NeurIPS 2026 论文列表

Protein-molecule virtual screening is increasingly cast as a problem of representation learning in a shared embedding space. Existing methods rely on dense holistic alignment, entangling invariant binding determinants with nuisance correlations and limiting transfer to new targets. It has been noted that binding in protein–molecule systems involves sparse cross-modality interactions: binding is governed by a small contact interface and a few decisive local interactions (e.g., hydrogen bonds, hydrophobic contacts, and salt bridges) rather than the global structures of the protein and molecule. We hypothesize that uncovering and leveraging sparse interaction patterns is critical for generalization beyond the training data, as these patterns are reusable and expected to improve performance across different scenarios. In this paper, we aim to identify and leverage sparse interaction patterns, and verify our hypothesis. Since the training data contain only observed binding pairs, we formalize this prior via a V-structure causal model under Heckman-style selection, and establish three theoretical results: (i) the latent concepts of interacting proteins and molecules are not identifiable without appropriate sparsity constraints;(ii) these concepts and their sparse interactions are component-wise identifiable under structural sparsity conditions; and (iii) a low-rank relaxation of these conditions yields subspace identifiability of the concepts and interactions. Inspired by these principles, we propose CausalBind with three implementation variants. Extensive experiments on DUD-E and LIT-PCBA benchmarks show that all variants consistently outperform strong baselines across all metrics, respectively.

Recent AI regulations increasingly emphasize the need for mechanisms that preserve the utility of data for AI innovation while preventing misuse, particularly by enforcing purpose limitation in downstream AI applications. In practice, enforcing this principle remains challenging, as released data can be trivially fed into arbitrary models beyond its declared intent. Existing approaches attempt to mitigate this risk by either perturbing data or retraining models to limit unintended use. These strategies, however, offer no protection against inference by unknown or externally trained models, or fundamentally rely on control over the training or deployment. In this work, we introduce non-transferable examples (NTEs), recoded data that act as a task-level "ciphertext" decodable only by a designated model. Where adversarial examples exploit sensitive input directions, NTEs use the complementary insensitive subspace: a training-free, data-agnostic recoding within a model-specific low-sensitivity subspace preserves the authorized model's outputs while degrading unauthorized ones through subspace misalignment. We establish formal bounds certifying output fidelity for the authorized model and showing unauthorized degradation scales with measurable spectral misalignment between models. Empirically, NTEs preserve authorized-model performance across diverse vision backbones and vision-language models, while unauthorized models collapse even under adaptive reconstruction attacks. These results establish NTEs as a practical means to preserve intended data utility while preventing unauthorized exploitation. Our source code and visual demos are available at: https://github.com/model-specific/non-transferable-examples.

Image Manipulation Localization (IML) is commonly formulated as a fully supervised learning task that estimates the optimal manipulation mask $y$ for a given image $x$. In this work, we first reveal the latent nature of artifacts and thus reinterpret IML as a latent-variable problem, $P(y| x)=\int P(y|z) P(z|x)dz$, where $z$ denotes the artifacts. Following this interpretation, we pinpoint the cause for the current IML models' insufficiency as their implicit artifacts modeling strategy, highlighting the necessity of modeling $z$ in an explicit manner. Without direct labels, feature disentanglement is the most appropriate solution for this explicit modeling. Accordingly, we propose a two-stage learning paradigm with the Pairwise Artifacts Learning (PAL) and Standard Localization (SL) phases to estimate $P(z|x)$ and $P (y|z)$ via edit relations. To support our edit-relation-based learning, we further curate EditGroup-45K, a source-anchored dataset organized into edit groups for pair construction. Extensive experiments show that our PAL paradigm yields consistent improvements across diverse IML architectures, and empirical analyses further verify that PAL does capture artifacts explicitly through feature disentanglement. Code and dataset will be publicly available.

