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 Deep Learning


ATMOSSCI-BENCH: Evaluating the Recent Advances of Large Language Models for Atmospheric Science

Neural Information Processing Systems

The rapid advancements in large language models (LLMs), particularly in their reasoning capabilities, hold transformative potential for addressing complex challenges and boosting scientific discovery in atmospheric science. However, leveraging LLMs effectively in this domain requires a robust and comprehensive evaluation benchmark. Toward this end, we present ATMOSSCI-BENCH, a novel benchmark designed to systematically assess LLM performance across five core categories of atmospheric science problems: hydrology, atmospheric dynamics, atmospheric physics, geophysics, and physical oceanography. ATMOSSCI-BENCH features a dual-format design comprising both multiple-choice questions (MCQs) and open-ended questions (OEQs), enabling scalable automated evaluation alongside deeper analysis of conceptual understanding. We employ a template-based MCQ generation framework to create diverse, graduate-level problems with symbolic perturbation, while OEQs are used to probe open-ended reasoning. We conduct a comprehensive evaluation of representative LLMs, categorized into four groups: instruction-tuned models, advanced reasoning models, math-augmented models, and domain-specific climate models. Our analysis provides some interesting insights into the reasoning and problem-solving capabilities of LLMs in atmospheric science. We believe ATMOSSCI-BENCH can serve as a critical step toward advancing LLM applications in climate services by offering a standard and rigorous evaluation framework.



Obliviator Reveals the Cost of Nonlinear Guardedness in Concept Erasure

Neural Information Processing Systems

Concept erasure aims to remove unwanted attributes, such as social or demographic factors, from learned representations, while preserving their task-relevant utility. While the goal of concept erasure is protection against all adversaries, existing methods remain vulnerable to nonlinear ones. This vulnerability arises from their failure to fully capture the complex, nonlinear statistical dependencies between learned representations and unwanted attributes. Moreover, although the existence of a trade-off between utility and erasure is expected, its progression during the erasure process, i.e., the cost of erasure, remains unstudied. In this work, we introduce Obliviator, a post-hoc erasure method designed to fully capture nonlinear statistical dependencies.


MVSMamba: Multi-View Stereo with State Space Model

Neural Information Processing Systems

Robust feature representations are essential for learning-based Multi-View Stereo (MVS), which relies on accurate feature matching. Recent MVS methods leverage Transformers to capture long-range dependencies based on local features extracted by conventional feature pyramid networks. However, the quadratic complexity of Transformer-based MVS methods poses challenges to balance performance and efficiency. Motivated by the global modeling capability and linear complexity of the Mamba architecture, we propose MVSMamba, the first Mamba-based MVS network. MVSMamba enables efficient global feature aggregation with minimal computational overhead. To fully exploit Mamba's potential in MVS, we propose a Dynamic Mamba module (DM-module) based on a novel referencecentered dynamic scanning strategy, which enables: (1) Efficient intra-and interview feature interaction from the reference to source views, (2) Omnidirectional multi-view feature representations, and (3) Multi-scale global feature aggregation. Extensive experimental results demonstrate MVSMamba outperforms state-of-theart MVS methods on the DTU dataset and the Tanks-and-Temples benchmark with both superior performance and efficiency.


HyPINO: Multi-Physics Neural Operators via HyperPINNs and the Method of Manufactured Solutions

Neural Information Processing Systems

We present HyPINO, a multi-physics neural operator designed for zero-shot generalization across a broad class of PDEs without requiring task-specific fine-tuning. Our approach combines a Swin Transformer-based hypernetwork with mixed supervision: (i) labeled data from analytical solutions generated via the Method of Manufactured Solutions (MMS), and (ii) unlabeled samples optimized using physics-informed objectives. The model maps PDE parameterizations to target Physics-Informed Neural Networks (PINNs) and can handle linear elliptic, hyperbolic, and parabolic equations in two dimensions with varying source terms, geometries, and mixed Dirichlet/Neumann boundary conditions, including interior boundaries. HyPINO achieves strong zero-shot accuracy on seven benchmark problems from PINN literature, outperforming U-Nets, Poseidon, and Physics-Informed Neural Operators (PINO). Further, we introduce an iterative refinement procedure that treats the residual of the generated PINN as "delta PDE" and performs another forward pass to generate a corrective PINN. Summing their contributions and repeating this process forms an ensemble whose combined solution progressively reduces the error on six benchmarks and achieves a >100 lower L2 loss in the best case, while retaining forward-only inference. Additionally, we evaluate the fine-tuning behavior of PINNs initialized by HyPINO and show that they converge faster and to lower final error than both randomly initialized and Reptilemeta-learned PINNs on five benchmarks, performing on par on the remaining two. Our results highlight the potential of this scalable approach as a foundation for extending neural operators toward solving increasingly complex, nonlinear, and high-dimensional PDE problems. The code and model weights are publicly available at https://github.com/rbischof/hypino.


