Daily Papers

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.

We use a Stochastic Hybrid Automaton (SHA) model of prostate cancer evolution under intermittent androgen suppression (IAS) to study a threshold-based policy for therapy design. IAS is currently one of the most widely used treatments for advanced prostate cancer. Patients undergoing IAS are submitted to cycles of treatment (in the form of androgen deprivation) and off-treatment periods in an alternating manner. One of the main challenges in IAS is to optimally design a therapy scheme, i.e., to determine when to discontinue and recommence androgen suppression. The level of prostate specific antigen (PSA) in a patient's serum is frequently monitored to determine when the patient will be taken off therapy and when therapy will resume. The threshold-based policy we propose is parameterized by lower and upper PSA threshold values and is associated with a cost metric that combines clinically relevant measures of therapy success. Using Infinitesimal Perturbation Analysis (IPA), we derive unbiased gradient estimators of this cost metric with respect to the controllable PSA threshold values based on actual data and show how these estimators can be used to adaptively adjust controllable parameters so as to improve therapy outcomes based on the cost metric defined.

Multi-attribute user records are inherently heterogeneous, often combining continuous, categorical, and binary attributes, and they frequently exhibit strong cross-attribute dependencies. Designing high-utility metric differential privacy (mDP) mechanisms for such records is challenging. Simple predefined mechanisms, such as distance-based noise, may be poorly aligned with task-specific utility loss, whereas fully optimization-based mechanisms can be computationally prohibitive for multi-attribute records. We propose Dependency-aware Heterogeneous Data Perturbation (DepHDP)}, a framework for multi-attribute mDP that combines dependency-aware attribute grouping with heterogeneous perturbation design. Rather than applying a one-size-fits-all mechanism, DepHDP selects an appropriate perturbation strategy for each attribute or attribute group, choosing between efficient predefined mechanisms, such as Laplace or Exponential mechanisms, and optimization-based designs. This selection is guided by both domain size and a predefined-noise adequacy criterion, which quantifies whether task-induced utility loss can be well explained by perturbation magnitude. To support scalable end-to-end optimization, DepHDP estimates group-level utility loss through sampling and lightweight surrogate modeling, and jointly optimizes privacy-budget allocation and group-wise mechanism design under a global ell_p-metric mDP constraint. Across three case studies, DepHDP improves privacy--utility trade-offs over uniform baselines at lower computational cost than full-record OPT on evaluated domains.

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.

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.

Human action understanding is crucial for the advancement of multimodal systems. While recent developments, driven by powerful large language models (LLMs), aim to be general enough to cover a wide range of categories, they often overlook the need for more specific capabilities. In this work, we address the more challenging task of Fine-grained Action Recognition (FAR), which focuses on detailed semantic labels within shorter temporal duration (e.g., "salto backward tucked with 1 turn"). Given the high costs of annotating fine-grained labels and the substantial data needed for fine-tuning LLMs, we propose to adopt semi-supervised learning (SSL). Our framework, SeFAR, incorporates several innovative designs to tackle these challenges. Specifically, to capture sufficient visual details, we construct Dual-level temporal elements as more effective representations, based on which we design a new strong augmentation strategy for the Teacher-Student learning paradigm through involving moderate temporal perturbation. Furthermore, to handle the high uncertainty within the teacher model's predictions for FAR, we propose the Adaptive Regulation to stabilize the learning process. Experiments show that SeFAR achieves state-of-the-art performance on two FAR datasets, FineGym and FineDiving, across various data scopes. It also outperforms other semi-supervised methods on two classical coarse-grained datasets, UCF101 and HMDB51. Further analysis and ablation studies validate the effectiveness of our designs. Additionally, we show that the features extracted by our SeFAR could largely promote the ability of multimodal foundation models to understand fine-grained and domain-specific semantics.

Large language models encode a vast amount of semantic knowledge and possess remarkable understanding and reasoning capabilities. Previous research has explored how to ground language models in robotic tasks to ensure that the sequences generated by the language model are both logically correct and practically executable. However, low-level execution may deviate from the high-level plan due to environmental perturbations or imperfect controller design. In this paper, we propose DoReMi, a novel language model grounding framework that enables immediate Detection and Recovery from Misalignments between plan and execution. Specifically, LLMs are leveraged for both planning and generating constraints for planned steps. These constraints can indicate plan-execution misalignments and we use a vision question answering (VQA) model to check constraints during low-level skill execution. If certain misalignment occurs, our method will call the language model to re-plan in order to recover from misalignments. Experiments on various complex tasks including robot arms and humanoid robots demonstrate that our method can lead to higher task success rates and shorter task completion times. Videos of DoReMi are available at https://sites.google.com/view/doremi-paper.

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.

The problem of attribution is concerned with identifying the parts of an input that are responsible for a model's output. An important family of attribution methods is based on measuring the effect of perturbations applied to the input. In this paper, we discuss some of the shortcomings of existing approaches to perturbation analysis and address them by introducing the concept of extremal perturbations, which are theoretically grounded and interpretable. We also introduce a number of technical innovations to compute extremal perturbations, including a new area constraint and a parametric family of smooth perturbations, which allow us to remove all tunable hyper-parameters from the optimization problem. We analyze the effect of perturbations as a function of their area, demonstrating excellent sensitivity to the spatial properties of the deep neural network under stimulation. We also extend perturbation analysis to the intermediate layers of a network. This application allows us to identify the salient channels necessary for classification, which, when visualized using feature inversion, can be used to elucidate model behavior. Lastly, we introduce TorchRay, an interpretability library built on PyTorch.

Vibe design agents turn natural-language briefs into rendered interfaces and frontend code. Yet a useful design agent should do more than produce one valid page: it should help users explore coherent alternatives. Increasing token-level temperature is a blunt solution because it varies aesthetic decisions and syntax-sensitive code at the same time. We instead separate exploration from implementation through an inference architecture that makes design direction an explicit intermediate decision. Inspired by Verbalized Sampling, a pre-pass proposes structured design specifications with typicality scores, an external selector samples one, and the downstream generator realizes the selected specification together with the original request under fixed settings. We apply this approach to UI themes and visual-asset prompts. Across 168 prompts, with 1,255 paired comparisons per temperature for each intervention, theme sampling broadens observed selection coverage and screenshot variation, while LLM-judge preferences vary across interventions, prompt complexity, and viewport. In an online experiment with more than 300,000 tasks, the observed code-export increase remains statistically uncertain, while fewer negative feedback events coexist with more correction interactions and modest operational costs. Together, these findings identify structured design specifications as a practical control point for exploring alternative UI concepts while keeping downstream generation settings fixed.

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

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).

GUI grounding models report over 85% accuracy on standard benchmarks, yet drop 27-56 percentage points when instructions require spatial reasoning rather than direct element naming. Current benchmarks miss this because they evaluate each screenshot once with a single fixed instruction. We introduce GUI-Perturbed, a controlled perturbation framework that independently varies visual scenes and instructions to measure grounding robustness. Evaluating three 7B models from the same architecture lineage, we find that relational instructions cause systematic accuracy collapse across all models, a 70% browser zoom produces statistically significant degradation, and rank-8 LoRA fine-tuning with augmented data degrades performance rather than improving it. By perturbing along independent axes, GUI-Perturbed isolates which specific capability axes are affected-spatial reasoning, visual robustness, reasoning calibration-providing diagnostic signal that aggregate benchmarks cannot. We release the dataset, augmentation pipeline, and a fine-tuned model.

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.

Instruction-tuning plays a vital role in enhancing the task-solving abilities of large language models (LLMs), improving their usability in generating helpful responses on various tasks. However, previous work has demonstrated that they are sensitive to minor variations in instruction phrasing. In this paper, we explore whether introducing perturbations in instruction-tuning data can enhance LLMs' resistance against noisy instructions. We focus on how instruction-tuning with perturbations, such as removing stop words or shuffling words, affects LLMs' performance on the original and perturbed versions of widely-used benchmarks (MMLU, BBH, GSM8K). We further assess learning dynamics and potential shifts in model behavior. Surprisingly, our results suggest that instruction-tuning on perturbed instructions can, in some cases, improve downstream performance. These findings highlight the importance of including perturbed instructions in instruction-tuning, which can make LLMs more resilient to noisy user inputs.

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.

To realize effective large-scale, real-world robotic applications, we must evaluate how well our robot policies adapt to changes in environmental conditions. Unfortunately, a majority of studies evaluate robot performance in environments closely resembling or even identical to the training setup. We present THE COLOSSEUM, a novel simulation benchmark, with 20 diverse manipulation tasks, that enables systematical evaluation of models across 14 axes of environmental perturbations. These perturbations include changes in color, texture, and size of objects, table-tops, and backgrounds; we also vary lighting, distractors, physical properties perturbations and camera pose. Using THE COLOSSEUM, we compare 5 state-of-the-art manipulation models to reveal that their success rate degrades between 30-50% across these perturbation factors. When multiple perturbations are applied in unison, the success rate degrades geq75%. We identify that changing the number of distractor objects, target object color, or lighting conditions are the perturbations that reduce model performance the most. To verify the ecological validity of our results, we show that our results in simulation are correlated (R^2 = 0.614) to similar perturbations in real-world experiments. We open source code for others to use THE COLOSSEUM, and also release code to 3D print the objects used to replicate the real-world perturbations. Ultimately, we hope that THE COLOSSEUM will serve as a benchmark to identify modeling decisions that systematically improve generalization for manipulation. See https://robot-colosseum.github.io/ for more details.

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.

Existing evaluation methods largely rely on clean, static benchmarks, which can overestimate true model performance by failing to capture the noise and variability inherent in real-world user inputs. This is especially true for language models, which can face human-generated text queries containing mistakes, typos, or alternative ways of phrasing the same question. In this work, we introduce a theoretical framework for quantifying model sensitivity to prompt variants, or brittleness, that can enable us to disentangle data-induced difficulty from prompt-related variability. Using this framework, we design a novel evaluation pipeline, Brittlebench, to holistically evaluate the sensitivity of frontier models. We apply semantics-preserving perturbations to a suite of popular benchmarks, and observe model performance to degrade as much as 12%. However, these perturbations do not affect all models equally: even a single perturbation alters the relative ranking of models in 63% of cases, impacting conclusions about comparative model performance. Decomposing the total variance of both state-of-the-art open-weight and commercial models, we find that semantics-preserving input perturbations can account for up to half of the performance variance for a given model. Brittlebench highlights the need for more robust evaluations and models, and allows us to systematically understand model brittleness.

Predicting cellular responses to unseen chemical perturbations is challenging due to unknown targets and mechanisms, high-dimensional expression responses, and limited experimental coverage of the large small-molecule design space. We propose PerturbPFN, a PFN-style amortized model for unknown-target perturbation prediction under a hierarchical synthetic structural prior. Instead of directly regressing high-dimensional expression responses, PerturbPFN infers a latent system graph, sparse atomic intervention targets, and intervention strengths, then propagates their effects through an SCM decoder. The model is trained entirely on prior-predictive synthetic episodes generated from biologically motivated graph and expression simulators, enabling structured in-context learning without test-time gradient updates. We evaluate PerturbPFN on both real single-cell perturbation data and synthetic benchmarks, covering effect prediction, target identification, and regulatory structure discovery. Our results show that PerturbPFN offers a complementary trade-off to specialized baselines, achieving competitive perturbation prediction with low inference cost while exposing interpretable intermediate estimates of targets, strengths, and system structure.

Hardware-aware training (HAT) is widely used to improve the robustness of neural networks on non-ideal AI accelerators, such as analog in-memory computing (IMC) systems. However, not all hardware-induced distortions are equally compensable by training. This paper presents a diagnostic framework that models hardware non-idealities as structured perturbations of the forward operator and evaluates their compatibility with gradient-based optimization. We analyze six representative perturbation classes--read noise, variability, drift, stuck-at faults, IR-drop, and ADC discretization--and identify three key diagnostics: gradient expectation consistency, bounded gradient variance, and non-degenerate sensitivity. Our results show a clear separation between perturbations that can be compensated by HAT and those that consistently break optimization. This provides practical guidance for hardware-software co-design, clarifying which non-idealities can be addressed at the training level and which require circuit-, architecture-, or calibration-level mitigation. This study should be interpreted as a controlled empirical analysis under vanilla forward-perturbation HAT, rather than as a universal theory of hardware-aware training.

