OpenRaiser/Intern-Atlas huggingface dataset:
MESS+: Dynamically Learned Inference-Time LLM Routing in Model Zoos with Service Level Guarantees
Venue: Conference NeurIPS 2025
Year: 2025

Open-weight large language model (LLM) zoos provide access to numerous high-quality models, but selecting the appropriate model for specific tasks remains challenging and requires technical expertise. Most users simply want factually correct, safe, and satisfying responses without concerning themselves with model technicalities, while inference service providers prioritize minimizing operating costs. These competing interests are typically mediated through service level agreements (SLAs) that guarantee minimum service quality. We introduce MESS+, a stochastic optimization algorithm for cost-optimal LLM request routing while providing rigorous SLA compliance guarantees. MESS+ learns request satisfaction probabilities of LLMs in real-time as users interact with the system, based on which model selection decisions are made by solving a per-request optimization problem. Our algorithm includes a novel combination of virtual queues and request satisfaction prediction, along with a theoretical analysis of cost optimality and constraint satisfaction. Across a wide range of state-of-the-art LLM benchmarks, MESS+ achieves an average of $2\times$ cost savings compared to existing LLM routing techniques.
A Differentiable Alignment Framework for Sequence-to-Sequence Modeling via Optimal Transport
Venue: Conference NeurIPS 2025
Year: 2025

Accurate sequence-to-sequence (seq2seq) alignment is critical for applications like medical speech analysis and language learning tools relying on automatic speech recognition (ASR). State-of-the-art end-to-end (E2E) ASR systems, such as the Connectionist Temporal Classification (CTC) and transducer-based models, suffer from peaky behavior and alignment inaccuracies. In this paper, we propose a novel differentiable alignment framework based on one-dimensional optimal transport, enabling the model to learn a single alignment and perform ASR in an E2E manner. We introduce a pseudo-metric, called Sequence Optimal Transport Distance (SOTD), over the sequence space and discuss its theoretical properties. Based on the SOTD, we propose Optimal Temporal Transport Classification (OTTC) loss for ASR and contrast its behavior with CTC. Experimental results on the TIMIT, AMI, and LibriSpeech datasets show that our method considerably improves alignment performance compared to CTC and the more recently proposed Consistency-Regularized CTC, though with a trade-off in ASR performance. We believe this work opens new avenues for seq2seq alignment research, providing a solid foundation for further exploration and development within the community. Our code is publicly available at: https://github.com/idiap/OTTC
AmorLIP: Efficient Language-Image Pretraining via Amortization
Venue: Conference NeurIPS 2025
Year: 2025

Contrastive Language-Image Pretraining (CLIP) has demonstrated strong zero-shot performance across diverse downstream text-image tasks. Existing CLIP methods typically optimize a contrastive objective using negative samples drawn from each minibatch. To achieve robust representation learning, these methods require extremely large batch sizes and escalate computational demands to hundreds or even thousands of GPUs. Prior approaches to mitigate this issue often compromise downstream performance, prolong training duration, or face scalability challenges with very large datasets. To overcome these limitations, we propose AmorLIP, an efficient CLIP pretraining framework that amortizes expensive computations involved in contrastive learning through lightweight neural networks, which substantially improves training efficiency and performance. Leveraging insights from a spectral factorization of energy-based models, we introduce novel amortization objectives along with practical techniques to improve training stability. Extensive experiments across 38 downstream tasks demonstrate the superior zero-shot classification and retrieval capabilities of AmorLIP, consistently outperforming standard CLIP baselines with substantial relative improvements of up to 12.24%.
Consistent Story Generation: Unlocking the Potential of Zigzag Sampling
Venue: Conference NeurIPS 2025
Year: 2025

