Daily Papers

The majority of methods for crafting adversarial attacks have focused on scenes with a single dominant object (e.g., images from ImageNet). On the other hand, natural scenes include multiple dominant objects that are semantically related. Thus, it is crucial to explore designing attack strategies that look beyond learning on single-object scenes or attack single-object victim classifiers. Due to their inherent property of strong transferability of perturbations to unknown models, this paper presents the first approach of using generative models for adversarial attacks on multi-object scenes. In order to represent the relationships between different objects in the input scene, we leverage upon the open-sourced pre-trained vision-language model CLIP (Contrastive Language-Image Pre-training), with the motivation to exploit the encoded semantics in the language space along with the visual space. We call this attack approach Generative Adversarial Multi-object scene Attacks (GAMA). GAMA demonstrates the utility of the CLIP model as an attacker's tool to train formidable perturbation generators for multi-object scenes. Using the joint image-text features to train the generator, we show that GAMA can craft potent transferable perturbations in order to fool victim classifiers in various attack settings. For example, GAMA triggers ~16% more misclassification than state-of-the-art generative approaches in black-box settings where both the classifier architecture and data distribution of the attacker are different from the victim. Our code is available here: https://abhishekaich27.github.io/gama.html

Vision-Language Pre-training (VLP) models have exhibited unprecedented capability in many applications by taking full advantage of the multimodal alignment. However, previous studies have shown they are vulnerable to maliciously crafted adversarial samples. Despite recent success, these methods are generally instance-specific and require generating perturbations for each input sample. In this paper, we reveal that VLP models are also vulnerable to the instance-agnostic universal adversarial perturbation (UAP). Specifically, we design a novel Contrastive-training Perturbation Generator with Cross-modal conditions (C-PGC) to achieve the attack. In light that the pivotal multimodal alignment is achieved through the advanced contrastive learning technique, we devise to turn this powerful weapon against themselves, i.e., employ a malicious version of contrastive learning to train the C-PGC based on our carefully crafted positive and negative image-text pairs for essentially destroying the alignment relationship learned by VLP models. Besides, C-PGC fully utilizes the characteristics of Vision-and-Language (V+L) scenarios by incorporating both unimodal and cross-modal information as effective guidance. Extensive experiments show that C-PGC successfully forces adversarial samples to move away from their original area in the VLP model's feature space, thus essentially enhancing attacks across various victim models and V+L tasks. The GitHub repository is available at https://github.com/ffhibnese/CPGC_VLP_Universal_Attacks.

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

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

Classifier-free guidance (CFG) has become an essential component of modern diffusion models to enhance both generation quality and alignment with input conditions. However, CFG requires specific training procedures and is limited to conditional generation. To address these limitations, we propose Token Perturbation Guidance (TPG), a novel method that applies perturbation matrices directly to intermediate token representations within the diffusion network. TPG employs a norm-preserving shuffling operation to provide effective and stable guidance signals that improve generation quality without architectural changes. As a result, TPG is training-free and agnostic to input conditions, making it readily applicable to both conditional and unconditional generation. We further analyze the guidance term provided by TPG and show that its effect on sampling more closely resembles CFG compared to existing training-free guidance techniques. Extensive experiments on SDXL and Stable Diffusion 2.1 show that TPG achieves nearly a 2times improvement in FID for unconditional generation over the SDXL baseline, while closely matching CFG in prompt alignment. These results establish TPG as a general, condition-agnostic guidance method that brings CFG-like benefits to a broader class of diffusion models. The code is available at https://github.com/TaatiTeam/Token-Perturbation-Guidance

Controlled text perturbation is useful for evaluating and improving model generalizability. However, current techniques rely on training a model for every target perturbation, which is expensive and hard to generalize. We present Tailor, a semantically-controlled text generation system. Tailor builds on a pretrained seq2seq model and produces textual outputs conditioned on control codes derived from semantic representations. We craft a set of operations to modify the control codes, which in turn steer generation towards targeted attributes. These operations can be further composed into higher-level ones, allowing for flexible perturbation strategies. We demonstrate the effectiveness of these perturbations in multiple applications. First, we use Tailor to automatically create high-quality contrast sets for four distinct natural language processing (NLP) tasks. These contrast sets contain fewer spurious artifacts and are complementary to manually annotated ones in their lexical diversity. Second, we show that Tailor perturbations can improve model generalization through data augmentation. Perturbing just 2% of training data leads to a 5.8-point gain on an NLI challenge set measuring reliance on syntactic heuristics.

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.

Predicting how cells respond to genetic perturbations is fundamental to understanding gene function, disease mechanisms, and therapeutic development. While recent deep learning approaches have shown promise in modeling single-cell perturbation responses, they struggle to generalize across cell types and perturbation contexts due to limited contextual information during generation. We introduce PT-RAG (Perturbation-aware Two-stage Retrieval-Augmented Generation), a novel framework that extends Retrieval-Augmented Generation beyond traditional language-model applications to cellular biology. Unlike standard RAG systems designed for text retrieval with pre-trained LLMs, perturbation retrieval lacks established similarity metrics and requires learning what constitutes relevant context, making differentiable retrieval essential. PT-RAG addresses this through a two-stage pipeline: first, retrieving candidate perturbations K using GenePT embeddings, then adaptively refining the selection through Gumbel-Softmax discrete sampling conditioned on both the cell state and the input perturbation. This cell-type-aware differentiable retrieval enables end-to-end optimization of the retrieval objective jointly with generation. On the Replogle-Nadig single-gene perturbation dataset, we demonstrate that PT-RAG outperforms both STATE and vanilla RAG under identical experimental conditions, with the strongest gains in distributional similarity metrics (W_1, W_2). Notably, vanilla RAG's dramatic failure is itself a key finding: it demonstrates that differentiable, cell-type-aware retrieval is essential in this domain, and that naive retrieval can actively harm performance. Our results establish retrieval-augmented generation as a promising paradigm for modelling cellular responses to gene perturbation. The code to reproduce our experiments is available at https://github.com/difra100/PT-RAG_ICLR.

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.

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 a framework for automatically defining and learning deep generative models with problem-specific structure. We tackle problem domains that are more traditionally solved by algorithms such as sorting, constraint satisfaction for Sudoku, and matrix factorization. Concretely, we train diffusion models with an architecture tailored to the problem specification. This problem specification should contain a graphical model describing relationships between variables, and often benefits from explicit representation of subcomputations. Permutation invariances can also be exploited. Across a diverse set of experiments we improve the scaling relationship between problem dimension and our model's performance, in terms of both training time and final accuracy. Our code can be found at https://github.com/plai-group/gsdm.

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

Linear relaxation based perturbation analysis (LiRPA) for neural networks, which computes provable linear bounds of output neurons given a certain amount of input perturbation, has become a core component in robustness verification and certified defense. The majority of LiRPA-based methods focus on simple feed-forward networks and need particular manual derivations and implementations when extended to other architectures. In this paper, we develop an automatic framework to enable perturbation analysis on any neural network structures, by generalizing existing LiRPA algorithms such as CROWN to operate on general computational graphs. The flexibility, differentiability and ease of use of our framework allow us to obtain state-of-the-art results on LiRPA based certified defense on fairly complicated networks like DenseNet, ResNeXt and Transformer that are not supported by prior works. Our framework also enables loss fusion, a technique that significantly reduces the computational complexity of LiRPA for certified defense. For the first time, we demonstrate LiRPA based certified defense on Tiny ImageNet and Downscaled ImageNet where previous approaches cannot scale to due to the relatively large number of classes. Our work also yields an open-source library for the community to apply LiRPA to areas beyond certified defense without much LiRPA expertise, e.g., we create a neural network with a probably flat optimization landscape by applying LiRPA to network parameters. Our opensource library is available at https://github.com/KaidiXu/auto_LiRPA.

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.

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

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

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

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

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.

Normalizing flows are a promising tool for modeling probability distributions in physical systems. While state-of-the-art flows accurately approximate distributions and energies, applications in physics additionally require smooth energies to compute forces and higher-order derivatives. Furthermore, such densities are often defined on non-trivial topologies. A recent example are Boltzmann Generators for generating 3D-structures of peptides and small proteins. These generative models leverage the space of internal coordinates (dihedrals, angles, and bonds), which is a product of hypertori and compact intervals. In this work, we introduce a class of smooth mixture transformations working on both compact intervals and hypertori. Mixture transformations employ root-finding methods to invert them in practice, which has so far prevented bi-directional flow training. To this end, we show that parameter gradients and forces of such inverses can be computed from forward evaluations via the inverse function theorem. We demonstrate two advantages of such smooth flows: they allow training by force matching to simulation data and can be used as potentials in molecular dynamics simulations.

The spatiotemporal resolution of Partial Differential Equations (PDEs) plays important roles in the mathematical description of the world's physical phenomena. In general, scientists and engineers solve PDEs numerically by the use of computationally demanding solvers. Recently, deep learning algorithms have emerged as a viable alternative for obtaining fast solutions for PDEs. Models are usually trained on synthetic data generated by solvers, stored on disk and read back for training. This paper advocates that relying on a traditional static dataset to train these models does not allow the full benefit of the solver to be used as a data generator. It proposes an open source online training framework for deep surrogate models. The framework implements several levels of parallelism focused on simultaneously generating numerical simulations and training deep neural networks. This approach suppresses the I/O and storage bottleneck associated with disk-loaded datasets, and opens the way to training on significantly larger datasets. Experiments compare the offline and online training of four surrogate models, including state-of-the-art architectures. Results indicate that exposing deep surrogate models to more dataset diversity, up to hundreds of GB, can increase model generalization capabilities. Fully connected neural networks, Fourier Neural Operator (FNO), and Message Passing PDE Solver prediction accuracy is improved by 68%, 16% and 7%, respectively.

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.

We introduce adversarial learning methods for data-driven generative modeling of the dynamics of n^{th}-order stochastic systems. Our approach builds on Generative Adversarial Networks (GANs) with generative model classes based on stable m-step stochastic numerical integrators. We introduce different formulations and training methods for learning models of stochastic dynamics based on observation of trajectory samples. We develop approaches using discriminators based on Maximum Mean Discrepancy (MMD), training protocols using conditional and marginal distributions, and methods for learning dynamic responses over different time-scales. We show how our approaches can be used for modeling physical systems to learn force-laws, damping coefficients, and noise-related parameters. The adversarial learning approaches provide methods for obtaining stable generative models for dynamic tasks including long-time prediction and developing simulations for stochastic systems.

The interest of the deep learning community in image synthesis has grown massively in recent years. Nowadays, deep generative methods, and especially Generative Adversarial Networks (GANs), are leading to state-of-the-art performance, capable of synthesizing images that appear realistic. While the efforts for improving the quality of the generated images are extensive, most attempts still consider the generator part as an uncorroborated "black-box". In this paper, we aim to provide a better understanding and design of the image generation process. We interpret existing generators as implicitly relying on sparsity-inspired models. More specifically, we show that generators can be viewed as manifestations of the Convolutional Sparse Coding (CSC) and its Multi-Layered version (ML-CSC) synthesis processes. We leverage this observation by explicitly enforcing a sparsifying regularization on appropriately chosen activation layers in the generator, and demonstrate that this leads to improved image synthesis. Furthermore, we show that the same rationale and benefits apply to generators serving inverse problems, demonstrated on the Deep Image Prior (DIP) method.

