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Probabilistic Methods · Structure Learning

Siqi Chen, Yachen Gao, Yanwei Fu, Xinwei Sun

Controlling the false discovery rate (FDR) under complex sparsity structures remains a fundamental challenge in large language model (LLM) analysis. Motivated by multiple comparison problems in LLMs, we consider a setting in which sparsity arises at the group level after a linear transformation of model parameters. We propose Split Group Knockoffs (SGKs), a general framework for group-wise variable selection under grouped transformational sparsity that extends the Split Knockoff procedure to grouped transformed variables. We establish theoretical guarantees for group-level FDR control and support recovery consistency, addressing challenges induced by group-wise penalties in transformed spaces. Applying SGK to LLM behavior auditing experiment reveals that model disagreement is not uniform across subjects, but instead concentrates in domains with greater semantic and reasoning complexity, where SGK effectively distinguishes genuine behavioral deviations from surface-level performance variation.

Deep Learning · Generative Models and Autoencoders

Pengfei Jiang, Jixiang Luo, Luxi Lin, Zhaohong Huang, Xuelong Li

Visual Autoregressive Modeling (VAR) based on next-scale prediction achieves strong generation quality, but their explicit deep stacks fix the amount of computation per scale and inflate memory at high resolutions. We introduce Visual Implicit Autoregressive Modeling (VIAR), a next-scale autoregressive generator that embeds an implicit equilibrium layer between shallow pre/post blocks. The implicit layer is trained with Jacobian‑Free Backpropagation, yielding constant training memory, while inference exposes a per‑scale iteration knob that enables compute control. On ImageNet 256 × 256 benchmark, VIAR attains FID 2.16, and sFID 8.07 with only 38.4\% parameters of VAR, matching or surpassing strong AR baselines and remaining competitive with large diffusion models. By controlling the per-scale knob, VIAR can reduce peak memory from 19.24 GB to 8.53 GB and doubles throughput from 15.16 to 32.08 images/s on a single RTX 4090, without retraining. Ablations show that fewer steps are sufficient for fixed-point iterations to converge and that VIAR consistently dominates VAR across quality efficiency operating points. In zero shot in-painting and class‑conditional editing, VIAR produces sharper details and smoother boundaries while preserving global structure, validating the benefits of implicit equilibria and per‑scale compute control for practical, deployable visual generation.

Social Aspects · Alignment

Bijean Ghafouri, Eun Cheol Choi, Priyanka Dey, Emilio Ferrara

RLHF assumes that annotation responses reflect genuine human preferences. We argue this assumption warrants systematic examination, and that behavioral science offers frameworks that bring clarity to when it holds and when it breaks down. Behavioral scientists have documented for sixty years that people routinely produce responses without holding genuine opinions, construct preferences on the spot based on contextual cues, and interpret identical questions differently. These phenomena are pervasive for precisely the value-laden judgments that matter most for alignment, yet this literature has not yet been systematically integrated into ML practice. In this position paper, we argue that the ML community must treat measurement validity as logically prior to preference aggregation. Specifically, our position is that measuring human preferences in RLHF is a social science problem. We present a taxonomy distinguishing genuine preferences from non-attitudes, constructed preferences, and measurement artifacts, along with diagnostic approaches for detecting each. This framework has two important implications. First, it raises the question of whether current RLHF practice may be systematically modeling noise as signal and elicitation artifacts as human values. Second, it provides a path forward by suggesting diagnostic tools that can distinguish valid preferences from artifacts before they enter the training pipeline.

Social Aspects · Privacy

Yanming Li, Cédric Eichler, Nicolas Anciaux, Alexandra Bensamoun, Lorena Gonzalez-Manzano, Seifeddine Ghozzi

We propose a system for marking sensitive or copyrighted texts to detect their use in fine-tuning large language models (LLMs) under black-box access with statistical guarantees. Our method builds digital "marks" using invisible Unicode characters organized into ("cue", "reply") pairs. During an audit, prompts containing only "cue" fragments are issued to trigger regurgitation of the corresponding "reply", indicating document usage. To control false positives, we compare against held-out counterfactual marks and apply a ranking test, yielding a verifiable bound on the false positive rate. The approach is minimally invasive, scalable across many sources, robust to standard processing pipelines, and achieves high detection power even when marked data is a small fraction of the fine-tuning corpus.

