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Applications · Neuroscience, Cognitive Science

Hyunmo Kang, Abdulkadir Canatar, SueYeon Chung

Understanding representational similarity between neural recordings and computational models is essential for neuroscience, yet remains challenging to measure reliably due to the constraints on the number of neurons that can be recorded simultaneously. In this work, we apply tools from Random Matrix Theory to investigate how such limitations affect similarity measures, focusing on Centered Kernel Alignment (CKA) and Canonical Correlation Analysis (CCA). We propose an analytical framework for representational similarity analysis that relates measured similarities to the spectral properties of the underlying representations. We demonstrate that neural similarities are systematically underestimated under finite neuron sampling, mainly due to eigenvector delocalization. To overcome this, we introduce a denoising method to infer population-level similarity, enabling accurate analysis even with small neuron samples. Theoretical predictions are validated on synthetic and real datasets, offering practical strategies for interpreting neural data under finite sampling constraints.

Deep Learning · Algorithms

Erel Naor, Ofir Lindenbaum

Deep neural networks often under-perform on tabular data due to their sensitivity to irrelevant features and a spectral bias toward smooth, low-frequency functions. These limitations hinder their ability to capture the sharp, high-frequency signals that often define tabular structure, especially under limited labeled samples. While self-supervised learning (SSL) offers promise in such settings, it remains challenging in tabular domains due to the lack of effective data augmentations. We propose a hybrid autoencoder that combines a neural encoder with an oblivious soft decision tree (OSDT) encoder, each guided by its own stochastic gating network that performs sample-specific feature selection. Together, these structurally different encoders and model-specific gating networks implement model-based augmentation, producing complementary input views tailored to each architecture. The two encoders, trained with a shared decoder and cross-reconstruction loss, learn distinct yet aligned representations that reflect their respective inductive biases. During training, the OSDT encoder (robust to noise and effective at modeling localized, high-frequency structure) guides the neural encoder toward representations more aligned with tabular data. At inference, only the neural encoder is used, preserving flexibility and SSL compatibility. Spectral analysis highlights the distinct inductive biases of each encoder. Our method achieves consistent gains in low-label classification and regression across diverse tabular datasets, outperforming deep and tree-based supervised baselines.

Applications · Climate

Eya Cherif, Arthur Ouaknine, Luke Brown, Phuong Dao, Kyle Kovach, Bing Lu, Daniel Mederer, Hannes Feilhauer, Teja Kattenborn, David Rolnick

Plant traits such as leaf carbon content and leaf mass are essential variables in the study of biodiversity and climate change. However, conventional field sampling cannot feasibly cover trait variation at ecologically meaningful spatial scales. Machine learning represents a valuable solution for plant trait prediction across ecosystems, leveraging hyperspectral data from remote sensing.Nevertheless, trait prediction from hyperspectral data is challenged by label scarcity and substantial domain shifts (\eg across sensors, ecological distributions), requiring robust cross-domain methods.Here, we present GreenHyperSpectra, a pretraining dataset encompassing real-world cross-sensor and cross-ecosystem samples designed to benchmark trait prediction with semi- and self-supervised methods. We adopt an evaluation framework encompassing in-distribution and out-of-distribution scenarios. We successfully leverage GreenHyperSpectra to pretrain label-efficient multi-output regression models that outperform the state-of-the-art supervised baseline. Our empirical analyses demonstrate substantial improvements in learning spectral representations for trait prediction, establishing a comprehensive methodological framework to catalyze research at the intersection of representation learning and plant functional traits assessment. We also share the dataset\footnotemark[1], code and pretrained model objects for this study \href{https://github.com/echerif18/HyspectraSSL}{here}.\footnotetext[1]{GreenHyperSpectra dataset: \href{https://huggingface.co/datasets/Avatarr05/GreenHyperSpectra}{https://huggingface.co/datasets/Avatarr05/GreenHyperSpectra}}

