OpenRaiser/Intern-Atlas huggingface dataset:
Quantum Doubly Stochastic Transformers
Venue: Conference NeurIPS 2025
Year: 2025

At the core of the Transformer, the softmax normalizes the attention matrix to be right stochastic. Previous research has shown that this often de-stabilizes training and that enforcing the attention matrix to be doubly stochastic (through Sinkhorn's algorithm) consistently improves performance across different tasks, domains and Transformer flavors. However, Sinkhorn's algorithm is iterative, approximative, non-parametric and thus inflexible w.r.t. the obtained doubly stochastic matrix (DSM). Recently, it has been proven that DSMs can be obtained with a parametric quantum circuit, yielding a novel quantum inductive bias for DSMs with no known classical analogue. Motivated by this, we demonstrate the feasibility of a hybrid classical-quantum doubly stochastic Transformer (QDSFormer) that replaces the softmax in the self-attention layer with a variational quantum circuit. We study the expressive power of the circuit and find that it yields more diverse DSMs that better preserve information than classical operators. Across multiple small-scale object recognition tasks, we find that our QDSFormer consistently surpasses both a standard ViT and other doubly stochastic Transformers. Beyond the Sinkformer, this comparison includes a novel quantum-inspired doubly stochastic Transformer (based on QR decomposition) that can be of independent interest. Our QDSFormer also shows improved training stability and lower performance variation suggesting that it may mitigate the notoriously unstable training of ViTs on small-scale data.
SUMO: Subspace-Aware Moment-Orthogonalization for Accelerating Memory-Efficient LLM Training
Venue: Conference NeurIPS 2025
Year: 2025

Low-rank gradient-based optimization methods have significantly improved memory efficiency during the training of large language models (LLMs), enabling operations within constrained hardware without sacrificing performance. However, these methods primarily emphasize memory savings, often overlooking potential acceleration in convergence due to their reliance on standard isotropic steepest descent techniques, which can perform suboptimally in the highly anisotropic landscapes typical of deep networks, particularly LLMs. In this paper, we propose SUMO (Subspace-Aware Moment-Orthogonalization), an optimizer that employs exact singular value decomposition (SVD) for moment orthogonalization within a dynamically adapted low-dimensional subspace, enabling norm-inducing steepest descent optimization steps. By explicitly aligning optimization steps with the spectral characteristics of the loss landscape, SUMO effectively mitigates approximation errors associated with commonly used methods like Newton-Schulz orthogonalization approximation. We theoretically establish an upper bound on these approximation errors, proving their dependence on the condition numbers of moments, conditions we analytically demonstrate are encountered during LLM training. Furthermore, we both theoretically and empirically illustrate that exact orthogonalization via SVD substantially improves convergence rates while reducing overall complexity. Empirical evaluations confirm that SUMO accelerates convergence, enhances stability, improves performance, and reduces memory requirements by up to 20% compared to state-of-the-art methods.
Learning from Interval Targets
Venue: Conference NeurIPS 2025
Year: 2025

We study the problem of regression with interval targets, where only upper and lower bounds on target values are available in the form of intervals. This problem arises when the exact target label is expensive or impossible to obtain, due to inherent uncertainties. In the absence of exact targets, traditional regression loss functions cannot be used. First, we study the methodology of using a loss functions compatible with interval targets, for which we establish non-asymptotic generalization bounds based on smoothness of the hypothesis class that significantly relaxing prior assumptions of realizability and small ambiguity degree. Second, we propose a novel min-max learning formulation: minimize against the worst-case (maximized) target labels within the provided intervals. The maximization problem in the latter is non-convex, but we show that good performance can be achieved with the incorporation of smoothness constraints. Finally, we perform extensive experiments on real-world datasets and show that our methods achieve state-of-the-art performance.
Omnipresent Yet Overlooked: Heat Kernels in Combinatorial Bayesian Optimization
Venue: Conference NeurIPS 2025
Year: 2025

