OpenRaiser/Intern-Atlas huggingface dataset:
Certified Unlearning for Neural Networks
Venue: Conference ICML 2025
Year: 2025

We address the problem of machine unlearning, where the goal is to remove the influence of specific training data from a model upon request, motivated by privacy concerns and regulatory requirements such as the "right to be forgotten." Unfortunately, existing methods rely on restrictive assumptions or lack formal guarantees. To this end, we propose a novel method for certified machine unlearning, leveraging the connection between unlearning and privacy amplification by stochastic post-processing. Our method uses noisy fine-tuning on the retain data, i.e., data that does not need to be removed, to ensure provable unlearning guarantees. This approach requires no assumptions about the underlying loss function, making it broadly applicable across diverse settings. We analyze the theoretical trade-offs in efficiency and accuracy and demonstrate empirically that our method not only achieves formal unlearning guarantees but also performs effectively in practice, outperforming existing baselines. Our code is available at https://github.com/stair-lab/certified-unlearning-neural-networks-icml-2025
Mastering Massive Multi-Task Reinforcement Learning via Mixture-of-Expert Decision Transformer
Venue: Conference ICML 2025
Year: 2025

Despite recent advancements in offline multi-task reinforcement learning (MTRL) have harnessed the powerful capabilities of the Transformer architecture, most approaches focus on a limited number of tasks, with scaling to extremely massive tasks remaining a formidable challenge. In this paper, we first revisit the key impact of task numbers on current MTRL method, and further reveal that naively expanding the parameters proves insufficient to counteract the performance degradation as the number of tasks escalates. Building upon these insights, we propose M3DT, a novel mixture-of-experts (MoE) framework that tackles task scalability by further unlocking the model's parameter scalability. Specifically, we enhance both the architecture and the optimization of the agent, where we strengthen the Decision Transformer (DT) backbone with MoE to reduce task load on parameter subsets, and introduce a three-stage training mechanism to facilitate efficient training with optimal performance. Experimental results show that, by increasing the number of experts, M3DT not only consistently enhances its performance as model expansion on the fixed task numbers, but also exhibits remarkable task scalability, successfully extending to 160 tasks with superior performance.
Latent Thought Models with Variational Bayes Inference-Time Computation
Venue: Conference ICML 2025
Year: 2025

We propose a novel class of language models, Latent Thought Models (LTMs), which incorporate explicit latent thought vectors that follow an explicit prior model in latent space. These latent thought vectors guide the autoregressive generation of ground tokens through a Transformer decoder. Training employs a dual-rate optimization process within the classical variational Bayes framework: fast learning of local variational parameters for the posterior distribution of latent vectors (inference-time computation), and slow learning of global decoder parameters. Empirical studies reveal that LTMs possess additional scaling dimensions beyond traditional Large Language Models (LLMs), such as the number of iterations in inference-time computation and number of latent thought vectors. Higher sample efficiency can be achieved by increasing training compute per token, with further gains possible by trading model size for more inference steps. Designed based on these scaling properties, LTMs demonstrate superior sample and parameter efficiency compared to autoregressive models and discrete diffusion models. They significantly outperform these counterparts in validation perplexity and zero-shot language modeling tasks. Additionally, LTMs exhibit emergent few-shot in-context reasoning capabilities that scale with model size, and achieve competitive performance in conditional and unconditional text generation.
UniMoMo: Unified Generative Modeling of 3D Molecules for De Novo Binder Design
Venue: Conference ICML 2025
Year: 2025

The design of target-specific molecules such as small molecules, peptides, and antibodies is vital for biological research and drug discovery. Existing generative methods are restricted to single-domain molecules, failing to address versatile therapeutic needs or utilize cross-domain transferability to enhance model performance. In this paper, we introduce Unified generative Modeling of 3D Molecules (UniMoMo), the first framework capable of designing binders of multiple molecular domains using a single model. In particular, UniMoMo unifies the representations of different molecules as graphs of blocks, where each block corresponds to either a standard amino acid or a molecular fragment. Subsequently, UniMoMo utilizes a geometric latent diffusion model for 3D molecular generation, featuring an iterative full-atom autoencoder to compress blocks into latent space points, followed by an E(3)-equivariant diffusion process. Extensive benchmarks across peptides, antibodies, and small molecules demonstrate the superiority of our unified framework over existing domain-specific models, highlighting the benefits of multi-domain training.
Enhancing Cooperative Multi-Agent Reinforcement Learning with State Modelling and Adversarial Exploration
Venue: Conference ICML 2025
Year: 2025

