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Deep Learning · Generative Models and Autoencoders

Xuyang Wang, Xinzhe Zhou, Xiaoming Duan, Jianping He

The trajectory prediction of N-body systems is of great significance and remains challenging with broad applications across various fields such as physics, chemistry and biology. Recent advances in generative models including flow matching and diffusion models have emerged as effective solutions to this problem, owing to their capacity to model the stochasticity and underlying distributions of complex system trajectories. However, existing approaches typically adopt trivial prior distributions that neglect the temporal correlations and spatial symmetries of N-body trajectories, which not only complicates the generation process but also limits model performance. To address these limitations, we propose GP-EquiFlow, an SE(3)-equivariant flow matching model incorporating vector-valued Gaussian processes. Based on observed trajectories, we employ vector-valued Gaussian processes to construct SE(3)-equivariant prior distributions, which exhibit enhanced consistency with the target data distribution in both spatial and temporal dynamics. Extensive experiments on N-body simulations and molecular dynamics demonstrate that the proposed GP-EquiFlow delivers more accurate predictions while requiring fewer sampling steps, underscoring the effectiveness of integrating Gaussian process-based SE(3)-equivariant prior distributions in geometric trajectory prediction.

Applications · Health / Medicine

Mehmet Yigit Balik, Harri Lähdesmäki

Single-cell RNA sequencing provides insights into gene expression at single-cell resolution, yet inferring temporal processes from these static snapshot measurements remains a fundamental challenge. Current approaches utilizing neural differential equations and flows are sensitive to overfitting and lack careful considerations of biological variability. In this work, we propose a generative framework that models population trends using a latent heteroscedastic Gaussian process (GP) approximated by Hilbert space methods. To address the absence of genuine cell trajectories, we leverage an optimal transport (OT) objective that aligns generated and observed population distributions. Our method explicitly captures biological heterogeneity by incorporating cell-specific latent time and cell type conditioning to disentangle temporal asynchrony and trajectories to different cell types. We demonstrate state-of-the-art performance on complex interpolation and extrapolation benchmarks and introduce a novel gradient-based strategy for inferring perturbation trajectories.

Deep Learning · Generative Models and Autoencoders

Yuehao Wang, Peihao Wang, Hanwen Jiang, Ziyi Yang, Qixing Huang, Zhangyang “Atlas” Wang

Diffusion models have shown remarkable performance on diverse generation tasks. Recent work finds that imposing representation alignment on the hidden states of diffusion networks can both facilitate training convergence and enhance sampling quality, yet the mechanism driving this synergy remains insufficiently understood. In this paper, we investigate the connection between self-supervised spectral representation learning and diffusion generative models through a shared perspective on perturbation kernels. On the diffusion side, samples (e.g., images, videos) are produced by reversing a stochastic noise-injection process specified by Gaussian kernels; on the spectral representation side, spectral embeddings emerge from contrasting positive and negative relations induced by random perturbation kernels. Motivated by this, we propose a self-supervised spectral representation alignment method to facilitate diffusion model training. In addition, we clarify how joint spectral learning can benefit diffusion training from a geometric perspective. Furthermore, we find that the optimization of the spectral alignment objective is in an equivalent form of diffusion score distillation in the representation space. Building on these findings, we integrate a spectral regularizer into diffusion training objectives to improve the performance of diffusion models on multiple datasets. Experiments across images and 3D point clouds show consistent gains in generation quality.

Deep Learning · Generative Models and Autoencoders

Xinya Chen, Christopher Wewer, Jiahao Xie, Xinting Hu, Jan Eric Lenssen

We present SemanticNVS, a camera-conditioned multi-view diffusion model for novel view synthesis (NVS), which improves generation quality and consistency by integrating pre-trained semantic feature extractors. Existing NVS methods perform well for views near the input view, however, they tend to generate semantically implausible and distorted images under long-range camera motion, revealing severe degradation. We speculate that this degradation is due to current models failing to fully understand their conditioning or intermediate generated scene content. Here, we propose to integrate pre-trained semantic feature extractors to incorporate stronger scene semantics as conditioning to achieve high-quality generation even at distant viewpoints. We investigate two different strategies, (1) warped semantic features and (2) an alternating scheme of understanding and generation at each denoising step. Experimental results on multiple datasets demonstrate the clear qualitative and quantitative (4.69%-15.26% in FID) improvement over state-of-the-art alternatives. Our codebase and trained models will be released upon acceptance of the paper.

