OpenRaiser/Intern-Atlas huggingface dataset:
Rethinking Losses for Diffusion Bridge Samplers
Venue: Conference NeurIPS 2025
Year: 2025

Diffusion bridges are a promising class of deep-learning methods for sampling from unnormalized distributions. Recent works show that the Log Variance (LV) loss consistently outperforms the reverse Kullback-Leibler (rKL) loss when using the reparametrization trick to compute rKL-gradients. While the on-policy LV loss yields identical gradients to the rKL loss when combined with the log-derivative trick for diffusion samplers with non-learnable forward processes, this equivalence does not hold for diffusion bridges or when diffusion coefficients are learned. Based on this insight we argue that for diffusion bridges the LV loss does not represent an optimization objective that can be motivated like the rKL loss via the data processing inequality. Our analysis shows that employing the rKL loss with the log-derivative trick (rKL-LD) does not only avoid these conceptual problems but also consistently outperforms the LV loss. Experimental results with different types of diffusion bridges on challenging benchmarks show that samplers trained with the rKL-LD loss achieve better performance. From a practical perspective we find that rKL-LD requires significantly less hyperparameter optimization and yields more stable training behavior.
MS-BART: Unified Modeling of Mass Spectra and Molecules for Structure Elucidation
Venue: Conference NeurIPS 2025
Year: 2025

Mass spectrometry (MS) plays a critical role in molecular identification, significantly advancing scientific discovery. However, structure elucidation from MS data remains challenging due to the scarcity of annotated spectra. While large-scale pretraining has proven effective in addressing data scarcity in other domains, applying this paradigm to mass spectrometry is hindered by the complexity and heterogeneity of raw spectral signals. To address this, we propose MS-BART, a unified modeling framework that maps mass spectra and molecular structures into a shared token vocabulary, enabling cross-modal learning through large-scale pretraining on reliably computed fingerprint-molecule datasets. Multi-task pretraining objectives further enhance MS-BART's generalization by jointly optimizing denoising and translation task. The pretrained model is subsequently transferred to experimental spectra through finetuning on fingerprint predictions generated with MIST, a pre-trained spectral inference model, thereby enhancing robustness to real-world spectral variability. While finetuning alleviates the distributional difference, MS-BART still suffers molecular hallucination and requires further alignment. We therefore introduce a chemical feedback mechanism that guides the model toward generating molecules closer to the reference structure. Extensive evaluations demonstrate that MS-BART achieves SOTA performance across 5/12 key metrics on MassSpecGym and NPLIB1 and is faster by one order of magnitude than competing diffusion-based methods, while comprehensive ablation studies systematically validate the model's effectiveness and robustness.
TrajMamba: An Efficient and Semantic-rich Vehicle Trajectory Pre-training Model
Venue: Conference NeurIPS 2025
Year: 2025

Vehicle GPS trajectories record how vehicles move over time, storing valuable travel semantics, including movement patterns and travel purposes. Learning travel semantics effectively and efficiently is crucial for real-world applications of trajectory data, which is hindered by two major challenges. First, travel purposes are tied to the functions of the roads and points-of-interest (POIs) involved in a trip. Such information is encoded in textual addresses and descriptions and introduces heavy computational burden to modeling. Second, real-world trajectories often contain redundant points, which harm both computational efficiency and trajectory embedding quality. To address these challenges, we propose TrajMamba, a novel approach for efficient and semantically rich vehicle trajectory learning. TrajMamba introduces a Traj-Mamba Encoder that captures movement patterns by jointly modeling both GPS and road perspectives of trajectories, enabling robust representations of continuous travel behaviors. It also incorporates a Travel Purpose-aware Pre-training procedure to integrate travel purposes into the learned embeddings without introducing extra overhead to embedding calculation. To reduce redundancy in trajectories, TrajMamba features a Knowledge Distillation Pre-training scheme to identify key trajectory points through a learnable mask generator and obtain effective compressed trajectory embeddings. Extensive experiments on two real-world datasets and three downstream tasks show that TrajMamba outperforms state-of-the-art baselines in both efficiency and accuracy.
Enhancing Temporal Understanding in Video-LLMs through Stacked Temporal Attention in Vision Encoders
Venue: Conference NeurIPS 2025
Year: 2025

