NeurIPS 2026 论文列表

Genomic events span multiple spatial scales, from single-nucleotide substitutions to large structural variants, yet existing foundation models process only reference DNA sequences, leaving methylation, short variants, and structural-variant boundaries as downstream labels or auxiliary inputs. We propose the Unified Genomic Model (UGM), an encoder-only genomic foundation model that learns multi-scale genomic events as native tokens within a unified 43-token vocabulary. UGM introduces three algorithmic components: (i) a unified event tokenizer that maps reference bases, SNPs, CpG methylation, short INDELs, and structural-variant boundaries into a single event-state space; (ii) event-balanced pretraining, which promotes adequate gradient coverage for rare but biologically important events; and (iii) Site-Level Joint Prediction (SJP), a masked-language-modeling objective that recovers the complete genomic state at a masked position as a single token rather than predicting base, methylation, and variant labels independently. We evaluate UGM against specialized and generalist baselines across functional variant classification, regulatory benchmarks (NT and GUE), structural-variant detection, and cross-event attention analysis. UGM achieves competitive performance, particularly on tasks where explicit event-state information is central. It obtains the highest score on all seven functional variant tasks, reaches competitive splicing prediction on NT, and notably outperforms DNA-only baselines on SV breakpoint detection. These results suggest that native multi-scale event pretraining is a promising direction for genomic representation learning.

The proliferation of multimodal data has underscored the imperative for efficiency in cross-modal retrieval. By mapping data into a unified Hamming space, Cross-modal hashing (CMH) significantly enhances both storage and computational efficiency, thereby establishing itself as a preferred favored paradigm for retrieval tasks. However most methods assume complete data, which rarely holds in practice. In incomplete settings, missing modalities (e.g., text or image) break semantic correspondence and make unsupervised hashing unreliable. Therefore, we propose Unsupervised Generative Completion and Graph-attention Refinement for Incomplete Cross-modal Hashing (UGGRH) method. Specifically, UGGRH leverages pretrained generative models for modality completion and employs a discriminator-guided similarity refinement module to fuse intra-modal relations with paired image-text matching signals, thereby constructing a robust cross-modal similarity matrix that yields a noise-tolerant similarity target for training. After that, it learns discriminative binary codes via hash-aware graph attention and cross-modal fusion, to refine modality embeddings and produce unified hash codes. Experiments on MIRFlickr25K, NUS-WIDE, and MS COCO datasets demonstrate that UGGRH consistently achieves superior performance under high missing rates and modality imbalance, showing significant improvements in retrieval accuracy and robustness across challenging incomplete scenarios.

Graph learning research has increasingly shifted toward continual graph learning (CGL), which better reflects real-world scenarios where graphs evolve over time. However, existing CGL methods largely assume clean supervision and overlook a critical challenge: the newly arriving portions of the graph are often noisy, due to annotation errors or adversarial corruption. This mismatch limits their applicability in practice. In this work, we study robust continual graph learning, where models must simultaneously handle catastrophic forgetting and noisy supervision in evolving graph data. We show that label noise introduces a new failure mode—catastrophic remembering, where models persistently reinforce corrupted knowledge across tasks. To address these challenges, we propose a Unified Flow-Oriented framework (UFO). First, UFO models conditional feature distributions via flow-based generative modeling and produces replay representations, mitigating forgetting without storing historical data. Second, UFO estimates instance-level reliability scores to distinguish clean from noisy nodes, reducing the impact of corrupted supervision and alleviating catastrophic remembering. Extensive experiments on four benchmark graph datasets under varying noise ratios demonstrate that UFO consistently outperforms existing methods in both accuracy and forgetting metrics. Code is available at: https://anonymous.4open.science/r/UFO.

Despite the promise of Neural Combinatorial Optimization (NCO), recent literature has increasingly coupled *decision paradigms*, *training objectives*, and *problem classes* with specific backbone architectures, limiting generic model design and fair cross-paradigm evaluation. We propose UECO, a simple yet effective **U**nified **E**ncoder for **C**ombinatorial **O**ptimization with a structure-aware attention mixture scheme, where a lightweight module defined upon graph-based locality is interleaved with conventional (global) node-focused attention blocks to dynamically evolve edge representations and inject local topological information into attention scores. Instead of fusing static edge features in a single step, UECO thereby integrates local and global messages in a progressive and problem-agnostic manner. UECO is orthogonal to task-specific decoders, and works seamlessly with *Local Construction* (LC), *Global Prediction* (GP), and *Adaptive Expansion* (AE) paradigms, across node- or edge-oriented problems, symmetric or asymmetric tasks, and sparse or dense graphs, for supervised, reinforcement, or generative learning. Extensive experiments show that, via plug-in substitution of encoders, UECO consistently improves solution and generalization quality over diverse backbones and task scales on TSP, ATSP, CVRP, ACVRP, MIS, MaxClique, and MaxCut.

