distribution families over R^d is a fundamental problem in unsupervised learning and statistics. A central question in this setting is whether a given family of distributions possesses sufficient structure to be (at least) information-theoretically learnable and, if so, to characterize its sample complexity. In 2018, Ashtiani et al. reframed sample compressibility, originally due to Littlestone and Warmuth (1986), as a structural property of distribution classes, proving that it guarantees PAC-learnability. This discovery subsequently enabled a series of recent advancements in deriving nearly tight sample complexity bounds for various high-dimensional open problems. It has been further conjectured that the converse also holds: every learnable class admits a tight sample compression scheme. In this work, we establish that sample compressible families remain learnable even from perturbed samples, subject to a set of necessary and sufficient conditions. We analyze two models of data perturbation: (i) an additive independent noise model, and (ii) an adversarial corruption model, where an adversary manipulates a limited subset of the samples unknown to the learner. Our results are general and rely on as minimal assumptions as possible. We develop a perturbation-quantization framework that interfaces naturally with the compression scheme and leads to sample complexity bounds that scale gracefully with the noise level and corruption budget. As concrete applications, we establish new sample complexity bounds for learning finite mixtures of high-dimensional uniform distributions under both noise and adversarial perturbations, as well as for learning Gaussian mixture models from adversarially corrupted samples, resolving two open problems in the literature.

  • 2 authors
·
Jun 6, 2025

Accelerating High-Fidelity Waveform Generation via Adversarial Flow Matching Optimization

This paper introduces PeriodWave-Turbo, a high-fidelity and high-efficient waveform generation model via adversarial flow matching optimization. Recently, conditional flow matching (CFM) generative models have been successfully adopted for waveform generation tasks, leveraging a single vector field estimation objective for training. Although these models can generate high-fidelity waveform signals, they require significantly more ODE steps compared to GAN-based models, which only need a single generation step. Additionally, the generated samples often lack high-frequency information due to noisy vector field estimation, which fails to ensure high-frequency reproduction. To address this limitation, we enhance pre-trained CFM-based generative models by incorporating a fixed-step generator modification. We utilized reconstruction losses and adversarial feedback to accelerate high-fidelity waveform generation. Through adversarial flow matching optimization, it only requires 1,000 steps of fine-tuning to achieve state-of-the-art performance across various objective metrics. Moreover, we significantly reduce inference speed from 16 steps to 2 or 4 steps. Additionally, by scaling up the backbone of PeriodWave from 29M to 70M parameters for improved generalization, PeriodWave-Turbo achieves unprecedented performance, with a perceptual evaluation of speech quality (PESQ) score of 4.454 on the LibriTTS dataset. Audio samples, source code and checkpoints will be available at https://github.com/sh-lee-prml/PeriodWave.

  • 3 authors
·
Aug 15, 2024 4

Inv-Entropy: A Fully Probabilistic Framework for Uncertainty Quantification in Language Models

Large language models (LLMs) have transformed natural language processing, but their reliable deployment requires effective uncertainty quantification (UQ). Existing UQ methods are often heuristic and lack a probabilistic foundation. This paper begins by providing a theoretical justification for the role of perturbations in UQ for LLMs. We then introduce a dual random walk perspective, modeling input-output pairs as two Markov chains with transition probabilities defined by semantic similarity. Building on this, we propose a fully probabilistic framework based on an inverse model, which quantifies uncertainty by evaluating the diversity of the input space conditioned on a given output through systematic perturbations. Within this framework, we define a new uncertainty measure, Inv-Entropy. A key strength of our framework is its flexibility: it supports various definitions of uncertainty measures, embeddings, perturbation strategies, and similarity metrics. We also propose GAAP, a perturbation algorithm based on genetic algorithms, which enhances the diversity of sampled inputs. In addition, we introduce a new evaluation metric, Temperature Sensitivity of Uncertainty (TSU), which directly assesses uncertainty without relying on correctness as a proxy. Extensive experiments demonstrate that Inv-Entropy outperforms existing semantic UQ methods. The code to reproduce the results can be found at https://github.com/UMDataScienceLab/Uncertainty-Quantification-for-LLMs.

