NeurIPS 2025 论文列表

Predicting protein function from sequence is a central challenge in computational biology. While existing methods rely heavily on structured ontologies or similarity-based techniques, they often lack the flexibility to express structure-free functional descriptions and novel biological functions. In this work, we introduce Prot2Text-V2, a novel multimodal sequence-to-text model that generates free-form natural language descriptions of protein function directly from amino acid sequences. Our method combines a protein language model as a sequence encoder (ESM-3B) and a decoder-only language model (LLaMA-3.1-8B-Instruct) through a lightweight nonlinear modality projector. A key innovation is our Hybrid Sequence-level Contrastive Alignment Learning (H-SCALE), which improves cross-modal learning by matching mean- and std-pooled protein embeddings with text representations via contrastive loss. After the alignment phase, we apply instruction-based fine-tuning using LoRA on the decoder to teach the model how to generate accurate protein function descriptions conditioned on the protein sequence. We train Prot2Text-V2 on about 250K curated entries from SwissProt and evaluate it under low-homology conditions, where test sequences have low similarity with training samples. Prot2Text-V2 consistently outperforms traditional and LLM-based baselines across various metrics.

Classical image filters, such as those for averaging or differencing, are carefully normalized to ensure consistency, interpretability, and to avoid artifacts like intensity shifts, halos, or ringing. In contrast, convolutional filters learned end-to-end in deep networks lack such constraints. Although they may resemble wavelets and blob/edge detectors, they are not normalized in the same or any way. Consequently, when images undergo atmospheric transfer, their responses become distorted, leading to incorrect outcomes. We address this limitation by proposing filter normalization, followed by learnable scaling and shifting, akin to batch normalization. This simple yet effective modification ensures that the filters are atmosphere-equivariant, enabling co-domain symmetry. By integrating classical filtering principles into deep learning (applicable to both convolutional neural networks and convolution-dependent vision transformers), our method achieves significant improvements on artificial and natural intensity variation benchmarks. Our ResNet34 could even outperform CLIP by a large margin. Our analysis reveals that unnormalized filters degrade performance, whereas filter normalization regularizes learning, promotes diversity, and improves robustness and generalization.

The Zero-shot Vision-and-Language Navigation in Continuous Environments (VLN-CE) task requires agents to navigate previously unseen 3D environments using natural language instructions, without any scene-specific training. A critical challenge in this setting lies in ensuring agents’ actions align with both spatial structure and task intent over long-horizon execution. Existing methods often fail to achieve robust navigation due to a lack of structured decision-making and insufficient integration of feedback from previous actions. To address these challenges, we propose STRIDER (Instruction-Aligned Structural Decision Space Optimization), a novel framework that systematically optimizes the agent’s decision space by integrating spatial layout priors and dynamic task feedback. Our approach introduces two key innovations: 1) a Structured Waypoint Generator that constrains the action space through spatial structure, and 2) a Task-Alignment Regulator that adjusts behavior based on task progress, ensuring semantic alignment throughout navigation. Extensive experiments on the R2R-CE and RxR-CE benchmarks demonstrate that STRIDER significantly outperforms strong SOTA across key metrics; in particular, it improves Success Rate (SR) from 29\% to 35\%, a relative gain of 20.7\%. Such results highlight the importance of spatially constrained decision-making and feedback-guided execution in improving navigation fidelity for zero-shot VLN-CE.

The ability to extract oriented edges from visual input is a core computation across animal vision systems. Orientation maps, long associated with the layered architecture of the mammalian visual cortex, systematically organise neurons by their preferred edge orientation. Despite lacking cortical structures, the *Drosophila melanogaster* brain contains feature-selective neurons and exhibits complex visual detection capacity, raising the question of whether map-like vision representations can emerge without cortical infrastructure. We integrate a complete fruit fly brain connectome with biologically grounded spiking neuron models to simulate neuroprocessing in the fly visual system. By driving the network with oriented stimuli and analysing downstream responses, we show that coherent orientation maps can emerge from purely connectome-constrained dynamics. These results suggest that species of independent origin could evolve similar visual structures.

