NeurIPS 2025 Papers

Identifying drug-drug interactions (DDIs) is critical for ensuring drug safety and advancing drug development, a topic that has garnered significant research interest. While existing methods have made considerable progress, approaches relying solely on known DDIs face a key challenge when applied to drugs with limited data: insufficient exploration of the space of unlabeled pairwise drugs. To address these issues, we innovatively introduce S$^2$VM, a Self-supervised Visual pretraining framework for pair-wise Molecules, to fully fuse structural representations and explore the space of drug pairs for DDI prediction. S$^2$VM incorporates the explicit structure and correlations of visual molecules, such as the positional relationships and connectivity between functional substructures. Specifically, we blend the visual fragments of drug pairs into a unified input for joint encoding and then recover molecule-specific visual information for each drug individually. This approach integrates fine-grained structural representations from unlabeled drug pair data. By using visual fragments as anchors, S$^2$VM effectively captures the spatial information of local molecular components within visual molecules, resulting in more comprehensive embeddings of drug pairs. Experimental results show that S$^2$VM achieves state-of-the-art performance on widely used benchmarks, with Macro-F1 score improvements of 4.21% and 3.31%, respectively. Further extensive results and theoretical analysis demonstrate the effectiveness of S$^2$VM for both few-shot and novel drugs.

Recent methods in language model interpretability employ techniques such as sparse autoencoders to decompose residual stream contributions into linear, semantically-meaningful features. Our work demonstrates that an underlying assumption of these methods—that residual stream contributions build additively upon each other—is insufficient to fully explain model behavior. Specifically, we identify the Transformer Layer Correction Mechanism (TLCM), wherein adjacent transformer layers systematically counteract each other's contributions to the residual stream. TLCM appears in 5 out of 7 major open-source model families and activates across nearly all tokens in diverse texts. To understand TLCM, we show that it emerges during pretraining, operates most strongly on punctuation and numbers, and adaptively calibrates its correction strength based on the preceding layer's output. We further show that TLCM actively corrects a small subspace and promotes other subspaces, different from standard model behavior. We advance the ``propose-and-reject'' hypothesis: layers may propose multiple candidate features, while subsequent layers selectively filter out inappropriate ones. Finally, we discuss how our findings help explain three persistent challenges in feature-based interpretability: why extracted features descriptions often suffer from low specificity; why feature-based interventions for model steering fail at low magnitude; why recent work finds cross-layer transcoders outperform SAEs.

Online structured prediction is a task of sequentially predicting outputs with complex structures based on inputs and past observations, encompassing online classification. Recent studies showed that in the full-information setting, we can achieve finite bounds on the *surrogate regret*, *i.e.,* the extra target loss relative to the best possible surrogate loss. In practice, however, full-information feedback is often unrealistic as it requires immediate access to the whole structure of complex outputs. Motivated by this, we propose algorithms that work with less demanding feedback, *bandit* and *delayed* feedback. For bandit feedback, by using a standard inverse-weighted gradient estimator, we achieve a surrogate regret bound of $O(\sqrt{KT})$ for the time horizon $T$ and the size of the output set $K$. However, $K$ can be extremely large when outputs are highly complex, resulting in an undesirable bound. To address this issue, we propose another algorithm that achieves a surrogate regret bound of $O(T^{2/3})$, which is independent of $K$. This is achieved with a carefully designed pseudo-inverse matrix estimator. Furthermore, we numerically compare the performance of these algorithms, as well as existing ones. Regarding delayed feedback, we provide algorithms and regret analyses that cover various scenarios, including full-information and bandit feedback, as well as fixed and variable delays.

The emergence of large-scale pre-trained point cloud models has significantly advanced 3D scene understanding, but adapting these models to specific downstream tasks typically demands full fine-tuning, incurring high computational and storage costs. Parameter-efficient fine-tuning (PEFT) techniques, successful in natural language processing and 2D vision tasks, would underperform when naively applied to 3D point cloud models due to significant geometric and spatial distribution shifts. Existing PEFT methods commonly treat points as orderless tokens, neglecting important local spatial structures and global geometric contexts in 3D modeling. To bridge this gap, we introduce the Geometric Encoding Mixer (GEM), a novel geometry-aware PEFT module specifically designed for 3D point cloud transformers. GEM explicitly integrates fine-grained local positional encodings with a lightweight latent attention mechanism to capture comprehensive global context, thereby effectively addressing the spatial and geometric distribution mismatch. Extensive experiments demonstrate that GEM achieves performance comparable to or sometimes even exceeding full fine-tuning, while only updating 1.6% of the model's parameters, fewer than other PEFT methods. With significantly reduced training time and memory requirements, our approach thus sets a new benchmark for efficient, scalable, and geometry-aware fine-tuning of large-scale 3D point cloud models. Code is available at https://github.com/LiyaoTang/GEM.