Multi-view transformers for feed-forward 3D reconstruction must jointly solve two tasks. They need to extract precise per-view features and reason about cross-view geometric correspondences. Existing architectures apply cross-view attention throughout the network, leaving each layer to handle both objectives together. We revisit this design through a layer-wise probing analysis of feed-forward geometry transformers and observe that trained models tend to divide these two roles across layers. Early layers tend to specialize in per-frame feature extraction, while spatial cognition and cross-view reasoning emerge predominantly in later layers. This suggests that separating the two roles across the network can allocate compute more effectively. Building on this observation, we propose U-MVP, a U-shaped multi-view transformer for feed-forward 3D Gaussian Splatting that reflects this structure in the architecture itself. The encoder applies frame-wise attention to preserve per-view detail, the decoder introduces multi-view attention for cross-view geometric reasoning, and skip connections fuse the two streams so that appearance and geometry are recombined at decoding time. To scale to dense view regimes, we replace several global interaction blocks at the bottleneck with a grouping and swapping scheme that preserves cross-view information flow at lower cost. U-MVP performs competitively with feed-forward and optimization-based baselines from 16 to 256 views, generalizes to unseen datasets, and achieves strong results on 3D reconstruction and novel-view synthesis in posed and unposed settings.

Recent long-tailed recognition methods increasingly adopt two-stage fine-tuning, where a generic representation is first learned and imbalance-aware adaptation is then performed in a lightweight second stage. However, existing second-stage designs often allocate objective emphasis using delayed empirical summaries, such as historical class-wise performance or validation feedback, and commonly restrict adaptation to classifier heads. These choices may make routing unreliable when empirical feedback is noisy or skewed, and may also limit the feature plasticity required for rare categories. In this paper, we propose U-MOF, an uncertainty-guided parameter-efficient multi-objective fine-tuning framework for long-tailed recognition. U-MOF introduces lightweight residual adapters into a shared-backbone expert committee, uses entropy-based committee statistics as diagnostic routing proxies to modulate tail-oriented and smoothing-oriented objectives, and applies conflict-aware orthogonal projection to coordinate heterogeneous objective gradients. Experiments on CIFAR-100-LT, ImageNet-LT, and iNaturalist 2018 show that U-MOF improves rare-category and overall performance in controlled stage-two comparisons and remains competitive with strong published long-tailed recognition baselines, while preserving the efficiency advantages of decoupled adaptation. These results indicate that reliable stage-two long-tailed fine-tuning benefits not only from selecting appropriate objectives, but also from diagnosing when each objective should dominate and from retaining limited feature-level plasticity. An anonymized implementation is included in the Supplementary Material.

Over the past decade, U-Net has been the dominant architecture in medical image segmentation, leading to the development of thousands of U-shaped variants. Despite its widespread adoption, there is still no comprehensive benchmark to systematically evaluate their performance and utility, largely because of insufficient statistical validation and limited consideration of efficiency and generalization across diverse datasets. To bridge this gap, we present U-Bench, the first large-scale, statistically rigorous 2D benchmark that evaluates 100 U-Net variants across 28 datasets and 10 imaging modalities. Our contributions are threefold: (1) Comprehensive Evaluation: U-Bench evaluates models along three key dimensions: statistical robustness, zero-shot generalization, and computational efficiency. We introduce a novel metric, U-Score, which jointly captures the performance-efficiency trade-off, offering a deployment-oriented perspective on model progress. (2) Systematic Analysis and Model Selection Guidance: We summarize key findings from the large-scale evaluation and systematically analyze the impact of dataset characteristics and architectural paradigms on model performance. Based on these insights, we propose a model advisor agent to guide researchers in selecting the most suitable models for specific datasets and tasks. (3) Public Availability: We provide all code, models, protocols, and weights, enabling the community to reproduce our results and extend the benchmark with future methods. In summary, U-Bench not only exposes gaps in previous evaluations but also establishes a foundation for fair, reproducible, and practically relevant benchmarking in the next decade of U-Net-based segmentation models. The weights, datasets, and results will be released after the acceptance.