Bayesian Optimization (BO) has the potential to solve various combinatorial tasks, ranging from materials science to neural architecture search. However, BO requires specialized kernels to effectively model combinatorial domains. Recent efforts have introduced several combinatorial kernels, but the relationships among them are not well understood. To bridge this gap, we develop a unifying framework based on heat kernels, which we derive in a systematic way and express as simple closed-form expressions. Using this framework, we prove that many successful combinatorial kernels are either related or equivalent to heat kernels, and validate this theoretical claim in our experiments. Moreover, our analysis confirms and extends the results presented in Bounce: certain algorithms' performance decreases substantially when the unknown optima of the function do not have a certain structure. In contrast, heat kernels are not sensitive to the location of the optima. Lastly, we show that a fast and simple pipeline, relying on heat kernels, is able to achieve state-of-the-art results, matching or even outperforming certain slow or complex algorithms.
Information-Computation Tradeoffs  for Noiseless Linear Regression with Oblivious Contamination
Venue: Conference NeurIPS 2025
Year: 2025

We study the task of noiseless linear regression under Gaussian covariates in the presence of additive oblivious contamination. Specifically, we are given i.i.d.\ samples from a distribution $(x, y)$ on $\mathbb{R}^d \times \mathbb{R}$ with $x \sim \mathcal{N}(0,\mathbf{I}_d)$ and $y = x^\top β+ z$, where $z$ is drawn independently of $x$ from an unknown distribution $E$. Moreover, $z$ satisfies $\mathbb{P}_E[z = 0] = α>0$. The goal is to accurately recover the regressor $β$ to small $\ell_2$-error. Ignoring computational considerations, this problem is known to be solvable using $O(d/α)$ samples. On the other hand, the best known polynomial-time algorithms require $Ω(d/α^2)$ samples. Here we provide formal evidence that the quadratic dependence in $1/α$ is inherent for efficient algorithms. Specifically, we show that any efficient Statistical Query algorithm for this task requires VSTAT complexity at least $\tildeΩ(d^{1/2}/α^2)$.
Know Thyself by Knowing Others: Learning Neuron Identity from Population Context
Venue: Conference NeurIPS 2025
Year: 2025

Neurons process information in ways that depend on their cell type, connectivity, and the brain region in which they are embedded. However, inferring these factors from neural activity remains a significant challenge. To build general-purpose representations that allow for resolving information about a neuron's identity, we introduce NuCLR, a self-supervised framework that aims to learn representations of neural activity that allow for differentiating one neuron from the rest. NuCLR brings together views of the same neuron observed at different times and across different stimuli and uses a contrastive objective to pull these representations together. To capture population context without assuming any fixed neuron ordering, we build a spatiotemporal transformer that integrates activity in a permutation-equivariant manner. Across multiple electrophysiology and calcium imaging datasets, a linear decoding evaluation on top of NuCLR representations achieves a new state-of-the-art for both cell type and brain region decoding tasks, and demonstrates strong zero-shot generalization to unseen animals. We present the first systematic scaling analysis for neuron-level representation learning, showing that increasing the number of animals used during pretraining consistently improves downstream performance. The learned representations are also label-efficient, requiring only a small fraction of labeled samples to achieve competitive performance. These results highlight how large, diverse neural datasets enable models to recover information about neuron identity that generalize across animals. Code is available at https://github.com/nerdslab/nuclr.
SpEx: A Spectral Approach to Explainable Clustering
Venue: Conference NeurIPS 2025
Year: 2025

Explainable clustering by axis-aligned decision trees was introduced by Moshkovitz et al. (2020) and has gained considerable interest. Prior work has focused on minimizing the price of explainability for specific clustering objectives, lacking a general method to fit an explanation tree to any given clustering, without restrictions. In this work, we propose a new and generic approach to explainable clustering, based on spectral graph partitioning. With it, we design an explainable clustering algorithm that can fit an explanation tree to any given non-explainable clustering, or directly to the dataset itself. Moreover, we show that prior algorithms can also be interpreted as graph partitioning, through a generalized framework due to Trevisan (2013) wherein cuts are optimized in two graphs simultaneously. Our experiments show the favorable performance of our method compared to baselines on a range of datasets.
Fast Last-Iterate Convergence of SGD in the Smooth Interpolation Regime
Venue: Conference NeurIPS 2025
Year: 2025

