OpenRaiser/Intern-Atlas huggingface dataset:
Curly Flow Matching for Learning Non-gradient Field Dynamics
Venue: Conference NeurIPS 2025
Year: 2025

Modeling the transport dynamics of natural processes from population-level observations is a ubiquitous problem in the natural sciences. Such models rely on key assumptions about the underlying process in order to enable faithful learning of governing dynamics that mimic the actual system behavior. The de facto assumption in current approaches relies on the principle of least action that results in gradient field dynamics and leads to trajectories minimizing an energy functional between two probability measures. However, many real-world systems, such as cell cycles in single-cell RNA, are known to exhibit non-gradient, periodic behavior, which fundamentally cannot be captured by current state-of-the-art methods such as flow and bridge matching. In this paper, we introduce Curly Flow Matching (Curly-FM), a novel approach that is capable of learning non-gradient field dynamics by designing and solving a Schrödinger bridge problem with a non-zero drift reference process -- in stark contrast to typical zero-drift reference processes -- which is constructed using inferred velocities in addition to population snapshot data. We showcase Curly-FM by solving the trajectory inference problems for single cells, computational fluid dynamics, and ocean currents with approximate velocities. We demonstrate that Curly-FM can learn trajectories that better match both the reference process and population marginals. Curly-FM expands flow matching models beyond the modeling of populations and towards the modeling of known periodic behavior in physical systems. Our code repository is accessible at: https://github.com/kpetrovicc/curly-flow-matching.git
SAM-R1: Leveraging SAM for Reward Feedback in Multimodal Segmentation via Reinforcement Learning
Venue: Conference NeurIPS 2025
Year: 2025

Leveraging multimodal large models for image segmentation has become a prominent research direction. However, existing approaches typically rely heavily on manually annotated datasets that include explicit reasoning processes, which are costly and time-consuming to produce. Recent advances suggest that reinforcement learning (RL) can endow large models with reasoning capabilities without requiring such reasoning-annotated data. In this paper, we propose SAM-R1, a novel framework that enables multimodal large models to perform fine-grained reasoning in image understanding tasks. Our approach is the first to incorporate fine-grained segmentation settings during the training of multimodal reasoning models. By integrating task-specific, fine-grained rewards with a tailored optimization objective, we further enhance the model's reasoning and segmentation alignment. We also leverage the Segment Anything Model (SAM) as a strong and flexible reward provider to guide the learning process. With only 3k training samples, SAM-R1 achieves strong performance across multiple benchmarks, demonstrating the effectiveness of reinforcement learning in equipping multimodal models with segmentation-oriented reasoning capabilities.
Continuous Q-Score Matching: Diffusion Guided Reinforcement Learning for Continuous-Time Control
Venue: Conference NeurIPS 2025
Year: 2025

Reinforcement learning (RL) has achieved significant success across a wide range of domains, however, most existing methods are formulated in discrete time. In this work, we introduce a novel RL method for continuous-time control, where stochastic differential equations govern state-action dynamics. Departing from traditional value function-based approaches, our key contribution is the characterization of continuous-time Q-functions via a martingale condition and the linking of diffusion policy scores to the action gradient of a learned continuous Q-function by the dynamic programming principle. This insight motivates Continuous Q-Score Matching (CQSM), a score-based policy improvement algorithm. Notably, our method addresses a long-standing challenge in continuous-time RL: preserving the action-evaluation capability of Q-functions without relying on time discretization. We further provide theoretical closed-form solutions for linear-quadratic (LQ) control problems within our framework. Numerical results in simulated environments demonstrate the effectiveness of our proposed method and compare it to popular baselines.
Orthogonal Survival Learners for Estimating Heterogeneous Treatment Effects from Time-to-Event Data
Venue: Conference NeurIPS 2025
Year: 2025

Estimating heterogeneous treatment effects (HTEs) is crucial for personalized decision-making. However, this task is challenging in survival analysis, which includes time-to-event data with censored outcomes (e.g., due to study dropout). In this paper, we propose a toolbox of novel orthogonal survival learners to estimate HTEs from time-to-event data under censoring. Our learners have three main advantages: (i) we show that learners from our toolbox are guaranteed to be orthogonal and thus come with favorable theoretical properties; (ii) our toolbox allows for incorporating a custom weighting function, which can lead to robustness against different types of low overlap, and (iii) our learners are model-agnostic (i.e., they can be combined with arbitrary machine learning models). We instantiate the learners from our toolbox using several weighting functions and, as a result, propose various neural orthogonal survival learners. Some of these coincide with existing survival learners (including survival versions of the DR- and R-learner), while others are novel and further robust w.r.t. low overlap regimes specific to the survival setting (i.e., survival overlap and censoring overlap). We then empirically verify the effectiveness of our learners for HTE estimation in different low-overlap regimes through numerical experiments. In sum, we provide practitioners with a large toolbox of learners that can be used for randomized and observational studies with censored time-to-event data.
UMoE: Unifying Attention and FFN with Shared Experts
Venue: Conference NeurIPS 2025
Year: 2025