Building a virtual cell capable of accurately simulating cellular behaviors in silico has long been a dream in computational biology. We introduce CellFlux, an image-generative model that simulates cellular morphology changes induced by chemical and genetic perturbations using flow matching. Unlike prior methods, CellFlux models distribution-wise transformations from unperturbed to perturbed cell states, effectively distinguishing actual perturbation effects from experimental artifacts such as batch effects -- a major challenge in biological data. Evaluated on chemical (BBBC021), genetic (RxRx1), and combined perturbation (JUMP) datasets, CellFlux generates biologically meaningful cell images that faithfully capture perturbation-specific morphological changes, achieving a 35% improvement in FID scores and a 12% increase in mode-of-action prediction accuracy over existing methods. Additionally, CellFlux enables continuous interpolation between cellular states, providing a potential tool for studying perturbation dynamics. These capabilities mark a significant step toward realizing virtual cell modeling for biomedical research. Project page: https://yuhui-zh15.github.io/CellFlux/.

The analysis of parametric and non-parametric uncertainties of very large dynamical systems requires the construction of a stochastic model of said system. Linear approaches relying on random matrix theory and principal componant analysis can be used when systems undergo low-frequency vibrations. In the case of fast dynamics and wave propagation, we investigate a random generator of boundary conditions for fast submodels by using machine learning. We show that the use of non-linear techniques in machine learning and data-driven methods is highly relevant. Physics-informed neural networks is a possible choice for a data-driven method to replace linear modal analysis. An architecture that support a random component is necessary for the construction of the stochastic model of the physical system for non-parametric uncertainties, since the goal is to learn the underlying probabilistic distribution of uncertainty in the data. Generative Adversarial Networks (GANs) are suited for such applications, where the Wasserstein-GAN with gradient penalty variant offers improved convergence results for our problem. The objective of our approach is to train a GAN on data from a finite element method code (Fenics) so as to extract stochastic boundary conditions for faster finite element predictions on a submodel. The submodel and the training data have both the same geometrical support. It is a zone of interest for uncertainty quantification and relevant to engineering purposes. In the exploitation phase, the framework can be viewed as a randomized and parametrized simulation generator on the submodel, which can be used as a Monte Carlo estimator.

We propose a general and efficient framework to control auto-regressive generation models with NeurAlly-Decomposed Oracle (NADO). Given a pre-trained base language model and a sequence-level boolean oracle function, we propose to decompose the oracle function into token-level guidance to steer the base model in text generation. Specifically, the token-level guidance is approximated by a neural model trained with examples sampled from the base model, demanding no additional auxiliary labeled data. Based on posterior regularization, we present the closed-form optimal solution to incorporate the token-level guidance into the base model for controllable generation. We further provide a theoretical analysis of how the approximation quality of NADO affects the controllable generation results. Experiments conducted on two applications: (1) text generation with lexical constraints and (2) machine translation with formality control demonstrate that our framework efficiently guides the base model towards the given oracle while maintaining high generation quality.

The prediction-based nonlinear reference governor (PRG) is an add-on algorithm to enforce constraints on pre-stabilized nonlinear systems by modifying, whenever necessary, the reference signal. The implementation of PRG carries a heavy computational burden, as it may require multiple numerical simulations of the plant model at each sample time. To this end, this paper proposes an alternative approach based on machine learning, where we first use a regression neural network (NN) to approximate the input-output map of the PRG from a set of training data. During the real-time operation, at each sample time, we use the trained NN to compute a nominal reference command, which may not be constraint admissible due to training errors and limited data. We adopt a novel sensitivity-based approach to minimally adjust the nominal reference while ensuring constraint enforcement. We thus refer to the resulting control strategy as the modified neural network reference governor (MNN-RG), which is significantly more computationally efficient than the PRG. The computational and theoretical properties of MNN-RG are presented. Finally, the effectiveness and limitations of the proposed method are studied by applying it as a load governor for constraint management in automotive fuel cell systems through simulation-based case studies.

Data-driven surrogate models improve the efficiency of simulating continuous dynamical systems, yet their autoregressive rollouts are often limited by instability and spectral blow-up. While global regularization techniques can enforce contractive dynamics, they uniformly damp high-frequency features, introducing a contraction-dissipation dilemma. Furthermore, long-horizon trajectory optimization methods that explicitly correct drift are bottlenecked by memory constraints. In this work, we propose Jacobian-Adaptive Weighting for Stability (JAWS), a probabilistic regularization strategy designed to mitigate these limitations. By framing operator learning as Maximum A Posteriori (MAP) estimation with spatially heteroscedastic uncertainty, JAWS dynamically modulates the regularization strength based on local physical complexity. This allows the model to enforce contraction in smooth regions to suppress noise, while relaxing constraints near singular features to preserve gradients, effectively realizing a behavior similar to numerical shock-capturing schemes. Experiments demonstrate that this spatially-adaptive prior serves as an effective spectral pre-conditioner, which reduces the base operator's burden of handling high-frequency instabilities. This reduction enables memory-efficient, short-horizon trajectory optimization to match or exceed the long-term accuracy of long-horizon baselines. Evaluated on the 1D viscous Burgers' equation, our hybrid approach improves long-term stability, shock fidelity, and out-of-distribution generalization while reducing training computational costs.

Unconditional video generation is a challenging task that involves synthesizing high-quality videos that are both coherent and of extended duration. To address this challenge, researchers have used pretrained StyleGAN image generators for high-quality frame synthesis and focused on motion generator design. The motion generator is trained in an autoregressive manner using heavy 3D convolutional discriminators to ensure motion coherence during video generation. In this paper, we introduce a novel motion generator design that uses a learning-based inversion network for GAN. The encoder in our method captures rich and smooth priors from encoding images to latents, and given the latent of an initially generated frame as guidance, our method can generate smooth future latent by modulating the inversion encoder temporally. Our method enjoys the advantage of sparse training and naturally constrains the generation space of our motion generator with the inversion network guided by the initial frame, eliminating the need for heavy discriminators. Moreover, our method supports style transfer with simple fine-tuning when the encoder is paired with a pretrained StyleGAN generator. Extensive experiments conducted on various benchmarks demonstrate the superiority of our method in generating long and high-resolution videos with decent single-frame quality and temporal consistency.

While counterfactual examples are useful for analysis and training of NLP models, current generation methods either rely on manual labor to create very few counterfactuals, or only instantiate limited types of perturbations such as paraphrases or word substitutions. We present Polyjuice, a general-purpose counterfactual generator that allows for control over perturbation types and locations, trained by finetuning GPT-2 on multiple datasets of paired sentences. We show that Polyjuice produces diverse sets of realistic counterfactuals, which in turn are useful in various distinct applications: improving training and evaluation on three different tasks (with around 70% less annotation effort than manual generation), augmenting state-of-the-art explanation techniques, and supporting systematic counterfactual error analysis by revealing behaviors easily missed by human experts.

We introduce a new family of physics-inspired generative models termed PFGM++ that unifies diffusion models and Poisson Flow Generative Models (PFGM). These models realize generative trajectories for N dimensional data by embedding paths in N{+}D dimensional space while still controlling the progression with a simple scalar norm of the D additional variables. The new models reduce to PFGM when D{=}1 and to diffusion models when D{to}infty. The flexibility of choosing D allows us to trade off robustness against rigidity as increasing D results in more concentrated coupling between the data and the additional variable norms. We dispense with the biased large batch field targets used in PFGM and instead provide an unbiased perturbation-based objective similar to diffusion models. To explore different choices of D, we provide a direct alignment method for transferring well-tuned hyperparameters from diffusion models (D{to} infty) to any finite D values. Our experiments show that models with finite D can be superior to previous state-of-the-art diffusion models on CIFAR-10/FFHQ 64{times}64 datasets, with FID scores of 1.91/2.43 when D{=}2048/128. In class-conditional setting, D{=}2048 yields current state-of-the-art FID of 1.74 on CIFAR-10. In addition, we demonstrate that models with smaller D exhibit improved robustness against modeling errors. Code is available at https://github.com/Newbeeer/pfgmpp

Generating realistic time series data is important for many engineering and scientific applications. Existing work tackles this problem using generative adversarial networks (GANs). However, GANs are often unstable during training, and they can suffer from mode collapse. While variational autoencoders (VAEs) are known to be more robust to these issues, they are (surprisingly) less often considered for time series generation. In this work, we introduce Koopman VAE (KVAE), a new generative framework that is based on a novel design for the model prior, and that can be optimized for either regular and irregular training data. Inspired by Koopman theory, we represent the latent conditional prior dynamics using a linear map. Our approach enhances generative modeling with two desired features: (i) incorporating domain knowledge can be achieved by leverageing spectral tools that prescribe constraints on the eigenvalues of the linear map; and (ii) studying the qualitative behavior and stablity of the system can be performed using tools from dynamical systems theory. Our results show that KVAE outperforms state-of-the-art GAN and VAE methods across several challenging synthetic and real-world time series generation benchmarks. Whether trained on regular or irregular data, KVAE generates time series that improve both discriminative and predictive metrics. We also present visual evidence suggesting that KVAE learns probability density functions that better approximate empirical ground truth distributions.

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

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

Efficient numerical solvers for partial differential equations empower science and engineering. One of the commonly employed numerical solvers is the preconditioned conjugate gradient (PCG) algorithm which can solve large systems to a given precision level. One challenge in PCG solvers is the selection of preconditioners, as different problem-dependent systems can benefit from different preconditioners. We present a new method to introduce inductive bias in preconditioning conjugate gradient algorithm. Given a system matrix and a set of solution vectors arise from an underlying distribution, we train a graph neural network to obtain an approximate decomposition to the system matrix to be used as a preconditioner in the context of PCG solvers. We conduct extensive experiments to demonstrate the efficacy and generalizability of our proposed approach in solving various 2D and 3D linear second-order PDEs.

Automatically generating coherent and semantically meaningful text has many applications in machine translation, dialogue systems, image captioning, etc. Recently, by combining with policy gradient, Generative Adversarial Nets (GAN) that use a discriminative model to guide the training of the generative model as a reinforcement learning policy has shown promising results in text generation. However, the scalar guiding signal is only available after the entire text has been generated and lacks intermediate information about text structure during the generative process. As such, it limits its success when the length of the generated text samples is long (more than 20 words). In this paper, we propose a new framework, called LeakGAN, to address the problem for long text generation. We allow the discriminative net to leak its own high-level extracted features to the generative net to further help the guidance. The generator incorporates such informative signals into all generation steps through an additional Manager module, which takes the extracted features of current generated words and outputs a latent vector to guide the Worker module for next-word generation. Our extensive experiments on synthetic data and various real-world tasks with Turing test demonstrate that LeakGAN is highly effective in long text generation and also improves the performance in short text generation scenarios. More importantly, without any supervision, LeakGAN would be able to implicitly learn sentence structures only through the interaction between Manager and Worker.

