ICLR 2025 Papers

Efficient physics simulations are essential for numerous applications, ranging from realistic cloth animations in video games, to analyzing pollutant dispersion in environmental sciences, to calculating vehicle drag coefficients in engineering applications. Unfortunately, analytical solutions to the underlying physical equations are rarely available, and numerical solutions are computationally demanding. Latest developments in the field of physics-based Deep Learning have led to promising efficiency gains but still suffer from limited generalization capabilities across multiple different PDEs. Thus, in this work, we introduce **Metamizer**, a novel neural optimizer that iteratively solves a wide range of physical systems without retraining by minimizing a physics-based loss function. To this end, our approach leverages a scale-invariant architecture that enhances gradient descent updates to accelerate convergence. Since the neural network itself acts as an optimizer, training this neural optimizer falls into the category of meta-optimization approaches. We demonstrate that Metamizer achieves high accuracy across multiple PDEs after training on the Laplace, advection-diffusion and incompressible Navier-Stokes equation as well as on cloth simulations. Remarkably, the model also generalizes to PDEs that were not covered during training such as the Poisson, wave and Burgers equation.

Policy evaluation estimates the performance of a policy by (1) collecting data from the environment and (2) processing raw data into a meaningful estimate. Due to the sequential nature of reinforcement learning, any improper data-collecting policy or data-processing method substantially deteriorates the variance of evaluation results over long time steps. Thus, policy evaluation often suffers from large variance and requires massive data to achieve the desired accuracy. In this work, we design an optimal combination of data-collecting policy and data-processing baseline. Theoretically, we prove our doubly optimal policy evaluation method is unbiased and guaranteed to have lower variance than previously best-performing methods. Empirically, compared with previous works, we show our method reduces variance substantially and achieves superior empirical performance.

Proteins are essential macromolecules defined by their amino acid sequences, which determine their three-dimensional structures and, consequently, their functions in all living organisms. Therefore, generative protein modeling necessitates a multimodal approach to simultaneously model, understand, and generate both sequences and structures. However, existing methods typically use separate models for each modality, limiting their ability to capture the intricate relationships between sequence and structure. This results in suboptimal performance in tasks that requires joint understanding and generation of both modalities. In this paper, we introduce DPLM-2, a multimodal protein foundation model that extends discrete diffusion protein language model (DPLM) to accommodate both sequences and structures. To enable structural learning with the language model, 3D coordinates are converted to discrete tokens using a lookup-free quantization-based tokenizer. By training on both experimental and high-quality synthetic structures, DPLM-2 learns the joint distribution of sequence and structure, as well as their marginals and conditionals. We also implement an efficient warm-up strategy to exploit the connection between large-scale evolutionary data and structural inductive biases from pre-trained sequence-based protein language models. Empirical evaluation shows that DPLM-2 can simultaneously generate highly compatible amino acid sequences and their corresponding 3D structures eliminating the need for a two-stage generation approach. Moreover, DPLM-2 demonstrates competitive performance in various conditional generation tasks, including folding, inverse folding, and scaffolding with multimodal motif inputs.

Problems in fields such as healthcare, robotics, and finance requires reasoning about the value both of what decision or action to take and when to take it. The prevailing hope is that artificial intelligence will support such decisions by estimating the causal effect of policies such as how to treat patients or how to allocate resources over time. However, existing methods for estimating the effect of a policy struggle with \emph{irregular time}. They either discretize time, or disregard the effect of timing policies. We present a new deep-Q algorithm that estimates the effect of both when and what to do called Earliest Disagreement Q-Evaluation (EDQ). EDQ makes use of recursion for the Q-function that is compatible with flexible sequence models, such as transformers. EDQ provides accurate estimates under standard assumptions. We validate the approach through experiments on survival time and tumor growth tasks.

Machine unlearning algorithms, designed for selective removal of training data from models, have emerged as a promising approach to growing privacy concerns. In this work, we expose a critical yet underexplored vulnerability in the deployment of unlearning systems: the assumption that the data requested for removal is always part of the original training set. We present a threat model where an attacker can degrade model accuracy by submitting adversarial unlearning requests for data \textit{not} present in the training set. We propose white-box and black-box attack algorithms and evaluate them through a case study on image classification tasks using the CIFAR-10 and ImageNet datasets, targeting a family of widely used unlearning methods. Our results show extremely poor test accuracy following the attack—3.6% on CIFAR-10 and 0.4% on ImageNet for white-box attacks, and 8.5% on CIFAR-10 and 1.3% on ImageNet for black-box attacks. Additionally, we evaluate various verification mechanisms to detect the legitimacy of unlearning requests and reveal the challenges in verification, as most of the mechanisms fail to detect stealthy attacks without severely impairing their ability to process valid requests. These findings underscore the urgent need for research on more robust request verification methods and unlearning protocols, should the deployment of machine unlearning systems become more prevalent in the future.