Arctic sea ice performs a vital role in global climate and has paramount impacts on both polar ecosystems and coastal communities. In the last few years, multiple deep learning based pan-Arctic sea ice concentration (SIC) forecasting methods have emerged and showcased superior performance over physics-based dynamical models. However, previous methods forecast SIC at a fixed temporal granularity, e.g. sub-seasonal or seasonal, thus only leveraging inter-granularity information and overlooking the plentiful inter-granularity correlations. SIC at various temporal granularities exhibits cumulative effects and are naturally consistent, with short-term fluctuations potentially impacting long-term trends and long-term trends provides effective hints for facilitating short-term forecasts in Arctic sea ice. Therefore, in this study, we propose to cultivate temporal multi-granularity that naturally derived from Arctic sea ice reanalysis data and provide a unified perspective for modeling SIC via our Sea Ice Fusion framework. SIFusion is delicately designed to leverage both intra-granularity and inter-granularity information for capturing granularity-consistent representations that promote forecasting skills. Our extensive experiments show that SIFusion outperforms off-the-shelf deep learning models for their specific temporal granularity.

LLM-based formal proof assistants (e.g., in Lean) hold great promise for automating mathematical discovery. But beyond syntactic correctness, do these systems truly understand mathematical structure as humans do? We investigate this question in context of mathematical inequalities---specifically the prover's ability to recognize that the given problem simplifies by applying a known inequality such as AM/GM. Specifically, we are interested in their ability to do this in a {\em compositional setting} where multiple inequalities must be applied as part of a solution. We introduce \ineqcomp, a benchmark built from elementary inequalities through systematic transformations, including variable duplication, algebraic rewriting, and multi-step composition. Although these problems remain easy for humans, we find that most provers---including Goedel, STP, and Kimina-7B---struggle significantly. DeepSeek-Prover-V2-7B shows relative robustness, but still suffers a 20\% performance drop (pass@32). Even for DeepSeek-Prover-V2-671B model, the gap between compositional variants and seed problems exists, implying that simply scaling up the model size alone does not fully solve the compositional weakness. Strikingly, performance remains poor for all models even when formal proofs of the constituent parts are provided in context, revealing that the source of weakness is indeed in compositional reasoning. Our results expose a persisting gap between the generalization behavior of current AI provers and human mathematical intuition. All data and evaluation code can be found at \url{https://github.com/haoyuzhao123/LeanIneqComp}.

Deployment of neural networks on resource-constrained devices demands models that are both compact and robust to adversarial inputs. However, compression and adversarial robustness often conflict. In this work, we introduce a dynamical low-rank training scheme enhanced with a novel spectral regularizer that controls the condition number of the low-rank core in each layer. This approach mitigates the sensitivity of compressed models to adversarial perturbations without sacrificing clean accuracy. The method is model- and data-agnostic, computationally efficient, and supports rank adaptivity to automatically compress the network at hand. Extensive experiments across standard architectures, datasets, and adversarial attacks show the regularized networks can achieve over 94 compression while recovering or improving adversarial accuracy relative to uncompressed baselines.

Zero-shot object navigation (ZSON) allows robots to find target objects in unfamiliar environments using natural language instructions, without relying on pre-built maps or task-specific training. Recent general-purpose models, such as large language models (LLMs) and vision-language models (VLMs), equip agents with semantic reasoning abilities to estimate target object locations in a zero-shot manner. However, these models often greedily select the next goal without maintaining a global understanding of the environment and are fundamentally limited in the spatial reasoning necessary for effective navigation. To overcome these limitations, we propose a novel 3D voxel-based belief map that estimates the target’s prior presence distribution within a voxelized 3D space. This approach enables agents to integrate semantic priors from LLMs and visual embeddings with hierarchical spatial structure, alongside real-time observations, to build a comprehensive 3D global posterior belief of the target’s location. Building on this 3D voxel map, we introduce BeliefMapNav, an efficient navigation system with two key advantages: i) grounding LLM semantic reasoning within the 3D hierarchical semantics voxel space for precise target position estimation, and ii) integrating sequential path planning to enable efficient global navigation decisions. Experiments on HM3D and HSSD benchmarks show that BeliefMapNav achieves state-of-the-art (SOTA) Success Rate (SR) and Success weighted by Path Length (SPL), with a notable 9.7 SPL improvement over the previous best SR method, validating its effectiveness and efficiency.