Machine unlearning (MU) aims to efficiently remove sensitive or harmful memory from a pre-trained model. The key challenge is to balance the potential tradeoff between unlearning efficacy and utility preservation, which involves forgetting undesirable information as defined while maintaining the model's original performance. One potential way to tackle this problem is to use multi-objective optimization to jointly optimize both the unlearning and utility preservation objectives. However, existing multi-objective methods only guarantee finding a Pareto-optimal solution without fine-grained control, which causes under-optimization of the unlearning objective. To this end, we first model MU as a constrained optimization problem, that is, optimizing the unlearning objective under the constraint of a bounded increase for utility loss. We then show that solving this optimization problem is equivalent to unilateral gradient surgery on the unlearning objective. To resolve the additional computational cost brought by gradient surgery, we propose an implicit gradient surgery method, which approximates the solution to the aforementioned constrained optimization problem via only one backpropagation, thereby achieving efficient utility-preserving MU. Theoretically, we provide a tight convergence analysis of the algorithm. Empirically, our extensive experiments show that the proposed algorithm achieves better tradeoff results than existing baselines. Codes are available at https://github.com/anseryuer/EUPMU-Efficient-Utility-Preserving-Machine-Unlearning.

While existing image‑guided composition methods may help insert a foreground object onto a user-specified region of a background image, achieving natural blending inside the region with the rest of the image unchanged, we observe that these existing methods often struggle in synthesizing seamless interaction-aware compositions when the task involves human-object interactions. In this paper, we first propose HOComp, a novel approach for compositing a foreground object onto a human-centric background image, while ensuring harmonious interactions between the foreground object and the background person and their consistent appearances. Our approach includes two key designs: (1) MLLMs-driven Region-based Pose Guidance (MRPG), which utilizes MLLMs to identify the interaction region as well as the interaction type (e.g., holding and lefting) to provide coarse-to-fine constraints to the generated pose for the interaction while incorporating human pose landmarks to track action variations and enforcing fine-grained pose constraints; and (2) Detail-Consistent Appearance Preservation (DCAP), which unifies a shape-aware attention modulation mechanism, a multi-view appearance loss, and a background consistency loss to ensure consistent shapes/textures of the foreground and faithful reproduction of the background human. We then propose the first dataset, named Interaction-aware Human-Object Composition (IHOC), for the task. Experimental results on our dataset show that HOComp effectively generates harmonious human-object interactions with consistent appearances, and outperforms relevant methods qualitatively and quantitatively.

Sparse variable selection improves interpretability and generalization in high-dimensional learning by selecting a small subset of informative features. Recent advances in Mixed Integer Programming (MIP) have enabled solving large-scale non-private sparse regression—known as Best Subset Selection (BSS)—with millions of variables in minutes. However, extending these algorithmic advances to the setting of Differential Privacy (DP) has remained largely unexplored. In this paper, we introduce two new differentially private estimators for sparse variable selection, levering modern MIP techniques. Our framework is general and applies broadly to problems like sparse regression or classification, and we provide theoretical support recovery guarantees in the case of BSS. Inspired by the exponential mechanism, we develop structured sampling procedures that efficiently explore the non-convex objective landscape, avoiding the exhaustive combinatorial search in the exponential mechanism. We complement our theoretical findings with extensive numerical experiments, using both least squares and hinge loss for our objective function, and demonstrate that our methods achieve state-of-the-art empirical support recovery, outperforming competing algorithms in settings with up to $p=10^4$.

