ICML 2025 Papers

Inverse problems (IPs) involve reconstructing signals from noisy observations. Recently, diffusion models (DMs) have emerged as a powerful framework for solving IPs, achieving remarkable reconstruction performance. However, existing DM-based methods frequently encounter issues such as heavy computational demands and suboptimal convergence. In this work, building upon the idea of the recent work DMPlug, we propose two novel methods, DMILO and DMILO-PGD, to address these challenges. Our first method, DMILO, employs intermediate layer optimization (ILO) to alleviate the memory burden inherent in DMPlug. Additionally, by introducing sparse deviations, we expand the range of DMs, enabling the exploration of underlying signals that may lie outside the range of the diffusion model. We further propose DMILO-PGD, which integrates ILO with projected gradient descent (PGD), thereby reducing the risk of suboptimal convergence. We provide an intuitive theoretical analysis of our approaches under appropriate conditions and validate their superiority through extensive experiments on diverse image datasets, encompassing both linear and nonlinear IPs. Our results demonstrate significant performance gains over state-of-the-art methods, highlighting the effectiveness of DMILO and DMILO-PGD in addressing common challenges in DM-based IP solvers.

We present a novel reasoning approach called Flow-of-Options (FoO), designed to address intrinsic biases in Large Language Models (LLMs). Flow-of-Options enables LLMs to systematically explore a diverse range of possibilities in their reasoning, as demonstrated by an FoO-based agentic framework developed for autonomously solving Machine Learning (ML) tasks. FoO enforces diversity in LLM solutions through compressed and interpretable task representations, resulting in improvements of 38.2% - 69.2% on standard data science tasks, and 37.4% - 47.9% on therapeutic chemistry tasks, as compared to state-of-the-art baselines. With an overall operation cost under $1 per task, our framework is well-suited for cost-sensitive applications. Going beyond tabular classification and regression, we show the broader applicability of our FoO-based agentic system to tasks such as reinforcement learning and image generation. Our code is open-sourced at: https://github.com/flagshippioneering/Flow-of-Options.

Existing PLMs generate protein sequences based on a single-condition constraint from a specific modality, struggling to simultaneously satisfy multiple constraints across different modalities. In this work, we introduce CFP-GEN, a novel diffusion language model for Combinatorial Functional Protein GENeration. CFP-GEN facilitates the de novo protein design by integrating multimodal conditions with functional, sequence, and structural constraints. Specifically, an Annotation-Guided Feature Modulation (AGFM) module is introduced to dynamically adjust the protein feature distribution based on composable functional annotations, e.g., GO terms, IPR domains and EC numbers. Meanwhile, the ResidueControlled Functional Encoding (RCFE) module captures residue-wise interaction to ensure more precise control. Additionally, off-the-shelf 3D structure encoders can be seamlessly integrated to impose geometric constraints. We demonstrate that CFP-GEN enables high-throughput generation of novel proteins with functionality comparable to natural proteins, while achieving a high success rate in designing multifunctional proteins.

Decoding functional magnetic resonance imaging (fMRI) signals into text has been a key challenge in the neuroscience community, with the potential to advance brain-computer interfaces and uncover deeper insights into brain mechanisms. However, existing approaches often struggle with suboptimal predictive performance, limited task variety, and poor generalization across subjects. In response to this, we propose MindLLM, a model designed for subject-agnostic and versatile fMRI-to-text decoding. MindLLM consists of an fMRI encoder and an off-the-shelf LLM. The fMRI encoder employs a neuroscience-informed attention mechanism, which is capable of accommodating subjects with varying input shapes and thus achieves high-performance subject-agnostic decoding. Moreover, we introduce Brain Instruction Tuning (BIT), a novel approach that enhances the model's ability to capture diverse semantic representations from fMRI signals, facilitating more versatile decoding. We evaluate MindLLM on comprehensive fMRI-to-text benchmarks. Results demonstrate that our model outperforms the baselines, improving downstream tasks by $12.0\%$, unseen subject generalization by $24.5\%$, and novel task adaptation by $25.0\%$. Furthermore, the attention patterns in MindLLM provide interpretable insights into its decision-making process.

Circular and non-flat data distribution are prevalent across diverse domains of data science, yet their specific geometric structures often remain underutilized in machine learning frameworks. A principled approach to accounting for the underlying geometry of such data is pivotal, particularly when extending statistical models, like the pervasive Gaussian distribution. In this work, we tackle those issue by focusing on the manifold of symmetric positive definite matrices, a key focus in information geometry. We introduced a non-isotropic wrapped Gaussian by leveraging the exponential map, we derive theoretical properties of this distribution and propose a maximum likelihood framework for parameter estimation. Furthermore, we reinterpret established classifiers on SPD through a probabilistic lens and introduce new classifiers based on the wrapped Gaussian model. Experiments on synthetic and real-world datasets demonstrate the robustness and flexibility of this geometry-aware distribution, underscoring its potential to advance manifold-based data analysis. This work lays the groundwork for extending classical machine learning and statistical methods to more complex and structured data.