Large language model-based web agents have demonstrated strong performance on realistic web interaction tasks. However, existing evaluations are predominantly conducted under relatively stable and well-behaved interaction conditions, which may overestimate agent robustness. High task success in such idealized settings does not necessarily reflect performance under realistic web interaction. To address this limitation, we introduce a diagnostic stress-testing benchmark for web agents. We first construct realistic and controllable web environments that provide clean and stable interaction workflows as reference baselines. We then introduce structured and controlled perturbations that emulate interaction variability, including shifting layouts, altered interaction semantics, and execution disruptions. By comparing agent behavior between clean and perturbed settings, our framework enables systematic diagnosis of robustness under what-if interaction scenarios. Through extensive evaluation of state-of-the-art multimodal web agents, we show that stress-based evaluation exposes failure modes and substantial robustness gaps that remain hidden under clean benchmark conditions.

Inverse design refers to the problem of optimizing the input of an objective function in order to enact a target outcome. For many real-world engineering problems, the objective function takes the form of a simulator that predicts how the system state will evolve over time, and the design challenge is to optimize the initial conditions that lead to a target outcome. Recent developments in learned simulation have shown that graph neural networks (GNNs) can be used for accurate, efficient, differentiable estimation of simulator dynamics, and support high-quality design optimization with gradient- or sampling-based optimization procedures. However, optimizing designs from scratch requires many expensive model queries, and these procedures exhibit basic failures on either non-convex or high-dimensional problems.In this work, we show how denoising diffusion models (DDMs) can be used to solve inverse design problems efficiently and propose a particle sampling algorithm for further improving their efficiency. We perform experiments on a number of fluid dynamics design challenges, and find that our approach substantially reduces the number of calls to the simulator compared to standard techniques.

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.

Inverse design, where we seek to design input variables in order to optimize an underlying objective function, is an important problem that arises across fields such as mechanical engineering to aerospace engineering. Inverse design is typically formulated as an optimization problem, with recent works leveraging optimization across learned dynamics models. However, as models are optimized they tend to fall into adversarial modes, preventing effective sampling. We illustrate that by instead optimizing over the learned energy function captured by the diffusion model, we can avoid such adversarial examples and significantly improve design performance. We further illustrate how such a design system is compositional, enabling us to combine multiple different diffusion models representing subcomponents of our desired system to design systems with every specified component. In an N-body interaction task and a challenging 2D multi-airfoil design task, we demonstrate that by composing the learned diffusion model at test time, our method allows us to design initial states and boundary shapes that are more complex than those in the training data. Our method generalizes to more objects for N-body dataset and discovers formation flying to minimize drag in the multi-airfoil design task. Project website and code can be found at https://github.com/AI4Science-WestlakeU/cindm.

Concept Design structures software systems around concepts: user-facing, self-contained units of functionality with a focused purpose. Concepts are composed into applications using synchronization rules called reactions, which specify how actions in one concept trigger actions in others. This paper first gives a formal semantics for concepts and reactions, enabling automatic verification of safety invariants in applications developed with this methodology. It then presents a CEGIS-style, LLM-driven synthesis procedure for generating reaction designs that satisfy such invariants. Because many different designs can satisfy the same invariant, we study two ways of steering synthesis toward the user's intended design: natural-language prompts and positive/negative scenarios. We also propose an LLM-driven scenario elicitation technique to support early design exploration. In an evaluation on three applications and twelve design variants using one LLM configuration, invariant-only synthesis reached verified designs quickly but often produced inconsistent designs across runs, some of which were implausible, showing that invariants alone underconstrain the design task. Scenario-guided synthesis recovered intended designs more consistently than natural-language prompting, although minimal scenarios can lead to overfitting. LLM-driven scenario elicitation, where the user classifies proposed scenarios rather than authoring them from scratch, recovered the intended designs in most variants when enough scenarios were elicited, but missed behaviors and non-determinism prevented reliable coverage in all cases.

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

A key challenge in machine learning is to explain how learning dynamics select among the many solutions that achieve identical loss values in overparameterized models - a phenomenon known as implicit bias. Controlling this bias provides a direct mechanism on learned representations, which are central to interpretability, robustness, and reasoning in modern AI systems. Yet, despite its importance, existing explanations remain largely ad hoc and lack a unifying mechanism. We develop a theoretical and constructive framework in which implicit bias emerges as a geometric correction induced by the interplay between gradient noise and continuous symmetries of the loss. We compute the induced bias across a range of architectures, predicting new behaviors and explaining known ones. The approach also enables inverse design: by engineering predictor - preserving parameterizations, it is possible to shape the bias, with sparsity and spectral sparsity emerging as canonical instances. Numerical experiments support the theory and validate the inverse - design framework in controlled settings.

Designing high-quality presentation slides can be challenging for non-experts due to the complexity involved in navigating various design choices. Numerous automated tools can suggest layouts and color schemes, yet often lack the ability to refine their own output, which is a key aspect in real-world workflows. We propose DesignLab, which separates the design process into two roles, the design reviewer, who identifies design-related issues, and the design contributor who corrects them. This decomposition enables an iterative loop where the reviewer continuously detects issues and the contributor corrects them, allowing a draft to be further polished with each iteration, reaching qualities that were unattainable. We fine-tune large language models for these roles and simulate intermediate drafts by introducing controlled perturbations, enabling the design reviewer learn design errors and the contributor learn how to fix them. Our experiments show that DesignLab outperforms existing design-generation methods, including a commercial tool, by embracing the iterative nature of designing which can result in polished, professional slides.

Recent benchmarks reveal that models for single-cell perturbation response are often outperformed by simply predicting the dataset mean. We trace this anomaly to a metric artifact: control-referenced deltas and unweighted error metrics reward mode collapse whenever the control is biased or the biological signal is sparse. Large-scale in silico simulations and analysis of two real-world perturbation datasets confirm that shared reference shifts, not genuine biological change, drives high performance in these evaluations. We introduce differentially expressed gene (DEG)-aware metrics, weighted mean-squared error (WMSE) and weighted delta R^{2} (R^{2}_{w}(Δ)) with respect to all perturbations, that measure error in niche signals with high sensitivity. We further introduce negative and positive performance baselines to calibrate these metrics. With these improvements, the mean baseline sinks to null performance while genuine predictors are correctly rewarded. Finally, we show that using WMSE as a loss function reduces mode collapse and improves model performance.

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.

Existing benchmarks evaluate Tool-Integrated Reasoning (TIR) in LLMs on idealized ''happy paths'', largely overlooking real-world tool failures. We introduce ToolMaze, a benchmark for dynamic path discovery and error recovery in TIR agents. To separate systematic replanning from blind trial-and-error, ToolMaze adopts a two-dimensional design: DAG-based topological complexity and a 2 times 2 taxonomy of tool perturbations (explicit/implicit, transient/permanent). Evaluations show that perturbations degrade performance across nearly all models, with the sharpest drops under implicit semantic failures. Driven by systemic over-trust in corrupted outputs, Perturbation Recovery Rate (PRR) plummets by around 37\% in these scenarios, while complex topologies trap agents in futile trial-and-error loops. Crucially, agentic fault-tolerance improves with model scale 3.66times slower than basic task execution, highlighting dynamic replanning as a distinct bottleneck unaddressed by model scaling or prompting. Data and code are available at https://github.com/Zhudongsheng75/ToolMaze.

Perturbation-based post-hoc image explanation methods are commonly used to explain image prediction models. These methods perturb parts of the input to measure how those parts affect the output. Since the methods only require the input and output, they can be applied to any model, making them a popular choice to explain black-box models. While many different methods exist and have been compared with one another, it remains poorly understood which parameters of the different methods are responsible for their varying performance. This work uses the Randomized Input Sampling for Explanations (RISE) method as a baseline to evaluate many combinations of mask sampling, segmentation techniques, smoothing, attribution calculation, and per-segment or per-pixel attribution, using a proxy metric. The results show that attribution calculation, which is frequently the focus of other works, has little impact on the results. Conversely, segmentation and per-pixel attribution, rarely examined parameters, have a significant impact. The implementation of and data gathered in this work are available online: https://github.com/guspih/post-hoc-image-perturbation and https://bit.ly/smooth-mask-perturbation.

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.

Structural vibrations are a source of unwanted noise in engineering systems like cars, trains or airplanes. Minimizing these vibrations is crucial for improving passenger comfort. This work presents a novel design optimization approach based on guided flow matching for reducing vibrations by placing beadings (indentations) in plate-like structures. Our method integrates a generative flow matching model and a surrogate model trained to predict structural vibrations. During the generation process, the flow matching model pushes towards manufacturability while the surrogate model pushes to low-vibration solutions. The flow matching model and its training data implicitly define the design space, enabling a broader exploration of potential solutions as no optimization of manually-defined design parameters is required. We apply our method to a range of differentiable optimization objectives, including direct optimization of specific eigenfrequencies through careful construction of the objective function. Results demonstrate that our method generates diverse and manufacturable plate designs with reduced structural vibrations compared to designs from random search, a criterion-based design heuristic and genetic optimization. The code and data are available from https://github.com/ecker-lab/Optimizing_Vibrating_Plates.

Engineering design optimization seeks to automatically determine the shapes, topologies, or parameters of components that maximize performance under given conditions. This process often depends on physics-based simulations, which are difficult to install, computationally expensive, and require domain-specific expertise. To mitigate these challenges, we introduce EngiBench, the first open-source library and datasets spanning diverse domains for data-driven engineering design. EngiBench provides a unified API and a curated set of benchmarks -- covering aeronautics, heat conduction, photonics, and more -- that enable fair, reproducible comparisons of optimization and machine learning algorithms, such as generative or surrogate models. We also release EngiOpt, a companion library offering a collection of such algorithms compatible with the EngiBench interface. Both libraries are modular, letting users plug in novel algorithms or problems, automate end-to-end experiment workflows, and leverage built-in utilities for visualization, dataset generation, feasibility checks, and performance analysis. We demonstrate their versatility through experiments comparing state-of-the-art techniques across multiple engineering design problems, an undertaking that was previously prohibitively time-consuming to perform. Finally, we show that these problems pose significant challenges for standard machine learning methods due to highly sensitive and constrained design manifolds.

Existing works have extensively studied adversarial examples, which are minimal perturbations that can mislead the output of deep neural networks (DNNs) while remaining imperceptible to humans. However, in this work, we reveal the existence of a harmless perturbation space, in which perturbations drawn from this space, regardless of their magnitudes, leave the network output unchanged when applied to inputs. Essentially, the harmless perturbation space emerges from the usage of non-injective functions (linear or non-linear layers) within DNNs, enabling multiple distinct inputs to be mapped to the same output. For linear layers with input dimensions exceeding output dimensions, any linear combination of the orthogonal bases of the nullspace of the parameter consistently yields no change in their output. For non-linear layers, the harmless perturbation space may expand, depending on the properties of the layers and input samples. Inspired by this property of DNNs, we solve for a family of general perturbation spaces that are redundant for the DNN's decision, and can be used to hide sensitive data and serve as a means of model identification. Our work highlights the distinctive robustness of DNNs (i.e., consistency under large magnitude perturbations) in contrast to adversarial examples (vulnerability for small imperceptible noises).

As multimodal resources are transformed into media outputs, agentic AI is expected to stay aligned with design intent over long horizons. Designers follow briefs specifying goals, constraints, and deliverables, with later work building on earlier decisions. Recent work reuses design experience across tasks, yet alignment among artifacts within one project remains challenging. Agents therefore need to preserve and apply this intent across domains and as projects grow. We introduce Design Anything, a graph-based harness that preserves design intent outside the model and binds deliverables to the workflow steps that produce them through an intent-execution graph. A task contract retains constraints and decisions, selected designs become explicit inputs to later generations, and a deterministic controller uses bindings and execution records to check output types and counts, identify outstanding deliverables, and guide subsequent turns. We also introduce DesignAnything-Bench, with 228 tasks across 19 design domains, including 38 project families at scales of 6, 14, and 24 artifacts. With the LLM held fixed, Design Anything satisfies 85.0% and 92.5% of the brief's factual constraints with DeepSeek V4.1 Flash High and GPT-5.6 Sol High, respectively, exceeding the strongest same-model baselines by 15.4% and 14.4%. These gains reach 25.1% and 23.0% on 24-artifact tasks. Under each model, Design Anything leads or ties in constraint satisfaction in 18 of 19 domains. Professional designers also prefer its complete deliverable sets over those of same-model baselines in a blind evaluation.

