Daily Papers

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

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

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

A central hypothesis in aging biology proposes that the gradual accumulation of stochastic molecular damage drives transcriptional deregulation (TD), ultimately leading to functional decline. However, existing single-cell analyses largely rely on static expression measurements and provide limited resolution of how regulatory responses change at the level of individual cells. Here, we leverage DKO, a deep learning framework that predicts cell-specific virtual gene perturbation effects from unperturbed transcriptomes, capturing cell-to-cell differences in regulatory context without requiring a reconstructed gene regulatory network or matched perturbation data. Applying DKO to single-cell transcriptomic datasets from humans, mice, Drosophila, and C. elegans revealed that the transcriptional consequences of perturbing the same gene became increasingly heterogeneous across cells with age, indicating that gene regulatory responses become less consistent and more dependent on cellular context. Furthermore, we find that cells with higher somatic mutation burdens have greater knockout-response variability, linking accumulated molecular damage to regulatory inconsistency. Within the same cellular populations, higher impact variability was also associated with higher senescence scores, linking transcriptional dysregulation to senescence-associated states. Our findings identify a progressive loss of regulatory robustness at both the gene and cell levels as a conserved feature of aging, linking stochastic molecular damage to increasing heterogeneity in cellular regulatory responses.

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).

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

Virtual-cell models aim to predict how cell populations respond to perturbations, but control and treated cells are measured as unpaired populations, complicating the learning of perturbation-specific effects. We present SCALE, a conditional transport model that represents cells as unordered sets and predicts treated populations without cell-level matching. A shared set-aware encoder and conditional DiT backbone learn latent transport, making endpoint supervision directly delta-aligned without an auxiliary delta objective. Across genetic, chemical, developmental and immune perturbations, SCALE recovered gene-expression changes, response directions and population structure. In CRISPR data with dominant cell-line effects, SCALE outperformed competing methods across seven metrics and maintained separation among gene-target representations rather than collapsing them into a shared region. SCALE further prioritized cytokines predicted to produce distinct immune activation and inflammatory responses. Experiments using matched PBMC samples from three donors confirmed these predicted differences. Together, SCALE enables perturbation-specific prediction from unpaired populations and supports experimental prioritization.

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.

Single-cell perturbation models can reduce costly wet-lab screening by predicting how cells respond transcriptionally to interventions. While recent generative models improve population-level prediction, individual generated cells are not explicitly checked for biological consistency. We introduce PerturbCellRL, a reinforcement learning (RL) framework that post-trains a pretrained single-cell transcriptomic generator using a suite of cell-level verifiers as rewards. These verifiers define four rewards: Pearson top-k similarity, RMSE top-k proximity, DE Spearman, and Pathway activity. The Pathway activity verifier rewards cells whose pathway responses match known perturbation biology. We evaluate PerturbCellRL on multiple genetic and chemical perturbation benchmarks. Across these benchmarks, PerturbCellRL improves over the pretrained flow-matching generator on reward-aligned evaluation metrics and a held-out evaluation metric. Moreover, PerturbCellRL remains competitive with state-of-the-art methods on population-level metrics. Together, these results frame trustworthy single-cell prediction as verifier-guided generative alignment, moving beyond matching expression distributions toward predictions whose single-cell perturbation effects are explicitly checked for biological consistency.

Predicting single-cell perturbation responses requires mapping between two unpaired populations of cells measured before and after the perturbation. Optimal transport (OT) provides a principled framework for constructing such mappings by minimizing the transport cost, and neural OT methods (e.g., CellOT) have been employed for this prediction task. However, these methods rely on a fixed transport cost, typically the squared Euclidean distance. This cost may connect cells with the wrong responses. Lineage tracing provides the information needed to learn the cost, as heritable barcodes link the cells of the same clone before and after the perturbation. Here, we propose \CloneOT, a neural inverse OT method that learns both the transport cost and the transport map from partially lineage-traced single-cell datasets. \CloneOT\ represents the cost as a neural network. It learns the cost by minimizing the extra cost that the lineage adds to the optimal transport, so that the cheapest transport keeps the cells of each clone together. Our experiments demonstrate that \CloneOT\ recovers the correct transport on 2D datasets, while the squared Euclidean cost fails. Moreover, \CloneOT\ outperforms five baselines on 14 lineage-tracing perturbation scenarios of cancer cells, for both seen and unseen clones. Furthermore, we show that \CloneOT\ reveals the clone-specific transcriptional programs of drug-tolerant persister cells and forecasts the fate of each clone from its cells before treatment. Our implementation is available at https://github.com/poseidonchan/CloneOT.

Stem cells can precisely and robustly undergo cellular differentiation and lineage commitment, referred to as stemness. However, how the gene network underlying stemness regulation reliably specifies cell fates is not well understood. To address this question, we applied a recently developed computational method, Random Circuit Perturbation (RACIPE), to a nine-component gene regulatory network (GRN) governing stemness, from which we identified fifteen robust gene states. Among them, four out of the five most probable gene states exhibit gene expression patterns observed in single mouse embryonic cells at 32-cell and 64-cell stages. These gene states can be robustly predicted by the stemness GRN but not by randomized versions of the stemness GRN. Strikingly, we found a hierarchical structure of the GRN with the Oct4/Cdx2 motif functioning as the first decision-making module followed by Gata6/Nanog. We propose that stem cell populations, instead of being viewed as all having a specific cellular state, can be regarded as a heterogeneous mixture including cells in various states. Upon perturbations by external signals, stem cells lose the capacity to access certain cellular states, thereby becoming differentiated. The findings demonstrate that the functions of the stemness GRN is mainly determined by its well-evolved network topology rather than by detailed kinetic parameters.

We study the response of mono-energetic stellar populations with initially isotropic kinematics to impulsive and adiabatic changes to an underlying dark matter potential. Half-light radii expand and velocity dispersions decrease as enclosed dark matter is removed. The details of this expansion and cooling depend on the time scale on which the underlying potential changes. In the adiabatic regime, the product of half-light radius and average velocity dispersion is conserved. We show that the stellar populations maintain centrally isotropic kinematics throughout their adiabatic evolution, and their densities can be approximated by a family of analytical radial profiles. Metallicity gradients within the galaxy flatten as dark matter is slowly removed. In the case of strong impulsive perturbations, stellar populations develop power-law-like density tails with radially biased kinematics. We show that the distribution of stellar binding energies within the dark matter halo substantially widens after an impulsive perturbation, no matter the sign of the perturbation. This allows initially energetically separated stellar populations to mix, to the extent that previously chemo-dynamically distinct populations may masquerade as a single population with large metallicity and energy spread. Finally, we show that in response to an impulsive perturbation, stellar populations that are deeply embedded in cored dark matter halos undergo a series of damped oscillations before reaching a virialised equilibrium state, driven by inefficient phase mixing in the harmonic potentials of cored halos. This slow return to equilibrium adds substantial systematic uncertainty to dynamical masses estimated from Jeans modeling or the virial theorem.

