ICML 2025 论文列表

Understanding cellular responses to stimuli is crucial for biological discovery and drug development. Transcriptomics provides interpretable, gene-level insights, while microscopy imaging offers rich predictive features but is harder to interpret. Weakly paired datasets, where samples share biological states, enable multimodal learning but are scarce, limiting their utility for training and multimodal inference. We propose a framework to enhance transcriptomics by distilling knowledge from microscopy images. Using weakly paired data, our method aligns and binds modalities, enriching gene expression representations with morphological information. To address data scarcity, we introduce (1) *Semi-Clipped*, an adaptation of CLIP for cross-modal distillation using pretrained foundation models, achieving state-of-the-art results, and (2) *PEA* (**P**erturbation **E**mbedding **A**ugmentation), a novel augmentation technique that enhances transcriptomics data while preserving inherent biological information. These strategies improve the predictive power and retain the interpretability of transcriptomics, enabling rich unimodal representations for complex biological tasks.

Conformal Prediction (CP) has proven to be an effective post-hoc method for improving the trustworthiness of neural networks by providing prediction sets with finite-sample guarantees. However, under adversarial attacks, classical conformal guarantees do not hold anymore: this problem is addressed in the field of Robust Conformal Prediction. Several methods have been proposed to provide robust CP sets with guarantees under adversarial perturbations, but, for large scale problems, these sets are either too large or the methods are too computationally demanding to be deployed in real life scenarios. In this work, we propose a new method that leverages Lipschitz-bounded networks to precisely and efficiently estimate robust CP sets. When combined with a 1-Lipschitz robust network, we demonstrate that our *lip-rcp* method outperforms state-of-the-art results in both the size of the robust CP sets and computational efficiency in medium and large-scale scenarios such as ImageNet. Taking a different angle, we also study vanilla CP under attack, and derive new worst-case coverage bounds of vanilla CP sets, which are valid simultaneously for all adversarial attack levels. Our *lip-rcp* method makes this second approach as efficient as vanilla CP while also allowing robustness guarantees.

The importance of higher-order relations is widely recognized in numerous real-world systems. However, annotating them is a tedious and sometimes even impossible task. Consequently, current approaches for data modelling either ignore the higher-order interactions altogether or simplify them into pairwise connections. To facilitate higher-order processing, even when a hypergraph structure is not available, we introduce SPHINX, a model that learns to infer a latent hypergraph structure in an unsupervised way, solely from the final task-dependent signal. To ensure broad applicability, we design the model to be end-to-end differentiable, capable of generating a discrete hypergraph structure compatible with any modern hypergraph networks, and easily optimizable without requiring additional regularization losses. Through extensive ablation studies and experiments conducted on four challenging datasets, we demonstrate that our model is capable of inferring suitable latent hypergraphs in both transductive and inductive tasks. Moreover, the inferred latent hypergraphs are interpretable and contribute to enhancing the final performance, outperforming existing methods for hypergraph prediction.

Conformal prediction is a powerful tool for constructing prediction intervals for black-box models, providing a finite sample coverage guarantee for exchangeable data. However, this exchangeability is compromised when some entries of the test feature are contaminated, such as in the case of cellwise outliers. To address this issue, this paper introduces a novel framework called *detect-then-impute conformal prediction*. This framework first employs an outlier detection procedure on the test feature and then utilizes an imputation method to fill in those cells identified as outliers. To quantify the uncertainty in the processed test feature, we adaptively apply the detection and imputation procedures to the calibration set, thereby constructing exchangeable features for the conformal prediction interval of the test label. We develop two practical algorithms, $\texttt{PDI-CP}$ and $\texttt{JDI-CP}$, and provide a distribution-free coverage analysis under some commonly used detection and imputation procedures. Notably, $\texttt{JDI-CP}$ achieves a finite sample $1-2\alpha$ coverage guarantee. Numerical experiments on both synthetic and real datasets demonstrate that our proposed algorithms exhibit robust coverage properties and comparable efficiency to the oracle baseline.

Quality statistical inference requires a sufficient amount of data, which can be missing or hard to obtain. To this end, prediction-powered inference has risen as a promising methodology, but existing approaches are largely limited to Z-estimation problems such as inference of means and quantiles. In this paper, we apply ideas of prediction-powered inference to e-values. By doing so, we inherit all the usual benefits of e-values -- such as anytime-validity, post-hoc validity and versatile sequential inference -- as well as greatly expand the set of inferences achievable in a prediction-powered manner. In particular, we show that every inference procedure that can be framed in terms of e-values has a prediction-powered counterpart, given by our method. We showcase the effectiveness of our framework across a wide range of inference tasks, from simple hypothesis testing and confidence intervals to more involved procedures for change-point detection and causal discovery, which were out of reach of previous techniques. Our approach is modular and easily integrable into existing algorithms, making it a compelling choice for practical applications.

