NeurIPS 2026 论文列表

Conference on Neural Information Processing Systems

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6,437篇论文

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Data-Driven Soft Labeling Scales DNA Read Classification to Whole-Body Cell-Type Deconvolution

Dmytro Rizdvanetskyi, Nathan Roos, Pavlo Lutsik

展开摘要

Cell-type deconvolution, the task of estimating the proportions of constituent cell types in a heterogeneous biological sample, is a core problem in computational biology. Methods that rely on epigenetic marks such as DNA methylation typically operate on aggregated methylation estimates, discarding the pattern-level information carried by individual DNA reads. Existing read-level approaches that exploit this information are scarce, and all remain restricted to few-class settings; scaling them further is an open problem because, at scale, non-discriminative reads dominate and hard labels conflict with the many-to-many mapping between methylation patterns and cell types, preventing classifier convergence. To overcome this, we propose data-driven soft labels that estimate the conditional cell-type distribution for each read, and integrate this scheme into *Syto*, a new modular framework for read-level classification-based deconvolution. On a whole-body atlas of 39 human cell types, *Syto* reduces MSE by $2.56\times$ over SoTA, with gains transferring to an out-of-distribution dataset spanning 16 tissues. *Syto* lays the foundation for modeling increasingly large cell-type panels, with improved applications in biology and healthcare. The proposed soft-labeling scheme is further translatable to any setting with a many-to-many signal-to-label mapping.

Poster
Classification Fields: Arbitrarily Fine Recursive Hierarchical Clustering From Few Examples

Yicen Li, Ruiyang Hong, Anastasis Kratsios, Haitz Sáez de Ocáriz Borde, Paul D. McNicholas

展开摘要

Classical clustering methods usually return either a finite partition of the observed data or a finite dendrogram over it. This finite-sample view is inadequate when the hierarchy of interest is a recursive geometric object with fine-scale refinements that continue beyond the levels directly observed. We introduce classification fields: infinite-depth hierarchical cluster structures on $\mathbb{R}^d$ generated by a local parent-to-child refinement rule. A classification field generator maps each parent centre to an ordered, bounded, and separated tuple of child residuals. Together with a root and a scale factor, this rule recursively generates cluster centres, Voronoi cells, and a metric DAG encoding the hierarchy. Given only a finite prefix of such a hierarchy, we learn a classification field predictor that approximates the generator and can be rolled out to unseen depths. We prove exponential truncation convergence in the completed cell metric and ReLU realizability with width $(O(\varepsilon^{-\gamma})$ and depth $\widetilde O(\varepsilon^{-3\gamma/2})$, where $\gamma=\log K/(-\log s)$, up to finite-window aspect-ratio factors. The approximation holds at the level of the induced compact metric structures, measured in the completed cell-metric Hausdorff distance. Experimental validation on matched CFG-generated hierarchies, IFS fractals, and image-induced recursive clustering hierarchies shows that learned predictors preserve ordered child slots, unordered geometry, and hierarchy-level path metrics under recursive rollout. These results support the claim that finite hierarchical observations can reveal local refinement rules capable of generating substantially deeper classification fields.

Poster
BrainCoT: A Multi-Task Zero-Shot Brain Signal Foundation Model with Neurometric-Anchored Chain-of-Thought Reasoning

Yiyu Gui, Mingzhi Chen, Guibo Luo, Yuchao Yang

展开摘要

Brain signals exhibit substantial multi-center heterogeneity, strong inter-subject variability, and highly diverse task settings, which makes it difficult to build models that generalize beyond a single task. While recent brain signal foundation models leverage large-scale pretraining to learn generalizable representations, they often fall short in practice because they still require target-data-specific supervised adaptation, lack multi-task zero-shot capability, and rarely provide verifiable evidence to support their predictions. In this work, we present **BrainCoT**, a multi-task zero-shot Brain signal foundation model with neurometric-anchored Chain-of-Thought (CoT) reasoning. BrainCoT unifies heterogeneous tasks into an instruction-driven framework so that, after pretraining, a single model can be directly applied to multiple tasks in zero-shot settings without additional adaptation. It further introduces neurometric-anchored chain-of-thought grounded in neurometric evidence for verifiable reasoning, and adopts Decision-Consistent Rationale Training to keep process learning aligned with correct predictions. Across extensive evaluations, BrainCoT achieves an average ACC of 67.41\% and AUC of 74.33\% in zero-shot classification without downstream training data, outperforming the strongest linear-probing baseline trained with 1\% labeled downstream data by 3.85\% in ACC and 5.97\% in AUC. Code will be released upon acceptance.

Poster
Black-box model classification under the discriminative factorization

Hayden Helm, Merrick Ohata, Carey E. Priebe

展开摘要

Access to modern generative systems is often restricted to querying an API (the ``black-box" setting) and many properties of the system are unknown to the user at inference time. While recent work has shown that low-dimensional representations of models based on the relationship between their embedded responses to a set of queries are useful for inferring model-level properties, the quality of these representations is highly sensitive to the query set. We introduce the discriminative factorization to distinguish between high- and low-quality query sets in the context of black-box model-level classification. Under this framework, the probability of chance-level classification decays exponentially in the query budget. On three auditing tasks, estimated factorization parameters predict the empirical performance decay rate. We conclude by showing that query sets selected using the estimated discriminative field reproduce the empirical ordering of oracle query sets.