Probabilistic weather forecasting requires not only accurate trajectories, but calibrated distributions over plausible atmospheric futures. Recent data-driven systems have achieved remarkable deterministic skill, and diffusion-based ensemble forecasters have substantially improved sample realism and uncertainty quantification. However, their inference cost scales with forecast horizon, ensemble size, and the number of denoising steps required for each transition, making large operational ensembles expensive. To address this, we present Tyche, a one-step conditional flow model for efficient probabilistic weather forecasting. Tyche models the conditional forecast distribution with a destination-aware average-velocity flow that maps Gaussian noise directly to future weather states in a single function evaluation (1-NFE). To make this one-step transport learnable in high-dimensional geophysical fields, we derive a JVP-regularized rectification objective that enforces temporal self-consistency across source and destination flow timesteps without explicitly forming Jacobians. The transport field is parameterized by an isotropic Swin-style transformer that preserves fine-scale spatial structure while remaining scalable on global grids. To improve ensemble reliability under autoregressive forecasting, we further introduce a rollout-based finetuning stage with curriculum CRPS calibration supervision. Experiments on ERA5 at 1.5$^\circ$ and 6-hour resolution show that our Tyche, using merely a single NFE, matches or exceeds the forecast skill and calibration of state-of-the-art multi-step generative baselines and the operational ECMWF IFS ensemble. Codes are available.

Two-sided matching platforms rely on preferences from both sides, yet participants can evaluate only a small fraction of potential partners. In practice, they use low-cost pre-match screening, e.g., interviews, profile views, or trial tasks, to form noisy impressions before committing to applications and offers. We study bandit learning in matching markets with interviews, modeling these interactions as queried *hints* [Bhaskara et al., 2022] that reveal partial preference information to both sides while constraining subsequent applications. Our framework also allows firm-side uncertainty: firms, like agents, learn their preferences and may make early hiring mistakes. To address this, we introduce strategic deferral, a firm-side action that permits temporary vacancy, corrects premature commitments, and enables decentralized learning under coarse anonymous feedback. We design algorithms for centralized and decentralized markets and show that a constant number of interviews per round suffices for horizon-independent regret, improving over the $O(\log T)$ guarantees known without interviews. Our bounds are near-optimal: the centralized guarantee is within a factor $m$ of an information-theoretic lower bound, while decentralized algorithms match it up to polynomial factors in structured markets and remain horizon-independent in general markets.

Sampling from a softmax distribution is a fundamental operation in machine learning, but its linear complexity in the number of items makes exact sampling impractical at scale. Two-level softmax (2LS) sampling is a popular alternative enabling sublinear-time sampling. Assuming items are partitioned into clusters, 2LS first samples a cluster and then an item within it. In this paper, we show that, despite its advantages, 2LS introduces systematic and undesirable sampling biases, which arise from misweighting clusters by ignoring both cluster size imbalance and intra-cluster similarity dispersion. We propose two sampling methods, Size-Corrected 2LS (S-2LS) and Size- and Dispersion-Corrected 2LS (SD-2LS), which correct these biases and provide provably better softmax approximations with negligible to non-existent computational overhead. In-depth experiments on five large-scale datasets validate the improved sampling properties of our methods. We recommend their consistent use in place of standard 2LS in future work.

We study fixed-confidence best-action identification (BAI) in stochastic minimax trees. This problem is increasingly relevant in modern AI planning, where deep minimax search and Monte Carlo Tree Search (MCTS) with language model long rollouts face a fundamental tradeoff: heuristic evaluations are cheap but biased, while accurate rollouts are reliable but prohibitively expensive. We propose 2FFS, a two-fidelity tree-search algorithm that brings multi-fidelity flat bandit ideas into trees. The algorithm combines minimax-style fast expansion with MCTS-style stochastic sampling, adaptively deciding when to exploit cheap biased evaluations and when to invoke expensive accurate evaluations for local certification. We prove fixed-confidence correctness, establish finite stopping for exact identification, and give a polynomial-depth cost upper bound for general-depth trees. Across numerical stochastic-tree experiments, 2FFS uses substantially fewer samples and computational operations comparing to existing BAI-MCTS baseline.

