The performance of pre-trained masked diffusion models is often constrained by their sampling procedure, which makes decisions irreversible and struggles in low-step generation regimes. We introduce a novel sampling algorithm that works with pre-trained models and, after a lightweight fine-tuning of a single layer, significantly improves sample quality and efficiency. Our method reformulates the generation process using a star-shaped paradigm, which inherently allows for error correction. To make this process effective, we augment it with a learnable re-masking scheduler that intelligently identifies and revises likely errors. This approach yields a substantial quality boost, particularly when using a small number of sampling steps. We extensively ablate key components of our approach and show its usability in different scenarios. In comprehensive experiments on text, and code generation, our sampling algorithm outperforms or matches existing methods.
Neural networks are typically optimized with variants of stochastic gradient descent. Under a squared loss, however, the optimal solution to the linear last layer weights is known in closed-form. We propose to leverage this during optimization, treating the last layer as a function of the backbone parameters, and optimizing solely for these parameters. We show this is equivalent to alternating between gradient descent steps on the backbone and closed-form updates on the last layer. We adapt the method for the setting of stochastic gradient descent, by trading off the loss on the current batch against the accumulated information from previous batches. We provide theoretical analyses showing convergence of the method to an optimal solution in the neural tangent kernel regime, as well as quantifying the gains compared to standard SGD in a one-step analysis. Finally, we demonstrate the effectiveness of our approach compared with SGD and Adam on a squared loss in several regression tasks, including neural operators and causal inference.
For the combinatorial graph alignment problem (GAP), finding the node correspondence that maximizes the number of common edges (nce) between two unlabeled graphs, the classical Frank-Wolfe heuristic FAQ remains a strong baseline once it is properly initialized, while existing GNN approaches struggle in the purely structural setting. We introduce a chaining procedure: a sequence of Folklore-type (2-FWL) GNNs in which each network is trained with cross-entropy after decoding the previous network's similarity matrix and ranking nodes by their current alignment quality. This non-differentiable ranking step injects discrete combinatorial feedback at every stage; at inference, we iterate the final network and keep the candidate with highest observed nce. On sparse Erdos-Renyi graphs at noise level 0.25, chained FGNNs used to initialize FAQ reach 85% accuracy versus 13% for FAQ initialized from the convex relaxation, and essentially 0% for prior GNN methods. On correlated regular graphs, where MPNNs with constant features produce identical node embeddings (1-WL fails to refine) and FAQ's convex initialization is degenerate, chaining is the only method among those we evaluate, including Gromov-Wasserstein solvers, that recovers a non-trivial alignment. On three real-world benchmarks (yeast PPI, coauthorship, and road networks), recent comparisons underestimate FAQ by initializing it from a uniform doubly stochastic matrix; initialized from the convex relaxation it already surpasses prior reported numbers, and dataset-specific chained FGNNs further improve on this strengthened baseline. Code and pretrained chains available at: https://github.com/mlelarge/chaining-gnn-graph-alignment.
Medical object detection suffers when a single detector is trained on mixed medical modalities (e.g., CXR, CT, MRI) due to heterogeneous statistics and disjoint representation spaces. To address this challenge, we turn to representation alignment, an approach that has proven effective for bringing features from different sources into a shared space. Specifically, we target the representations of DETR-style object queries and propose a simple, detector-agnostic framework to align them with modality context. First, we define modality tokens: compact, text-derived embeddings encoding imaging modality that are lightweight and require no extra annotations. We integrate the modality tokens into the detection process via Multimodality Context Attention (MoCA), mixing object-query representations via self-attention to propagate modality context within the query set. This preserves DETR-style architectures and adds negligible latency while injecting modality cues into object queries. We further introduce QueryREPA, a short pretraining stage that aligns query representations to their modality tokens using a task-specific contrastive objective with modality-balanced batches. Together, MoCA and QueryREPA produce modality-aware, class-faithful queries that transfer effectively to downstream training. Across diverse modalities trained altogether, the proposed approach consistently improves AP with minimal overhead and no architectural modifications, offering a practical path toward robust multimodality medical object detection.