We establish a continuous-time framework for analyzing Deep Q-Networks (DQNs) via stochastic control and Forward-Backward Stochastic Differential Equations (FBSDEs). Considering a continuous-time Markov Decision Process (MDP) driven by a square-integrable martingale, we analyze DQN approximation properties. We show that DQNs can approximate the optimal Q-function on compact sets with arbitrary accuracy and high probability, leveraging residual network approximation theorems and large deviation bounds for the state-action process. We then analyze the convergence of a general Q-learning algorithm for training DQNs in this setting, adapting stochastic approximation theorems. Our analysis emphasizes the interplay between DQN layer count, time discretization, and the role of viscosity solutions (primarily for the value function $V^*$) in addressing potential non-smoothness of the optimal Q-function. This work bridges deep reinforcement learning and stochastic control, offering insights into DQNs in continuous-time settings, relevant for applications with physical systems or high-frequency data.

While the activations of neurons in deep neural networks usually do not have a simple human-understandable interpretation, sparse autoencoders (SAEs) can be used to transform these activations into a higher-dimensional latent space which can be more easily interpretable. However, SAEs can have millions of distinct latents, making it infeasible for humans to manually interpret each one. In this work, we build an open-source automated pipeline to generate and evaluate natural language interpretations for SAE latents using LLMs. We test our framework on SAEs of varying sizes, activation functions, and losses, trained on two different open-weight LLMs. We introduce five new techniques to score the quality of interpretations that are cheaper to run than the previous state of the art. One of these techniques, intervention scoring, evaluates the interpretability of the effects of intervening on a latent, which we find explains latents that are not recalled by existing methods. We propose guidelines for generating better interpretations that remain valid for a broader set of activating contexts, and discuss pitfalls with existing scoring techniques. Our code is available at https://github.com/EleutherAI/delphi.

We study the task of Multiclass Linear Classification (MLC) in the distribution-free PAC model with Random Classification Noise (RCN). Specifically, the learner is given a set of labeled examples $(x, y)$, where $x$ is drawn from an unknown distribution on $R^d$ and the labels are generated by a multiclass linear classifier corrupted with RCN. That is, the label $y$ is flipped from $i$ to $j$ with probability $H_{ij}$ according to a known noise matrix $H$ with non-negative separation $\sigma: = \min_{i \neq j} H_{ii}-H_{ij}$. The goal is to compute a hypothesis with small 0-1 error. For the special case of two labels, prior work has given polynomial-time algorithms achieving the optimal error. Surprisingly, little is known about the complexity of this task even for three labels. As our main contribution, we show that the complexity of MLC with RCN becomes drastically different in the presence of three or more labels. Specifically, we prove super-polynomial Statistical Query (SQ) lower bounds for this problem. In more detail, even for three labels and constant separation, we give a super-polynomial lower bound on the complexity of any SQ algorithm achieving optimal error. For a larger number of labels and smaller separation, we show a super-polynomial SQ lower bound even for the weaker goal of achieving any constant factor approximation to the optimal loss or even beating the trivial hypothesis.

Submodular functions, defined on continuous or discrete domains, arise in numerous applications. We study the minimization of the difference of submodular (DS) functions, over both domains, extending prior work restricted to set functions. We show that all functions on discrete domains and all smooth functions on continuous domains are DS. For discrete domains, we observe that DS minimization is equivalent to minimizing the difference of two convex (DC) functions, as in the set function case. We propose a novel variant of the DC Algorithm (DCA) and apply it to the resulting DC Program, obtaining comparable theoretical guarantees as in the set function case. The algorithm can be applied to continuous domains via discretization. Experiments demonstrate that our method outperforms baselines in integer compressive sensing and integer least squares.

Autoregressive models (ARMs) have become the workhorse for sequence generation tasks, since many problems can be modeled as next-token prediction. While there appears to be a natural ordering for text (i.e., left-to-right), for many data types, such as graphs, the canonical ordering is less obvious. To address this problem, we introduce a variant of ARM that generates high-dimensional data using a probabilistic ordering that is sequentially inferred from data. This model incorporates a trainable probability distribution, referred to as an order-policy, that dynamically decides the autoregressive order in a state-dependent manner. To train the model, we introduce a variational lower bound on the exact log-likelihood, which we optimize with stochastic gradient estimation. We demonstrate experimentally that our method can learn meaningful autoregressive orderings in image and graph generation. On the challenging domain of molecular graph generation, we achieve state-of-the-art results on the QM9 and ZINC250k benchmarks, evaluated using the Fréchet ChemNet Distance (FCD), Synthetic Accessibility Score (SAS), Quantitative Estimate of Drug-likeness (QED).