General Machine Learning · Supervised Learning

Thibault Pautrel, François Portier

Gradient-based sufficient dimension reduction methods face a fundamental tradeoff: computing local gradients in the ambient space yields closed-form solutions but suffers from the curse of dimensionality, while iterative refinement in the projected space improves statistical efficiency at $O(n^2 p)$ cost per iteration. We show that minimizers of the Minimum Average Variance Estimation (MAVE) criterion recover the span of the regression function's gradients---the same target as the Outer Product of Gradients method---but through local regression in the projected space. We then reformulate MAVE as a Riemannian maximization problem on the Stiefel manifold and derive a closed-form gradient, enabling efficient stochastic optimization. The resulting algorithm, SMAVE, combines mini-batch Riemannian gradient ascent with adaptive $k$-nearest neighbor localization that evolves with the subspace estimate. On synthetic benchmarks, SMAVE matches or exceeds the accuracy of existing methods while running 10--50$\times$ faster; on real regression tasks, these gains translate to improved prediction with speedups exceeding three orders of magnitude.

Deep Learning · Foundation Models

Hongyu Ke, Jack Morris, Yongkang Liu, Satoshi Kitai, Kentaro Oguchi, Yi Ding, Haoxin Wang

State Space Models (SSMs) have emerged as a powerful and efficient alternative to Transformers, demonstrating linear-time complexity and exceptional sequence modeling capabilities. However, their application to vision tasks remains challenging. First, existing vision SSMs largely depend on manually designed fixed scanning methods to flatten image patches into sequences, which imposes predefined geometric structures and increases the complexity. Second, the broader adoption of vision SSMs is hindered in domains that require query-based interactions between distinct information streams. This is a result of the inherently causal and self-referential nature of SSMs designed for 1D sequence modeling tasks. This fusion mechanism is indispensable for critical perception tasks such as multi-view 3D fusion. To address these limitations, we propose Deformba, a context adaptive method that dynamically augments the spatial structural information while maintaining the linear complexity of SSMs. Deformba also allows multi-modal fusion, analogous to standard cross attention. To demonstrate the effectiveness and general applicability of Deformba, we test its performance on general 2D vision tasks such as image classification, object detection, instance segmentation, and semantic segmentation, as well as 3D vision tasks like BEV perception. Extensive experiments show that Deformba achieves strong performance across various visual perception benchmarks.

Theory · Deep Learning

Blanka Kövér, Alexandra Butoi, Anej Svete, Michael Hahn, Ryan Cotterell

Transformers consistently fail to learn certain simple functions such as Parity---which returns whether the input has an even number of ones---even when they can provably compute them with specific parameter settings. This gap between *learnability* and *expressivity* is particularly prominent for sensitive functions---functions whose output is likely to change if a single bit of the input is changed. While prior work has established that transformers exhibit a bias toward low-sensitivity functions, the precise mechanism underlying this bias remains poorly understood. To shed light onto this phenomenon, we study the geometry of transformers' parameter space. We show that sensitive functions---even when representable---occupy a vanishingly small region that random initialization is unlikely to reach. More specifically, we prove that randomly initialized transformers almost surely compute functions with many low-sensitivity inputs, where flipping a bit is unlikely to change the output. Our results provide a novel theoretical grounding for the empirical observation that transformers exhibit a strong bias toward low-sensitivity functions, shifting the focus from average sensitivity to the full *sensitivity profile*.