We introduce Multi-Objective Counterfactuals for Design (MCD), a novel method for counterfactual optimization in design problems. Counterfactuals are hypothetical situations that can lead to a different decision or choice. In this paper, the authors frame the counterfactual search problem as a design recommendation tool that can help identify modifications to a design, leading to better functional performance. MCD improves upon existing counterfactual search methods by supporting multi-objective queries, which are crucial in design problems, and by decoupling the counterfactual search and sampling processes, thus enhancing efficiency and facilitating objective tradeoff visualization. The paper demonstrates MCD's core functionality using a two-dimensional test case, followed by three case studies of bicycle design that showcase MCD's effectiveness in real-world design problems. In the first case study, MCD excels at recommending modifications to query designs that can significantly enhance functional performance, such as weight savings and improvements to the structural safety factor. The second case study demonstrates that MCD can work with a pre-trained language model to suggest design changes based on a subjective text prompt effectively. Lastly, the authors task MCD with increasing a query design's similarity to a target image and text prompt while simultaneously reducing weight and improving structural performance, demonstrating MCD's performance on a complex multimodal query. Overall, MCD has the potential to provide valuable recommendations for practitioners and design automation researchers looking for answers to their ``What if'' questions by exploring hypothetical design modifications and their impact on multiple design objectives. The code, test problems, and datasets used in the paper are available to the public at decode.mit.edu/projects/counterfactuals/.

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.

While LLM agents can generate visually plausible CAD assemblies, these designs often fail to fulfill their intended physical functions. We study functional CAD design, a setting where agents interpret underspecified requests to construct and iteratively revise mechanisms that satisfy functional requirements in physical simulation. Verifying these requirements is nontrivial: different candidate mechanisms may realize the same function through entirely different components, controls, and operating sequences. To bridge this gap, we propose FunCAD-Harness, a framework that translates abstract requirements into candidate-specific physical tests and uses simulation feedback to guide design revisions. To systematically evaluate this capability, we introduce FunCADBench, a benchmark spanning 46 mechanism families with interdependent and multi-step operations. Experiments across frontier LLM agents show that FunCAD-Harness exposes subtle mechanical failures invisible to visual inspection, substantially improving functional success rates over standard simulation-augmented baselines. Ultimately, our work marks a step toward CAD agents capable of translating human intent into working mechanisms.

This paper introduces a generative model designed for multimodal control over text-to-image foundation generative AI models such as Stable Diffusion, specifically tailored for engineering design synthesis. Our model proposes parametric, image, and text control modalities to enhance design precision and diversity. Firstly, it handles both partial and complete parametric inputs using a diffusion model that acts as a design autocomplete co-pilot, coupled with a parametric encoder to process the information. Secondly, the model utilizes assembly graphs to systematically assemble input component images, which are then processed through a component encoder to capture essential visual data. Thirdly, textual descriptions are integrated via CLIP encoding, ensuring a comprehensive interpretation of design intent. These diverse inputs are synthesized through a multimodal fusion technique, creating a joint embedding that acts as the input to a module inspired by ControlNet. This integration allows the model to apply robust multimodal control to foundation models, facilitating the generation of complex and precise engineering designs. This approach broadens the capabilities of AI-driven design tools and demonstrates significant advancements in precise control based on diverse data modalities for enhanced design generation.

Real-world design tasks - such as picture book creation, film storyboard development using character sets, photo retouching, visual effects, and font transfer - are highly diverse and complex, requiring deep interpretation and extraction of various elements from instructions, descriptions, and reference images. The resulting images often implicitly capture key features from references or user inputs, making it challenging to develop models that can effectively address such varied tasks. While existing visual generative models can produce high-quality images based on prompts, they face significant limitations in professional design scenarios that involve varied forms and multiple inputs and outputs, even when enhanced with adapters like ControlNets and LoRAs. To address this, we introduce IDEA-Bench, a comprehensive benchmark encompassing 100 real-world design tasks, including rendering, visual effects, storyboarding, picture books, fonts, style-based, and identity-preserving generation, with 275 test cases to thoroughly evaluate a model's general-purpose generation capabilities. Notably, even the best-performing model only achieves 22.48 on IDEA-Bench, while the best general-purpose model only achieves 6.81. We provide a detailed analysis of these results, highlighting the inherent challenges and providing actionable directions for improvement. Additionally, we provide a subset of 18 representative tasks equipped with multimodal large language model (MLLM)-based auto-evaluation techniques to facilitate rapid model development and comparison. We releases the benchmark data, evaluation toolkits, and an online leaderboard at https://github.com/ali-vilab/IDEA-Bench, aiming to drive the advancement of generative models toward more versatile and applicable intelligent design systems.

Graphic design plays a vital role in visual communication across advertising, marketing, and multimedia entertainment. Prior work has explored automated graphic design generation using diffusion models, aiming to streamline creative workflows and democratize design capabilities. However, complex graphic design scenarios require accurately adhering to design intent specified by multiple heterogeneous user-provided elements (\eg images, layouts, and texts), which pose multi-condition control challenges for existing methods. Specifically, previous single-condition control models demonstrate effectiveness only within their specialized domains but fail to generalize to other conditions, while existing multi-condition methods often lack fine-grained control over each sub-condition and compromise overall compositional harmony. To address these limitations, we introduce CreatiDesign, a systematic solution for automated graphic design covering both model architecture and dataset construction. First, we design a unified multi-condition driven architecture that enables flexible and precise integration of heterogeneous design elements with minimal architectural modifications to the base diffusion model. Furthermore, to ensure that each condition precisely controls its designated image region and to avoid interference between conditions, we propose a multimodal attention mask mechanism. Additionally, we develop a fully automated pipeline for constructing graphic design datasets, and introduce a new dataset with 400K samples featuring multi-condition annotations, along with a comprehensive benchmark. Experimental results show that CreatiDesign outperforms existing models by a clear margin in faithfully adhering to user intent.

It is not fully understood why adversarial examples can deceive neural networks and transfer between different networks. To elucidate this, several studies have hypothesized that adversarial perturbations, while appearing as noises, contain class features. This is supported by empirical evidence showing that networks trained on mislabeled adversarial examples can still generalize well to correctly labeled test samples. However, a theoretical understanding of how perturbations include class features and contribute to generalization is limited. In this study, we provide a theoretical framework for understanding learning from perturbations using a one-hidden-layer network trained on mutually orthogonal samples. Our results highlight that various adversarial perturbations, even perturbations of a few pixels, contain sufficient class features for generalization. Moreover, we reveal that the decision boundary when learning from perturbations matches that from standard samples except for specific regions under mild conditions. The code is available at https://github.com/s-kumano/learning-from-adversarial-perturbations.

The Perturbation Discrimination Score (PDS) is increasingly used to evaluate whether predicted perturbation effects remain distinguishable, including in Systema and the Virtual Cell Challenge. However, its behavior in high-dimensional gene-expression settings has not been examined in detail. We show that PDS is highly sensitive to the choice of similarity or distance measure and to the scale of predicted effects. Analysis of observed perturbation responses reveals that ell_1 and ell_2-based PDS behave very differently from cosine-based measures, even after norm matching. We provide geometric insight and discuss implications for future discrimination-based evaluation metrics.

This paper presents a novel generative model for Computer Aided Design (CAD) that 1) represents high-level design concepts of a CAD model as a three-level hierarchical tree of neural codes, from global part arrangement down to local curve geometry; and 2) controls the generation or completion of CAD models by specifying the target design using a code tree. Concretely, a novel variant of a vector quantized VAE with "masked skip connection" extracts design variations as neural codebooks at three levels. Two-stage cascaded auto-regressive transformers learn to generate code trees from incomplete CAD models and then complete CAD models following the intended design. Extensive experiments demonstrate superior performance on conventional tasks such as random generation while enabling novel interaction capabilities on conditional generation tasks. The code is available at https://github.com/samxuxiang/hnc-cad.

Scientific LLM agents have shown promise in literature reasoning, tool use, and experiment planning, but it remains unclear whether they can autonomously improve large, tightly coupled scientific machine-learning systems through executable code changes and computationally expensive validation. We study this question in protein folding, where progress requires coordinated architectural modifications, multi-objective evaluation, and domain-aware interpretation. We present AgentFold, a multi-agent framework that formulates folding-model development as a closed-loop search over executable code variants. Starting from ESMFold, AgentFold proposes hypotheses, implements and debugs code-level modifications, evaluates model variants, analyzes experimental outcomes, and stores both successful and failed interventions in structured memory. An MCTS-style policy allocates computational resources across high-scoring search branches. On an engineering-scale protein-folding codebase comprising more than 2,000 lines of code, AgentFold explores approximately 80 model variants using approximately 5,000 GPU-hours and 170 million LLM tokens. Under a matched computational budget, AgentFold improves the best lDDT by 7.5% over independent Codex proposals and outperforms a random-search control. Beyond model improvement, the resulting intervention traces reveal recurring empirical design patterns: stable gains tend to arise from early, soft, learnable priors and gated refinement, whereas direct geometric perturbations and geometry-conditioned feedback often destabilize training. The code and experimental resources are publicly available at https://github.com/lmqfly/AgentFold.

A variety of methods have been proposed to try to explain how deep neural networks make their decisions. Key to those approaches is the need to sample the pixel space efficiently in order to derive importance maps. However, it has been shown that the sampling methods used to date introduce biases and other artifacts, leading to inaccurate estimates of the importance of individual pixels and severely limit the reliability of current explainability methods. Unfortunately, the alternative -- to exhaustively sample the image space is computationally prohibitive. In this paper, we introduce EVA (Explaining using Verified perturbation Analysis) -- the first explainability method guarantee to have an exhaustive exploration of a perturbation space. Specifically, we leverage the beneficial properties of verified perturbation analysis -- time efficiency, tractability and guaranteed complete coverage of a manifold -- to efficiently characterize the input variables that are most likely to drive the model decision. We evaluate the approach systematically and demonstrate state-of-the-art results on multiple benchmarks.

Generative models, such as large language models and text-to-image diffusion models, are increasingly used to create visual designs like user interfaces (UIs) and presentation slides. Finetuning and benchmarking these generative models have often relied on datasets of human-annotated design preferences. Yet, due to the subjective and highly personalized nature of visual design, preference varies widely among individuals. In this paper, we study this problem by introducing DesignPref, a dataset of 12k pairwise comparisons of UI design generation annotated by 20 professional designers with multi-level preference ratings. We found that among trained designers, substantial levels of disagreement exist (Krippendorff's alpha = 0.25 for binary preferences). Natural language rationales provided by these designers indicate that disagreements stem from differing perceptions of various design aspect importance and individual preferences. With DesignPref, we demonstrate that traditional majority-voting methods for training aggregated judge models often do not accurately reflect individual preferences. To address this challenge, we investigate multiple personalization strategies, particularly fine-tuning or incorporating designer-specific annotations into RAG pipelines. Our results show that personalized models consistently outperform aggregated baseline models in predicting individual designers' preferences, even when using 20 times fewer examples. Our work provides the first dataset to study personalized visual design evaluation and support future research into modeling individual design taste.

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.

Large language models have demonstrated impressive performance on challenging mathematical reasoning tasks, which has triggered the discussion of whether the performance is achieved by true reasoning capability or memorization. To investigate this question, prior work has constructed mathematical benchmarks when questions undergo simple perturbations -- modifications that still preserve the underlying reasoning patterns of the solutions. However, no work has explored hard perturbations, which fundamentally change the nature of the problem so that the original solution steps do not apply. To bridge the gap, we construct MATH-P-Simple and MATH-P-Hard via simple perturbation and hard perturbation, respectively. Each consists of 279 perturbed math problems derived from level-5 (hardest) problems in the MATH dataset (Hendrycksmath et. al., 2021). We observe significant performance drops on MATH-P-Hard across various models, including o1-mini (-16.49%) and gemini-2.0-flash-thinking (-12.9%). We also raise concerns about a novel form of memorization where models blindly apply learned problem-solving skills without assessing their applicability to modified contexts. This issue is amplified when using original problems for in-context learning. We call for research efforts to address this challenge, which is critical for developing more robust and reliable reasoning models.