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.

Modern representation learning methods often struggle to adapt quickly under non-stationarity because they suffer from catastrophic forgetting and decaying plasticity. Such problems prevent learners from fast adaptation since they may forget useful features or have difficulty learning new ones. Hence, these methods are rendered ineffective for continual learning. This paper proposes Utility-based Perturbed Gradient Descent (UPGD), an online learning algorithm well-suited for continual learning agents. UPGD protects useful weights or features from forgetting and perturbs less useful ones based on their utilities. Our empirical results show that UPGD helps reduce forgetting and maintain plasticity, enabling modern representation learning methods to work effectively in continual learning.

Can we build continuous generative models which generalize across scales, can be evaluated at any coordinate, admit calculation of exact derivatives, and are conceptually simple? Existing MLP-based architectures generate worse samples than the grid-based generators with favorable convolutional inductive biases. Models that focus on generating images at different scales do better, but employ complex architectures not designed for continuous evaluation of images and derivatives. We take a signal-processing perspective and treat continuous image generation as interpolation from samples. Indeed, correctly sampled discrete images contain all information about the low spatial frequencies. The question is then how to extrapolate the spectrum in a data-driven way while meeting the above design criteria. Our answer is FunkNN -- a new convolutional network which learns how to reconstruct continuous images at arbitrary coordinates and can be applied to any image dataset. Combined with a discrete generative model it becomes a functional generator which can act as a prior in continuous ill-posed inverse problems. We show that FunkNN generates high-quality continuous images and exhibits strong out-of-distribution performance thanks to its patch-based design. We further showcase its performance in several stylized inverse problems with exact spatial derivatives.

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

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.

Prompting interfaces allow users to quickly adjust the output of generative models in both vision and language. However, small changes and design choices in the prompt can lead to significant differences in the output. In this work, we develop a black-box framework for generating adversarial prompts for unstructured image and text generation. These prompts, which can be standalone or prepended to benign prompts, induce specific behaviors into the generative process, such as generating images of a particular object or generating high perplexity text.

Model attribution is a popular tool to explain the rationales behind model predictions. However, recent work suggests that the attributions are vulnerable to minute perturbations, which can be added to input samples to fool the attributions while maintaining the prediction outputs. Although empirical studies have shown positive performance via adversarial training, an effective certified defense method is eminently needed to understand the robustness of attributions. In this work, we propose to use uniform smoothing technique that augments the vanilla attributions by noises uniformly sampled from a certain space. It is proved that, for all perturbations within the attack region, the cosine similarity between uniformly smoothed attribution of perturbed sample and the unperturbed sample is guaranteed to be lower bounded. We also derive alternative formulations of the certification that is equivalent to the original one and provides the maximum size of perturbation or the minimum smoothing radius such that the attribution can not be perturbed. We evaluate the proposed method on three datasets and show that the proposed method can effectively protect the attributions from attacks, regardless of the architecture of networks, training schemes and the size of the datasets.

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

Generative models have demonstrated remarkable success in domains such as text, image, and video synthesis. In this work, we explore the application of generative models to fluid dynamics, specifically for turbulence simulation, where classical numerical solvers are computationally expensive. We propose a novel stochastic generative model based on stochastic interpolants, which enables probabilistic forecasting while incorporating physical constraints such as energy stability and divergence-freeness. Unlike conventional stochastic generative models, which are often agnostic to underlying physical laws, our approach embeds energy consistency by making the parameters of the stochastic interpolant learnable coefficients. We evaluate our method on a benchmark turbulence problem - Kolmogorov flow - demonstrating superior accuracy and stability over state-of-the-art alternatives such as autoregressive conditional diffusion models (ACDMs) and PDE-Refiner. Furthermore, we achieve stable results for significantly longer roll-outs than standard stochastic interpolants. Our results highlight the potential of physics-aware generative models in accelerating and enhancing turbulence simulations while preserving fundamental conservation properties.

Advancements in DNA sequencing technologies have significantly improved our ability to decode genomic sequences. However, the prediction and interpretation of these sequences remain challenging due to the intricate nature of genetic material. Large language models (LLMs) have introduced new opportunities for biological sequence analysis. Recent developments in genomic language models have underscored the potential of LLMs in deciphering DNA sequences. Nonetheless, existing models often face limitations in robustness and application scope, primarily due to constraints in model structure and training data scale. To address these limitations, we present GENERator, a generative genomic foundation model featuring a context length of 98k base pairs (bp) and 1.2B parameters. Trained on an expansive dataset comprising 386B bp of eukaryotic DNA, the GENERator demonstrates state-of-the-art performance across both established and newly proposed benchmarks. The model adheres to the central dogma of molecular biology, accurately generating protein-coding sequences that translate into proteins structurally analogous to known families. It also shows significant promise in sequence optimization, particularly through the prompt-responsive generation of promoter sequences with specific activity profiles. These capabilities position the GENERator as a pivotal tool for genomic research and biotechnological advancement, enhancing our ability to interpret and predict complex biological systems and enabling precise genomic interventions.

Cross-domain speech enhancement (SE) is often faced with severe challenges due to the scarcity of noise and background information in an unseen target domain, leading to a mismatch between training and test conditions. This study puts forward a novel data simulation method to address this issue, leveraging noise-extractive techniques and generative adversarial networks (GANs) with only limited target noisy speech data. Notably, our method employs a noise encoder to extract noise embeddings from target-domain data. These embeddings aptly guide the generator to synthesize utterances acoustically fitted to the target domain while authentically preserving the phonetic content of the input clean speech. Furthermore, we introduce the notion of dynamic stochastic perturbation, which can inject controlled perturbations into the noise embeddings during inference, thereby enabling the model to generalize well to unseen noise conditions. Experiments on the VoiceBank-DEMAND benchmark dataset demonstrate that our domain-adaptive SE method outperforms an existing strong baseline based on data simulation.

Video anomaly detection (VAD) is a vital yet complex open-set task in computer vision, commonly tackled through reconstruction-based methods. However, these methods struggle with two key limitations: (1) insufficient robustness in open-set scenarios, where unseen normal motions are frequently misclassified as anomalies, and (2) an overemphasis on, but restricted capacity for, local motion reconstruction, which are inherently difficult to capture accurately due to their diversity. To overcome these challenges, we introduce a novel frequency-guided diffusion model with perturbation training. First, we enhance robustness by training a generator to produce perturbed samples, which are similar to normal samples and target the weakness of the reconstruction model. This training paradigm expands the reconstruction domain of the model, improving its generalization to unseen normal motions. Second, to address the overemphasis on motion details, we employ the 2D Discrete Cosine Transform (DCT) to separate high-frequency (local) and low-frequency (global) motion components. By guiding the diffusion model with observed high-frequency information, we prioritize the reconstruction of low-frequency components, enabling more accurate and robust anomaly detection. Extensive experiments on five widely used VAD datasets demonstrate that our approach surpasses state-of-the-art methods, underscoring its effectiveness in open-set scenarios and diverse motion contexts. Our project website is https://xiaofeng-tan.github.io/projects/FG-Diff/index.html.

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).

Neural networks have shown great potential in accelerating the solution of partial differential equations (PDEs). Recently, there has been a growing interest in introducing physics constraints into training neural PDE solvers to reduce the use of costly data and improve the generalization ability. However, these physics constraints, based on certain finite dimensional approximations over the function space, must resolve the smallest scaled physics to ensure the accuracy and stability of the simulation, resulting in high computational costs from large input, output, and neural networks. This paper proposes a general acceleration methodology called NeuralStagger by spatially and temporally decomposing the original learning tasks into several coarser-resolution subtasks. We define a coarse-resolution neural solver for each subtask, which requires fewer computational resources, and jointly train them with the vanilla physics-constrained loss by simply arranging their outputs to reconstruct the original solution. Due to the perfect parallelism between them, the solution is achieved as fast as a coarse-resolution neural solver. In addition, the trained solvers bring the flexibility of simulating with multiple levels of resolution. We demonstrate the successful application of NeuralStagger on 2D and 3D fluid dynamics simulations, which leads to an additional 10sim100times speed-up. Moreover, the experiment also shows that the learned model could be well used for optimal control.

In this work, we introduce ChemBFN, a language model that handles chemistry tasks based on Bayesian flow networks working on discrete data. A new accuracy schedule is proposed to improve the sampling quality by significantly reducing the reconstruction loss. We show evidence that our method is appropriate for generating molecules with satisfied diversity even when a smaller number of sampling steps is used. A classifier-free guidance method is adapted for conditional generation. It is also worthwhile to point out that after generative training, our model can be fine-tuned on regression and classification tasks with the state-of-the-art performance, which opens the gate of building all-in-one models in a single module style. Our model has been open sourced at https://github.com/Augus1999/bayesian-flow-network-for-chemistry.

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

Inference-time scaling offers a versatile paradigm for aligning visual generative models with downstream objectives without parameter updates. However, existing approaches that optimize the high-dimensional initial noise suffer from severe inefficiency, as many search directions exert negligible influence on the final generation. We show that this inefficiency is closely related to a spectral bias in generative dynamics: model sensitivity to initial perturbations diminishes rapidly as frequency increases. Building on this insight, we propose Spectral Evolution Search (SES), a plug-and-play framework for initial noise optimization that executes gradient-free evolutionary search within a low-frequency subspace. Theoretically, we derive the Spectral Scaling Prediction from perturbation propagation dynamics, which explains the systematic differences in the impact of perturbations across frequencies. Extensive experiments demonstrate that SES significantly advances the Pareto frontier of generation quality versus computational cost, consistently outperforming strong baselines under equivalent budgets.

The evaluation of Retrieval-Augmented Generation (RAG) systems typically examines retrieval quality and generation parameters like temperature in isolation, overlooking their interaction. This work presents a systematic investigation of how text perturbations (simulating noisy retrieval) interact with temperature settings across multiple LLM runs. We propose a comprehensive RAG Perturbation-Temperature Analysis Framework that subjects retrieved documents to three distinct perturbation types across varying temperature settings. Through extensive experiments on HotpotQA with both open-source and proprietary LLMs, we demonstrate that performance degradation follows distinct patterns: high-temperature settings consistently amplify vulnerability to perturbations, while certain perturbation types exhibit non-linear sensitivity across the temperature range. Our work yields three key contributions: (1) a diagnostic benchmark for assessing RAG robustness, (2) an analytical framework for quantifying perturbation-temperature interactions, and (3) practical guidelines for model selection and parameter tuning under noisy retrieval conditions.

In this work, we introduce Boolformer, the first Transformer architecture trained to perform end-to-end symbolic regression of Boolean functions. First, we show that it can predict compact formulas for complex functions which were not seen during training, when provided a clean truth table. Then, we demonstrate its ability to find approximate expressions when provided incomplete and noisy observations. We evaluate the Boolformer on a broad set of real-world binary classification datasets, demonstrating its potential as an interpretable alternative to classic machine learning methods. Finally, we apply it to the widespread task of modelling the dynamics of gene regulatory networks. Using a recent benchmark, we show that Boolformer is competitive with state-of-the art genetic algorithms with a speedup of several orders of magnitude. Our code and models are available publicly.