Predicting cellular responses to perturbations supports the study of gene function, disease mechanisms, and therapeutic strategies. Despite advances in single-cell perturbation modeling, existing models typically optimize surrogate losses that do not directly reflect the biological criteria used for evaluation, so better data fitting need not yield better biological predictions. To address this mismatch, we introduce CellRFT, a reinforcement fine-tuning framework that uses biological evaluation as direct training feedback. CellRFT uses policy-gradient optimization to learn from non-differentiable evaluations of generated cell populations and integrates multiple biological rewards through hierarchical reward aggregation. Comprehensive experiments demonstrate CellRFT's applicability across different pretrained models and effectiveness in improving perturbation prediction, reveal that optimizing one biological criterion can help or hinder others, and show that complementary rewards can improve criteria beyond those directly optimized, offering a way to probe how biological metrics shape model behavior, with the potential to inform evaluation design. Code will be made available.

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

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.

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

Predicting transcriptional responses to genetic perturbations is central to understanding gene function. Existing predictors primarily rely on transcriptomic measurements, although chromatin accessibility provides complementary information about the cellular context in which perturbations act. Using this information requires linking chromatin context to specific perturbations and accounting for baseline differences between independently sampled control and perturbed populations. We propose ChromaPert, a chromatin-informed framework for predicting state-dependent perturbation responses. ChromaPert combines molecular and DNA-informed locus priors with paired control RNA--ATAC features to jointly represent target identity and measured cellular context. Its Chromatin-Guided Response Router (CGRR) builds a source bank of control-derived expression offsets and retrieves relevant sources using perturbation/locus or control-ATAC similarity. These offsets account for baseline differences, while conditional transport flow learns the remaining response. Across three unseen-target and held-out-state settings on K562 CAT-ATAC and Perturb-Multiome, ChromaPert achieves the highest all-gene response correlation among evaluated methods. When transferring known perturbations to held-out states, it improves correlation by 23.2% across all genes and 46.2% for the twenty most responsive genes over the strongest respective baselines. Correct RNA--ATAC pairing improves recovery of chromatin-associated response slopes over shuffled pairing, while cross-state predictions retain state-specific responses to the same perturbation.

In order to study oscillators coupled by pulses emitted at discrete times, it is generally assumed that the effect of each pulse is an instantaneous phase shift, with a possible conduction delay between emission and receipt. However, we are interested in neural oscillators in which each pulse (action potential) activates a biexponential synapse, and at high frequencies, the duration of the synaptic conductance may be greater than the network period. Therefore, the effect of received pulses can summate over the course of several cycles. To overcome this limitation, we previously defined a mean field approach for a single synchronous population. Here, we extend it to two alternating synchronous populations by assuming a perturbation of a single oscillator from one of the synchronous populations which is represented by a single self-connected neural oscillator. The train of delayed biexponential synapses emitted by each oscillator is divided into a tonic and a phasic component. Because of the continuous rather than pulsatile nature of the input, we had to drop the concept of oscillator phase and derive self-consistent criteria for the existence and stability of an alternating firing pattern between two synchronous populations based solely on the perturbation of time intervals from their steady state values. Simulations showed that for high frequency oscillations as defined above, the mean field approach predicts the existence and stability of phase-locking between two synchronous populations better than the instantaneous phase shift approach. This approach may generalize to other forms of coupling amongst non-neural oscillators.

Weight-perturbation evolution strategies (ES) can fine-tune billion-parameter language models with surprisingly small populations (e.g., N!approx!30), contradicting classical zeroth-order curse-of-dimensionality intuition. We also observe a second seemingly separate phenomenon: under fixed hyperparameters, the stochastic fine-tuning reward often rises, peaks, and then degrades in both ES and GRPO. We argue that both effects reflect a shared geometric property of fine-tuning landscapes: they are low-dimensional in curvature. A small set of high-curvature dimensions dominates improvement, producing (i) heterogeneous time scales that yield rise-then-decay under fixed stochasticity, as captured by a minimal quadratic stochastic-ascent model, and (ii) degenerate improving updates, where many random perturbations share similar components along these directions. Using ES as a geometric probe on fine-tuning reward landscapes of GSM8K, ARC-C, and WinoGrande across Qwen2.5-Instruct models (0.5B--7B), we show that reward-improving perturbations remain empirically accessible with small populations across scales. Together, these results reconcile ES scalability with non-monotonic training dynamics and suggest that high-dimensional fine-tuning may admit a broader class of viable optimization methods than worst-case theory implies.

In this paper, by introducing Generalized Bernstein condition, we propose the first Obig(sqrt{p}{nepsilon}big) high probability excess population risk bound for differentially private algorithms under the assumptions G-Lipschitz, L-smooth, and Polyak-{\L}ojasiewicz condition, based on gradient perturbation method. If we replace the properties G-Lipschitz and L-smooth by alpha-H{\"o}lder smoothness (which can be used in non-smooth setting), the high probability bound comes to Obig(n^{-alpha{1+2alpha}}big) w.r.t n, which cannot achieve Oleft(1/nright) when alphain(0,1]. To solve this problem, we propose a variant of gradient perturbation method, max{1,g-Normalized Gradient Perturbation} (m-NGP). We further show that by normalization, the high probability excess population risk bound under assumptions alpha-H{\"o}lder smooth and Polyak-{\L}ojasiewicz condition can achieve Obig(sqrt{p}{nepsilon}big), which is the first Oleft(1/nright) high probability excess population risk bound w.r.t n for differentially private algorithms under non-smooth conditions. Moreover, we evaluate the performance of the new proposed algorithm m-NGP, the experimental results show that m-NGP improves the performance of the differentially private model over real datasets. It demonstrates that m-NGP improves the utility bound and the accuracy of the DP model on real datasets simultaneously.

Many real-world problems require reasoning across multiple scales, demanding models which operate not on single data points, but on entire distributions. We introduce generative distribution embeddings (GDE), a framework that lifts autoencoders to the space of distributions. In GDEs, an encoder acts on sets of samples, and the decoder is replaced by a generator which aims to match the input distribution. This framework enables learning representations of distributions by coupling conditional generative models with encoder networks which satisfy a criterion we call distributional invariance. We show that GDEs learn predictive sufficient statistics embedded in the Wasserstein space, such that latent GDE distances approximately recover the W_2 distance, and latent interpolation approximately recovers optimal transport trajectories for Gaussian and Gaussian mixture distributions. We systematically benchmark GDEs against existing approaches on synthetic datasets, demonstrating consistently stronger performance. We then apply GDEs to six key problems in computational biology: learning representations of cell populations from lineage-tracing data (150K cells), predicting perturbation effects on single-cell transcriptomes (1M cells), predicting perturbation effects on cellular phenotypes (20M single-cell images), modeling tissue-specific DNA methylation patterns (253M sequences), designing synthetic yeast promoters (34M sequences), and spatiotemporal modeling of viral protein sequences (1M sequences).