Operational disaster response goes beyond damage assessment, requiring responders to integrate multi-sensor signals, reason over road networks, populations and key facilities, plan evacuations, and produce actionable reports. However, prior work largely isolates remote-sensing perception or evaluates generic tool use, leaving the end-to-end workflows of emergency operations underexplored. In this paper, we introduce **D**isaster **O**perational **R**esponse **A**gent benchmark (**DORA**), the first agentic benchmark for end-to-end disaster response: 515 expert-authored tasks across 45 real-world disaster events spanning 10 types, paired with expert-verified, replayable gold trajectories totaling 3,500 tool-call steps. Tasks span five dimensions that cover the operational disaster-response pipeline: disaster perception, spatial relational analysis, rescue and evacuation planning, temporal evolution reasoning, and multi-modal report synthesis. Agents compose calls from a 108-tool MCP library over heterogeneous geospatial data: optical, SAR, and multi-spectral imagery across single-, bi-, and multi-temporal sequences (0.015-10m GSD), complemented by elevation and social vector layers. We comprehensively evaluate 13 frontier LLMs on our benchmark, revealing three persistent challenges: 1) disaster-domain grounding exposes unique failure modes (damage-semantic grounding, sensor-modality mismatch, and disaster-pipeline composition); 2) agents are doubly bottlenecked by tool selection and argument grounding, where gold tool-order hints improve accuracy by only 1.08-4.40%, and alternative scaffolds yield at most a 3.24% gain; 3) compositional fragility scales with trajectory length, the agent-to-gold gap widening from 7% to 56% on long pipelines. DORA establishes a rigorous testbed for operationally reliable disaster-response agents.

Effective machine learning depends not only on how we model data, but also on what data we choose to collect. While large sequence models have revolutionized data modeling, the problem of automated data selection, or "intrinsic curiosity", remains a significant challenge. Classic approaches incentivize exploration by rewarding an agent based on its "learning progress", which measures how much a newly acquired observation improves a world model's predictive ability. However, evaluating these rewards traditionally requires expensive inner loops of gradient descent updates within each trajectory, rendering them computationally impractical at scale. In this work, we investigate whether the emergent in-context learning (ICL) capabilities of sequence models can eliminate this bottleneck by serving as immediate, update-free world models. Specifically, we evaluate whether an exploration policy can be trained to maximize learning progress, using solely the prediction errors and counterfactual context manipulations of an in-context learner. We first prove that in general Markov decision processes, this is in fact impossible in an unbiased way: the resulting intrinsic rewards either suffer from nuisance terms that bias their estimation of true learning progress, or they cannot be implemented using an in-context learner's prediction errors. Conversely, we prove a positive result for a broad subclass of non-temporal settings, encompassing active learning and Bayesian Experimental Design: here, ICL-derived rewards successfully bound and asymptotically converge to the true learning progress. We corroborate our theory with controlled experiments across continuous and symbolic environments, demonstrating that our ICL-driven framework successfully trains curious data-collection policies that explore optimally.

The widespread adoption of AI assistants has prompted the development of privacy-aware platforms designed to extract insights from real-world usage. Their privacy protections primarily rely on layering multiple heuristic techniques, such as PII redaction, clustering, and aggregation. In this paper, we put their privacy claims to the test by presenting CLIOPATRA, the first attack against privacy-preserving LLM-based insights systems. Our attack involves an adversary that carefully designs and inserts malicious chats into the system to break multiple layers of protections and induce the leakage of sensitive information from a target user’s chat. We evaluate CLIOPATRA on one such platform, Anthropic’s Clio, and target synthetically generated medical chats to show that an adversary can successfully and confidently (with nearly 100% precision) extract the medical history contained in these chats in up to 65% of cases. We also show that CLIOPATRA can stealthily extract information by obfuscating the private information in the generated insights. Finally, we demonstrate that existing ad hoc mitigations, such as LLM-based privacy auditing, are unreliable and fail to detect major leaks. Taken together, our findings indicate that, even when layered, current heuristic protections are insufficient to adequately protect user data, and that prompt injection has been an understudied risk in LLM-based insight systems.

Intrinsic rewards for exploration in reinforcement learning condition on different contexts: lifelong rewards score each transition against accumulated experience but ignore within-rollout redundancy; episodic rewards penalize intra-trajectory repetition but discard lifetime progress. Hybrid methods combine both signals through heuristic weights or require Gaussian-process dynamics that do not scale beyond low-dimensional state spaces. Trajectory-level information gain decomposes into per-step terms that condition on the replay buffer and rollout prefix simultaneously, but remains intractable for deep models. We derive the Conditional Information Gain (CIG) reward as a tractable surrogate: a log-determinant objective over an ensemble disagreement kernel whose Cholesky factorization yields causal per-step rewards that retain both conditioning sets while scaling to high-dimensional state spaces. We instantiate CIG in a model-based setting, where rollouts are short and within-rollout corrections remain largely unexplored. Across twelve tasks spanning discrete (MiniGrid) and continuous control (OGBench), in both clean and stochastic-distractor settings, CIG outperforms or matches prior exploration methods while remaining robust to stochastic distractors.