Despite significant advances in Multimodal Large Language Models (MLLMs), understanding complex temporal dynamics in videos remains a major challenge. Our experiments show that current Video Large Language Model (Video-LLM) architectures have critical limitations in temporal understanding, struggling with tasks that require detailed comprehension of action sequences and temporal progression. In this work, we propose a Video-LLM architecture that introduces stacked temporal attention modules directly within the vision encoder. This design incorporates a temporal attention in vision encoder, enabling the model to better capture the progression of actions and the relationships between frames before passing visual tokens to the LLM. Our results show that this approach significantly improves temporal reasoning and outperforms existing models in video question answering tasks, specifically in action recognition. We improve on benchmarks including VITATECS, MVBench, and Video-MME by up to +5.5%. By enhancing the vision encoder with temporal structure, we address a critical gap in video understanding for Video-LLMs. Project page and code are available at: https://alirasekh.github.io/STAVEQ2/.
ShapeEmbed: a self-supervised learning framework for 2D contour quantification
Venue: Conference NeurIPS 2025
Year: 2025

The shape of objects is an important source of visual information in a wide range of applications. One of the core challenges of shape quantification is to ensure that the extracted measurements remain invariant to transformations that preserve an object's intrinsic geometry, such as changing its size, orientation, and position in the image. In this work, we introduce ShapeEmbed, a self-supervised representation learning framework designed to encode the contour of objects in 2D images, represented as a Euclidean distance matrix, into a shape descriptor that is invariant to translation, scaling, rotation, reflection, and point indexing. Our approach overcomes the limitations of traditional shape descriptors while improving upon existing state-of-the-art autoencoder-based approaches. We demonstrate that the descriptors learned by our framework outperform their competitors in shape classification tasks on natural and biological images. We envision our approach to be of particular relevance to biological imaging applications.
Put CASH on Bandits: A Max K-Armed Problem for Automated Machine Learning
Venue: Conference NeurIPS 2025
Year: 2025

The Combined Algorithm Selection and Hyperparameter optimization (CASH) is a challenging resource allocation problem in the field of AutoML. We propose MaxUCB, a max k-armed bandit method to trade off exploring different model classes and conducting hyperparameter optimization. MaxUCB is specifically designed for the light-tailed and bounded reward distributions arising in this setting and, thus, provides an efficient alternative compared to classic max k-armed bandit methods assuming heavy-tailed reward distributions. We theoretically and empirically evaluate our method on four standard AutoML benchmarks, demonstrating superior performance over prior approaches. We make our code and data available at https://github.com/amirbalef/CASH_with_Bandits
Disentangled Representation Learning via Modular Compositional Bias
Venue: Conference NeurIPS 2025
Year: 2025

Recent disentangled representation learning (DRL) methods heavily rely on factor specific strategies-either learning objectives for attributes or model architectures for objects-to embed inductive biases. Such divergent approaches result in significant overhead when novel factors of variation do not align with prior assumptions, such as statistical independence or spatial exclusivity, or when multiple factors coexist, as practitioners must redesign architectures or objectives. To address this, we propose a compositional bias, a modular inductive bias decoupled from both objectives and architectures. Our key insight is that different factors obey distinct recombination rules in the data distribution: global attributes are mutually exclusive, e.g., a face has one nose, while objects share a common support (any subset of objects can co-exist). We therefore randomly remix latents according to factor-specific rules, i.e., a mixing strategy, and force the encoder to discover whichever factor structure the mixing strategy reflects through two complementary objectives: (i) a prior loss that ensures every remix decodes into a realistic image, and (ii) the compositional consistency loss introduced by Wiedemer et al. (arXiv:2310.05327), which aligns each composite image with its corresponding composite latent. Under this general framework, simply adjusting the mixing strategy enables disentanglement of attributes, objects, and even both, without modifying the objectives or architectures. Extensive experiments demonstrate that our method shows competitive performance in both attribute and object disentanglement, and uniquely achieves joint disentanglement of global style and objects. Code is available at https://github.com/whieya/Compositional-DRL.
FairImagen: Post-Processing for Bias Mitigation in Text-to-Image Models
Venue: Conference NeurIPS 2025
Year: 2025

