ICLR 2025 论文列表

Recent advances in protein backbone generation have achieved promising results under structural, functional, or physical constraints. However, existing methods lack the flexibility for precise topology control, limiting navigation of the backbone space. We present $\textbf{ProtPainter}$, a diffusion-based approach for generating protein backbones conditioned on 3D curves. ProtPainter follows a two-stage process: curve-based sketching and sketch-guided backbone generation. For the first stage, we propose $\textbf{CurveEncoder}$, which predicts secondary structure annotations from a curve to parametrize sketch generation. For the second stage, the sketch guides the generative process in Denoising Diffusion Probabilistic Modeling (DDPM) to generate backbones. During the process, we further introduce a fusion scheduling scheme, Helix-Gating, to control the scaling factors. To evaluate, we propose the first benchmark for topology-conditioned protein generation, introducing Protein Restoration Task and a new metric, self-consistency Topology Fitness (scTF). Experiments demonstrate ProtPainter's ability to generate topology-fit (scTF $>$ 0.8) and designable (scTM $>$ 0.5) backbones, with drawing and dragging tasks showcasing its flexibility and versatility.

Masked autoencoders (MAEs) represent a prominent self-supervised learning paradigm in computer vision. Despite their empirical success, the underlying mechanisms of MAEs remain insufficiently understood. Recent studies have attempted to elucidate the functioning of MAEs through contrastive learning and feature representation analysis, yet these approaches often provide only implicit insights. In this paper, we propose a new perspective for understanding MAEs by leveraging the information bottleneck principle in information theory. Our theoretical analyses reveal that optimizing the latent features to balance relevant and irrelevant information is key to improving MAE performance. Building upon our proofs, we introduce MI-MAE, a novel method that optimizes MAEs through mutual information maximization and minimization. By enhancing latent features to retain maximal relevant information between them and the output, and minimizing irrelevant information between them and the input, our approach achieves better performance. Extensive experiments on standard benchmarks show that MI-MAE significantly outperforms MAE models in tasks such as image classification, object detection, and semantic segmentation. Our findings validate the theoretical framework and highlight the practical advantages of applying the information bottleneck principle to MAEs, offering deeper insights for developing more powerful self-supervised learning models.

While message passing neural networks (MPNNs) have convincing success in a range of applications, they exhibit limitations such as the oversquashing problem and their inability to capture long-range interactions. Augmenting MPNNs with a virtual node (VN) removes the locality constraint of the layer aggregation and has been found to improve performance on a range of benchmarks. We provide a comprehensive theoretical analysis of the role of VNs and benefits thereof, through the lenses of oversquashing and sensitivity analysis. First, we characterize, precisely, how the improvement afforded by VNs on the mixing abilities of the network and hence in mitigating oversquashing, depends on the underlying topology. We then highlight that, unlike Graph-Transformers (GTs), classical instantiations of the VN are often constrained to assign uniform importance to different nodes. Consequently, we propose a variant of VN with the same computational complexity, which can have different sensitivity to nodes based on the graph structure. We show that this is an extremely effective and computationally efficient baseline for graph-level tasks.

We consider a class of conditional forward-backward diffusion models for conditional generative modeling, that is, generating new data given a covariate (or control variable). To formally study the theoretical properties of these conditional generative models, we adopt a statistical framework of distribution regression to characterize the large sample properties of the conditional distribution estimators induced by these conditional forward-backward diffusion models. Here, the conditional distribution of data is assumed to smoothly change over the covariate. In particular, our derived convergence rate is minimax-optimal under the total variation metric within the regimes covered by the existing literature. Additionally, we extend our theory by allowing both the data and the covariate variable to potentially admit a low-dimensional manifold structure. In this scenario, we demonstrate that the conditional forward-backward diffusion model can adapt to both manifold structures, meaning that the derived estimation error bound (under the Wasserstein metric) depends only on the intrinsic dimensionalities of the data and the covariate.