We study the selection of agents based on mutual nominations, a theoretical problem with many applications from committee selection to AI alignment. As agents both select and are selected, they may be incentivized to misrepresent their true opinion about the eligibility of others to influence their own chances of selection. Impartial mechanisms circumvent this issue by guaranteeing that the selection of an agent is independent of the nominations cast by that agent. Previous research has established strong bounds on the performance of impartial mechanisms, measured by their ability to approximate the number of nominations for the most highly nominated agents. We study to what extent the performance of impartial mechanisms can be improved if they are given a prediction of a set of agents receiving a maximum number of nominations. Specifically, we provide bounds on the consistency and robustness of such mechanisms, where consistency measures the performance of the mechanisms when the prediction is correct and robustness its performance when the prediction is incorrect. For the general setting where up to $k$ agents are to be selected and agents nominate any number of other agents, we give a mechanism with consistency $1-O\big(\frac{1}{k}\big)$ and robustness $1-\frac{1}{e}-O\big(\frac{1}{k}\big)$. For the special case of selecting a single agent based on a single nomination per agent, we prove that $1$-consistency can be achieved while guaranteeing $\frac{1}{2}$-robustness. A close comparison with previous results shows that (asymptotically) optimal consistency can be achieved with little to no sacrifice in terms of robustness.

Do LLMs robustly generalize critical safety facts to novel situations? Lacking this ability is dangerous when users ask naive questions—for instance, ``I'm considering packing melon balls for my 10-month-old's lunch. What other foods would be good to include?'' Before offering food options, the LLM should warn that melon balls pose a choking hazard to toddlers, as documented by the CDC. Failing to provide such warnings could result in serious injuries or even death. To evaluate this, we introduce SAGE-Eval, SAfety-fact systematic GEneralization evaluation, the first benchmark that tests whether LLMs properly apply well‑established safety facts to naive user queries. SAGE-Eval comprises 104 facts manually sourced from reputable organizations, systematically augmented to create 10,428 test scenarios across 7 common domains (e.g., Outdoor Activities, Medicine). We find that the top model, Claude-3.7-sonnet, passes only 58% of all the safety facts tested. We also observe that model capabilities and training compute weakly correlate with performance on SAGE-Eval, implying that scaling up is not the golden solution. Our findings suggest frontier LLMs still lack robust generalization ability. We recommend developers use SAGE-Eval in pre-deployment evaluations to assess model reliability in addressing salient risks.

Discrete diffusion models, like continuous diffusion models, generate high-quality samples by gradually undoing noise applied to datapoints with a Markov process. Gradual generation in theory comes with many conceptual benefits; for example, inductive biases can be incorporated into the noising Markov process. In practice, however, the consistently best performing discrete diffusion model is masking diffusion, which does not denoise gradually. Here we explain the superior performance of masking diffusion by noting that it makes use of a fundamental difference between continuous and discrete Markov processes: discrete Markov processes evolve by discontinuous jumps at a fixed rate and, unlike other discrete diffusion models, masking diffusion builds in the known distribution of jump times and only learns where to jump to. We show that we can similarly bake in the known distribution of jump times into any discrete diffusion model. The resulting models -- schedule-conditioned diffusion (SCUD) -- generalize classical discrete diffusion and masking diffusion. By applying SCUD to models with noising processes that incorporate inductive biases on images, text, and protein data, we build diffusion models that outperform masking.

Distributed training often suffers from high communication overhead due to large-scale gradient synchronization. Although gradient compression—particularly at 4-bit or even lower precision—significantly reduces transfer volume, it typically results in sacrifice in precision and degradation of the final model accuracy. In this work, we introduce DUO, a distributed training framework designed to mitigate accuracy degradation incurred by gradient compression without involving additional overhead. DUO achieves this by inserting an additional high-precision gradient synchronization step into a previously computation-only phase, so that its communication is fully hidden by computation. We provide a comprehensive theoretical proof of convergence for DUO and validate its effectiveness through extensive pre-training experiments on GPT models. Our results indicate that DUO effectively restores accuracy when using 4-bit gradient compression, achieving performance comparable to uncompressed training. Remarkably, DUO maintains minimal accuracy degradation even under extreme compression scenarios, including 1-bit gradients or complete omission of the low-precision gradient communication step (0-bit transmission).