Poster
Beyond MNIST: Limitations of Amplitude Encoding on Quantum Classification

Xin Wang, Yabo Wang, Rebing Wu

展开摘要

It remains unclear whether quantum machine learning (QML) truly holds an advantage when tackling practical and meaningful tasks. In exploring this question, the importance of classical data encoding, often overlooked, becomes increasingly evident. Amplitude encoding, which can embed $2^n$ classical data into $n$ qubits, is widely used due to its apparent efficiency. However, its potential limitations for QML have yet to be fully explored. In this paper, we establish a theoretical result for the limitations caused by quantum encoding and point out the existence of a concentration phenomenon in amplitude encoding. Compared to prior work, our theoretical result operates under more general conditions and leads to a stronger conclusion. This concentration phenomenon causes the classification predictions to remain close to random guessing, regardless of the training process. Our findings shed new light on a long-standing puzzle in the field of QML: why some QML models perform well on simple datasets like MNIST but fail to generalize to more complex practical tasks. By highlighting the pivotal role of encoding design in QML, our work clearly indicates that future research needs to focus more on the design of classical data encoding to advance the effectiveness of QML.

Poster
Alignment Imprint: Zero-Shot AI-Generated Text Detection via Provable Preference Discrepancy

Junxi Wu, Kailin Huang, Dongjian Hu, Bin CHEN, Hao Wu, Shu-Tao Xia, Changliang Zou

展开摘要

Detecting AI-generated text is an important but challenging problem. Existing likelihood-based detection methods are often sensitive to content complexity and may exhibit unstable performance. In this paper, our key insight is that modern Large Language Models (LLMs) undergo alignment (including fine-tuning and preference tuning), leaving a measurable distributional imprint. We theoretically derive this imprint by abstracting the alignment process as a sequence of constrained optimization steps, showing that the log-likelihood ratio can naturally decompose into implicit instructional biases and preference rewards. We refer to this quantity as the Alignment Imprint. Furthermore, to mitigate the instability in high-entropy regions, we introduce Log-likelihood Alignment Preference Discrepancy (LAPD), a standardized information-weighted statistic based on alignment imprint. We provide statistical guarantee that alignment-based statistics dominate Fast-DetectGPT in performance. We also theoretically show that LAPD strictly improves the unweighted alignment scores when the aligned and base models are close in distribution. Extensive experiments show that LAPD achieves an improvement 45.82% relative to the strongest existing baselines, yielding large and consistent gains across all settings

Poster
Align3D-AD: Cross-Modal Feature Alignment and Dual-Prompt Learning for Zero-shot 3D Anomaly Detection

Letian Bai, Xuanming Cao, Juan Du, Chengyu Tao

展开摘要

Zero-shot 3D anomaly detection aims to identify anomalies without access to training data from target categories. However, existing methods mainly rely on projecting 3D observations into multi-view representations that primarily capture geometric cues rather than realistic visual semantics and process them with vision encoders pretrained on RGB data, leading to a significant domain gap between the encoder and the projected representations. To address this issue, we propose Align3D-AD, a unified two-stage framework that leverages the RGB modality from auxiliary categories as cross-modal guidance for zero-shot 3D anomaly detection. First, we introduce a cross-modal feature alignment paradigm that maps rendering features into the RGB semantic space. Unlike prior works that implicitly rely on pretrained encoders, our method enables direct semantic transfer from RGB observations. A semantic consistency reweighting strategy is further introduced to refine feature alignment by reweighting local regions according to holistic semantic consistency. Second, we propose a modality-aware prompt learning framework with dual-prompt contrastive alignment. By assigning independent prompts to RGB-aligned and rendering features, our method captures complementary semantics across modalities, while the contrastive alignment further enhances prompt representations to improve discriminability. Extensive experiments on MVTec3D-AD, Eyecandies, and Real3D-AD demonstrate that Align3D-AD consistently outperforms existing zero-shot methods under both one-vs-rest and cross-dataset settings, highlighting its generalization capability and robustness. Code and the dataset will be made available once our paper is accepted.

Poster
A Minimal Interpretable Architecture for Zero-Shot Reconstruction of Dynamical Systems

Christoph Jürgen Hemmer, Florian Plaswig, Daniel Durstewitz

展开摘要

Recent foundation models (FMs) for zero-shot reconstruction of dynamical systems (DS) achieve strong out-of-domain generalization but provide little insight into the *mechanisms* that underlie their forecasts. Such an understanding could help to strip down overladen FM architectures to their bare essence and expose the minimal requirements for in-context learning in the DS domain. Toward this goal, here we iteratively reduce a recent powerful SOTA model for DS reconstruction, DynaMix (Hemmer & Durstewitz, 2025), to a minimal interpretable two-parameter form, which we call *DynaBase*. DynaBase produces forecasts through a linear blend of the current latent state and the nearest in-context neighbor and its temporal successor. Surprisingly, despite its extreme simplicity, DynaBase produces highly competitive zero-shot DS reconstructions across chaotic and cyclic systems, with a negligible parameter load, many orders of magnitude below that of other FMs. Even more, this extreme simplicity permits direct model optimization on DS reconstruction measures, as well as closed-form one-step analytical solutions on prediction MSE. Theoretical and empirical analysis of DynaBase further leads to a 1-parameter family of maps, with the context-parroting algorithm of (Zhang & Gilpin, 2026) recovered at one end, and chaotic (divergent but bounded) behavior at the other. We further show how different training strategies lead to models either optimal for short-term prediction or for DS reconstruction. Thus, DynaBase not only exposes the minimal mechanisms required for producing zero-shot DS reconstruction, but also reconciles within an accessible mathematical frame divergent observations in the literature.

Poster