The rise of parallel computing hardware has made it increasingly important to understand which nonlinear state space models can be efficiently parallelized. Recent advances have shown that evaluating a state space model can be recast as solving a parallelizable optimization problem, and sometimes this approach yields dramatic speed-ups in evaluation time. However, the factors that govern the difficulty of these optimization problems remain unclear, limiting the larger adoption of the technique. In this work, we establish a precise relationship between the dynamics of a nonlinear system and the conditioning of its corresponding optimization formulation. We show that the predictability of a system, defined as the degree to which small perturbations in state influence future behavior, directly governs the number of optimization steps required for evaluation. In predictable systems, the state trajectory can be computed in $\mathcal{O}((\log T)^2)$ time, where $T$ is the sequence length, a major improvement over the conventional sequential approach. In contrast, chaotic or unpredictable systems exhibit poor conditioning, with the consequence that parallel evaluation converges too slowly to be useful. Importantly, our theoretical analysis demonstrates that for predictable systems, the optimization problem is always well-conditioned, whereas for unpredictable systems, the conditioning degrades exponentially as a function of the sequence length. We validate our claims through extensive experiments, providing practical guidance on when nonlinear dynamical systems can be efficiently parallelized, and highlighting predictability as a key design principle for parallelizable models.

Most work on adaptive data analysis assumes that samples in the dataset are independent. When correlations are allowed, even the non-adaptive setting can become intractable, unless some structural constraints are imposed. To address this, Bassily and Freund [2016] introduced the elegant framework of *concentrated queries*, which requires the analyst to restrict itself to queries that are concentrated around their expected value. While this assumption makes the problem trivial in the non-adaptive setting, in the adaptive setting it remains quite challenging. In fact, all known algorithms in this framework support significantly fewer queries than in the independent case: At most $O(n)$ queries for a sample of size $n$, compared to $O(n^2)$ in the independent setting. In this work, we prove that this utility gap is inherent under the current formulation of the concentrated queries framework, assuming some natural conditions on the algorithm. Additionally, we present a simplified version of the best-known algorithms that match our impossibility result.

Federated Learning enables collaborative training across decentralized edge devices while preserving data privacy. However, fine-tuning large-scale pre-trained models in federated learning is hampered by substantial communication overhead and client resource limitations. Parameter-efficient fine-tuning methods like Low-Rank Adaptation (LoRA) reduce resource demands but suffer from aggregation discrepancies and heightened vulnerability to label noise, particularly in heterogeneous federated settings. In this paper, we introduce RFedLR, a robust federated PEFT framework designed to overcome these challenges. RFedLR integrates two key components: (1) Sensitivity-aware robust tuning, which identifies and selectively updates noise-sensitive parameters to bolster local robustness against label noise, and (2) Adaptive federated LoRA aggregation, which dynamically weights and aggregates LoRA updates based on their importance and stability to minimize bias and noise propagation. Comprehensive experimental validation shows RFedLR outperforms existing methods, achieving superior accuracy and robustness in noisy federated scenarios. Our code is available at: https://github.com/FangXiuwen/RFedLR

Existing machine unlearning (MU) approaches exhibit significant sensitivity to hyperparameters, requiring meticulous tuning that limits practical deployment. In this work, we first empirically demonstrate the instability and suboptimal performance of existing popular MU methods when deployed in different scenarios. To address this issue, we propose Dual Optimizer (DualOptim), which incorporates adaptive learning rate and decoupled momentum factors. Empirical and theoretical evidence demonstrates that DualOptim contributes to effective and stable unlearning. Through extensive experiments, we show that DualOptim can significantly boost MU efficacy and stability across diverse tasks, including image classification, image generation, and large language models, making it a versatile approach to empower existing MU algorithms.