Existing benchmarks for tool-using LLM agents primarily report single-run success rates and miss reliability properties required in production. We introduce ReliabilityBench, a benchmark for evaluating agent reliability across three dimensions: (i) consistency under repeated execution using pass^k, (ii) robustness to semantically equivalent task perturbations at intensity ε, and (iii) fault tolerance under controlled tool/API failures at intensity λ. ReliabilityBench contributes a unified reliability surface R(k,ε,λ), action metamorphic relations that define correctness via end-state equivalence rather than text similarity, and a chaos-engineering-style fault injection framework (timeouts, rate limits, partial responses, schema drift). We evaluate two models (Gemini 2.0 Flash, GPT-4o) and two agent architectures (ReAct, Reflexion) across four domains (scheduling, travel, customer support, e-commerce) over 1,280 episodes. Perturbations alone reduce success from 96.9% at ε=0 to 88.1% at ε=0.2. Rate limiting is the most damaging fault in ablations. ReAct is more robust than Reflexion under combined stress, and Gemini 2.0 Flash achieves comparable reliability to GPT-4o at much lower cost. ReliabilityBench provides a systematic framework for assessing production readiness of LLM agents.

Predicting the effects of perturbations in-silico on cell state can identify drivers of cell behavior at scale and accelerate drug discovery. However, modeling challenges remain due to the inherent heterogeneity of single cell gene expression and the complex, latent gene dependencies. Here, we present PRiMeFlow, an end-to-end flow matching based approach to directly model the effects of genetic and small molecule perturbations in the gene expression space. The distribution-fitting approach taken by PRiMeFlow enables it to accurately approximate the empirical distribution of single-cell gene expression, which we demonstrate through extensive benchmarking inside PerturBench. Through ablation studies, we also validate important model design choices such as operating in gene expression space and parameterizing the velocity field with a U-Net architecture. Finally, by scaling PRiMeFlow to a broad perturbation data atlas spanning multiple datasets and employing a carefully designed pretraining-finetuning strategy, we demonstrate its outstanding performance on the H1 human embryonic stem cells from the ARC Virtual Cell Challenge benchmark.

Artefact descriptions are the primary carriers of engineering design knowledge that is both an outcome and a driver of the design process. While an artefact could be described in different connotations, the design process requires a description to embody engineering design knowledge, which is expressed in the text through intricate placement of entities and relationships. As large-language models learn from all kinds of text merely as a sequence of characters/tokens, these are yet to generate text that embodies explicit engineering design facts. Existing ontological design theories are less likely to guide the large-language models whose applications are currently limited to ideation and learning purposes. In this article, we explicate engineering design knowledge as knowledge graphs from a large sample of 33,881 patent documents. We examine the constituents of these knowledge graphs to understand the linguistic and structural basis of engineering design knowledge. In terms of linguistic basis, we observe that entities and relationships could be generalised to 64 and 24 linguistic syntaxes. While relationships mainly capture attributes ('of'), structure ('in', 'with'), purpose ('to', 'for'), hierarchy ('include'), exemplification ('such as'), and behaviour ('to', 'from'), the hierarchical relationships could specifically be identified using 75 unique syntaxes. To understand the structural basis, we draw inspiration from various studies on biological/ecological networks and discover motifs from patent knowledge graphs. We identify four 3-node and four 4-node patterns that could further be converged and simplified into sequence [->...->], aggregation [->...<-], and hierarchy [<-...->]. Expected to guide large-language model based design tools, we propose few regulatory precepts for concretising abstract entities and relationships within subgraphs, while explicating hierarchical structures.

Generative modeling has shown increasing promise for predicting cellular perturbation effects under chemical compound treatments. Existing approaches either model perturbation as a distribution-to-distribution mapping without explicit concentration handling, or treat concentration as a discrete class label, precluding continuous dose control. We introduce a joint flow matching approach that simultaneously models cell latents and drug concentration via a dual-timestep formulation, enabling dose-conditioned single-cell morphing through the invertibility of flow matching. The joint formulation induces a monotonic dose-response geometry in latent space and additionally supports concentration estimation from cell morphology. As proof of concept, we further demonstrate generalization to an unseen dose held out during training. Empirically, our method achieves competitive or improved per-concentration metrics on two compounds compared with representative baselines, while enabling capabilities structurally unavailable to discrete-class methods.

Topology optimization (TO) provides a principled mathematical approach for optimizing the performance of a structure by designing its material spatial distribution in a pre-defined domain and subject to a set of constraints. The majority of existing TO approaches leverage numerical solvers for design evaluations during the optimization and hence have a nested nature and rely on discretizing the design variables. Contrary to these approaches, herein we develop a new class of TO methods based on the framework of Gaussian processes (GPs) whose mean functions are parameterized via deep neural networks. Specifically, we place GP priors on all design and state variables to represent them via parameterized continuous functions. These GPs share a deep neural network as their mean function but have as many independent kernels as there are state and design variables. We estimate all the parameters of our model in a single for loop that optimizes a penalized version of the performance metric where the penalty terms correspond to the state equations and design constraints. Attractive features of our approach include (1) having a built-in continuation nature since the performance metric is optimized at the same time that the state equations are solved, and (2) being discretization-invariant and accommodating complex domains and topologies. To test our method against conventional TO approaches implemented in commercial software, we evaluate it on four problems involving the minimization of dissipated power in Stokes flow. The results indicate that our approach does not need filtering techniques, has consistent computational costs, and is highly robust against random initializations and problem setup.

Large Language Models (LLMs) have become key components of modern software, with prompts acting as their de-facto programming interface. However, prompt design remains largely empirical and small mistakes can cascade into unreliable, insecure, or inefficient behavior. This paper presents the first systematic survey and taxonomy of prompt defects, recurring ways that prompts fail to elicit their intended behavior from LLMs. We organize defects along six dimensions: (1) Specification and Intent, (2) Input and Content, (3) Structure and Formatting, (4) Context and Memory, (5) Performance and Efficiency, and (6) Maintainability and Engineering. Each dimension is refined into fine-grained subtypes, illustrated with concrete examples and root cause analysis. Grounded in software engineering principles, we show how these defects surface in real development workflows and examine their downstream effects. For every subtype, we distill mitigation strategies that span emerging prompt engineering patterns, automated guardrails, testing harnesses, and evaluation frameworks. We then summarize these strategies in a master taxonomy that links defect, impact, and remedy. We conclude with open research challenges and a call for rigorous engineering-oriented methodologies to ensure that LLM-driven systems are dependable by design.

State-of-the-art deep neural networks have achieved impressive results on many image classification tasks. However, these same architectures have been shown to be unstable to small, well sought, perturbations of the images. Despite the importance of this phenomenon, no effective methods have been proposed to accurately compute the robustness of state-of-the-art deep classifiers to such perturbations on large-scale datasets. In this paper, we fill this gap and propose the DeepFool algorithm to efficiently compute perturbations that fool deep networks, and thus reliably quantify the robustness of these classifiers. Extensive experimental results show that our approach outperforms recent methods in the task of computing adversarial perturbations and making classifiers more robust.

Recent work found that LLMs are sensitive to a wide range of arbitrary prompt dimensions, including the type of delimiters, answer enumerators, instruction wording, and more. This throws into question popular single-prompt evaluation practices. We present DOVE (Dataset Of Variation Evaluation) a large-scale dataset containing prompt perturbations of various evaluation benchmarks. In contrast to previous work, we examine LLM sensitivity from an holistic perspective, and assess the joint effects of perturbations along various dimensions, resulting in thousands of perturbations per instance. We evaluate several model families against DOVE, leading to several findings, including efficient methods for choosing well-performing prompts, observing that few-shot examples reduce sensitivity, and identifying instances which are inherently hard across all perturbations. DOVE consists of more than 250M prompt perturbations and model outputs, which we make publicly available to spur a community-wide effort toward meaningful, robust, and efficient evaluation. Browse the data, contribute, and more: https://slab-nlp.github.io/DOVE/

Building credible simulators from data is difficult because structure design, parameter calibration, and out-of-distribution (OOD) robustness are tightly coupled. We introduce SOCIA (Simulation Orchestration for Computational Intelligence with Agents), a framework that treats simulator construction as joint structure-parameter co-optimization: it elicits mechanism-rich blueprints, exposes explicit tunable parameters, and instantiates a calibration schema, producing an executable simulator with built-in calibration hooks. SOCIA couples Bayesian Optimization for sample-efficient point calibration with Simulation-Based Inference for uncertainty-aware fitting; diagnostics trigger targeted structural edits in an outer refinement loop to co-optimize design and parameters under tight budgets. Across three diverse tasks, SOCIA consistently outperforms strong baselines, excelling on both in-distribution (ID) fitting and OOD shift. Ablations that weaken structure, calibration design, or tuning yield near-monotone degradations, underscoring the necessity of unified structure-parameter optimization. We will release the code soon.

Modern recommender systems may output considerably different recommendations due to small perturbations in the training data. Changes in the data from a single user will alter the recommendations as well as the recommendations of other users. In applications like healthcare, housing, and finance, this sensitivity can have adverse effects on user experience. We propose a method to stabilize a given recommender system against such perturbations. This is a challenging task due to (1) the lack of a ``reference'' rank list that can be used to anchor the outputs; and (2) the computational challenges in ensuring the stability of rank lists with respect to all possible perturbations of training data. Our method, FINEST, overcomes these challenges by obtaining reference rank lists from a given recommendation model and then fine-tuning the model under simulated perturbation scenarios with rank-preserving regularization on sampled items. Our experiments on real-world datasets demonstrate that FINEST can ensure that recommender models output stable recommendations under a wide range of different perturbations without compromising next-item prediction accuracy.

Training deep neural networks for classification often includes minimizing the training loss beyond the zero training error point. In this phase of training, a "neural collapse" behavior has been observed: the variability of features (outputs of the penultimate layer) of within-class samples decreases and the mean features of different classes approach a certain tight frame structure. Recent works analyze this behavior via idealized unconstrained features models where all the minimizers exhibit exact collapse. However, with practical networks and datasets, the features typically do not reach exact collapse, e.g., because deep layers cannot arbitrarily modify intermediate features that are far from being collapsed. In this paper, we propose a richer model that can capture this phenomenon by forcing the features to stay in the vicinity of a predefined features matrix (e.g., intermediate features). We explore the model in the small vicinity case via perturbation analysis and establish results that cannot be obtained by the previously studied models. For example, we prove reduction in the within-class variability of the optimized features compared to the predefined input features (via analyzing gradient flow on the "central-path" with minimal assumptions), analyze the minimizers in the near-collapse regime, and provide insights on the effect of regularization hyperparameters on the closeness to collapse. We support our theory with experiments in practical deep learning settings.

Modern engineering, spanning electrical, mechanical, aerospace, civil, and computer disciplines, stands as a cornerstone of human civilization and the foundation of our society. However, engineering design poses a fundamentally different challenge for large language models (LLMs) compared with traditional textbook-style problem solving or factual question answering. Although existing benchmarks have driven progress in areas such as language understanding, code synthesis, and scientific problem solving, real-world engineering design demands the synthesis of domain knowledge, navigation of complex trade-offs, and management of the tedious processes that consume much of practicing engineers' time. Despite these shared challenges across engineering disciplines, no benchmark currently captures the unique demands of engineering design work. In this work, we introduce EngDesign, an Engineering Design benchmark that evaluates LLMs' abilities to perform practical design tasks across nine engineering domains. Unlike existing benchmarks that focus on factual recall or question answering, EngDesign uniquely emphasizes LLMs' ability to synthesize domain knowledge, reason under constraints, and generate functional, objective-oriented engineering designs. Each task in EngDesign represents a real-world engineering design problem, accompanied by a detailed task description specifying design goals, constraints, and performance requirements. EngDesign pioneers a simulation-based evaluation paradigm that moves beyond textbook knowledge to assess genuine engineering design capabilities and shifts evaluation from static answer checking to dynamic, simulation-driven functional verification, marking a crucial step toward realizing the vision of engineering Artificial General Intelligence (AGI).

Generative AI is known for its tendency to homogenize, often reproducing dominant style conventions found in training data. However, it remains unclear how these homogenizing effects extend to complex structural tasks like web design. As lay creators increasingly turn to LLMs to 'vibe-code' websites -- prompting for aesthetic and functional goals rather than writing code -- they may inadvertently narrow the diversity of their designs, and limit creative expression throughout the internet. In this paper, we interrogate the possibility of design homogenization in web vibe coding. We first characterize the vibe coding lifecycle, pinpointing stages where homogenization risks may arise. We then conduct a sociotechnical risk analysis unpacking the potential harms of web vibe coding and their interaction with design homogenization. We identify that the push for frictionless generation can exacerbate homogenization and its harms. Finally, we propose a mitigation framework centered on the idea of productive friction. Through case studies at the micro, meso, and macro levels, we show how centering productive friction can empower creators to challenge default outputs and preserve diverse expression in AI-mediated web design.

