NeurIPS 2025 论文列表

Multimodal molecular models often suffer from 3D conformer unreliability and modality collapse, limiting their robustness and generalization. We propose MuMo, a structured multimodal fusion framework that addresses these challenges in molecular representation through two key strategies. To reduce the instability of conformer-dependent fusion, we design a Structured Fusion Pipeline (SFP) that combines 2D topology and 3D geometry into a unified and stable structural prior. To mitigate modality collapse caused by naive fusion, we introduce a Progressive Injection (PI) mechanism that asymmetrically integrates this prior into the sequence stream, preserving modality-specific modeling while enabling cross-modal enrichment. Built on a state space backbone, MuMo supports long-range dependency modeling and robust information propagation. Across 29 benchmark tasks from Therapeutics Data Commons (TDC) and MoleculeNet, MuMo achieves an average improvement of 2.7% over the best-performing baseline on each task, ranking first on 22 of them, including a 27% improvement on the LD50 task. These results validate its robustness to 3D conformer noise and the effectiveness of multimodal fusion in molecular representation. The code is available at: github.com/selmiss/MuMo.

We present LrcSSM, a $\textit{non-linear}$ recurrent model that processes long sequences as fast as today's linear state-space layers. By forcing its Jacobian matrix to be diagonal, the full sequence can be solved in parallel, giving $\mathcal{O}(TD)$ time and memory and only $\mathcal{O}(\log T)$ sequential depth, for input-sequence length $T$ and a state dimension $D$. Moreover, LrcSSM offers a formal gradient-stability guarantee that other input-varying systems such as Liquid-S4 and Mamba do not provide. Importantly, the diagonal Jacobian structure of our model results in no performance loss compared to the original model with dense Jacobian, and the approach can be generalized to other non-linear recurrent models, demonstrating broader applicability. On a suite of long-range forecasting tasks, we demonstrate that LrcSSM outperforms Transformers, LRU, S5, and Mamba.

Characterizing the cellular properties of neurons is fundamental to understanding their function in the brain. In this quest, the generation of bio-realistic models is central towards integrating multimodal cellular data sets and establishing causal relationships. However, current modeling approaches remain constrained by the limited availability and intrinsic variability of experimental neuronal data. The deterministic formalism of bio-realistic models currently precludes accounting for the natural variability observed experimentally. While deep learning is becoming increasingly relevant in this space, it fails to capture the full biophysical complexity of neurons, their nonlinear voltage dynamics, and variability. To address these shortcomings, we introduce $\texttt{NOBLE}$, a neural operator framework that learns a mapping from a continuous frequency-modulated embedding of interpretable neuron features to the somatic voltage response induced by current injection. Trained on synthetic data generated from bio-realistic neuron models, $\texttt{NOBLE}$ predicts distributions of neural dynamics accounting for the intrinsic experimental variability. Unlike conventional bio-realistic neuron models, interpolating within the embedding space offers models whose dynamics are consistent with experimentally observed responses. $\texttt{NOBLE}$ enables the efficient generation of synthetic neurons that closely resemble experimental data and exhibit trial-to-trial variability, offering a $4200$× speedup over the numerical solver. $\texttt{NOBLE}$ is the first scaled-up deep learning framework that validates its generalization with real experimental data. To this end, $\texttt{NOBLE}$ captures fundamental neural properties in a unique and emergent manner that opens the door to a better understanding of cellular composition and computations, neuromorphic architectures, large-scale brain circuits, and general neuroAI applications.

Accurate prediction of continuous properties is essential to many scientific and engineering tasks. Although deep-learning regressors excel with abundant labels, their accuracy deteriorates in data-scarce regimes. We introduce RankRefine, a model-agnostic, plug-and-play post-hoc refinement technique that injects expert knowledge through pairwise rankings. Given a query item and a small reference set with known properties, RankRefine combines the base regressor’s output with a rank-based estimate via inverse-variance weighting, requiring no retraining. In molecular property prediction task, RankRefine achieves up to 10\% relative reduction in mean absolute error using only 20 pairwise comparisons obtained through a general-purpose large language model (LLM) with no finetuning. As rankings provided by human experts or general-purpose LLMs are sufficient for improving regression across diverse domains, RankRefine offers practicality and broad applicability, especially in low-data settings.