Landmark universal function approximation results for neural networks with trained weights and biases provided the impetus for the ubiquitous use of neural networks as learning models in neuroscience and Artificial Intelligence (AI). Recent work has extended these results to networks in which a smaller subset of weights (e.g., output weights) are tuned, leaving other parameters random. However, it remains an open question whether universal approximation holds when only biases are learned, despite evidence from neuroscience and AI that biases significantly shape neural responses. The current paper answers this question. We provide theoretical and numerical evidence demonstrating that feedforward neural networks with fixed random weights can approximate any continuous function on compact sets. We further show an analogous result for the approximation of dynamical systems with recurrent neural networks. Our findings are relevant to neuroscience, where they demonstrate the potential for behaviourally relevant changes in dynamics without modifying synaptic weights, as well as for AI, where they shed light on recent fine-tuning methods for large language models, like bias and prefix-based approaches.

Diffusion models have demonstrated significant potential for generating high-quality images, audio, and videos. However, their iterative inference process entails substantial computational costs, limiting practical applications. Recently, researchers have introduced accelerated sampling methods that enable diffusion models to generate samples with far fewer timesteps than those used during training. Nonetheless, as the number of sampling steps decreases, the prediction errors significantly degrade the quality of generated outputs. Additionally, the exposure bias in diffusion models further amplifies these errors. To address these challenges, we leverage a manifold hypothesis to explore the exposure bias problem in depth. Based on this geometric perspective, we propose a manifold constraint that effectively reduces exposure bias during accelerated sampling of diffusion models. Notably, our method involves no additional training and requires only minimal hyperparameter tuning. Extensive experiments demonstrate the effectiveness of our approach, achieving a FID score of 15.60 with 10-step SDXL on MS-COCO, surpassing the baseline by a reduction of 2.57 in FID.

Multi-goal long-horizon problems are prevalent in real-world applications. The additional goal space introduced by multi-goal problems intensifies the spatial complexity of exploration; meanwhile, the long interaction sequences in long-horizon problems exacerbate the temporal complexity of exploration. Addressing the great exploration challenge posed by multi-goal long-horizon problems depends not only on the design of algorithms but also on the design of environments and the availability of demonstrations to assist in training. To facilitate the above research, we propose a multi-goal long-horizon Reinforcement Learning (RL) environment based on realistic fixed-wing UAV's velocity vector control, named VVC-Gym, and generate multiple demonstration sets of various quality. Through experimentation, we analyze the impact of different environment designs on training, assess the quantity and quality of demonstrations and their influence on training, and assess the effectiveness of various RL algorithms, providing baselines on VVC-Gym and its corresponding demonstrations. The results suggest that VVC-Gym is suitable for studying: (1) the influence of environment designs on addressing multi-goal long-horizon problems with RL. (2) the assistance that demonstrations can provide in overcoming the exploration challenges of multi-goal long-horizon problems. (3) the RL algorithm designs with the least possible impact from environment designs on the efficiency and effectiveness of training.

Knowledge editing aims to update outdated information in Large Language Models (LLMs). A representative line of study is locate-then-edit methods, which typically employ causal tracing to identify the modules responsible for recalling factual knowledge about entities. However, we find these methods are often sensitive only to changes in the subject entity, leaving them less effective at adapting to changes in relations. This limitation results in poor editing locality, which can lead to the persistence of irrelevant or inaccurate facts, ultimately compromising the reliability of LLMs. We believe this issue arises from the insufficient precision of knowledge localization. To address this, we propose a Fine-grained Neuron-level Knowledge Editing (FiNE) method that enhances editing locality without affecting overall success rates. By precisely identifying and modifying specific neurons within feed-forward networks, FiNE significantly improves knowledge localization and editing. Quantitative experiments demonstrate that FiNE efficiently achieves better overall performance compared to existing techniques, providing new insights into the localization and modification of knowledge within LLMs.

Graph condensation has emerged as a promising avenue to enable scalable training of GNNs by compressing the training dataset while preserving essential graph characteristics. Our study uncovers significant shortcomings in current graph condensation techniques. First, the majority of the algorithms paradoxically require training on the full dataset to perform condensation. Second, due to their gradient-emulating approach, these methods require fresh condensation for any change in hyperparameters or GNN architecture, limiting their flexibility and reusability. To address these challenges, we present Bonsai, a novel graph condensation method empowered by the observation that *computation trees* form the fundamental processing units of message-passing GNNs. Bonsai condenses datasets by encoding a careful selection of *exemplar* trees that maximize the representation of all computation trees in the training set. This unique approach imparts Bonsai as the first linear-time, model-agnostic graph condensation algorithm for node classification that outperforms existing baselines across $7$ real-world datasets on accuracy, while being $22$ times faster on average. Bonsai is grounded in rigorous mathematical guarantees on the adopted approximation strategies, making it robust to GNN architectures, datasets, and parameters.