  • 5 authors
·
Jun 11, 2025

Towards Robust Defense against Customization via Protective Perturbation Resistant to Diffusion-based Purification

Diffusion models like Stable Diffusion have become prominent in visual synthesis tasks due to their powerful customization capabilities, which also introduce significant security risks, including deepfakes and copyright infringement. In response, a class of methods known as protective perturbation emerged, which mitigates image misuse by injecting imperceptible adversarial noise. However, purification can remove protective perturbations, thereby exposing images again to the risk of malicious forgery. In this work, we formalize the anti-purification task, highlighting challenges that hinder existing approaches, and propose a simple diagnostic protective perturbation named AntiPure. AntiPure exposes vulnerabilities of purification within the "purification-customization" workflow, owing to two guidance mechanisms: 1) Patch-wise Frequency Guidance, which reduces the model's influence over high-frequency components in the purified image, and 2) Erroneous Timestep Guidance, which disrupts the model's denoising strategy across different timesteps. With additional guidance, AntiPure embeds imperceptible perturbations that persist under representative purification settings, achieving effective post-customization distortion. Experiments show that, as a stress test for purification, AntiPure achieves minimal perceptual discrepancy and maximal distortion, outperforming other protective perturbation methods within the purification-customization workflow.

  • 4 authors
·
Sep 18, 2025

Random Sub-Samples Generation for Self-Supervised Real Image Denoising

With sufficient paired training samples, the supervised deep learning methods have attracted much attention in image denoising because of their superior performance. However, it is still very challenging to widely utilize the supervised methods in real cases due to the lack of paired noisy-clean images. Meanwhile, most self-supervised denoising methods are ineffective as well when applied to the real-world denoising tasks because of their strict assumptions in applications. For example, as a typical method for self-supervised denoising, the original blind spot network (BSN) assumes that the noise is pixel-wise independent, which is much different from the real cases. To solve this problem, we propose a novel self-supervised real image denoising framework named Sampling Difference As Perturbation (SDAP) based on Random Sub-samples Generation (RSG) with a cyclic sample difference loss. Specifically, we dig deeper into the properties of BSN to make it more suitable for real noise. Surprisingly, we find that adding an appropriate perturbation to the training images can effectively improve the performance of BSN. Further, we propose that the sampling difference can be considered as perturbation to achieve better results. Finally we propose a new BSN framework in combination with our RSG strategy. The results show that it significantly outperforms other state-of-the-art self-supervised denoising methods on real-world datasets. The code is available at https://github.com/p1y2z3/SDAP.

  • 5 authors
·
Jul 31, 2023

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
·
Oct 18

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
·
Mar 26, 2024

Spectral Bottleneck in Deep Neural Networks: Noise is All You Need

Deep neural networks are known to exhibit a spectral learning bias, wherein low-frequency components are learned early in training, while high-frequency modes emerge more gradually in later epochs. However, when the target signal lacks low-frequency components and is dominated by broadband high frequencies, training suffers from a 'spectral bottleneck', and the model fails to reconstruct the entire signal, including the frequency components that lie within the network's representational capacity. We examine such a scenario in the context of implicit neural representations (INRs) with sinusoidal representation networks (SIRENs), focusing on the challenge of fitting high-frequency-dominant signals that are susceptible to spectral bottleneck. To effectively fit any target signal irrespective of it's frequency content, we propose a generalized target-aware 'weight perturbation scheme' (WINNER - weight initialization with noise for neural representations) for network initialization. The scheme perturbs uniformly initialized weights with Gaussian noise, where the noise scales are adaptively determined by the spectral centroid of the target signal. We show that the noise scales can provide control over the spectra of network activations and the eigenbasis of the empirical neural tangent kernel. This method not only addresses the spectral bottleneck but also yields faster convergence and with improved representation accuracy, outperforming state-of-the-art approaches in audio fitting and achieving notable gains in image fitting and denoising tasks. Beyond signal reconstruction, our approach opens new directions for adaptive weight initialization strategies in computer vision and scientific machine learning.

  • 5 authors
·
Sep 9, 2025

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
·
Feb 9

Unlasting: Unpaired Single-Cell Multi-Perturbation Estimation by Dual Conditional Diffusion Implicit Bridges