Applications · Time Series

Md Atik Ahamed, Mihir Parmar, Palash Goyal, Yiwen Song, Long T. Le, Qiang (Shaun) Cheng, Chun-Liang Li, Hamid Palangi, Jinsung Yoon, Tomas Pfister

We introduce TFRBench, the first benchmark designed to evaluate the reasoning capabilities of forecasting systems. Traditionally, time-series forecasting has been evaluated solely on numerical accuracy, treating foundation models as "black boxes." Unlike existing benchmarks, TFRBench provides a protocol for evaluating the reasoning generated by forecasting systems--specifically their analysis of cross-channel dependencies, trends, and external events. To enable this, we propose a systematic multi-agent framework that utilizes an iterative verification loop to synthesize numerically grounded reasoning traces. Spanning ten datasets across five domains, our evaluation confirms that this reasoning is causally effective; useful for evaluation; and prompting LLMs with our generated traces significantly improves forecasting accuracy compared to direct numerical prediction (e.g., avg. $\sim40.2$% $\rightarrow$ $\sim56.6$%), validating the quality of our reasoning. Conversely, benchmarking experiments reveal that off-the-shelf LLMs consistently struggle with both reasoning (lower LLM-as-a-Judge scores) and numerical forecasting, frequently failing to capture domain-specific dynamics. TFRBench thus establishes a new standard for interpretable, reasoning-based evaluation in time-series forecasting.

Deep Learning · Generative Models and Autoencoders

Shanchuan Lin, Ceyuan Yang, Zhijie Lin, Hao Chen, Haoqi Fan

We present adversarial flow models, a class of generative models that belongs to both adversarial and flow families of models. Our method supports native one-step or multi-step generation and is trained using the adversarial objective. Unlike traditional GANs, where the generator learns an arbitrary transport plan between the noise and the data distributions, our generator learns a deterministic noise-to-data mapping, which is the same optimal transport as in flow-matching models. This significantly stabilizes adversarial training. Also, unlike consistency-based methods, our model directly learns one-step or few-step generation without having to learn the intermediate timesteps of the probability flow for propagation. This saves model capacity, reduces training iterations, and avoids error accumulation. Under the same 1NFE setting on ImageNet-256px, our B/2 model approaches the performance of consistency-based XL/2 models, while our XL/2 model creates a new best FID of 2.38. We additionally show the possibility of end-to-end training of 56-layer and 112-layer models through depth repetition without any intermediate supervision, and achieve FIDs of 2.08 and 1.94 using a single forward pass, surpassing their 28-layer 2NFE and 4NFE counterparts.

Deep Learning · Large Language Models

Ziwen Zhao, Menglin Yang

Retrieval-augmented generation (RAG) enhances large language models with external knowledge, and tree-based RAG organizes documents into hierarchical indexes to support queries at multiple granularities. However, existing Tree-RAG methods designed for single-document retrieval face critical challenges in scaling to cross-document multi-hop questions: *(1) poor distribution adaptability*, where $k$-means clustering introduces noise due to rigid distribution assumptions; *(2) structural isolation*, as tree indexes lack explicit cross-document connections; and *(3) coarse abstraction*, which obscures fine-grained details. To address these limitations, we propose **$\Psi$-RAG**, a tree-RAG framework with two key components. *First*, a hierarchical abstract tree index built through an iterative "merging and collapse" process that adapts to data distributions without a priori assumption. *Second*, a multi-granular retrieval agent that intelligently interacts with the knowledge base with reorganized queries and an agent-powered hybrid retriever. $\Psi$-RAG supports diverse tasks from token-level question answering to document-level summarization. On cross-document multi-hop QA benchmarks, it outperforms RAPTOR by 25.9\% and HippoRAG 2 by 7.4\% in average F1 score. Code is available at https://anonymous.4open.science/r/Psi-RAG-7831/.