*De novo* peptide sequencing is a fundamental computational technique for ascertaining amino acid sequences of peptides directly from tandem mass spectrometry data, eliminating the need for reference databases. Cutting-edge models encode the observed mass spectra into latent representations from which peptides are predicted auto-regressively. However, the issue of missing fragmentation, attributable to factors such as suboptimal fragmentation efficiency and instrumental constraints, presents a formidable challenge in practical applications. To tackle this obstacle, we propose a novel computational paradigm called $\underline{\textbf{L}}$atent $\underline{\textbf{I}}$mputation before $\underline{\textbf{P}}$rediction (LIPNovo). LIPNovo is devised to compensate for missing fragmentation information within observed spectra before executing the final peptide prediction. Rather than generating raw missing data, LIPNovo performs imputation in the latent space, guided by the theoretical peak profile of the target peptide sequence. The imputation process is conceptualized as a set-prediction problem, utilizing a set of learnable peak queries to reason about the relationships among observed peaks and directly generate the latent representations of theoretical peaks through optimal bipartite matching. In this way, LIPNovo manages to supplement missing information during inference and thus boosts performance. Despite its simplicity, experiments on three benchmark datasets demonstrate that LIPNovo outperforms state-of-the-art methods by large margins. Code is available at https://github.com/usr922/LIPNovo.

Weak-to-strong (W2S) generalization is a type of finetuning (FT) where a strong (large) student model is trained on pseudo-labels generated by a weak teacher. Surprisingly, W2S FT often outperforms the weak teacher. We seek to understand this phenomenon through the observation that FT often occurs in intrinsically low-dimensional spaces. Leveraging the low intrinsic dimensionality of FT, we analyze W2S in the ridgeless regression setting from a variance reduction perspective. For a strong student-weak teacher pair with sufficiently expressive low-dimensional feature subspaces $\mathcal{V}_s, \mathcal{V}_w$, we provide an exact characterization of the variance that dominates the generalization error of W2S. This unveils a virtue of discrepancy between the strong and weak models in W2S: the variance of the weak teacher is inherited by the strong student in $\mathcal{V}_s \cap \mathcal{V}_w$, while reduced by a factor of $\mathrm{dim}(\mathcal{V}_s)/N$ in the subspace of discrepancy $\mathcal{V}_w \setminus \mathcal{V}_s$ with $N$ pseudo-labels for W2S. Our analysis further casts light on the sample complexities and the scaling of performance gap recovery in W2S. The analysis is supported by experiments on synthetic regression problems, as well as real vision and NLP tasks.

Handling missing values at test time is challenging for machine learning models, especially when aiming for both high accuracy and interpretability. Established approaches often add bias through imputation or excessive model complexity via missingness indicators. Moreover, either method can obscure interpretability, making it harder to understand how the model utilizes the observed variables in predictions. We propose *missingness-avoiding* (MA) machine learning, a general framework for training models to rarely require the values of missing (or imputed) features at test time. We create tailored MA learning algorithms for decision trees, tree ensembles, and sparse linear models by incorporating classifier-specific regularization terms in their learning objectives. The tree-based models leverage contextual missingness by reducing reliance on missing values based on the observed context. Experiments on real-world datasets demonstrate that **MA-DT, MA-LASSO, MA-RF**, and **MA-GBT** effectively reduce the reliance on features with missing values while maintaining predictive performance competitive with their unregularized counterparts. This shows that our framework gives practitioners a powerful tool to maintain interpretability in predictions with test-time missing values.