Statistical watermarking techniques are well-established for sequentially decoded language models (LMs). However, these techniques cannot be directly applied to order-agnostic LMs, as the tokens in order-agnostic LMs are not generated sequentially. In this work, we introduce PATTERN-MARK, a pattern-based watermarking framework specifically designed for order-agnostic LMs. We develop a Markov-chain-based watermark generator that produces watermark key sequences with high-frequency key patterns. Correspondingly, we propose a statistical pattern-based detection algorithm that recovers the key sequence during detection and conducts statistical tests based on the count of high-frequency patterns. Our extensive evaluations on order-agnostic LMs, such as ProteinMPNN and CMLM, demonstrate PATTERN-MARK’s enhanced detection efficiency, generation quality, and robustness, positioning it as a superior watermarking technique for order-agnostic LMs.

Current approaches to genomic sequence modeling often struggle to align the inductive biases of machine learning models with the evolutionarily-informed structure of biological systems. To this end, we formulate a novel application of hyperbolic CNNs that exploits this structure, enabling more expressive DNA sequence representations. Our strategy circumvents the need for explicit phylogenetic mapping while discerning key properties of sequences pertaining to core functional and regulatory behavior. Across 37 out of 42 genome interpretation benchmark datasets, our hyperbolic models outperform their Euclidean equivalents. Notably, our approach even surpasses state-of-the-art performance on seven GUE benchmark datasets, consistently outperforming many DNA language models while using orders of magnitude fewer parameters and avoiding pretraining. Our results include a novel set of benchmark datasets---the Transposable Elements Benchmark---which explores a major but understudied component of the genome with deep evolutionary significance. We further motivate our work by exploring how our hyperbolic models recognize genomic signal under various data-generating conditions and by constructing an empirical method for interpreting the hyperbolicity of dataset embeddings. Throughout these assessments, we find persistent evidence highlighting the potential of our hyperbolic framework as a robust paradigm for genome representation learning. Our code and benchmark datasets are available at https://github.com/rrkhan/HGE.

Understanding neural representations will help open the black box of neural networks and advance our scientific understanding of modern AI systems. However, how complex, structured, and transferable representations emerge in modern neural networks has remained a mystery. Building on previous results, we propose the Canonical Representation Hypothesis (CRH), which posits a set of six alignment relations to universally govern the formation of representations in most hidden layers of a neural network. Under the CRH, the latent representations (R), weights (W), and neuron gradients (G) become mutually aligned during training. This alignment implies that neural networks naturally learn compact representations, where neurons and weights are invariant to task-irrelevant transformations. We then show that the breaking of CRH leads to the emergence of reciprocal power-law relations between R, W, and G, which we refer to as the Polynomial Alignment Hypothesis (PAH). We present a minimal-assumption theory proving that the balance between gradient noise and regularization is crucial for the emergence of the canonical representation. The CRH and PAH lead to an exciting possibility of unifying major key deep learning phenomena, including neural collapse and the neural feature ansatz, in a single framework.

Recent advances in language model (LM) agents and function calling have enabled autonomous, feedback-driven systems to solve problems across various digital domains. To better understand the unique limitations of LM agents, we introduce RefactorBench, a benchmark consisting of 100 large handcrafted multi-file refactoring tasks in popular open-source repositories. Solving tasks within RefactorBench requires thorough exploration of dependencies across multiple files and strong adherence to relevant instructions. Every task is defined by 3 natural language instructions of varying specificity and is mutually exclusive, allowing for the creation of longer combined tasks on the same repository. Baselines on RefactorBench reveal that current LM agents struggle with simple compositional tasks, solving only 22\% of tasks with base instructions, in contrast to a human developer with short time constraints solving 87\%. Through trajectory analysis, we identify various unique failure modes of LM agents, and further explore the failure mode of tracking past actions. By adapting a baseline agent to condition on representations of state, we achieve a 43.9\% improvement in solving RefactorBench tasks. We further extend our state-aware approach to encompass entire digital environments and outline potential directions for future research. RefactorBench aims to support the study of LM agents by providing a set of real-world, multi-hop tasks within the realm of code.