Despite the increasing scale of genome language models (gLMs), their ability to decode the function of regulatory sequences remains unclear. gLM pretraining relies on sequence reconstruction, which may struggle due to the noisy, rapidly evolving nature of regulatory DNA. Self-supervised contrastive approaches provide a promising alternative. Inspired by language-image architectures like CLIP, we demonstrate contrastive promoter-protein pretraining (C3P). By learning to align promoters to their corresponding proteins, we leverage the rich representations of proteins learned by protein language models as supervisory signal for the learning of promoter representations. After training on 88 million bacterial promoter-protein pairs, we evaluate the predictive power of C3P-learned promoter representations for inference of curated regulatory annotations, finding multi-fold improvement over leading gLMs. We also introduce zero-shot co-regulated gene retrieval, the ability to find co-regulated genes in a genome using no experimental data. We find that compared to a randomly initialized baseline, C3P training consistently provides significant zero-shot performance gains, unlike gLMs. Scaling analysis reveals the potential for further improvement as well as the efficiency of C3P, which achieved strong performance at a fraction of the training cost of leading gLMs. In addition to demonstrating that C3P training is effective for learning representations of bacterial regulatory sequences, our strong zero-shot co-regulated gene retrieval performance suggests the possibility of decoding gene regulation for millions of bacteria from their genomes alone.

Classical compute-optimal scaling laws assume an unbounded supply of fresh pretraining data, yet pretraining is increasingly entering the regime where compute is growing faster than high-quality data. We propose *Compute-Data (CD) scaling laws*, a unified framework that bridges *compute-optimal* scaling, in which data scales freely with compute, and *data-optimal* scaling, in which the corpus is fixed and compute can grow unbounded. CD scaling extends classic scaling by introducing a *token effectiveness function* that quantifies how much a *derived* token, produced for instance by multi-epoch repetition or paraphrasing, is worth relative to a fresh one, ranging from a perfect substitute to no value at all. Fitting $\eta$ for two data expansion strategies (multi-epoch repetition, paraphrasing) across model sizes ranging from 14M to 600M parameters on the Dolma-3 corpus, we find that it is far from constant: it depends jointly on model size, the tokens-per-parameter ratio, and the amount of derived data, and saturates as the corpus is expanded. The functional form of $\eta$ implies that substituting compute for data *diminishes* with both model size and data availability, and partitions training into three operational regimes: compute-bound, data-bound, and model-bound, showing that classic compute-optimal allocation is suboptimal across most of the practically relevant regime.

Neural surrogate solvers of partial differential equations (PDEs) promise dramatic speedups over numerical methods, especially in scenarios requires many solves. However, current accuracy-based evaluations do not fully consider two central issues: (i) neural solvers incur substantial up-front costs for data generation, training, and tuning; and (ii) classical solvers can also generate low-fidelity solutions at a sufficiently low simulation cost. To explicitly account for these realities and fully incorporate end-to-end costs, we propose an evaluation framework centered on **breakeven complexity**, a metric that counts the forward solves before a learned solver is cost-effective relative to an error-equivalent traditional solver. To evaluate this measure, we apply scaling laws to determine how much training budget to allocate to data generation and discuss how to achieve smooth error-matching in diverse settings. We evaluate the breakeven complexity of many modern neural PDE solvers on three PDEs on 2D periodic domains from APEBench and a novel benchmark of flows past multiple obstacles generated by the GPU-native PyFR code. Among other findings, our results suggest that neural PDE solvers will be *more effective* on problems as problems get harder in terms of cost, dimension, rollout, physics regime (e.g. higher Re), etc.

Whole-brain 4D fMRI generation is valuable for modeling functional brain dynamics, yet existing fMRI foundation models mainly target representation learning and downstream prediction rather than conditional predictive generation. We introduce BrainWorld, a structural-prior-conditioned generative model for whole-brain 4D fMRI dynamics. BrainWorld uses sMRI as subject-level anatomical context to guide future fMRI generation, integrating structural information into the denoising process rather than treating it as a parallel modality. Evaluated on 22 datasets spanning diverse cohorts and brain states, BrainWorld generates stable 4D fMRI trajectories up to 400 frames, improves downstream performance through generated-example augmentation, and learns transferable multimodal representations that outperform baselines. Together, these results establish BrainWorld as a condition-aware generative framework for long-horizon brain dynamics modeling and multimodal representation learning.

