ICML 2025 Papers

LongRoPE2 is a novel approach that extends the effective context window of pre-trained large language models (LLMs) to the target length, while preserving the performance on the original shorter context window. This is achieved by three contributions: (1) a hypothesis that insufficient training in higher RoPE dimensions contributes to the persistent out-of-distribution (OOD) issues observed in existing methods; (2) an effective RoPE rescaling algorithm that adopts evolutionary search guided by "needle-driven" perplexity to address the insufficient training problem; (3) a mixed context window training approach that fine-tunes model weights to adopt rescaled RoPE for long-context sequences while preserving the short-context performance with the original RoPE. Extensive experiments on LLaMA3-8B and Phi3-mini-3.8B across various benchmarks validate the hypothesis and demonstrate the effectiveness of LongRoPE2. Remarkably, LongRoPE2 extends LLaMA3-8B to achieve a 128K effective context length while retaining over 98.5% of short-context performance, using only 10B tokens -- 80x fewer than Meta's approach, which fails to reach the target effective context length.

Large Language Models (LLMs) have been observed to process non-human-readable text sequences, such as jailbreak prompts, often viewed as a bug for aligned LLMs. In this work, we present a systematic investigation challenging this perception, demonstrating that unnatural languages - strings that appear incomprehensible to humans but maintain semantic meanings for LLMs - contain latent features usable by models. Notably, unnatural languages possess latent features that can be generalized across different models and tasks during inference. Furthermore, models fine-tuned on unnatural versions of instruction datasets perform on-par with those trained on natural language, achieving \(49.71\) win rates in Length-controlled AlpacaEval 2.0 in average across various base models. In addition, through comprehensive analysis, we demonstrate that LLMs process unnatural languages by filtering noise and inferring contextual meaning from filtered words. Our code is publicly available at https://github.com/John-AI-Lab/Unnatural_Language.

With the rapid scaling of large language models (LLMs), structured pruning has become a widely used technique to learn efficient, smaller models from larger ones, delivering superior performance compared to training similarly sized models from scratch. In this paper, we move beyond the traditional static pruning approach of determining a fixed pruning mask for a model, and propose a dynamic approach to structured pruning. In our method, the pruning mask is input-dependent and adapts dynamically based on the information described in a user instruction. Our approach, termed "instruction-following pruning'', introduces a sparse mask predictor that takes the user instruction as input and dynamically selects the most relevant model parameters for the given task. To identify and activate effective parameters, we jointly optimize the sparse mask predictor and the LLM, leveraging both instruction-following data and the pre-training corpus. Experimental results demonstrate the effectiveness of our approach on a wide range of evaluation benchmarks. For example, our 3B activated model improves over the 3B dense model by 5-8 points of absolute margin on domains such as math and coding, and rivals the performance of a 9B model.

While the capabilities of generative foundational models have advanced rapidly in recent years, methods to prevent harmful and unsafe behaviors remain underdeveloped. Among the pressing challenges in AI safety, machine unlearning (MU) has become increasingly critical to meet upcoming safety regulations. Most existing MU approaches focus on altering the most significant parameters of the model. However, these methods often require fine-tuning substantial portions of the model, resulting in high computational costs and training instabilities, which are typically mitigated by access to the original training dataset. In this work, we address these limitations by leveraging Singular Value Decomposition (SVD) to create a compact, low-dimensional projection that enables the selective forgetting of specific data points. We propose Singular Value Decomposition for Efficient Machine Unlearning (SEMU), a novel approach designed to optimize MU in two key aspects. First, SEMU minimizes the number of model parameters that need to be modified, effectively removing unwanted knowledge while making only minimal changes to the model's weights. Second, SEMU eliminates the dependency on the original training dataset, preserving the model's previously acquired knowledge without additional data requirements. Extensive experiments demonstrate that SEMU achieves competitive performance while significantly improving efficiency in terms of both data usage and the number of modified parameters.

Conformal prediction is a popular framework of uncertainty quantification that constructs prediction sets with coverage guarantees. To uphold the exchangeability assumption, many conformal prediction methods necessitate an additional hold-out set for parameter tuning. Yet, the impact of violating this principle on coverage remains underexplored, making it ambiguous in practical applications. In this work, we empirically find that the tuning bias - the coverage gap introduced by leveraging the same dataset for tuning and calibration, is negligible for simple parameter tuning in many conformal prediction methods. In particular, we observe the scaling law of the tuning bias: this bias increases with parameter space complexity and decreases with calibration set size. Formally, we establish a theoretical framework to quantify the tuning bias and provide rigorous proof for the scaling law of the tuning bias by deriving its upper bound. In the end, we discuss how to reduce the tuning bias, guided by the theories we developed.