Text-to-image generation models have made significant progress in producing high-quality images from textual descriptions, yet they continue to struggle with maintaining subject consistency across multiple images, a fundamental requirement for visual storytelling. Existing methods attempt to address this by either fine-tuning models on large-scale story visualization datasets, which is resource-intensive, or by using training-free techniques that share information across generations, which still yield limited success. In this paper, we introduce a novel training-free sampling strategy called Zigzag Sampling with Asymmetric Prompts and Visual Sharing to enhance subject consistency in visual story generation. Our approach proposes a zigzag sampling mechanism that alternates between asymmetric prompting to retain subject characteristics, while a visual sharing module transfers visual cues across generated images to %further enforce consistency. Experimental results, based on both quantitative metrics and qualitative evaluations, demonstrate that our method significantly outperforms previous approaches in generating coherent and consistent visual stories. The code is available at https://github.com/Mingxiao-Li/Asymmetry-Zigzag-StoryDiffusion.
Nested Learning: The Illusion of Deep Learning Architectures
Venue: Conference NeurIPS 2025
Year: 2025

Despite the recent progresses, particularly in developing Language Models, there are fundamental challenges and unanswered questions about how such models can continually learn/memorize, self-improve, and find effective solutions. In this paper, we present a new learning paradigm, called Nested Learning (NL), that coherently represents a machine learning model with a set of nested, multi-level, and/or parallel optimization problems, each of which with its own context flow. Through the lenses of NL, existing deep learning methods learns from data through compressing their own context flow, and in-context learning naturally emerges in large models. NL suggests a philosophy to design more expressive learning algorithms with more levels, resulting in higher-order in-context learning and potentially unlocking effective continual learning capabilities. We advocate for NL by presenting three core contributions: (1) Expressive Optimizers: We show that known gradient-based optimizers, such as Adam, SGD with Momentum, etc., are in fact associative memory modules that aim to compress the gradients' information (by gradient descent). Building on this insight, we present other more expressive optimizers with deep memory and/or more powerful learning rules; (2) Self-Modifying Learning Module: Taking advantage of NL's insights on learning algorithms, we present a sequence model that learns how to modify itself by learning its own update algorithm; and (3) Continuum Memory System: We present a new formulation for memory system that generalizes the traditional viewpoint of long/short-term memory. Combining our self-modifying sequence model with the continuum memory system, we present a continual learning module, called Hope, showing promising results in language modeling, knowledge incorporation, and few-shot generalization tasks, continual learning, and long-context reasoning tasks.
Diffusion Models Meet Contextual Bandits
Venue: Conference NeurIPS 2025
Year: 2025

Efficient online decision-making in contextual bandits is challenging, as methods without informative priors often suffer from computational or statistical inefficiencies. In this work, we leverage pre-trained diffusion models as expressive priors to capture complex action dependencies and develop a practical algorithm that efficiently approximates posteriors under such priors, enabling both fast updates and sampling. Empirical results demonstrate the effectiveness and versatility of our approach across diverse contextual bandit settings.
Exploiting LLMs for Automatic Hypothesis Assessment via a Logit-Based Calibrated Prior
Venue: Conference NeurIPS 2025
Year: 2025

As hypothesis generation becomes increasingly automated, a new bottleneck has emerged: hypothesis assessment. Modern systems can surface thousands of statistical relationships-correlations, trends, causal links-but offer little guidance on which ones are novel, non-trivial, or worthy of expert attention. In this work, we study the complementary problem to hypothesis generation: automatic hypothesis assessment. Specifically, we ask: given a large set of statistical relationships, can we automatically assess which ones are novel and worth further exploration? We focus on correlations as they are a common entry point in exploratory data analysis that often serve as the basis for forming deeper scientific or causal hypotheses. To support automatic assessment, we propose to leverage the vast knowledge encoded in LLMs' weights to derive a prior distribution over the correlation value of a variable pair. If an LLM's prior expects the correlation value observed, then such correlation is not surprising, and vice versa. We propose the Logit-based Calibrated Prior, an LLM-elicited correlation prior that transforms the model's raw output logits into a calibrated, continuous predictive distribution over correlation values. We evaluate the prior on a benchmark of 2,096 real-world variable pairs and it achieves a sign accuracy of 78.8%, a mean absolute error of 0.26, and 95% credible interval coverage of 89.2% in predicting Pearson correlation coefficient. It also outperforms a fine-tuned RoBERTa classifier in binary correlation prediction and achieves higher precision@K in hypothesis ranking. We further show that the prior generalizes to correlations not seen during LLM pretraining, reflecting context-sensitive reasoning rather than memorization.
Understanding and Enhancing Mask-Based Pretraining towards Universal Representations
Venue: Conference NeurIPS 2025
Year: 2025

