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Born a Transformer -- Always a Transformer? On the Effect of Pretraining on Architectural Abilities

Neural Information Processing Systems

Transformers have theoretical limitations in modeling certain sequence-to-sequence tasks, yet it remains largely unclear if these limitations play a role in large-scale pretrained LLMs, or whether LLMs might effectively overcome these constraints in practice due to the scale of both the models themselves and their pretraining data. We explore how these architectural constraints manifest after pretraining by studying a family of and tasks inspired by Liu et al. [2024a]. We use a recently proposed framework for studying length generalization [Huang et al., 2025] to provide guarantees for each of our settings. Empirically, we observe an, where pretrained models are better at retrieving tokens to the right (induction) rather than the left (anti-induction) of a query token. This asymmetry disappears upon targeted fine-tuning if length-generalization is guaranteed by theory. Mechanistic analysis reveals that this asymmetry is connected to the differences in the strength of induction versus anti-induction circuits within pretrained transformers.



NavBench: Probing Multimodal Large Language Models for Embodied Navigation

Neural Information Processing Systems

Multimodal Large Language Models (MLLMs) have demonstrated strong generalization in vision-language tasks, yet their ability to understand and act within embodied environments remains underexplored. We present NavBench, a benchmark to evaluate the embodied navigation capabilities of MLLMs under zero-shot settings. NavBench consists of two components: (1) navigation comprehension, assessed through three cognitively grounded tasks including global instruction alignment, temporal progress estimation, and local observation-action reasoning, covering 3,200 question-answer pairs; and (2) step-by-step execution in 432 episodes across 72 indoor scenes, stratified by spatial, cognitive, and execution complexity. To support real-world deployment, we introduce a pipeline that converts MLLMs' outputs into robotic actions. We evaluate both proprietary and open-source models, finding that GPT-4o performs well across tasks, while lighter open-source models succeed in simpler cases. Results also show that models with higher comprehension scores tend to achieve better execution performance. Providing map-based context improves decision accuracy, especially in medium-difficulty scenarios. However, most models struggle with temporal understanding, particularly in estimating progress during navigation, which may pose a key challenge.


SCOUT: Teaching Pre-trained Language Models to Enhance Reasoning via Flow Chain-of-Thought

Neural Information Processing Systems

Chain-of-Thought (CoT) prompting improves the reasoning performance of large language models (LLMs) by encouraging step-by-step thinking. However, CoT-based methods depend on intermediate reasoning steps, which limits scalability and generalization. Recent work explores recursive reasoning, where LLMs reuse internal layers across iterations to refine latent representations without explicit CoT supervision. While promising, these approaches often require costly pretraining and lack a principled framework for how reasoning should evolve across iterations.


A Little Depth Goes a Long Way: The Expressive Power of Log-Depth Transformers

Neural Information Processing Systems

Recent theoretical results show transformers cannot express sequential reasoning problems over long inputs, intuitively because their computational *depth* is bounded. However, prior work treats the depth as a constant, leaving it unclear to what degree bounded depth may suffice for solving problems over short inputs, or how increasing the transformer's depth affects its expressive power. We address these questions by analyzing transformers whose depth can grow minimally with context length $n$. We show even highly uniform transformers with depth $\Theta(\log n)$ can express two important problems: *recognizing regular languages*, which captures state tracking abilities and was known to be expressible only by an unconventional, non-uniform model of transformers, and *graph connectivity*, which underlies multi-step reasoning. Notably, both of these problems cannot be expressed by fixed-depth transformers under standard complexity conjectures, demonstrating the expressivity benefit of growing depth. Moreover, our theory quantitatively predicts how depth must grow with input length to express these problems, showing that depth scaling is more efficient than scaling width or chain-of-thought steps. Empirically, our detailed experiments designed to bridge the expressivity vs. learnability gap reveal that our theoretical depth requirements for regular language recognition closely match the practical depth requirements for successfully training transformers. Thus, our results clarify how depth affects a transformer's reasoning capabilities, and provide practical guidance for effective depth selection for sequential reasoning.