Deep Learning · Self-Supervised Learning

Fabian A Mikulasch, Friedemann Zenke

Self-supervised learning (SSL) excels at finding general-purpose latent representations from complex data, yet lacks a unifying theoretical framework that explains the diverse existing methods and guides the design of new ones. We cast SSL as latent distribution matching (DM): learning representations that maximize their log-probability under an assumed latent model (alignment), while maximizing latent entropy to prevent collapse (uniformity). This view unifies independent component analysis with contrastive, non-contrastive, and predictive SSL methods, including stop-gradient approaches. Leveraging DM, we derive a nonlinear, sampling-free Bayesian filtering model with a Kalman-based predictor for high-dimensional timeseries. We further prove that predictive DM yields identifiable latent representations under mild assumptions, even with nonlinear predictors. Overall, DM clarifies the assumptions behind established SSL methods and provides principled guidance for developing new approaches.

Probabilistic Methods · Bayesian Models and Methods

Xiaoxian Zhu, Yingmeng Li, Shuangge Ma, Mengyun Wu

In modern applications such as ECG monitoring, neuroimaging, wearable sensing, and industrial equipment diagnostics, complex and continuously structured data are ubiquitous, presenting both challenges and opportunities for functional data analysis. However, existing methods face a critical trade-off: conventional functional models are limited by linearity, whereas deep learning approaches lack interpretable region selection for sparse effects. To bridge these gaps, we propose a sparse Bayesian functional deep neural network (sBayFDNN). It learns adaptive functional embeddings through a deep Bayesian architecture to capture complex nonlinear relationships, while a structured prior enables interpretable, region-wise selection of influential domains with quantified uncertainty. Theoretically, we establish rigorous approximation error bounds, posterior consistency, and region selection consistency. These results provide the first theoretical guarantees for a Bayesian deep functional model, ensuring its reliability and statistical rigor. Empirically, comprehensive simulations and real‑world studies confirm the effectiveness and superiority of sBayFDNN. Crucially, sBayFDNN excels in recognizing intricate dependencies for accurate predictions and more precisely identifies functionally meaningful regions, capabilities fundamentally beyond existing approaches.

Social Aspects · Safety

Yujie Lin, Chengyi Yang, Zhishang Xiang, YIPING SONG, Jinsong Su

Large language models inevitably retain sensitive information, defined as inputs that may induce harmful generations, due to training on massive web corpora, raising concerns for privacy and safety. Existing machine unlearning methods primarily rely on retraining or aggressive fine-tuning, which are either computationally expensive or prone to degrading related knowledge and overall model utility. In this work, we reformulate machine unlearning as a precise knowledge re-mapping problem via model editing. We propose ZeroUnlearn, a few-shot unlearning framework. It overwrites sensitive inputs by mapping them to a neutral target state and removing their original representations. ZeroUnlearn enforces representational orthogonality through a multiplicative parameter update with a closed-form solution, enabling efficient and targeted unlearning. We further extend ZeroUnlearn to a gradient-based variant for multi-sample unlearning. Experiments demonstrate that our approach outperforms existing baselines while preserving general model utility. Our code is available at the anonymous link: https://anonymous.4open.science/r/ZeroUnlearn-9B87.