Proteolysis-targeting chimeras (PROTACs) are a groundbreaking technology for targeted protein degradation, but designing effective linkers that connect two molecular fragments to form a drug-candidate PROTAC molecule remains a key challenge. While diffusion models show promise in molecular generation, current diffusion models for PROTAC linker design are typically trained on small molecule datasets, introducing distribution mismatches in the chemical space between small molecules and target PROTACs. Direct fine-tuning on limited PROTAC datasets often results in overfitting and poor generalization. In this work, we propose DAD-PROTAC, a domain-adapted diffusion model for PROTAC linker design, which addresses this distribution mismatch in chemical space through density ratio estimation to bridge the gap between small-molecule and PROTAC domains. By decomposing the target score estimator into a pre-trained score function and a lightweight score correction term, DAD-PROTAC achieves efficient fine-tuning without full retraining. Experimental results demonstrate its superior ability to generate high-quality PROTAC linkers.

With the growing interest in embodied and spatial intelligence, accurately predicting trajectories in 3D environments has become increasingly critical. However, no datasets have been explicitly designed to study 3D trajectory prediction. To this end, we contribute a 3D motion trajectory (3DMoTraj) dataset collected from unmanned underwater vehicles (UUVs) operating in oceanic environments. Mathematically, trajectory prediction becomes significantly more complex when transitioning from 2D to 3D. To tackle this challenge, we analyze the prediction complexity of 3D trajectories and propose a new method consisting of two key components: decoupled trajectory prediction and correlated trajectory refinement. The former decouples inter-axis correlations, thereby reducing prediction complexity and generating coarse predictions. The latter refines the coarse predictions by modeling their inter-axis correlations. Extensive experiments show that our method significantly improves 3D trajectory prediction accuracy and outperforms state-of-the-art methods. Both the 3DMoTraj dataset and the method are available at https://github.com/zhouhao94/3DMoTraj.

In this work, we propose a new architecture-agnostic method for training idempotent neural networks. An idempotent operator satisfies $f(x) = f(f(x))$, meaning it can be applied iteratively with no effect beyond the first application. Some neural networks used in data transformation tasks, such as image generation and augmentation, can represent non-linear idempotent projections. Using methods from perturbation theory we derive the recurrence relation ${\mathbf{K}' \leftarrow 3\mathbf{K}^2 - 2\mathbf{K}^3}$ for iteratively projecting a real-valued matrix $\mathbf{K}$ onto the manifold of idempotent matrices. Our analysis shows that for linear, single-layer MLP networks this projection 1) has idempotent fixed points, and 2) is attracting only around idempotent points. We give an extension to non-linear networks by considering our approach as a substitution of the gradient for the canonical loss function, achieving an architecture-agnostic training scheme. We provide experimental results for MLP- and CNN-based architectures with significant improvement in idempotent error over the canonical gradient-based approach. Finally, we demonstrate practical applications of the method as we train a generative network successfully using only a simple reconstruction loss paired with our method.

Digital twins are models of real-world systems that can simulate their dynamics in response to potential actions. In complex settings, the state and action variables, and available data and knowledge relevant to a system can constantly change, requiring digital twins to continuously update with these changes to remain relevant. Current approaches struggle in this regard, as they require fixed, well-defined modelling environments, and they cannot adapt to novel variables without re-designs, or incorporate new information without re-training. To address this, we frame digital twinning as an in-context learning problem using large language models, enabling seamless updates to the twin at inference time. We develop CALM-DT, a Context-Adaptive Language Model-based Digital Twin that can accurately simulate across diverse state-action spaces using in-context learning alone by utilising fine-tuned encoders for sample retrieval. We empirically demonstrate CALM-DT's competitive performance with existing digital twin approaches, and its unique ability to adapt to changes in its modelling environment without parameter updates.