This paper presents Representation-Conditioned image Generation (RCG), a simple yet effective image generation framework which sets a new benchmark in class-unconditional image generation. RCG does not condition on any human annotations. Instead, it conditions on a self-supervised representation distribution which is mapped from the image distribution using a pre-trained encoder. During generation, RCG samples from such representation distribution using a representation diffusion model (RDM), and employs a pixel generator to craft image pixels conditioned on the sampled representation. Such a design provides substantial guidance during the generative process, resulting in high-quality image generation. Tested on ImageNet 256times256, RCG achieves a Frechet Inception Distance (FID) of 3.31 and an Inception Score (IS) of 253.4. These results not only significantly improve the state-of-the-art of class-unconditional image generation but also rival the current leading methods in class-conditional image generation, bridging the long-standing performance gap between these two tasks. Code is available at https://github.com/LTH14/rcg.

Taming the generation outcome of state of the art Diffusion and Flow-Matching (FM) models without having to re-train a task-specific model unlocks a powerful tool for solving inverse problems, conditional generation, and controlled generation in general. In this work we introduce D-Flow, a simple framework for controlling the generation process by differentiating through the flow, optimizing for the source (noise) point. We motivate this framework by our key observation stating that for Diffusion/FM models trained with Gaussian probability paths, differentiating through the generation process projects gradient on the data manifold, implicitly injecting the prior into the optimization process. We validate our framework on linear and non-linear controlled generation problems including: image and audio inverse problems and conditional molecule generation reaching state of the art performance across all.

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

Neural surrogates for partial differential equations (PDEs) have become popular due to their potential to quickly simulate physics. With a few exceptions, neural surrogates generally treat the forward evolution of time-dependent PDEs as a black box by directly predicting the next state. While this is a natural and easy framework for applying neural surrogates, it can be an over-simplified and rigid framework for predicting physics. In this work, we propose an alternative framework in which neural solvers predict the temporal derivative and an ODE integrator forwards the solution in time, which has little overhead and is broadly applicable across model architectures and PDEs. We find that by simply changing the training target and introducing numerical integration during inference, neural surrogates can gain accuracy and stability. Predicting temporal derivatives also allows models to not be constrained to a specific temporal discretization, allowing for flexible time-stepping during inference or training on higher-resolution PDE data. Lastly, we investigate why this new framework can be beneficial and in what situations does it work well.

Generative Adversarial Networks (GANs) are a popular formulation to train generative models for complex high dimensional data. The standard method for training GANs involves a gradient descent-ascent (GDA) procedure on a minimax optimization problem. This procedure is hard to analyze in general due to the nonlinear nature of the dynamics. We study the local dynamics of GDA for training a GAN with a kernel-based discriminator. This convergence analysis is based on a linearization of a non-linear dynamical system that describes the GDA iterations, under an isolated points model assumption from [Becker et al. 2022]. Our analysis brings out the effect of the learning rates, regularization, and the bandwidth of the kernel discriminator, on the local convergence rate of GDA. Importantly, we show phase transitions that indicate when the system converges, oscillates, or diverges. We also provide numerical simulations that verify our claims.

Explaining predictions based on multivariate time series data carries the additional difficulty of handling not only multiple features, but also time dependencies. It matters not only what happened, but also when, and the same feature could have a very different impact on a prediction depending on this time information. Previous work has used perturbation-based saliency methods to tackle this issue, perturbing an input using a trainable mask to discover which features at which times are driving the predictions. However these methods introduce fixed perturbations, inspired from similar methods on static data, while there seems to be little motivation to do so on temporal data. In this work, we aim to explain predictions by learning not only masks, but also associated perturbations. We empirically show that learning these perturbations significantly improves the quality of these explanations on time series data.

We present HyPINO, a multi-physics neural operator designed for zero-shot generalization across a broad class of parametric PDEs without requiring task-specific fine-tuning. Our approach combines a Swin Transformer-based hypernetwork with mixed supervision: (i) labeled data from analytical solutions generated via the Method of Manufactured Solutions (MMS), and (ii) unlabeled samples optimized using physics-informed objectives. The model maps PDE parametrizations to target Physics-Informed Neural Networks (PINNs) and can handle linear elliptic, hyperbolic, and parabolic equations in two dimensions with varying source terms, geometries, and mixed Dirichlet/Neumann boundary conditions, including interior boundaries. HyPINO achieves strong zero-shot accuracy on seven benchmark problems from PINN literature, outperforming U-Nets, Poseidon, and Physics-Informed Neural Operators (PINO). Further, we introduce an iterative refinement procedure that compares the physics of the generated PINN to the requested PDE and uses the discrepancy to generate a "delta" PINN. Summing their contributions and repeating this process forms an ensemble whose combined solution progressively reduces the error on six benchmarks and achieves over 100x gain in average L_2 loss in the best case, while retaining forward-only inference. Additionally, we evaluate the fine-tuning behavior of PINNs initialized by HyPINO and show that they converge faster and to lower final error than both randomly initialized and Reptile-meta-learned PINNs on five benchmarks, performing on par on the remaining two. Our results highlight the potential of this scalable approach as a foundation for extending neural operators toward solving increasingly complex, nonlinear, and high-dimensional PDE problems with significantly improved accuracy and reduced computational cost.

We investigate the theoretical foundations of classifier-free guidance (CFG). CFG is the dominant method of conditional sampling for text-to-image diffusion models, yet unlike other aspects of diffusion, it remains on shaky theoretical footing. In this paper, we disprove common misconceptions, by showing that CFG interacts differently with DDPM (Ho et al., 2020) and DDIM (Song et al., 2021), and neither sampler with CFG generates the gamma-powered distribution p(x|c)^gamma p(x)^{1-gamma}. Then, we clarify the behavior of CFG by showing that it is a kind of predictor-corrector method (Song et al., 2020) that alternates between denoising and sharpening, which we call predictor-corrector guidance (PCG). We prove that in the SDE limit, CFG is actually equivalent to combining a DDIM predictor for the conditional distribution together with a Langevin dynamics corrector for a gamma-powered distribution (with a carefully chosen gamma). Our work thus provides a lens to theoretically understand CFG by embedding it in a broader design space of principled sampling methods.

Solving parametric partial differential equations (PDEs) and associated PDE-based, inverse problems is a central task in engineering and physics, yet existing neural operator methods struggle with high-dimensional, discontinuous inputs and require large amounts of {\em labeled} training data. We propose the Deep Generative Neural Operator (DGNO), a physics-aware framework that addresses these challenges by leveraging a deep, generative, probabilistic model in combination with a set of lower-dimensional, latent variables that simultaneously encode PDE-inputs and PDE-outputs. This formulation can make use of unlabeled data and significantly improves inverse problem-solving, particularly for discontinuous or discrete-valued input functions. DGNO enforces physics constraints without labeled data by incorporating as virtual observables, weak-form residuals based on compactly supported radial basis functions (CSRBFs). These relax regularity constraints and eliminate higher-order derivatives from the objective function. We also introduce MultiONet, a novel neural operator architecture, which is a more expressive generalization of the popular DeepONet that significantly enhances the approximating power of the proposed model. These innovations make DGNO particularly effective for challenging forward and inverse, PDE-based problems, such as those involving multi-phase media. Numerical experiments demonstrate that DGNO achieves higher accuracy across multiple benchmarks while exhibiting robustness to noise and strong generalization to out-of-distribution cases. Its adaptability, and the ability to handle sparse, noisy data while providing probabilistic estimates, make DGNO a powerful tool for scientific and engineering applications.

We consider the general class of time-homogeneous stochastic dynamical systems, both discrete and continuous, and study the problem of learning a representation of the state that faithfully captures its dynamics. This is instrumental to learning the transfer operator or the generator of the system, which in turn can be used for numerous tasks, such as forecasting and interpreting the system dynamics. We show that the search for a good representation can be cast as an optimization problem over neural networks. Our approach is supported by recent results in statistical learning theory, highlighting the role of approximation error and metric distortion in the learning problem. The objective function we propose is associated with projection operators from the representation space to the data space, overcomes metric distortion, and can be empirically estimated from data. In the discrete-time setting, we further derive a relaxed objective function that is differentiable and numerically well-conditioned. We compare our method against state-of-the-art approaches on different datasets, showing better performance across the board.

Autoregressive models have achieved promising results in natural language processing. However, for image generation tasks, they encounter substantial challenges in effectively capturing long-range dependencies, managing computational costs, and most crucially, defining meaningful autoregressive sequences that reflect natural image hierarchies. To address these issues, we present Next-Frequency Image Generation (NFIG), a novel framework that decomposes the image generation process into multiple frequency-guided stages. Our approach first generates low-frequency components to establish global structure with fewer tokens, then progressively adds higher-frequency details, following the natural spectral hierarchy of images. This principled autoregressive sequence not only improves the quality of generated images by better capturing true causal relationships between image components, but also significantly reduces computational overhead during inference. Extensive experiments demonstrate that NFIG achieves state-of-the-art performance with fewer steps, offering a more efficient solution for image generation, with 1.25times speedup compared to VAR-d20 while achieving better performance (FID: 2.81) on the ImageNet-256 benchmark. We hope that our insight of incorporating frequency-domain knowledge to guide autoregressive sequence design will shed light on future research. We will make our code publicly available upon acceptance of the paper.

In recent years, trace generation has emerged as a significant challenge within the Process Mining community. Deep Learning (DL) models have demonstrated accuracy in reproducing the features of the selected processes. However, current DL generative models are limited in their ability to adapt the learned distributions to generate data samples based on specific conditions or attributes. This limitation is particularly significant because the ability to control the type of generated data can be beneficial in various contexts, enabling a focus on specific behaviours, exploration of infrequent patterns, or simulation of alternative 'what-if' scenarios. In this work, we address this challenge by introducing a conditional model for process data generation based on a conditional variational autoencoder (CVAE). Conditional models offer control over the generation process by tuning input conditional variables, enabling more targeted and controlled data generation. Unlike other domains, CVAE for process mining faces specific challenges due to the multiperspective nature of the data and the need to adhere to control-flow rules while ensuring data variability. Specifically, we focus on generating process executions conditioned on control flow and temporal features of the trace, allowing us to produce traces for specific, identified sub-processes. The generated traces are then evaluated using common metrics for generative model assessment, along with additional metrics to evaluate the quality of the conditional generation

Large-scale Causal Language Models (CLMs), e.g., GPT3 and ChatGPT, have brought great success in text generation. However, it is still an open challenge to control the generation process of CLM while balancing flexibility, control granularity, and generation efficiency. In this paper, we provide a new alternative for controllable text generation (CTG), by designing a non-intrusive, lightweight control plugin to accompany the generation of CLM at arbitrary time steps. The proposed control plugin, namely Residual Memory Transformer (RMT), has an encoder-decoder setup, which can accept any types of control conditions and cooperate with CLM through a residual learning paradigm, to achieve a more flexible, general, and efficient CTG. Extensive experiments are carried out on various control tasks, in the form of both automatic and human evaluations. The results show the superiority of RMT over a range of state-of-the-art approaches, proving the effectiveness and versatility of our approach.