We study population convergence guarantees of stochastic gradient descent (SGD) for smooth convex objectives in the interpolation regime, where the noise at optimum is zero or near zero. The behavior of the last iterate of SGD in this setting -- particularly with large (constant) stepsizes -- has received growing attention in recent years due to implications for the training of over-parameterized models, as well as to analyzing forgetting in continual learning and to understanding the convergence of the randomized Kaczmarz method for solving linear systems. We establish that after $T$ steps of SGD on $β$-smooth convex loss functions with stepsize $0 < η< 2/β$, the last iterate exhibits expected excess risk $\widetilde{O}(\frac{1}{η(2-βη) T^{1-βη/2}} + \fracη{(2-βη)^2} T^{βη/2} σ_\star^2)$, where $σ_\star^2$ denotes the variance of the stochastic gradients at the optimum. In particular, for a well-tuned stepsize we obtain a near optimal $\widetilde{O}(1/T + σ_\star/\sqrt{T})$ rate for the last iterate, extending the results of Varre et al. (2021) beyond least squares regression; and when $σ_\star=0$ we obtain a rate of $\smash{O(1/\sqrt T)}$ with $η=1/β$, improving upon the best-known $\smash{O(T^{-1/4})}$ rate recently established by Evron et al. (2025) in the special case of realizable linear regression.
Adaptive Distraction: Probing LLM Contextual Robustness with Automated Tree Search
Venue: Conference NeurIPS 2025
Year: 2025

Large Language Models (LLMs) often struggle to maintain their original performance when faced with semantically coherent but task-irrelevant contextual information. Although prior studies have explored this issue using fixed-template or retrieval-based distractions, such static methods show limited effectiveness against contemporary models. To address this problem, we propose a dynamic distraction generation framework based on tree search, where the generation process is guided by model behavior. Without modifying the original question or answer, the method efficiently produces challenging adaptive distractions across multiple datasets, enabling systematic stress testing of LLMs' contextual robustness. Experiments on four benchmarks demonstrate that the generated distractions lead to an average performance drop of over 45\% for mainstream models. Further comparisons of mitigation strategies show that prompt-based optimization methods yield limited gains, whereas post-training approaches (e.g., DPO) significantly enhance the model's contextual robustness. The results indicate that these issues do not stem from knowledge deficits in LLMs, but from a fundamental inability to maintain consistent reasoning under contextual distraction, posing a major challenge to the reliability of LLMs in real-world applications. The code is publicly available at https://github.com/wyf23187/Adaptive_Distractions.
ExGra-Med: Extended Context Graph Alignment for Medical Vision-Language Models
Venue: Conference NeurIPS 2025
Year: 2025

State-of-the-art medical multi-modal LLMs (med-MLLMs), such as LLaVA-Med and BioMedGPT, primarily depend on scaling model size and data volume, with training driven largely by autoregressive objectives. However, we reveal that this approach can lead to weak vision-language alignment, making these models overly dependent on costly instruction-following data. To address this, we introduce ExGra-Med, a novel multi-graph alignment framework that jointly aligns images, instruction responses, and extended captions in the latent space, advancing semantic grounding and cross-modal coherence. To scale to large LLMs (e.g., LLaMA-7B), we develop an efficient end-to-end training scheme using black-box gradient estimation, enabling fast and scalable optimization. Empirically, ExGra-Med matches LLaVA-Med's performance using just 10% of the pre-training data, achieving a 20.13% gain on VQA-RAD and approaching full-data performance. It also outperforms strong baselines like BioMedGPT and RadFM on visual chatbot and zero-shot classification tasks, demonstrating its promise for efficient, high-quality vision-language integration in medical AI.
Explaining and Mitigating Crosslingual Tokenizer Inequities
Venue: Conference NeurIPS 2025
Year: 2025