Heterogeneous Graph Neural Networks (HGNNs), have demonstrated excellent capabilities in processing heterogeneous information networks. Self-supervised learning on heterogeneous graphs, especially contrastive self-supervised strategy, shows great potential when there are no labels. However, this approach requires the use of carefully designed graph augmentation strategies and the selection of positive and negative samples. Determining the exact level of similarity between sample pairs is non-trivial.To solve this problem, we propose a novel self-supervised Heterogeneous graph neural network with Optimal Transport (HGOT) method which is designed to facilitate self-supervised learning for heterogeneous graphs without graph augmentation strategies. Different from traditional contrastive self-supervised learning, HGOT employs the optimal transport mechanism to relieve the laborious sampling process of positive and negative samples. Specifically, we design an aggregating view (central view) to integrate the semantic information contained in the views represented by different meta-paths (branch views). Then, we introduce an optimal transport plan to identify the transport relationship between the semantics contained in the branch view and the central view. This allows the optimal transport plan between graphs to align with the representations, forcing the encoder to learn node representations that are more similar to the graph space and of higher quality. Extensive experiments on four real-world datasets demonstrate that our proposed HGOT model can achieve state-of-the-art performance on various downstream tasks. In particular, in the node classification task, HGOT achieves an average of more than 6\% improvement in accuracy compared with state-of-the-art methods.

In the field of machine learning (ML), an essential type of decision-related problem is known as AUF (Avoiding Undesired Future): if an ML model predicts an undesired outcome, how can decisions be made to prevent it? Recently, a novel framework called *rehearsal learning* has been proposed to address the AUF problem. Despite its utility in modeling uncertainty for decision-making, it remains unclear *under what conditions* and *how* optimal actions that maximize the *AUF probability* can be identified. In this paper, we propose *CARE* (CAnonical REctangle), a condition under which the maximum AUF probability can be achieved. Under the CARE condition, we present a projection-Newton algorithm to select actions and prove that the algorithm achieves superlinear convergence to the optimal one. Besides, we provide a generalization method for adopting the algorithm to AUF scenarios beyond the CARE condition. Finally, we demonstrate that a closed-form solution exists when the outcome is a singleton variable, substantially reducing the time complexity of decision-making. Experiments validate the effectiveness and efficiency of our method.

Spatially Resolved Transcriptomics (SRT) is a cutting-edge technique that captures the spatial context of cells within tissues, enabling the study of complex biological networks. Recent graph-based methods leverage both gene expression and spatial information to identify relevant spatial domains. However, these approaches fall short in obtaining meaningful spot representations, especially for spots near spatial domain boundaries, as they heavily emphasize adjacent spots that have minimal feature differences from an anchor node. To address this, we propose Spotscape, a novel framework that introduces the Similarity Telescope module to capture global relationships between multiple spots. Additionally, we propose a similarity scaling strategy to regulate the distances between intra- and inter-slice spots, facilitating effective multi-slice integration. Extensive experiments demonstrate the superiority of Spotscape in various downstream tasks, including single-slice and multi-slice scenarios.

We investigate the problem of identifying the optimal scoring rule within the principal-agent framework for online information acquisition problem. We focus on the principal's perspective, seeking to determine the desired scoring rule through interactions with the agent. To address this challenge, we propose two algorithms: OIAFC and OIAFB, tailored for fixed confidence and fixed budget settings, respectively. Our theoretical analysis demonstrates that OIAFC can extract the desired $(\epsilon, \delta)$-scoring rule with a efficient instance-dependent sample complexity or an instance-independent sample complexity. Our analysis also shows that OIAFB matches the instance-independent performance bound of OIAFC, while both algorithms share the same complexity across fixed confidence and fixed budget settings.

Language model agents are poised to mediate how people navigate and act online. If the companies that already dominate internet search, communication, and commerce—or the firms trying to unseat them—control these agents, the resulting *platform agents* will likely deepen surveillance, tighten lock-in, and further entrench incumbents. To resist that trajectory, this position paper argues that we should promote *agent advocates*: user-controlled agents that safeguard individual autonomy and choice. Doing so demands three coordinated moves: broad public access to both compute and capable AI models that are not platform-owned, open interoperability and safety standards, and market regulation that prevents platforms from foreclosing competition.