Applications · Physics

Hong Wang, Yixuan Jiang, Jie Wang, Xinyi Li, Jian Luo, huanshuo dong

Operator eigenvalue problems play a critical role in various scientific fields and engineering applications, yet numerical methods are hindered by the curse of dimensionality. Recent deep learning methods provide an efficient approach to address this challenge by iteratively updating neural networks. These methods' performance relies heavily on the spectral distribution of the given operator: larger gaps between the operator's eigenvalues will improve precision, thus tailored spectral transformations that leverage the spectral distribution can enhance their performance. Based on this observation, we propose the **S**pectral **T**ransformation **Net**work (**STNet**). During each iteration, STNet uses approximate eigenvalues and eigenfunctions to perform spectral transformations on the original operator, turning it into an equivalent but easier problem. Specifically, we employ deflation projection to exclude the subspace corresponding to already solved eigenfunctions, thereby reducing the search space and avoiding converging to existing eigenfunctions. Additionally, our filter transform magnifies eigenvalues in the desired region and suppresses those outside, further improving performance. Extensive experiments demonstrate that STNet consistently outperforms existing learning-based methods, achieving state-of-the-art performance in accuracy.

Deep Learning · Robustness

Wei Chen, Yuxuan Liang

Spatio-temporal forecasting is crucial in many domains, such as transportation, meteorology, and energy. However, real-world scenarios frequently present challenges such as signal anomalies, noise, and distributional shifts. Existing solutions primarily enhance robustness by modifying network architectures or training procedures. Nevertheless, these approaches are computationally intensive and resource-demanding, especially for large-scale applications. In this paper, we explore a _novel **t**est-**t**ime **c**omputing paradigm, namely learning with calibration, **ST-TTC**_, for **s**patio-**t**emporal forecasting. Through learning with calibration, we aim to capture periodic structural biases arising from non-stationarity during the testing phase and perform real-time bias correction on predictions to improve accuracy. Specifically, we first introduce a spectral-domain calibrator with phase-amplitude modulation to mitigate periodic shift and then propose a flash updating mechanism with a streaming memory queue for efficient test-time computation. _**ST-TTC**_ effectively bypasses complex training-stage techniques, offering an efficient and generalizable paradigm. Extensive experiments on real-world datasets demonstrate the effectiveness, universality, flexibility and efficiency of our proposed method.

General Machine Learning · Everything Else

En Yu, Jie Lu, Xiaoyu Yang, Guangquan Zhang, Zhen Fang

Modern machine learning models struggle to maintain performance in dynamic environments where temporal distribution shifts, \textit{i.e., concept drift}, are prevalent. Temporal Domain Generalization (TDG) seeks to enable model generalization across evolving domains, yet existing approaches typically assume smooth incremental changes, struggling with complex real-world drifts involving both long-term structure (incremental evolution/periodicity) and local uncertainties. To overcome these limitations, we introduce FreKoo, which tackles these challenges through a novel frequency-domain analysis of parameter trajectories. It leverages the Fourier transform to disentangle parameter evolution into distinct spectral bands. Specifically, the low-frequency components with dominant dynamics are learned and extrapolated using the Koopman operator, robustly capturing diverse drift patterns including both incremental and periodic drifts. Simultaneously, potentially disruptive high-frequency variations are smoothed via targeted temporal regularization, preventing overfitting to transient noise and domain uncertainties. In addition, this dual-spectral strategy is rigorously grounded through theoretical analysis, providing stability guarantees for the Koopman prediction, a principled Bayesian justification for the high-frequency regularization, and culminating in a multiscale generalization bound connecting spectral dynamics to improved generalization. Extensive experiments demonstrate FreKoo's significant superiority over state-of-the-art TDG methods, particularly excelling in real-world streaming scenarios with complex drifts and uncertainties.

