OpenRaiser/Intern-Atlas huggingface dataset:
Fantastic Features and Where to Find Them: A Probing Method to combine Features from Multiple Foundation Models
Venue: Conference NeurIPS 2025
Year: 2025

Foundation models (FMs) trained with different objectives and data learn diverse representations, making some more effective than others for specific downstream tasks. Existing adaptation strategies, such as parameter-efficient fine-tuning, focus on individual models and do not exploit the complementary strengths across models. Probing methods offer a promising alternative by extracting information from frozen models, but current techniques do not scale well with large feature sets and often rely on dataset-specific hyperparameter tuning. We propose Combined backBones (ComBo), a simple and scalable probing-based adapter that effectively integrates features from multiple models and layers. ComBo compresses activations from layers of one or more FMs into compact token-wise representations and processes them with a lightweight transformer for task-specific prediction. Crucially, ComBo does not require dataset-specific tuning or backpropagation through the backbone models. However, not all models are equally relevant for all tasks. To address this, we introduce a mechanism that leverages ComBo's joint multi-backbone probing to efficiently evaluate each backbone's task-relevance, enabling both practical model comparison and improved performance through selective adaptation. On the 19 tasks of the VTAB-1k benchmark, ComBo outperforms previous probing methods, matches or surpasses more expensive alternatives, such as distillation-based model merging, and enables efficient probing of tuned models. Our results demonstrate that ComBo offers a practical and general-purpose framework for combining diverse representations from multiple FMs.
Simplicity Prevails: Rethinking Negative Preference Optimization for LLM Unlearning
Venue: Conference NeurIPS 2025
Year: 2025

This work studies the problem of large language model (LLM) unlearning, aiming to remove unwanted data influences (e.g., copyrighted or harmful content) while preserving model utility. Despite the increasing demand for unlearning, a technically-grounded optimization framework is lacking. Gradient ascent (GA)-type methods, though widely used, are suboptimal as they reverse the learning process without controlling optimization divergence (i.e., deviation from the pre-trained state), leading to risks of over-forgetting and potential model collapse. Negative preference optimization (NPO) has been proposed to address this issue and is considered one of the state-of-the-art LLM unlearning approaches. In this work, we revisit NPO and identify another critical issue: reference model bias. This bias arises from using the reference model (i.e., the model prior to unlearning) to evaluate the unlearning success, which can compromise NPO's effectiveness. Specifically, it leads to (a) uneven allocation of optimization power across forget data with varying difficulty levels and (b) ineffective gradient weight smoothing during the early stages of unlearning optimization. To overcome these challenges, we propose a simple yet effective unlearning optimization framework, called SimNPO, showing that `simplicity' in removing the reliance on a reference model (through the lens of simple preference optimization) benefits unlearning. We provide deeper insights into SimNPO's advantages through an analysis based on mixtures of Markov chains. Extensive experiments further validate SimNPO's efficacy on benchmarks like TOFU and MUSE, as well as its robustness against relearning attacks. Codes are available at https://github.com/OPTML-Group/Unlearn-Simple.
On Fitting Flow Models with Large Sinkhorn Couplings
Venue: Conference NeurIPS 2025
Year: 2025

Flow models transform data gradually from one modality (e.g. noise) onto another (e.g. images). Such models are parameterized by a time-dependent velocity field, trained to fit segments connecting pairs of source and target points. When the pairing between source and target points is given, training flow models boils down to a supervised regression problem. When no such pairing exists, as is the case when generating data from noise, training flows is much harder. A popular approach lies in picking source and target points independently. This can, however, lead to velocity fields that are slow to train, but also costly to integrate at inference time. In theory, one would greatly benefit from training flow models by sampling pairs from an optimal transport (OT) measure coupling source and target, since this would lead to a highly efficient flow solving the Benamou and Brenier dynamical OT problem. In practice, recent works have proposed to sample mini-batches of $n$ source and $n$ target points and reorder them using an OT solver to form better pairs. These works have advocated using batches of size $n\approx 256$, and considered OT solvers that return couplings that are either sharp (using e.g. the Hungarian algorithm) or blurred (using e.g. entropic regularization, a.k.a. Sinkhorn). We follow in the footsteps of these works by exploring the benefits of increasing $n$ by three to four orders of magnitude, and look more carefully on the effect of the entropic regularization $\varepsilon$ used in the Sinkhorn algorithm. Our analysis is facilitated by new scale invariant quantities to report the sharpness of a coupling, while our sharded computations across multiple GPU or GPU nodes allow scaling up $n$. We show that in both synthetic and image generation tasks, flow models greatly benefit when fitted with large Sinkhorn couplings, with a low entropic regularization $\varepsilon$.
CAR-Flow: Condition-Aware Reparameterization Aligns Source and Target for Better Flow Matching
Venue: Conference NeurIPS 2025
Year: 2025