Estimating single-cell responses across various perturbations facilitates the identification of key genes and enhances drug screening, significantly boosting experimental efficiency. However, single-cell sequencing is a destructive process, making it impossible to capture the same cell's phenotype before and after perturbation. Consequently, data collected under perturbed and unperturbed conditions are inherently unpaired. Existing methods either attempt to forcibly pair unpaired data using random sampling, or neglect the inherent relationship between unperturbed and perturbed cells during the modeling. In this work, we propose a framework based on Dual Diffusion Implicit Bridges (DDIB) to learn the mapping between different data distributions, effectively addressing the challenge of unpaired data. We further interpret this framework as a form of data augmentation. We integrate gene regulatory network (GRN) information to propagate perturbation signals in a biologically meaningful way, and further incorporate a masking mechanism to predict silent genes, improving the quality of generated profiles. Moreover, gene expression under the same perturbation often varies significantly across cells, frequently exhibiting a bimodal distribution that reflects intrinsic heterogeneity. To capture this, we introduce a more suitable evaluation metric. We propose Unlasting, dual conditional diffusion models that overcome the problem of unpaired single-cell perturbation data and strengthen the model's insight into perturbations under the guidance of the GRN, with a dedicated mask model designed to improve generation quality by predicting silent genes. In addition, we introduce a biologically grounded evaluation metric that better reflects the inherent heterogeneity in single-cell responses.

  • 8 authors
·
Jun 26, 2025

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
·
Aug 31

Adaptive Activation Cancellation for Hallucination Mitigation in Large Language Models

Large Language Models frequently generate fluent but factually incorrect text. We propose Adaptive Activation Cancellation (AAC), a real-time inference-time framework that treats hallucination-associated neural activations as structured interference within the transformer residual stream, drawing an explicit analogy to classical adaptive noise cancellation from signal processing. The framework identifies Hallucination Nodes (H-Nodes) via layer-wise linear probing and suppresses them using a confidence-weighted forward hook during auto-regressive generation -- requiring no external knowledge, no fine-tuning, and no additional inference passes. Evaluated across OPT-125M, Phi-3-mini, and LLaMA 3-8B on TruthfulQA and HaluEval, the real-time hook is the only intervention that consistently improves downstream accuracy on all three scales. Critically, the method is strictly surgical: WikiText-103 perplexity and MMLU reasoning accuracy are preserved at exactly 0.0% degradation across all three model scales, a property that distinguishes AAC from interventions that trade fluency or general capability for factual improvement. On the LLaMA 3-8B scale, the hook additionally yields positive generation-level gains (MC1 +0.04; MC2 +0.003; Token-F1 +0.003) while achieving probe-space selectivity 5.94x - 3.5x higher than the ITI baseline -- demonstrating that targeted neuron-level suppression can simultaneously improve factual accuracy and preserve model capability.

  • 6 authors
·
Mar 9

Towards High-Quality and Efficient Speech Bandwidth Extension with Parallel Amplitude and Phase Prediction

Speech bandwidth extension (BWE) refers to widening the frequency bandwidth range of speech signals, enhancing the speech quality towards brighter and fuller. This paper proposes a generative adversarial network (GAN) based BWE model with parallel prediction of Amplitude and Phase spectra, named AP-BWE, which achieves both high-quality and efficient wideband speech waveform generation. The proposed AP-BWE generator is entirely based on convolutional neural networks (CNNs). It features a dual-stream architecture with mutual interaction, where the amplitude stream and the phase stream communicate with each other and respectively extend the high-frequency components from the input narrowband amplitude and phase spectra. To improve the naturalness of the extended speech signals, we employ a multi-period discriminator at the waveform level and design a pair of multi-resolution amplitude and phase discriminators at the spectral level, respectively. Experimental results demonstrate that our proposed AP-BWE achieves state-of-the-art performance in terms of speech quality for BWE tasks targeting sampling rates of both 16 kHz and 48 kHz. In terms of generation efficiency, due to the all-convolutional architecture and all-frame-level operations, the proposed AP-BWE can generate 48 kHz waveform samples 292.3 times faster than real-time on a single RTX 4090 GPU and 18.1 times faster than real-time on a single CPU. Notably, to our knowledge, AP-BWE is the first to achieve the direct extension of the high-frequency phase spectrum, which is beneficial for improving the effectiveness of existing BWE methods.

  • 4 authors
·
Jan 12, 2024

The Differentiable Auditory Loop (DAL): An ML Framework for Hyper-Personalized Hearing Aids