Deep Learning · Everything Else

Reece Shuttleworth, Jacob Andreas, Antonio Torralba, Pratyusha Sharma

Fine-tuning is a crucial paradigm for adapting pre-trained large language models to downstream tasks. Recently, methods like Low-Rank Adaptation (LoRA) have been shown to effectively fine-tune LLMs with an extreme reduction in trainable parameters. But, \emph{are their learned solutions really equivalent?} We study how LoRA and full-finetuning change pre-trained models by analyzing the model's weight matrices through the lens of their spectral properties. We find that LoRA and full fine-tuning yield weight matrices whose singular value decompositions exhibit very different structure: weight matrices trained with LoRA have new, high-ranking singular vectors, which we call \emph{intruder dimensions}, while those trained with full fine-tuning do not. Further, we extend the finding that LoRA forgets less than full fine-tuning and find its forgetting is vastly localized to the intruder dimension -- by causally intervening on the intruder dimensions by changing their associated singular values post-fine-tuning, we show that they cause forgetting. Moreover, scaling them down significantly improves modeling of the pre-training distribution with a minimal drop in downstream task performance. Given this, we should expect accumulating intruder dimensions to be harmful and lead to more forgetting. This will be amplified during continual learning because of sequentially fine-tuning, and we show that LoRA models do accumulate intruder dimensions here tend to perform worse in this setting, emphasizing the practicality of our findings.

Probabilistic Methods · Gaussian Processes

Zi Yang, Ying Li, Zhidi Lin, Michael Minyi Zhang, Pablo Martinez Olmos

The multi-view Gaussian process latent variable model (MV-GPLVM) aims to learn a unified representation from multi-view data but is hindered by challenges such as limited kernel expressiveness and low computational efficiency. To overcome these issues, we first introduce a new duality between the spectral density and the kernel function. By modeling the spectral density with a bivariate Gaussian mixture, we then derive a generic and expressive kernel termed Next-Gen Spectral Mixture (NG-SM) for MV-GPLVMs. To address the inherent computational inefficiency of the NG-SM kernel, we propose a random Fourier feature approximation. Combined with a tailored reparameterization trick, this approximation enables scalable variational inference for both the model and the unified latent representations. Numerical evaluations across a diverse range of multi-view datasets demonstrate that our proposed method consistently outperforms state-of-the-art models in learning meaningful latent representations.

Deep Learning · Attention Mechanisms

Pengbo Wang, Chaozhuo Li, Chenxu Wang, Liwen Zheng, Litian Zhang, Xi Zhang

LLMs have demonstrated unprecedented capabilities in natural language processing, yet their practical deployment remains hindered by persistent factuality and faithfulness hallucinations. While existing methods address these hallucination types independently, they inadvertently induce performance trade-offs, as interventions targeting one type often exacerbate the other. Through empirical and theoretical analysis of activation space dynamics in LLMs, we reveal that these hallucination categories share overlapping subspaces within neural representations, presenting an opportunity for concurrent mitigation. To harness this insight, we propose SPACE, a unified framework that jointly enhances factuality and faithfulness by editing shared activation subspaces. SPACE establishes a geometric foundation for shared subspace existence through dual-task feature modeling, then identifies and edits these subspaces via a hybrid probe strategy combining spectral clustering and attention head saliency scoring. Experimental results across multiple benchmark datasets demonstrate the superiority of our approach.

Deep Learning · Graph Neural Networks

Javad Aliakbari, Johan Oestman, Ashkan Panahi, Alexandre Graell i Amat

We consider the problem of federated learning (FL) with graph-structured data distributed across multiple clients. In particular, we address the common scenario of interconnected subgraphs, where interconnections between clients significantly influence the learning process. Existing approaches suffer from critical limitations, either requiring the exchange of sensitive node embeddings, thereby posing privacy risks, or relying on computationally-intensive steps, which hinders scalability. To tackle these challenges, we propose FedLap, a novel framework that leverages global structure information via Laplacian smoothing in the spectral domain to effectively capture inter-node dependencies while ensuring privacy and scalability. We provide a formal analysis of the privacy of FedLap, demonstrating that it preserves privacy. Notably, FedLap is the first subgraph FL scheme with strong privacy guarantees. Extensive experiments on benchmark datasets demonstrate that the proposed method achieves competitive or superior utility compared to existing techniques.

