OpenRaiser/Intern-Atlas huggingface dataset:
CellCLIP - Learning Perturbation Effects in Cell Painting via Text-Guided Contrastive Learning
Venue: Conference NeurIPS 2025
Year: 2025

High-content screening (HCS) assays based on high-throughput microscopy techniques such as Cell Painting have enabled the interrogation of cells' morphological responses to perturbations at an unprecedented scale. The collection of such data promises to facilitate a better understanding of the relationships between different perturbations and their effects on cellular state. Towards achieving this goal, recent advances in cross-modal contrastive learning could, in theory, be leveraged to learn a unified latent space that aligns perturbations with their corresponding morphological effects. However, the application of such methods to HCS data is not straightforward due to substantial differences in the semantics of Cell Painting images compared to natural images, and the difficulty of representing different classes of perturbations (e.g., small molecule vs CRISPR gene knockout) in a single latent space. In response to these challenges, here we introduce CellCLIP, a cross-modal contrastive learning framework for HCS data. CellCLIP leverages pre-trained image encoders coupled with a novel channel encoding scheme to better capture relationships between different microscopy channels in image embeddings, along with natural language encoders for representing perturbations. Our framework outperforms current open-source models, demonstrating the best performance in both cross-modal retrieval and biologically meaningful downstream tasks while also achieving significant reductions in computation time.
T-SHIRT: Token-Selective Hierarchical Data Selection for Instruction Tuning
Venue: Conference NeurIPS 2025
Year: 2025

Instruction tuning is essential for Large Language Models (LLMs) to effectively follow user instructions. To improve training efficiency and reduce data redundancy, recent works use LLM-based scoring functions, e.g., Instruction-Following Difficulty (IFD), to select high-quality instruction-tuning data with scores above a threshold. While these data selection methods often lead to models that can match or even exceed the performance of models trained on the full datasets, we identify two key limitations: (i) they assess quality at the sample level, ignoring token-level informativeness; and (ii) they overlook the robustness of the scoring method, often selecting a sample due to superficial lexical features instead of its true quality. In this work, we propose Token-Selective HIeRarchical Data Selection for Instruction Tuning (T-SHIRT), a novel data selection framework that introduces a new scoring method to include only informative tokens in quality evaluation and also promotes robust and reliable samples whose neighbors also show high quality with less local inconsistencies. We demonstrate that models instruction-tuned on a curated dataset (only 5% of the original size) using T-SHIRT can outperform those trained on the entire large-scale dataset by up to 5.48 points on average across eight benchmarks. Across various LLMs and training set scales, our method consistently surpasses existing state-of-the-art data selection techniques, while also remaining both cost-effective and highly efficient. For instance, by using GPT-2 for score computation, we are able to process a dataset of 52k samples in 40 minutes on a single GPU. Our code is available at https://github.com/Dynamite321/T-SHIRT.
Temperature is All You Need for Generalization in Langevin Dynamics and other Markov Processes
Venue: Conference NeurIPS 2025
Year: 2025

We analyze the generalization gap (gap between the training and test errors) when training a potentially over-parametrized model using a Markovian stochastic training algorithm, initialized from some distribution $θ_0 \sim p_0$. We focus on Langevin dynamics with a positive temperature $β^{-1}$, i.e. gradient descent on a training loss $L$ with infinitesimal step size, perturbed with $β^{-1}$-variances Gaussian noise, and lightly regularized or bounded. There, we bound the generalization gap, at any time during training, by $\sqrt{(β\mathbb{E} L (θ_0) + \log(1/δ))/N}$ with probability $1-δ$ over the dataset, where $N$ is the sample size, and $\mathbb{E} L (θ_0) =O(1)$ with standard initialization scaling. In contrast to previous guarantees, we have no dependence on either training time or reliance on mixing, nor a dependence on dimensionality, gradient norms, or any other properties of the loss or model. This guarantee follows from a general analysis of any Markov process-based training that has a Gibbs-style stationary distribution. The proof is surprisingly simple, once we observe that the marginal distribution divergence from initialization remains bounded, as implied by a generalized second law of thermodynamics.
Eliciting Reasoning in Language Models with Cognitive Tools
Venue: Conference NeurIPS 2025
Year: 2025