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

This paper introduces PDEformer, a neural solver for partial differential equations (PDEs) capable of simultaneously addressing various types of PDEs. We advocate representing the PDE in the form of a computational graph, facilitating the seamless integration of both symbolic and numerical information inherent in a PDE. A graph Transformer and an implicit neural representation (INR) are employed to generate mesh-free predicted solutions. Following pretraining on data exhibiting a certain level of diversity, our model achieves zero-shot accuracies on benchmark datasets that surpass those of adequately trained expert models. Additionally, PDEformer demonstrates promising results in the inverse problem of PDE coefficient recovery.

Conditional Text Generation has drawn much attention as a topic of Natural Language Generation (NLG) which provides the possibility for humans to control the properties of generated contents. Current conditional generation models cannot handle emerging conditions due to their joint end-to-end learning fashion. When a new condition added, these techniques require full retraining. In this paper, we present a new framework named Pre-train and Plug-in Variational Auto-Encoder (PPVAE) towards flexible conditional text generation. PPVAE decouples the text generation module from the condition representation module to allow "one-to-many" conditional generation. When a fresh condition emerges, only a lightweight network needs to be trained and works as a plug-in for PPVAE, which is efficient and desirable for real-world applications. Extensive experiments demonstrate the superiority of PPVAE against the existing alternatives with better conditionality and diversity but less training effort.

Effective regularization techniques are highly desired in deep learning for alleviating overfitting and improving generalization. This work proposes a new regularization scheme, based on the understanding that the flat local minima of the empirical risk cause the model to generalize better. This scheme is referred to as adversarial model perturbation (AMP), where instead of directly minimizing the empirical risk, an alternative "AMP loss" is minimized via SGD. Specifically, the AMP loss is obtained from the empirical risk by applying the "worst" norm-bounded perturbation on each point in the parameter space. Comparing with most existing regularization schemes, AMP has strong theoretical justifications, in that minimizing the AMP loss can be shown theoretically to favour flat local minima of the empirical risk. Extensive experiments on various modern deep architectures establish AMP as a new state of the art among regularization schemes. Our code is available at https://github.com/hiyouga/AMP-Regularizer.

Time-dependent partial differential equations (PDEs) are ubiquitous in science and engineering. Recently, mostly due to the high computational cost of traditional solution techniques, deep neural network based surrogates have gained increased interest. The practical utility of such neural PDE solvers relies on their ability to provide accurate, stable predictions over long time horizons, which is a notoriously hard problem. In this work, we present a large-scale analysis of common temporal rollout strategies, identifying the neglect of non-dominant spatial frequency information, often associated with high frequencies in PDE solutions, as the primary pitfall limiting stable, accurate rollout performance. Based on these insights, we draw inspiration from recent advances in diffusion models to introduce PDE-Refiner; a novel model class that enables more accurate modeling of all frequency components via a multistep refinement process. We validate PDE-Refiner on challenging benchmarks of complex fluid dynamics, demonstrating stable and accurate rollouts that consistently outperform state-of-the-art models, including neural, numerical, and hybrid neural-numerical architectures. We further demonstrate that PDE-Refiner greatly enhances data efficiency, since the denoising objective implicitly induces a novel form of spectral data augmentation. Finally, PDE-Refiner's connection to diffusion models enables an accurate and efficient assessment of the model's predictive uncertainty, allowing us to estimate when the surrogate becomes inaccurate.

The design of fusion devices is typically based on computationally expensive simulations. This can be alleviated using high aspect ratio models that employ a reduced number of free parameters, especially in the case of stellarator optimization where non-axisymmetric magnetic fields with a large parameter space are optimized to satisfy certain performance criteria. However, optimization is still required to find configurations with properties such as low elongation, high rotational transform, finite plasma beta, and good fast particle confinement. In this work, we train a machine learning model to construct configurations with favorable confinement properties by finding a solution to the inverse design problem, that is, obtaining a set of model input parameters for given desired properties. Since the solution of the inverse problem is non-unique, a probabilistic approach, based on mixture density networks, is used. It is shown that optimized configurations can be generated reliably using this method.

Discrete diffusion or flow models could enable faster and more controllable sequence generation than autoregressive models. We show that na\"ive linear flow matching on the simplex is insufficient toward this goal since it suffers from discontinuities in the training target and further pathologies. To overcome this, we develop Dirichlet flow matching on the simplex based on mixtures of Dirichlet distributions as probability paths. In this framework, we derive a connection between the mixtures' scores and the flow's vector field that allows for classifier and classifier-free guidance. Further, we provide distilled Dirichlet flow matching, which enables one-step sequence generation with minimal performance hits, resulting in O(L) speedups compared to autoregressive models. On complex DNA sequence generation tasks, we demonstrate superior performance compared to all baselines in distributional metrics and in achieving desired design targets for generated sequences. Finally, we show that our classifier-free guidance approach improves unconditional generation and is effective for generating DNA that satisfies design targets. Code is available at https://github.com/HannesStark/dirichlet-flow-matching.

Partial Differential Equations are precise in modelling the physical, biological and graphical phenomena. However, the numerical methods suffer from the curse of dimensionality, high computation costs and domain-specific discretization. We aim to explore pros and cons of different PDE solvers, and apply them to specific scientific simulation problems, including forwarding solution, inverse problems and equations discovery. In particular, we extend the recent CNF (NeurIPS 2023) framework solver to multi-dependent-variable and non-linear settings, together with down-stream applications. The outcomes include implementation of selected methods, self-tuning techniques, evaluation on benchmark problems and a comprehensive survey of neural PDE solvers and scientific simulation applications.

Generating time series data using Generative Adversarial Networks (GANs) presents several prevalent challenges, such as slow convergence, information loss in embedding spaces, instability, and performance variability depending on the series length. To tackle these obstacles, we introduce a robust framework aimed at addressing and mitigating these issues effectively. This advanced framework integrates the benefits of an Autoencoder-generated embedding space with the adversarial training dynamics of GANs. This framework benefits from a time series-based loss function and oversight from a supervisory network, both of which capture the stepwise conditional distributions of the data effectively. The generator functions within the latent space, while the discriminator offers essential feedback based on the feature space. Moreover, we introduce an early generation algorithm and an improved neural network architecture to enhance stability and ensure effective generalization across both short and long time series. Through joint training, our framework consistently outperforms existing benchmarks, generating high-quality time series data across a range of real and synthetic datasets with diverse characteristics.

There has been a recent surge of interest in modeling neural networks (NNs) as Gaussian processes. In the limit of a NN of infinite width the NN becomes equivalent to a Gaussian process. Here we demonstrate that for an ensemble of large, finite, fully connected networks with a single hidden layer the distribution of outputs at initialization is well described by a Gaussian perturbed by the fourth Hermite polynomial for weights drawn from a symmetric distribution. We show that the scale of the perturbation is inversely proportional to the number of units in the NN and that higher order terms decay more rapidly, thereby recovering the Edgeworth expansion. We conclude by observing that understanding how this perturbation changes under training would reveal the regimes in which the Gaussian process framework is valid to model NN behavior.

Even for known nonlinear dynamical systems, feedback controller synthesis is a difficult problem that often requires leveraging the particular structure of the dynamics to induce a stable closed-loop system. For general nonlinear models, including those fit to data, there may not be enough known structure to reliably synthesize a stabilizing feedback controller. In this paper, we discuss a state-dependent nonlinear tracking controller formulation based on a state-dependent Riccati equation for general nonlinear control-affine systems. This formulation depends on a nonlinear factorization of the system of vector fields defining the control-affine dynamics, which always exists under mild smoothness assumptions. We propose a method for learning this factorization from a finite set of data. On a variety of simulated nonlinear dynamical systems, we empirically demonstrate the efficacy of learned versions of this controller in stable trajectory tracking. Alongside our learning method, we evaluate recent ideas in jointly learning a controller and stabilizability certificate for known dynamical systems; we show experimentally that such methods can be frail in comparison.

Denoising Diffusion Probabilistic Models have shown an impressive generation quality, although their long sampling chain leads to high computational costs. In this paper, we observe that a long sampling chain also leads to an error accumulation phenomenon, which is similar to the exposure bias problem in autoregressive text generation. Specifically, we note that there is a discrepancy between training and testing, since the former is conditioned on the ground truth samples, while the latter is conditioned on the previously generated results. To alleviate this problem, we propose a very simple but effective training regularization, consisting in perturbing the ground truth samples to simulate the inference time prediction errors. We empirically show that, without affecting the recall and precision, the proposed input perturbation leads to a significant improvement in the sample quality while reducing both the training and the inference times. For instance, on CelebA 64times64, we achieve a new state-of-the-art FID score of 1.27, while saving 37.5% of the training time. The code is publicly available at https://github.com/forever208/DDPM-IP

Recent image generation models show remarkable generation performance. However, they mirror strong location preference in datasets, which we call spatial bias. Therefore, generators render poor samples at unseen locations and scales. We argue that the generators rely on their implicit positional encoding to render spatial content. From our observations, the generator's implicit positional encoding is translation-variant, making the generator spatially biased. To address this issue, we propose injecting explicit positional encoding at each scale of the generator. By learning the spatially unbiased generator, we facilitate the robust use of generators in multiple tasks, such as GAN inversion, multi-scale generation, generation of arbitrary sizes and aspect ratios. Furthermore, we show that our method can also be applied to denoising diffusion probabilistic models.

Straight line equation y=mx with slope m, when singularly perturbed as ay^3+y=mx with a positive parameter a, results in S-shaped curves or S-curves on a real plane. As arightarrow 0, we get back y=mx which is a cumulative distribution function of a continuous uniform distribution that describes the occurrence of every event in an interval to be equally probable. As arightarrowinfty, the derivative of y has finite support only at y=0 resembling a degenerate distribution. Based on these arguments, in this work, we propose that these S-curves can represent maximum entropy uniform distribution to a zero entropy single value. We also argue that these S-curves are superposable as they are only parametrically nonlinear but fundamentally linear. So far, the superposed forms have been used to capture the patterns of natural systems such as nonlinear dynamics of biological growth and kinetics of enzyme reactions. Here, we attempt to use the S-curve and its superposed form as statistical models. We fit the models on a classical dataset containing flower measurements of iris plants and analyze their usefulness in pattern recognition. Based on these models, we claim that any non-uniform pattern can be represented as a singular perturbation to uniform distribution. However, our parametric estimation procedure have some limitations such as sensitivity to initial conditions depending on the data at hand.

Image animation consists of generating a video sequence so that an object in a source image is animated according to the motion of a driving video. Our framework addresses this problem without using any annotation or prior information about the specific object to animate. Once trained on a set of videos depicting objects of the same category (e.g. faces, human bodies), our method can be applied to any object of this class. To achieve this, we decouple appearance and motion information using a self-supervised formulation. To support complex motions, we use a representation consisting of a set of learned keypoints along with their local affine transformations. A generator network models occlusions arising during target motions and combines the appearance extracted from the source image and the motion derived from the driving video. Our framework scores best on diverse benchmarks and on a variety of object categories. Our source code is publicly available.