Conventional hearing aids rely on fixed, frequency-dependent amplification and compression to manage reduced sensitivity, which often fails to provide sufficient listening support in complex environments, such as situations with multiple speakers (the ``cocktail party'' problem). To more comprehensively address the underlying encoding dysfunctions of hearing loss, we introduce the Differentiable Auditory Loop (DAL), a new open-source framework for personalized hearing aid design and fitting. Our first implementation of DAL incorporates CARFAC, a differentiable model of human cochlear function, which we ported to JAX, to optimize a deep neural network to match impaired auditory neural activity patterns with a normal-hearing reference. To build a hearing aid with the fine-grained spectro-temporal signal processing required, we adopt SEANet, a waveform-to-waveform fully convolutional UNet generator. We fine-tune the network by comparing the outputs of a CARFAC model fitted to normal hearing with that of a CARFAC model fitted to match each subject's individual hearing impairment. The comparison is done using loss functions derived from the respective CARFAC neural activity pattern (NAP) outputs and stabilized auditory images (SAIs), the latter providing a 2D representation that captures phase-insensitive temporal structure in the auditory nerve output. Through gradient descent, the SEANet model learns to both denoise the input and compensate for the hearing loss modelled by the impaired CARFAC model. Across neural-representation and signal-fidelity metrics, the DAL-optimized SEANet model outperformed the tested master hearing aid (MHA) baselines. The DAL framework provides a practical path toward model-based, machine-learning-driven personalization of hearing aid signal processing. Next steps include hardware deployment to enable real-world clinical testing.

  • 6 authors
·
Jun 1

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
·
Oct 19

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
·
Jul 14, 2025

Diagnosing and Mitigating Modality Interference in Multimodal Large Language Models

Multimodal Large Language Models have demonstrated impressive capabilities across tasks, yet they often exhibit difficulty in distinguishing task-relevant from irrelevant signals -- particularly in tasks like Visual Question Answering -- which can lead to susceptibility to misleading or spurious inputs. We refer to this broader limitation as the Cross-Modality Competency Problem -- the model's inability to fairly evaluate all modalities. This vulnerability becomes more evident in modality-specific tasks -- such as image classification or pure text question answering -- where models are expected to rely solely on one modality. In such tasks, spurious information from irrelevant modalities often leads to significant performance degradation. We refer to this failure as Modality Interference, which serves as a concrete and measurable instance of the cross-modality competency problem, and we further design a perturbation-based causal diagnostic experiment to verify and quantify this problem. To mitigate modality interference, we propose a novel framework to finetune MLLMs, including perturbation-based data augmentations with both heuristic perturbations and adversarial perturbations, and a consistency regularization strategy applying on model outputs with original and perturbed inputs. Experiments on multiple benchmark datasets (image-heavy, text-heavy and multimodal tasks) and multiple model families with different scales demonstrate significant improvements in robustness and cross-modality competency, indicating our method's effectiveness in boosting unimodal reasoning ability while enhancing performance on multimodal tasks.

ucdavis UC Davis
·
May 26, 2025

Image Tokenizer Needs Post-Training

Recent image generative models typically capture the image distribution in a pre-constructed latent space, relying on a frozen image tokenizer. However, there exists a significant discrepancy between the reconstruction and generation distribution, where current tokenizers only prioritize the reconstruction task that happens before generative training without considering the generation errors during sampling. In this paper, we comprehensively analyze the reason for this discrepancy in a discrete latent space, and, from which, we propose a novel tokenizer training scheme including both main-training and post-training, focusing on improving latent space construction and decoding respectively. During the main training, a latent perturbation strategy is proposed to simulate sampling noises, \ie, the unexpected tokens generated in generative inference. Specifically, we propose a plug-and-play tokenizer training scheme, which significantly enhances the robustness of tokenizer, thus boosting the generation quality and convergence speed, and a novel tokenizer evaluation metric, \ie, pFID, which successfully correlates the tokenizer performance to generation quality. During post-training, we further optimize the tokenizer decoder regarding a well-trained generative model to mitigate the distribution difference between generated and reconstructed tokens. With a sim400M generator, a discrete tokenizer trained with our proposed main training achieves a notable 1.60 gFID and further obtains 1.36 gFID with the additional post-training. Further experiments are conducted to broadly validate the effectiveness of our post-training strategy on off-the-shelf discrete and continuous tokenizers, coupled with autoregressive and diffusion-based generators.