We develop a new method for generating prediction sets that combines the flexibility of conformal methods with an estimate of the conditional distribution $\textup{P}_{Y \mid X}$. Existing methods, such as conformalized quantile regression and probabilistic conformal prediction, usually provide only a marginal coverage guarantee. In contrast, our approach extends these frameworks to achieve approximately conditional coverage, which is crucial for many practical applications. Our prediction sets adapt to the behavior of the predictive distribution, making them effective even under high heteroscedasticity. While exact conditional guarantees are infeasible without assumptions on the underlying data distribution, we derive non-asymptotic bounds that depend on the total variation distance of the conditional distribution and its estimate. Using extensive simulations, we show that our method consistently outperforms existing approaches in terms of conditional coverage, leading to more reliable statistical inference in a variety of applications.

Large Language Models (LLMs) are increasingly being used in workflows involving generating content to be consumed by humans (*e.g.,* marketing) and also in directly interacting with humans (*e.g.,* through chatbots). The development of such systems that are capable of generating verifiably persuasive messages presents both opportunities and challenges for society. On the one hand, such systems could positively impact domains like advertising and social good, such as addressing drug addiction, and on the other, they could be misused for spreading misinformation and shaping political opinions. To channel LLMs' impact on society, we need to develop systems to measure and benchmark their persuasiveness. With this motivation, we introduce **PersuasionBench** and **PersuasionArena**, the first large-scale benchmark and arena containing a battery of tasks to automatically measure the simulative and generative persuasion abilities of large language models. We introduce **transsuasion** (trans = carrying across, suasion = the act of persuading), a novel task of transforming non-persuasive language into persuasive content while preserving other factors determining persuasiveness (sender, receiver, time, and channel). Our findings indicate that the simulative persuasion capabilities of LLMs are barely above random; however, their generative persuasion capabilities are much better. For instance, GPT-4o loses only 36% of the time when playing against the best human persuader. Further, we find that LLMs' persuasiveness correlates positively with model size, but smaller models can also be made to have a higher persuasiveness than much larger models. Notably, targeted training using synthetic and natural datasets significantly enhances smaller models' persuasive capabilities, challenging scale-dependent assumptions. Our findings carry key implications for both model developers and policymakers. For instance, while the EU AI Act and California's SB-1047 aim to regulate AI models based on the number of floating point operations, we demonstrate that simple metrics like this alone fail to capture the full scope of AI's societal impact. We invite the community to explore and contribute to PersuasionArena and PersuasionBench, available at [behavior-in-the-wild.github.io/measure-persuasion](https://behavior-in-the-wild.github.io/measure-persuasion), to advance our understanding of AI-driven persuasion and its societal implications.

Optimizing the performance of many objectives (instantiated by tasks or clients) jointly with a few Pareto stationary solutions (models) is critical in machine learning. However, previous multi-objective optimization methods often focus on a few objectives and cannot scale to many objectives that outnumber the solutions, leading to either subpar performance or ignored objectives. We introduce ''Many-objective multi-solution Transport (MosT)'', a framework that finds multiple diverse solutions in the Pareto front of many objectives. Our insight is to seek multiple solutions, each performing as a domain expert and focusing on a specific subset of objectives while collectively covering all of them. MosT formulates the problem as a bi-level optimization of weighted objectives for each solution, where the weights are defined by an optimal transport between objectives and solutions. Our algorithm ensures convergence to Pareto stationary solutions for complementary subsets of objectives. On a range of applications in federated learning, multi-task learning, and mixture-of-prompt learning for LLMs, MosT distinctly outperforms strong baselines, delivering high-quality, diverse solutions that profile the entire Pareto frontier, thus ensuring balanced trade-offs across many objectives.

