NeurIPS 2025 Papers

Diffusion-based virtual staining methods of histopathology images have demonstrated outstanding potential for stain normalization and cross-dye staining (e.g., hematoxylin-eosin to immunohistochemistry). However, achieving pathology-correct cross-dye virtual staining with versatile tone controls poses significant challenges due to the difficulty of decoupling the given pathology and tone conditions. This issue would cause non-pathologic regions to be mistakenly stained like pathologic ones, and vice versa, which we term “pathology leakage.” To address this issue, we propose diffusion virtual staining Transformer (D-VST), a new framework with versatile tone control for cross-dye virtual staining. Specifically, we introduce a pathology encoder in conjunction with a tone encoder, combined with a two-stage curriculum learning scheme that decouples pathology and tone conditions, to enable tone control while eliminating pathology leakage. Further, to extend our method for billion-pixel whole slide image (WSI) staining, we introduce a novel frequency-aware adaptive patch sampling strategy for high-quality yet efficient inference of ultra-high resolution images in a zero-shot manner. Integrating these two innovative components facilitates a pathology-correct, tone-controllable, cross-dye WSI virtual staining process. Extensive experiments on three virtual staining tasks that involve translating between four different dyes demonstrate the superiority of our approach in generating high-quality and pathologically accurate images compared to existing methods based on generative adversarial networks and diffusion models. Our code and trained models will be released.

We study contextual dynamic pricing when a target market can leverage $K$ auxiliary markets—offline logs or concurrent streams—whose *mean utilities differ by a structured preference shift*. We propose *Cross-Market Transfer Dynamic Pricing (CM-TDP)*, the first algorithm that *provably* handles such model-shift transfer and delivers minimax-optimal regret for *both* linear and non-parametric utility models. For linear utilities of dimension $d$, where the *difference* between source- and target-task coefficients is $s_{0}$-sparse, CM-TDP attains regret $\tilde{\mathcal{O}}\bigl((dK^{-1}+s_{0})\log T\bigr)$. For nonlinear demand residing in a reproducing kernel Hilbert space with effective dimension $\alpha$, complexity $\beta$ and task-similarity parameter $H$, the regret becomes $\tilde{\mathcal{O}}\bigl(K^{-2\alpha\beta/(2\alpha\beta+1)}T^{1/(2\alpha\beta+1)} + H^{2/(2\alpha+1)}T^{1/(2\alpha+1)}\bigr)$, matching information-theoretic lower bounds up to logarithmic factors. The RKHS bound is the first of its kind for transfer pricing and is of independent interest. Extensive simulations show up to 38\% higher cumulative revenue and $6\times$ faster convergence relative to single-market pricing baselines. By bridging transfer learning, robust aggregation, and revenue optimization, CM-TDP moves toward pricing systems that *transfer faster, price smarter*.

Aiming to generalize the well-trained gaze estimation model to new target domains, Cross-domain Gaze Estimation (CDGE) is developed for real-world application scenarios. Existing CDGE methods typically extract the domain-invariant features to mitigate domain shift in feature space, which is proved insufficient by Generalized Label Shift (GLS) theory. In this paper, we introduce a novel GLS perspective to CDGE and modelize the cross-domain problem by label and conditional shift problem. A GLS correction framework is presented and a feasible realization is proposed, in which a importance reweighting strategy based on truncated Gaussian distribution is introduced to overcome the continuity challenges in label shift correction. To embed the reweighted source distribution to conditional invariant learning, we further derive a probability-aware estimation of conditional operator discrepancy. Extensive experiments on standard CDGE tasks with different backbone models validate the superior generalization capability across domain and applicability on various models of proposed method.

In machine learning, effective modeling requires a holistic consideration of how to encode inputs, make predictions (i.e., decoding), and train the model. However, in time-series forecasting, prior work has predominantly focused on encoder design, often treating prediction and training as separate or secondary concerns. In this paper, we propose TimePerceiver, a unified encoder-decoder forecasting framework that is tightly aligned with an effective training strategy. To be specific, we first generalize the forecasting task to include diverse temporal prediction objectives such as extrapolation, interpolation, and imputation. Since this generalization requires handling input and target segments that are arbitrarily positioned along the temporal axis, we design a novel encoder-decoder architecture that can flexibly perceive and adapt to these varying positions. For encoding, we introduce a set of latent bottleneck representations that can interact with all input segments to jointly capture temporal and cross-channel dependencies. For decoding, we leverage learnable queries corresponding to target timestamps to effectively retrieve relevant information. Extensive experiments demonstrate that our framework consistently and significantly outperforms prior state-of-the-art baselines across a wide range of benchmark datasets.

Time-resolved single-cell omics data offers high-throughput, genome-wide measurements of cellular states, which are instrumental to reverse-engineer the processes underpinning cell fate. Such technologies are inherently destructive, allowing only cross-sectional measurements of the underlying stochastic dynamical system. Furthermore, cells may divide or die in addition to changing their molecular state. Collectively these present a major challenge to inferring realistic biophysical models. We present a novel approach, unbalanced probability flow inference, that addresses this challenge for biological processes modelled as stochastic dynamics with growth. By leveraging a Lagrangian formulation of the Fokker-Planck equation, our method accurately disentangles drift from intrinsic noise and growth. We showcase the applicability of our approach through evaluation on a range of simulated and real single-cell RNA-seq datasets. Comparing to several existing methods, we find our method achieves higher accuracy while enjoying a simple two-step training scheme.