Reconstructing ocean surface nutrients from sparse observations is critical for understanding long-term biogeochemical cycles. Most prior work focuses on reconstructing atmospheric fields and treats the reconstruction problem as image inpainting, assuming smooth, single-scale dynamics. In contrast, nutrient transport follows advection–diffusion dynamics under nonstationary, multiscale ocean flow. This mismatch leads to instability, as small errors in unresolved eddies can propagate through time and distort nutrient predictions. To address this, we introduce NUTS, a two-scale reconstruction model that decouples large-scale transport and mesoscale variability. The homogenized solver captures stable, coarse-scale advection under filtered flow. A refinement module then restores mesoscale detail conditioned on the residual eddy field. NUTS is stable, interpretable, and robust to mesoscale perturbations, with theoretical guarantees from homogenization theory. NUTS outperforms all data-driven baselines in global reconstruction and achieves site-wise accuracy comparable to numerical models. On real observations, NUTS reduces NRMSE by 79.9% for phosphate and 19.3% for nitrate over the best baseline. Ablation studies validate the effectiveness of each module.

Reinforcement learning (RL) has become a predominant technique to align language models (LMs) with human preferences or promote outputs which are deemed to be desirable by a given reward function. Standard RL approaches optimize average reward, while methods explicitly focused on reducing the probability of undesired outputs typically come at a cost to average-case performance. To improve this tradeoff, we introduce RePULSe, a new training method that augments the standard RL loss with an additional loss that uses learned proposals to guide sampling low-reward outputs, and then reduces those outputs’ probability. We run experiments demonstrating that RePULSe produces a better tradeoff of expected reward versus the probability of undesired outputs and is more adversarially robust, compared to standard RL alignment approaches and alternatives.

Diffusion models, though originally designed for generative tasks, have demonstrated impressive self-supervised representation learning capabilities. A particularly intriguing phenomenon in these models is the emergence of unimodal representation dynamics, where the quality of learned features peaks at an intermediate noise level. In this work, we conduct a comprehensive theoretical and empirical investigation of this phenomenon. Leveraging the inherent low-dimensionality structure of image data, we theoretically demonstrate that the unimodal dynamic emerges when the diffusion model successfully captures the underlying data distribution. The unimodality arises from an interplay between denoising strength and class confidence across noise scales. Empirically, we further show that, in classification tasks, the presence of unimodal dynamics reliably reflects the diffusion model’s generalization: it emerges when the model generate novel images and gradually transitions to a monotonically decreasing curve as the model begins to memorize the training data.

Linear Transformers and State Space Models have emerged as efficient alternatives to softmax Transformers for causal sequence modeling, enabling parallel training via matrix multiplication and efficient RNN-style inference. However, despite their success in causal tasks, no unified framework exists for applying Linear Transformers to bidirectional sequence modeling. We introduce LION, the first framework to systematically extend Linear Transformers to the bidirectional setting. LION generalizes three core representations commonly used in the causal case—full Linear Attention , bidirectional RNN, and chunkwise parallel form—to the bidirectional setting. These forms are theoretically equivalent and enable models to exploit the strengths of each during training and inference. We prove that a broad class of Linear Transformers can be extended using LION and validate our framework via three core examples based on the choice of decay type: LION-LIT, the bidirectional extension of [25]; LION-D, based on [44]; and LION-S, a variant using selective decay [34, 13]. Across standard bidirectional tasks, LION enables models to match or exceed the performance of softmax Transformers, while offering significantly faster training and more efficient inference than existing State Space Models.