Mask-based pretraining has become a cornerstone of modern large-scale models across language, vision, and recently biology. Despite its empirical success, its role and limits in learning data representations have been unclear. In this work, we show that the behavior of mask-based pretraining can be directly characterized by test risk in high-dimensional minimum-norm ("ridge-less") linear regression, without relying on further model specifications. Further analysis of linear models uncovers several novel aspects of mask-based pretraining. The theoretical framework and its implications have been validated across diverse neural architectures (including MLPs, CNNs, and Transformers) applied to both vision and language tasks. Guided by our theory, we propose an embarrassingly simple yet overlooked pretraining scheme named Randomly Random Mask AutoEncoding (R$^2$MAE), which enforces capturing multi-scale features from data and is able to outperform optimal fixed mask ratio settings in our linear model framework. We implement R$^2$MAE in vision, language, DNA sequence, and single-cell models, where it consistently outperforms standard and more complicated masking schemes, leading to improvements for state-of-the-art models. Our code is available at: https://github.com/MingzeDong/r2mae
The Boundaries of Fair AI in Medical Image Prognosis: A Causal Perspective
Venue: Conference NeurIPS 2025
Year: 2025

As machine learning (ML) algorithms are increasingly used in medical image analysis, concerns have emerged about their potential biases against certain social groups. Although many approaches have been proposed to ensure the fairness of ML models, most existing works focus only on medical image diagnosis tasks, such as image classification and segmentation, and overlooked prognosis scenarios, which involve predicting the likely outcome or progression of a medical condition over time. To address this gap, we introduce FairTTE, the first comprehensive framework for assessing fairness in time-to-event (TTE) prediction in medical imaging. FairTTE encompasses a diverse range of imaging modalities and TTE outcomes, integrating cutting-edge TTE prediction and fairness algorithms to enable systematic and fine-grained analysis of fairness in medical image prognosis. Leveraging causal analysis techniques, FairTTE uncovers and quantifies distinct sources of bias embedded within medical imaging datasets. Our large-scale evaluation reveals that bias is pervasive across different imaging modalities and that current fairness methods offer limited mitigation. We further demonstrate a strong association between underlying bias sources and model disparities, emphasizing the need for holistic approaches that target all forms of bias. Notably, we find that fairness becomes increasingly difficult to maintain under distribution shifts, underscoring the limitations of existing solutions and the pressing need for more robust, equitable prognostic models.
Mitigating Overthinking in Large Reasoning Models via Manifold Steering
Venue: Conference NeurIPS 2025
Year: 2025

Recent advances in Large Reasoning Models (LRMs) have demonstrated remarkable capabilities in solving complex tasks such as mathematics and coding. However, these models frequently exhibit a phenomenon known as overthinking during inference, characterized by excessive validation loops and redundant deliberation, leading to substantial computational overheads. In this paper, we aim to mitigate overthinking by investigating the underlying mechanisms from the perspective of mechanistic interpretability. We first showcase that the tendency of overthinking can be effectively captured by a single direction in the model's activation space and the issue can be eased by intervening the activations along this direction. However, this efficacy soon reaches a plateau and even deteriorates as the intervention strength increases. We therefore systematically explore the activation space and find that the overthinking phenomenon is actually tied to a low-dimensional manifold, which indicates that the limited effect stems from the noises introduced by the high-dimensional steering direction. Based on this insight, we propose Manifold Steering, a novel approach that elegantly projects the steering direction onto the low-dimensional activation manifold given the theoretical approximation of the interference noise. Extensive experiments on DeepSeek-R1 distilled models validate that our method reduces output tokens by up to 71% while maintaining and even improving the accuracy on several mathematical benchmarks. Our method also exhibits robust cross-domain transferability, delivering consistent token reduction performance in code generation and knowledge-based QA tasks. Code is available at: https://github.com/Aries-iai/Manifold_Steering.
Synthetic-powered predictive inference
Venue: Conference NeurIPS 2025
Year: 2025