The role of reinforcement learning (RL) in enhancing the reasoning of large language models (LLMs) is becoming increasingly significant. Despite the success of RL in many scenarios, there are still many challenges in improving the reasoning of LLMs. One key challenge is the sparse reward, which introduces more training variance in policy optimization and makes it difficult to obtain a good estimation for value function in Actor-Critic (AC) methods. To address these issues, we introduce Direct Advantage-Based Policy Optimization (DAPO), a novel step-level offline RL algorithm with theoretical guarantees for enhancing the reasoning abilities of LLMs. Unlike response-level methods (such as DPO and GRPO) that the update directions of all reasoning steps are governed by the outcome reward uniformly, DAPO employs a critic function to provide step-level dense signals for policy optimization. Additionally, the actor and critic in DAPO are trained independently, ensuring that critic is a good estimation of true state value function and avoiding the co-training instability observed in standard AC methods. We train DAPO on mathematical and code problems and then evaluate its performance on multiple benchmarks. Our results show that DAPO can effectively enhance the mathematical and code capabilities on both SFT models and RL models, demonstrating the effectiveness of DAPO.

Graph heterophily, where connected nodes have different labels, has attracted significant interest recently. Most existing works adopt a simplified approach - using low-pass filters for homophilic graphs and high-pass filters for heterophilic graphs. However, we discover that the relationship between graph heterophily and spectral filters is more complex - the optimal filter response varies across frequency components and does not follow a strict monotonic correlation with heterophily degree. This finding challenges conventional fixed filter designs and suggests the need for adaptive filtering to preserve expressiveness in graph embeddings. Formally, natural questions arise: Given a heterophilic graph $\mathcal{G}$ , how and to what extent will the varying heterophily degree of $\mathcal{G}$ affect the performance of GNNs? How can we design adaptive filters to fit those varying heterophilic connections? Our theoretical analysis reveals that the average frequency response of GNNs and graph heterophily degree do not follow a strict monotonic correlation, necessitating adaptive graph filters to guarantee good generalization performance. Hence, we propose HeroFilter, a simple yet powerful GNN, which extracts information across the heterophily spectrum and combines salient representations through adaptive mixing. HeroFilter's superior performance achieves up to 9.2% accuracy improvement over leading baselines across homophilic and heterophilic graphs.

Retrieval-Augmented Generation (RAG) provides additional contextual knowledge to complement the parametric knowledge in Large Language Models (LLMs). These two knowledge interweave to enhance the accuracy and timeliness of LLM responses. However, the internal mechanisms by which LLMs utilize these knowledge remain unclear. We propose modeling the forward propagation of knowledge as an entity flow, employing this framework to trace LLMs' internal behaviors when processing mixed-source knowledge. Linear probing utilizes a trainable linear classifier to detect specific attributes in hidden layers. However, once trained, a probe cannot adapt to dynamically specified entities. To address this challenge, we construct an entity-aware probe, which introduces special tokens to mark probing targets and employs a small trainable rank-8 lora update to process these special markers. We first verify this approach through an attribution experiment, demonstrating that it can accurately detect information about ad-hoc entities from complex hidden states. Next, we trace entity flows across layers to understand how LLMs reconcile conflicting knowledge internally. Our probing results reveal that contextual and parametric knowledge are routed between tokens through distinct sets of attention heads, supporting attention competition only within knowledge types. While conflicting knowledge maintains a residual presence across layers, aligned knowledge from multiple sources gradually accumulates, with the magnitude of this accumulation directly determining its influence on final outputs.

We consider the problem of validating whether a neural posterior estimate $q(\theta \mid x)$ is an accurate approximation to the true, unknown true posterior $p(\theta \mid x)$. Existing methods for evaluating the quality of an NPE estimate are largely derived from classifier-based tests or divergence measures, but these suffer from several practical drawbacks. As an alternative, we introduce the *Conditional Localization Test* (**CoLT**), a principled method designed to detect discrepancies between $p(\theta \mid x)$ and $q(\theta \mid x)$ across the full range of conditioning inputs. Rather than relying on exhaustive comparisons or density estimation at every $x$, CoLT learns a localization function that adaptively selects points $\theta_l(x)$ where the neural posterior $q$ deviates most strongly from the true posterior $p$ for that $x$. This approach is particularly advantageous in typical simulation-based inference settings, where only a single draw $\theta \sim p(\theta \mid x)$ from the true posterior is observed for each conditioning input, but where the neural posterior $q(\theta \mid x)$ can be sampled an arbitrary number of times. Our theoretical results establish necessary and sufficient conditions for assessing distributional equality across all $x$, offering both rigorous guarantees and practical scalability. Empirically, we demonstrate that CoLT not only performs better than existing methods at comparing $p$ and $q$, but also pinpoints regions of significant divergence, providing actionable insights for model refinement. These properties position CoLT as a state-of-the-art solution for validating neural posterior estimates.