Learning to cooperate in distributed partially observable environments with no communication abilities poses significant challenges for multi-agent deep reinforcement learning (MARL). This paper addresses key concerns in this domain, focusing on inferring state representations from individual agent observations and leveraging these representations to enhance agents' exploration and collaborative task execution policies. To this end, we propose a novel state modelling framework for cooperative MARL, where agents infer meaningful belief representations of the non-observable state, with respect to optimizing their own policies, while filtering redundant and less informative joint state information. Building upon this framework, we propose the MARL SMPE algorithm. In SMPE, agents enhance their own policy's discriminative abilities under partial observability, explicitly by incorporating their beliefs into the policy network, and implicitly by adopting an adversarial type of exploration policies which encourages agents to discover novel, high-value states while improving the discriminative abilities of others. Experimentally, we show that SMPE outperforms state-of-the-art MARL algorithms in complex fully cooperative tasks from the MPE, LBF, and RWARE benchmarks.
FlowDrag: 3D-aware Drag-based Image Editing with Mesh-guided Deformation Vector Flow Fields
Venue: Conference ICML 2025
Year: 2025

Drag-based editing allows precise object manipulation through point-based control, offering user convenience. However, current methods often suffer from a geometric inconsistency problem by focusing exclusively on matching user-defined points, neglecting the broader geometry and leading to artifacts or unstable edits. We propose FlowDrag, which leverages geometric information for more accurate and coherent transformations. Our approach constructs a 3D mesh from the image, using an energy function to guide mesh deformation based on user-defined drag points. The resulting mesh displacements are projected into 2D and incorporated into a UNet denoising process, enabling precise handle-to-target point alignment while preserving structural integrity. Additionally, existing drag-editing benchmarks provide no ground truth, making it difficult to assess how accurately the edits match the intended transformations. To address this, we present VFD (VidFrameDrag) benchmark dataset, which provides ground-truth frames using consecutive shots in a video dataset. FlowDrag outperforms existing drag-based editing methods on both VFD Bench and DragBench.
Identifiable Object Representations under Spatial Ambiguities
Venue: Conference ICML 2025
Year: 2025

Modular object-centric representations are essential for *human-like reasoning* but are challenging to obtain under spatial ambiguities, *e.g. due to occlusions and view ambiguities*. However, addressing challenges presents both theoretical and practical difficulties. We introduce a novel multi-view probabilistic approach that aggregates view-specific slots to capture *invariant content* information while simultaneously learning disentangled global *viewpoint-level* information. Unlike prior single-view methods, our approach resolves spatial ambiguities, provides theoretical guarantees for identifiability, and requires *no viewpoint annotations*. Extensive experiments on standard benchmarks and novel complex datasets validate our method's robustness and scalability.
Improved Sample Complexity for Private Nonsmooth Nonconvex Optimization
Venue: Conference ICML 2025
Year: 2025

We study differentially private (DP) optimization algorithms for stochastic and empirical objectives which are neither smooth nor convex, and propose methods that return a Goldstein-stationary point with sample complexity bounds that improve on existing works. We start by providing a single-pass $(ε,δ)$-DP algorithm that returns an $(α,β)$-stationary point as long as the dataset is of size $\widetildeΩ(\sqrt{d}/αβ^{3}+d/εαβ^{2})$, which is $Ω(\sqrt{d})$ times smaller than the algorithm of Zhang et al. [2024] for this task, where $d$ is the dimension. We then provide a multi-pass polynomial time algorithm which further improves the sample complexity to $\widetildeΩ\left(d/β^2+d^{3/4}/εα^{1/2}β^{3/2}\right)$, by designing a sample efficient ERM algorithm, and proving that Goldstein-stationary points generalize from the empirical loss to the population loss.
Laplace Transform Based Low-Complexity Learning of Continuous Markov Semigroups
Venue: Conference ICML 2025
Year: 2025