Efficient vision transformer remains a bottleneck for high-resolution images and long-video related real-world applications. Generalized Spatial Propagation Network (GSPN) \cite{wang2025parallel} addresses this by replacing quadratic self-attention with a line-scan propagation scheme, bringing the cost close to linear in the number of rows or columns, while retaining accuracy. Despite this advancement, the existing GSPN implementation still suffers from (i) heavy overhead due to repeatedly launching GPU kernels, (ii) excessive data transfers from global GPU memory, and (iii) redundant computations caused by maintaining separate propagation weights for each channel. We introduce GSPN-2, a joint algorithm–system redesign. In particular, we eliminate thousands of micro-launches from the previous implementation into one single 2D kernel, explicitly pin one warp to each channel slice, and stage the previous column's activations in shared memory. On the model side, we introduce a set of channel-shared propagation weights that replace per-channel matrices, trimming parameters, and align naturally with the affinity map used in transformer attention. Experiments demonstrate GSPN-2's effectiveness across image classification and text-to-image synthesis tasks, matching transformer-level accuracy with significantly lower computational cost. GSPN-2 establishes a new efficiency frontier for modeling global spatial context in vision applications through its unique combination of structured matrix transformations and GPU-optimized implementation.

Understanding cellular responses to chemical interventions is critical to the discovery of effective therapeutics. Because individual biological techniques often measure only one axis of cellular response at a time, high-quality multimodal datasets are needed to unlock a holistic understanding of how cells respond to treatments and to advance computational methods that integrate modalities. However, many techniques destroy cells and thus preclude paired measurements, and attempts to match disparate unimodal datasets are often confounded by data being generated in incompatible experimental settings. Here we introduce scGeneScope, a multimodal single‑cell RNA sequencing (scRNA-seq) and Cell Painting microscopy image dataset conditionally paired by chemical treatment, designed to facilitate the development and benchmarking of unimodal, multimodal, and multiple profile machine learning methods for cellular profiling. 28 chemicals, each acting on distinct biological pathways or mechanisms of action (MoAs), were applied to U2-OS cells in two experimental data generation rounds, creating paired sets of replicates that were then profiled independently by scRNA‑seq or Cell Painting. Using scGeneScope, we derive a replicate- and experiment-split treatment identification benchmark simulating MoA discovery under realistic laboratory variability conditions and evaluate unimodal, multimodal, and multiprofile models ranging in complexity from linear approaches to recent foundation models. Multiprofile integration improved performance in both the unimodal and multimodal settings, with gains more consistent in the former. Evaluation of unimodal models for MoA identification demonstrated that recent scRNA-seq foundation models deployed zero-shot were consistently outperformed by classic fit-to-data methods, underscoring the need for careful, realistic benchmarking in machine learning for biology. We release the scGeneScope dataset and benchmarking code to support further research.

Conformational ensembles of protein structures are immensely important both for understanding protein function and drug discovery in novel modalities such as cryptic pockets. Current techniques for sampling ensembles such as molecular dynamics (MD) are computationally inefficient, while many recent machine learning methods do not transfer to systems outside their training data. We propose JAMUN which performs MD in a smoothed, noised space of all-atom 3D conformations of molecules by utilizing the framework of walk-jump sampling. JAMUN enables ensemble generation for small peptides at rates of an order of magnitude faster than traditional molecular dynamics. The physical priors in JAMUN enables transferability to systems outside of its training data, even to peptides that are longer than those originally trained on. Our model, code and weights are available at https://github.com/prescient-design/jamun.