Conformal prediction is a framework for predictive inference with a distribution-free, finite-sample guarantee. However, it tends to provide uninformative prediction sets when calibration data are scarce. This paper introduces Synthetic-powered predictive inference (SPI), a novel framework that incorporates synthetic data -- e.g., from a generative model -- to improve sample efficiency. At the core of our method is a score transporter: an empirical quantile mapping that aligns nonconformity scores from trusted, real data with those from synthetic data. By carefully integrating the score transporter into the calibration process, SPI provably achieves finite-sample coverage guarantees without making any assumptions about the real and synthetic data distributions. When the score distributions are well aligned, SPI yields substantially tighter and more informative prediction sets than standard conformal prediction. Experiments on image classification -- augmenting data with synthetic diffusion-model generated images -- and on tabular regression demonstrate notable improvements in predictive efficiency in data-scarce settings.
Align Your Flow: Scaling Continuous-Time Flow Map Distillation
Venue: Conference NeurIPS 2025
Year: 2025

Diffusion- and flow-based models have emerged as state-of-the-art generative modeling approaches, but they require many sampling steps. Consistency models can distill these models into efficient one-step generators; however, unlike flow- and diffusion-based methods, their performance inevitably degrades when increasing the number of steps, which we show both analytically and empirically. Flow maps generalize these approaches by connecting any two noise levels in a single step and remain effective across all step counts. In this paper, we introduce two new continuous-time objectives for training flow maps, along with additional novel training techniques, generalizing existing consistency and flow matching objectives. We further demonstrate that autoguidance can improve performance, using a low-quality model for guidance during distillation, and an additional boost can be achieved by adversarial finetuning, with minimal loss in sample diversity. We extensively validate our flow map models, called Align Your Flow, on challenging image generation benchmarks and achieve state-of-the-art few-step generation performance on both ImageNet 64x64 and 512x512, using small and efficient neural networks. Finally, we show text-to-image flow map models that outperform all existing non-adversarially trained few-step samplers in text-conditioned synthesis.
ChA-MAEViT: Unifying Channel-Aware Masked Autoencoders and Multi-Channel Vision Transformers for Improved Cross-Channel Learning
Venue: Conference NeurIPS 2025
Year: 2025

Prior work using Masked Autoencoders (MAEs) typically relies on random patch masking based on the assumption that images have significant redundancies across different channels, allowing for the reconstruction of masked content using cross-channel correlations. However, this assumption does not hold in Multi-Channel Imaging (MCI), where channels may provide complementary information with minimal feature overlap. Thus, these MAEs primarily learn local structures within individual channels from patch reconstruction, failing to fully leverage cross-channel interactions and limiting their MCI effectiveness. In this paper, we present ChA-MAEViT, an MAE-based method that enhances feature learning across MCI channels via four key strategies: (1) dynamic channel-patch masking, which compels the model to reconstruct missing channels in addition to masked patches, thereby enhancing cross-channel dependencies and improving robustness to varying channel configurations; (2) memory tokens, which serve as long-term memory aids to promote information sharing across channels, addressing the challenges of reconstructing structurally diverse channels; (3) hybrid token fusion module, which merges fine-grained patch tokens with a global class token to capture richer representations; and (4) Channel-Aware Decoder, a lightweight decoder utilizes channel tokens to effectively reconstruct image patches. Experiments on satellite and microscopy datasets, CHAMMI, JUMP-CP, and So2Sat, show that ChA-MAEViT significantly outperforms state-of-the-art MCI-ViTs by 3.0-21.5%, highlighting the importance of cross-channel interactions in MCI. Our code is publicly available at https://github.com/chaudatascience/cha_mae_vit.
Transferring Causal Effects using Proxies
Venue: Conference NeurIPS 2025
Year: 2025