Loss of plasticity (LoP) is the primary cause of cognitive decline in normal aging brains next to cell loss. Recent works show that similar LoP also plagues neural networks during deep continual learning (DCL). While it has been shown that random perturbations of learned weights can alleviate LoP, its underlying mechanisms remain insufficiently understood. Here we offer a unique view of LoP and dissect its mechanisms through the lenses of an innovative framework combining the theory of neural collapse and finite-time Lyapunov exponents (FTLE) analysis. We show that LoP actually consists of two contrasting types: (i) type-1 LoP is characterized by highly negative FTLEs, where the network is prevented from learning due to the collapse of representations; (ii) while type-2 LoP is characterized by excessively positive FTLEs, where the network can train well but the growingly chaotic behaviors reduce its test accuracy. Based on these understandings, we introduce Generalized Mixup, designed to relax the representation space for prolonged DCL and demonstrate its superior efficacy vs. existing methods.

In this paper, we propose a new method called \textit{Self-Training with Dynamic Weighting} (STDW), which aims to enhance robustness in Gradual Domain Adaptation (GDA) by addressing the challenge of smooth knowledge migration from the source to the target domain. Traditional GDA methods mitigate domain shift through intermediate domains and self-training but often suffer from inefficient knowledge migration or incomplete intermediate data. Our approach introduces a dynamic weighting mechanism that adaptively balances the loss contributions of the source and target domains during training. Specifically, we design an optimization framework governed by a time-varying hyperparameter $\varrho$ (progressing from 0 to 1), which controls the strength of domain-specific learning and ensures stable adaptation. The method leverages self-training to generate pseudo-labels and optimizes a weighted objective function for iterative model updates, maintaining robustness across intermediate domains. Experiments on rotated MNIST, color-shifted MNIST, portrait datasets, and the Cover Type dataset demonstrate that STDW outperforms existing baselines. Ablation studies further validate the critical role of $\varrho$'s dynamic scheduling in achieving progressive adaptation, confirming its effectiveness in reducing domain bias and improving generalization. This work provides both theoretical insights and a practical framework for robust gradual domain adaptation, with potential applications in dynamic real-world scenarios.

Graph Neural Networks (GNNs) have achieved significant success in various real-world applications, including social networks, finance systems, and traffic management. Recent researches highlight their vulnerability to backdoor attacks in node classification, where GNNs trained on a poisoned graph misclassify a test node only when specific triggers are attached. These studies typically focus on single attack categories and use adaptive trigger generators to create node-specific triggers. However, adaptive trigger generators typically have a simple structure, limited parameters, and lack category-aware graph knowledge, which makes them struggle to handle backdoor attacks across multiple categories as the number of target categories increases. We address this gap by proposing a novel approach for Effective and Unnoticeable Multi-Category (EUMC) graph backdoor attacks, leveraging subgraph from the attacked graph as category-aware triggers to precisely control the target category. To ensure the effectiveness of our method, we construct a Multi-Category Subgraph Triggers Pool (MC-STP) using the subgraphs of the attacked graph as triggers. We then exploit the attachment probability shifts of each subgraph trigger as category-aware priors for target category determination. Moreover, we develop a ``select then attach'' strategy that connects suitable category-aware trigger to attacked nodes for unnoticeability. Extensive experiments across different real-world datasets confirm the efficacy of our method in conducting multi-category graph backdoor attacks on various GNN models and defense strategies.

Recent advances in text-to-image models have increased the exposure of powerful image editing techniques as a tool, raising concerns about their potential for malicious use. An emerging line of research to address such threats focuses on implanting “protective” adversarial noise into images before their public release, so future attempts to edit them using text-to-image models can be impeded. However, subsequent works have shown that these adversarial noises are often easily “reversed,” e.g., with techniques as simple as JPEG compression, casting doubt on the practicality of the approach. In this paper, we argue that adversarial noise for image protection should not only be imperceptible, as has been a primary focus of prior work, but also irreversible, viz., it should be difficult to detect as noise provided that the original image is hidden. We propose a surprisingly simple method to enhance the robustness of image protection methods against noise reversal techniques. Specifically, it applies an adaptive per-region Gaussian blur on the noise to adjust the overall frequency spectrum. Through extensive experiments, we show that our method consistently improves the per-sample worst-case protection performance of existing methods against a wide range of reversal techniques on diverse image editing scenarios, while also reducing quality degradation due to noise in terms of perceptual metrics. Code is available at https://github.com/jsu-kim/BlurGuard.