We partially resolve Conjecture 1 of \textit{Karagodin et al., Clustering in Causal Attention Masking (NeurIPS 2024)} and extend it to time-dependent parameter regimes. The conjecture predicts that causal attention dynamics converge to two clusters aligned with the eigenvectors associated with the largest eigenvalue $\lambda_{\max}$ of the value transformation. We prove that this behavior holds when $\lambda_{\max}>0$ and is generally false when $\lambda_{\max}\le0$. The resulting two-cluster regime is common in practice and substantially more challenging than the classical single-cluster setting studied previously. A central contribution of our work is the identification of a rigorous dimension deduction phenomenon: despite evolving in a high-dimensional embedding space, token trajectories collapse onto a two-dimensional structure governed by a small number of dominant directions. Building on this insight, we introduce a new analytical framework--instability within the flow--inspired by instability phenomena in physical systems. This framework enables the analysis of steady-regime behavior in non-monotone, non-autonomous attention dynamics. Our theoretical findings are illustrated through simulations and experimental studies using Group Query Attention (GQA) layers.

Online platforms often struggle with inflated, uninformative user ratings. This issue can be mitigated by better design of the data collection mechanism, for example through changing the phrasing of user questions. Previous work optimizes a single rating scale to best distinguish the inherent qualities of items under binary feedback. In this paper, we demonstrate the power of utilizing different rating scales for different users. First, we show that a designer can always split a single rating scale into two to improve item rankings. Next, we formally characterize the optimal design of multiple scales as a series of 0-1 step functions whose threshold values are evenly spaced. Finally, we consider an adaptive model where subsequent rating scales can depend on the responses from previous users and show that adaptivity leads to even greater distinguishing power. All in all, our theoretical results show that using heterogeneous scales significantly improves item rankings on platforms.

How do protein structure prediction models fold proteins? We investigate this question through causal interventions on the folding trunks of ESMFold, OpenFold, and Boltz-1. Across all three models, we find a shared two-stage computational structure. In the first stage, early blocks initialize *pairwise biochemical signals*: features like charge propagate from sequence into pairwise representations through architecture-specific pathways. In the second stage, late blocks develop *pairwise spatial features*: distance and contact information accumulate in the pairwise representation. We verify these mechanisms causally by showing that steering charge and distance features induces predictable structural changes. Furthermore, these representations are functionally interchangeable: pairwise states can be linearly aligned and substituted across models. Together, these results suggest that folding trunks with different architectures, inputs, and training procedures converge on a shared representational organization for mapping sequence chemistry into spatial geometry.

Training loss and accuracy are the standard signals used to monitor generalization during deep neural network training. Two well-documented phenomena complicate this picture: in grokking, train loss falls rapidly while test performance improves abruptly only after a long delay; in epoch-wise double descent, train loss decreases monotonically while test loss or error rises and falls. Existing accounts are often task-specific, and a task-agnostic analysis framework for diagnosing and explaining these phenomena across realistic tasks and architectures is missing. We address this challenge by analyzing two competing processes that underlie learning dynamics: representation learning in the encoder and readout calibration in the final classifier. Using tools from representational geometry, neural tangent kernels, and linear probing, we show that both processes are active throughout training, with the fluctuations of their relative speed giving rise to seemingly anomalous generalization dynamics. Applying the representation-readout decomposition to grokking across a wide range of tasks and architectures, we find that the readout is train-biased before grokking onset, and representation learning is gradual but not absent—contrary to the lazy-to-rich account. The framework further provides diagnostic signatures distinguishing spurious from genuine generalization: in a previously reported MNIST grokking example and an epoch-wise double descent example, apparent delayed or non-monotone generalization is shown to arise from representation degradation and readout misalignment induced by non-standard training recipes. Together, these results establish the representation-readout decomposition as a top-down framework for understanding learning dynamics and revealing underlying algorithms for interpretability research.