Understanding complex three-dimensional (3D) structures of graphs is essential for accurately modeling various properties, yet many existing approaches struggle with fully capturing the intricate spatial relationships and symmetries inherent in such systems, especially in large-scale, dynamic molecular datasets. These methods often must balance trade-offs between expressiveness and computational efficiency, limiting their scalability. To address this gap, we propose a novel Geometric Tensor Network (GotenNet) that effectively models the geometric intricacies of 3D graphs while ensuring strict equivariance under the Euclidean group E(3). Our approach directly tackles the expressiveness-efficiency trade-off by leveraging effective geometric tensor representations without relying on irreducible representations or Clebsch-Gordan transforms, thereby reducing computational overhead. We introduce a unified structural embedding, incorporating geometry-aware tensor attention and hierarchical tensor refinement that iteratively updates edge representations through inner product operations on high-degree steerable features, allowing for flexible and efficient representations for various tasks. We evaluated models on QM9, rMD17, MD22, and Molecule3D datasets, where the proposed model consistently outperforms state-of-the-art methods in both scalar and high-degree property predictions, demonstrating exceptional robustness across diverse datasets, and establishes GotenNet as a versatile and scalable framework for 3D equivariant Graph Neural Networks.

Predictive coding has been established as a promising neuroscientific theory to describe the mechanism of information processing in the retina or cortex. This theory hypothesises that cortex predicts sensory inputs at various levels of abstraction to minimise prediction errors. Inspired by predictive coding, Chen et al. (2024) proposed another theory, temporal prediction hypothesis, to claim that sequence memory residing in hippocampus has emerged through predicting input signals from the past sensory inputs. Specifically, they supposed that the CA3 predictor in hippocampus creates synaptic delay between input signals, which is compensated by the following CA1 predictor. Though recorded neural activities were replicated based on the temporal prediction hypothesis, its validity has not been fully explored. In this work, we aim to explore the temporal prediction hypothesis from the perspective of self-supervised learning (SSL). Specifically, we focus on non-contrastive learning, which generates two augmented views of an input image and predicts one from another. Non-contrastive learning is intimately related to the temporal prediction hypothesis because the synaptic delay is implicitly created by StopGradient. Building upon a popular non-contrastive learner, SimSiam, we propose PhiNet, an extension of SimSiam to have two predictors explicitly corresponding to the CA3 and CA1, respectively. Through studying the PhiNet model, we discover two findings. First, meaningful data representations emerge in PhiNet more stably than in SimSiam. This is initially supported by our learning dynamics analysis: PhiNet is more robust to the representational collapse. Second, PhiNet adapts more quickly to newly incoming patterns in online and continual learning scenarios. For practitioners, we additionally propose an extension called X-PhiNet integrated with a momentum encoder, excelling in continual learning. All in all, our work reveals that the temporal prediction hypothesis is a reasonable model in terms of the robustness and adaptivity.

Deep learning models often struggle with generalization when deploying on real-world data, due to the common distributional shift to the training data. Test-time adaptation (TTA) is an emerging scheme used at inference time to address this issue. In TTA, models are adapted online at the same time when making predictions to test data. Neighbor-based approaches have gained attention recently, where prototype embeddings provide location information to alleviate the feature shift between training and testing data. However, due to their inherit limitation of simplicity, they often struggle to learn useful patterns and encounter performance degradation. To confront this challenge, we study the TTA problem from a geometric point of view. We first reveal that the underlying structure of neighbor-based methods aligns with the Voronoi Diagram, a classical computational geometry model for space partitioning. Building on this observation, we propose the Test-Time adjustment by Voronoi Diagram guidance (TTVD), a novel framework that leverages the benefits of this geometric property. Specifically, we explore two key structures: 1) Cluster-induced Voronoi Diagram (CIVD): This integrates the joint contribution of self-supervision and entropy-based methods to provide richer information. 2) Power Diagram (PD): A generalized version of the Voronoi Diagram that refines partitions by assigning weights to each Voronoi cell. Our experiments under rigid, peer-reviewed settings on CIFAR-10-C, CIFAR-100-C, ImageNet-C, and ImageNet-R shows that TTVD achieves remarkable improvements compared to state-of-the-art methods. Moreover, extensive experimental results also explore the effects of batch size and class imbalance, which are two scenarios commonly encountered in real-world applications. These analyses further validate the robustness and adaptability of our proposed framework.