High-dimensional count data are common in scientific applications, but most diffusion and flow models are designed for continuous or categorical data, and generation often requires many sequential model evaluations. We propose Count Flow Map, a generative model that learns finite-time transitions directly in count space for one- or few-step generation. Our model directly learns stochastic transitions over finite time intervals, using Poisson births and Binomial deaths to preserve nonnegative integer counts without a predefined maximum. These transition models are trained to match the underlying local birth--death dynamics and to maintain consistency across step sizes. We characterize the connection between local dynamics and finite-time transition consistency and derive a bound on the generation error. After validating Count Flow Map in several simulations, including a high-dimensional, high-count setting, we apply it to single-cell drug perturbation prediction and neural population forecasting, where it captures perturbation responses and supports forecasts of high-activity events with only one or a few model evaluations. Together, these experiments demonstrate that Count Flow Map enables high-quality generation directly in count space across inference budgets, from one-step to few-step generation, using a single trained model.

We develop a model-free policy gradient method for discrete-time mean-field control (MFC). In MFC, the policy affects the objective both through the controlled dynamics and through the population distribution. Standard REINFORCE estimators capture the first effect but not the second. We introduce Transport REINFORCE, a transport map-based approach that perturbs a suitable transformation of the population distribution to estimate this missing mean-field contribution. The method applies to both finite and continuous state spaces. In finite state spaces, we perturb the population distribution directly on the probability simplex through a convex combination of the current population weights and random weights. In continuous state spaces, we project the population distribution onto the manifold of Gaussian mixtures, and then randomize it via a transport map that ensures the perturbed law remains within this manifold. We prove consistency of the perturbed objective and gradient as the perturbation vanishes, and derive bias and mean-square error bounds for the resulting sample-based gradient estimator. Numerical experiments on several MFC benchmarks show that Transport REINFORCE improves over standard REINFORCE.

Simulating trajectories of multi-particle systems on complex energy landscapes is a central task in molecular dynamics (MD) and drug discovery, but remains challenging at scale due to computationally expensive and long simulations. Previous approaches leverage techniques such as flow or Schrödinger bridge matching to implicitly learn joint trajectories through data snapshots. However, many systems, including biomolecular systems and heterogeneous cell populations, undergo dynamic interactions that evolve over their trajectory and cannot be captured through static snapshots. To close this gap, we introduce Entangled Schrödinger Bridge Matching (EntangledSBM), a framework that learns the first- and second-order stochastic dynamics of interacting, multi-particle systems where the direction and magnitude of each particle's path depend dynamically on the paths of the other particles. We define the Entangled Schrödinger Bridge (EntangledSB) problem as solving a coupled system of bias forces that entangle particle velocities. We show that our framework accurately simulates heterogeneous cell populations under perturbations and rare transitions in high-dimensional biomolecular systems.

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.

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.

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.

Objective perturbation adds a random linear term to a regularized empirical risk and releases the exact perturbed minimizer. We study the finite computation obtained by releasing the N-th iterate of deterministic gradient descent on wmapsto F(w;S)+langle z,wrangle, where zsimmathcal N(0,σ^2I_d) is drawn once before optimization. For strongly convex and smooth objectives with Lipschitz Hessian, we prove an explicit condition under which the map zmapsto w_N is a C^1-diffeomorphism on the bounded domains used in the privacy argument, with a quantitative lower bound on the smallest singular value of its Jacobian. This permits a direct change-of-variables analysis of the finite iterate. For generalized linear models, the resulting privacy-profile bound has no explicit ambient-dimension factor once the iteration condition holds, and its finite-iteration correction decreases geometrically. By letting the free truncation parameter grow slowly with N, we recover the corresponding exact-minimizer certificate in the limit. We also bound the expected excess empirical risk by dσ^2/(2μ) plus a geometrically decreasing optimization term, and transfer the result to population risk without an additional multiplicative condition-number factor in the leading statistical terms.

Rate-induced tipping ("R-tipping") in ecological modelling is characterised by too-rapid change of an environmental parameter causing collapse of a population without any bifurcation being crossed ("B-tipping"). A well-known example of a slow-fast predator-prey model in which R-tipping is observed [Vanselow, Wieczorek, Feudel, Journal of Theoretical Biology, 479, 64-72 (2019)] suffers from unecological "resurgence", whereby populations driven to functional extinction recover towards stable coexistence. We propose an analytically tractable model, incorporating a strong Allee effect into the prey dynamics in a slow-fast Lotka-Volterra-type predator-prey system, which induces bistability and thus renders the extinction state a genuine attractor. Applying geometric singular perturbation theory (GSPT), we describe the dynamics of the extended model that is obtained by "ramping" of the inverse prey carrying capacity. We show the presence of a parabolic-shaped, folded critical manifold which admits a folded saddle singularity, the strong canard of which separates solutions that track the moving coexistence state from those that tip to extinction. The analytical simplicity of our model allows us to derive explicit expressions for the critical rate that separates "tracking" from "tipping" dynamics. Finally, we argue that our system represents a minimal model for rate-induced tipping to extinction, in that it incorporates three essential ingredients: bistability, a folded critical manifold, and a folded-saddle-type canard.

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

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.

Post-training of language models is commonly framed as a sample-score-update loop implemented by gradient descent. A recent line of work, exemplified by RandOpt, relocates this loop to weight space, sampling Gaussian perturbations around a pretrained model and ensembling the top-K rewarded specialists at inference. While competitive with PPO and GRPO under matched training compute, this prediction-level ensemble incurs K forward passes per test example and does not extend cleanly to free-form generation. We ask whether the rewarded population can instead be folded into a single deployable model, replacing the inference-time ensemble with one consolidated update. A split-half analysis over 25 model-task pairs reveals reproducible low-rank structure in every case. We turn this geometry into CoRP (Consolidating Rewarded Perturbations), a gradient-free operator that combines reward-weighted aggregation, compatibility-aware reweighting, and a held-out validation gate, with no gradient flowing through the language model. Across five language models from 0.5B to 8B and five tasks covering math, code, and creative writing, CoRP improves the base model by 8.1 points on average. Using one tenth of RandOpt's perturbation budget, CoRP exceeds single-inference RandOpt by 6.5 points and recovers more than half of the gain of the 50-pass majority-vote ensemble, at one forward pass per test example.