We study value-iteration (VI) algorithms for solving general (a.k.a. multichain) Markov decision processes (MDPs) under the average-reward criterion, a fundamental but theoretically challenging setting. Beyond the difficulties inherent to all average-reward problems posed by the lack of contractivity and non-uniqueness of solutions to the Bellman operator, in the multichain setting an optimal policy must solve the navigation subproblem of steering towards the best connected component, in addition to optimizing long-run performance within each component. We develop algorithms which better solve this navigational subproblem in order to achieve faster convergence for multichain MDPs, obtaining improved rates of convergence and sharper measures of complexity relative to prior work. Many key components of our results are of potential independent interest, including novel connections between average-reward and discounted problems, optimal fixed-point methods for discounted VI which extend to general Banach spaces, new sublinear convergence rates for the discounted value error, and refined suboptimality decompositions for multichain MDPs. Overall our results yield faster convergence rates for discounted and average-reward problems and expand the theoretical foundations of VI approaches.

This work establishes that sparse Bayesian neural networks achieve optimal posterior contraction rates over anisotropic Besov spaces and their hierarchical compositions. These structures reflect the intrinsic dimensionality of the underlying function, thereby mitigating the curse of dimensionality. Our analysis shows that Bayesian neural networks equipped with either sparse or continuous shrinkage priors attain the optimal rates which are dependent on the intrinsic dimension of the true structures. Moreover, we show that these priors enable rate adaptation, allowing the posterior to contract at the optimal rate even when the smoothness level of the true function is unknown. The proposed framework accommodates a broad class of functions, including additive and multiplicative Besov functions as special cases. These results advance the theoretical foundations of Bayesian neural networks and provide rigorous justification for their practical effectiveness in high-dimensional, structured estimation problems.

Open-source foundation models have seen rapid adoption and development, enabling powerful general-purpose capabilities across diverse domains. However, fine-tuning large foundation models for domain-specific or personalized tasks remains prohibitively expensive for most users due to the significant memory overhead beyond that of inference. We introduce EMLoC, an Emulator-based Memory-efficient fine-tuning framework with LoRA Correction, which enables model fine-tuning within the same memory budget required for inference. EMLoC constructs a task-specific light-weight emulator using activation-aware singular value decomposition (SVD) on a small downstream calibration set. Fine-tuning then is performed on this lightweight emulator via LoRA. To tackle the misalignment between the original model and the compressed emulator, we propose a novel compensation algorithm to correct the fine-tuned LoRA module, which thus can be merged into the original model for inference. EMLoC supports flexible compression ratios and standard training pipelines, making it adaptable to a wide range of applications. Extensive experiments demonstrate that EMLoC outperforms other baselines across multiple datasets and modalities. Moreover, without quantization, EMLoC enables fine-tuning of a 38B model, which originally required 95GB of memory, on a single 24GB consumer GPU—bringing efficient and practical model adaptation to individual users.

Consistent pose‐driven character animation has achieved remarkable progress in single‐character scenarios. However, extending these advances to multi‐character settings is non‐trivial, especially when position swap is involved. Beyond mere scaling, the core challenge lies in enforcing correct Identity Correspondence (IC) between characters in reference and generated frames. To address this, we introduce EverybodyDance, a systematic solution targeting IC correctness in multi-character animation. EverybodyDance is built around the **Identity Matching Graph (IMG)**, which models characters in the generated and reference frames as two node sets in a weighted complete bipartite graph. Edge weights, computed via our proposed Mask–Query Attention (MQA), quantify the affinity between each pair of characters. Our key insight is to formalize IC correctness as a graph structural metric and to optimize it during training. We also propose a series of targeted strategies tailored for multi-character animation, including identity-embedded guidance, a multi-scale matching strategy, and pre-classified sampling, which work synergistically. Finally, to evaluate IC performance, we curate the **Identity Correspondence Evaluation** benchmark, dedicated to multi‐character IC correctness. Extensive experiments demonstrate that EverybodyDance substantially outperforms state‐of‐the‐art baselines in both IC and visual fidelity.