Graphic design often involves exploring different stylistic directions, which can be time-consuming for non-experts. We address this problem of stylistically improving designs based on natural language instructions. While VLMs have shown initial success in graphic design, their pretrained knowledge on styles is often too general and misaligned with specific domain data. For example, VLMs may associate minimalism with abstract designs, whereas designers emphasize shape and color choices. Our key insight is to leverage design data -- a collection of real-world designs that implicitly capture designer's principles -- to learn design knowledge and guide stylistic improvement. We propose PRISM (PRior-Informed Stylistic Modification) that constructs and applies a design knowledge base through three stages: (1) clustering high-variance designs to capture diversity within a style, (2) summarizing each cluster into actionable design knowledge, and (3) retrieving relevant knowledge during inference to enable style-aware improvement. Experiments on the Crello dataset show that PRISM achieves the highest average rank of 1.49 (closer to 1 is better) over baselines in style alignment. User studies further validate these results, showing that PRISM is consistently preferred by designers.

Prediction models can exhibit sensitivity with respect to training data: small changes in the training data can produce models that assign conflicting predictions to individual data points during test time. In this work, we study this sensitivity in recommender systems, where users' recommendations are drastically altered by minor perturbations in other unrelated users' interactions. We introduce a measure of stability for recommender systems, called Rank List Sensitivity (RLS), which measures how rank lists generated by a given recommender system at test time change as a result of a perturbation in the training data. We develop a method, CASPER, which uses cascading effect to identify the minimal and systematical perturbation to induce higher instability in a recommender system. Experiments on four datasets show that recommender models are overly sensitive to minor perturbations introduced randomly or via CASPER - even perturbing one random interaction of one user drastically changes the recommendation lists of all users. Importantly, with CASPER perturbation, the models generate more unstable recommendations for low-accuracy users (i.e., those who receive low-quality recommendations) than high-accuracy ones.

Predicting cellular responses to genetic perturbations is a central capability for virtual cells and a key step toward computational modeling of biological interventions. Most existing models directly map an unperturbed molecular profile and perturba- tion to the resulting observation without explicitly representing the latent cellular transition induced by the intervention. We introduce a mechanism-centric virtual cell world model that represents cellular state as a set of Latent Mechanism Units (LMUs) and treats genetic perturbations as actions on these latent states. Each LMU combines a reusable identity grounded in multimodal biological evidence with an observation-specific state, allowing a perturbation to induce mechanism- specific stochastic transitions before decoding the resulting transcriptional response. We train VCLMU through two-stage pretraining, first on around 200K pseudo-bulk perturbation profiles and then on gene-aligned single-cell perturbation data. Across six perturbation-disjoint benchmarks, VCLMU consistently improves perturbation- specific response recovery over strong baselines while maintaining competitive global response accuracy. We further analyze learned LMUs through enrichment between perturbation responses and LMU gene sets and show that they capture structured biological response programs. These results support mechanism-level latent state transition as a useful formulation for virtual cell models that aim to predict and interpret cellular responses to biological interventions.

Recent works exploring deep learning application to dynamical systems modeling have demonstrated that embedding physical priors into neural networks can yield more effective, physically-realistic, and data-efficient models. However, in the absence of complete prior knowledge of a dynamical system's physical characteristics, determining the optimal structure and optimization strategy for these models can be difficult. In this work, we explore methods for discovering neural state space dynamics models for system identification. Starting with a design space of block-oriented state space models and structured linear maps with strong physical priors, we encode these components into a model genome alongside network structure, penalty constraints, and optimization hyperparameters. Demonstrating the overall utility of the design space, we employ an asynchronous genetic search algorithm that alternates between model selection and optimization and obtains accurate physically consistent models of three physical systems: an aerodynamics body, a continuous stirred tank reactor, and a two tank interacting system.

The robustness of Vision Language Models (VLMs) is commonly assessed through output-level invariance, implicitly assuming that stable predictions reflect stable multimodal processing. In this work, we argue that this assumption is insufficient. We introduce a representation-aware and frequency-aware evaluation framework that measures internal embedding drift, spectral sensitivity, and structural smoothness (spatial consistency of vision tokens), alongside standard label-based metrics. Applying this framework to modern VLMs across the SEEDBench, MMMU, and POPE datasets reveals three distinct failure modes. First, models frequently preserve predicted answers while undergoing substantial internal representation drift; for perturbations such as text overlays, this drift approaches the magnitude of inter-image variability, indicating that representations move to regions typically occupied by unrelated inputs despite unchanged outputs. Second, robustness does not improve with scale; larger models achieve higher accuracy but exhibit equal or greater sensitivity, consistent with sharper yet more fragile decision boundaries. Third, we find that perturbations affect tasks differently: they harm reasoning when they disrupt how models combine coarse and fine visual cues, but on the hallucination benchmarks, they can reduce false positives by making models generate more conservative answers.

Slide design requires personalizing both deck themes and page layouts. Yet, current AI agent-based methods struggle with fine-grained, page-level design. Solely relying on prespecified templates or user verbose instructions, they fail to capture latent design intents, leaving Page-level Slide Personalization (PSP) unresolved. To close this gap, this work formulates PSP as an inverse planning problem. We propose to learn a design intent without assuming any knowledge of the specific executing tools (e.g., PowerPoint, Beamer) being used. However, relinquishing control over these tools makes the problem intractable to optimize end-to-end. To overcome this, we propose SPIRE, a principled framework to solve PSP approximately. By intentionally corrupting the visual structures of clean slides, SPIRE creates a verifiable task to denoise the corruption, whereby two agents learn to collaboratively refine executable designs via reinforcement learning (RL). We present a proof that structural denoising is a consistent surrogate for PSP, and that the multi-agent formulation strictly reduces policy gradient variance in RL. Extensive experiments demonstrate the superiority of SPIRE.

Feedback is crucial for every design process, such as user interface (UI) design, and automating design critiques can significantly improve the efficiency of the design workflow. Although existing multimodal large language models (LLMs) excel in many tasks, they often struggle with generating high-quality design critiques -- a complex task that requires producing detailed design comments that are visually grounded in a given design's image. Building on recent advancements in iterative refinement of text output and visual prompting methods, we propose an iterative visual prompting approach for UI critique that takes an input UI screenshot and design guidelines and generates a list of design comments, along with corresponding bounding boxes that map each comment to a specific region in the screenshot. The entire process is driven completely by LLMs, which iteratively refine both the text output and bounding boxes using few-shot samples tailored for each step. We evaluated our approach using Gemini-1.5-pro and GPT-4o, and found that human experts generally preferred the design critiques generated by our pipeline over those by the baseline, with the pipeline reducing the gap from human performance by 50% for one rating metric. To assess the generalizability of our approach to other multimodal tasks, we applied our pipeline to open-vocabulary object and attribute detection, and experiments showed that our method also outperformed the baseline.

Front-end development accumulates change after change at the repository level, weaving complex cross-file dependencies that current LLM coding agents tuned for single-shot tasks cannot reliably track across multiple iterations, leading to functional regressions and code that resists maintenance. We argue the missing piece is design knowledge: architectural principles, module responsibilities, and structural constraints that developers lean on to keep code readable, maintainable, and evolvable as a system scales. To operationalize this, we propose WebDesignIter, a framework built around a persistent knowledge graph (WebAppArchKG) that fuses repository structure with design knowledge and keeps both in sync across development cycles. WebDesignIter works in two stages: design-informed planning pulls historical context and architectural overviews from WebAppArchKG to produce an implementation plan with corresponding test scripts, and design-aware generation executes that plan through targeted diff-based patches, validated by sandbox execution and automatic syntax repair. On Web-Bench, WebDesignIter delivers an average Pass@2 gain of 9.55 percentage points across nine foundation models over existing baselines. More importantly, WebDesignIter outperforms every general-purpose coding agent Claude Code, OpenHands, SWE-Agent, Codex CLI on every model configuration, posting the highest Pass@1 and Pass@2 while consuming 2530 fewer input tokens. Ablation singles out design knowledge as the most impactful component: stripping it drops Pass@1 by 11.40 percentage points, a degradation far larger than removing code-graph retrieval, patch-based generation, or sandbox verification, confirming that design knowledge provides a fundamentally more efficient and reliable path to repository-level code generation.

Large Language Models (LLMs) can generate Computer-Aided Design (CAD), yet lack physical comprehension required for reliable engineering design. Instead of attempting to implicitly learn physical laws from data, we propose a Hybrid Agentic-Physical Architecture that embeds validated knowledge-based engineering tools directly into the decision making loop of autonomous AI agents. In this framework, engineering design is formulated as a closed-loop, sequential decision making process guided by explicit physical verification. Based on a load case, dedicated agents iteratively plan, generate, evaluate, and revise engineering designs using knowledge-based tools as a feedback signal. We introduce a benchmark dataset and metrics for assessing functional validity in generative CAD. Our system generates more complex and physically verified designs, with a 4.2 increase in structural complexity and improving compile rate by 3.5% compared to similar agentic methods. The codebase, prompts and dataset will be made publicly available to support reproducibility and future research.

Although model editing has shown promise in revising knowledge in Large Language Models (LLMs), its impact on the inherent capabilities of LLMs is often overlooked. In this work, we reveal a critical phenomenon: even a single edit can trigger model collapse, manifesting as significant performance degradation in various benchmark tasks. However, benchmarking LLMs after each edit, while necessary to prevent such collapses, is impractically time-consuming and resource-intensive. To mitigate this, we propose using perplexity as a surrogate metric, validated by extensive experiments demonstrating changes in an edited model's perplexity are strongly correlated with its downstream task performances. We further conduct an in-depth study on sequential editing, a practical setting for real-world scenarios, across various editing methods and LLMs, focusing on hard cases from our previous single edit studies. The results indicate that nearly all examined editing methods result in model collapse after only few edits. To facilitate further research, we have utilized GPT-3.5 to develop a new dataset, HardEdit, based on those hard cases. This dataset aims to establish the foundation for pioneering research in reliable model editing and the mechanisms underlying editing-induced model collapse. We hope this work can draw the community's attention to the potential risks inherent in model editing practices.

High-Level Synthesis (HLS) design space exploration (DSE) seeks Pareto-optimal designs within expansive pragma configuration spaces. To accelerate HLS DSE, graph neural networks (GNNs) are commonly employed as surrogates for HLS tools to predict quality of results (QoR) metrics, while multi-objective optimization algorithms expedite the exploration. However, GNN-based prediction methods may not fully capture the rich semantic features inherent in behavioral descriptions, and conventional multi-objective optimization algorithms often do not explicitly account for the domain-specific knowledge regarding how pragma directives influence QoR. To address these limitations, this paper proposes the MPM-LLM4DSE framework, which incorporates a multimodal prediction model (MPM) that simultaneously fuses features from behavioral descriptions and control and data flow graphs. Furthermore, the framework employs a large language model (LLM) as an optimizer, accompanied by a tailored prompt engineering methodology. This methodology incorporates pragma impact analysis on QoR to guide the LLM in generating high-quality configurations (LLM4DSE). Experimental results demonstrate that our multimodal predictive model significantly outperforms state-of-the-art work ProgSG by up to 10.25times. Furthermore, in DSE tasks, the proposed LLM4DSE achieves an average performance gain of 39.90\% over prior methods, validating the effectiveness of our prompting methodology. Code and models are available at https://github.com/wslcccc/MPM-LLM4DSE.

User interface (UI) design is an iterative process in which designers progressively refine their work with design software such as Figma or Sketch. Recent advances in vision language models (VLMs) with tool invocation suggest these models can operate design software to edit a UI design through iteration. Understanding and enhancing this capacity is important, as it highlights VLMs' potential to collaborate with designers within conventional software. However, as no existing benchmark evaluates tool-based design performance, the capacity remains unknown. To address this, we introduce CANVAS, a benchmark for VLMs on tool-based user interface design. Our benchmark contains 598 tool-based design tasks paired with ground-truth references sampled from 3.3K mobile UI designs across 30 function-based categories (e.g., onboarding, messaging). In each task, a VLM updates the design step-by-step through context-based tool invocations (e.g., create a rectangle as a button background), linked to design software. Specifically, CANVAS incorporates two task types: (i) design replication evaluates the ability to reproduce a whole UI screen; (ii) design modification evaluates the ability to modify a specific part of an existing screen. Results suggest that leading models exhibit more strategic tool invocations, improving design quality. Furthermore, we identify common error patterns models exhibit, guiding future work in enhancing tool-based design capabilities.