Listwise reranking with large language models (LLMs) enhances top-ranked results in retrieval-based applications. Due to the limit in context size and high inference cost of long context, reranking is typically performed over a fixed size of small subsets, with the final ranking aggregated from these partial results. This fixed computation disregards query difficulty and document distribution, leading to inefficiencies. We propose AcuRank, an adaptive reranking framework that dynamically adjusts both the amount and target of computation based on uncertainty estimates over document relevance. Using a Bayesian TrueSkill model, we iteratively refine relevance estimates until reaching sufficient confidence levels, and our explicit modeling of ranking uncertainty enables principled control over reranking behavior and avoids unnecessary updates to confident predictions. Results on the TREC-DL and BEIR benchmarks show that our method consistently achieves a superior accuracy–efficiency trade-off and scales better with compute than fixed-computation baselines. These results highlight the effectiveness and generalizability of our method across diverse retrieval tasks and LLM-based reranking models.

Brain-computer interfaces have shown great potential in motor and speech rehabilitation, but still suffer from low performance stability across days, mostly due to the instabilities in neural signals. These instabilities, partially caused by neuron deaths and electrode shifts, leading to channel-level variabilities among different recording days. Previous studies mostly focused on aligning multi-day neural signals of onto a low-dimensional latent manifold to reduce the variabilities, while faced with difficulties when neural signals exhibit significant drift. Here, we propose to learn a channel-level invariant neural representation to address the variabilities in channels across days. It contains a channel-rearrangement module to learn stable representations against electrode shifts, and a channel reconstruction module to handle the missing neurons. The proposed method achieved the state-of-the-art performance with cross-day decoding tasks over two months, on multiple benchmark BCI datasets. The proposed approach showed good generalization ability that can be incorporated to different neural networks.

Distillation has shown remarkable success in transferring knowledge from a Large Language Model (LLM) teacher to a student LLM. However, current distillation methods require similar tokenizers between the teacher and the student, restricting their applicability to only a small subset of teacher--student pairs. In this work, we develop a principled cross-tokenizer distillation method to solve this crucial deficiency. Our method is the first to enable effective distillation across fundamentally different tokenizers, while also substantially outperforming prior methods in all other cases. We verify the efficacy of our method on three distinct use cases. First, we show that viewing tokenizer transfer as self-distillation enables unprecedentedly effective transfer across tokenizers, including rapid transfer of subword models to the byte-level. Transferring different models to the same tokenizer also enables ensembling to boost performance. Secondly, we distil a large maths-specialised LLM into a small general-purpose model with a different tokenizer, achieving competitive maths problem-solving performance. Thirdly, we use our method to train state-of-the-art embedding prediction hypernetworks for training-free tokenizer transfer. Our results unlock an expanded range of teacher--student pairs for distillation, enabling new ways to adapt and enhance interaction between LLMs.

Precise, generalizable subject-agnostic seizure prediction (SASP) remains a fundamental challenge due to the intrinsic complexity and significant spectral variability of electrophysiologial signals across individuals and recording modalities. We propose \model{FAPEX}, a novel architecture that introduces a learnable \emph{fractional neural frame operator} (FrNFO) for adaptive time–frequency decomposition. Unlike conventional models that exhibit spectral bias toward low frequencies, our FrNFO employs fractional-order convolutions to capture both high and low-frequency dynamics, achieving approximately $10\%$ improvement in F1-score and sensitivity over state-of-the-art baselines. The FrNFO enables the extraction of \emph{instantaneous phase and amplitude representations} that are particularly informative for preictal biomarker discovery and enhance out-of-distribution generalization. \model{FAPEX} further integrates structural state-space modeling and channelwise attention, allowing it to handle heterogeneous electrode montages. Evaluated across 12 benchmarks spanning species (human, rat, dog, macaque) and modalities (Scalp‑EEG, SEEG, ECoG, LFP), \model{FAPEX} consistently outperforms 23 supervised and 10 self-supervised baselines under nested cross-validation, with gains of up to $15\%$ in sensitivity on complex cross-domain scenarios. It further demonstrates superior performance in several external validation cohorts. To our knowledge, these establish \model{FAPEX} as the first epilepsy model to show consistent superiority in SASP, offering a promising solution for discovering epileptic biomarker evidence supporting the existence of a distinct and identifiable preictal state for and clinical translation.

Multimodal dataset distillation aims to synthesize a small set of image-text pairs that enables efficient training of large-scale vision-language models. While dataset distillation has shown promise in unimodal tasks, extending it to multimodal contrastive learning presents key challenges: learning cross-modal alignment and managing the high computational cost of large encoders. Prior approaches address scalability by freezing the text encoder and update only the image encoder and text projection layer. However, we find this severely limits semantic alignment and becomes a bottleneck for performance scaling. We propose CovMatch, a scalable dataset distillation framework that aligns the cross-covariance of real and synthetic features while regularizing feature distributions within each modality. Unlike prior approaches, CovMatch enables joint optimization of both encoders, leading to stronger cross-modal alignment and improved performance. Evaluated on Flickr30K and COCO, CovMatch outperforms state-of-the-art multimodal distillation methods and achieves up to 6.8\% absolute gains in retrieval accuracy using only 500 synthetic pairs.