Recent breakthroughs in the analysis of multi-objective evolutionary algorithms (MOEAs) are mathematical runtime analyses of those algorithms which are intensively used in practice. So far, most of these results show the same performance as previously known for simple algorithms like the GSEMO. The few results indicating advantages of the popular MOEAs share the same shortages: They consider the performance for the problem of computing the full Pareto front, (of some algorithms enriched with newly invented mechanisms,) and this on newly designed benchmarks. In this work, we overcome these shortcomings by analyzing how existing popular MOEAs approximate the Pareto front of the established LargeFront benchmark. We prove that all popular MOEAs, including NSGA-II (sequential version), NSGA-III, SMS-EMOA, and SPEA2, only need an expected time of $O(n^2 \log n)$ function evaluations to compute an additive $\varepsilon$-approximation of the Pareto front of the LargeFront benchmark. This contrasts with the already proven exponential runtime (with high probability) of the GSEMO on the same task. This result is the first mathematical runtime analysis showing and explaining the superiority of popular MOEAs over simple ones like the GSEMO for the central task of computing good approximations to the Pareto front.

Signed networks can reflect more complex connections through positive and negative edges, and cost-effective signed network sketching can significantly benefit an important link sign prediction task in the era of big data. Existing signed network embedding algorithms mainly learn node representation in the Graph Neural Network (GNN) framework with the balance theory. However, the node-wise representation learning methods either limit the representational power because they primarily rely on node pairwise relationship in the network, or suffer from severe efficiency issues. Recent research has explored simplicial complexes to capture higher-order interactions and integrated them into GNN frameworks. Motivated by that, we propose EdgeSketch+, a simple and effective edge embedding algorithm beyond traditional node-centric modeling that directly represents edges as low-dimensional vectors without transitioning from node embeddings. The proposed approach maintains a good balance between accuracy and efficiency by exploiting the Locality Sensitive Hashing (LSH) technique to swiftly capture the higher-order information derived from the simplicial complex in a manner of no learning processes. Experiments show that EdgeSketch+ matches state-of-the-art accuracy while significantly reducing runtime, achieving speedups of up to $546.07\times$ compared to GNN-based methods.

Developing improved predictive models for multi-molecular systems is crucial, as nearly every chemical product used results from a mixture of chemicals. While being a vital part of the industry pipeline, the chemical mixture space remains relatively unexplored by the Machine Learning (ML) community. In this paper, we introduce CheMixHub, a holistic benchmark for molecular mixtures spanning a corpus of 11 chemical mixtures property prediction tasks. With applications ranging from drug delivery formulations to battery electrolytes, CheMixHub currently totals approximately 500k data points gathered and curated from 7 publicly available datasets. We devise various data splitting techniques to assess context-specific generalization and model robustness, providing a foundation for the development of predictive models for chemical mixture properties. Furthermore, we map out the modelling space of deep learning models for chemical mixtures, establishing initial benchmarks for the community. This dataset has the potential to accelerate chemical mixture development, encompassing reformulation, optimization, and discovery. The dataset and code for the benchmarks can be found at: https://github.com/chemcognition-lab/chemixhub

Optimization modeling is fundamental to decision-making in fields such as supply chain management, logistics, and financial engineering, but its complexity presents a major barrier to adoption. Automating model creation from natural language is key to improving efficiency and access. However, while Large Language Models (LLMs) are a promising tool for this, they often produce flawed or infeasible results due to errors and hallucinations. To address this issue, we propose Solver-Informed Reinforcement Learning (SIRL), a framework that uses Reinforcement Learning with Verifiable Reward to improve LLMs’ ability to generate accurate and executable optimization models. Specifically, SIRL automatically assesses the executable code and the instance-level mathematical model represented by the associated .lp files. This process yields precise feedback on syntactic validity, feasibility, and solution quality, which serves as a direct reward signal to guide the reinforcement learning process. Furthermore, this verification mechanism also supports our instance-enhanced self-consistency method for creating high-quality training data. Extensive experiments on diverse public benchmarks demonstrate that models trained with our SIRL framework achieve state-of-the-art performance, substantially outperforming existing methods in generating accurate and executable optimization models. Specifically, our SIRL-32B model surpasses DeepSeek-V3 and OpenAI-o3 on the majority of these benchmarks. Our code is publicly available at https://github.com/Cardinal-Operations/SIRL.