Sparse Mixture of Experts (MoE) architectures have emerged as a promising approach for scaling Transformer models. While initial works primarily incorporated MoE into feed-forward network (FFN) layers, recent studies have explored extending the MoE paradigm to attention layers to enhance model performance. However, existing attention-based MoE layers require specialized implementations and demonstrate suboptimal performance compared to their FFN-based counterparts. In this paper, we aim to unify MoE designs in attention and FFN layers by introducing a novel reformulation of the attention mechanism, that reveals an underlying FFN-like structure within attention modules. Our proposed architecture, UMoE, achieves superior performance through attention-based MoE layers while enabling efficient parameter sharing between FFN and attention components.
PRESCRIBE: Predicting Single-Cell Responses with Bayesian Estimation
Venue: Conference NeurIPS 2025
Year: 2025

In single-cell perturbation prediction, a central task is to forecast the effects of perturbing a gene unseen in the training data. The efficacy of such predictions depends on two factors: (1) the similarity of the target gene to those covered in the training data, which informs model (epistemic) uncertainty, and (2) the quality of the corresponding training data, which reflects data (aleatoric) uncertainty. Both factors are critical for determining the reliability of a prediction, particularly as gene perturbation is an inherently stochastic biochemical process. In this paper, we propose PRESCRIBE (PREdicting Single-Cell Response wIth Bayesian Estimation), a multivariate deep evidential regression framework designed to measure both sources of uncertainty jointly. Our analysis demonstrates that PRESCRIBE effectively estimates a confidence score for each prediction, which strongly correlates with its empirical accuracy. This capability enables the filtering of untrustworthy results, and in our experiments, it achieves steady accuracy improvements of over 3% compared to comparable baselines.
Scaling Laws for Optimal Data Mixtures
Venue: Conference NeurIPS 2025
Year: 2025

Large foundation models are typically trained on data from multiple domains, with the data mixture--the proportion of each domain used--playing a critical role in model performance. The standard approach to selecting this mixture relies on trial and error, which becomes impractical for large-scale pretraining. We propose a systematic method to determine the optimal data mixture for any target domain using scaling laws. Our approach accurately predicts the loss of a model of size $N$ trained with $D$ tokens and a specific domain weight vector $h$. We validate the universality of these scaling laws by demonstrating their predictive power in three distinct and large-scale settings: large language model (LLM), native multimodal model (NMM), and large vision models (LVM) pretraining. We further show that these scaling laws can extrapolate to new data mixtures and across scales: their parameters can be accurately estimated using a few small-scale training runs, and used to estimate the performance at larger scales and unseen domain weights. The scaling laws allow to derive the optimal domain weights for any target domain under a given training budget ($N$,$D$), providing a principled alternative to costly trial-and-error methods.
Generative RLHF-V: Learning Principles from Multi-modal Human Preference
Venue: Conference NeurIPS 2025
Year: 2025

Training multi-modal large language models (MLLMs) that align with human intentions is a long-term challenge. Traditional score-only reward models for alignment suffer from low accuracy, weak generalization, and poor interpretability, blocking the progress of alignment methods, e.g., reinforcement learning from human feedback (RLHF). Generative reward models (GRMs) leverage MLLMs' intrinsic reasoning capabilities to discriminate pair-wise responses, but their pair-wise paradigm makes it hard to generalize to learnable rewards. We introduce Generative RLHF-V, a novel alignment framework that integrates GRMs with multi-modal RLHF. We propose a two-stage pipeline: $\textbf{multi-modal generative reward modeling from RL}$, where RL guides GRMs to actively capture human intention, then predict the correct pair-wise scores; and $\textbf{RL optimization from grouped comparison}$, which enhances multi-modal RL scoring precision by grouped responses comparison. Experimental results demonstrate that, besides out-of-distribution generalization of RM discrimination, our framework improves 4 MLLMs' performance across 7 benchmarks by $18.1\%$, while the baseline RLHF is only $5.3\%$. We further validate that Generative RLHF-V achieves a near-linear improvement with an increasing number of candidate responses. Our code and models can be found at https://generative-rlhf-v.github.io.
Counterfactual reasoning: an analysis of in-context emergence
Venue: Conference NeurIPS 2025
Year: 2025