In autoregressive language models, each token is sampled by conditioning on all the past tokens; the overall string has thus been sampled from the correct underlying joint distribution represented by the model. In contrast, masked diffusion language models generate text by unmasking tokens out of order and potentially in parallel. Generating an overall string sampled from the correct underlying joint distribution would (again) require exactly one token unmasking in every full-model forward pass. The more tokens unmasked in parallel, the further away the string is from the true joint; this can be seen in the resulting drop in accuracy (but, increase in speed). In this paper we devise a way to {\em approximately} sample multiple tokens from the joint distribution in a single full-model forward pass; we do so by developing a new lightweight single-layer ``sampler" on top of an existing large diffusion LM. One forward pass of the full model can now be followed by multiple forward passes of only this sampler layer, to yield multiple unmasked tokens. Our sampler is trained to mimic exact joint sampling from the (frozen) full model. We show the effectiveness of our approximate joint sampling for both pretrained-only (Dream-7B-Base, Llada-7B-Base) and instruction-tuned (Dream-7B-Instruct, Dream-7B-Coder) models on language modeling and math \& coding tasks. When four tokens are unmasked for each full-model denoising step, our sampling algorithm achieves a MAUVE score of 0.87 (vs marginal baseline of 0.31) with respect to the true joint distribution.
Clinical notes contain rich patient information, such as diagnoses or medications, making them valuable for patient representation learning. Recent advances in large language models have further improved the ability to extract meaningful representations from clinical texts. However, clinical notes are often missing. For example, in our MIMIC-IV cohort, 35.15% of patients have no eligible discharge summaries. In such cases, representations can be learned from other modalities such as structured data, chest X-rays, or radiology reports. Yet the availability of these modalities is influenced by clinical decision-making and varies across patients, potentially producing modality missing-not-at-random (MMNAR) patterns. We propose a causal representation learning framework that leverages observed data and informative missingness in multimodal clinical records. It consists of: (1) an MMNAR-aware modality fusion component that integrates structured data, imaging, and text while conditioning on missingness patterns to capture patient health and clinician-driven assignment; (2) a modality reconstruction component with latent alignment to preserve modality information in the learned representation; and (3) a multitask outcome prediction model with a rectifier that corrects for residual bias from specific modality observation patterns. Comprehensive evaluations across MIMIC-IV and eICU show consistent gains over the strongest baselines, achieving relative AUC improvements of up to 4.3% for hospital readmission and 2.7% for ICU admission.
Restricted Boltzmann machines (RBMs) are energy-based models originating from statistical physics. In this study, we investigate how musical structures are represented in the hidden layer of a Bernoulli-Bernoulli RBM trained on binary piano-roll representations of J.~S.~Bach's music. By examining the visible patterns induced by individual hidden units, we find that the hidden layer primarily captures local temporal and pitch-statistical features rather than explicit musical concepts such as melodies, chords, or keys. Free-energy comparisons show that the trained RBM assigns higher probabilities to the examined musical inputs than to digit or noise patterns. Analysis using t-SNE, cosine similarity, and PCA reveals that hidden representations are sensitive to absolute pitch and input overlap, with transposed versions of the same piece not necessarily mapped close together. Generated samples exhibit local pitch organization but limited long-range coherence. These findings illustrate how a simple statistical-physics model captures certain regularities in structured musical data while highlighting its limitations in representing higher-level musical relationships.
Quantization reduces the deployment cost of large language models (LLMs). However, post-training quantization (PTQ) cannot fine-tune model parameters and often degrades accuracy in low-bit settings, while quantization-aware training (QAT) requires backpropagation and incurs high memory overhead. We propose ZeroQAT, a zeroth-order QAT framework supporting both weight and activation quantization. By using forward-only gradient estimation, ZeroQAT removes backpropagation and substantially reduces memory and computation while retaining end-to-end optimization benefits. We further introduce a lightweight variant of ZeroQAT for quantized fine-tuning, which freezes and pre-quantizes most parameters to further cut memory usage. Experiments show that ZeroQAT consistently outperforms representative PTQ and QAT baselines while requiring significantly less memory. For example, ZeroQAT enables fine-tuning of a 13B model at extremely low bit-widths (e.g., 2-4 bits) on a single 8GB GPU, and even allows fine-tuning a 6.7B model on a OnePlus 12 smartphone, demonstrating its practicality for end-to-end QAT on resource-limited edge devices.