The recent advent of reasoning models like OpenAI's o1 was met with excited speculation by the AI community about the mechanisms underlying these capabilities in closed models, followed by a rush of replication efforts, particularly from the open source community. These speculations were largely settled by the demonstration from DeepSeek-R1 that chains-of-thought and reinforcement learning (RL) can effectively replicate reasoning on top of base LLMs. However, it remains valuable to explore alternative methods for theoretically eliciting reasoning that could help elucidate the underlying mechanisms, as well as providing additional methods that may offer complementary benefits. Here, we build on the long-standing literature in cognitive psychology and cognitive architectures, which postulates that reasoning arises from the orchestrated, sequential execution of a set of modular, predetermined cognitive operations. Crucially, we implement this key idea within a modern agentic tool-calling framework. In particular, we endow an LLM with a small set of "cognitive tools" encapsulating specific reasoning operations, each executed by the LLM itself. Surprisingly, this simple strategy results in considerable gains in performance on standard mathematical reasoning benchmarks compared to base LLMs, for both closed and open-weight models. For instance, providing our "cognitive tools" to GPT-4.1 increases its pass@1 performance on AIME2024 from 32% to 53%, even surpassing the performance of o1-preview. In addition to its practical implications, this demonstration contributes to the debate regarding the role of post-training methods in eliciting reasoning in LLMs versus the role of inherent capabilities acquired during pre-training, and whether post-training merely uncovers these latent abilities.
Through the River: Understanding the Benefit of Schedule-Free Methods for Language Model Training
Venue: Conference NeurIPS 2025
Year: 2025

As both model and dataset sizes continue to scale rapidly, conventional pretraining strategies with fixed compute budgets-such as cosine learning rate schedules-are increasingly inadequate for large-scale training. Recent alternatives, including warmup-stable-decay (WSD) schedules and weight averaging, offer greater flexibility. However, WSD relies on explicit decay phases to track progress, while weight averaging addresses this limitation at the cost of additional memory. In search of a more principled and scalable alternative, we revisit the Schedule-Free (SF) method [Defazio et al., 2024], which has shown strong empirical performance across diverse settings. We show that SF-AdamW effectively navigates the "river" structure of the loss landscape without decay phases or auxiliary averaging, making it particularly suitable for continuously scaling training workloads. To understand this behavior, we conduct a theoretical and empirical analysis of SF dynamics, revealing that it implicitly performs weight averaging without memory overhead. Guided by this analysis, we propose a refined variant of SF that improves robustness to momentum and performs better under large batch sizes, addressing key limitations of the original method. Together, these results establish SF as a practical, scalable, and theoretically grounded approach for language model training.
Exploration from a Primal-Dual Lens: Value-Incentivized Actor-Critic Methods for Sample-Efficient Online RL
Venue: Conference NeurIPS 2025
Year: 2025

Online reinforcement learning (RL) with complex function approximations such as transformers and deep neural networks plays a significant role in the modern practice of artificial intelligence. Despite its popularity and importance, balancing the fundamental trade-off between exploration and exploitation remains a long-standing challenge; in particular, we are still in lack of efficient and practical schemes that are backed by theoretical performance guarantees. Motivated by recent developments in exploration via optimistic regularization, this paper provides an interpretation of the principle of optimism through the lens of primal-dual optimization. From this fresh perspective, we set forth a new value-incentivized actor-critic (VAC) method, which optimizes a single easy-to-optimize objective integrating exploration and exploitation -- it promotes state-action and policy estimates that are both consistent with collected data transitions and result in higher value functions. Theoretically, the proposed VAC method has near-optimal regret guarantees under linear Markov decision processes (MDPs) in both finite-horizon and infinite-horizon settings, which can be extended to the general function approximation setting under appropriate assumptions.
RoPECraft: Training-Free Motion Transfer with Trajectory-Guided RoPE Optimization on Diffusion Transformers
Venue: Conference NeurIPS 2025
Year: 2025