Applications · Time Series

Jie Yang, Yifan Hu, Yuante Li, Kexin Zhang, Kaize Ding, Philip Yu

Deep learning has achieved strong performance in Time Series Forecasting (TSF). However, we identify a critical representation paradox, termed Latent Chaos: models with accurate predictions often learn latent representations that are temporally disordered and lack continuity. We attribute this phenomenon to the dominant observation-space forecasting paradigm. Most TSF models minimize point-wise errors on noisy and partially observed data, which encourages shortcut solutions instead of the recovery of underlying system dynamics. To address this issue, we propose Latent Time Series Forecasting (LatentTSF), a novel paradigm that shifts TSF from observation regression to latent state prediction. Specifically, LatentTSF employs an AutoEncoder to project observations at each time step into a higher-dimensional latent state space. This expanded representation aims to capture underlying system variables and impose a smoother temporal structure. Forecasting is then performed entirely in the latent space, allowing the model to focus on learning structured temporal dynamics. Theoretical analysis demonstrates that our proposed latent objectives implicitly maximize mutual information between predicted latent states and ground-truth states and observations. Extensive experiments on widely-used benchmarks confirm that LatentTSF effectively mitigates latent chaos, achieving superior performance. Our code is available in [https://anonymous.4open.science/r/LatentTSF-CC99](https://anonymous.4open.science/r/LatentTSF-CC99).

Theory · Everything Else

Junxian Liu, Hao Zeng, Hongxin Wei

Conformal Prediction (CP) provides a statistical framework for uncertainty quantification that constructs prediction sets with coverage guarantees. While CP yields uncontrolled prediction set sizes, Backward Conformal Prediction (BCP) inverts this paradigm by enforcing a predefined upper bound on set size and estimating the resulting coverage guarantee. However, the looseness induced by Markov's inequality within the BCP framework causes a significant gap between the estimated coverage bound and the empirical coverage. In this work, we introduce ST-BCP, a novel method that introduces a data-dependent transformation of nonconformity scores to narrow the coverage gap. In particular, we develop a computable transformation and prove that it outperforms the baseline identity transformation. Extensive experiments demonstrate the effectiveness of our method, reducing the average coverage gap from 4.20\% to 1.12\% on common benchmarks.

Applications · Everything Else

Fei Wei, Daoyuan Chen, Ce Wang, Yilun Huang, Yushuo Chen, Xuchen Pan, Yaliang Li, Bolin Ding

Large language models (LLMs) are strong passive responders, but learning to proactively elicit information—asking the right questions and stopping at the right time—remains difficult. Existing approaches, such as optimizing turn-level attributes or relying on user simulators to generate training trajectories, often struggle with a persistent reality gap. We propose \texttt{Learn-to-Ask}, a simulator-free framework that learns proactive questioning policies directly from offline expert conversations. Our key insight is to leverage the \textbf{observed future} of each expert trajectory to derive dense, turn-level rewards that reflect expert long-horizon strategy, reducing policy learning to a sequence of supervised learning tasks that jointly enable LLMs to know \textbf{what to ask} and \textbf{when to stop}. To ensure the LLM-generated contents, such as reward fidelity and sampling quality, align with expectations, we further introduce an automated pipeline that calibrates the prompts with minimal human supervision. Across multiple datasets and model scales, \texttt{Learn-to-Ask} consistently improves proactive information-seeking behavior. We also report a large-scale real-world deployment where the trained agent surpasses an internal expert baseline under professional audit, which demonstrates the effectiveness of our framework and our rewards as a reality-validated proxy metric for LLM proactivity.