Optimizing high-dimensional and complex black-box functions is crucial in numerous scientific applications. While Bayesian optimization (BO) is a powerful method for sample-efficient optimization, it struggles with the curse of dimensionality and scaling to thousands of evaluations. Recently, leveraging generative models to solve black-box optimization problems has emerged as a promising framework. However, those methods often underperform compared to BO methods due to limited expressivity and difficulty of uncertainty estimation in high-dimensional spaces. To overcome these issues, we introduce \textbf{DiBO}, a novel framework for solving high-dimensional black-box optimization problems. Our method iterates two stages. First, we train a diffusion model to capture the data distribution and deep ensembles to predict function values with uncertainty quantification. Second, we cast the candidate selection as a posterior inference problem to balance exploration and exploitation in high-dimensional spaces. Concretely, we fine-tune diffusion models to amortize posterior inference. Extensive experiments demonstrate that our method outperforms state-of-the-art baselines across synthetic and real-world tasks. Our code is publicly available \href{https://github.com/umkiyoung/DiBO}{here}.

In this paper, we introduce a geometric framework to analyze memorization in diffusion models through the sharpness of the log probability density. We mathematically justify a previously proposed score-difference-based memorization metric by demonstrating its effectiveness in quantifying sharpness. Additionally, we propose a novel memorization metric that captures sharpness at the initial stage of image generation in latent diffusion models, offering early insights into potential memorization. Leveraging this metric, we develop a mitigation strategy that optimizes the initial noise of the generation process using a sharpness-aware regularization term.

Multimodal retrieval-augmented generation (RAG) plays a crucial role in domains such as knowledge-based visual question answering (KB-VQA), where models should effectively integrate additional knowledge to generate a response. However, existing vision and language models (VLMs) are not inherently designed for context-augmented generation, limiting their effectiveness in such tasks. While synthetic data generation has recently gained attention for training large VLMs, its application for context-augmented generation remains underexplored. To address this gap, we introduce SKVQA, a large-scale synthetic multimodal dataset containing over 2 million visual question-answer pairs, each associated with external knowledge sources to determine the final answer. Compared to previous datasets, SKVQA exhibits 11× more unique questions, greater domain diversity, and a broader spectrum of image sources. Through human evaluations, we confirm the high quality of the generated question-answer pairs and their contextual relevance. Extensive experiments show that SKVQA serves both as a challenging benchmark for knowledge-based VQA and as an effective training resource for adapting generative multimodal models to context-augmented generation. Our results further indicate that models trained on SKVQA demonstrate enhanced generalization in both context-aware VQA and multimodal RAG settings.

Sparse tensor programs are essential in deep learning and graph analytics, driving the need for optimized processing. To meet this demand, specialized hardware accelerators are being developed. Optimizing these programs for accelerators is challenging for two reasons: program performance is highly sensitive to variations in sparse inputs, and early-stage accelerators rely on expensive simulators. Therefore, ML-based cost models used for optimizing such programs on general-purpose hardware are often ineffective for early-stage accelerators, as they require large datasets for proper training. To this end, we introduce COGNATE, a novel framework that leverages inexpensive data samples from general-purpose hardware (e.g., CPUs) to train cost models, followed by few-shot fine-tuning on emerging hardware. COGNATE exploits the homogeneity of input features across hardware platforms while effectively mitigating heterogeneity, enabling cost model training with just 5% of the data samples needed by accelerator-specific models to achieve comparable performance. We conduct extensive experiments to demonstrate that COGNATE outperforms existing techniques, achieving average speedups of 1.47× (up to 5.46×) for SpMM and 1.39× (up to 4.22×) for SDDMM.

Arena-based evaluation is a fundamental yet significant evaluation paradigm for modern AI models, especially large language models (LLMs). Existing framework based on ELO rating system suffers from the inevitable instability problem due to ranking inconsistency and the lack of attention to the varying abilities of annotators. In this paper, we introduce a novel stable arena framework to address these issues by enhancing the ELO Rating System. Specifically, we replace the iterative update method with a Maximum Likelihood Estimation (MLE) approach, m-ELO, and provide theoretical proof of the consistency and stability of the MLE approach for model ranking. Additionally, we proposed the am-ELO, which modify the Elo Rating’s probability function to incorporate annotator abilities, enabling the simultaneous estimation of model scores and annotator reliability. Experiments demonstrate that this method ensures stability, proving that this framework offers a more robust, accurate, and stable evaluation method for LLMs.