We consider the problem of estimating a causal effect in a multi-domain setting. The causal effect of interest is confounded by an unobserved confounder and can change between the different domains. We assume that we have access to a proxy of the hidden confounder and that all variables are discrete or categorical. We propose methodology to estimate the causal effect in the target domain, where we assume to observe only the proxy variable. Under these conditions, we prove identifiability (even when treatment and response variables are continuous). We introduce two estimation techniques, prove consistency, and derive confidence intervals. The theoretical results are supported by simulation studies and a real-world example studying the causal effect of website rankings on consumer choices.
Hephaestus: Mixture Generative Modeling with Energy Guidance for Large-scale QoS Degradation
Venue: Conference NeurIPS 2025
Year: 2025

We study the Quality of Service Degradation (QoSD) problem, in which an adversary perturbs edge weights to degrade network performance. This setting arises in both network infrastructures and distributed ML systems, where communication quality, not just connectivity, determines functionality. While classical methods rely on combinatorial optimization, and recent ML approaches address only restricted linear variants with small-size networks, no prior model directly tackles the QoSD problem under nonlinear edge-weight functions. This work proposes \PIMMA, a self-reinforcing generative framework that synthesizes feasible solutions in latent space, to fill this gap. Our method includes three phases: (1) Forge: a Predictive Path-Stressing (PPS) algorithm that uses graph learning and approximation to produce feasible solutions with performance guarantee, (2) Morph: a new theoretically grounded training paradigm for Mixture of Conditional VAEs guided by an energy-based model to capture solution feature distributions, and (3) Refine: a reinforcement learning agent that explores this space to generate progressively near-optimal solutions using our designed differentiable reward function. Experiments on both synthetic and real-world networks show that our approach consistently outperforms classical and ML baselines, particularly in scenarios with nonlinear cost functions where traditional methods fail to generalize.
CPO: Condition Preference Optimization for Controllable Image Generation
Venue: Conference NeurIPS 2025
Year: 2025

To enhance controllability in text-to-image generation, ControlNet introduces image-based control signals, while ControlNet++ improves pixel-level cycle consistency between generated images and the input control signal. To avoid the prohibitive cost of back-propagating through the sampling process, ControlNet++ optimizes only low-noise timesteps (e.g., $t < 200$) using a single-step approximation, which not only ignores the contribution of high-noise timesteps but also introduces additional approximation errors. A straightforward alternative for optimizing controllability across all timesteps is Direct Preference Optimization (DPO), a fine-tuning method that increases model preference for more controllable images ($I^{w}$) over less controllable ones ($I^{l}$). However, due to uncertainty in generative models, it is difficult to ensure that win--lose image pairs differ only in controllability while keeping other factors, such as image quality, fixed. To address this, we propose performing preference learning over control conditions rather than generated images. Specifically, we construct winning and losing control signals, $\mathbf{c}^{w}$ and $\mathbf{c}^{l}$, and train the model to prefer $\mathbf{c}^{w}$. This method, which we term \textit{Condition Preference Optimization} (CPO), eliminates confounding factors and yields a low-variance training objective. Our approach theoretically exhibits lower contrastive loss variance than DPO and empirically achieves superior results. Moreover, CPO requires less computation and storage for dataset curation. Extensive experiments show that CPO significantly improves controllability over the state-of-the-art ControlNet++ across multiple control types: over $10\%$ error rate reduction in segmentation, $70$--$80\%$ in human pose, and consistent $2$--$5\%$ reductions in edge and depth maps.