Probabilistic Methods · Bayesian Models and Methods

Theodore Papamarkou, Pierre Alquier, Matthias Bauer, Wray Buntine, Andrew Davison, Gintare Karolina Dziugaite, Maurizio Filippone, Andrew Y. K. Foong, Vincent Fortuin, Dimitris Fouskakis 等

LLMs excel at predictive tasks and complex reasoning tasks, but many high-value deployments rely on decisions under uncertainty, for example, which tool to call, which expert to consult, or how many resources to invest. While the usefulness and feasibility of Bayesian approaches remain unclear for LLM inference, this position paper argues that the control layer of an agentic AI system (that orchestrates LLMs and tools) is a clear case where Bayesian principles should shine. Bayesian decision theory provides a framework for agentic systems that can help to maintain beliefs over task-relevant latent quantities, to update these beliefs from observed agentic and human-AI interactions, and to choose actions. Making LLMs themselves explicitly Bayesian belief-updating engines remains computationally intensive and conceptually nontrivial as a general modeling target. In contrast, this paper argues that coherent decision-making requires Bayesian principles at the level of the agentic system, not necessarily the LLM agent parameters. This paper articulates practical properties for Bayesian control that fit modern agentic AI systems and human-AI collaboration, and provides concrete examples and design patterns to illustrate how calibrated beliefs and utility-aware policies can improve agentic AI orchestration.

Deep Learning · Large Language Models

Artem Vazhentsev, Lyudmila Rvanova, Gleb Kuzmin, Ekaterina Fadeeva, Ivan Lazichny, Alexander Panchenko, Maxim Panov, Mrinmaya Sachan, Preslav Nakov, Tim Baldwin 等

Recent progress in large language models (LLMs) has led to systems capable of producing text with remarkable fluency. However, these models are still prone to factual inaccuracies, often referred to as \``hallucinations''. One strategy to alleviate this issue is uncertainty quantification (UQ), but most existing approaches are computationally intensive or require supervision. In this work, we propose Recurrent Attention-based Uncertainty Quantification (RAUQ), an unsupervised and efficient framework for identifying hallucinations. The method leverages an observation about transformer attention behavior: when incorrect information is generated, certain ``uncertainty-aware'' attention heads, tend to reduce their focus on preceding tokens. RAUQ automatically detects these attention heads and combines their activation patterns with token-level confidence measures in a recurrent scheme, producing a sequence-level uncertainty estimate in just a single forward pass. Through experiments on twelve tasks spanning question answering, summarization, and translation across four different LLMs, we show that RAUQ consistently outperforms state-of-the-art UQ baselines. Importantly, it does so with minimal cost, less than 1% additional computation. Since it requires neither labeled data nor extensive parameter tuning, RAUQ serves as a lightweight, plug-and-play solution for real-time hallucination detection in white-box LLMs.

Applications · Health / Medicine

Silas Ruhrberg Estevez, Chris Chiu, Mihaela van der Schaar

Modern clinical practice relies on evidence-based guidelines implemented as compact scoring systems composed of a small number of interpretable decision rules. While machine-learning models achieve strong performance, many fail to translate into routine clinical use due to misalignment with workflow constraints such as memorability, auditability, and bedside execution. We argue that this gap arises not from insufficient predictive power, but from optimizing over model classes that are incompatible with guideline deployment. Deployable guidelines often take the form of unit-weighted clinical checklists, formed by thresholding the sum of binary rules, but learning such scores requires searching an exponentially large discrete space of possible rule sets. We introduce $\texttt{AgentScore}$, which performs semantically guided optimization in this space by using LLMs to propose candidate rules and a deterministic, data-grounded verification-and-selection loop to enforce statistical validity and deployability constraints. Across eight clinical prediction tasks, $\texttt{AgentScore}$ outperforms existing score-generation methods and achieves AUC comparable to more flexible interpretable models despite operating under stronger structural constraints. On two additional externally validated tasks, $\texttt{AgentScore}$ achieves higher discrimination than established guideline-based scores.