Single-cell perturbation atlases rarely measure every intervention in every cellular context: a query perturbation is often observed in one or more source contexts but missing in the recipient context where its effect is needed. Ignoring those measured responses discards query-specific experimental evidence, whereas copying or weakly calibrating them across contexts risks transferring the wrong signal. We propose PerturbMap, which predicts a missing recipient-context effect by combining a recipient-local low-rank base with accepted proposals that transport the same perturbation's measured source responses through source-to-recipient ridge experts fit on paired training perturbations, with proposal weights determined by route reliability estimated on validation anchors. On the Perturb-CITE-seq melanoma cohort, PerturbMap improves full-effect MSE by 4.1\% over a recipient-local low-rank base and achieves lower MSE than FedAvg, zero-response, raw-copy, calibrated-copy, and identity-shuffled affine controls. It remains within 2.82times10^{-6} MSE of our centralized token-matched pooled reference, which uses a stronger training interface. A condition-mean specificity diagnostic shows the same direction: same-recipient top-10 counterpart retrieval by cosine increases from 74.5\% for the low-rank base to 80.5\% for PerturbMap.

Adversarial examples are often cited by neuroscientists and machine learning researchers as an example of how computational models diverge from biological sensory systems. Recent work has proposed adding biologically-inspired components to visual neural networks as a way to improve their adversarial robustness. One surprisingly effective component for reducing adversarial vulnerability is response stochasticity, like that exhibited by biological neurons. Here, using recently developed geometrical techniques from computational neuroscience, we investigate how adversarial perturbations influence the internal representations of standard, adversarially trained, and biologically-inspired stochastic networks. We find distinct geometric signatures for each type of network, revealing different mechanisms for achieving robust representations. Next, we generalize these results to the auditory domain, showing that neural stochasticity also makes auditory models more robust to adversarial perturbations. Geometric analysis of the stochastic networks reveals overlap between representations of clean and adversarially perturbed stimuli, and quantitatively demonstrates that competing geometric effects of stochasticity mediate a tradeoff between adversarial and clean performance. Our results shed light on the strategies of robust perception utilized by adversarially trained and stochastic networks, and help explain how stochasticity may be beneficial to machine and biological computation.

Evolving borrower behaviors, shifting economic conditions, and changing regulatory landscapes continuously reshape the data distributions underlying modern credit-scoring systems. Conventional explainability techniques, such as SHAP, assume static data and fixed background distributions, making their explanations unstable and potentially unfair when concept drift occurs. This study addresses that challenge by developing adaptive explanation frameworks that recalibrate interpretability and fairness in dynamically evolving credit models. Using a multi-year credit dataset, we integrate predictive modeling via XGBoost with three adaptive SHAP variants: (A) per-slice explanation reweighting that adjusts for feature distribution shifts, (B) drift-aware SHAP rebaselining with sliding-window background samples, and (C) online surrogate calibration using incremental Ridge regression. Each method is benchmarked against static SHAP explanations using metrics of predictive performance (AUC, F1), directional and rank stability (cosine, Kendall tau), and fairness (demographic parity and recalibration). Results show that adaptive methods, particularly rebaselined and surrogate-based explanations, substantially improve temporal stability and reduce disparate impact across demographic groups without degrading predictive accuracy. Robustness tests, including counterfactual perturbations, background sensitivity analysis, and proxy-variable detection, confirm the resilience of adaptive explanations under real-world drift conditions. These findings establish adaptive explainability as a practical mechanism for sustaining transparency, accountability, and ethical reliability in data-driven credit systems, and more broadly, in any domain where decision models evolve with population change.

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.

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 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 introduce a new predator-prey model by replacing the growth and predation constant by a square matrix, and the population density as a population vector. The classical Lotka-Volterra model describes a population that either modulates or converges. Stability analysis of such models have been extensively studied by the works of Merdan (https://doi.org/10.1016/j.chaos.2007.06.062). The new model adds complexity by introducing an age group structure where the population of each age group evolves as prescribed by the Leslie matrix. The added complexity changes the behavior of the model such that the population either displays roughly an exponential growth or decay. We first provide an exact equation that describes a time evolution and use analytic techniques to obtain an approximate growth factor. We also discuss the variants of the Leslie model, i.e., the complex value predator-prey model and the competitive model. We then prove the Last Species Standing theorem that determines the dominant population in the large time limit. The recursive structure of the model denies the application of simple regression. We discuss a machine learning scheme that allows an admissible fit for the population evolution of Paramecium Aurelia and Paramecium Caudatum. Another potential avenue to simplify the computation is to use the machinery of quantum operators. We demonstrate the potential of this approach by computing the Hamiltonian of a simple Leslie system.

In this paper, we study the problem of sampling from a probability distribution using Langevin-type dynamics. We consider overdamped Langevin dynamics perturbed by adding a Stratonovich perturbation that preserves reversibility. We prove an optimal scaling for the Stratonovich perturbation applied to Gaussian target distributions and derive an algorithm to construct such perturbation. Our theoretical results are supplemented by numerical experiments in which we compare our proposed method with nonreversible samplers and overdamped Langevin dynamics. Our numerical experiments demonstrate the efficiency of the approach beyond the quadratic case.

Planning effective interventions in biological systems requires treatment-effect models that adapt to unseen biological contexts by identifying their specific underlying mechanisms. Yet single-cell perturbation datasets span only a handful of biological contexts, and existing methods cannot leverage new interventional evidence at inference time to adapt beyond their training data. To meta-learn a perturbation effect estimator, we present MapPFN, a prior-data fitted network (PFN) pretrained on synthetic data generated from a prior over causal perturbations. Given a set of experiments, MapPFN uses in-context learning to predict post-perturbation distributions, without gradient-based optimization. Despite being pretrained on in silico gene knockouts alone, MapPFN identifies differentially expressed genes, matching the performance of models trained on real single-cell data. Our code and data are available at https://github.com/marvinsxtr/MapPFN.

Cosmological first-order phase transitions can generate curvature perturbations through inhomogeneous quantum tunneling, as studied previously on superhorizon scales. In this work, we for the first time conduct three-dimensional lattice simulations that incorporate scalar metric perturbations and radiation perturbations, covering a range from bubble wall scales to super-horizon scales. We obtain the precise scalar perturbation power spectrum and the probability density function of energy density perturbations. Furthermore, we simulate the gravitational-wave energy spectra generated by each source during the first-order phase transition, including the scalar field itself, scalar metric perturbations, and the energy density and velocity perturbations of radiation. For gravitational waves, the contribution from other sources can exceed 1/3 of that from the scalar field at superhorizon scales. Additionally, we compare the effects of different values of the transition strength and rate on the results. This paper provides more accurate numerical results for research aimed at detecting or constraining first-order phase transitions via gravitational waves and curvature perturbations.

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.