Federated learning (FL), aimed at leveraging vast distributed datasets, confronts a crucial challenge: the heterogeneity of data across different silos. While previous studies have explored discrete representations to enhance model generalization across minor distributional shifts, these approaches often struggle to adapt to new data silos with significantly divergent distributions. In response, we have identified that models derived from FL exhibit markedly increased uncertainty when applied to data silos with unfamiliar distributions. Consequently, we propose an innovative yet straightforward iterative framework, termed \emph{Uncertainty-Based Extensible-Codebook Federated Learning (UEFL)}. This framework dynamically maps latent features to trainable discrete vectors, assesses the uncertainty, and specifically extends the discretization dictionary or codebook for silos exhibiting high uncertainty. Our approach aims to simultaneously enhance accuracy and reduce uncertainty by explicitly addressing the diversity of data distributions, all while maintaining minimal computational overhead in environments characterized by heterogeneous data silos. Extensive experiments across multiple datasets demonstrate that UEFL outperforms state-of-the-art methods, achieving significant improvements in accuracy (by 3\%--22.1\%) and uncertainty reduction (by 38.83\%--96.24\%). The source code is available at https://github.com/destiny301/uefl.

Aligning large language models (LLMs) with human preferences requires balancing policy optimization with computational stability. While recent offline methods like DPO and SimPO bypass reinforcement learning’s complexity, they face critical limitations: DPO relies on static reference models that degrade with policy updates, and SimPO assumes a uniform target reward margin that ignores instance-wise preference strength. We propose AlphaDPO, an adaptive preference optimization framework that dynamically reparameterizes the reference distribution to address these issues. Our key innovation lies in an implicit reference model \(\hat{\pi}_{\text{ref}} \propto U(y|x)(\pi_\theta/\pi_{\text{ref}})^\alpha\), which interpolates between policy-driven specialization and uniform exploration while enabling instance-adaptive reward margins. Theoretically, we prove AlphaDPO implicitly controls sequential KL divergence between iterative policy updates, ensuring stability even with poorly calibrated reference models. Empirically, AlphaDPO achieves state-of-the-art performance on AlpacaEval 2 (58.7\% LC win rate) and Arena-Hard (35.7\% win rate) across Mistral2-7B, Llama3-8B, and Gemma2-9B, demonstrating robust alignment without multi-stage training. Our work establishes adaptive reference reparameterization as a principled mechanism for preference optimization.

Benchmark contamination has become a significant concern in the LLM evaluation community. Previous Agents-as-an-Evaluator address this issue by involving agents in the generation of questions. Despite their success, the biases in Agents-as-an-Evaluator methods remain largely unexplored. In this paper, we present a theoretical formulation of evaluation bias, providing valuable insights into designing unbiased evaluation protocols. Furthermore, we identify two type of bias in Agents-as-an-Evaluator through carefully designed probing tasks on a minimal Agents-as-an-Evaluator setup. To address these issues, we propose the Unbiased Evaluator, an evaluation protocol that delivers a more comprehensive, unbiased, and interpretable assessment of LLMs. Extensive experiments reveal significant room for improvement in current LLMs. Additionally, we demonstrate that the Unbiased Evaluator not only offers strong evidence of benchmark contamination but also provides interpretable evaluation results.

Self-Supervised Learning (SSL) powers many current AI systems. As research interest and investment grow, the SSL design space continues to expand. The Platonic view of SSL, following the Platonic Representation Hypothesis (PRH), suggests that despite different methods and engineering approaches, all representations converge to the same Platonic ideal. However, this phenomenon lacks precise theoretical explanation. By synthesizing evidence from Identifiability Theory (IT), we show that the PRH can emerge in SSL. There is a gap between SSL theory and practice: Current IT cannot explain SSL's empirical success, though it has practically relevant insights. Our work formulates a blueprint for SSL research to bridge this gap: we propose expanding IT into what we term Singular Identifiability Theory (SITh), a broader theoretical framework encompassing the entire SSL pipeline. SITh would allow deeper insights into the implicit data assumptions in SSL and advance the field towards learning more interpretable and generalizable representations. We highlight three critical directions for future research: 1) training dynamics and convergence properties of SSL; 2) the impact of finite samples, batch size, and data diversity; and 3) the role of inductive biases in architecture, augmentations, initialization schemes, and optimizers.