Research and practice in Intelligent Design (ID) have significantly enhanced engineering innovation, efficiency, quality, and productivity over recent decades, fundamentally reshaping how engineering designers think, behave, and interact with design processes. The recent emergence of Foundation Models (FMs), particularly Large Language Models (LLMs), has demonstrated general knowledge-based reasoning capabilities, and open new paths and avenues for further transformation in engineering design. In this context, this paper introduces Intelligent Design 4.0 (ID 4.0) as an emerging paradigm empowered by agentic AI systems. We review the historical evolution of ID across four distinct stages: rule-based expert systems, task-specific machine learning models, large-scale foundation AI models, and the recent emerging paradigm of multi-agent collaboration. We propose a conceptual framework for ID 4.0 and discuss its potential to support end-to-end automation of engineering design processes through coordinated, autonomous multi-agent-based systems. Furthermore, we discuss future perspectives to enhance and fully realize ID 4.0's potential, including more complex design scenarios, more practical design implementations, novel agent coordination mechanisms, and autonomous design goal-setting with better human value alignment. In sum, these insights lay a foundation for advancing Intelligent Design toward greater adaptivity, autonomy, and effectiveness in addressing increasingly complex design challenges.

Perturbation-based explanation methods often measure the contribution of an input feature to an image classifier's outputs by heuristically removing it via e.g. blurring, adding noise, or graying out, which often produce unrealistic, out-of-samples. Instead, we propose to integrate a generative inpainter into three representative attribution methods to remove an input feature. Our proposed change improved all three methods in (1) generating more plausible counterfactual samples under the true data distribution; (2) being more accurate according to three metrics: object localization, deletion, and saliency metrics; and (3) being more robust to hyperparameter changes. Our findings were consistent across both ImageNet and Places365 datasets and two different pairs of classifiers and inpainters.

Data-driven design is emerging as a powerful strategy to accelerate engineering innovation. However, its application to vehicle wheel design remains limited due to the lack of large-scale, high-quality datasets that include 3D geometry and physical performance metrics. To address this gap, this study proposes a synthetic design-performance dataset generation framework using generative AI. The proposed framework first generates 2D rendered images using Stable Diffusion, and then reconstructs the 3D geometry through 2.5D depth estimation. Structural simulations are subsequently performed to extract engineering performance data. To further expand the design and performance space, topology optimization is applied, enabling the generation of a more diverse set of wheel designs. The final dataset, named DeepWheel, consists of over 6,000 photo-realistic images and 900 structurally analyzed 3D models. This multi-modal dataset serves as a valuable resource for surrogate model training, data-driven inverse design, and design space exploration. The proposed methodology is also applicable to other complex design domains. The dataset is released under the Creative Commons Attribution-NonCommercial 4.0 International(CC BY-NC 4.0) and is available on the https://www.smartdesignlab.org/datasets

Predicting high-dimensional transcriptional responses to genetic perturbations is challenging due to severe experimental noise and sparse gene-level effects. Existing methods often suffer from mean collapse, where high correlation is achieved by predicting global average expression rather than perturbation-specific responses, leading to many false positives and limited biological interpretability. Recent approaches incorporate biological knowledge graphs into perturbation models, but these graphs are typically treated as dense and static, which can propagate noise and obscure true perturbation signals. We propose AdaPert, a perturbation-conditioned framework that addresses mean collapse by explicitly modeling sparsity and biological structure. AdaPert learns perturbation-specific subgraphs from biological knowledge graphs and applies adaptive learning to separate true signals from noise. Across multiple genetic perturbation benchmarks, AdaPert consistently outperforms existing baselines and achieves substantial improvements on DEG-aware evaluation metrics, indicating more accurate recovery of perturbation-specific transcriptional changes.

We demonstrate how images and sounds can be used for indirect prompt and instruction injection in multi-modal LLMs. An attacker generates an adversarial perturbation corresponding to the prompt and blends it into an image or audio recording. When the user asks the (unmodified, benign) model about the perturbed image or audio, the perturbation steers the model to output the attacker-chosen text and/or make the subsequent dialog follow the attacker's instruction. We illustrate this attack with several proof-of-concept examples targeting LLaVa and PandaGPT.

Tool-use language agents are evaluated on benchmarks that assume clean inputs, unambiguous tool registries, and reliable APIs. Real deployments violate all these assumptions: user typos propagate into hallucinated tool names, a misconfigured request timeout can stall an agent indefinitely, and duplicate tool names across servers can freeze an SDK. We study these failures as a sim-to-real gap in the tool-use partially observable Markov decision process (POMDP), where deployment noise enters through the observation, action space, reward-relevant metadata, or transition dynamics. We introduce RobustBench-TC, a benchmark with 22 perturbation types organized by these four POMDP components, each grounded in a verified GitHub issue or documented tool-calling failure. Across 21 models from 1.5B to 32B parameters (including the closed-source o4-mini), the robustness profile is sharply uneven: observation perturbations reduce accuracy by less than 5%, while reward-relevant and transition perturbations reduce accuracy by roughly 40% and 30%, respectively; scale alone does not close these gaps. We then propose ToolRL-DR, a domain-randomization reinforcement learning (RL) recipe that trains a tool-use agent on perturbation-augmented trajectories spanning the three statically encodable POMDP components. On a 3B backbone, ToolRL-DR-Full retains roughly three-quarters of clean accuracy and reaches an aggregate perturbed accuracy comparable to open-source 14B function-calling baselines while substantially narrowing the gap to o4-mini. It closes approximately 27% of the Transition gap despite never seeing transition perturbations in training, suggesting that RL on adversarial static tool-use inputs induces a more persistent retry policy that transfers to unseen runtime failures. The dataset, code and benchmark leaderboard are publicly available.

Iterative repair loops have become a core design pattern in LLM-based software engineering systems. These workflows repeatedly generate, validate, and repair artifacts using feedback such as compiler errors or test failures. Despite their widespread use, the impact of repair-loop iteration limits remains poorly understood, as most prior work adopts fixed, often arbitrary, repair budgets. We study repair-loop effectiveness across multiple software engineering tasks, including code generation, test generation, and code translation. Across several representative workflows, datasets, and contemporary low-cost LLMs, we observe a consistent pattern of diminishing returns: the first three to four repair iterations account for most achievable gains, while later iterations contribute only marginal improvements. We further find that repair behavior is influenced more strongly by workflow orchestration and feedback design than by the underlying model itself. These results suggest that repair budgets should be treated as an explicit experimental variable, as they directly affect evaluation outcomes, computational cost, runtime, and reproducibility in LLM-based software engineering research.

Contrastive methods have led a recent surge in the performance of self-supervised representation learning (SSL). Recent methods like BYOL or SimSiam purportedly distill these contrastive methods down to their essence, removing bells and whistles, including the negative examples, that do not contribute to downstream performance. These "non-contrastive" methods work surprisingly well without using negatives even though the global minimum lies at trivial collapse. We empirically analyze these non-contrastive methods and find that SimSiam is extraordinarily sensitive to dataset and model size. In particular, SimSiam representations undergo partial dimensional collapse if the model is too small relative to the dataset size. We propose a metric to measure the degree of this collapse and show that it can be used to forecast the downstream task performance without any fine-tuning or labels. We further analyze architectural design choices and their effect on the downstream performance. Finally, we demonstrate that shifting to a continual learning setting acts as a regularizer and prevents collapse, and a hybrid between continual and multi-epoch training can improve linear probe accuracy by as many as 18 percentage points using ResNet-18 on ImageNet. Our project page is at https://alexanderli.com/noncontrastive-ssl/.

With the rapid advancement of Large Language Models (LLMs), there is growing interest in applying them to hardware design and verification. Among these stages, design verification remains the most time-consuming and resource-intensive phase, where generating effective stimuli for the design under test (DUT) is both critical and labor-intensive. We present {\it TB or not TB}, a framework for automated stimulus generation using LLMs fine-tuned through Coverage-Driven Direct Preference Optimization (CD-DPO). To enable preference-based training, we introduce PairaNet, a dataset derived from PyraNet that pairs high- and low-quality testbenches labeled using simulation-derived coverage metrics. The proposed CD-DPO method integrates quantitative coverage feedback directly into the optimization objective, guiding the model toward generating stimuli that maximize verification coverage. Experiments on the CVDP CID12 benchmark show that {\it TB or not TB} outperforms both open-source and commercial baselines, achieving up to 77.27\% improvement in code coverage, demonstrating the effectiveness of Coverage-driven preference optimization for LLM-based hardware verification.

The current advances in generative AI for learning large neural network models with the capability to produce essays, images, music and even 3D assets from text prompts create opportunities for a manifold of disciplines. In the present paper, we study the potential of deep text-to-3D models in the engineering domain, with focus on the chances and challenges when integrating and interacting with 3D assets in computational simulation-based design optimization. In contrast to traditional design optimization of 3D geometries that often searches for the optimum designs using numerical representations, such as B-Spline surface or deformation parameters in vehicle aerodynamic optimization, natural language challenges the optimization framework by requiring a different interpretation of variation operators while at the same time may ease and motivate the human user interaction. Here, we propose and realize a fully automated evolutionary design optimization framework using Shap-E, a recently published text-to-3D asset network by OpenAI, in the context of aerodynamic vehicle optimization. For representing text prompts in the evolutionary optimization, we evaluate (a) a bag-of-words approach based on prompt templates and Wordnet samples, and (b) a tokenisation approach based on prompt templates and the byte pair encoding method from GPT4. Our main findings from the optimizations indicate that, first, it is important to ensure that the designs generated from prompts are within the object class of application, i.e. diverse and novel designs need to be realistic, and, second, that more research is required to develop methods where the strength of text prompt variations and the resulting variations of the 3D designs share causal relations to some degree to improve the optimization.

Generative UI tools promise to democratize UI design by turning natural language descriptions into complete interfaces. Alongside the interface, these tools generate user-facing design rationales that explain their layout, accessibility, and design choices. However, it remains unclear whether these stated rationales are actually reflected in the interfaces they produce. We call this disconnect ``Design Theater'': plausible and confident design rationales that have little relationship to the actual implementation. To study this phenomenon, we introduce a benchmark and three metrics for measuring Design Theater. The benchmark includes 24 UI generation tasks spanning structural, styling, and functional design requirements. Using this benchmark, we evaluate 120 interfaces created by five generative UI tools. On average, over 25\% of user-facing design rationales are not implemented in the generated interface, and the implementation failure increases to 34\% for functional requirements. Tools recognize roughly half of the UX principles embedded in prompts (mean = 0.54), with four of five tools implementing 6\% or fewer functional principles. We also measure interface similarity across tools and find convergence in visual appearance and layout organization, with greater variation in color choices. Overall, we contribute: 1) the concept of Design Theater; 2) a benchmark with metrics for assessing whether the stated reasoning of generative UI tools is reflected in their implementations; 3) and findings from a systematic evaluation of these tools. We discuss what these findings mean for the design and evaluation of generative UI tools.

As leading LLMs improve on capability evaluations, their limitations in producing creative outputs on design tasks remain insufficiently characterised. Our work introduces Design Creativity Bench, a benchmark that evaluates diversity and appropriateness in UI designs. It measures distinctiveness among models on the same prompt (originality), how much a model's designs change between two prompts for the same UI goal in different product domains (creative range), and the share of a brief's acceptance criteria each design meets (appropriateness). Originality is 0.592 for same-prompt design pairs from different models (95% CI [0.582, 0.602]), far below the 0.764 for same-prompt human-model pairs (95% CI [0.751, 0.778]). Creative range is 0.581 across models (95% CI [0.567, 0.597]), against 0.902 for human designs (95% CI [0.884, 0.919]). Appropriateness is above 90% for every model, and the best model reaches 99.2%, slightly above the 98.0% for human designs. Our work shows that the default output of LLMs, though generally appropriate, is substantially more repetitive than the human baseline. This calls for strong measures to address the issue.