Quantifying the uncertainty of forecasting models is essential to assess and mitigate the risks associated with data-driven decisions, especially in volatile domains such as electricity markets. In this paper, we propose a computationally efficient isotonic variant of Quantile Regression Averaging (QRA), called Isotonic Quantile Regression Averaging (iQRA), for generating probabilistic forecasts from ensembles of point forecasts. Building on QRA, we introduce stochastic order constraints as a hyperparameter-free regularization mechanism that reduces computational complexity while maintaining competitive forecast accuracy. We further demonstrate that the same isotonic regularization principle can be applied to the smoothed estimator of QRA. In an extensive forecasting study of two European day-ahead electricity markets, we show that iQRA and its smoothed variant consistently rank among the top state-of-the-art postprocessing methods in terms of reliability and sharpness. It produces well-calibrated prediction intervals, with smoothed iQRA providing superior reliability even when compared against coverage-oriented conformal prediction. We further introduce a battery arbitrage evaluation, showing that the leading probabilistic methods achieve the highest profit per trade and that probabilistic risk control improves the economic value of trading decisions. Isotonic regularization offers a scalable hyperparameter-free variable selection for linear quantile regression, making iQRA attractive for practical decision-support systems in energy markets.
Phase retrieval is an ill-posed inverse problem in which existing methods often struggle to balance reconstruction fidelity and perceptual quality. We propose a novel Langevin-based framework for phase retrieval that bridges model-driven and data-driven approaches by combining stochastic posterior sampling, learned denoising, and model-based updates to better navigate the perception-distortion tradeoff. The framework consists of three progressively more advanced variants. The first, prNet-Small, provides a theoretically grounded and lightweight pipeline that integrates Langevin dynamics with learned noise and denoising processes and alternating projection-based updates. Building upon this foundation, prNet-Large exploits parallel sampling of diverse reconstructions and aggregates them to approximate the MMSE solution, significantly improving distortion metrics. Finally, prNet-Large-Adversarial enhances perceptual quality by replacing simple averaging with an adversarially trained aggregation network while preserving reconstruction fidelity. In addition, we incorporate test time augmentation to further improve the performance. Extensive experiments demonstrate that the proposed framework consistently outperforms classical, deep learning-based, and diffusion-based baselines across multiple benchmarks in both reconstruction fidelity and perceptual quality. The source code and trained models are available at https://github.com/METU-SPACE-Lab/prNet-for-Phase-Retrieval
Language model agents are increasingly used to automate scientific research, yet evaluating their scientific contributions remains a challenge. A key mechanism to obtain such insights is through ablation experiments. To this end, we introduce AblationBench, a benchmark suite for evaluating agents on ablation planning tasks in empirical AI research. It includes two tasks: AuthorAblation, which helps authors propose ablation experiments based on a method section and contains 83 instances, and ReviewerAblation, which helps reviewers find missing ablations in a full paper and contains 350 instances. For both tasks, we develop LM-based judges that serve as an automatic evaluation framework. Our experiments with frontier LMs show that these tasks remain challenging, with the best-performing LM system identifying only 45% of the original ablations on average, below human-level performance. We observe an inverse performance trend between the author and reviewer tasks, which we attribute to differences in model grounding. Lastly, we analyze the limitations of current LMs on these tasks, and find that chain-of-thought prompting outperforms an agent-based approach. Our data is available on https://huggingface.co/collections/ai-coscientist/ablationbench, and our code is available on https://github.com/ai-scientist-bench/ablation-bench .
Oral squamous cell carcinoma OSCC is a major global health burden, particularly in several regions across Asia, Africa, and South America, where it accounts for a significant proportion of cancer cases. Early detection dramatically improves outcomes, with stage I cancers achieving up to 90 percent survival. However, traditional diagnosis based on histopathology has limited accessibility in low-resource settings because it is invasive, resource-intensive, and reliant on expert pathologists. On the other hand, oral cytology of brush biopsy offers a minimally invasive and lower cost alternative, provided that the remaining challenges, inter observer variability and unavailability of expert pathologists can be addressed using artificial intelligence. Development and validation of robust AI solutions requires access to large, labeled, and multi-source datasets to train high capacity models that generalize across domain shifts. We introduce the first large and multicenter oral cytology dataset, comprising annotated slides stained with Papanicolaou(PAP) and May-Grunwald-Giemsa(MGG) protocols, collected from ten tertiary medical centers in India. The dataset is labeled and annotated by expert pathologists for cellular anomaly classification and detection, is designed to advance AI driven diagnostic methods. By filling the gap in publicly available oral cytology datasets, this resource aims to enhance automated detection, reduce diagnostic errors, and improve early OSCC diagnosis in resource-constrained settings, ultimately contributing to reduced mortality and better patient outcomes worldwide.