Symbolic regression is a key task in machine learning, aiming to discover mathematical expressions that best describe a dataset. While deep learning has increased interest in using neural networks for symbolic regression, many existing approaches rely on pre-trained models. These models require significant computational resources and struggle with regression tasks involving unseen functions and variables. A pre-training-free paradigm is needed to better integrate with search-based symbolic regression algorithms. To address these limitations, we propose a novel framework for symbolic regression that integrates evolutionary feature construction with a neural network, without the need for pre-training. Our approach adaptively generates symbolic trees that align with the desired semantics in real-time using a language model trained via online supervised learning, providing effective building blocks for feature construction. To mitigate hallucinations from the language model, we design a retrieval-augmented generation mechanism that explicitly leverages searched symbolic expressions. Additionally, we introduce a scale-invariant data augmentation technique that further improves the robustness and generalization of the model. Experimental results demonstrate that our framework achieves state-of-the-art accuracy across 25 regression algorithms and 120 regression tasks.

Recent advances in deep learning have inspired numerous works on data-driven solutions to partial differential equation (PDE) problems. These neural PDE solvers can often be much faster than their numerical counterparts; however, each presents its unique limitations and generally balances training cost, numerical accuracy, and ease of applicability to different problem setups. To address these limitations, we introduce several methods to apply latent diffusion models to physics simulation. Firstly, we introduce a mesh autoencoder to compress arbitrarily discretized PDE data, allowing for efficient diffusion training across various physics. Furthermore, we investigate full spatiotemporal solution generation to mitigate autoregressive error accumulation. Lastly, we investigate conditioning on initial physical quantities, as well as conditioning solely on a text prompt to introduce text2PDE generation. We show that language can be a compact, interpretable, and accurate modality for generating physics simulations, paving the way for more usable and accessible PDE solvers. Through experiments on both uniform and structured grids, we show that the proposed approach is competitive with current neural PDE solvers in both accuracy and efficiency, with promising scaling behavior up to $\sim$3 billion parameters. By introducing a scalable, accurate, and usable physics simulator, we hope to bring neural PDE solvers closer to practical use.

Motivated by applications in chemistry and other sciences, we study the expressive power of message-passing neural networks for geometric graphs, whose node features correspond to 3-dimensional positions. Recent work has shown that such models can separate generic pairs of non-isomorphic geometric graphs, though they may fail to separate some rare and complicated instances. However, these results assume a fully connected graph, where each node possesses complete knowledge of all other nodes. In contrast, often, in application, every node only possesses knowledge of a small number of nearest neighbors. This paper shows that generic pairs of non-isomorphic geometric graphs can be separated by message-passing networks with rotation equivariant features as long as the underlying graph is connected. When only invariant intermediate features are allowed, generic separation is guaranteed for generically globally rigid graphs. We introduce a simple architecture, EGENNET, which achieves our theoretical guarantees and compares favorably with alternative architecture on synthetic and chemical benchmarks

Accurate interpretation and visualization of human instructions are crucial for text-to-image (T2I) synthesis. However, current models struggle to capture semantic variations from word order changes, and existing evaluations, relying on indirect metrics like text-image similarity, fail to reliably assess these challenges. This often obscures poor performance on complex or uncommon linguistic patterns by the focus on frequent word combinations. To address these deficiencies, we propose a novel metric called SemVarEffect and a benchmark named SemVarBench, designed to evaluate the causality between semantic variations in inputs and outputs in T2I synthesis. Semantic variations are achieved through two types of linguistic permutations, while avoiding easily predictable literal variations. Experiments reveal that the CogView-3-Plus and Ideogram 2 performed the best, achieving a score of 0.2/1. Semantic variations in object relations are less understood than attributes, scoring 0.07/1 compared to 0.17-0.19/1. We found that cross-modal alignment in UNet or Transformers plays a crucial role in handling semantic variations, a factor previously overlooked by a focus on textual encoders. Our work establishes an effective evaluation framework that advances the T2I synthesis community's exploration of human instruction understanding. Our benchmark and code are available at https://github.com/zhuxiangru/SemVarBench.