Model uncertainty and limited data are fundamental challenges to robust management of human intervention in a natural system. These challenges are acutely highlighted by concerns that many ecological systems may contain tipping points, such as Allee population sizes. Before a collapse, we do not know where the tipping points lie, if they exist at all. Hence, we know neither a complete model of the system dynamics nor do we have access to data in some large region of state-space where such a tipping point might exist. We illustrate how a Bayesian Non-Parametric (BNP) approach using a Gaussian Process (GP) prior provides a flexible representation of this inherent uncertainty. We embed GPs in a Stochastic Dynamic Programming (SDP) framework in order to make robust management predictions with both model uncertainty and limited data. We use simulations to evaluate this approach as compared with the standard approach of using model selection to choose from a set of candidate models. We find that model selection erroneously favors models without tipping points -- leading to harvest policies that guarantee extinction. The GPDP performs nearly as well as the true model and significantly outperforms standard approaches. We illustrate this using examples of simulated single-species dynamics, where the standard model selection approach should be most effective, and find that it still fails to account for uncertainty appropriately and leads to population crashes, while management based on the GPDP does not, since it does not underestimate the uncertainty outside of the observed data.

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.

The origin of supermassive black holes, especially those already present at high redshift, remains an open problem. We propose that their seeds are primordial black holes formed from rare overdense regions of conventional thermal DM. A spectator scalar with two degenerate vacua gives the DM different masses, and hence different freeze-out abundances, in the two vacua. Inflationary fluctuations populate the vacuum containing the heavier relic only in exponentially rare patches. As the Universe cools, the density contrast of these patches grows sufficiently large for the patches to collapse into PBHs after horizon re-entry. We derive the resulting PBH mass function and show that it is sharply concentrated near a lower cutoff while reproducing the mass scale and abundance required for SMBH seeds. Since the overdensities originate from a rare, non-Gaussian population rather than from an enhancement of nearly Gaussian primordial curvature perturbations, the usual CMB spectral-distortion constraint does not directly apply. The construction also correlates the seed population with the dark-sector spectrum and the inflation scale, providing complementary avenues for testing the scenario.

Density peak clustering (DPC) connects each observation to its nearest neighbor of higher density and identifies cluster centers as high-density observations with unusually large nearest neighbor uphill shifts. The resulting uphill paths from observations to cluster centers, however, can be irregular and unstable in low-density regions, making the clustering assignments sensitive to local perturbations and obscuring the population geometry of the DPC graph. In this paper, we introduce gradient-guided density peak clustering (GGDPC), which performs a gradient ascent step before each nearest neighbor uphill search. We develop a stability theory that relates the GGDPC graph to the gradient ascent flow of the population density. In particular, we establish consistency of GGDPC under five complementary criteria: recovery of local modes, adjusted Rand index, dendrogram (cluster tree), path length, and waterfall measure. Together, these results provide new statistical, geometric, and topological interpretations of DPC-type clustering algorithms.

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.

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.

On a global level, ecological communities are being perturbed at an unprecedented rate by human activities and environmental instabilities. Yet, we understand little about what factors facilitate or impede long-term persistence of these communities. While observational studies indicate that increased biodiversity must, somehow, be driving stability, theoretical studies have argued the exact opposite viewpoint instead. This encouraged many researchers to participate in the ongoing diversity-stability debate. Within this context, however, there has been a severe lack of studies that consider spatial features explicitly, even though nearly all habitats are spatially embedded. To this end, we study here the linear stability of meta-ecosystems on networks that describe how discrete patches are connected by dispersal between them. By combining results from random-matrix theory and network theory, we are able to show that there are three distinct features that underlie stability: edge density, tendency to triadic closure, and isolation or fragmentation. Our results appear to further indicate that network sparsity does not necessarily reduce stability, and that connections between patches are just as, if not more, important to consider when studying the stability of large ecological systems.

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.

Flow-based generative models have been employed for sampling the Boltzmann distribution, but their application to high-dimensional systems is hindered by the significant computational cost of obtaining the Jacobian of the flow. To overcome this challenge, we introduce the flow perturbation method, which incorporates optimized stochastic perturbations into the flow. By reweighting trajectories generated by the perturbed flow, our method achieves unbiased sampling of the Boltzmann distribution with orders of magnitude speedup compared to both brute force Jacobian calculations and the Hutchinson estimator. Notably, it accurately sampled the Chignolin protein with all atomic Cartesian coordinates explicitly represented, which, to our best knowledge, is the largest molecule ever Boltzmann sampled in such detail using generative models.

Predicting how a cell will change its transcriptional state under a developmental signal or a genetic perturbation is the computational core of in-silico biology and the AI Virtual Cell program. Existing approaches either fit static control-to-treated maps that discard time, or solve multi-step ODE / Schrödinger-bridge problems on each dataset independently. We introduce Chreode, a one-step cell world model that predicts action-conditioned cell-state transitions through a structured residual transition operator. It shifts distributional evolution from inference time to training time, enabling single-pass generation while preserving a Waddington-inspired decomposition into downhill landscape flow, rotational in-tangent dynamics, and stochastic spread. The model is pretrained with a shared scVI encoder and a DiT-based dynamics backbone on a 2.4M-cell mouse embryonic atlas spanning 7 datasets. As a fine-tuning initialization, Chreode improves per-target Sinkhorn distance on Weinreb hematopoiesis and Veres islet differentiation over matched scratch models, PI-SDE, and PRESCIENT. As a transferable gene-state embedding for GEARS, the pretrained dynamics representation reduces shared-vocabulary DE20 mean squared error on Norman Perturb-seq from 0.2121 to 0.1858, a 12.4% relative improvement, without changing the GEARS training procedure. We interpret this transfer to perturbation prediction as evidence that pretrained developmental-trajectory dynamics encode differentiation primitives transferable to CRISPR-induced state shifts, since both involve cell-state transitions in a shared latent geometry. The pretrained backbone additionally produces zero-shot clonal fate scores on Weinreb that are competitive with strong dynamic-OT baselines.

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

Accurate prediction of extreme weather events remains a major challenge for artificial intelligence-based weather prediction systems. While deterministic models such as FuXi, GraphCast, and SFNO have achieved competitive forecast skill relative to numerical weather prediction, their ability to represent uncertainty and capture extremes is still limited. This study investigates how state-of-the-art deterministic artificial intelligence-based models respond to initial-condition perturbations and evaluates the resulting ensembles in forecasting extremes. Using four perturbation strategies (Gaussian, Perlin noise, Hemispheric Centered Bred Vectors, and Huge Ensembles), we generate 50 member ensembles for the August 2022 Pakistan floods and China heatwave, and complement these case studies with a global threshold-based evaluation. Ensemble skill is assessed against ERA5 and compared with IFS ENS and the AIFS ENS probabilistic model using deterministic and probabilistic metrics. Results show that simpler perturbations like Gaussian and Perlin noise produce similarly realistic ensemble spread and probabilistic skill as flow-based approaches like HCBV and HENS, narrowing but not closing the performance gap with numerical weather prediction ensembles, or native probabilistic models which retain the highest probabilistic skill across variables. Model choice is the dominant factor for ensemble performance, not perturbation method. Across variables, models capture temperature extremes more effectively than precipitation. These findings demonstrate that simple input perturbations can extend deterministic models toward probabilistic forecasting in hardware-constrained settings, supporting artificial intelligence-driven early warning systems.