General Machine Learning · Representation Learning

Panagiotis Koromilas, Theodoros Giannakopoulos, Mihalis Nicolaou, Yannis Panagakis

Supervised classifier learning has a theoretical optimum — Neural Collapse (NC) — yet standard training does not reach it in practice. We trace this failure to a geometric limitation: cross-entropy is invariant to joint rescaling of features and weights, leaving radial degrees of freedom unconstrained and the loss landscape degenerate. Projecting optimization onto the unit hypersphere eliminates this degeneracy and exposes a hidden equivalence: normalized softmax classification and supervised contrastive learning are conceptually the same, both optimizing angular similarity to class prototypes. We formalize this unification by proving that supervised contrastive learning already produces an optimal classifier during training, the prototype classifier whose weights are given by class-wise feature means, rendering subsequent classifier learning through linear probing redundant. Building on this framework, we identify two computational bottlenecks that slow convergence to NC: the small effective negative set in classifier learning (limited to K class prototypes), and the coupling of competing optimization terms through a shared normalization. We address these with NTCE, which expands the negative set from K classes to M batch instances, and NONL, which normalizes only over negatives to decouple intra-class alignment from inter-class repulsion. Empirically, our methods surpass cross-entropy accuracy on four benchmarks including ImageNet-1K, achieve $\ge$95\% NC across all metrics, and yield consistent gains in transfer learning (+5.5\% mean relative improvement), long-tailed classification (up to +8.7\%), and robustness (lower mCE), while eliminating hours of post-hoc classifier training.

Social Aspects · Accountability, Transparency, and Interpretability

Panagiotis Koromilas, Andreas Demou, James Oldfield, Yannis Panagakis, Mihalis Nicolaou

Sparse autoencoders (SAEs) have emerged as a promising method for interpreting neural network representations by decomposing activations into sparse combinations of dictionary atoms. However, SAEs assume that features combine additively through linear reconstruction, an assumption that cannot capture compositional structure: linear models cannot distinguish whether "Starbucks" arises from the composition of "star" and "coffee" features or merely their co-occurrence. This forces SAEs to allocate monolithic features for compound concepts rather than decomposing them into interpretable constituents. We introduce PolySAE, which extends the SAE decoder with higher-order terms to model feature interactions while preserving the linear encoder essential for interpretability. Through low-rank tensor factorization on a shared projection subspace, PolySAE captures pairwise and triple feature interactions with small parameter overhead (3\% on GPT2). Across four language models and three SAE variants, PolySAE achieves an average improvement of approximately 8\% in probing F1 while maintaining comparable reconstruction error, and produces 2-10$\times$ larger Wasserstein distances between class-conditional feature distributions. Critically, learned interaction weights exhibit negligible correlation with co-occurrence frequency ($r = 0.06$ vs. $r = 0.82$ for SAE feature covariance), suggesting that polynomial terms capture compositional structure, such as morphological binding and phrasal composition, largely independent of surface statistics.

Deep Learning · Foundation Models

Tianbo Wang, Yuqing Ma, Lingyan Meng, Zhange Zhang, Kewei Liao, Jian Yang, Simin Li, Jinyang Guo, Xianglong Liu

Medical Large Vision-Language Models (Med-LVLMs) suffer from severe hallucinations, posing critical safety risks in clinical deployment. Editing LVLM activations has shown promise for mitigating hallucination with minimal cost. However, due to the requirements of medical domain expertise, existing methods struggle to capture imaging manifestations and diagnostic principles that are critical for clinical interpretation, thereby limiting their effectiveness. To address these limitations, we propose the first MEDical-oriented Activation Editing (MEDA) method by integrating Query-decisive Manifestation Steering (QMS) and Principle-driven Diagnosis Induction (PDI) to promote Med-LVLM's expertise elicitation. Specifically, QMS retrieves positive query-decisive imaging manifestations as trusted guidance for activation steering, while PDI constructs positive principle-embedded diagnostic prompts to induce expert-like clinical reasoning. Extensive experiments across six benchmarks and six LVLMs demonstrate that MEDA efficiently improves the response factuality with up to a 10.2\% gain on IU-Xray, while exhibiting strong generalization and few-shot robustness.