Towards General Modality Translation with Contrastive and Predictive Latent Diffusion Bridge

Neural Information Processing Systems

Recent advances in generative modeling have positioned diffusion models as stateof-the-art tools for sampling from complex data distributions. While these models have shown remarkable success across single-modality domains such as images and audio, extending their capabilities to Modality Translation (MT), translating information across different sensory modalities, remains an open challenge. Existing approaches often rely on restrictive assumptions, including shared dimensionality, Gaussian source priors, and modality-specific architectures, which limit their generality and theoretical grounding. In this work, we propose the Latent Denoising Diffusion Bridge Model (LDDBM), a general-purpose framework for modality translation based on a latent-variable extension of Denoising Diffusion Bridge Models. By operating in a shared latent space, our method learns a bridge between arbitrary modalities without requiring aligned dimensions. We introduce a contrastive alignment loss to enforce semantic consistency between paired samples and design a domain-agnostic encoder-decoder architecture tailored for noise prediction in latent space. Additionally, we propose a predictive loss to guide training toward accurate cross-domain translation and explore several training strategies to improve stability. Our approach supports arbitrary modality pairs and performs strongly on diverse MT tasks, including multi-view to 3D shape generation, image super-resolution, and multi-view scene synthesis.


d531364f1771e0972c1d11c334a0efb4-Paper-Conference.pdf

Neural Information Processing Systems

Personalized models have demonstrated remarkable success in understanding and generating concepts provided by users. However, existing methods use separate concept tokens for understanding and generation, treating these tasks in isolation. This may result in limitations for generating images with complex prompts. For example, given the concept bo, generating " bo wearing its hat" without additional textual descriptions of its hat. We call this kind of generation personalized attribute-reasoning generation. To address the limitation, we present UniCTokens, a novel framework that effectively integrates personalized information into a unified vision language model (VLM) for understanding and generation. UniCTokens trains a set of unified concept tokens to leverage complementary semantics, boosting two personalized tasks. Moreover, we propose a progressive training strategy with three stages: understanding warm-up, bootstrapping generation from under-Equal contribution.


Explicit dynamic modelingtime-then-graph model Frequency dynamics Theorem 1. Theorem 2

Neural Information Processing Systems

Dynamic GNNs, which integrate temporal and spatial features in Electroencephalography (EEG) data, have shown great potential in automating seizure detection. However, fully capturing the underlying dynamics necessary to represent brain states, such as seizure and non-seizure, remains a non-trivial task and presents two fundamental challenges. First, most existing dynamic GNN methods are built on temporally fixed static graphs, which fail to reflect the evolving nature of brain connectivity during seizure progression. Second, current efforts to jointly model temporal signals and graph structures and, more importantly, their interactions remain nascent, often resulting in inconsistent performance. To address these challenges, we present the first theoretical analysis of these two problems, demonstrating the effectiveness and necessity of explicit dynamic modeling and time-then-graph dynamic GNN method. Building on these insights, we propose EvoBrain, a novel seizure detection model that integrates a two-stream Mamba architecture with a GCN enhanced by Laplacian Positional Encoding, following neurological insights. Moreover, EvoBrainincorporates explicitly dynamic graph structures, allowing both nodes and edges to evolve over time. Our contributions include (a) a theoretical analysis proving the expressivity advantage of explicit dynamic modeling and time-then-graph over other approaches, (b) a novel and efficient model that significantly improves AUROC by 23% and F1 score by 30%, compared with the dynamic GNN baseline, and (c) broad evaluations of our method on the challenging early seizure prediction task.


Towards Interpretability Without Sacrifice: Faithful Dense Layer Decomposition with Mixture of Decoders

Neural Information Processing Systems

Multilayer perceptrons (MLPs) are an integral part of large language models, yet their dense representations render them difficult to understand, edit, and steer. Recent methods learn interpretable approximations via neuron-level sparsity, yet fail to faithfully reconstruct the original mapping-significantly increasing model's next-token cross-entropy loss. In this paper, we advocate for moving to layer-level sparsity to overcome the accuracy trade-off in sparse layer approximation. Under this paradigm, we introduce Mixture of Decoders (MxDs). MxDs generalize MLPs and Gated Linear Units, expanding pre-trained dense layers into tens of thousands of specialized sublayers. Through a flexible form of tensor factorization, each sparsely activating MxD sublayer implements a linear transformation with fullrank weights-preserving the original decoders' expressive capacity even under heavy sparsity. Experimentally, we show that MxDs significantly outperform state-of-the-art methods (e.g., Transcoders) on the sparsity-accuracy frontier in language models with up to 3B parameters. Further evaluations on sparse probing and feature steering demonstrate that MxDs learn similarly specialized features of natural language-opening up a promising new avenue for designing interpretable yet faithful decompositions. Our code is included at: https://github.com/


Manipulating 3DMolecules in a Fixed-Dimensional E(3)-Equivariant Latent Space

Neural Information Processing Systems

Medicinal chemists often optimize drugs considering their 3D structures and designing structurally distinct molecules that retain key features, such as shapes, pharmacophores, or chemical properties. Previous deep learning approaches address this through supervised tasks like molecule inpainting or property-guided optimization. In this work, we propose a flexible zero-shot molecule manipulation method by navigating in a shared latent space of 3D molecules. We introduce a Variational AutoEncoder (VAE) for 3D molecules, named MolFLAE, which learns a fixed-dimensional, E(3)-equivariant latent space independent of atom counts. MolFLAE encodes 3D molecules using an E(3)-equivariant neural network into fixed number of latent nodes, distinguished by learned embeddings. The latent space is regularized, and molecular structures are reconstructed via a Bayesian Flow Network (BFN) conditioned on the encoder's latent output. MolFLAE achieves competitive performance on standard unconditional 3D molecule generation benchmarks. Moreover, the latent space of MolFLAE enables zero-shot molecule manipulation, including atom number editing, structure reconstruction, and coordinated latent interpolation for both structure and properties. We further demonstrate our approach on a drug optimization task for the human glucocorticoid receptor, generating molecules with improved hydrophilicity while preserving key interactions, under computational evaluations.