Applications · Neuroscience, Cognitive Science

Noga Mudrik, Yuxi Chen, Gal Mishne, Adam Charles

Many fields collect large-scale temporal data through repeated measurements (`trials’), where each trial is labeled with a set of metadata variables spanning several categories. For example, a trial in a neuroscience study may be linked to a value from category (a): task difficulty, and category (b): animal choice. A critical challenge in time-series analysis is to understand how these labels are encoded within the multi-trial observations, and disentangle the distinct effect of each label entry across categories. Here, we present MILCCI, a novel data-driven method that i) identifies the interpretable components underlying the data, ii) captures cross-trial variability, and iii) integrates label information to understand each category's representation within the data. MILCCI extends a sparse per-trial decomposition that leverages label similarities within each category to enable subtle, label-driven cross-trial adjustments in component compositions and to distinguish the contribution of each category. MILCCI also learns each component’s corresponding temporal trace, which evolves over time within each trial and varies flexibly across trials. We demonstrate MILCCI’s performance through both synthetic and real-world examples, including voting patterns, online page view trends, and neuronal recordings.

Applications · Health / Medicine

Hao Zhou, Simon Lee, Cyrus Tanade, Keum San Chun, Juhyeon Lee, Migyeong Gwak, Megha Thukral, Justin Sung, Eugene Hwang, Mehrab Bin Morshed 等

Biosignals acquired from different locations on the body often provide temporally ordered views of the same underlying physiological process. However, most existing self-supervised learning methods treat these signals as interchangeable views, overlooking the directional temporal dynamics that link them. A canonical example is the relationship between electrocardiography (ECG), which captures the electrical activation initiating each heartbeat, and photoplethysmography (PPG), which records the resulting peripheral pulse delayed by vascular dynamics. To capture this structured relationship, we introduce xMAE, a biosignal pretraining framework that leverages masked cross-modal reconstruction across temporally ordered biosignals as a training-time constraint to encourage physiologically meaningful timing structure in the learned representations. We show that pretraining with xMAE yields representations that outperform both unimodal and multimodal baselines on 15 of 19 downstream tasks, including cardiovascular outcome prediction, abnormal laboratory test detection, sleep staging, and demographic inference, while generalizing across devices, body locations, and acquisition settings. Further analysis suggests that the ECG--PPG timing structure is reflected in the learned PPG representations. More broadly, xMAE demonstrates the effectiveness of incorporating temporal structure into multimodal pretraining when signals observe different stages of a shared underlying process.

Deep Learning · Attention Mechanisms

Sai Surya Duvvuri, Nirmal Patel, Nilesh Gupta, Inderjit Dhillon

Softmax-based dot-product attention is a cornerstone of Transformer architectures, enabling remarkable capabilities such as in-context learning. However, as context lengths increase, a fundamental limitation of the softmax function emerges: it tends to diffuse probability mass to irrelevant tokens degrading performance in long-sequence scenarios. Furthermore, attempts to sharpen focus by lowering softmax temperature hinder learnability due to vanishing gradients. We introduce LUCID Attention, an architectural modification that applies a preconditioner to the attention probabilities. This preconditioner, derived from exponentiated key-key similarities, minimizes overlap between the keys in a Reproducing Kernel Hilbert Space, thus allowing the query to focus on important keys among large number of keys accurately with same computational complexity as standard attention. Additionally, LUCID's preconditioning-based approach to retrieval bypasses the need for low temperature and the learnability problems associated with it. We validate our approach by training $\sim$1 billion parameter language models evaluated on up to 128K tokens. Our results demonstrate significant gains on long-context retrieval tasks, specifically retrieval tasks from BABILong, RULER, SCROLLS and LongBench. For instance, LUCID achieves up to 18\% improvement in BABILong and 14\% improvement in RULER multi-needle performance compared to standard attention.