Markov processes serve as a universal model for many real-world random processes. This paper presents a data-driven approach for learning these models through the spectral decomposition of the infinitesimal generator (IG) of the Markov semigroup. The unbounded nature of IGs complicates traditional methods such as vector-valued regression and Hilbert-Schmidt operator analysis. Existing techniques, including physics-informed kernel regression, are computationally expensive and limited in scope, with no recovery guarantees for transfer operator methods when the time-lag is small. We propose a novel method that leverages the IG's resolvent, characterized by the Laplace transform of transfer operators. This approach is robust to time-lag variations, ensuring accurate eigenvalue learning even for small time-lags. Our statistical analysis applies to a broader class of Markov processes than current methods while reducing computational complexity from quadratic to linear in the state dimension. Finally, we illustrate the behaviour of our method in two experiments.
Orthus: Autoregressive Interleaved Image-Text Generation with Modality-Specific Heads
Venue: Conference ICML 2025
Year: 2025

We introduce Orthus, an autoregressive (AR) transformer that excels in generating images given textual prompts, answering questions based on visual inputs, and even crafting lengthy image-text interleaved contents. Unlike prior arts on unified multimodal modeling, Orthus simultaneously copes with discrete text tokens and continuous image features under the AR modeling principle. The continuous treatment of visual signals minimizes the information loss for both image understanding and generation while the fully AR formulation renders the characterization of the correlation between modalities straightforward. The key mechanism enabling Orthus to leverage these advantages lies in its modality-specific heads -- one regular language modeling (LM) head predicts discrete text tokens and one diffusion head generates continuous image features conditioning on the output of the backbone. We devise an efficient strategy for building Orthus -- by substituting the Vector Quantization (VQ) operation in the existing unified AR model with a soft alternative, introducing a diffusion head, and tuning the added modules to reconstruct images, we can create an Orthus-base model effortlessly (e.g., within mere 72 A100 GPU hours). Orthus-base can further embrace post-training to better model interleaved images and texts. Empirically, Orthus surpasses competing baselines including Show-o and Chameleon across standard benchmarks, achieving a GenEval score of 0.58 and an MME-P score of 1265.8 using 7B parameters. Orthus also shows exceptional mixed-modality generation capabilities, reflecting the potential for handling intricate practical generation tasks.
EQ-VAE: Equivariance Regularized Latent Space for Improved Generative Image Modeling
Venue: Conference ICML 2025
Year: 2025

Latent generative models have emerged as a leading approach for high-quality image synthesis. These models rely on an autoencoder to compress images into a latent space, followed by a generative model to learn the latent distribution. We identify that existing autoencoders lack equivariance to semantic-preserving transformations like scaling and rotation, resulting in complex latent spaces that hinder generative performance. To address this, we propose EQ-VAE, a simple regularization approach that enforces equivariance in the latent space, reducing its complexity without degrading reconstruction quality. By finetuning pre-trained autoencoders with EQ-VAE, we enhance the performance of several state-of-the-art generative models, including DiT, SiT, REPA and MaskGIT, achieving a 7 speedup on DiT-XL/2 with only five epochs of SD-VAE fine-tuning. EQ-VAE is compatible with both continuous and discrete autoencoders, thus offering a versatile enhancement for a wide range of latent generative models. Project page and code: https://eq-vae.github.io/.
Privacy Attacks on Image AutoRegressive Models
Venue: Conference ICML 2025
Year: 2025