Conditional generative modeling aims to learn a conditional data distribution from samples containing data-condition pairs. For this, diffusion and flow-based methods have attained compelling results. These methods use a learned (flow) model to transport an initial standard Gaussian noise that ignores the condition to the conditional data distribution. The model is hence required to learn both mass transport and conditional injection. To ease the demand on the model, we propose Condition-Aware Reparameterization for Flow Matching (CAR-Flow) -- a lightweight, learned shift that conditions the source, the target, or both distributions. By relocating these distributions, CAR-Flow shortens the probability path the model must learn, leading to faster training in practice. On low-dimensional synthetic data, we visualize and quantify the effects of CAR-Flow. On higher-dimensional natural image data (ImageNet-256), equipping SiT-XL/2 with CAR-Flow reduces FID from 2.07 to 1.68, while introducing less than 0.6% additional parameters.
Technical Debt in In-Context Learning: Diminishing Efficiency in Long Context
Venue: Conference NeurIPS 2025
Year: 2025

Transformers have demonstrated remarkable in-context learning (ICL) capabilities, adapting to new tasks by simply conditioning on demonstrations without parameter updates. Compelling empirical and theoretical evidence suggests that ICL, as a general-purpose learner, could outperform task-specific models. However, it remains unclear to what extent the transformers optimally learn in-context compared to principled learning algorithms. To investigate this, we employ a meta ICL framework in which each prompt defines a distinctive regression task whose target function is drawn from a hierarchical distribution, requiring inference over both the latent model class and task-specific parameters. Within this setup, we benchmark sample complexity of ICL against principled learning algorithms, including the Bayes optimal estimator, under varying performance requirements. Our findings reveal a striking dichotomy: while ICL initially matches the efficiency of a Bayes optimal estimator, its efficiency significantly deteriorates in long context. Through an information-theoretic analysis, we show that the diminishing efficiency is inherent to ICL. These results clarify the trade-offs in adopting ICL as a universal problem solver, motivating a new generation of on-the-fly adaptive methods without the diminishing efficiency.
Causality-Induced Positional Encoding for Transformer-Based Representation Learning of Non-Sequential Features
Venue: Conference NeurIPS 2025
Year: 2025

Positional encoding is essential for supplementing transformer with positional information of tokens. Existing positional encoding methods demand predefined token/feature order, rendering them unsuitable for real-world data with non-sequential yet causally-related features. To address this limitation, we propose CAPE, a novel method that identifies underlying causal structure over non-sequential features as a weighted directed acyclic graph (DAG) using generalized structural equation modeling. The DAG is then embedded in hyperbolic space where its geometric structure is well-preserved using a hyperboloid model-based approach that effectively captures two important causal graph properties (causal strength & causal specificity). This step yields causality-aware positional encodings for the features, which are converted into their rotary form for integrating with transformer's self-attention mechanism. Theoretical analysis reveals that CAPE-generated rotary positional encodings possess three valuable properties for enhanced self-attention, including causal distance-induced attenuation, causal generality-induced attenuation, and robustness to positional disturbances. We evaluate CAPE over both synthetic and real-word datasets, empirically demonstrating its theoretical properties and effectiveness in enhancing transformer for data with non-sequential features. Our code is available at https://github.com/Catchxu/CAPE.
Training-Free Constrained Generation With Stable Diffusion Models
Venue: Conference NeurIPS 2025
Year: 2025