  • 10 authors
·
Sep 15, 2025 2

ISOMORPH: A Supply Chain Digital Twin for Simulation, Dataset Generation, and Forecasting Benchmarks

Open time-series forecasting (TSF) benchmarks cover retail, energy, weather, and traffic, but supply-chain logistics remains underserved. We introduce ISOMORPH, the first public digital twin of a multi-echelon logistics network with fully interpretable, user-configurable parameters and modular topology, demand process, and control rules. The simulator advances a directed routing graph in discrete time: demand arrives at the destination, is served from stock or recorded as backlog, and triggers replenishment through the network. The state vector tracks per-node on-hand inventory with outstanding orders, in-transit shipments, and a smoothed demand estimate, so the dynamics close as a Markov chain on a tractable state space whose transition kernel acts linearly on the empirical distribution of the state. The released data reproduces the bullwhip effect at empirically consistent magnitudes, and three conservation laws encoded in the Markov chain serve as verification tools when users extend the simulator. We release datasets at two catalogue scales (C=50 and C=200) with six scenario sweeps producing 30 additional rollouts and 20 Latin-hypercube perturbations, exhibiting dynamics absent from fixed TSF benchmarks: variance amplification, cascading bottlenecks, regime shifts, and cross-channel coupling through shared macro shocks. Zero-shot evaluation of four foundation models (Chronos, Moirai, TimesFM, Lag-Llama) shows MASE values exceeding public GIFT-Eval references at low-to-moderate horizons, supporting incorporation into existing benchmarks. The same pairing produces forecast confidence bands via Latin-hypercube perturbation of demand-side knobs, forward UQ from parameter uncertainty unavailable on standard TSF datasets, demonstrating that foundation models can serve as fast surrogates for the digital twin's forward UQ. Code (MIT): https://github.com/tuhinsahai/ISOMORPH.

  • 9 authors
·
May 11

VirusCascade: Hijacking Collaborative Reflection in LLM-Powered Recommender Agents

Advancing beyond traditional static scoring models, LLM-powered agentic recommender systems (LLM-ARS) instantiate users and items as autonomous agents, whose semantic states are dynamically refined through a recurrent process known as collaborative reflection. While this mechanism improves recommendation quality, it simultaneously introduces a systemic vulnerability: adversarial evidence injected into a single agent can be rationalised into a legitimate preference narrative, written back into memory, and propagated to other agents through interaction contexts. We term the local rationalisation process reflection laundering, and its system-wide escalation through collaborative reflection collaborative-reflection hijacking. Existing attacks on recommender systems, whether based on interaction-level data poisoning or text-level adversarial perturbations, assume static pipelines and thus cannot exploit this recurrent, multi-agent amplification pathway. To bridge this gap, we first conduct a controlled vulnerability analysis that establishes two exploitable properties underlying collaborative-reflection hijacking: reflective persistence and cross-agent propagation. Then building on these findings, we propose VirusCascade, the first black-box targeted promotion attack that jointly shapes semantic and structural attack surfaces: the former ensures the target item is naturally rationalised as satisfying broad user preferences, the latter positions it for system-wide propagation. Extensive experiments on four real-world datasets across diverse LLM-ARS architectures demonstrate that VirusCascade consistently achieves state-of-the-art targeted exposure under evaluated stealth constraints, reaching a mean E@20 of 0.384 and surpassing the strongest baseline by an absolute margin of +0.185.

  • 6 authors
·
Sep 28

Fidelity Is Not Safety: Gently-Compressed LLMs Pass Every Data-Free Quality Guard Yet Invent Procedure Steps in Agentic Execution

Practitioners accept a compressed language model once it clears a stack of data-cheap quality guards: perplexity within a small factor of the original, downstream accuracy (for example MMLU) inside a confidence interval, and data-free output-fidelity signals that compare the compressed and original network's internal representations under random probe inputs. This stack has a blind spot. Across three model families, gently-compressed models clear every guard and then invent procedure steps that were never in the instructions when they run a standard operating procedure (SOP) as an agent. The effect is operator-specific: coherent low-rank (SVD) truncation induces it, and magnitude pruning matched to the same perplexity does not. One dissociation isolates the cause. The same compressed weights that CI-win a paired output-fidelity test CI-fail the invented-step canary. The governing axis is the coherence of the compression error times its rate; the magnitude of the damage does not predict it. The data-free fidelity probe is a fidelity oracle by construction, so it cannot see this axis. We characterize the blindspot and dissociation with paired confidence intervals on a pre-registered, powered canary across three architectures. Operator-specificity replicates on all three, and the perplexity-guard evasion appears where the model admits in-guard low-rank headroom. We then give a data-free screen: a two-axis statistic of the compression error (coherent-fraction and error-rate) that flags the failing builds with fixed thresholds across architectures and matches the coherence-times-rate mechanism. Perplexity, MMLU, and fidelity acceptance do not certify agent safety. Screen gently-compressed low-rank builds before agentic deployment

  • 2 authors
·
Jul 29

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
·
Mar 21, 2025