The classical development of neural networks has primarily focused on learning mappings between finite dimensional Euclidean spaces or finite sets. We propose a generalization of neural networks to learn operators, termed neural operators, that map between infinite dimensional function spaces. We formulate the neural operator as a composition of linear integral operators and nonlinear activation functions. We prove a universal approximation theorem for our proposed neural operator, showing that it can approximate any given nonlinear continuous operator. The proposed neural operators are also discretization-invariant, i.e., they share the same model parameters among different discretization of the underlying function spaces. Furthermore, we introduce four classes of efficient parameterization, viz., graph neural operators, multi-pole graph neural operators, low-rank neural operators, and Fourier neural operators. An important application for neural operators is learning surrogate maps for the solution operators of partial differential equations (PDEs). We consider standard PDEs such as the Burgers, Darcy subsurface flow, and the Navier-Stokes equations, and show that the proposed neural operators have superior performance compared to existing machine learning based methodologies, while being several orders of magnitude faster than conventional PDE solvers.

Virtual cell modeling represents an emerging frontier at the intersection of artificial intelligence and biology, aiming to predict quantities such as responses to diverse perturbations quantitatively. However, autonomously building computational models for virtual cells is challenging due to the complexity of biological systems, the heterogeneity of data modalities, and the need for domain-specific expertise across multiple disciplines. Here, we introduce CellForge, an agentic system that leverages a multi-agent framework that transforms presented biological datasets and research objectives directly into optimized computational models for virtual cells. More specifically, given only raw single-cell multi-omics data and task descriptions as input, CellForge outputs both an optimized model architecture and executable code for training virtual cell models and inference. The framework integrates three core modules: Task Analysis for presented dataset characterization and relevant literature retrieval, Method Design, where specialized agents collaboratively develop optimized modeling strategies, and Experiment Execution for automated generation of code. The agents in the Design module are separated into experts with differing perspectives and a central moderator, and have to collaboratively exchange solutions until they achieve a reasonable consensus. We demonstrate CellForge's capabilities in single-cell perturbation prediction, using six diverse datasets that encompass gene knockouts, drug treatments, and cytokine stimulations across multiple modalities. CellForge consistently outperforms task-specific state-of-the-art methods. Overall, CellForge demonstrates how iterative interaction between LLM agents with differing perspectives provides better solutions than directly addressing a modeling challenge. Our code is publicly available at https://github.com/gersteinlab/CellForge.

Approximating nonlinear differential equations using a neural network provides a robust and efficient tool for various scientific computing tasks, including real-time predictions, inverse problems, optimal controls, and surrogate modeling. Previous works have focused on embedding dynamical systems into networks through two approaches: learning a single solution operator (i.e., the mapping from input parametrized functions to solutions) or learning the governing system of equations (i.e., the constitutive model relative to the state variables). Both of these approaches yield different representations for the same underlying data or function. Additionally, observing that families of differential equations often share key characteristics, we seek one network representation across a wide range of equations. Our method, called Predicting Operators and Symbolic Expressions (PROSE), learns maps from multimodal inputs to multimodal outputs, capable of generating both numerical predictions and mathematical equations. By using a transformer structure and a feature fusion approach, our network can simultaneously embed sets of solution operators for various parametric differential equations using a single trained network. Detailed experiments demonstrate that the network benefits from its multimodal nature, resulting in improved prediction accuracy and better generalization. The network is shown to be able to handle noise in the data and errors in the symbolic representation, including noisy numerical values, model misspecification, and erroneous addition or deletion of terms. PROSE provides a new neural network framework for differential equations which allows for more flexibility and generality in learning operators and governing equations from data.

Agents based on large language models have shown great potential in accelerating scientific discovery by leveraging their rich background knowledge and reasoning capabilities. In this paper, we introduce BioDiscoveryAgent, an agent that designs new experiments, reasons about their outcomes, and efficiently navigates the hypothesis space to reach desired solutions. We demonstrate our agent on the problem of designing genetic perturbation experiments, where the aim is to find a small subset out of many possible genes that, when perturbed, result in a specific phenotype (e.g., cell growth). Utilizing its biological knowledge, BioDiscoveryAgent can uniquely design new experiments without the need to train a machine learning model or explicitly design an acquisition function as in Bayesian optimization. Moreover, BioDiscoveryAgent, using Claude 3.5 Sonnet, achieves an average of 21% improvement in predicting relevant genetic perturbations across six datasets, and a 46% improvement in the harder task of non-essential gene perturbation, compared to existing Bayesian optimization baselines specifically trained for this task. Our evaluation includes one dataset that is unpublished, ensuring it is not part of the language model's training data. Additionally, BioDiscoveryAgent predicts gene combinations to perturb more than twice as accurately as a random baseline, a task so far not explored in the context of closed-loop experiment design. The agent also has access to tools for searching the biomedical literature, executing code to analyze biological datasets, and prompting another agent to critically evaluate its predictions. Overall, BioDiscoveryAgent is interpretable at every stage, representing an accessible new paradigm in the computational design of biological experiments with the potential to augment scientists' efficacy.

Despite recent advances in natural language generation, it remains challenging to control attributes of generated text. We propose DExperts: Decoding-time Experts, a decoding-time method for controlled text generation that combines a pretrained language model with "expert" LMs and/or "anti-expert" LMs in a product of experts. Intuitively, under the ensemble, tokens only get high probability if they are considered likely by the experts, and unlikely by the anti-experts. We apply DExperts to language detoxification and sentiment-controlled generation, where we outperform existing controllable generation methods on both automatic and human evaluations. Moreover, because DExperts operates only on the output of the pretrained LM, it is effective with (anti-)experts of smaller size, including when operating on GPT-3. Our work highlights the promise of tuning small LMs on text with (un)desirable attributes for efficient decoding-time steering.

Generative models have advanced significantly in sampling material systems with continuous variables, such as atomistic structures. However, their application to discrete variables, like atom types or spin states, remains underexplored. In this work, we introduce a Boltzmann generator built on discrete flow matching, specifically tailored for systems with discrete phase-space coordinates (e.g., the Ising model or crystalline compounds). This approach enables a single model to sample free energy surfaces over a wide temperature range with minimal training overhead. In addition, the model generation is scalable to larger lattice sizes than those in the training set. We demonstrate the effectiveness of our approach on the 2D Ising model, showing efficient and reliable free energy sampling. This framework provides a scalable and computationally efficient solution for discrete coordinate systems and can be extended to sample the alchemical degrees of freedom in crystalline compounds.

Generative modeling of single-cell RNA-seq data has shown invaluable potential in community-driven tasks such as trajectory inference, batch effect removal and gene expression generation. However, most recent deep models generating synthetic single cells from noise operate on pre-processed continuous gene expression approximations, ignoring the inherently discrete and over-dispersed nature of single-cell data, which limits downstream applications and hinders the incorporation of robust noise models. Moreover, crucial aspects of deep-learning-based synthetic single-cell generation remain underexplored, such as controllable multi-modal and multi-label generation and its role in the performance enhancement of downstream tasks. This work presents Cell Flow for Generation (CFGen), a flow-based conditional generative model for multi-modal single-cell counts, which explicitly accounts for the discrete nature of the data. Our results suggest improved recovery of crucial biological data characteristics while accounting for novel generative tasks such as conditioning on multiple attributes and boosting rare cell type classification via data augmentation. By showcasing CFGen on a diverse set of biological datasets and settings, we provide evidence of its value to the fields of computational biology and deep generative models.

Given an unconditional generative model and a predictor for a target property (e.g., a classifier), the goal of training-free guidance is to generate samples with desirable target properties without additional training. As a highly efficient technique for steering generative models toward flexible outcomes, training-free guidance has gained increasing attention in diffusion models. However, existing methods only handle data in continuous spaces, while many scientific applications involve both continuous and discrete data (referred to as multimodality). Another emerging trend is the growing use of the simple and general flow matching framework in building generative foundation models, where guided generation remains under-explored. To address this, we introduce TFG-Flow, a novel training-free guidance method for multimodal generative flow. TFG-Flow addresses the curse-of-dimensionality while maintaining the property of unbiased sampling in guiding discrete variables. We validate TFG-Flow on four molecular design tasks and show that TFG-Flow has great potential in drug design by generating molecules with desired properties.

Given ample experimental data from a system governed by differential equations, it is possible to use deep learning techniques to construct the underlying differential operators. In this work we perform symbolic discovery of differential operators in a situation where there is sparse experimental data. This small data regime in machine learning can be made tractable by providing our algorithms with prior information about the underlying dynamics. Physics Informed Neural Networks (PINNs) have been very successful in this regime (reconstructing entire ODE solutions using only a single point or entire PDE solutions with very few measurements of the initial condition). We modify the PINN approach by adding a neural network that learns a representation of unknown hidden terms in the differential equation. The algorithm yields both a surrogate solution to the differential equation and a black-box representation of the hidden terms. These hidden term neural networks can then be converted into symbolic equations using symbolic regression techniques like AI Feynman. In order to achieve convergence of these neural networks, we provide our algorithms with (noisy) measurements of both the initial condition as well as (synthetic) experimental data obtained at later times. We demonstrate strong performance of this approach even when provided with very few measurements of noisy data in both the ODE and PDE regime.

Vibration rendering is essential for creating realistic tactile experiences in human-virtual object interactions, such as in video game controllers and VR devices. By dynamically adjusting vibration parameters based on user actions, these systems can convey spatial features and contribute to texture representation. However, generating arbitrary vibrations to replicate real-world material textures is challenging due to the large parameter space. This study proposes a human-in-the-loop vibration generation model based on user preferences. To enable users to easily control the generation of vibration samples with large parameter spaces, we introduced an optimization model based on Differential Subspace Search (DSS) and Generative Adversarial Network (GAN). With DSS, users can employ a one-dimensional slider to easily modify the high-dimensional latent space to ensure that the GAN can generate desired vibrations. We trained the generative model using an open dataset of tactile vibration data and selected five types of vibrations as target samples for the generation experiment. Extensive user experiments were conducted using the generated and real samples. The results indicated that our system could generate distinguishable samples that matched the target characteristics. Moreover, we established a correlation between subjects' ability to distinguish real samples and their ability to distinguish generated samples.

We introduce Poseidon, a foundation model for learning the solution operators of PDEs. It is based on a multiscale operator transformer, with time-conditioned layer norms that enable continuous-in-time evaluations. A novel training strategy leveraging the semi-group property of time-dependent PDEs to allow for significant scaling-up of the training data is also proposed. Poseidon is pretrained on a diverse, large scale dataset for the governing equations of fluid dynamics. It is then evaluated on a suite of 15 challenging downstream tasks that include a wide variety of PDE types and operators. We show that Poseidon exhibits excellent performance across the board by outperforming baselines significantly, both in terms of sample efficiency and accuracy. Poseidon also generalizes very well to new physics that is not seen during pretraining. Moreover, Poseidon scales with respect to model and data size, both for pretraining and for downstream tasks. Taken together, our results showcase the surprising ability of Poseidon to learn effective representations from a very small set of PDEs during pretraining in order to generalize well to unseen and unrelated PDEs downstream, demonstrating its potential as an effective, general purpose PDE foundation model. Finally, the Poseidon model as well as underlying pretraining and downstream datasets are open sourced, with code being available at https://github.com/camlab-ethz/poseidon and pretrained models and datasets at https://huggingface.co/camlab-ethz.