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

Overfitting widely exists in adversarial robust training of deep networks. An effective remedy is adversarial weight perturbation, which injects the worst-case weight perturbation during network training by maximizing the classification loss on adversarial examples. Adversarial weight perturbation helps reduce the robust generalization gap; however, it also undermines the robustness improvement. A criterion that regulates the weight perturbation is therefore crucial for adversarial training. In this paper, we propose such a criterion, namely Loss Stationary Condition (LSC) for constrained perturbation. With LSC, we find that it is essential to conduct weight perturbation on adversarial data with small classification loss to eliminate robust overfitting. Weight perturbation on adversarial data with large classification loss is not necessary and may even lead to poor robustness. Based on these observations, we propose a robust perturbation strategy to constrain the extent of weight perturbation. The perturbation strategy prevents deep networks from overfitting while avoiding the side effect of excessive weight perturbation, significantly improving the robustness of adversarial training. Extensive experiments demonstrate the superiority of the proposed method over the state-of-the-art adversarial training methods.

We investigate the spectral statistics of random perturbations of semiclassical Schrödinger operators on compact manifolds, near energy levels corresponding to chaotic classical dynamics. The prototypical example is that of an operator h^2Δ+V(x) that is perturbed by a smooth potential h^αV_ω with αin (0,1), and V_ω is a random potential that decorrelates on distances h^β, with 0<β<2α. We show that for a generic perturbation, the spectral fluctuations of the smoothed counting function of eigenvalues obey a universal behavior at a certain mesoscopic scale, which is coherent with the predictions of random matrix theory.

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.

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.

We examine the geometry of neural network training using the Jacobian of trained network parameters with respect to their initial values. Our analysis reveals low-dimensional structure in the training process which is dependent on the input data but largely independent of the labels. We find that the singular value spectrum of the Jacobian matrix consists of three distinctive regions: a "chaotic" region of values orders of magnitude greater than one, a large "bulk" region of values extremely close to one, and a "stable" region of values less than one. Along each bulk direction, the left and right singular vectors are nearly identical, indicating that perturbations to the initialization are carried through training almost unchanged. These perturbations have virtually no effect on the network's output in-distribution, yet do have an effect far out-of-distribution. While the Jacobian applies only locally around a single initialization, we find substantial overlap in bulk subspaces for different random seeds. Our code is available at https://github.com/EleutherAI/training-jacobian

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.

Large language models (LLMs) are widely used as information sources, yet small changes in semantic assumptions can destabilize their beliefs. We introduce P-StaT (Perturbation Stability of Truth), a framework for evaluating belief stability under matched semantic perturbations in both representational and behavioral settings. Across 21 LLMs and three domains, we compare perturbations involving familiar Fictional statements against synthetically generated and unfamiliar Synthetic statements. Unfamiliar Synthetic perturbations generally induce greater epistemic instability than familiar Fictional perturbations, with behavioral belief retraction rates frequently exceeding 0.5 (50%). Finally, exploratory clustering analyses reveal recurring themes among retracted statements, including ambiguity, technical terminology, and obscure concepts. These results show that epistemic familiarity is systematically associated with stability under semantic reframing, suggesting that stability-based analyses can complement accuracy-based benchmarks when evaluating LLM robustness and reliability. Code and data are available at https://github.com/samanthadies/P-StaT.

Outer-learning algorithms use infinitesimal sensitivities to propose finite changes to initialization or training parameters. For hard-ReLU training, the derivative of the finite program and the derivative of its flow limit do not by themselves specify the response at a chosen radius. We characterize the intervening regime in which the perturbation radius is proportional to the GD step. Integer event rounding then survives at leading order: smooth Euler bias shifts each discrete phase, and upstream rounding moves downstream branch boundaries. We derive the crossing indices and a uniform endpoint expansion for finitely many separated transverse events in piecewise-C^2 dynamics, away from recursive phase boundaries. In contractive affine regions, an explicit remainder and complete branch verification certify finite candidate comparisons. Scalar phase frequencies and a coupled feedback ablation test the mechanism; frozen nonlinear-network experiments show radius-dependent prediction accuracy, including incomplete branch matches and failed-word tails. Together with local AD and uniform flow consistency, the result identifies sufficient response regimes: differentiating training is a choice of perturbation resolution as well as a choice of derivative.

Guided diffusion samplers are increasingly used to reconstruct physical fields from sparse observations, but standard diagnostics do not say how much of the reconstruction was actually determined by the data. We introduce effective data resolution for black-box generative posteriors: a comparison between the resolution warranted by the inverse problem, dof_{ref}, and the resolution realised by the sampler, dof_{samp}. A perturbation estimator measures dof_{samp} and the spatial map R(x,x) from sampler queries alone. We validate the estimator against exact references and use it to study guided diffusion. The resulting measurements show that guidance weight can strongly alter apparent information transfer, that mean, spread and resolution are not jointly corrected by one weight even with an exact prior and score, and that resolution fidelity does not follow reliably from the apparent principledness of a guidance rule.

Perturbative availability poisons (PAPs) add small changes to images to prevent their use for model training. Current research adopts the belief that practical and effective approaches to countering PAPs do not exist. In this paper, we argue that it is time to abandon this belief. We present extensive experiments showing that 12 state-of-the-art PAP methods are vulnerable to Image Shortcut Squeezing (ISS), which is based on simple compression. For example, on average, ISS restores the CIFAR-10 model accuracy to 81.73%, surpassing the previous best preprocessing-based countermeasures by 37.97% absolute. ISS also (slightly) outperforms adversarial training and has higher generalizability to unseen perturbation norms and also higher efficiency. Our investigation reveals that the property of PAP perturbations depends on the type of surrogate model used for poison generation, and it explains why a specific ISS compression yields the best performance for a specific type of PAP perturbation. We further test stronger, adaptive poisoning, and show it falls short of being an ideal defense against ISS. Overall, our results demonstrate the importance of considering various (simple) countermeasures to ensure the meaningfulness of analysis carried out during the development of PAP methods.

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.

We formulate gene regulatory network reconstruction from RNA velocity as a sparse dynamical inverse problem. We show that control-only data can be structurally nonidentifying and characterize excitation conditions under which controlled perturbations restore identifiability by generating complementary regulator trajectories. To enable stable reconstruction from noisy data, we develop an integral sparse estimator that avoids numerical differentiation and derive recovery bounds separating stochastic error from systematic contributions due to latent-time uncertainty, kinetic-parameter error, numerical quadrature, and model misspecification. Synthetic experiments illustrate perturbation-assisted identifiability, improved conditioning, and the robustness of integral reconstruction. Applied to perturbation-resolved RPE1 RNA-velocity data, the framework yields an empirically full-rank design whose conditioning improves with perturbational diversity and a reconstructed network core stable under perturbation subsampling. Held-out evaluation further shows that identifiability and reconstruction stability do not imply uniform predictive improvement. These results connect perturbational excitation, identifiability, and stable sparse recovery in regulatory dynamical systems.