We introduce DEsignBench, a text-to-image (T2I) generation benchmark tailored for visual design scenarios. Recent T2I models like DALL-E 3 and others, have demonstrated remarkable capabilities in generating photorealistic images that align closely with textual inputs. While the allure of creating visually captivating images is undeniable, our emphasis extends beyond mere aesthetic pleasure. We aim to investigate the potential of using these powerful models in authentic design contexts. In pursuit of this goal, we develop DEsignBench, which incorporates test samples designed to assess T2I models on both "design technical capability" and "design application scenario." Each of these two dimensions is supported by a diverse set of specific design categories. We explore DALL-E 3 together with other leading T2I models on DEsignBench, resulting in a comprehensive visual gallery for side-by-side comparisons. For DEsignBench benchmarking, we perform human evaluations on generated images in DEsignBench gallery, against the criteria of image-text alignment, visual aesthetic, and design creativity. Our evaluation also considers other specialized design capabilities, including text rendering, layout composition, color harmony, 3D design, and medium style. In addition to human evaluations, we introduce the first automatic image generation evaluator powered by GPT-4V. This evaluator provides ratings that align well with human judgments, while being easily replicable and cost-efficient. A high-resolution version is available at https://github.com/design-bench/design-bench.github.io/raw/main/designbench.pdf?download=

We present an open-source database of superconducting quantum device designs that may be used as the starting point for customized devices. Each design can be generated programmatically using the open-source Qiskit Metal package, and simulated using finite-element electromagnetic solvers. We present a robust workflow for achieving high accuracy on design simulations. Many designs in the database are experimentally validated, showing excellent agreement between simulated and measured parameters. Our database includes a front-end interface that allows users to generate ``best-guess'' designs based on desired circuit parameters. This project lowers the barrier to entry for research groups seeking to make a new class of devices by providing them a well-characterized starting point from which to refine their designs.

Nowadays, developers increasingly rely on solutions powered by Large Language Models (LLM) to assist them with their coding tasks. This makes it crucial to align these tools with human values to prevent malicious misuse. In this paper, we propose a comprehensive framework for assessing the potential harmfulness of LLMs within the software engineering domain. We begin by developing a taxonomy of potentially harmful software engineering scenarios and subsequently, create a dataset of prompts based on this taxonomy. To systematically assess the responses, we design and validate an automatic evaluator that classifies the outputs of a variety of LLMs both open-source and closed-source models, as well as general-purpose and code-specific LLMs. Furthermore, we investigate the impact of models size, architecture family, and alignment strategies on their tendency to generate harmful content. The results show significant disparities in the alignment of various LLMs for harmlessness. We find that some models and model families, such as Openhermes, are more harmful than others and that code-specific models do not perform better than their general-purpose counterparts. Notably, some fine-tuned models perform significantly worse than their base-models due to their design choices. On the other side, we find that larger models tend to be more helpful and are less likely to respond with harmful information. These results highlight the importance of targeted alignment strategies tailored to the unique challenges of software engineering tasks and provide a foundation for future work in this critical area.

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.

The proliferation of applications using artificial intelligence (AI) systems has led to a growing number of users interacting with these systems through sophisticated interfaces. Human-computer interaction research has long shown that interfaces shape both user behavior and user perception of technical capabilities and risks. Yet, practitioners and researchers evaluating the social and ethical risks of AI systems tend to overlook the impact of anthropomorphic, deceptive, and immersive interfaces on human-AI interactions. Here, we argue that design features of interfaces with adaptive AI systems can have cascading impacts, driven by feedback loops, which extend beyond those previously considered. We first conduct a scoping review of AI interface designs and their negative impact to extract salient themes of potentially harmful design patterns in AI interfaces. Then, we propose Design-Enhanced Control of AI systems (DECAI), a conceptual model to structure and facilitate impact assessments of AI interface designs. DECAI draws on principles from control systems theory -- a theory for the analysis and design of dynamic physical systems -- to dissect the role of the interface in human-AI systems. Through two case studies on recommendation systems and conversational language model systems, we show how DECAI can be used to evaluate AI interface designs.

Deploying compound LLM agents in adversarial, partially observable sequential environments requires navigating several design dimensions: (1) what the agent sees, (2) how it reasons, and (3) how tasks are decomposed across components. Yet practitioners lack guidance on which design choices improve performance versus merely increase inference costs. We present a controlled study of compound LLM agent design in CybORG CAGE-2, a cyber defense environment modeled as a Partially Observable Markov Decision Process (POMDP). Reward is non-positive, so all configurations operate in a failure-mitigation mode. Our evaluation spans five model families, six models, and twelve configurations (3,475 episodes) with token-level cost accounting. We vary context representation (raw observations vs. a deterministic state-tracking layer with compressed history), deliberation (self-questioning, self-critique, and self-improvement tools, with optional chain-of-thought prompting), and hierarchical decomposition (monolithic ReAct vs. delegation to specialized sub-agents). We find that: (1) Programmatic state abstraction delivers the largest returns per token spent (RPTS), improving mean return by up to 76% over raw observations. (2) Distributing deliberation tools across a hierarchy degrades performance relative to hierarchy alone for all five model families, reaching up to 3.4times worse mean return while using 1.8-2.7times more tokens. We call this destructive pattern a deliberation cascade. (3) Hierarchical decomposition without deliberation achieves the best absolute performance for most models, and context engineering is generally more cost-effective than deliberation. These findings suggest a design principle for structured adversarial POMDPs: invest in programmatic infrastructure and clean task decomposition rather than deeper per-agent reasoning, as these strategies can interfere when combined.

The automation of analog integrated circuit (IC) design remains a longstanding challenge, primarily due to the intricate interdependencies among physical layout, parasitic effects, and circuit-level performance. These interactions impose complex constraints that are difficult to accurately capture and optimize using conventional design methodologies. Although recent advances in machine learning (ML) have shown promise in automating specific stages of the analog design flow, the development of holistic, end-to-end frameworks that integrate these stages and iteratively refine layouts using post-layout, parasitic-aware performance feedback is still in its early stages. Furthermore, progress in this direction is hindered by the limited availability of open, high-quality datasets tailored to the analog domain, restricting both the benchmarking and the generalizability of ML-based techniques. To address these limitations, we present OSIRIS, a scalable dataset generation pipeline for analog IC design. OSIRIS systematically explores the design space of analog circuits while producing comprehensive performance metrics and metadata, thereby enabling ML-driven research in electronic design automation (EDA). In addition, we release a dataset consisting of 87,100 circuit variations generated with OSIRIS, accompanied by a reinforcement learning (RL)-based baseline method that exploits OSIRIS for analog design optimization.

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.

Design of reliable systems must guarantee stability against input perturbations. In machine learning, such guarantee entails preventing overfitting and ensuring robustness of models against corruption of input data. In order to maximize stability, we analyze and develop a computationally efficient implementation of Jacobian regularization that increases classification margins of neural networks. The stabilizing effect of the Jacobian regularizer leads to significant improvements in robustness, as measured against both random and adversarial input perturbations, without severely degrading generalization properties on clean data.

Despite being trained on vast amounts of data, most LLMs are unable to reliably generate well-designed UIs. Designer feedback is essential to improving performance on UI generation; however, we find that existing RLHF methods based on ratings or rankings are not well-aligned with with designers' workflows and ignore the rich rationale used to critique and improve UI designs. In this paper, we investigate several approaches for designers to give feedback to UI generation models, using familiar interactions such as commenting, sketching and direct manipulation. We first perform an evaluation with 21 designers where they gave feedback using these interactions, which resulted in 1500 design annotations. We then use this data to finetune a series of LLMs to generate higher quality UIs. Finally, we evaluate these models with human judges, and we find that our designer-aligned approaches outperform models trained with traditional ranking feedback and all tested baselines, including GPT-5.

Parametric computer-aided design (CAD) tools are the predominant way that engineers specify physical structures, from bicycle pedals to airplanes to printed circuit boards. The key characteristic of parametric CAD is that design intent is encoded not only via geometric primitives, but also by parameterized constraints between the elements. This relational specification can be viewed as the construction of a constraint program, allowing edits to coherently propagate to other parts of the design. Machine learning offers the intriguing possibility of accelerating the design process via generative modeling of these structures, enabling new tools such as autocompletion, constraint inference, and conditional synthesis. In this work, we present such an approach to generative modeling of parametric CAD sketches, which constitute the basic computational building blocks of modern mechanical design. Our model, trained on real-world designs from the SketchGraphs dataset, autoregressively synthesizes sketches as sequences of primitives, with initial coordinates, and constraints that reference back to the sampled primitives. As samples from the model match the constraint graph representation used in standard CAD software, they may be directly imported, solved, and edited according to downstream design tasks. In addition, we condition the model on various contexts, including partial sketches (primers) and images of hand-drawn sketches. Evaluation of the proposed approach demonstrates its ability to synthesize realistic CAD sketches and its potential to aid the mechanical design workflow.

In this paper, we study the content-aware layout generation problem, which aims to automatically generate layouts that are harmonious with a given background image. Existing methods usually deal with this task with a single-step reasoning framework. The lack of a feedback-based self-correction mechanism leads to their failure rates significantly increasing when faced with complex element layout planning. To address this challenge, we introduce SEGA, a novel Stepwise Evolution Paradigm for Content-Aware Layout Generation. Inspired by the systematic mode of human thinking, SEGA employs a hierarchical reasoning framework with a coarse-to-fine strategy: first, a coarse-level module roughly estimates the layout planning results; then, another refining module performs fine-level reasoning regarding the coarse planning results. Furthermore, we incorporate layout design principles as prior knowledge into the model to enhance its layout planning ability. Besides, we present GenPoster-100K that is a new large-scale poster dataset with rich meta-information annotation. The experiments demonstrate the effectiveness of our approach by achieving the state-of-the-art results on multiple benchmark datasets. Our project page is at: https://brucew91.github.io/SEGA.github.io/

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.

Visual-Language-Action (VLA) models report impressive success rates on robotic manipulation benchmarks, yet these results may mask fundamental weaknesses in robustness. We perform a systematic vulnerability analysis by introducing controlled perturbations across seven dimensions: objects layout, camera viewpoints, robot initial states, language instructions, light conditions, background textures and sensor noise. We comprehensively analyzed multiple state-of-the-art models and revealed consistent brittleness beneath apparent competence. Our analysis exposes critical weaknesses: models exhibit extreme sensitivity to perturbation factors, including camera viewpoints and robot initial states, with performance dropping from 95% to below 30% under modest perturbations. Surprisingly, models are largely insensitive to language variations, with further experiments revealing that models tend to ignore language instructions completely. Our findings challenge the assumption that high benchmark scores equate to true competency and highlight the need for evaluation practices that assess reliability under realistic variation.

Computer Aided Design (CAD) is indispensable across various industries. Text-based CAD editing, which automates the modification of CAD models based on textual instructions, holds great potential but remains underexplored. Existing methods primarily focus on design variation generation or text-based CAD generation, either lacking support for text-based control or neglecting existing CAD models as constraints. We introduce CAD-Editor, the first framework for text-based CAD editing. To address the challenge of demanding triplet data with accurate correspondence for training, we propose an automated data synthesis pipeline. This pipeline utilizes design variation models to generate pairs of original and edited CAD models and employs Large Vision-Language Models (LVLMs) to summarize their differences into editing instructions. To tackle the composite nature of text-based CAD editing, we propose a locate-then-infill framework that decomposes the task into two focused sub-tasks: locating regions requiring modification and infilling these regions with appropriate edits. Large Language Models (LLMs) serve as the backbone for both sub-tasks, leveraging their capabilities in natural language understanding and CAD knowledge. Experiments show that CAD-Editor achieves superior performance both quantitatively and qualitatively.

In engineering design, navigating complex decision-making landscapes demands a thorough exploration of the design, performance, and constraint spaces, often impeded by resource-intensive simulations. Data-driven methods can mitigate this challenge by harnessing historical data to delineate feasible domains, accelerate optimization, or evaluate designs. However, the implementation of these methods usually demands machine-learning expertise and multiple trials to choose the right method and hyperparameters. This makes them less accessible for numerous engineering situations. Additionally, there is an inherent trade-off between training speed and accuracy, with faster methods sometimes compromising precision. In our paper, we demonstrate that a recently released general-purpose transformer-based classification model, TabPFN, is both fast and accurate. Notably, it requires no dataset-specific training to assess new tabular data. TabPFN is a Prior-Data Fitted Network, which undergoes a one-time offline training across a broad spectrum of synthetic datasets and performs in-context learning. We evaluated TabPFN's efficacy across eight engineering design classification problems, contrasting it with seven other algorithms, including a state-of-the-art AutoML method. For these classification challenges, TabPFN consistently outperforms in speed and accuracy. It is also the most data-efficient and provides the added advantage of being differentiable and giving uncertainty estimates. Our findings advocate for the potential of pre-trained models that learn from synthetic data and require no domain-specific tuning to make data-driven engineering design accessible to a broader community and open ways to efficient general-purpose models valid across applications. Furthermore, we share a benchmark problem set for evaluating new classification algorithms in engineering design.