UAV tracking can be widely applied in scenarios such as disaster rescue, environmental monitoring, and logistics transportation. However, existing UAV tracking methods predominantly emphasize speed and lack exploration in semantic awareness, which hinders the search region from extracting accurate localization information from the template. The limitation results in suboptimal performance under typical UAV tracking challenges such as camera motion, fast motion, and low resolution, etc. To address this issue, we propose a dynamic semantic aware correlation modeling tracking framework. The core of our framework is a Dynamic Semantic Relevance Generator, which, in combination with the correlation map from the Transformer, explore semantic relevance. The approach enhances the search region's ability to extract important information from the template, improving accuracy and robustness under the aforementioned challenges. Additionally, to enhance the tracking speed, we design a pruning method for the proposed framework. Therefore, we present multiple model variants that achieve trade-offs between speed and accuracy, enabling flexible deployment according to the available computational resources. Experimental results validate the effectiveness of our method, achieving competitive performance on multiple UAV tracking datasets.

Molecular property prediction is a fundamental task in computational chemistry with critical applications in drug discovery and materials science. While recent works have explored Large Language Models (LLMs) for this task, they primarily rely on textual molecular representations such as SMILES/SELFIES, which can be ambiguous and structurally uninformative. In this work, we introduce MolVision, a novel approach that leverages Vision-Language Models (VLMs) by integrating both molecular structure images and textual descriptions to enhance property prediction. We construct a benchmark spanning nine diverse datasets, covering both classification and regression tasks. Evaluating nine different VLMs in zero-shot, few-shot, and fine-tuned settings, we find that visual information improves prediction performance, particularly when combined with efficient fine-tuning strategies such as LoRA. Our results reveal that while visual information alone is insufficient, multimodal fusion significantly enhances generalization across molecular properties. Adaptation of vision encoder for molecular images in conjunction with LoRA further improves the performance. The code and data is available at : https://molvision.github.io/MolVision/.

Large-scale pre-trained models hold significant potential for learning universal EEG representations. However, most existing methods, particularly autoregressive (AR) frameworks, primarily rely on straightforward temporal sequencing of multi-channel EEG data, which fails to capture the rich physiological characteristics inherent to EEG signals. Moreover, their time-centered modeling approach also limits the effective representation of the dynamic spatial topology of brain activity. To address these challenges and fully exploit the potential of large-scale EEG models, we propose a novel Topology Hierarchical Derived Brain Autoregressive Modeling (THD-BAR) for EEG generic representations. The core innovation of THD-BAR lies in the introduction of the Brain Topology Hierarchy (BTH), which establishes a multi-scale spatial order for EEG channels. This hierarchical structure enables a redefinition of autoregressive learning as a "next-scale-time prediction" problem, effectively capturing both spatial and temporal dynamics. Based on BTH, we design a Topology-Hierarchical Vector Quantized-Variational Autoencoder (THVQ-VAE) for multi-scale tokenization and develop an enhanced Brain Autoregressive (BAR) module with specialized masking strategies for prediction. Through extensive large-scale pre-training on 17 datasets, followed by rigorous validation on 10 downstream datasets spanning 5 distinct tasks, THD-BAR consistently outperforms existing methods. These results highlight the superior generalization and modeling capabilities of our proposed approach.

Estimating heterogeneous treatment effects (HTEs) of continuous-valued interventions on survival, that is, time-to-event (TTE) outcomes, is crucial in various fields, notably in clinical decision-making and in driving the advancement of next-generation clinical trials. However, while HTE estimation for continuous-valued (i.e., dosage-dependent) interventions and for TTE outcomes have been separately explored, their combined application remains largely overlooked in the machine learning literature. We propose DoseSurv, a varying-coefficient network designed to estimate HTEs for different dosage-dependent and non-dosage treatment options from TTE data. DoseSurv uses radial basis functions to model continuity in dose-response relationships and learns balanced representations to address covariate shifts arising in HTE estimation from observational TTE data. We present experiments across various treatment scenarios on both simulated and real-world data, demonstrating DoseSurv's superior performance over existing baseline models.