Recovering 3D pose and shape of birds from single images is bottlenecked by the long tail of avian diversity: out of $\sim 10{,}000$ species, only a few dozen have 3D-labeled training data, and in-the-wild test sets routinely contain species never seen at training. Generalizing across clades is therefore a load-bearing problem. The current state of the art, AniMer+, mitigates it with a family-level contrastive loss that conveys only a binary same-family indicator per pair and discards the continuous structure of the species tree. We propose a **taxonomic Ornstein--Uhlenbeck prior** on the AVES shape code: a multivariate Gaussian whose covariance decays exponentially with Linnaean rank distance, with a learnable selection strength and noise scale. The prior generalizes family contrastive into a continuous, generative form, exposing the graded cross- and within-family similarity that a binary indicator cannot, and brings continuous comparative phylogenetics in as a biology-grounded inductive bias for the long tail. Our method consistently improves over AniMer+ on every reported avian benchmark cell, with the largest gains on the unseen-species CowBird benchmark. A permutation ablation isolates taxonomic structure from generic Gaussian smoothing, and a rank-granularity ablation identifies cross-order distinctions—the structure beyond a family-vs-not indicator—as the dominant source of the unseen-species gain.

Current video foundation models, including the strongest self-supervised models such as V-JEPA2, fail to capture how humans organize social information in dynamic scenes. For example, across a range of diverse vision models tested, none were able to predict human similarity judgments to social video clips as well as a sentence embedding model of the caption text (MPNet). We show this gap in vision model performance can be closed by a compact behavioral supervisory signal. We introduce behavioral geometric supervision (BGS): a hybrid objective that constrains local and global pairwise embedding geometry to match the relational similarity structure across videos. We apply this method using a new human similarity dataset, containing 49,484 odd-one-out judgments from 250 naturalistic social video clips, and low-rank adaptation across four ViT backbones (V-JEPA 2/2.1, TimeSformer, VideoMAE, and CLIP). We find that one of the best fine-tuned models, V-JEPA 2.1, nearly triples in performance compared to the pre-trained baseline and reaches close to the noise ceiling, exceeding the strongest sentence-embedding baseline. In addition, finetuned models (i) capture unique variance in human judgments that caption-based language embeddings do not, (ii) develop interpretable social-affective attributes (valence, arousal, and dominance) despite never being trained on any of these attributes, (iii) zero-shot transfer to a separate dataset of out-of-distribution abstract social interactions, and (iv) shift spatial attention from scene context to socially informative regions (faces, gaze, and interacting bodies). A matched language-distillation control fails to reproduce these gains, ruling out caption transfer as the mechanism. Our results show how a modest amount of human behavioral data can steer video models toward human-like social visual understanding.

Multi-view video recordings are increasingly used to capture the 3D movements of animals in experimental settings, yet extracting rich 3D representations from these recordings remains challenging. Supervised pose estimation requires extensive manual annotation, while general-purpose 3D reconstruction models trained on generic scene datasets fail on the specialized imagery and sparse-view setting of laboratory experiments. We address these limitations with BEAST3D, a self-supervised pretraining framework that learns 3D visual representations from unlabeled, calibrated multi-view video. BEAST3D uses a vision transformer to predict 3D Gaussian splats that reconstruct held-out views through differentiable rendering, while simultaneously segmenting the animal from the background. BEAST3D reconstructs 3D structure with as few as four views by conditioning directly on known camera parameters---unlike general-purpose models, which must estimate camera geometry from dense overlapping viewpoints that are seldom available in lab settings. Through comprehensive evaluation across four species, we demonstrate that BEAST3D produces rich, viewpoint-invariant features that transfer effectively to three downstream tasks: novel view synthesis, which validates the quality of the learned 3D representations; multi-view pose estimation, which provides the sparse keypoint trajectories widely used in behavioral analysis; and neural encoding, which relates 3D behavioral features to simultaneously recorded neural activity. BEAST3D thus establishes a versatile framework for behavioral analysis that leverages 3D structure in modern multi-view laboratory recordings.