Message-passing graph neural networks (MPGNNs) dominate modern graph learning. Typical efforts enhance MPGNN's expressive power by enriching the adjacency-based aggregation. In contrast, we introduce a graph-level aggregation over walk incidence-based matrices that are constructed to deliberately trade off some expressivity for stronger and more structured inductive bias. This approach allows for gradual scaling between classical message-passing and simpler methods based on walks. Drawing on weighted automata, we ensure our gradual scaling is polynomial-time and avoids the combinatorial explosion of colored walks. Our second result characterizes the expressive power at each scale using homomorphism counts over a hierarchy of generalized caterpillar graphs. Based on these foundations, we propose Caterpillar GNNs that substantially reduce the number of nodes in the hidden layers of the computational graphs on real-world datasets. This gradual reduction does not obstruct learning, enabling a systematic study of lower-order expressivity. We further describe benchmark settings where task-aligned expressivity supports learning.
Reinforcement learning with rule-based, binary-valued reward functions has been shown to significantly enhance the reasoning capabilities of large language models. These models typically rely on REINFORCE-based policy optimization methods, such as REINFORCE with baseline and group relative policy optimization (GRPO). However, a key limitation is that existing methods either ignore reward normalization or use static normalization schemes, which fail to adapt to the evolving policy during training. This mismatch can lead to unstable gradient estimates and hinder training stability. To address this issue, we propose Beta Normalization Policy Optimization (BNPO), a novel method that adaptively normalizes rewards using a Beta distribution with dynamically updated parameters. By aligning normalization with the changing policy distribution, BNPO enables more accurate, lower-variance gradient estimation and promotes stable training dynamics. We provide theoretical analysis showing that BNPO reduces variance and generalizes both REINFORCE and GRPO under binary-valued rewards. In addition, we introduce an advantage decomposition mechanism to extend BNPO to more complex reward settings. Experimental results demonstrate that BNPO achieves state-of-the-art performance among policy optimization methods on reasoning tasks.
Transformer-based models have gained increasing attention in time series research, driving interest in Large Language Models (LLMs) and foundation models for time series analysis. As the field moves toward multi-modality, Large Vision Models (LVMs) are emerging as a promising direction. In the past, the effectiveness of Transformer and LLMs in time series has been debated. When it comes to LVMs, a similar question arises: are LVMs truely useful for time series analysis? To address it, we design and conduct the first principled study involving 4 LVMs, 8 imaging methods, 18 datasets and 26 baselines across both high-level (classification) and low-level (forecasting) tasks, with extensive ablation analysis. Our findings indicate LVMs are indeed useful for time series classification but face challenges in forecasting. Although effective, the contemporary best LVM forecasters are limited to specific types of LVMs and imaging methods, exhibit a bias toward forecasting periods, and have limited ability to utilize long look-back windows. We hope our findings could serve as a cornerstone for future research on LVM- and multimodal-based solutions to different time series tasks.
Real-world multimodal systems routinely face missing-input scenarios, and in reality, robots lose audio in a factory or a clinical record omits lab tests at inference time. Standard fusion layers either preserve robustness or calibration but never both. We introduce Adaptive Entropy-Gated Contrastive Fusion (AECF), a single light-weight layer that (i) adapts its entropy coefficient per instance, (ii) enforces monotone calibration across all modality subsets, and (iii) drives a curriculum mask directly from training-time entropy. On AV-MNIST and MS-COCO, AECF improves masked-input mAP by +18 pp at a 50% drop rate while reducing ECE by up to 200%, yet adds 1% run-time. All back-bones remain frozen, making AECF an easy drop-in layer for robust, calibrated multimodal inference.