The number of tokens it takes to encode parallel text in different languages is known to vary. These disparities are called token premiums. Having high token premiums leads to less throughput during training and increases costs at inference. In this paper, we show that even after controlling for dataset size, vocabulary size, and data content, monolingual tokenizers exhibit a wide range of token premiums across languages. To understand the cross-linguistic differences that cause these token premiums, we train a suite of approximately 7,000 comparable monolingual tokenizers for 97 languages, manipulating tokenization algorithm, vocabulary size, and dataset size. We measure token premiums and test for a relationship between factors such as data similarity (between tokenizer training and evaluation), vocabulary size, and pre-tokenization. We also investigate the role of language-specific features such as writing system and word length. We find that similarity between training and test data does not impact token premiums, but vocabulary size and pre-tokenization do. While simply increasing vocabulary size does not lead to reduced token premium effects, we can determine an ``optimal'' vocabulary size for each language to achieve significantly reduced token premium effects. We also train superword tokenizers which allow merges over whitespaces, and we find that they both reduce token premium effects and improve compression overall. Thus, intervening on the vocabulary size or the pre-tokenizer significantly reduces crosslingual token premium effects.
Curl Descent : Non-Gradient Learning Dynamics with Sign-Diverse Plasticity
Venue: Conference NeurIPS 2025
Year: 2025

Gradient-based algorithms are a cornerstone of artificial neural network training, yet it remains unclear whether biological neural networks use similar gradient-based strategies during learning. Experiments often discover a diversity of synaptic plasticity rules, but whether these amount to an approximation to gradient descent is unclear. Here we investigate a previously overlooked possibility: that learning dynamics may include fundamentally non-gradient "curl"-like components while still being able to effectively optimize a loss function. Curl terms naturally emerge in networks with inhibitory-excitatory connectivity or Hebbian/anti-Hebbian plasticity, resulting in learning dynamics that cannot be framed as gradient descent on any objective. To investigate the impact of these curl terms, we analyze feedforward networks within an analytically tractable student-teacher framework, systematically introducing non-gradient dynamics through neurons exhibiting rule-flipped plasticity. Small curl terms preserve the stability of the original solution manifold, resulting in learning dynamics similar to gradient descent. Beyond a critical value, strong curl terms destabilize the solution manifold. Depending on the network architecture, this loss of stability can lead to chaotic learning dynamics that destroy performance. In other cases, the curl terms can counterintuitively speed learning compared to gradient descent by allowing the weight dynamics to escape saddles by temporarily ascending the loss. Our results identify specific architectures capable of supporting robust learning via diverse learning rules, providing an important counterpoint to normative theories of gradient-based learning in neural networks.
Non-Markovian Discrete Diffusion with Causal Language Models
Venue: Conference NeurIPS 2025
Year: 2025

Discrete diffusion models offer a flexible, controllable approach to structured sequence generation, yet they still lag behind causal language models in expressive power. A key limitation lies in their reliance on the Markovian assumption, which restricts each step to condition only on the current state, leading to potential uncorrectable error accumulation. In this paper, we introduce CaDDi (Causal Discrete Diffusion Model), a discrete diffusion model that conditions on the entire generative trajectory, thereby lifting the Markov constraint and allowing the model to revisit and improve past states. By unifying sequential (causal) and temporal (diffusion) reasoning in a single non-Markovian transformer, CaDDi also treats standard causal language models as a special case and permits the direct reuse of pretrained LLM weights with no architectural changes. Empirically, CaDDi outperforms state-of-the-art discrete diffusion baselines on natural-language benchmarks, substantially narrowing the remaining gap to large autoregressive transformers.
Gaussian-Augmented Physics Simulation and System Identification with Complex Colliders
Venue: Conference NeurIPS 2025
Year: 2025