Image AutoRegressive generation has emerged as a new powerful paradigm with image autoregressive models (IARs) matching state-of-the-art diffusion models (DMs) in image quality (FID: 1.48 vs. 1.58) while allowing for a higher generation speed. However, the privacy risks associated with IARs remain unexplored, raising concerns regarding their responsible deployment. To address this gap, we conduct a comprehensive privacy analysis of IARs, comparing their privacy risks to the ones of DMs as reference points. Concretely, we develop a novel membership inference attack (MIA) that achieves a remarkably high success rate in detecting training images (with a True Positive Rate at False Positive Rate = 1% of 86.38% vs. 6.38% for DMs with comparable attacks). We leverage our novel MIA to provide dataset inference (DI) for IARs, and show that it requires as few as 6 samples to detect dataset membership (compared to 200 for DI in DMs), confirming a higher information leakage in IARs. Finally, we are able to extract hundreds of training data points from an IAR (e.g., 698 from VAR-d30). Our results suggest a fundamental privacy-utility trade-off: while IARs excel in image generation quality and speed, they are empirically significantly more vulnerable to privacy attacks compared to DMs that achieve similar performance. We release the code at https://github.com/sprintml/privacy_attacks_against_iars for reproducibility.
Improved Learning via k-DTW: A Novel Dissimilarity Measure for Curves
Venue: Conference ICML 2025
Year: 2025

This paper introduces $k$-Dynamic Time Warping ($k$-DTW), a novel dissimilarity measure for polygonal curves. $k$-DTW has stronger metric properties than Dynamic Time Warping (DTW) and is more robust to outliers than the Fréchet distance, which are the two gold standards of dissimilarity measures for polygonal curves. We show interesting properties of $k$-DTW and give an exact algorithm as well as a $(1+\varepsilon)$-approximation algorithm for $k$-DTW by a parametric search for the $k$-th largest matched distance. We prove the first dimension-free learning bounds for curves and further learning theoretic results. $k$-DTW not only admits smaller sample size than DTW for the problem of learning the median of curves, where some factors depending on the curves' complexity $m$ are replaced by $k$, but we also show a surprising separation on the associated Rademacher and Gaussian complexities: $k$-DTW admits strictly smaller bounds than DTW, by a factor $\tildeΩ(\sqrt{m})$ when $k\ll m$. We complement our theoretical findings with an experimental illustration of the benefits of using $k$-DTW for clustering and nearest neighbor classification.
Categorical Schrödinger Bridge Matching
Venue: Conference ICML 2025
Year: 2025

The Schrödinger Bridge (SB) is a powerful framework for solving generative modeling tasks such as unpaired domain translation. Most SB-related research focuses on continuous data space $\mathbb{R}^{D}$ and leaves open theoretical and algorithmic questions about applying SB methods to discrete data, e.g, on finite spaces $\mathbb{S}^{D}$. Notable examples of such sets $\mathbb{S}$ are codebooks of vector-quantized (VQ) representations of modern autoencoders, tokens in texts, categories of atoms in molecules, etc. In this paper, we provide a theoretical and algorithmic foundation for solving SB in discrete spaces using the recently introduced Iterative Markovian Fitting (IMF) procedure. Specifically, we theoretically justify the convergence of discrete-time IMF (D-IMF) to SB in discrete spaces. This enables us to develop a practical computational algorithm for SB, which we call Categorical Schrödinger Bridge Matching (CSBM). We show the performance of CSBM via a series of experiments with synthetic data and VQ representations of images. The code of CSBM is available at https://github.com/gregkseno/csbm.
HybridGS: High-Efficiency Gaussian Splatting Data Compression using Dual-Channel Sparse Representation and Point Cloud Encoder
Venue: Conference ICML 2025
Year: 2025

Most existing 3D Gaussian Splatting (3DGS) compression schemes focus on producing compact 3DGS representation via implicit data embedding. They have long coding times and highly customized data format, making it difficult for widespread deployment. This paper presents a new 3DGS compression framework called HybridGS, which takes advantage of both compact generation and standardized point cloud data encoding. HybridGS first generates compact and explicit 3DGS data. A dual-channel sparse representation is introduced to supervise the primitive position and feature bit depth. It then utilizes a canonical point cloud encoder to perform further data compression and form standard output bitstreams. A simple and effective rate control scheme is proposed to pivot the interpretable data compression scheme. At the current stage, HybridGS does not include any modules aimed at improving 3DGS quality during generation. But experiment results show that it still provides comparable reconstruction performance against state-of-the-art methods, with evidently higher encoding and decoding speed. The code is publicly available at https://github.com/Qi-Yangsjtu/HybridGS.
Customizing the Inductive Biases of Softmax Attention using Structured Matrices
Venue: Conference ICML 2025
Year: 2025