Large-scale neural language models exhibit remarkable performance in in-context learning: the ability to learn and reason about the input context on the fly. This work studies in-context counterfactual reasoning in language models, that is, the ability to predict consequences of a hypothetical scenario. We focus on a well-defined, synthetic linear regression task that requires noise abduction. Accurate prediction is based on (1) inferring an unobserved latent concept and (2) copying contextual noise from factual observations. We show that language models are capable of counterfactual reasoning. Further, we enhance existing identifiability results and reduce counterfactual reasoning for a broad class of functions to a transformation on in-context observations. In Transformers, we find that self-attention, model depth and pre-training data diversity drive performance. Moreover, we provide mechanistic evidence that the latent concept is linearly represented in the residual stream and we introduce designated \textit{noise abduction heads} central to performing counterfactual reasoning. Lastly, our findings extend to counterfactual reasoning under SDE dynamics and reflect that Transformers can perform noise abduction on sequential data, providing preliminary evidence on the potential for counterfactual story generation. Our code is available under https://github.com/mrtzmllr/iccr.
PhysioWave: A Multi-Scale Wavelet-Transformer for Physiological Signal Representation
Venue: Conference NeurIPS 2025
Year: 2025

Physiological signals are often corrupted by motion artifacts, baseline drift, and other low-SNR disturbances, which pose significant challenges for analysis. Additionally, these signals exhibit strong non-stationarity, with sharp peaks and abrupt changes that evolve continuously, making them difficult to represent using traditional time-domain or filtering methods. To address these issues, a novel wavelet-based approach for physiological signal analysis is presented, aiming to capture multi-scale time-frequency features in various physiological signals. Leveraging this technique, two large-scale pretrained models specific to EMG and ECG are introduced for the first time, achieving superior performance and setting new baselines in downstream tasks. Additionally, a unified multi-modal framework is constructed by integrating pretrained EEG model, where each modality is guided through its dedicated branch and fused via learnable weighted fusion. This design effectively addresses challenges such as low signal-to-noise ratio, high inter-subject variability, and device mismatch, outperforming existing methods on multi-modal tasks. The proposed wavelet-based architecture lays a solid foundation for analysis of diverse physiological signals, while the multi-modal design points to next-generation physiological signal processing with potential impact on wearable health monitoring, clinical diagnostics, and broader biomedical applications. Code and data are available at: github.com/ForeverBlue816/PhysioWave
Infrequent Exploration in Linear Bandits
Venue: Conference NeurIPS 2025
Year: 2025

We study the problem of infrequent exploration in linear bandits, addressing a significant yet overlooked gap between fully adaptive exploratory methods (e.g., UCB and Thompson Sampling), which explore potentially at every time step, and purely greedy approaches, which require stringent diversity assumptions to succeed. Continuous exploration can be impractical or unethical in safety-critical or costly domains, while purely greedy strategies typically fail without adequate contextual diversity. To bridge these extremes, we introduce a simple and practical framework, INFEX, explicitly designed for infrequent exploration. INFEX executes a base exploratory policy according to a given schedule while predominantly choosing greedy actions in between. Despite its simplicity, our theoretical analysis demonstrates that INFEX achieves instance-dependent regret matching standard provably efficient algorithms, provided the exploration frequency exceeds a logarithmic threshold. Additionally, INFEX is a general, modular framework that allows seamless integration of any fully adaptive exploration method, enabling wide applicability and ease of adoption. By restricting intensive exploratory computations to infrequent intervals, our approach can also enhance computational efficiency. Empirical evaluations confirm our theoretical findings, showing state-of-the-art regret performance and runtime improvements over existing methods.
One SPACE to Rule Them All: Jointly Mitigating Factuality and Faithfulness Hallucinations in LLMs
Venue: Conference NeurIPS 2025
Year: 2025

LLMs have demonstrated unprecedented capabilities in natural language processing, yet their practical deployment remains hindered by persistent factuality and faithfulness hallucinations. While existing methods address these hallucination types independently, they inadvertently induce performance trade-offs, as interventions targeting one type often exacerbate the other. Through empirical and theoretical analysis of activation space dynamics in LLMs, we reveal that these hallucination categories share overlapping subspaces within neural representations, presenting an opportunity for concurrent mitigation. To harness this insight, we propose SPACE, a unified framework that jointly enhances factuality and faithfulness by editing shared activation subspaces. SPACE establishes a geometric foundation for shared subspace existence through dual-task feature modeling, then identifies and edits these subspaces via a hybrid probe strategy combining spectral clustering and attention head saliency scoring. Experimental results across multiple benchmark datasets demonstrate the superiority of our approach.
Benford’s Curse: Tracing Digit Bias to Numerical Hallucination in LLMs
Venue: Conference NeurIPS 2025
Year: 2025