Computer Vision · Vision Models & Multimodal

Hritam Basak, Zhaozheng Yin

We address the problem of language-guided 3D affordance prediction, a core capability for embodied agents interacting with unstructured environments. Existing methods often rely on fixed affordance categories or require external expert prompts, limiting their ability to generalize across different objects and interpret multi-step instructions. In this work, we introduce $\textit{ViSPLA}$, a novel iterative self-prompting framework that leverages the intrinsic geometry of predicted masks for continual refinement. We redefine affordance detection as a language-conditioned segmentation task: given a 3D point cloud and language instruction, our model predicts a sequence of refined affordance masks, each guided by differential geometric feedback including Laplacians, normal derivatives, and curvature fields. This feedback is encoded into visual prompts that drive a multi-stage refinement decoder, enabling the model to self-correct and adapt to complex spatial structures. To further enhance precision and coherence, we introduce Implicit Neural Affordance Fields, which define continuous probabilistic regions over the 3D surface without additional supervision. Additionally, our Spectral Convolutional Self-Prompting module operates in the frequency domain of the point cloud, enabling multi-scale refinement that captures both coarse and fine affordance structures. Extensive experiments demonstrate that $\textit{ViSPLA}$ achieves state-of-the-art results on both seen and unseen objects on two benchmark datasets. Our framework establishes a new paradigm for open-world 3D affordance reasoning by unifying language comprehension with low-level geometric perception through iterative refinement.

Steffen Schotthöfer, Lexie Yang, Stefan Schnake

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

Phuc Tran, Van Vu, Nisheeth K. Vishnoi

A central challenge in machine learning is to understand how noise or measurement errors affect low-rank approximations, particularly in the spectral norm. This question is especially important in differentially private low-rank approximation, where one aims to preserve the top-$p$ structure of a data-derived matrix while ensuring privacy. Prior work often analyzes Frobenius norm error or changes in reconstruction quality, but these metrics can over- or under-estimate true subspace distortion. The spectral norm, by contrast, captures worst-case directional error and provides the strongest utility guarantees. We establish new high-probability spectral-norm perturbation bounds for symmetric matrices that refine the classical Eckart--Young--Mirsky theorem and explicitly capture interactions between a matrix $A \in \mathbb{R}^{n \times n}$ and an arbitrary symmetric perturbation $E$. Under mild eigengap and norm conditions, our bounds yield sharp estimates for $\| (A + E)_p - A_p \|$, where $A_p$ is the best rank-$p$ approximation of $A$, with improvements of up to a factor of $\sqrt{n}$. As an application, we derive improved utility guarantees for differentially private PCA, resolving an open problem in the literature. Our analysis relies on a novel contour bootstrapping method from complex analysis and extends it to a broad class of spectral functionals, including polynomials and matrix exponentials. Empirical results on real-world datasets confirm that our bounds closely track the actual spectral error under diverse perturbation regimes.

Applications · Neuroscience, Cognitive Science

Valentin Schmutz, Ali Haydaroğlu, Shuqi Wang, Yixiao Feng, Matteo Carandini, Kenneth D Harris

Computation in recurrent networks of neurons has been hypothesized to occur at the level of low-dimensional latent dynamics, both in artificial systems and in the brain. This hypothesis seems at odds with evidence from large-scale neuronal recordings in mice showing that neuronal population activity is high-dimensional. To demonstrate that low-dimensional latent dynamics and high-dimensional activity can be two sides of the same coin, we present an analytically solvable recurrent neural network (RNN) model whose dynamics can be exactly reduced to a low-dimensional dynamical system, but generates an activity manifold that has a high linear embedding dimension. This raises the question: Do low-dimensional latents explain the high-dimensional activity observed in mouse visual cortex? Spectral theory tells us that the covariance eigenspectrum alone does not allow us to recover the dimensionality of the latents, which can be low or high, when neurons are nonlinear. To address this indeterminacy, we develop Neural Cross-Encoder (NCE), an interpretable, nonlinear latent variable modeling method for neuronal recordings, and find that high-dimensional neuronal responses to drifting gratings and spontaneous activity in visual cortex can be reduced to low-dimensional latents, while the responses to natural images cannot. We conclude that the high-dimensional activity measured in certain conditions, such as in the absence of a stimulus, is explained by low-dimensional latents that are nonlinearly processed by individual neurons.