The core component of attention is the scoring function, which transforms the inputs into low-dimensional queries and keys and takes the dot product of each pair. While the low-dimensional projection improves efficiency, it causes information loss for certain tasks that have intrinsically high-dimensional inputs. Additionally, attention uses the same scoring function for all input pairs, without imposing a distance-dependent compute bias for neighboring tokens in the sequence. In this work, we address these shortcomings by proposing new scoring functions based on computationally efficient structured matrices with high ranks, including Block Tensor-Train (BTT) and Multi-Level Low Rank (MLR) matrices. On in-context regression tasks with high-dimensional inputs, our proposed scoring functions outperform standard attention for any fixed compute budget. On language modeling, a task that exhibits locality patterns, our MLR-based attention method achieves improved scaling laws compared to both standard attention and variants of sliding window attention. Additionally, we show that both BTT and MLR fall under a broader family of efficient structured matrices capable of encoding either full-rank or distance-dependent compute biases, thereby addressing significant shortcomings of standard attention. Finally, we show that MLR attention has promising results for long-range time-series forecasting.
Reconstructing Cell Lineage Trees from Phenotypic Features with Metric Learning
Venue: Conference ICML 2025
Year: 2025

How a single fertilized cell gives rise to a complex array of specialized cell types in development is a central question in biology. The cells grow, divide, and acquire differentiated characteristics through poorly understood molecular processes. A key approach to studying developmental processes is to infer the tree graph of cell lineage division and differentiation histories, providing an analytical framework for dissecting individual cells' molecular decisions during replication and differentiation. Although genetically engineered lineage-tracing methods have advanced the field, they are either infeasible or ethically constrained in many organisms. In contrast, modern single-cell technologies can measure high-content molecular profiles (e.g., transcriptomes) in a wide range of biological systems. Here, we introduce CellTreeQM, a novel deep learning method based on transformer architectures that learns an embedding space with geometric properties optimized for tree-graph inference. By formulating lineage reconstruction as a tree-metric learning problem, we have systematically explored supervised, weakly supervised, and unsupervised training settings and present a Lineage Reconstruction Benchmark to facilitate comprehensive evaluation of our learning method. We benchmarked the method on (1) synthetic data modeled via Brownian motion with independent noise and spurious signals and (2) lineage-resolved single-cell RNA sequencing datasets. Experimental results show that CellTreeQM recovers lineage structures with minimal supervision and limited data, offering a scalable framework for uncovering cell lineage relationships in challenging animal models. To our knowledge, this is the first method to cast cell lineage inference explicitly as a metric learning task, paving the way for future computational models aimed at uncovering the molecular dynamics of cell lineage.
How to Train Your Multi-Exit Model? Analyzing the Impact of Training Strategies
Venue: Conference ICML 2025
Year: 2025

Early exits enable the network's forward pass to terminate early by attaching trainable internal classifiers to the backbone network. Existing early-exit methods typically adopt either a joint training approach, where the backbone and exit heads are trained simultaneously, or a disjoint approach, where the heads are trained separately. However, the implications of this choice are often overlooked, with studies typically adopting one approach without adequate justification. This choice influences training dynamics and its impact remains largely unexplored. In this paper, we introduce a set of metrics to analyze early-exit training dynamics and guide the choice of training strategy. We demonstrate that conventionally used joint and disjoint regimes yield suboptimal performance. To address these limitations, we propose a mixed training strategy: the backbone is trained first, followed by the training of the entire multi-exit network. Through comprehensive evaluations of training strategies across various architectures, datasets, and early-exit methods, we present the strengths and weaknesses of the early exit training strategies. In particular, we show consistent improvements in performance and efficiency using the proposed mixed strategy.