We propose RoPECraft, a training-free video motion transfer method for diffusion transformers that operates solely by modifying their rotary positional embeddings (RoPE). We first extract dense optical flow from a reference video, and utilize the resulting motion offsets to warp the complex-exponential tensors of RoPE, effectively encoding motion into the generation process. These embeddings are then further optimized during denoising time steps via trajectory alignment between the predicted and target velocities using a flow-matching objective. To keep the output faithful to the text prompt and prevent duplicate generations, we incorporate a regularization term based on the phase components of the reference video's Fourier transform, projecting the phase angles onto a smooth manifold to suppress high-frequency artifacts. Experiments on benchmarks reveal that RoPECraft outperforms all recently published methods, both qualitatively and quantitatively.
Nearly-Linear Time Private Hypothesis Selection with the Optimal Approximation Factor
Venue: Conference NeurIPS 2025
Year: 2025

Estimating the density of a distribution from its samples is a fundamental problem in statistics. Hypothesis selection addresses the setting where, in addition to a sample set, we are given $n$ candidate distributions -- referred to as hypotheses -- and the goal is to determine which one best describes the underlying data distribution. This problem is known to be solvable very efficiently, requiring roughly $O(\log n)$ samples and running in $\tilde{O}(n)$ time. The quality of the output is measured via the total variation distance to the unknown distribution, and the approximation factor of the algorithm determines how large this distance is compared to the optimal distance achieved by the best candidate hypothesis. It is known that $α= 3$ is the optimal approximation factor for this problem. We study hypothesis selection under the constraint of differential privacy. We propose a differentially private algorithm in the central model that runs in nearly-linear time with respect to the number of hypotheses, achieves the optimal approximation factor, and incurs only a modest increase in sample complexity, which remains polylogarithmic in $n$. This resolves an open question posed by [Bun, Kamath, Steinke, Wu, NeurIPS 2019]. Prior to our work, existing upper bounds required quadratic time.
Teaching Humans Subtle Differences with DIFFusion
Venue: Conference NeurIPS 2025
Year: 2025

Scientific expertise often requires recognizing subtle visual differences that remain challenging to articulate even for domain experts. We present a system that leverages generative models to automatically discover and visualize minimal discriminative features between categories while preserving instance identity. Our method generates counterfactual visualizations with subtle, targeted transformations between classes, performing well even in domains where data is sparse, examples are unpaired, and category boundaries resist verbal description. Experiments across six domains, including black hole simulations, butterfly taxonomy, and medical imaging, demonstrate accurate transitions with limited training data, highlighting both established discriminative features and novel subtle distinctions that measurably improved category differentiation. User studies confirm our generated counterfactuals significantly outperform traditional approaches in teaching humans to correctly differentiate between fine-grained classes, showing the potential of generative models to advance visual learning and scientific research.
Scalable Utility-Aware Multiclass Calibration
Venue: Conference NeurIPS 2025
Year: 2025

Ensuring that classifiers are well-calibrated, i.e., their predictions align with observed frequencies, is a minimal and fundamental requirement for classifiers to be viewed as trustworthy. Existing methods for assessing multiclass calibration often focus on specific aspects associated with prediction (e.g., top-class confidence, class-wise calibration) or utilize computationally challenging variational formulations. In this work, we study scalable \emph{evaluation} of multiclass calibration. To this end, we propose utility calibration, a general framework that measures the calibration error relative to a specific utility function that encapsulates the goals or decision criteria relevant to the end user. We demonstrate how this framework can unify and re-interpret several existing calibration metrics, particularly allowing for more robust versions of the top-class and class-wise calibration metrics, and, going beyond such binarized approaches, toward assessing calibration for richer classes of downstream utilities.
Diffusion Beats Autoregressive in Data-Constrained Settings
Venue: Conference NeurIPS 2025
Year: 2025