Probabilistic Methods · Bayesian Models and Methods

Ibne Farabi Shihab, SANJEDA AKTER, Anuj Sharma

Deep protein structure predictors such as AlphaFold provide confidence estimates (e.g., pLDDT) that are not calibrated and degrade under distribution shifts across experimental modalities, temporal changes, and disordered regions. We introduce **CalPro**, a prior-aware evidential conformal framework for shift-robust uncertainty quantification. CalPro combines three components: (i) a geometric evidential head outputting Normal Inverse Gamma distributions via graph neural networks; (ii) a differentiable calibration surrogate that shapes representations during training, followed by split-conformal calibration for finite-sample coverage; and (iii) domain priors (disorder, flexibility) encoded as soft constraints on predicted uncertainty. Theoretically, we derive structure-aware *sensitivity bounds* for coverage degradation under distribution shift using PAC-Bayesian control over ambiguity sets, quantifying how miscoverage increases with model complexity and shift magnitude. Empirically, CalPro achieves at most 5 percentage points coverage degradation across modalities compared to 15 to 25 points for baselines, reduces calibration error by 30\% to 50\%, and improves downstream docking success from 52\% to 75\% when filtering by uncertainty. The framework extends beyond proteins to structured regression tasks where priors encode local reliability.

Probabilistic Methods · Variational Inference

Nico Daheim, Thomas Moellenhoff, James Ming Liang Ang, Mohammad Emtiyaz Khan

Stochastic Variance Reduced Gradient (SVRG) and its variants aim to speed-up training by using gradient corrections. In their decade of existence, these methods have never been connected to any Bayesian methods, at least not at a fundamental level. Here, we fill this gap and show surprising new connections of SVRG to a recently proposed Bayesian method called ‘posterior correction’. Our main contribution is to show that SVRG can be recovered as a special case of posterior correction when applied over isotropic-Gaussian posteriors. Novel extensions of SVRG are automatically obtained by using more flexible exponential-family posteriors. We derive two new such extensions by using Gaussian families: a Newton-like variant with novel Hessian corrections, and an Adam-like extension that scales to large problems. Our work is the first to connect SVRG to Bayes and use it to boost training.

Deep Learning · Generative Models and Autoencoders

Naoki Murata, Chieh-Hsin Lai, Yuhta Takida, Toshimitsu Uesaka, Bac Nguyen, Stefano Ermon, Yuki Mitsufuji

Recent literature has effectively leveraged diffusion models trained on continuous variables as priors for solving inverse problems. Notably, discrete diffusion models with discrete latent codes have shown strong performance, particularly in modalities suited for discrete compressed representations, such as image and motion generation. However, their discrete and non-differentiable nature has limited their application to inverse problems formulated in continuous spaces. This paper presents a novel method for addressing linear inverse problems by leveraging generative models based on discrete diffusion as priors. We overcome these limitations by approximating the true posterior distribution with a variational distribution constructed from categorical distributions and continuous relaxation techniques. Furthermore, we employ a star-shaped noise process to mitigate the drawbacks of traditional discrete diffusion models with absorbing states, demonstrating that our method performs comparably to continuous diffusion techniques with lower GPU memory consumption.

Social Aspects · Privacy

Omri Lev, Moshe Shenfeld, Vishwak Srinivasan, Katrina Ligett, Ashia Wilson

We study differentially private ordinary least squares (DP-OLS) with bounded data $(X,Y)$ via sketching-based mechanisms. While Gaussian sketching approaches have been explored for DP-OLS \citep{sheffet2017differentially}, they are typically viewed as less competitive than the Adaptive Sufficient Statistics Perturbation (AdaSSP) method \citep{wang_adassp}, which directly perturbs the sufficient statistics $(X^{\top}X, X^{\top}Y)$ and is information theoretically optimal while also exhibiting strong empirical performance. In this work, we propose the \emph{Iterative Hessian Mixing} (IHM), an algorithm that builds on Gaussian sketching approaches to DP-OLS and is inspired by the Iterative Hessian Sketch of \citet{pilanci_hessiansketch}. We prove that IHM is differentially private and provide utility guarantees in the form of excess empirical risk bounds. These bounds improve upon those of AdaSSP by removing a multiplicative factor that can be as large as the square root of the data dimension. The design of the IHM is based on new accuracy guarantees that we present for prior Gaussian sketching approaches for DP-OLS, which clarify when these methods are expected to perform well and how IHM circumvents their inherent limitations. We also conduct a rigorous empirical evaluation on a large suite of datasets, demonstrating that IHM consistently outperforms prior baselines, including AdaSSP.