Deep learning methods incorporate PDE residuals as the loss function for solving Fokker-Planck equations, and usually impose the proper normalization condition to avoid a trivial solution. However, soft constraints require careful balancing of multi-objective loss functions, and specific network architectures may limit representation capacity under hard constraints. In this paper, we propose a novel framework: Fokker-Planck neural network (FPNN) that adopts a score PDE loss to decouple the score learning and the density normalization into two stages. Our method allows free-form network architectures to model the unnormalized density and strictly satisfy normalization constraints by post-processing. We demonstrate the effectiveness on various high-dimensional steady-state Fokker-Planck (SFP) equations, achieving superior accuracy and over a 20$\times$ speedup compared to state-of-the-art methods. Without any labeled data, FPNNs achieve the mean absolute percentage error (MAPE) of 11.36%, 13.87% and 12.72% for 4D Ring, 6D Unimodal and 6D Multi-modal problems respectively, requiring only 256, 980, and 980 parameters. Experimental results highlights the potential as a universal fast solver for handling more than 20-dimensional SFP equations, with great gains in efficiency, accuracy, memory and computational resource usage.

Subgraph matching is vital in knowledge graph (KG) question answering, molecule design, scene graph, code and circuit search, etc. Neural methods have shown promising results for subgraph matching. Our study of recent systems suggests refactoring them into a unified design space for graph matching networks. Existing methods occupy only a few isolated patches in this space, which remains largely uncharted. We undertake the first comprehensive exploration of this space, featuring such axes as attention-based vs. soft permutation-based interaction between query and corpus graphs, aligning nodes vs. edges, and the form of the final scoring network that integrates neural representations of the graphs. Our extensive experiments reveal that judicious and hitherto-unexplored combinations of choices in this space lead to large performance benefits. Beyond better performance, our study uncovers valuable insights and establishes general design principles for neural graph representation and interaction, which may be of wider interest.

The probabilistic forecasting of time series is a well-recognized challenge, particularly in disentangling correlations among interacting time series and addressing the complexities of distribution modeling. By treating time series as temporal dynamics, we introduce **KooNPro**, a novel probabilistic time series forecasting model that combines variance-aware deep **Koo**pman model with **N**eural **Pro**cess. KooNPro introduces a variance-aware continuous spectrum using Gaussian distributions to capture complex temporal dynamics with improved stability. It further integrates the Neural Process to capture fine dynamics, enabling enhanced dynamics capture and prediction. Extensive experiments on nine real-world datasets demonstrate that KooNPro consistently outperforms state-of-the-art baselines. Ablation studies highlight the importance of the Neural Process component and explore the impact of key hyperparameters. Overall, KooNPro presents a promising novel approach for probabilistic time series forecasting.

Offline reinforcement learning (RL) has garnered significant attention for its ability to learn effective policies from pre-collected datasets without the need for further environmental interactions. While promising results have been demonstrated in single-agent settings, offline multi-agent reinforcement learning (MARL) presents additional challenges due to the large joint state-action space and the complexity of multi-agent behaviors. A key issue in offline RL is the distributional shift, which arises when the target policy being optimized deviates from the behavior policy that generated the data. This problem is exacerbated in MARL due to the interdependence between agents' local policies and the expansive joint state-action space. Prior approaches have primarily addressed this challenge by incorporating regularization in the space of either Q-functions or policies. In this work, we propose a novel type of regularizer in the space of stationary distributions to address the distributional shift more effectively. Our algorithm, ComaDICE, provides a principled framework for offline cooperative MARL to correct the stationary distribution of the global policy, which is then leveraged to derive local policies for individual agents. Through extensive experiments on the offline multi-agent MuJoCo and StarCraft II benchmarks, we demonstrate that ComaDICE achieves superior performance compared to state-of-the-art offline MARL methods across nearly all tasks.

Many time series classification tasks, where labels vary over time, are affected by label noise that also varies over time. Such noise can cause label quality to improve, worsen, or periodically change over time. We first propose and formalize temporal label noise, an unstudied problem for sequential classification of time series. In this setting, multiple labels are recorded over time while being corrupted by a time-dependent noise function. We first demonstrate the importance of modeling the temporal nature of the label noise function and how existing methods will consistently underperform. We then propose methods to train noise-tolerant classifiers by estimating the temporal label noise function directly from data. We show that our methods lead to state-of-the-art performance under diverse types of temporal label noise on real-world datasets.

In the field of equivariant networks, achieving affine equivariance, particularly for general group representations, has long been a challenge. In this paper, we propose the steerable EquivarLayer, a generalization of InvarLayer (Li et al., 2024), by building on the concept of equivariants beyond invariants. The steerable EquivarLayer supports affine equivariance with arbitrary input and output representations, marking the first model to incorporate steerability into networks for the affine group. To integrate it with canonicalization, a promising approach for making pre-trained models equivariant, we introduce a novel Det-Pooling module, expanding the applicability of EquivarLayer and the range of groups suitable for canonicalization. We conduct experiments on image classification tasks involving group transformations to validate the steerable EquivarLayer in the role of a canonicalization function, demonstrating its effectiveness over data augmentation.