*Statistical adversarial data detection* (SADD) detects whether an upcoming batch contains *adversarial examples* (AEs) by measuring the distributional discrepancies between *clean examples* (CEs) and AEs. In this paper, we explore the strength of SADD-based methods by theoretically showing that minimizing distributional discrepancy can help reduce the expected loss on AEs. Despite these advantages, SADD-based methods have a potential limitation: they discard inputs that are detected as AEs, leading to the loss of clean information within those inputs. To address this limitation, we propose a two-pronged adversarial defense method, named ***D***istributional-discrepancy-based ***A***dversarial ***D***efense (DAD). In the training phase, DAD first optimizes the test power of the *maximum mean discrepancy* (MMD) to derive MMD-OPT, which is *a stone that kills two birds*. MMD-OPT first serves as a *guiding signal* to minimize the distributional discrepancy between CEs and AEs to train a denoiser. Then, it serves as a *discriminator* to differentiate CEs and AEs during inference. Overall, in the inference stage, DAD consists of a two-pronged process: (1) directly feeding the detected CEs into the classifier, and (2) removing noise from the detected AEs by the distributional-discrepancy-based denoiser. Extensive experiments show that DAD outperforms current *state-of-the-art* (SOTA) defense methods by *simultaneously* improving clean and robust accuracy on CIFAR-10 and ImageNet-1K against adaptive white-box attacks. Codes are publicly available at: https://github.com/tmlr-group/DAD.

The isomorphism problem is a key challenge in both graph and hypergraph domains, crucial for applications like protein design, chemical pathways, and community detection. Hypergraph isomorphism, which models high-order relationships in real-world scenarios, remains underexplored compared to the graph isomorphism. Current algorithms for hypergraphs, like the 1-dimensional generalized Weisfeiler-Lehman test (1-GWL), lag behind advancements in graph isomorphism tests, limiting most hypergraph neural networks to 1-GWL's expressive power. To address this, we propose the high-dimensional GWL (k-GWL), generalizing k-WL from graphs to hypergraphs. We prove that k-GWL reduces to k-WL for simple graphs, and thus develop a unified isomorphism method for both graphs and hypergraphs. We also successfully establish a clear and complete understanding of the GWL hierarchy of expressivity, showing that (k+1)-GWL is more expressive than k-GWL with illustrative examples. Based on k-GWL, we develop a hypergraph neural network model named k-HNN with improved expressive power of k-GWL, which achieves superior performance on real-world datasets, including a 6\% accuracy improvement on the Steam-Player dataset over the runner-up. Our code is available at https://github.com/talence-zcq/KGWL.

Conformal Prediction is a widely studied technique to construct prediction sets of future observations. Most conformal prediction methods focus on achieving the necessary coverage guarantees, but do not provide formal guarantees on the size (volume) of the prediction sets. We first prove the impossibility of volume optimality where any distribution-free method can only find a trivial solution. We then introduce a new notion of volume optimality by restricting the prediction sets to belong to a set family (of finite VC-dimension), specifically a union of $k$-intervals. Our main contribution is an efficient distribution-free algorithm based on dynamic programming (DP) to find a union of $k$-intervals that is guaranteed for any distribution to have near-optimal volume among all unions of $k$-intervals satisfying the desired coverage property. By adopting the framework of distributional conformal prediction (Chernozhukov et al., 2021), the new DP based conformity score can also be applied to achieve approximate conditional coverage and conditional restricted volume optimality, as long as a reasonable estimator of the conditional CDF is available. While the theoretical results already establish volume-optimality guarantees, they are complemented by experiments that demonstrate that our method can significantly outperform existing methods in many settings.

Transforming complex actions into discrete skill abstractions has demonstrated strong potential for robotic manipulation.Existing approaches mainly leverage latent variable models, e.g., VQ-VAE, to learn skill abstractions through learned vectors (codebooks), while they suffer from codebook collapse and modeling the causal relationship between learned skills. To address these limitations, we present **S**kill **T**raining with **A**ugmented **R**otation (**STAR**), a framework that advances both skill learning and composition to complete complex behaviors. Specifically, to prevent codebook collapse, we devise rotation-augmented residual skill quantization (RaRSQ).It encodes relative angles between encoder outputs into the gradient flow by rotation-based gradient mechanism. Points within the same skill code are forced to be either pushed apart or pulled closer together depending on gradient directions.Further, to capture the casual relationship between skills, we present causal skill transformer (CST) which explicitly models dependencies between skill representations through an autoregressive mechanism for coherent action generation.Extensive experiments demonstrate the superiority of STAR on both LIBERO benchmark and realworld tasks, with around 12% improvement over the baselines.