We consider linear stochastic bandits where the set of actions is an ellipsoid. We provide the first known minimax optimal algorithm for this problem. We first derive a novel information-theoretic lower bound on the regret of any algorithm, which must be at least $\Omega(\min(d \sigma \sqrt{T} + d \|\theta\|_{A}, \|\theta\|_{A} T))$ where $d$ is the dimension, $T$ the time horizon, $\sigma^2$ the noise variance, $A$ a matrix defining the set of actions and $\theta$ the vector of unknown parameters. We then provide an algorithm whose regret matches this bound to a multiplicative universal constant. The algorithm is non-classical in the sense that it is not optimistic, and it is not a sampling algorithm. The main idea is to combine a novel sequential procedure to estimate $\|\theta\|$, followed by an explore-and-commit strategy informed by this estimate. The algorithm is highly computationally efficient, and a run requires only time $O(dT + d^2 \log(T/d) + d^3)$ and memory $O(d^2)$, in contrast with known optimistic algorithms, which are not implementable in polynomial time. We go beyond minimax optimality and show that our algorithm is locally asymptotically minimax optimal, a much stronger notion of optimality. We further provide numerical experiments to illustrate our theoretical findings.
Recent studies have revealed the vulnerability of large language models to adversarial attacks, where adversaries craft specific inputs to induce incorrect or harmful outputs. Although various empirical defenses have been proposed, their worst-case robustness remains poorly understood, raising concerns about how they would behave against stronger future attacks. Here, we study the worst-case robustness of LLMs from both empirical and theoretical perspectives. First, we provide tighter empirical upper bounds for the tested deterministic defenses using stronger white-box attacks, under which most tested configurations achieve nearly 0\% robustness. Second, we formulate randomized-smoothing certification for bounded and binary base functions as fractional and 0-1 knapsack problems, respectively, and derive grouped solvers for two token kernels. For example, on AdvBench, we certify a GPT-4o safety detector smoothed by a uniform kernel to an average certified $\ell_0$ radius of 2.02. In our stated suffix-attack setting, the same kernel certifies a Llama-3-8B safety detector to an average certified radius of 6.41.
Traditional similarity-based schema matching methods fail to resolve semantic ambiguities and conflicts in complex, domain-specific mappings due to a lack of commonsense and domain-specific knowledge. In parallel, large language models (LLMs) without sufficient background knowledge tend to hallucinate, further complicating schema matching. To overcome these limitations, we introduce KG-RAG4SM, a Knowledge Graph-based Retrieval-Augmented Generation for Schema Matching. This method integrates novel retrieval mechanisms, including LLM-based, vector-based, graph traversal-based, and hybrid techniques with advanced reranking schemes to extract the most relevant subgraphs from large external KGs. Our approach achieves superior results without requiring re-training, as evidenced by improvements of 39.79% in precision and 30.56% in F1 score over LLM-based state-of-the-art (SOTA) methods (e.g., Jellyfish-8B) on the MIMIC dataset, and enhancements of 69.20% in precision and 21.99% in F1 score over pre-trained language model (PLM)-based SOTA methods (e.g., SMAT) on the Synthea dataset. Additionally, KG-RAG4SM scales effectively across KGs from commonsense KGs to domain-specific ones, while its instruction-tuning knowledge exclusion component ensures truthful performance in end-to-end schema matching tasks despite the suboptimal relevance of KG context. Our empirical analysis and case studies from real-world scenarios show that the hallucination problem in LLMs for schema matching is well mitigated by our solution.
PolSAR data presents unique challenges due to its rich and complex characteristics. Existing data representations, such as complex-valued data, polarimetric features, and amplitude images, are widely used. However, these formats often face issues related to usability, interpretability, and data integrity. Most feature extraction networks for PolSAR are small, limiting their ability to capture features effectively. To address these issues, We propose the Polarimetric Scattering Mechanism-Informed SAM (PolSAM), an enhanced Segment Anything Model (SAM) that integrates domain-specific scattering characteristics and a novel prompt generation strategy. PolSAM introduces Microwave Vision Data (MVD), a lightweight and interpretable data representation derived from polarimetric decomposition and semantic correlations. We propose two key components: the Feature-Level Fusion Prompt (FFP), which fuses visual tokens from pseudo-colored SAR images and MVD to address modality incompatibility in the frozen SAM encoder, and the Semantic-Level Fusion Prompt (SFP), which refines sparse and dense segmentation prompts using semantic information. Experimental results on the PhySAR-Seg datasets demonstrate that PolSAM significantly outperforms existing SAM-based and multimodal fusion models, improving segmentation accuracy, reducing data storage, and accelerating inference time. The source code and datasets will be made publicly available at https://github.com/XAI4SAR/PolSAM.