Large Language Models (LLMs) exhibit impressive performance on complex reasoning tasks, yet they frequently fail on basic numerical problems, producing incorrect outputs. Inspired by Benford's Law, a statistical pattern in which lower digits occur more frequently as leading digits, we hypothesize that the skewed digit distributions in web-collected corpora may be learned by LLMs during pretraining, leading to biased numerical generation. To investigate the hypothesis, we first examine whether digits frequencies in pretraining corpus (OLMo2) follows Benford's law. We then construct an evaluation benchmark in which the ground-truth digits are uniformly distributed within each of the seven numerical reasoning tasks. Our evaluation results demonstrate that leading open-source LLMs show a consistent pattern of digit bias that resembles Benford's law. Through logit-lens tracing and neuron-level dissection, we identify that this bias arises predominantly from a small subset of highly digit-selective feed-forward network (FFN) neurons in the deeper layers. Finally, we demonstrate that pruning these neurons mitigates imbalanced overgeneration and partially corrects erroneous outputs, providing causal evidence that fine-grained pretraining digit bias can propagate into model behavior. Our findings reveal a fundamental connection between corpus-level statistics and symbolic failure modes in LLMs, offering a new lens for diagnosing and mitigating hallucinations in numerical tasks.
Treatment Effect Estimation for Optimal Decision-Making
Venue: Conference NeurIPS 2025
Year: 2025

Decision-making across various fields, such as medicine, heavily relies on conditional average treatment effects (CATEs). Practitioners commonly make decisions by checking whether the estimated CATE is positive, even though the decision-making performance of modern CATE estimators is poorly understood from a theoretical perspective. In this paper, we study optimal decision-making based on two-stage CATE estimators (e.g., DR-learner), which are considered state-of-the-art and widely used in practice. We prove that, while such estimators may be optimal for estimating CATE, they can be suboptimal when used for decision-making. Intuitively, this occurs because such estimators prioritize CATE accuracy in regions far away from the decision boundary, which is ultimately irrelevant to decision-making. As a remedy, we propose a novel two-stage learning objective that retargets the CATE to balance CATE estimation error and decision performance. We then propose a neural method that optimizes an adaptively-smoothed approximation of our learning objective. Finally, we confirm the effectiveness of our method both empirically and theoretically. In sum, our work is the first to show how two-stage CATE estimators can be adapted for optimal decision-making.
Computational Algebra with Attention: Transformer Oracles for Border Basis Algorithms
Venue: Conference NeurIPS 2025
Year: 2025

Solving systems of polynomial equations, particularly those with finitely many solutions, is a crucial challenge across many scientific fields. Traditional methods like Gröbner and Border bases are fundamental but suffer from high computational costs, which have motivated recent Deep Learning approaches to improve efficiency, albeit at the expense of output correctness. In this work, we introduce the Oracle Border Basis Algorithm, the first Deep Learning approach that accelerates Border basis computation while maintaining output guarantees. To this end, we design and train a Transformer-based oracle that identifies and eliminates computationally expensive reduction steps, which we find to dominate the algorithm's runtime. By selectively invoking this oracle during critical phases of computation, we achieve substantial speedup factors of up to 3.5x compared to the base algorithm, without compromising the correctness of results. To generate the training data, we develop a sampling method and provide the first sampling theorem for border bases. We construct a tokenization and embedding scheme tailored to monomial-centered algebraic computations, resulting in a compact and expressive input representation, which reduces the number of tokens to encode an $n$-variate polynomial by a factor of $O(n)$. Our learning approach is data efficient, stable, and a practical enhancement to traditional computer algebra algorithms and symbolic computation.
Iterative Self-Incentivization Empowers Large Language Models as Agentic Searchers
Venue: Conference NeurIPS 2025
Year: 2025

Large language models (LLMs) have been widely integrated into information retrieval to advance traditional techniques. However, effectively enabling LLMs to seek accurate knowledge in complex tasks remains a challenge due to the complexity of multi-hop queries as well as the irrelevant retrieved content. To address these limitations, we propose EXSEARCH, an agentic search framework, where the LLM learns to retrieve useful information as the reasoning unfolds through a self-incentivized process. At each step, the LLM decides what to retrieve (thinking), triggers an external retriever (search), and extracts fine-grained evidence (recording) to support next-step reasoning. To enable LLM with this capability, EXSEARCH adopts a Generalized Expectation-Maximization algorithm. In the E-step, the LLM generates multiple search trajectories and assigns an importance weight to each; the M-step trains the LLM on them with a re-weighted loss function. This creates a self-incentivized loop, where the LLM iteratively learns from its own generated data, progressively improving itself for search. We further theoretically analyze this training process, establishing convergence guarantees. Extensive experiments on four knowledge-intensive benchmarks show that EXSEARCH substantially outperforms baselines, e.g., +7.8% improvement on exact match score. Motivated by these promising results, we introduce EXSEARCH-Zoo, an extension that extends our method to broader scenarios, to facilitate future work.