Stable diffusion models represent the state-of-the-art in data synthesis across diverse domains and hold transformative potential for applications in science and engineering, e.g., by facilitating the discovery of novel solutions and simulating systems that are computationally intractable to model explicitly. While there is increasing effort to incorporate physics-based constraints into generative models, existing techniques are either limited in their applicability to latent diffusion frameworks or lack the capability to strictly enforce domain-specific constraints. To address this limitation this paper proposes a novel integration of stable diffusion models with constrained optimization frameworks, enabling the generation of outputs satisfying stringent physical and functional requirements. The effectiveness of this approach is demonstrated through material design experiments requiring adherence to precise morphometric properties, challenging inverse design tasks involving the generation of materials inducing specific stress-strain responses, and copyright-constrained content generation tasks. All code has been released at https://github.com/RAISELab-atUVA/Constrained-Stable-Diffusion.
Power Lines: Scaling laws for weight decay and batch size in LLM pre-training
Venue: Conference NeurIPS 2025
Year: 2025

Efficient LLM pre-training requires well-tuned hyperparameters (HPs), including learning rate $η$ and weight decay $λ$. We study scaling laws for HPs: formulas for how to scale HPs as we scale model size N, dataset size D, and batch size B. Recent work suggests the AdamW timescale, $τ= B/(ηλD)$, should remain constant across training settings, and we verify the implication that optimal $λ$ scales linearly with B, for a fixed N and D. However, as N and D scale, we show optimal $τ$ obeys a precise power law in the tokens-per-parameter ratio, D/N. This law thus provides a method to accurately predict $λ$opt in advance of large-scale training. We also study scaling laws for optimal batch size Bopt (the B enabling lowest loss at a given N,D) and critical batch size Bcrit (the B beyond which further data parallelism becomes ineffective). In contrast to prior work, we find both Bopt and Bcrit scale as power laws in D, independent of model size, N. Finally, we analyze how these findings inform the real-world selection of Pareto-optimal N and D under dual training time and compute objectives. All experiments were run on Cerebras CS-3 systems.
No, of Course I Can! Deeper Fine-Tuning Attacks That Bypass Token-Level Safety Mechanisms
Venue: Conference NeurIPS 2025
Year: 2025

Leading language model (LM) providers like OpenAI and Anthropic allow customers to fine-tune frontier LMs for specific use cases. To prevent abuse, these providers apply filters to block fine-tuning on overtly harmful data. In this setting, we make three contributions: First, while past work has shown that safety alignment is "shallow", we correspondingly demonstrate that existing fine-tuning attacks are shallow -- attacks target only the first several tokens of the model response, and consequently can be blocked by generating the first several response tokens with an aligned model. Second, we conceptually illustrate how to make attacks deeper by introducing a new fine-tuning attack that trains models to first refuse harmful requests before answering them; this "refuse-then-comply" strategy bypasses shallow defenses and produces harmful responses that evade output filters. Third, we demonstrate the potency of our new fine-tuning attack by jailbreaking both open-source models equipped with defenses and production models, achieving attack success rates of 57% and 72% against GPT-4o and Claude Haiku, respectively. Our attack received a $2000 bug bounty from OpenAI and was acknowledged as a vulnerability by Anthropic. Our work undermines the notion that models are safe because they initially refuse harmful requests and broadens awareness of the scope of attacks that face production fine-tuning APIs.
Optimal Policy Minimum Bayesian Risk
Venue: Conference NeurIPS 2025
Year: 2025