Xixi Wan, AIHUA ZHENG, Bo Jiang, Beibei Wang, Chenglong Li, Jin Tang

Multi-modal object Re-IDentification (ReID) has gained considerable attention with the goal of retrieving specific targets across cameras using heterogeneous visual data sources. At present, multi-modal object ReID faces two core challenges: (1) learning robust features under fine-grained local noise caused by occlusion, frame loss, and other disruptions; and (2) effectively integrating heterogeneous modalities to enhance multi-modal representation. To address the above challenges, we propose a robust approach named Uncertainty-Guided Graph model for multi-modal object ReID (UGG-ReID). UGG-ReID is designed to mitigate noise interference and facilitate effective multi-modal fusion by estimating both local and sample-level aleatoric uncertainty and explicitly modeling their dependencies. Specifically, we first propose the Gaussian patch-graph representation model that leverages uncertainty to quantify fine-grained local cues and capture their structural relationships. This process boosts the expressiveness of modal-specific information, ensuring that the generated embeddings are both more informative and robust. Subsequently, we design an uncertainty-guided mixture of experts strategy that dynamically routes samples to experts exhibiting low uncertainty. This strategy effectively suppresses noise-induced instability, leading to enhanced robustness. Meanwhile, we design an uncertainty-guided routing to strengthen the multi-modal interaction, improving the performance. UGG-ReID is comprehensively evaluated on five representative multi-modal object ReID datasets, encompassing diverse spectral modalities. Experimental results show that the proposed method achieves excellent performance on all datasets and is significantly better than current methods in terms of noise immunity. Our code is available at https://github.com/wanxixi11/UGG-ReID.

Applications · Physics

Yiheng Du, Aditi Krishnapriyan

Computationally resolving turbulence remains a central challenge in fluid dynamics due to its multi-scale interactions. Fully resolving large-scale turbulence through direct numerical simulation (DNS) is computationally prohibitive, motivating data-driven machine learning alternatives. In this work, we propose EddyFormer, a Transformer-based spectral-element (SEM) architecture for large-scale turbulence simulation that combines the accuracy of spectral methods with the scalability of the attention mechanism. We introduce an SEM tokenization that decomposes the flow into grid-scale and subgrid-scale components, enabling capture of both local and global features. We create a new three-dimensional isotropic turbulence dataset and train EddyFormer to achieves DNS-level accuracy at 256^3 resolution, providing a 30x speedup over DNS. When applied to unseen domains up to 4x larger than in training, EddyFormer preserves accuracy on physics-invariant metrics-energy spectra, correlation functions, and structure functions-showing domain generalization. On The Well benchmark suite of diverse turbulent flows, EddyFormer resolves cases where prior ML models fail to converge, accurately reproducing complex dynamics across a wide range of physical conditions.

Probabilistic Methods

Jeffrey Alido, Tongyu Li, Yu Sun, Lei Tian

Conventional score-based diffusion models (DMs) may struggle with anisotropic Gaussian diffusion processes due to the required inversion of covariance matrices in the denoising score matching training objective \cite{vincent_connection_2011}. We propose Whitened Score (WS) diffusion models, a novel framework based on stochastic differential equations that learns the Whitened Score function instead of the standard score. This approach circumvents covariance inversion, extending score-based DMs by enabling stable training of DMs on arbitrary Gaussian forward noising processes. WS DMs establish equivalence with flow matching for arbitrary Gaussian noise, allow for tailored spectral inductive biases, and provide strong Bayesian priors for imaging inverse problems with structured noise. We experiment with a variety of computational imaging tasks using the CIFAR, CelebA ($64\times64$), and CelebA-HQ ($256\times256$) datasets and demonstrate that WS diffusion priors trained on anisotropic Gaussian noising processes consistently outperform conventional diffusion priors based on isotropic Gaussian noise.