Diffusion models have emerged as a formidable tool for training-free conditional generation.However, a key hurdle in inference-time guidance techniques is the need for compute-heavy backpropagation through the diffusion network for estimating the guidance direction. Moreover, these techniques often require handcrafted parameter tuning on a case-by-case basis. Although some recent works have introduced minimal compute methods for linear inverse problems, a generic lightweight guidance solution to both linear and non-linear guidance problems is still missing. To this end, we propose Dreamguider, a method that enables inference-time guidance without compute-heavy backpropagation through the diffusion network. The key idea is to regulate the gradient flow through a time-varying factor. Moreover, we propose an empirical guidance scale that works for a wide variety of tasks, hence removing the need for handcrafted parameter tuning. We further introduce an effective lightweight augmentation strategy that significantly boosts the performance during inference-time guidance. We present experiments using Dreamguider on multiple tasks across multiple datasets and models to show the effectiveness of the proposed modules. To facilitate further research, we will make the code public after the review process.

Classifier-free guidance (CFG) is a core technique powering state-of-the-art image generation systems, yet its underlying mechanisms remain poorly understood. In this work, we begin by analyzing CFG in a simplified linear diffusion model, where we show its behavior closely resembles that observed in the nonlinear case. Our analysis reveals that linear CFG improves generation quality via three distinct components: (i) a mean-shift term that approximately steers samples in the direction of class means, (ii) a positive Contrastive Principal Components (CPC) term that amplifies class-specific features, and (iii) a negative CPC term that suppresses generic features prevalent in unconditional data. We then verify that these insights in real-world, nonlinear diffusion models: over a broad range of noise levels, linear CFG resembles the behavior of its nonlinear counterpart. Although the two eventually diverge at low noise levels, we discuss how the insights from the linear analysis still shed light on the CFG's mechanism in the nonlinear regime.

This paper describes a method for learning low-dimensional approximations of nonlinear dynamical systems, based on neural-network approximations of the underlying Koopman operator. Extended Dynamic Mode Decomposition (EDMD) provides a useful data-driven approximation of the Koopman operator for analyzing dynamical systems. This paper addresses a fundamental problem associated with EDMD: a trade-off between representational capacity of the dictionary and over-fitting due to insufficient data. A new neural network architecture combining an autoencoder with linear recurrent dynamics in the encoded state is used to learn a low-dimensional and highly informative Koopman-invariant subspace of observables. A method is also presented for balanced model reduction of over-specified EDMD systems in feature space. Nonlinear reconstruction using partially linear multi-kernel regression aims to improve reconstruction accuracy from the low-dimensional state when the data has complex but intrinsically low-dimensional structure. The techniques demonstrate the ability to identify Koopman eigenfunctions of the unforced Duffing equation, create accurate low-dimensional models of an unstable cylinder wake flow, and make short-time predictions of the chaotic Kuramoto-Sivashinsky equation.

We incorporate discrete and continuous time Markov processes as building blocks into probabilistic graphical models with latent and observed variables. We introduce the automatic Backward Filtering Forward Guiding (BFFG) paradigm (Mider et al., 2021) for programmable inference on latent states and model parameters. Our starting point is a generative model, a forward description of the probabilistic process dynamics. We backpropagate the information provided by observations through the model to transform the generative (forward) model into a pre-conditional model guided by the data. It approximates the actual conditional model with known likelihood-ratio between the two. The backward filter and the forward change of measure are suitable to be incorporated into a probabilistic programming context because they can be formulated as a set of transformation rules. The guided generative model can be incorporated in different approaches to efficiently sample latent states and parameters conditional on observations. We show applicability in a variety of settings, including Markov chains with discrete state space, interacting particle systems, state space models, branching diffusions and Gamma processes.

Deep generative models based on neural differential equations have quickly become the state-of-the-art for numerous generation tasks across many different applications. These models rely on ODE/SDE solvers which integrate from a prior distribution to the data distribution. In many applications it is highly desirable to then integrate in the other direction. The standard solvers, however, accumulate discretization errors which don't align with the forward trajectory, thereby prohibiting an exact inversion. In applications where the precision of the generative model is paramount this inaccuracy in inversion is often unacceptable. Current approaches to solving the inversion of these models results in significant downstream issues with poor stability and low-order of convergence; moreover, they are strictly limited to the ODE domain. In this work, we propose a new family of reversible exponential (stochastic) Runge-Kutta solvers which we refer to as Rex developed by an application of Lawson methods to convert any explicit (stochastic) Runge-Kutta scheme into a reversible one. In addition to a rigorous theoretical analysis of the proposed solvers, we also empirically demonstrate the utility of Rex on improving the sampling of Boltzmann distributions with flow models, and improving image generation and editing capabilities with diffusion models.

Machine learning for differential equations paves the way for computationally efficient alternatives to numerical solvers, with potentially broad impacts in science and engineering. Though current algorithms typically require simulated training data tailored to a given setting, one may instead wish to learn useful information from heterogeneous sources, or from real dynamical systems observations that are messy or incomplete. In this work, we learn general-purpose representations of PDEs from heterogeneous data by implementing joint embedding methods for self-supervised learning (SSL), a framework for unsupervised representation learning that has had notable success in computer vision. Our representation outperforms baseline approaches to invariant tasks, such as regressing the coefficients of a PDE, while also improving the time-stepping performance of neural solvers. We hope that our proposed methodology will prove useful in the eventual development of general-purpose foundation models for PDEs.

While large-scale language models (LMs) are able to imitate the distribution of natural language well enough to generate realistic text, it is difficult to control which regions of the distribution they generate. This is especially problematic because datasets used for training large LMs usually contain significant toxicity, hate, bias, and negativity. We propose GeDi as an efficient method for using smaller LMs as generative discriminators to guide generation from large LMs to make them safer and more controllable. GeDi guides generation at each step by computing classification probabilities for all possible next tokens via Bayes rule by normalizing over two class-conditional distributions; one conditioned on the desired attribute, or control code, and another conditioned on the undesired attribute, or anti control code. We find that GeDi gives stronger controllability than the state of the art method while also achieving generation speeds more than 30 times faster. Additionally, training GeDi on only four topics allows us to controllably generate new topics zero-shot from just a keyword, unlocking a new capability that previous controllable generation methods do not have. Lastly, we show that GeDi can make GPT-2 (1.5B parameters) significantly less toxic without sacrificing linguistic quality, making it by far the most practical existing method for detoxifying large language models while maintaining a fast generation speed.

In offline multi-objective optimization (MOO), we leverage an offline dataset of designs and their associated labels to simultaneously minimize multiple objectives. This setting more closely mirrors complex real-world problems compared to single-objective optimization. Recent works mainly employ evolutionary algorithms and Bayesian optimization, with limited attention given to the generative modeling capabilities inherent in such data. In this study, we explore generative modeling in offline MOO through flow matching, noted for its effectiveness and efficiency. We introduce ParetoFlow, specifically designed to guide flow sampling to approximate the Pareto front. Traditional predictor (classifier) guidance is inadequate for this purpose because it models only a single objective. In response, we propose a multi-objective predictor guidance module that assigns each sample a weight vector, representing a weighted distribution across multiple objective predictions. A local filtering scheme is introduced to address non-convex Pareto fronts. These weights uniformly cover the entire objective space, effectively directing sample generation towards the Pareto front. Since distributions with similar weights tend to generate similar samples, we introduce a neighboring evolution module to foster knowledge sharing among neighboring distributions. This module generates offspring from these distributions, and selects the most promising one for the next iteration. Our method achieves state-of-the-art performance across various tasks.

Recent research has adopted a new experimental field centered around the concept of text perturbations which has revealed that shuffled word order has little to no impact on the downstream performance of Transformer-based language models across many NLP tasks. These findings contradict the common understanding of how the models encode hierarchical and structural information and even question if the word order is modeled with position embeddings. To this end, this paper proposes nine probing datasets organized by the type of controllable text perturbation for three Indo-European languages with a varying degree of word order flexibility: English, Swedish and Russian. Based on the probing analysis of the M-BERT and M-BART models, we report that the syntactic sensitivity depends on the language and model pre-training objectives. We also find that the sensitivity grows across layers together with the increase of the perturbation granularity. Last but not least, we show that the models barely use the positional information to induce syntactic trees from their intermediate self-attention and contextualized representations.

This paper presents a continuous-time optimal control framework for the generation of reference trajectories in driving scenarios with uncertainty. A previous work presented a discrete-time stochastic generator for autonomous vehicles; those results are extended to continuous time to ensure the robustness of the generator in a real-time setting. We show that the stochastic model in continuous time can capture the uncertainty of information by producing better results, limiting the risk of violating the problem's constraints compared to a discrete approach. Dynamic solvers provide faster computation and the continuous-time model is more robust to a wider variety of driving scenarios than the discrete-time model, as it can handle further time horizons, which allows trajectory planning outside the framework of urban driving scenarios.

Learning image classification and image generation using the same set of network parameters is a challenging problem. Recent advanced approaches perform well in one task often exhibit poor performance in the other. This work introduces an energy-based classifier and generator, namely EGC, which can achieve superior performance in both tasks using a single neural network. Unlike a conventional classifier that outputs a label given an image (i.e., a conditional distribution p(y|x)), the forward pass in EGC is a classifier that outputs a joint distribution p(x,y), enabling an image generator in its backward pass by marginalizing out the label y. This is done by estimating the energy and classification probability given a noisy image in the forward pass, while denoising it using the score function estimated in the backward pass. EGC achieves competitive generation results compared with state-of-the-art approaches on ImageNet-1k, CelebA-HQ and LSUN Church, while achieving superior classification accuracy and robustness against adversarial attacks on CIFAR-10. This work represents the first successful attempt to simultaneously excel in both tasks using a single set of network parameters. We believe that EGC bridges the gap between discriminative and generative learning.

We develop a data-driven deep neural operator framework to approximate multiple output states for a diesel engine and generate real-time predictions with reasonable accuracy. As emission norms become more stringent, the need for fast and accurate models that enable analysis of system behavior have become an essential requirement for system development. The fast transient processes involved in the operation of a combustion engine make it difficult to develop accurate physics-based models for such systems. As an alternative to physics based models, we develop an operator-based regression model (DeepONet) to learn the relevant output states for a mean-value gas flow engine model using the engine operating conditions as input variables. We have adopted a mean-value model as a benchmark for comparison, simulated using Simulink. The developed approach necessitates using the initial conditions of the output states to predict the accurate sequence over the temporal domain. To this end, a sequence-to-sequence approach is embedded into the proposed framework. The accuracy of the model is evaluated by comparing the prediction output to ground truth generated from Simulink model. The maximum mathcal L_2 relative error observed was approximately 6.5%. The sensitivity of the DeepONet model is evaluated under simulated noise conditions and the model shows relatively low sensitivity to noise. The uncertainty in model prediction is further assessed by using a mean ensemble approach. The worst-case error at the (mu + 2sigma) boundary was found to be 12%. The proposed framework provides the ability to predict output states in real-time and enables data-driven learning of complex input-output operator mapping. As a result, this model can be applied during initial development stages, where accurate models may not be available.