Agent systems based on Large Language Models (LLMs) are increasingly deployed for autonomous tasks, yet existing evaluations mostly focus on task success rather than whether agents know when to abstain. This gap poses real risks: under ambiguity, conflicting constraints, or tool failures, agents may execute unintended and irreversible actions. To close this gap, we present the first systematic evaluation framework for agentic abstention: the ability to recognize when not to act. At its core, AgentAbstain is a paired-task benchmark that defines 8 abstention categories spanning pre-execution reasoning and runtime discovery, with 263 paired tasks across 42 executable sandbox environments, each pairing a should-act task with a should-abstain variant produced by a controlled perturbation to the instruction, tool, or environment state. Scaling such paired evaluations poses two practical challenges: manually authoring diverse tasks is expensive, and static benchmarks risk data contamination as models evolve. To address both, we propose AbstainGen, a fully automated pipeline that synthesizes sandbox environments and generates paired tasks end-to-end, validated by deterministic replay and semantic LLM judges. Its scalable design enables on-demand regeneration of fresh task instances, and human validation rates 96% of generated tasks as well-designed. Evaluating 17 frontier LLMs across 4 agent harnesses, the best model (Gemini 3.1 Pro) achieves only 59.5% paired accuracy (correct on both the act and abstain sides of each paired task). More importantly, abstention capability is largely independent of general task-solving capability, indicating that scaling task-solving alone will not close this gap. We identify failure modes such as Post-hoc Abstention, in which agents execute irreversible actions before recognizing abstention triggers. For instance, an agent may cancel a flight reservation before noticing contradictory rebooking instructions, leaving the user stranded. These findings underscore the need for rigorous abstention evaluation to develop more trustworthy LLM agents.

Recommendation unlearning (RU) aims to remove the influence of specified user--item interactions from a trained recommender while preserving utility on the remaining data. Existing RU methods usually require access to the original training data, especially the remaining data, to recover recommendation utility after unlearning. However, access to such data is often restricted or unavailable in practice due to privacy constraints, storage costs, or third-party deployment, giving rise to source-free recommendation unlearning. To address this challenge, we propose an adaptive source-free recommendation unlearning (**AdaSRU**) method that enables effective unlearning without accessing the original remaining data. **AdaSRU** first estimates the inaccessible gradient on the remaining data. It exploits the first-order optimality condition of the trained recommender and approximates the remaining gradient using the forgetting data and squared gradient accumulators from adaptive optimizers, e.g., Adam. **AdaSRU** then formulates unlearning as a gradient-constrained update, where the estimated remaining gradient is used as a constraint to limit utility degradation while maximizing the unlearning objective. **AdaSRU** adaptively adjusts the utility-preserving correction according to the current gradient geometry. We further theoretically prove that **AdaSRU** approaches an approximate Pareto stationary solution. Extensive experiments on three real-world datasets demonstrate that **AdaSRU** achieves strong performance in both unlearning and recommendation. The code is available at https://anonymous.4open.science/r/AdaSRU-94D9/.

Despite the critical role of temporal reasoning in Large Language Models (LLMs), current synthetic benchmarks fall short: they either introduce information leakage or, upon addressing this issue, merely assess questions with explicit time points, failing to rigorously evaluate implicit temporal reasoning capabilities. To bridge this gap, we propose a formally grounded evaluation framework, ALTER, based on Allen’s Interval Algebra. By combining basic relations into complex networks and converting these structures into natural language forms through an automated pipeline, we construct a validated benchmark of 2,500 question-answer pairs, ensuring a controllable and scalable evaluation environment. We conduct experiments on a representative selection of LLMs. Empirical evaluations on diverse LLMs yield three key findings: (1) identifying performance decline of LLMs in highly complex scenarios involving dense events; (2) isolating complex logical interactions—rather than linguistic comprehension—as an unresolved bottleneck; and (3) revealing a critical evaluation bias induced by narrative chronology, with LLMs exploiting textual shortcuts. In summary, these findings reveal the blind spots of current evaluation paradigms, providing a rigorous foundation for the robust evaluation of complex temporal reasoning.

Understanding how neural population responses represent sensory information is a central problem in systems neuroscience. One approach is to define a representational geometry on stimulus space in which distances reflect how reliably stimuli can be distinguished from neural activity. However, different constructions of these distances can lead to qualitatively different conclusions about the neural code. Here, we show that a unique Riemannian representational geometry emerges from first principles governing how distances contract as stimulus resolution is lost through coarse-graining. This results in a multi-scale extension of the Fisher information metric, capturing encoding structure from fine stimulus details to coarse global distinctions. The resulting geometry is exactly related to the mutual information encoded by the population: well encoded stimulus directions -- those contributing more to mutual information -- are expanded, whereas poorly encoded directions are contracted. The metric tensor can be estimated using diffusion models, making the framework practical for large neural populations and high-dimensional stimuli. Applied to visual cortical responses to natural images, the eigenvectors of the metric tensor identify stimulus variations that contribute most to information transmission, yielding interpretable features that are robust to modelling choices. Together, these results provide a principled, information-theoretic framework for characterising neural population codes.