Autoregressive (AR) models have long dominated the landscape of large language models, driving progress across a wide range of tasks. Recently, diffusion-based language models have emerged as a promising alternative, though their advantages over AR models remain underexplored. In this paper, we systematically study masked diffusion models in data-constrained settings where training involves repeated passes over limited data and find that they significantly outperform AR models when compute is abundant but data is scarce. Diffusion models make better use of repeated data, achieving lower validation loss and superior downstream performance. We find new scaling laws for diffusion models and derive a closed-form expression for the critical compute threshold at which diffusion begins to outperform AR. Finally, we explain why diffusion models excel in this regime: their randomized masking objective implicitly trains over a rich distribution of token orderings, acting as an implicit data augmentation that AR's fixed left-to-right factorization lacks. Our results suggest that when data, not compute, is the bottleneck, diffusion models offer a compelling alternative to the standard AR paradigm. Our code is available at: https://diffusion-scaling.github.io.
Latent Space Factorization in LoRA
Venue: Conference NeurIPS 2025
Year: 2025

Low-rank adaptation (LoRA) is a widely used method for parameter-efficient finetuning. However, existing LoRA variants lack mechanisms to explicitly disambiguate task-relevant information within the learned low-rank subspace, potentially limiting downstream performance. We propose Factorized Variational Autoencoder LoRA (FVAE-LoRA), which leverages a VAE to learn two distinct latent spaces. Our novel Evidence Lower Bound formulation explicitly promotes factorization between the latent spaces, dedicating one latent space to task-salient features and the other to residual information. Extensive experiments on text, audio, and image tasks demonstrate that FVAE-LoRA consistently outperforms standard LoRA. Moreover, spurious correlation evaluations confirm that FVAE-LoRA better isolates task-relevant signals, leading to improved robustness under distribution shifts. Our code is publicly available at: https://github.com/idiap/FVAE-LoRA
Fully Dynamic Algorithms for Chamfer Distance
Venue: Conference NeurIPS 2025
Year: 2025

We study the problem of computing Chamfer distance in the fully dynamic setting, where two set of points $A, B \subset \mathbb{R}^{d}$, each of size up to $n$, dynamically evolve through point insertions or deletions and the goal is to efficiently maintain an approximation to $\mathrm{dist}_{\mathrm{CH}}(A,B) = \sum_{a \in A} \min_{b \in B} \textrm{dist}(a,b)$, where $\textrm{dist}$ is a distance measure. Chamfer distance is a widely used dissimilarity metric for point clouds, with many practical applications that require repeated evaluation on dynamically changing datasets, e.g., when used as a loss function in machine learning. In this paper, we present the first dynamic algorithm for maintaining an approximation of the Chamfer distance under the $\ell_p$ norm for $p \in \{1,2 \}$. Our algorithm reduces to approximate nearest neighbor (ANN) search with little overhead. Plugging in standard ANN bounds, we obtain $(1+ε)$-approximation in $\tilde{O}(ε^{-d})$ update time and $O(1/ε)$-approximation in $\tilde{O}(d n^{ε^2} ε^{-4})$ update time. We evaluate our method on real-world datasets and demonstrate that it performs competitively against natural baselines.
Robust Distortion-Free Watermark for Autoregressive Audio Generation Models
Venue: Conference NeurIPS 2025
Year: 2025

The rapid advancement of next-token-prediction models has led to widespread adoption across modalities, enabling the creation of realistic synthetic media. In the audio domain, while autoregressive speech models have propelled conversational interactions forward, the potential for misuse, such as impersonation in phishing schemes or crafting misleading speech recordings, has also increased. Security measures such as watermarking have thus become essential to ensuring the authenticity of digital media. Traditional statistical watermarking methods used for autoregressive language models face challenges when applied to autoregressive audio models, due to the inevitable ``retokenization mismatch'' - the discrepancy between original and retokenized discrete audio token sequences. To address this, we introduce Aligned-IS, a novel, distortion-free watermark, specifically crafted for audio generation models. This technique utilizes a clustering approach that treats tokens within the same cluster equivalently, effectively countering the retokenization mismatch issue. Our comprehensive testing on prevalent audio generation platforms demonstrates that Aligned-IS not only preserves the quality of generated audio but also significantly improves the watermark detectability compared to the state-of-the-art distortion-free watermarking adaptations, establishing a new benchmark in secure audio technology applications.
AltLoRA: Towards Better Gradient Approximation in Low-Rank Adaptation with Alternating Projections
Venue: Conference NeurIPS 2025
Year: 2025