Chris Chiu, Simpson Zhang, Mihaela van der Schaar

Emerging agentic marketplaces provide the economic infrastructure for matching and coordinating the large amounts of AI agents used in agentic swarms. Unlike human workers, AI agents can operate on multiple jobs simultaneously, acquire skills rapidly, and labor without wage floors. These differences introduce a new segment of AI labor markets, where AI agents interact with each other at a much higher frequency than human markets. Yet we lack frameworks to understand how such markets behave in light of economic forces that shape labor markets, such as adverse selection and reputation dynamics. To explore this, we introduce AI-Work, a tractable, simulated gig economy where Large Language Model (LLM) agents compete for jobs, develop skills, and adapt their strategies under uncertainty and competitive pressure. Our experiments examine three domains of capabilities that successful agents possess: metacognition (accurate self-assessment of skills), competitive awareness (modeling rivals and market dynamics), and long-horizon strategic planning. Agents with these capabilities consistently achieve higher profits, reputations, and market share than competing agents. Through AI-Work, we hope to provide a foundation to explore the microeconomic properties of AI-only labour markets, and a conceptual framework to study the strategic reasoning capabilities of participating AI agents.

Applications · Everything Else

Jan Melechovsky, Ambuj Mehrish, Abhinaba Roy, Dorien Herremans

Music recordings often suffer from audio quality issues such as excessive reverberation, distortion, clipping, tonal imbalances, and a narrowed stereo image, especially when created in non-professional settings without specialized equipment or expertise. These problems are typically corrected using separate specialized tools and manual adjustments. In this paper, we introduce SonicMaster, the first unified generative model for music restoration and mastering that addresses a broad spectrum of audio artifacts with text-based control. SonicMaster is conditioned on natural language instructions to apply targeted enhancements, or can operate in an automatic mode for general restoration. To train this model, we construct the SonicMaster dataset, a large dataset of paired degraded and high-quality tracks by simulating common degradation types with nineteen degradation functions belonging to five enhancements groups: equalization, dynamics, reverb, amplitude, and stereo. Our approach leverages a flow-matching generative training paradigm to learn an audio transformation that maps degraded inputs to their cleaned, mastered versions guided by text prompts. Objective audio quality metrics demonstrate that SonicMaster significantly improves sound quality across all artifact categories. Furthermore, subjective listening tests confirm that listeners prefer SonicMaster’s enhanced outputs over other baselines. Demo samples are available through https://msonic793.github.io/SonicMaster/

Applications · Computer Vision

Ho Hin Lee, Quan Liu, Shunxing Bao, Yuankai Huo, Bennett Landman

Large kernel convolutions offer a scalable alternative to vision transformers for high-resolution 3D volumetric analysis, yet naïvely increasing kernel size often leads to optimization instability. Motivated by the spatial bias inherent in effective receptive fields (ERFs), we theoretically demonstrate that structurally re-parameterized blocks induce spatially varying learning rates that are crucial for convergence. Leveraging this insight, we introduce Rep3D, a framework that employs a lightweight modulation network to generate receptive-biased scaling masks, adaptively re-weighting kernel updates within a plain encoder architecture. This approach unifies spatial inductive bias with optimization-aware learning, avoiding the complexity of multi-branch designs while ensuring robust local-to-global convergence. Extensive evaluations on five 3D segmentation benchmarks demonstrate that Rep3D consistently outperforms state-of-the-art transformer and fixed-prior baselines.

Deep Learning · Foundation Models

Seunghan Lee

TabPFN has recently gained attention as a foundation model for tabular datasets, achieving strong performance by leveraging in-context learning on synthetic data. However, we find that TabPFN is vulnerable to label shift, often overfitting to the majority class in the training dataset. To address this limitation, we propose DistPFN, the first test-time posterior adjustment method designed for tabular foundation models. DistPFN rescales predicted class probabilities by downweighting the influence of the training prior (i.e., the class distribution of the context) and emphasizing the contribution of the model’s predicted posterior, without architectural modification or additional training. We further introduce DistPFN-T, which incorporates temperature scaling to adaptively control the adjustment strength based on the discrepancy between prior and posterior. We evaluate our methods on over 250 OpenML datasets, demonstrating substantial improvements for various TabPFN-based models in classification tasks under label shift, while maintaining strong performance in standard settings without label shift.