We consider the problem of computing stationary points in min-max optimization, with a focus on the special case of Nash equilibria in (two-)team zero-sum games. We first show that computing $\epsilon$-Nash equilibria in $3$-player $\text{\emph{adversarial}}$ team games---wherein a team of $2$ players competes against a $\text{\emph{single}}$ adversary---is $\textsf{CLS}$-complete, resolving the complexity of Nash equilibria in such settings. Our proof proceeds by reducing from $\text{\emph{symmetric}}$ $\epsilon$-Nash equilibria in $\text{\emph{symmetric}}$, identical-payoff, two-player games, by suitably leveraging the adversarial player so as to enforce symmetry---without disturbing the structure of the game. In particular, the class of instances we construct comprises solely polymatrix games, thereby also settling a question left open by Hollender, Maystre, and Nagarajan (2024). Moreover, we establish that computing $\text{\emph{symmetric}}$ (first-order) equilibria in $\text{\emph{symmetric}}$ min-max optimization is $\textsf{PPAD}$-complete, even for quadratic functions. Building on this reduction, we show that computing symmetric $\epsilon$-Nash equilibria in symmetric, $6$-player ($3$ vs. $3$) team zero-sum games is also $\textsf{PPAD}$-complete, even for $\epsilon = \text{poly}(1/n)$. As a corollary, this precludes the existence of symmetric dynamics---which includes many of the algorithms considered in the literature---converging to stationary points. Finally, we prove that computing a $\text{\emph{non-symmetric}}$ $\text{poly}(1/n)$-equilibrium in symmetric min-max optimization is $\textsf{FNP}$-hard.

In federated learning (FL), models must \emph{converge quickly} under tight communication budgets while \emph{generalizing} across non-IID client distributions. These twin requirements have naturally led to two widely used techniques: client/server \emph{momentum} to accelerate progress, and \emph{sharpness-aware minimization} (SAM) to prefer flat solutions. However, simply combining momentum and SAM leaves two structural issues unresolved in non-IID FL. We identify and formalize two failure modes: \emph{local–global curvature misalignment} (local SAM directions need not reflect the global loss geometry) and \emph{momentum-echo oscillation} (late-stage instability caused by accumulated momentum). To our knowledge, these failure modes have not been jointly articulated and addressed in the FL literature. We propose \textbf{FedWMSAM} to address both failure modes. First, we construct a momentum-guided global perturbation from server-aggregated momentum to align clients' SAM directions with the global descent geometry, enabling a \emph{single-backprop} SAM approximation that preserves efficiency. Second, we couple momentum and SAM via a cosine-similarity adaptive rule, yielding an early-momentum, late-SAM two-phase training schedule. We provide a non-IID convergence bound that \emph{explicitly models the perturbation-induced variance} $\sigma_\rho^2=\sigma^2+(L\rho)^2$ and its dependence on $(S,K,R,N)$ on the theory side. We conduct extensive experiments on multiple datasets and model architectures, and the results validate the effectiveness, adaptability, and robustness of our method, demonstrating its superiority in addressing the optimization challenges of Federated Learning. Our code is available at \url{https://github.com/Li-Tian-Le/NeurlPS_FedWMSAM}.

Marked temporal point processes (MTPPs) model sequences of events occurring at irregular time intervals, with wide-ranging applications in fields such as healthcare, finance and social networks. We propose the _state-space point process_ (S2P2) model, a novel and performant model that leverages techniques derived for modern deep state-space models (SSMs) to overcome limitations of existing MTPP models, while simultaneously imbuing strong inductive biases for continuous-time event sequences that other discrete sequence models (i.e., RNNs, transformers) do not capture. Inspired by the classical linear Hawkes processes, we propose an architecture that interleaves stochastic jump differential equations with nonlinearities to create a highly expressive intensity-based MTPP model, without the need for restrictive parametric assumptions for the intensity. Our approach enables efficient training and inference with a parallel scan, bringing linear complexity and sublinear scaling while retaining expressivity to MTPPs. Empirically, S2P2 achieves state-of-the-art predictive likelihoods across eight real-world datasets, delivering an average improvement of 33% over the best existing approaches.