Low-Rank Adaptation (LoRA) has emerged as an effective technique for reducing memory overhead in fine-tuning large language models. However, it often suffers from sub-optimal performance compared with full fine-tuning since the update is constrained in the low-rank space. Recent variants such as LoRA-Pro attempt to mitigate this by adjusting the gradients of the low-rank matrices to approximate the full gradient. However, LoRA-Pro's solution is not unique, and different solutions can lead to significantly varying performance in ablation studies. Besides, to incorporate momentum or adaptive optimization design, approaches like LoRA-Pro must first compute the equivalent gradient, causing a higher memory cost close to full fine-tuning. A key challenge remains in integrating momentum properly into the low-rank space with lower memory cost. In this work, we propose AltLoRA, an alternating projection method that avoids the difficulties in gradient approximation brought by the joint update design, meanwhile integrating momentum without higher memory complexity. Our theoretical analysis provides convergence guarantees and further shows that AltLoRA enables stable feature learning and robustness to transformation invariance. Extensive experiments across multiple tasks demonstrate that AltLoRA outperforms LoRA and its variants, narrowing the gap toward full fine-tuning while preserving superior memory efficiency.
Corporate Needs You to Find the Difference: Revisiting Submodular and Supermodular Ratio Optimization Problems
Venue: Conference NeurIPS 2025
Year: 2025

We study the problem of minimizing or maximizing the average value $ f(S)/|S| $ of a submodular or supermodular set function $ f: 2^V \to \mathbb{R} $ over non-empty subsets $ S \subseteq V $. This generalizes classical problems such as Densest Subgraph (DSG), Densest Supermodular Set (DSS), and Submodular Function Minimization (SFM). Motivated by recent applications, we introduce two broad formulations: Unrestricted Sparsest Submodular Set (USSS) and Unrestricted Densest Supermodular Set (UDSS), which allow for negative and non-monotone functions. We show that DSS, SFM, USSS, UDSS, and the Minimum Norm Point (MNP) problem are equivalent under strongly polynomial-time reductions, enabling algorithmic crossover. In particular, viewing these through the lens of the MNP in the base polyhedron, we connect Fujishige's theory with dense decomposition, and show that both Fujishige-Wolfe's algorithm and the heuristic \textsc{SuperGreedy++} act as universal solvers for all these problems, including sub-modular function minimization. Theoretically, we explain why \textsc{SuperGreedy++} is effective beyond DSS, including for tasks like submodular minimization and minimum $ s $-$ t $ cut. Empirically, we test several solvers, including the Fujishige-Wolfe algorithm on over 400 experiments across seven problem types and large-scale real/synthetic datasets. Surprisingly, general-purpose convex and flow-based methods outperform task-specific baselines, demonstrating that with the right framing, general optimization techniques can be both scalable and state-of-the-art for submodular and supermodular ratio problems.
Doubly Robust Alignment for Large Language Models
Venue: Conference NeurIPS 2025
Year: 2025

This paper studies reinforcement learning from human feedback (RLHF) for aligning large language models with human preferences. While RLHF has demonstrated promising results, many algorithms are highly sensitive to misspecifications in the underlying preference model (e.g., the Bradley-Terry model), the reference policy, or the reward function, resulting in undesirable fine-tuning. To address model misspecification, we propose a doubly robust preference optimization algorithm that remains consistent when either the preference model or the reference policy is correctly specified (without requiring both). Our proposal demonstrates superior and more robust performance than state-of-the-art algorithms, both in theory and in practice. The code is available at https://github.com/DRPO4LLM/DRPO4LLM