Learned denoisers play a fundamental role in various signal generation (e.g., diffusion models) and reconstruction (e.g., compressed sensing) architectures, whose success derives from their ability to leverage low-dimensional structure in data. Existing denoising methods, however, either rely on local approximations that require a linear scan of the entire dataset or treat denoising as generic function approximation problems, sacrificing efficiency and interpretability. We consider the problem of efficiently denoising a new noisy data point sampled from an unknown manifold $\mathcal M \in \mathbb{R}^D$, using only noisy samples. This work proposes a framework for test-time efficient manifold denoising, by framing the concept of "learning-to-denoise" as *"learning-to-optimize"*. We have two technical innovations: (i) *online learning* methods which learn to optimize over the manifold of clean signals using only noisy data, effectively "growing" an optimizer one sample at a time. (ii) *mixed-order* methods which guarantee that the learned optimizers achieve global optimality, ensuring both efficiency and near-optimal denoising performance. We corroborate these claims with theoretical analyses of both the complexity and denoising performance of mixed-order traversal. Our experiments on scientific manifolds demonstrate significantly improved complexity-performance tradeoffs compared to nearest neighbor search, which underpins existing provable denoising approaches based on exhaustive search.

A fundamental problem in combinatorial optimization is identifying equivalent formulations. Despite the growing need for automated equivalence checks---driven, for example, by *optimization copilots*, which generate problem formulations from natural language descriptions---current approaches rely on simple heuristics that fail to reliably check formulation equivalence. Inspired by Karp reductions, in this work we introduce *Quasi-Karp equivalence*, a formal criterion for determining when two optimization formulations are equivalent based on the existence of a mapping between their decision variables. We propose *EquivaMap*, a framework that leverages large language models to automatically discover such mappings for scalable, reliable equivalence checking, with a verification stage that ensures mapped solutions preserve feasibility and optimality without additional solver calls. To evaluate our approach, we construct *EquivaFormulation*, the first open-source dataset of equivalent optimization formulations, generated by applying transformations such as adding slack variables or valid inequalities to existing formulations. Empirically, *EquivaMap* significantly outperforms existing methods, achieving substantial improvements in correctly identifying formulation equivalence.

Multimodal learning with variational autoencoders (VAEs) requires estimating joint distributions to evaluate the evidence lower bound (ELBO). Current methods, the product and mixture of experts, aggregate single-modality distributions assuming independence for simplicity, which is an overoptimistic assumption. This research introduces a novel methodology for aggregating single-modality distributions by exploiting the principle of *consensus of dependent experts* (CoDE), which circumvents the aforementioned assumption. Utilizing the CoDE method, we propose a novel ELBO that approximates the joint likelihood of the multimodal data by learning the contribution of each subset of modalities. The resulting CoDE-VAE model demonstrates better performance in terms of balancing the trade-off between generative coherence and generative quality, as well as generating more precise log-likelihood estimations. CoDE-VAE further minimizes the generative quality gap as the number of modalities increases. In certain cases, it reaches a generative quality similar to that of unimodal VAEs, which is a desirable property that is lacking in most current methods. Finally, the classification accuracy achieved by CoDE-VAE is comparable to that of state-of-the-art multimodal VAE models.

We propose a novel prompt design paradigm that challenges conventional wisdom in large language model (LLM) prompting. While conventional wisdom prioritizes well-crafted instructions and demonstrations for in-context learning (ICL), we show that pruning random demonstrations into seemingly incoherent ''gibberish'' can remarkably improve performance across diverse tasks. Notably, the ''gibberish'' always matches or surpasses state-of-the-art automatic prompt optimization techniques, achieving substantial gains regardless of LLM alignment. Nevertheless, discovering an effective pruning strategy is non-trivial, as existing attribution methods and prompt compression algorithms fail to deliver robust results, let alone human intuition. In terms of this, we propose a self-discover prompt optimization framework, PromptQuine, an evolutionary search framework that automatically searches for the pruning strategy by itself using only low-data regimes. Much like the emergent complexity in nature—such as symbiosis and self-organization—arising in response to resource constraints, our framework evolves and refines unconventional yet highly effective prompts by leveraging only the tokens present within the context. We demonstrate its effectiveness across classification, multi-choice question answering, generation and math reasoning tasks across LLMs, while achieving decent runtime efficiency. We hope our findings can guide mechanistic studies on in-context learning, and provide a call to action, to pave the way for more open-ended search algorithms for more effective LLM prompting.

Pre-trained vision language models still fall short of human visual cognition. In an effort to improve visual cognition and align models with human behavior, we introduce visual stimuli and human judgments on visual cognition tasks, allowing us to systematically evaluate performance across cognitive domains under a consistent environment. We fine-tune models on ground truth data for intuitive physics and causal reasoning and find that this improves model performance in the respective fine-tuning domain. Furthermore, it can improve model alignment with human behavior. However, we find that task-specific fine-tuning does not contribute to robust human-like generalization to data with other visual characteristics or to tasks in other cognitive domains.