Deep representation learning methods struggle with continual learning, suffering from both catastrophic forgetting of useful units and loss of plasticity, often due to rigid and unuseful units. While many methods address these two issues separately, only a few currently deal with both simultaneously. In this paper, we introduce Utility-based Perturbed Gradient Descent (UPGD) as a novel approach for the continual learning of representations. UPGD combines gradient updates with perturbations, where it applies smaller modifications to more useful units, protecting them from forgetting, and larger modifications to less useful units, rejuvenating their plasticity. We use a challenging streaming learning setup where continual learning problems have hundreds of non-stationarities and unknown task boundaries. We show that many existing methods suffer from at least one of the issues, predominantly manifested by their decreasing accuracy over tasks. On the other hand, UPGD continues to improve performance and surpasses or is competitive with all methods in all problems. Finally, in extended reinforcement learning experiments with PPO, we show that while Adam exhibits a performance drop after initial learning, UPGD avoids it by addressing both continual learning issues.

Controllable text generation systems often leverage control codes to direct various properties of the output like style and length. Inspired by recent work on causal inference for NLP, this paper reveals a previously overlooked flaw in these control code-based conditional text generation algorithms. Spurious correlations in the training data can lead models to incorrectly rely on parts of the input other than the control code for attribute selection, significantly undermining downstream generation quality and controllability. We demonstrate the severity of this issue with a series of case studies and then propose two simple techniques to reduce these correlations in training sets. The first technique is based on resampling the data according to an example's propensity towards each linguistic attribute (IPS). The second produces multiple counterfactual versions of each example and then uses an additional feedback mechanism to remove noisy examples (feedback aware self-training, FAST). We evaluate on 3 tasks -- news headline, meta review, and search ads generation -- and demonstrate that FAST can significantly improve the controllability and language quality of generated outputs when compared to state-of-the-art controllable text generation approaches.

Conditional neural text generation models generate high-quality outputs, but often concentrate around a mode when what we really want is a diverse set of options. We present a search algorithm to construct lattices encoding a massive number of generation options. First, we restructure decoding as a best-first search, which explores the space differently than beam search and improves efficiency by avoiding pruning paths. Second, we revisit the idea of hypothesis recombination: we can identify pairs of similar generation candidates during search and merge them as an approximation. On both summarization and machine translation, we show that our algorithm encodes thousands of diverse options that remain grammatical and high-quality into one lattice. This algorithm provides a foundation for building downstream generation applications on top of massive-scale diverse outputs.

Prefix-tuning is a powerful lightweight technique for adapting a large pre-trained language model to a downstream application. However, it uses the same dataset-level tuned prompt for all examples in the dataset. We extend this idea and propose a dynamic method, Control Prefixes, which allows for the inclusion of conditional input-dependent information, combining the benefits of prompt tuning and controlled generation. The method incorporates attribute-level learnable representations into different layers of a pre-trained transformer, allowing for the generated text to be guided in a particular direction. We provide a systematic evaluation of the technique and apply it to five datasets from the GEM benchmark for natural language generation (NLG). Although the aim is to develop a parameter-efficient model, we show Control Prefixes can even outperform full fine-tuning methods. We present state-of-the-art results on several data-to-text datasets, including WebNLG.

Recent advances in scientific machine learning (SciML) have enabled neural operators (NOs) to serve as powerful surrogates for modeling the dynamic evolution of physical systems governed by partial differential equations (PDEs). While existing approaches focus primarily on learning simulations from the target PDE, they often overlook more fundamental physical principles underlying these equations. Inspired by how numerical solvers are compatible with simulations of different settings of PDEs, we propose a multiphysics training framework that jointly learns from both the original PDEs and their simplified basic forms. Our framework enhances data efficiency, reduces predictive errors, and improves out-of-distribution (OOD) generalization, particularly in scenarios involving shifts of physical parameters and synthetic-to-real transfer. Our method is architecture-agnostic and demonstrates consistent improvements in normalized root mean square error (nRMSE) across a wide range of 1D/2D/3D PDE problems. Through extensive experiments, we show that explicit incorporation of fundamental physics knowledge significantly strengthens the generalization ability of neural operators. We will release models and codes at https://sites.google.com/view/sciml-fundemental-pde.

Offline optimization is an important task in numerous material engineering domains where online experimentation to collect data is too expensive and needs to be replaced by an in silico maximization of a surrogate of the black-box function. Although such a surrogate can be learned from offline data, its prediction might not be reliable outside the offline data regime, which happens when the surrogate has narrow prediction margin and is (therefore) sensitive to small perturbations of its parameterization. This raises the following questions: (1) how to regulate the sensitivity of a surrogate model; and (2) whether conditioning an offline optimizer with such less sensitive surrogate will lead to better optimization performance. To address these questions, we develop an optimizable sensitivity measurement for the surrogate model, which then inspires a sensitivity-informed regularizer that is applicable to a wide range of offline optimizers. This development is both orthogonal and synergistic to prior research on offline optimization, which is demonstrated in our extensive experiment benchmark.

Conditional time series generation plays a critical role in addressing data scarcity and enabling causal analysis in real-world applications. Despite its increasing importance, the field lacks a standardized and systematic benchmarking framework for evaluating generative models across diverse conditions. To address this gap, we introduce the Conditional Time Series Generation Benchmark (ConTSG-Bench). ConTSG-Bench comprises a large-scale, well-aligned dataset spanning diverse conditioning modalities and levels of semantic abstraction, first enabling systematic evaluation of representative generation methods across these dimensions with a comprehensive suite of metrics for generation fidelity and condition adherence. Both the quantitative benchmarking and in-depth analyses of conditional generation behaviors have revealed the traits and limitations of the current approaches, highlighting critical challenges and promising research directions, particularly with respect to precise structural controllability and downstream task utility under complex conditions.

Dynamical systems provide a comprehensive way to study complex and changing behaviors across various sciences. Many modern systems are too complicated to analyze directly or we do not have access to models, driving significant interest in learning methods. Koopman operators have emerged as a dominant approach because they allow the study of nonlinear dynamics using linear techniques by solving an infinite-dimensional spectral problem. However, current algorithms face challenges such as lack of convergence, hindering practical progress. This paper addresses a fundamental open question: When can we robustly learn the spectral properties of Koopman operators from trajectory data of dynamical systems, and when can we not? Understanding these boundaries is crucial for analysis, applications, and designing algorithms. We establish a foundational approach that combines computational analysis and ergodic theory, revealing the first fundamental barriers -- universal for any algorithm -- associated with system geometry and complexity, regardless of data quality and quantity. For instance, we demonstrate well-behaved smooth dynamical systems on tori where non-trivial eigenfunctions of the Koopman operator cannot be determined by any sequence of (even randomized) algorithms, even with unlimited training data. Additionally, we identify when learning is possible and introduce optimal algorithms with verification that overcome issues in standard methods. These results pave the way for a sharp classification theory of data-driven dynamical systems based on how many limits are needed to solve a problem. These limits characterize all previous methods, presenting a unified view. Our framework systematically determines when and how Koopman spectral properties can be learned.

Boltzmann generators approach the sampling problem in many-body physics by combining a normalizing flow and a statistical reweighting method to generate samples in thermodynamic equilibrium. The equilibrium distribution is usually defined by an energy function and a thermodynamic state. Here we propose temperature-steerable flows (TSF) which are able to generate a family of probability densities parametrized by a choosable temperature parameter. TSFs can be embedded in generalized ensemble sampling frameworks to sample a physical system across multiple thermodynamic states.

Classifier-Free Guidance (CFG) significantly enhances controllability in generative models by interpolating conditional and unconditional predictions. However, standard CFG often employs a static unconditional input, which can be suboptimal for iterative generation processes where model uncertainty varies dynamically. We introduce Adaptive Classifier-Free Guidance (A-CFG), a novel method that tailors the unconditional input by leveraging the model's instantaneous predictive confidence. At each step of an iterative (masked) diffusion language model, A-CFG identifies tokens in the currently generated sequence for which the model exhibits low confidence. These tokens are temporarily re-masked to create a dynamic, localized unconditional input. This focuses CFG's corrective influence precisely on areas of ambiguity, leading to more effective guidance. We integrate A-CFG into a state-of-the-art masked diffusion language model and demonstrate its efficacy. Experiments on diverse language generation benchmarks show that A-CFG yields substantial improvements over standard CFG, achieving, for instance, a 3.9 point gain on GPQA. Our work highlights the benefit of dynamically adapting guidance mechanisms to model uncertainty in iterative generation.

Recent advancements in generative modeling have made it possible to generate high-quality content from context information, but a key question remains: how to teach models to know when to generate content? To answer this question, this study proposes a novel event generative model that draws its statistical intuition from marked temporal point processes, and offers a clean, flexible, and computationally efficient solution for a wide range of applications involving multi-dimensional marks. We aim to capture the distribution of the point process without explicitly specifying the conditional intensity or probability density. Instead, we use a conditional generator that takes the history of events as input and generates the high-quality subsequent event that is likely to occur given the prior observations. The proposed framework offers a host of benefits, including exceptional efficiency in learning the model and generating samples, as well as considerable representational power to capture intricate dynamics in multi- or even high-dimensional event space. Our numerical results demonstrate superior performance compared to other state-of-the-art baselines.

We propose using Normalizing Flows as a trainable kernel within the molecular dynamics update of Hamiltonian Monte Carlo (HMC). By learning (invertible) transformations that simplify our dynamics, we can outperform traditional methods at generating independent configurations. We show that, using a carefully constructed network architecture, our approach can be easily scaled to large lattice volumes with minimal retraining effort. The source code for our implementation is publicly available online at https://github.com/nftqcd/fthmc.

Simulations of turbulent flows in 3D are one of the most expensive simulations in computational fluid dynamics (CFD). Many works have been written on surrogate models to replace numerical solvers for fluid flows with faster, learned, autoregressive models. However, the intricacies of turbulence in three dimensions necessitate training these models with very small time steps, while generating realistic flow states requires either long roll-outs with many steps and significant error accumulation or starting from a known, realistic flow state - something we aimed to avoid in the first place. Instead, we propose to approach turbulent flow simulation as a generative task directly learning the manifold of all possible turbulent flow states without relying on any initial flow state. For our experiments, we introduce a challenging 3D turbulence dataset of high-resolution flows and detailed vortex structures caused by various objects and derive two novel sample evaluation metrics for turbulent flows. On this dataset, we show that our generative model captures the distribution of turbulent flows caused by unseen objects and generates high-quality, realistic samples amenable for downstream applications without access to any initial state.