Inference scaling helps LLMs solve complex reasoning problems through extended runtime computation. On top of long chain-of-thought (long-CoT) models, purely inference-time techniques such as best-of-N (BoN) sampling, majority voting, or more generally, minimum Bayes risk decoding (MBRD), can further improve LLM accuracy by generating multiple candidate solutions and aggregating over them. These methods typically leverage additional signals in the form of reward models and risk/similarity functions that compare generated samples, e.g., exact match in some normalized space or standard similarity metrics such as Rouge. Here we present a novel method for incorporating reward and risk/similarity signals into MBRD. Based on the concept of optimal policy in KL-controlled reinforcement learning, our framework provides a simple and well-defined mechanism for leveraging such signals, offering several advantages over traditional inference-time methods: higher robustness, improved accuracy, and well-understood asymptotic behavior. In addition, it allows for the development of a sample-efficient variant of MBRD that can adjust the number of samples to generate according to the difficulty of the problem, without relying on majority vote counts. We empirically demonstrate the advantages of our approach on math (MATH-$500$) and coding (HumanEval) tasks using recent open-source models. We also present a comprehensive analysis of its accuracy-compute trade-offs.
BioReason: Incentivizing Multimodal Biological Reasoning within a DNA-LLM Model
Venue: Conference NeurIPS 2025
Year: 2025

Unlocking deep and interpretable biological reasoning from complex genomic data remains a major AI challenge limiting scientific progress. While current DNA foundation models excel at representing sequences, they struggle with multi-step reasoning and lack transparent, biologically meaningful explanations. BioReason addresses this by tightly integrating a DNA foundation model with a large language model (LLM), enabling the LLM to directly interpret and reason over genomic information. Through supervised fine-tuning and reinforcement learning, BioReason learns to produce logical, biologically coherent deductions. It achieves major performance gains, boosting KEGG-based disease pathway prediction accuracy from 86% to 98% and improving variant effect prediction by an average of 15% over strong baselines. BioReason can reason over unseen biological entities and explain its decisions step by step, offering a transformative framework for interpretable, mechanistic AI in biology. All data, code, and checkpoints are available at https://github.com/bowang-lab/BioReason
Aligning Evaluation with Clinical Priorities: Calibration, Label Shift, and Error Costs
Venue: Conference NeurIPS 2025
Year: 2025

Machine learning-based decision support systems are increasingly deployed in clinical settings, where probabilistic scoring functions are used to inform and prioritize patient management decisions. However, widely used scoring rules, such as accuracy and AUC-ROC, fail to adequately reflect key clinical priorities, including calibration, robustness to distributional shifts, and sensitivity to asymmetric error costs. In this work, we propose a principled yet practical evaluation framework for selecting calibrated thresholded classifiers that explicitly accounts for the uncertainty in class prevalences and domain-specific cost asymmetries often found in clinical settings. Building on the theory of proper scoring rules, particularly the Schervish representation, we derive an adjusted variant of cross-entropy (log score) that averages cost-weighted performance over clinically relevant ranges of class balance. The resulting evaluation is simple to apply, sensitive to clinical deployment conditions, and designed to prioritize models that are both calibrated and robust to real-world variations.
Anti-Aliased 2D Gaussian Splatting
Venue: Conference NeurIPS 2025
Year: 2025

2D Gaussian Splatting (2DGS) has recently emerged as a promising method for novel view synthesis and surface reconstruction, offering better view-consistency and geometric accuracy than volumetric 3DGS. However, 2DGS suffers from severe aliasing artifacts when rendering at different sampling rates than those used during training, limiting its practical applications in scenarios requiring camera zoom or varying fields of view. We identify that these artifacts stem from two key limitations: the lack of frequency constraints in the representation and an ineffective screen-space clamping approach. To address these issues, we present AA-2DGS, an anti-aliased formulation of 2D Gaussian Splatting that maintains its geometric benefits while significantly enhancing rendering quality across different scales. Our method introduces a world-space flat smoothing kernel that constrains the frequency content of 2D Gaussian primitives based on the maximal sampling frequency from training views, effectively eliminating high-frequency artifacts when zooming in. Additionally, we derive a novel object-space Mip filter by leveraging an affine approximation of the ray-splat intersection mapping, which allows us to efficiently apply proper anti-aliasing directly in the local space of each splat.
SPOT-Trip: Dual-Preference Driven Out-of-Town Trip Recommendation
Venue: Conference NeurIPS 2025
Year: 2025