Many of society's most pressing challenges, from pandemic response to supply chain disruptions to climate adaptation, emerge from the collective behavior of millions of autonomous agents making decisions over time. Large Population Models (LPMs) offer an approach to understand these complex systems by simulating entire populations with realistic behaviors and interactions at unprecedented scale. LPMs extend traditional modeling approaches through three key innovations: computational methods that efficiently simulate millions of agents simultaneously, mathematical frameworks that learn from diverse real-world data streams, and privacy-preserving communication protocols that bridge virtual and physical environments. This allows researchers to observe how agent behavior aggregates into system-level outcomes and test interventions before real-world implementation. While current AI advances primarily focus on creating "digital humans" with sophisticated individual capabilities, LPMs develop "digital societies" where the richness of interactions reveals emergent phenomena. By bridging individual agent behavior and population-scale dynamics, LPMs offer a complementary path in AI research illuminating collective intelligence and providing testing grounds for policies and social innovations before real-world deployment. We discuss the technical foundations and some open problems here. LPMs are implemented by the AgentTorch framework (github.com/AgentTorch/AgentTorch)

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.

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.

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

We prove that all excited states -sin(nx), ngeq2, of the De Gregorio equation on the torus are nonlinearly unstable in the sense of Hadamard. More precisely, perturbations arbitrarily small in H^2 leave a fixed H^1 neighborhood of the state. For every ngeq2, the linearized operator has a real eigenvalue λ_nin(0.56,0.6). To prove this, we transform the eigenvalue problem into a Fuchsian equation on the complex disk and obtain a matching condition for the eigenvalue. This condition is verified rigorously using interval arithmetic. The nonlinear instability follows from a bootstrap argument in the spirit of Guo, Hallstrom, and Spirn.

The antenna-elements that make up a radio interferometer form a spatial filter that samples components of the Fourier transform of a target radio astronomical source brightness. Along the signal path, there are multiplicative and additive perturbation effects that alter the signal and that should be corrected. The process of mitigating these perturbation effects is called calibration. In this work, we develop a new and fast Maximum Likelihood based estimator of these perturbation effects using the Exponential Map and Lie groups. To evaluate its performance, we compare it to the Cramér-Rao Lower Bound and, to test the estimation time, we compare it with the Expectation Maximization algorithm, another fast Maximum Likelihood estimator. Finally, we apply our estimator to a real observation of the protoplanetary disk AS 209 made with the Submillimeter Array. We found that our proposed estimator meets the Cramér-Rao Lower Bound and it was approximately 40 times faster than the Expectation Maximization algorithm.

This paper investigates the problem of forecasting multivariate aggregated human mobility while preserving the privacy of the individuals concerned. Differential privacy, a state-of-the-art formal notion, has been used as the privacy guarantee in two different and independent steps when training deep learning models. On one hand, we considered gradient perturbation, which uses the differentially private stochastic gradient descent algorithm to guarantee the privacy of each time series sample in the learning stage. On the other hand, we considered input perturbation, which adds differential privacy guarantees in each sample of the series before applying any learning. We compared four state-of-the-art recurrent neural networks: Long Short-Term Memory, Gated Recurrent Unit, and their Bidirectional architectures, i.e., Bidirectional-LSTM and Bidirectional-GRU. Extensive experiments were conducted with a real-world multivariate mobility dataset, which we published openly along with this paper. As shown in the results, differentially private deep learning models trained under gradient or input perturbation achieve nearly the same performance as non-private deep learning models, with loss in performance varying between 0.57% to 2.8%. The contribution of this paper is significant for those involved in urban planning and decision-making, providing a solution to the human mobility multivariate forecast problem through differentially private deep learning models.

We develop a linear perturbative formalism to compute the response of an inhomogeneous stellar disk embedded in a non-responsive dark matter halo to perturbations like bars, spiral arms and satellite galaxy encounters. Without self-gravity to reinforce it, the response of a Fourier mode phase mixes away due to an intrinsic spread in the vertical (Omega_z), radial (Omega_r) and azimuthal (Omega_phi) frequencies, giving rise to local phase-space spirals. Collisional diffusion due to scattering of stars by structures like giant molecular clouds causes super-exponential damping of the phase-spiral amplitude. The z-v_z phase-spiral is 1-armed (2-armed) for vertically anti-symmetric (symmetric) bending (breathing) modes. Only transient perturbations with timescales (tau_{P}) comparable to the vertical oscillation period (tau_z sim 1/Omega_z) trigger z-v_z phase-spirals. Each (n,l,m) mode of the response to impulsive (tau_{P}<tau=1/(nOmega_z+lOmega_r+mOmega_phi)) perturbations is power law (sim tau_{P}/tau) suppressed, but that to adiabatic (tau_{P}>tau) perturbations is exponentially weak (sim left[-left(tau_{mathrm{P}/tauright)^alpharight]}) except resonant (tauto infty) modes. Slower (tau_{P}>tau_z) perturbations, e.g., distant encounters with satellite galaxies, induce stronger bending modes. If the Gaia phase-spiral was triggered by a satellite, Sagittarius is the leading contender as it dominates the Solar neighborhood response of the Milky Way disk to satellite encounters. However, survival against collisional damping necessitates that the impact occurred within sim 0.6-0.7 Gyr ago. We discuss how the detailed galactic potential dictates the phase-spiral shape: phase mixing occurs slower and phase-spirals are less wound in the outer disk and in presence of an ambient halo.

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.

The Wilson-Cowan model for metapopulation, a Neural Mass Network Model, treats different subcortical regions of the brain as connected nodes, with connections representing various types of structural, functional, or effective neuronal connectivity between these regions. Each region comprises interacting populations of excitatory and inhibitory cells, consistent with the standard Wilson-Cowan model. By incorporating stable attractors into such a metapopulation model's dynamics, we transform it into a learning algorithm capable of achieving high image and text classification accuracy. We test it on MNIST and Fashion MNIST, in combination with convolutional neural networks, on CIFAR-10 and TF-FLOWERS, and, in combination with a transformer architecture (BERT), on IMDB, always showing high classification accuracy. These numerical evaluations illustrate that minimal modifications to the Wilson-Cowan model for metapopulation can reveal unique and previously unobserved dynamics.