Reinforcement Learning · Deep RL

Chunyu Wei, Wenji Hu, Xingjia Hao, Xin Wang, Yifan Yang, Yunhai Wang, Yang Tian, Yueguo Chen

Large Language Models (LLMs) face significant limitations when applied to large-scale graphs, struggling with context constraints and inflexible reasoning. We introduce GraphChain, a novel framework enabling LLMs to analyze large graphs by orchestrating dynamic sequences of specialized tools, mimicking human exploratory processes. GraphChain incorporates two core technical contributions: (1) Progressive Graph Distillation, a reinforcement learning approach that learns to generate tool sequences balancing task relevance and intermediate state compression, thereby overcoming LLM context limitations. (2) Structure-aware Test-Time Adaptation (STTA), a mechanism using a lightweight, self-supervised adapter conditioned on graph spectral properties to efficiently adapt a frozen LLM policy to diverse graph structures via soft prompts without retraining. Experiments show GraphChain significantly outperforms prior methods, enabling scalable and adaptive LLM-driven graph analysis.

Applications · Neuroscience, Cognitive Science

Valentin Schmutz, Ali Haydaroğlu, Shuqi Wang, Yixiao Feng, Matteo Carandini, Kenneth D Harris

Computation in recurrent networks of neurons has been hypothesized to occur at the level of low-dimensional latent dynamics, both in artificial systems and in the brain. This hypothesis seems at odds with evidence from large-scale neuronal recordings in mice showing that neuronal population activity is high-dimensional. To demonstrate that low-dimensional latent dynamics and high-dimensional activity can be two sides of the same coin, we present an analytically solvable recurrent neural network (RNN) model whose dynamics can be exactly reduced to a low-dimensional dynamical system, but generates an activity manifold that has a high linear embedding dimension. This raises the question: Do low-dimensional latents explain the high-dimensional activity observed in mouse visual cortex? Spectral theory tells us that the covariance eigenspectrum alone does not allow us to recover the dimensionality of the latents, which can be low or high, when neurons are nonlinear. To address this indeterminacy, we develop Neural Cross-Encoder (NCE), an interpretable, nonlinear latent variable modeling method for neuronal recordings, and find that high-dimensional neuronal responses to drifting gratings and spontaneous activity in visual cortex can be reduced to low-dimensional latents, while the responses to natural images cannot. We conclude that the high-dimensional activity measured in certain conditions, such as in the absence of a stimulus, is explained by low-dimensional latents that are nonlinearly processed by individual neurons.

Data-centric AI · Data-centric AI methods and tools

Hadi Askari, Shivanshu Gupta, Fei Wang, Anshuman Chhabra, Muhao Chen

Pretrained Large Language Models (LLMs) achieve strong performance across a wide range of tasks, yet exhibit substantial variability in the various layers' training quality with respect to specific downstream applications, limiting their downstream performance. It is therefore critical to estimate layer-wise training quality in a manner that accounts for both model architecture and training data. However, existing approaches predominantly rely on model-centric heuristics (such as spectral statistics, outlier detection, or uniform allocation) while overlooking the influence of data. To address these limitations, we propose **LayerIF**, a data-driven framework that leverages *Influence Functions* to quantify the training quality of individual layers in a principled and task-sensitive manner. By isolating each layer's gradients and measuring the sensitivity of the validation loss to training examples by computing layer-wise influences, we derive data-driven estimates of layer importance. Notably, our method produces *task-specific* layer importance estimates for the *same* LLM, revealing how layers specialize for different test-time evaluation tasks. We demonstrate the utility of our scores by leveraging them for two downstream applications: (a) expert allocation in LoRA-MoE architectures and (b) layer-wise sparsity distribution for LLM pruning. Experiments across multiple LLM architectures demonstrate that our model-agnostic, influence-guided allocation leads to consistent gains in task performance.