We introduce Rapid Simulation Based Inference (RSBI), a diffusion-based variational approach to likelihood-free Bayesian inference that achieves high posterior sample efficiency under large and multi-dimensional prior-to-posterior volumes. RSBI builds on recent advances in Schrödinger Bridge (SB) diffusion sampling to handle multi-modal posteriors, with the likelihood supplied either by a neural ratio estimator or kernal surrogate via a differentiable simulator. Furthermore, a key observation is that an appropriate surrogate likelihood gives a proposal distribution covering most of the generally multi-modal posterior mass, replacing the sequential rounds of standard methods with a one-shot proposal step. Subsequent NRE refinement recovers exact inference under the simulator and original model prior. As a variational method, RSBI does not suffer from prior leakage and implicit target drift commonly observed in standard sequential posterior estimation methods. To improve mode coverage we optionally utilize the well-tempered meta-dynamics framework, which also provides a mechanism through which to encourage exploration of the prior volume. We observe strong performance not only on standard SBI benchmarks, but also as prior volume is scaled up to 2500 times the original, achieving a performance degradation of only $\sim$5% on the two moons benchmark under a highly constrained simulation budget. Additionally, we evaluate RSBI's potential for gravitational wave ring-down posterior estimation, highlighting a real-world use-case where our method excels.

Multimodal continual learning requires MLLMs to acquire new domains and abilities sequentially while retaining previous capabilities. MoE-based methods preserve task-specific knowledge, but inference relies on reliable routing. We instead study unified continual multimodal consolidation, which forms one shared model from sequential LoRA updates and projector shifts. LoRA merging naturally supports language-side consolidation, but extending it to MLLMs raises two challenges. First, sequential LoRA updates may interfere and overwrite directions important to earlier tasks. Second, projector mismatch may make the consolidated LoRA update incompatible with the final visual-language alignment. To address these challenges, we propose **CASC** (**C**onflict-**A**ware **S**pectral **C**onsolidation), a method that jointly consolidates LoRA and projector updates. CASC maintains fixed-rank spectral banks and uses a shared protected subspace memory rule to preserve dominant historical directions while incorporating compatible new updates under fixed rank budgets, yielding a single model without replay data or inference time routing. Both theoretical analysis and experimental results demonstrate the effectiveness of CASC in addressing multimodal continual learning.

Over the past few years, diffusion-based Schrödinger bridge models have been proposed to approximate optimal transport dynamics between two prescribed boundary distributions, with successful applications to generative modeling. More precisely, these methods aim to estimate a path measure whose initial and terminal marginals match the two boundary distributions, while minimizing the Kullback–Leibler divergence with respect to a reference Markov process. In this work, we consider the generalized Schrödinger bridge problem, in which the reference process is a twisted Brownian motion, that is, a Feynman–Kac transform of a Brownian motion induced by a time-dependent differentiable potential. Building on the Iterative Markovian Fitting (IMF) paradigm, and in particular on its special case Diffusion Schrödinger Bridge Matching (DSBM), which corresponds to the zero potential, we introduce Twisted Schrödinger Bridge Matching (TSBM), a diffusion-based method designed to handle both continuous- and discrete-time potentials. Unlike previous approaches, TSBM provides a rigorous extension of the IMF scheme to the generalized Schrödinger bridge problem. This derivation leads to a new bridge-matching loss that depends explicitly on the gradient of the potential and recovers the DSBM objective when the potential vanishes, yielding improved performance. We further introduce trajectory-based variance-reduction techniques that substantially stabilize optimization and may be useful beyond the present setting. Finally, we empirically demonstrate the benefits of TSBM on several experimental settings.

LLM routing matters most in long-horizon applications such as coding agents, deep research systems, and computer-use agents, where a single user request triggers many model calls. Routing each call to the cheapest sufficient model can cut costs without sacrificing quality, yet existing router benchmarks evaluate only which model should answer a whole prompt. They never expose the router-visible prefix at an intermediate agent step, never test whether a cheaper replacement preserves downstream task success, and often rely on online LLM judges at evaluation time. We introduce TwinRouterBench, a step-level routing benchmark with two tracks. The static track provides 970 router-visible prefixes from 520 instances across SWE-bench, BFCL, mtRAG, QMSum, and PinchBench, each paired with an execution-verified target tier estimated under a released downgrade-and-cascade protocol; scoring is deterministic arithmetic over tier labels, trajectory membership, and token costs, with no online evaluator-side LLM judge. The dynamic track supplies a harness that runs routers on the full 500-case SWE-bench Verified suite; in this paper we report a 100-case held-out evaluation disjoint from the static SWE supervision split. At each LLM call the router selects a concrete model from a locked pool, and success is measured by official task resolution and realized API spend. The two tracks support fast offline iteration followed by end-to-end validation under live agent execution. Code and data are available at https://anonymous.4open.science/r/TwinRouterBench-8820.