Vovk (2015) introduced cross-conformal prediction, a modification of split conformal designed to improve the width of prediction sets. The method, when trained with a miscoverage rate equal to $\alpha$ and $n \gg K$, ensures a marginal coverage of at least $1 - 2\alpha - 2(1-\alpha)(K-1)/(n+K)$, where $n$ is the number of observations and $K$ denotes the number of folds. A simple modification of the method achieves coverage of at least $1-2\alpha$. In this work, we propose new variants of both methods that yield smaller prediction sets without compromising the latter theoretical guarantees. The proposed methods are based on recent results deriving more statistically efficient combination of p-values that leverage exchangeability and randomization. Simulations confirm the theoretical findings and bring out some important tradeoffs.

The availability of machine learning systems that can effectively perform arbitrary tasks has led to synthetic labels from these systems being used in applications of statistical inference, such as data analysis or model evaluation. The Prediction Powered Inference (PPI) framework provides a way of leveraging both a large pool of pseudo-labelled data and a small sample with real, high-quality labels to produce a low-variance, unbiased estimate of the quantity being evaluated for. Most work on PPI considers a relatively sizable set of labelled samples, which can be resource intensive to obtain. However, we find that when labelled data is scarce, the PPI++ method can perform even worse than classical inference. We analyze this phenomenon by relating PPI++ to ordinary least squares regression, which also experiences high variance with small sample sizes, and use this regression framework to better understand the efficacy of PPI. Motivated by this, we present two new PPI-based techniques that leverage robust regressors to produce even lower variance estimators in the few-label regime

Conformal Prediction (CP) is a principled framework for quantifying uncertainty in black-box learning models, by constructing prediction sets with finite-sample coverage guarantees. Traditional approaches rely on scalar nonconformity scores, which fail to fully exploit the geometric structure of multivariate outputs, such as in multi-output regression or multiclass classification. Recent methods addressing this limitation impose predefined convex shapes for the prediction sets, potentially misaligning with the intrinsic data geometry. We introduce a novel CP procedure handling multivariate score functions through the lens of optimal transport. Specifically, we leverage Monge-Kantorovich vector ranks and quantiles to construct prediction region with flexible, potentially non-convex shapes, better suited to the complex uncertainty patterns encountered in multivariate learning tasks. We prove that our approach ensures finite-sample, distribution-free coverage properties, similar to typical CP methods. We then adapt our method for multi-output regression and multiclass classification, and also propose simple adjustments to generate adaptive prediction regions with asymptotic conditional coverage guarantees. Finally, we evaluate our method on practical regression and classification problems, illustrating its advantages in terms of (conditional) coverage and efficiency.

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.

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.

Diffusion models have demonstrated exceptional performances in various fields of generative modeling, but suffer from slow sampling speed due to their iterative nature. While this issue is being addressed in continuous domains, discrete diffusion models face unique challenges, particularly in capturing dependencies between elements (e.g., pixel relationships in image, sequential dependencies in language) mainly due to the computational cost of processing high-dimensional joint distributions. In this paper, (i) we propose "mixture" models for discrete diffusion that are capable of treating dimensional correlations while remaining scalable, and (ii) we provide a set of loss functions for distilling the iterations of existing models. Two primary theoretical insights underpin our approach: First, conventional models with element-wise independence can well approximate the data distribution, but essentially require *many sampling steps*. Second, our loss functions enable the mixture models to distill such many-step conventional models into just a few steps by learning the dimensional correlations. Our experimental results show the effectiveness of the proposed method in distilling pretrained discrete diffusion models across image and language domains. The code used in the paper is available at https://github.com/sony/di4c.

Unconscious bias has been shown to influence how we assess our peers, with consequences for hiring, promotions and admissions. In this work, we focus on affinity bias, the component of unconscious bias which leads us to prefer people who are similar to us, despite no deliberate intention of favoritism. In a world where the people hired today become part of the hiring committee of tomorrow, we are particularly interested in understanding (and mitigating) how affinity bias affects this feedback loop. This problem has two distinctive features: 1) we only observe the _biased value_ of a candidate, but we want to optimize with respect to their _real value_ 2) the bias towards a candidate with a specific set of traits depends on the _fraction_ of people in the hiring committee with the same set of traits. We introduce a new bandits variant that exhibits those two features, which we call affinity bandits. Unsurprisingly, classical algorithms such as UCB often fail to identify the best arm in this setting. We prove a new instance-dependent regret lower bound, which is larger than that in the standard bandit setting by a multiplicative function of $K$. Since we treat rewards that are _time-varying_ and _dependent on the policy's past actions_, deriving this lower bound requires developing proof techniques beyond the standard bandit techniques. Finally, we design an elimination-style algorithm which nearly matches this regret, despite never observing the real rewards.