Reasoning about Actions and Change (RAC) has historically played a pivotal role in solving foundational AI problems, such as the frame problem. It has driven advancements in AI fields, such as non-monotonic and commonsense reasoning. RAC remains crucial for AI systems that operate in dynamic environments, engage in interactive scenarios, or rely on commonsense reasoning. Despite substantial advances made by Large Language Models (LLMs) in various AI domains, their performance in RAC remains underexplored. To address this gap, we introduce a new diagnostic benchmark, $\textbf{ActionReasoningBench}$, which encompasses 8 domains and includes questions for up to 19 action sequences. This benchmark rigorously evaluates LLMs across six key RAC dimensions: $\textit{Fluent Tracking}$, $\textit{State Tracking}$, $\textit{Action Executability}$, $\textit{Effects of Actions}$, $\textit{Numerical RAC}$, and $\textit{Composite Questions}$. LLMs demonstrate average accuracy rates of 73.55%, 65.63%, 58.73%, and 62.38% on the former four dimensions, which are frequently discussed in RAC literature. However, the performance on the latter two dimensions, which introduce complex and novel reasoning questions, the average performance of LLMs is lowered to 33.16% and 51.19%, respectively, reflecting a 17.9% performance decline. We also introduce new ramification constraints to capture the indirect effects of actions, providing deeper insights into RAC challenges. Our evaluation of state-of-the-art LLMs, including both open-source and commercial models, reveals challenges across all RAC dimensions, particularly in handling ramifications, with GPT-4o failing to solve any question and o1-preview achieving a score of only 18.4%.

A significant challenge in machine learning, particularly in noisy and low-data environments, lies in effectively incorporating inductive biases to enhance data efficiency and robustness. Despite the success of informed machine learning methods, designing algorithms with explicit inductive biases remains largely a manual process. In this work, we explore how prior knowledge represented in its native formats, e.g. in natural language, can be integrated into machine learning models in an automated manner. Inspired by the learning to learn principles of meta-learning, we consider the approach of learning to integrate knowledge via conditional meta-learning, a paradigm we refer to as informed meta-learning. We introduce and motivate theoretically the principles of informed meta-learning enabling automated and controllable inductive bias selection. To illustrate our claims, we implement an instantiation of informed meta-learning--the Informed Neural Process, and empirically demonstrate the potential benefits and limitations of informed meta-learning in improving data efficiency and generalisation.

The task of Visual Place Recognition (VPR) is to predict the location of a query image from a database of geo-tagged images. Recent studies in VPR have highlighted the significant advantage of employing pre-trained foundation models like DINOv2 for the VPR task. However, these models are often deemed inadequate for VPR without further fine-tuning on VPR-specific data. In this paper, we present an effective approach to harness the potential of a foundation model for VPR. We show that features extracted from self-attention layers can act as a powerful re-ranker for VPR, even in a zero-shot setting. Our method not only outperforms previous zero-shot approaches but also introduces results competitive with several supervised methods. We then show that a single-stage approach utilizing internal ViT layers for pooling can produce global features that achieve state-of-the-art performance, with impressive feature compactness down to 128D. Moreover, integrating our local foundation features for re-ranking further widens this performance gap. Our method also demonstrates exceptional robustness and generalization, setting new state-of-the-art performance, while handling challenging conditions such as occlusion, day-night transitions, and seasonal variations.

Recent efforts in fine-tuning language models often rely on automatic data selection, commonly using Nearest Neighbors retrieval from large datasets. However, we theoretically show that this approach tends to select redundant data, limiting its effectiveness or even hurting performance. To address this, we introduce SIFT, a data selection algorithm designed to reduce uncertainty about the model's response given a prompt, which unifies ideas from retrieval and active learning. Whereas Nearest Neighbor retrieval typically fails in the presence of information duplication, SIFT accounts for information duplication and optimizes the overall information gain of the selected examples. We focus our evaluations on fine-tuning at test-time for prompt-specific language modeling on the Pile dataset, and show that SIFT consistently outperforms Nearest Neighbor retrieval, with minimal computational overhead. Moreover, we show that our uncertainty estimates can predict the performance gain of test-time fine-tuning, and use this to develop an adaptive algorithm that invests test-time compute proportional to realized performance gains. We provide the `activeft` (Active Fine-Tuning) library which can be used as a drop-in replacement for Nearest Neighbor retrieval.