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.

This work addresses minimum-weight design of undamped Euler-Bernoulli frame structures under subresonant single-frequency harmonic excitations, focusing on (robust) dynamic compliance and (robust) peak input power with ellipsoidal load uncertainty. We develop a semidefinite reformulation of robust dynamic compliance for subresonant single-frequency excitation and prove its equivalence to robust peak input power. We show that both these response measures admit an exact reformulation as a free-vibration eigenvalue constraint with design-independent mass augmentation, unifying static, dynamic, and modal requirements. Despite the nonconvex polynomial dependence on cross-sectional areas, certified bounds on global minimizers are obtained via the moment-sum-of-squares hierarchy of semidefinite relaxations. Benchmark studies on 10- and 35-segment frames corroborate the theory. For the 10-segment problem, we obtain the global optimum; for the 35-segment frame, we find high-quality locally-optimal designs that substantially improve on the best known one. We further fabricate and experimentally validate an additional design that closely matches the predictions of the model.

Large language model (LLM) agents now perform well on correctness-oriented repository-level tasks, including SWE-Bench issue resolution and feature implementation in real codebases. However, they still struggle with repository-level code optimization, which requires preserving behavior while improving runtime performance. Passing tests is not enough in this setting; a patch must preserve behavior, implement code optimization, and approach expert speedups. Current agents often miss bottlenecks hidden behind abstraction layers and native extensions, stop after shallow speedups, or insufficiently test the code patches that thus may silently break edge cases. We present PerfAgent, a profiler-guided, verifier-in-the-loop workflow that gives an off-the-shelf coding agent the feedback needed to find real hotspots, improve beyond the first passing patch, and use profiler evidence rather than timing alone to decide what to optimize next. On two challenging optimization benchmarks, GSO and SWE-fficiency-Lite, PerfAgent more than doubles the rate of expert-matching patches over OpenHands with GPT-5.1, improving from 19.6% to 39.2% on GSO and from 26% to 74% on SWE-fficiency-Lite. It also surpasses an oracle best-of-five baseline at substantially lower cost, showing that the gains come from better feedback rather than additional test-time sampling.

Layout design is an important task in various design fields, including user interface, document, and graphic design. As this task requires tedious manual effort by designers, prior works have attempted to automate this process using generative models, but commonly fell short of providing intuitive user controls and achieving design objectives. In this paper, we build a conditional latent diffusion model, PLay, that generates parametrically conditioned layouts in vector graphic space from user-specified guidelines, which are commonly used by designers for representing their design intents in current practices. Our method outperforms prior works across three datasets on metrics including FID and FD-VG, and in user study. Moreover, it brings a novel and interactive experience to professional layout design processes.

Generative AI models have made significant progress in automating the creation of 3D shapes, which has the potential to transform car design. In engineering design and optimization, evaluating engineering metrics is crucial. To make generative models performance-aware and enable them to create high-performing designs, surrogate modeling of these metrics is necessary. However, the currently used representations of three-dimensional (3D) shapes either require extensive computational resources to learn or suffer from significant information loss, which impairs their effectiveness in surrogate modeling. To address this issue, we propose a new two-dimensional (2D) representation of 3D shapes. We develop a surrogate drag model based on this representation to verify its effectiveness in predicting 3D car drag. We construct a diverse dataset of 9,070 high-quality 3D car meshes labeled by drag coefficients computed from computational fluid dynamics (CFD) simulations to train our model. Our experiments demonstrate that our model can accurately and efficiently evaluate drag coefficients with an R^2 value above 0.84 for various car categories. Moreover, the proposed representation method can be generalized to many other product categories beyond cars. Our model is implemented using deep neural networks, making it compatible with recent AI image generation tools (such as Stable Diffusion) and a significant step towards the automatic generation of drag-optimized car designs. We have made the dataset and code publicly available at https://decode.mit.edu/projects/dragprediction/.

Engineering design operates through hierarchical abstraction from system specifications to component implementations, requiring visual understanding coupled with mathematical reasoning at each level. While Multi-modal Large Language Models (MLLMs) excel at natural image tasks, their ability to extract mathematical models from technical diagrams remains unexplored. We present CircuitSense, a comprehensive benchmark evaluating circuit understanding across this hierarchy through 8,006+ problems spanning component-level schematics to system-level block diagrams. Our benchmark uniquely examines the complete engineering workflow: Perception, Analysis, and Design, with a particular emphasis on the critical but underexplored capability of deriving symbolic equations from visual inputs. We introduce a hierarchical synthetic generation pipeline consisting of a grid-based schematic generator and a block diagram generator with auto-derived symbolic equation labels. Comprehensive evaluation of six state-of-the-art MLLMs, including both closed-source and open-source models, reveals fundamental limitations in visual-to-mathematical reasoning. Closed-source models achieve over 85\% accuracy on perception tasks involving component recognition and topology identification, yet their performance on symbolic derivation and analytical reasoning falls below 19\%, exposing a critical gap between visual parsing and symbolic reasoning. Models with stronger symbolic reasoning capabilities consistently achieve higher design task accuracy, confirming the fundamental role of mathematical understanding in circuit synthesis and establishing symbolic reasoning as the key metric for engineering competence.

The advancement of Large Language Models (LLMs) for domain applications in fields such as materials science and engineering depends on the development of fine-tuning strategies that adapt models for specialized, technical capabilities. In this work, we explore the effects of Continued Pretraining (CPT), Supervised Fine-Tuning (SFT), and various preference-based optimization approaches, including Direct Preference Optimization (DPO) and Odds Ratio Preference Optimization (ORPO), on fine-tuned LLM performance. Our analysis shows how these strategies influence model outcomes and reveals that the merging of multiple fine-tuned models can lead to the emergence of capabilities that surpass the individual contributions of the parent models. We find that model merging leads to new functionalities that neither parent model could achieve alone, leading to improved performance in domain-specific assessments. Experiments with different model architectures are presented, including Llama 3.1 8B and Mistral 7B models, where similar behaviors are observed. Exploring whether the results hold also for much smaller models, we use a tiny LLM with 1.7 billion parameters and show that very small LLMs do not necessarily feature emergent capabilities under model merging, suggesting that model scaling may be a key component. In open-ended yet consistent chat conversations between a human and AI models, our assessment reveals detailed insights into how different model variants perform and show that the smallest model achieves a high intelligence score across key criteria including reasoning depth, creativity, clarity, and quantitative precision. Other experiments include the development of image generation prompts based on disparate biological material design concepts, to create new microstructures, architectural concepts, and urban design based on biological materials-inspired construction principles.

Structural modeling is a fundamental component of computational engineering science, in which even minor physical inconsistencies or specification violations may invalidate downstream simulations. The potential of large language models (LLMs) for automatic generation of modeling code has been demonstrated. However, non-executable or physically inconsistent outputs remain prevalent under stringent engineering constraints. A framework for physics-consistent automatic building modeling is therefore proposed, integrating domain knowledge construction, constraint-oriented model alignment, and verification-driven evaluation. CivilInstruct is introduced as a domain-specific dataset that formalizes structural engineering knowledge and constraint reasoning to enable simulation-ready model generation. A two-stage fine-tuning strategy is further employed to enforce constraint satisfaction and application programming interface compliance, substantially reducing hallucinated and non-conforming outputs. MBEval is presented as a verification-driven benchmark that evaluates executability and structural dynamics consistency through closed-loop validation. Experimental results show consistent improvements over baselines across rigorous verification metrics. Our code is available at https://github.com/Jovanqing/AutoBM.

Text-to-image diffusion models are nothing but a revolution, allowing anyone, even without design skills, to create realistic images from simple text inputs. With powerful personalization tools like DreamBooth, they can generate images of a specific person just by learning from his/her few reference images. However, when misused, such a powerful and convenient tool can produce fake news or disturbing content targeting any individual victim, posing a severe negative social impact. In this paper, we explore a defense system called Anti-DreamBooth against such malicious use of DreamBooth. The system aims to add subtle noise perturbation to each user's image before publishing in order to disrupt the generation quality of any DreamBooth model trained on these perturbed images. We investigate a wide range of algorithms for perturbation optimization and extensively evaluate them on two facial datasets over various text-to-image model versions. Despite the complicated formulation of DreamBooth and Diffusion-based text-to-image models, our methods effectively defend users from the malicious use of those models. Their effectiveness withstands even adverse conditions, such as model or prompt/term mismatching between training and testing. Our code will be available at https://github.com/VinAIResearch/Anti-DreamBooth.git{https://github.com/VinAIResearch/Anti-DreamBooth.git}.

Predicting phenotypic and transcriptional responses to perturbations at single-cell resolution provides a powerful tool for probing biological systems. However, existing methods typically rely on fixed mappings learned during training, making it challenging to calibrate distribution shifts or adapt to novel perturbation conditions during inference. Here, we present scEGFlow, an energy-guided flow matching framework that dynamically bridges control and perturbed cellular states. scEGFlow models continuous transitions from control cell populations to perturbed states using conditional flow matching. It then applies condition-specific energy gradients to correct and steer these predictions, enabling flexible adjustments without retraining the flow model. Evaluations across benchmarks spanning imaging phenotypes and transcriptomic profiles show that scEGFlow outperforms existing methods in reconstructing response distributions under both seen and unseen perturbation conditions, faithfully preserving cellular manifold geometry and population heterogeneity. This advantage is notable when adapting to new conditions with only a few measured cells, consistently improving prediction accuracy. Furthermore, scEGFlow accurately recapitulates perturbation-induced up- and down-regulation patterns across consensus gene expression signatures, where energy guidance improves the agreement between predicted and observed regulatory directions. Ultimately, these findings demonstrate that scEGFlow provides a modular, generalizable, and steerable solution for single-cell perturbation modeling. By grounding generative flows in learned biological landscapes, this architecture establishes a new computational paradigm for navigating and manipulating cellular behavior in silico.

We introduce a new method of generating Computer Aided Design (CAD) profiles via a sequence of simple geometric constructions including curve offsetting, rotations and intersections. These sequences start with geometry provided by a designer and build up the points and curves of the final profile step by step. We demonstrate that adding construction steps between the designer's input geometry and the final profile improves generation quality in a similar way to the introduction of a chain of thought in language models. Similar to the constraints in a parametric CAD model, the construction sequences reduce the degrees of freedom in the modeled shape to a small set of parameter values which can be adjusted by the designer, allowing parametric editing with the constructed geometry evaluated to floating point precision. In addition we show that applying reinforcement learning to the construction sequences gives further improvements over a wide range of metrics, including some which were not explicitly optimized.

Text-to-3D systems can now synthesize a model from a single sentence, yet the result is a shape to render, not a design to edit. We present Arko-T, a 4B-parameter text-to-design model that maps natural-language intent directly into executable, parametric CAD programs. Rather than optimizing for code executability alone, Arko-T aligns every stage of the pipeline to a formal notion of design state, so that data curation, code normalization, and execution-grounded supervision all work to preserve the features, parameters, and construction logic that make a CAD artifact editable. Benchmarked against seven frontier LLMs across 12 metrics, Arko-T attains the best score on 8 and the second-best on 3 more, at roughly one-tenth the per-benchmark cost. The results suggest that targeted design-level training at moderate scale can match frontier general-purpose models on structured CAD generation.

Graphics design is important for various applications, including movie production and game design. To create a high-quality scene, designers usually need to spend hours in software like Blender, in which they might need to interleave and repeat operations, such as connecting material nodes, hundreds of times. Moreover, slightly different design goals may require completely different sequences, making automation difficult. In this paper, we propose a system that leverages Vision-Language Models (VLMs), like GPT-4V, to intelligently search the design action space to arrive at an answer that can satisfy a user's intent. Specifically, we design a vision-based edit generator and state evaluator to work together to find the correct sequence of actions to achieve the goal. Inspired by the role of visual imagination in the human design process, we supplement the visual reasoning capabilities of VLMs with "imagined" reference images from image-generation models, providing visual grounding of abstract language descriptions. In this paper, we provide empirical evidence suggesting our system can produce simple but tedious Blender editing sequences for tasks such as editing procedural materials from text and/or reference images, as well as adjusting lighting configurations for product renderings in complex scenes.

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.

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.