System identification involving the geometry, appearance, and physical properties from video observations is a challenging task with applications in robotics and graphics. Recent approaches have relied on fully differentiable Material Point Method (MPM) and rendering for simultaneous optimization of these properties. However, they are limited to simplified object-environment interactions with planar colliders and fail in more challenging scenarios where objects collide with non-planar surfaces. We propose AS-DiffMPM, a differentiable MPM framework that enables physical property estimation with arbitrarily shaped colliders. Our approach extends existing methods by incorporating a differentiable collision handling mechanism, allowing the target object to interact with complex rigid bodies while maintaining end-to-end optimization. We show AS-DiffMPM can be easily interfaced with various novel view synthesis methods as a framework for system identification from visual observations.
On the Stability of Graph Convolutional Neural Networks: A Probabilistic Perspective
Venue: Conference NeurIPS 2025
Year: 2025

Graph convolutional neural networks (GCNNs) have emerged as powerful tools for analyzing graph-structured data, achieving remarkable success across diverse applications. However, the theoretical understanding of the stability of these models, i.e., their sensitivity to small changes in the graph structure, remains in rather limited settings, hampering the development and deployment of robust and trustworthy models in practice. To fill this gap, we study how perturbations in the graph topology affect GCNN outputs and propose a novel formulation for analyzing model stability. Unlike prior studies that focus only on worst-case perturbations, our distribution-aware formulation characterizes output perturbations across a broad range of input data. This way, our framework enables, for the first time, a probabilistic perspective on the interplay between the statistical properties of the node data and perturbations in the graph topology. We conduct extensive experiments to validate our theoretical findings and demonstrate their benefits over existing baselines, in terms of both representation stability and adversarial attacks on downstream tasks. Our results demonstrate the practical significance of the proposed formulation and highlight the importance of incorporating data distribution into stability analysis.
SHAP zero Explains Biological Sequence Models with Near-zero Marginal Cost for Future Queries
Venue: Conference NeurIPS 2025
Year: 2025

The growing adoption of machine learning models for biological sequences has intensified the need for interpretable predictions, with Shapley values emerging as a theoretically grounded standard for model explanation. While effective for local explanations of individual input sequences, scaling Shapley-based interpretability to extract global biological insights requires evaluating thousands of sequences--incurring exponential computational cost per query. We introduce SHAP zero, a novel algorithm that amortizes the cost of Shapley value computation across large-scale biological datasets. After a one-time model sketching step, SHAP zero enables near-zero marginal cost for future queries by uncovering an underexplored connection between Shapley values, high-order feature interactions, and the sparse Fourier transform of the model. Applied to models of guide RNA efficacy, DNA repair outcomes, and protein fitness, SHAP zero explains predictions orders of magnitude faster than existing methods, recovering rich combinatorial interactions previously inaccessible at scale. This work opens the door to principled, efficient, and scalable interpretability for black-box sequence models in biology.
Non-equilibrium Annealed Adjoint Sampler
Venue: Conference NeurIPS 2025
Year: 2025

Recently, there has been significant progress in learning-based diffusion samplers, which aim to sample from a given unnormalized density. Many of these approaches formulate the sampling task as a stochastic optimal control (SOC) problem using a canonical uninformative reference process, which limits their ability to efficiently guide trajectories toward the target distribution. In this work, we propose the Non-Equilibrium Annealed Adjoint Sampler (NAAS), a novel SOC-based diffusion framework that employs annealed reference dynamics as a non-stationary base SDE. This annealing structure provides a natural progression toward the target distribution and generates informative reference trajectories, thereby enhancing the stability and efficiency of learning the control. Owing to our SOC formulation, our framework can incorporate a variety of SOC solvers, thereby offering high flexibility in algorithmic design. As one instantiation, we employ a lean adjoint system inspired by adjoint matching, enabling efficient and scalable training. We demonstrate the effectiveness of NAAS across a range of tasks, including sampling from classical energy landscapes and molecular Boltzmann distributions.