Out-of-town trip recommendation aims to generate a sequence of Points of Interest (POIs) for users traveling from their hometowns to previously unvisited regions based on personalized itineraries, e.g., origin, destination, and trip duration. Modeling the complex user preferences--which often exhibit a two-fold nature of static and dynamic interests--is critical for effective recommendations. However, the sparsity of out-of-town check-in data presents significant challenges in capturing such user preferences. Meanwhile, existing methods often conflate the static and dynamic preferences, resulting in suboptimal performance. In this paper, we for the first time systematically study the problem of out-of-town trip recommendation. A novel framework SPOT-Trip is proposed to explicitly learns the dual static-dynamic user preferences. Specifically, to handle scarce data, we construct a POI attribute knowledge graph to enrich the semantic modeling of users' hometown and out-of-town check-ins, enabling the static preference modeling through attribute relation-aware aggregation. Then, we employ neural ordinary differential equations (ODEs) to capture the continuous evolution of latent dynamic user preferences and innovatively combine a temporal point process to describe the instantaneous probability of each preference behavior. Further, a static-dynamic fusion module is proposed to merge the learned static and dynamic user preferences. Extensive experiments on real data offer insight into the effectiveness of the proposed solutions, showing that SPOT-Trip achieves performance improvement by up to 17.01%.
A Data-Driven Prism: Multi-View Source Separation with Diffusion Model Priors
Venue: Conference NeurIPS 2025
Year: 2025

A common challenge in the natural sciences is to disentangle distinct, unknown sources from observations. Examples of this source separation task include deblending galaxies in a crowded field, distinguishing the activity of individual neurons from overlapping signals, and separating seismic events from an ambient background. Traditional analyses often rely on simplified source models that fail to accurately reproduce the data. Recent advances have shown that diffusion models can directly learn complex prior distributions from noisy, incomplete data. In this work, we show that diffusion models can solve the source separation problem without explicit assumptions about the source. Our method relies only on multiple views, or the property that different sets of observations contain different linear transformations of the unknown sources. We show that our method succeeds even when no source is individually observed and the observations are noisy, incomplete, and vary in resolution. The learned diffusion models enable us to sample from the source priors, evaluate the probability of candidate sources, and draw from the joint posterior of the source distribution given an observation. We demonstrate the effectiveness of our method on a range of synthetic problems as well as real-world galaxy observations.
Two‑Stage Learning of Stabilizing Neural Controllers via Zubov Sampling and Iterative Domain Expansion
Venue: Conference NeurIPS 2025
Year: 2025

Learning-based neural network (NN) control policies have shown impressive empirical performance. However, obtaining stability guarantees and estimates of the region of attraction of these learned neural controllers is challenging due to the lack of stable and scalable training and verification algorithms. Although previous works in this area have achieved great success, much conservatism remains in their frameworks. In this work, we propose a novel two-stage training framework to jointly synthesize a controller and a Lyapunov function for continuous-time systems. By leveraging a Zubov-inspired region of attraction characterization to directly estimate stability boundaries, we propose a novel training-data sampling strategy and a domain-updating mechanism that significantly reduces the conservatism in training. Moreover, unlike existing works on continuous-time systems that rely on an SMT solver to formally verify the Lyapunov condition, we extend state-of-the-art neural network verifier $α,\!β$-CROWN with the capability of performing automatic bound propagation through the Jacobian of dynamical systems and a novel verification scheme that avoids expensive bisection. To demonstrate the effectiveness of our approach, we conduct numerical experiments by synthesizing and verifying controllers on several challenging nonlinear systems across multiple dimensions. We show that our training can yield region of attractions with volume $5 - 1.5\cdot 10^{5}$ times larger compared to the baselines, and our verification on continuous systems can be up to $40-10{,}000$ times faster compared to the traditional SMT solver dReal. Our code is available at https://github.com/Verified-Intelligence/Two-Stage_Neural_Controller_Training.