Applications · Health / Medicine

Maria Elkjær Montgomery, Christian Igel, Mikkel Odgaard, Martin Sillesen, Mads Nielsen

How do we map numeric values to representations in transformer-based sequence processing, particularly in electronic health record (EHR) data? We systematically compare discrete, continuous, and hybrid value embeddings using synthetic arithmetic tasks embedded within real-world EHR data, as well as real-world clinical prediction tasks. Our study reveals trade-offs between numeric precision, optimisation stability, and architectural flexibility. We find that representations that explicitly model value-concept interactions perform best on precision-sensitive arithmetic tasks when architectural constraints permit. Hybrid token-based approaches that retain numeric values but apply binning prior to projection provide a more robust and broadly applicable alternative, with the optimal number of bins following a simple empirically derived power-law in dataset size. Across tasks, models consistently exhibit reliable “good enough” numeric computation rather than exact arithmetic, while clinical gains from incorporating laboratory values are task-dependent. This suggests that robustness and deployability often outweigh maximal numeric precision in practice, motivating hybrid token-based approaches as a practical default.

Social Aspects · Accountability, Transparency, and Interpretability

André Duarte, Brian Tufts, Aditya Oke, Fei Fang, Arlindo Oliveira, Lei Li

*How can we distinguish whether a peer review was written by a human or generated by an AI model?* We argue that, in this setting, authorship should not be attributed solely from the textual features of a review, but also from the ideas, judgments, and claims it expresses. To this end, we propose Sem-Detect, an authorship detection method for peer reviews that operationalizes this principle by combining textual features with claim-level semantic analysis. Sem-Detect compares a target review against multiple AI-generated reviews of the same paper, leveraging the observation that different AI models tend to converge on similar points, while human reviewers introduce more unique and diverse ones. As a result, Sem-Detect is able to distinguish fully AI-generated reviews from authentic human-written ones, including those that have been refined using an LLM but still reflect human judgment. Across a dataset of over 20,000 peer reviews from ICLR and NeurIPS conferences, Sem-Detect improves over the strongest prior detector by 36.5% in TPR@1% FPR in the binary setting. More importantly, in the three-class scenario, we empirically show that LLM refinement preserves the semantic signals of human reviews, which remain distinct from the patterns exhibited by fully AI-generated text; as a result, fewer than 3.5% of LLM-refined human reviews are misclassified as AI-generated.

Deep Learning · Generative Models and Autoencoders

Ziseok Lee, Minyeong Hwang, Sanghyun Jo, Wooyeol Lee, Jihyung Ko, Young Bin Park, Jae-Mun Choi, Eunho Yang, Kyungsu Kim

Inference-time steering adapts pretrained diffusion and flow models to new tasks without retraining, often utilizing ratio-of-densities constructions that reweight time-indexed marginals with fixed exponents. We identify Marginal Path Collapse, a failure mode in which the intermediate density defined by such compositions becomes non-normalizable despite valid endpoints. This collapse can arise when composing heterogeneous experts trained with mismatched noise schedules (and/or negative exponents / partial supports). To address this, we provide (i) a necessary-and-sufficient Path Existence Criterion that characterizes when the composed intermediate densities are mathematically well-defined, and (ii) Adaptive path Correction with Exponents (ACE), which generalizes Feynman–Kac steering to support time-varying exponents. Our analysis reveals that ACE controls the quantile radius of the intermediate distributions, providing a theoretical mechanism for path stabilization observed in experiments. On flexible-pose scaffold decoration, a drug design task composed of de-novo, conformer, and protein-conditioned experts, ACE prevents collapse and significantly outperforms constant-exponent baselines. Furthermore, ACE improves attribute success rates in compositional image generation, establishing it as a general framework for compositional sampling.