Uncover Governing Law of Pathology Propagation Mechanism Through A Mean-Field Game

Neural Information Processing Systems

Alzheimer's disease (AD) is marked by cognitive decline along with the widespread of tau aggregates across the brain cortex. Due to the challenges of imaging pathology spreading flows \textit{in vivo}, however, quantitative analysis on the cortical pathways of tau propagation and its interaction with the cascade of amyloid-beta (A$\beta$) plaques lags behind the experimental insights of underlying pathophysiological mechanisms. To address this challenge, we present a physics-informed neural network, empowered by mean-field theory, to uncover the biologically meaningful spreading pathways of tau aggregates between two longitudinal snapshots. Following the notion of `prion-like' mechanism in AD, we first formulate the dynamics of tau propagation as a mean-field game (MFG), where the spread of tau aggregate at each location (aka.


Neural Collapse under Gradient Flow on Shallow ReLU Networks for Orthogonally Separable Data

Neural Information Processing Systems

Among many mysteries behind the success of deep networks lies the exceptional discriminative power of their learned representations as manifested by the intriguing Neural Collapse (NC) phenomenon, where simple feature structures emerge at the last layer of a trained neural network. Prior works on the theoretical understandings of NC have focused on analyzing the optimization landscape of matrix-factorization-like problems by considering the last-layer features as unconstrained free optimization variables and showing that their global minima exhibit NC. In this paper, we show that gradient flow on a two-layer ReLU network for classifying orthogonally separable data provably exhibits NC, thereby advancing prior results in two ways: First, we relax the assumption of unconstrained features, showing the effect of data structure and nonlinear activations on NC characterizations. Second, we reveal the role of the implicit bias of the training dynamics in facilitating the emergence of NC.


When Data Can't Meet: Estimating Correlation Across Privacy Barriers

Neural Information Processing Systems

We consider the problem of estimating the correlation of two random variables $X$ and $Y$, where the pairs $(X,Y)$ are not observed together, but are instead separated co-ordinate-wise at two servers: server 1 contains all the $X$ observations, and server 2 contains the corresponding $Y$ observations. In this vertically distributed setting, we assume that each server has its own privacy constraints, owing to which they can only share suitably privatized statistics of their own component observations. We consider differing privacy budgets $(\varepsilon_1,\delta_1)$ and $(\varepsilon_2,\delta_2)$ for the two servers and determine the minimax optimal rates for correlation estimation allowing for both non-interactive and interactive mechanisms. We also provide correlation estimators that achieve these rates and further develop inference procedures, namely, confidence intervals, for the estimated correlations. Our results are characterized by an interesting rate in terms of the sample size $n$, $\varepsilon_1$, $\varepsilon_2$, which is strictly slower than the usual central privacy estimation rates. More interestingly, we find that the interactive mechanism is always better than its non-interactive counterpart whenever the two privacy budgets are different. Results from extensive numerical experiments support our theoretical findings.


Hybrid Autoencoders for Tabular Data: Leveraging Model-Based Augmentation in Low-Label Settings

Neural Information Processing Systems

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.


Diffusion Adaptive Text Embedding for Text-to-Image Diffusion Models

Neural Information Processing Systems

Text-to-image diffusion models rely on text embeddings from a pre-trained text encoder, but these embeddings remain fixed across all diffusion timesteps, limiting their adaptability to the generative process. We propose Diffusion Adaptive Text Embedding (DATE), which dynamically updates text embeddings at each diffusion timestep based on intermediate perturbed data. We formulate an optimization problem and derive an update rule that refines the text embeddings at each sampling step to improve alignment and preference between the mean predicted image and the text. This allows DATE to dynamically adapts the text conditions to the reverse-diffused images throughout diffusion sampling without requiring additional model training. Through theoretical analysis and empirical results, we show that DATE maintains the generative capability of the model while providing superior text-image alignment over fixed text embeddings across various tasks, including multi-concept generation and text-guided image editing.