Text-to-image diffusion models, such as Stable Diffusion, have demonstrated remarkable capabilities in generating high-quality and diverse images from natural language prompts. However, recent studies reveal that these models often replicate and amplify societal biases, particularly along demographic attributes like gender and race. In this paper, we introduce FairImagen (https://github.com/fuzihaofzh/FairImagen), a post-hoc debiasing framework that operates on prompt embeddings to mitigate such biases without retraining or modifying the underlying diffusion model. Our method integrates Fair Principal Component Analysis to project CLIP-based input embeddings into a subspace that minimizes group-specific information while preserving semantic content. We further enhance debiasing effectiveness through empirical noise injection and propose a unified cross-demographic projection method that enables simultaneous debiasing across multiple demographic attributes. Extensive experiments across gender, race, and intersectional settings demonstrate that FairImagen significantly improves fairness with a moderate trade-off in image quality and prompt fidelity. Our framework outperforms existing post-hoc methods and offers a simple, scalable, and model-agnostic solution for equitable text-to-image generation.
TreeSynth: Synthesizing Diverse Data from Scratch via Tree-Guided Subspace Partitioning
Venue: Conference NeurIPS 2025
Year: 2025

Model customization necessitates high-quality and diverse datasets, but acquiring such data remains time-consuming and labor-intensive. Despite the great potential of large language models (LLMs) for data synthesis, current approaches are constrained by limited seed data, model biases, and low-variation prompts, resulting in limited diversity and biased distributions with the increase of data scales. To tackle this challenge, we introduce TREESYNTH, a tree-guided subspace-based data synthesis approach inspired by decision trees. It constructs a spatial partitioning tree to recursively divide a task-specific full data space (i.e., root node) into numerous atomic subspaces (i.e., leaf nodes) with mutually exclusive and exhaustive attributes to ensure both distinctiveness and comprehensiveness before synthesizing samples within each atomic subspace. This globally dividing-and-synthesizing method finally collects subspace samples into a comprehensive dataset, effectively circumventing repetition and space collapse to ensure the diversity of large-scale data synthesis. Furthermore, the spatial partitioning tree enables sample allocation into atomic subspaces, allowing the rebalancing of existing datasets for more balanced and comprehensive distributions. Empirically, extensive experiments across diverse benchmarks consistently demonstrate the superior data diversity, model performance, and robust scalability of TREESYNTH compared to both human-crafted datasets and peer data synthesis methods, with an average performance gain reaching 10%. Besides, the consistent improvements of TREESYNTH-balanced datasets highlight its efficacious application to redistribute existing datasets for more comprehensive coverage and the induced performance enhancement. The code is available at https://github.com/cpa2001/TreeSynth.
Equilibrium Policy Generalization: A Reinforcement Learning Framework for Cross-Graph Zero-Shot Generalization in Pursuit-Evasion Games
Venue: Conference NeurIPS 2025
Year: 2025

Equilibrium learning in adversarial games is an important topic widely examined in the fields of game theory and reinforcement learning (RL). Pursuit-evasion game (PEG), as an important class of real-world games from the fields of robotics and security, requires exponential time to be accurately solved. When the underlying graph structure varies, even the state-of-the-art RL methods require recomputation or at least fine-tuning, which can be time-consuming and impair real-time applicability. This paper proposes an Equilibrium Policy Generalization (EPG) framework to effectively learn a generalized policy with robust cross-graph zero-shot performance. In the context of PEGs, our framework is generally applicable to both pursuer and evader sides in both no-exit and multi-exit scenarios. These two generalizability properties, to our knowledge, are the first to appear in this domain. The core idea of the EPG framework is to train an RL policy across different graph structures against the equilibrium policy for each single graph. To construct an equilibrium oracle for single-graph policies, we present a dynamic programming (DP) algorithm that provably generates pure-strategy Nash equilibrium with near-optimal time complexity. To guarantee scalability with respect to pursuer number, we further extend DP and RL by designing a grouping mechanism and a sequence model for joint policy decomposition, respectively. Experimental results show that, using equilibrium guidance and a distance feature proposed for cross-graph PEG training, the EPG framework guarantees desirable zero-shot performance in various unseen real-world graphs. Besides, when trained under an equilibrium heuristic proposed for the graphs with exits, our generalized pursuer policy can even match the performance of the fine-tuned policies from the state-of-the-art PEG methods.
DeCaFlow: A deconfounding causal generative model
Venue: Conference NeurIPS 2025
Year: 2025