Despite being trained specifically to follow user instructions, today's instructiontuned language models perform poorly when instructed to produce random outputs. For example, when prompted to pick a number uniformly between one and ten Llama-2-13B-chat disproportionately favors the number five, and when tasked with picking a first name at random, Mistral-7B-Instruct chooses Avery 40 times more often than we would expect based on the U.S. population. When these language models are used for real-world tasks where diversity of outputs is crucial, such as language model assisted dataset construction, their inability to produce diffuse distributions over valid choices is a major hurdle. In this work, we propose a fine-tuning method that encourages language models to output distributions that are diffuse over valid outcomes. The methods we introduce generalize across a variety of tasks and distributions and make large language models practical for synthetic dataset generation with little human intervention.

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).

We introduce rd-spiral, an open-source Python library for simulating 2D reaction-diffusion systems using pseudo-spectral methods. The framework combines FFT-based spatial discretization with adaptive Dormand-Prince time integration, achieving exponential convergence while maintaining pedagogical clarity. We analyze three dynamical regimes: stable spirals, spatiotemporal chaos, and pattern decay, revealing extreme non-Gaussian statistics (kurtosis >96) in stable states. Information-theoretic metrics show 10.7% reduction in activator-inhibitor coupling during turbulence versus 6.5% in stable regimes. The solver handles stiffness ratios >6:1 with features including automated equilibrium classification and checkpointing. Effect sizes (delta=0.37--0.78) distinguish regimes, with asymmetric field sensitivities to perturbations. By balancing computational rigor with educational transparency, rd-spiral bridges theoretical and practical nonlinear dynamics.

The recent proliferation of research into transformer based natural language processing has led to a number of studies which attempt to detect the presence of human-like cognitive behavior in the models. We contend that, as is true of human psychology, the investigation of cognitive behavior in language models must be conducted in an appropriate population of an appropriate size for the results to be meaningful. We leverage work in uncertainty estimation in a novel approach to efficiently construct experimental populations. The resultant tool, PopulationLM, has been made open source. We provide theoretical grounding in the uncertainty estimation literature and motivation from current cognitive work regarding language models. We discuss the methodological lessons from other scientific communities and attempt to demonstrate their application to two artificial population studies. Through population based experimentation we find that language models exhibit behavior consistent with typicality effects among categories highly represented in training. However, we find that language models don't tend to exhibit structural priming effects. Generally, our results show that single models tend to over estimate the presence of cognitive behaviors in neural models.

We investigate statistical properties of a likelihood approach to nonparametric estimation of a singular distribution using deep generative models. More specifically, a deep generative model is used to model high-dimensional data that are assumed to concentrate around some low-dimensional structure. Estimating the distribution supported on this low-dimensional structure, such as a low-dimensional manifold, is challenging due to its singularity with respect to the Lebesgue measure in the ambient space. In the considered model, a usual likelihood approach can fail to estimate the target distribution consistently due to the singularity. We prove that a novel and effective solution exists by perturbing the data with an instance noise, which leads to consistent estimation of the underlying distribution with desirable convergence rates. We also characterize the class of distributions that can be efficiently estimated via deep generative models. This class is sufficiently general to contain various structured distributions such as product distributions, classically smooth distributions and distributions supported on a low-dimensional manifold. Our analysis provides some insights on how deep generative models can avoid the curse of dimensionality for nonparametric distribution estimation. We conduct a thorough simulation study and real data analysis to empirically demonstrate that the proposed data perturbation technique improves the estimation performance significantly.

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.

Ecological interactions are often mediated by feedbacks between organisms and their resource environments. Yet, how resource supply dynamics dictate collective dynamical phases of an ecosystem remains unclear. Here, we analyse a generalised consumer--resource model with non-reciprocal interactions to demonstrate that self-renewing versus externally-supplied resources yield fundamentally different dynamical phase diagrams. As interactions become increasingly non-reciprocal, ecosystems relying on self-renewing resources transition from stable dynamics to chaos and ultimately to infeasibility. By contrast, ecosystems with externally-supplied resources remain stable over a broader parameter range and transition to infeasibility without experiencing an intervening chaotic phase. Using the cavity method, we derive a unified stability condition applicable to a broad class of resource supply functions, explaining why externally-supplied resources can expand the stable region. We show that stability hinges crucially on the susceptibility of resources to perturbations, which depends strongly on their supply. Further, we show that external resource supply suppresses chaos in the unstable region by drastically reducing the susceptibility of resources closest to extinction. Our findings demonstrate that resource dynamics fundamentally reshape the accessible dynamical behaviours of an ecosystem, with implications for interpreting microbial community experiments.

Unwanted and often harmful social biases are becoming ever more salient in NLP research, affecting both models and datasets. In this work, we ask whether training on demographically perturbed data leads to fairer language models. We collect a large dataset of human annotated text perturbations and train a neural perturbation model, which we show outperforms heuristic alternatives. We find that (i) language models (LMs) pre-trained on demographically perturbed corpora are typically more fair, and (ii) LMs finetuned on perturbed GLUE datasets exhibit less demographic bias on downstream tasks, and (iii) fairness improvements do not come at the expense of performance on downstream tasks. Lastly, we discuss outstanding questions about how best to evaluate the (un)fairness of large language models. We hope that this exploration of neural demographic perturbation will help drive more improvement towards fairer NLP.

We present an approach to mitigating the risks of malicious image editing posed by large diffusion models. The key idea is to immunize images so as to make them resistant to manipulation by these models. This immunization relies on injection of imperceptible adversarial perturbations designed to disrupt the operation of the targeted diffusion models, forcing them to generate unrealistic images. We provide two methods for crafting such perturbations, and then demonstrate their efficacy. Finally, we discuss a policy component necessary to make our approach fully effective and practical -- one that involves the organizations developing diffusion models, rather than individual users, to implement (and support) the immunization process.

Most Galactic Globular Clusters (GCs) harbour multiple populations of stars (MPs), composed of at least two generations: the first characterized by a "standard" α-enhanced metal mixture, as observed in field halo stars of the Milky Way, and the second displaying anti-correlated CN--ONa chemical abundance pattern in combination with an enhanced helium fraction. Adequate collections of stellar spectra are needed to characterize the effect of such stellar abundance changes on the integrated light of GCs. We present a grid of synthetic stellar spectra covering the atmospheric parameters relevant to old stellar populations at four subsolar metallicities and two abundance patterns, representative of first- and second-generations of stars in GCs. Integrated spectra of populations were computed using our stellar grid and empirical stellar populations, namely, colour-magnitude diagrams from literature for Galactic GCs. The spectra range from 290 to 1000nm, where we measured the effect on several spectrophotometric indices due to the surface abundance variations attributed to MPs. We find non-negligible effects of the MPs on spectroscopic indices sensitive to C, N, Ca, or Na, and on Balmer indices; we also describe how MPs modify specific regions in the near-UV and near-IR that can be measured with narrow or medium photometric passbands. The effects vary with metallicity. A number of these changes remain detectable even when accounting for the stochastic fluctuations due to the finite nature of the stellar population cluster.