We introduce DeCaFlow, a deconfounding causal generative model. Training once per dataset using just observational data and the underlying causal graph, DeCaFlow enables accurate causal inference on continuous variables under the presence of hidden confounders. Specifically, we extend previous results on causal estimation under hidden confounding to show that a single instance of DeCaFlow provides correct estimates for all causal queries identifiable with do-calculus, leveraging proxy variables to adjust for the causal effects when do-calculus alone is insufficient. Moreover, we show that counterfactual queries are identifiable as long as their interventional counterparts are identifiable, and thus are also correctly estimated by DeCaFlow. Our empirical results on diverse settings (including the Ecoli70 dataset, with 3 independent hidden confounders, tens of observed variables and hundreds of causal queries) show that DeCaFlow outperforms existing approaches, while demonstrating its out-of-the-box applicability to any given causal graph. An implementation can be found in https://github.com/aalmodovares/DeCaFlow
Hierarchical Frequency Tagging Probe (HFTP): A Unified Approach to Investigate Syntactic Structure Representations in Large Language Models and the Human Brain
Venue: Conference NeurIPS 2025
Year: 2025

Large Language Models (LLMs) demonstrate human-level or even superior language abilities, effectively modeling syntactic structures, yet the specific computational modules responsible remain unclear. A key question is whether LLM behavioral capabilities stem from mechanisms akin to those in the human brain. To address these questions, we introduce the Hierarchical Frequency Tagging Probe (HFTP), a tool that utilizes frequency-domain analysis to identify neuron-wise components of LLMs (e.g., individual Multilayer Perceptron (MLP) neurons) and cortical regions (via intracranial recordings) encoding syntactic structures. Our results show that models such as GPT-2, Gemma, Gemma 2, Llama 2, Llama 3.1, and GLM-4 process syntax in analogous layers, while the human brain relies on distinct cortical regions for different syntactic levels. Representational similarity analysis reveals a stronger alignment between LLM representations and the left hemisphere of the brain (dominant in language processing). Notably, upgraded models exhibit divergent trends: Gemma 2 shows greater brain similarity than Gemma, while Llama 3.1 shows less alignment with the brain compared to Llama 2. These findings offer new insights into the interpretability of LLM behavioral improvements, raising questions about whether these advancements are driven by human-like or non-human-like mechanisms, and establish HFTP as a valuable tool bridging computational linguistics and cognitive neuroscience. This project is available at https://github.com/LilTiger/HFTP.
Mind the Gap: Bridging Thought Leap for Improved Chain-of-Thought Tuning
Venue: Conference NeurIPS 2025
Year: 2025

Large language models (LLMs) have achieved remarkable progress on mathematical tasks through Chain-of-Thought (CoT) reasoning. However, existing mathematical CoT datasets often suffer from Thought Leaps due to experts omitting intermediate steps, which negatively impacts model learning and generalization. We propose the CoT Thought Leap Bridge Task, which aims to automatically detect leaps and generate missing intermediate reasoning steps to restore the completeness and coherence of CoT. To facilitate this, we constructed a specialized training dataset called ScaleQM+, based on the structured ScaleQuestMath dataset, and trained CoT-Bridge to bridge thought leaps. Through comprehensive experiments on mathematical reasoning benchmarks, we demonstrate that models fine-tuned on bridged datasets consistently outperform those trained on original datasets, with improvements of up to +5.87% on NuminaMath. Our approach effectively enhances distilled data (+3.02%) and provides better starting points for reinforcement learning (+3.1%), functioning as a plug-and-play module compatible with existing optimization techniques. Furthermore, CoT-Bridge demonstrate improved generalization to out-of-domain logical reasoning tasks, confirming that enhancing reasoning completeness yields broadly applicable benefits.
Gradual Binary Search and Dimension Expansion : A general method for activation quantization in LLMs
Venue: Conference NeurIPS 2025
Year: 2025

Large language models (LLMs) have become pivotal in artificial intelligence, demonstrating strong capabilities in reasoning, understanding, and generating data. However, their deployment on edge devices is hindered by their substantial size, often reaching several billion parameters. Quantization is a widely used method to reduce memory usage and inference time, however LLMs present unique challenges due to the prevalence of outliers in their activations. In this work, we leverage the theoretical advantages of Hadamard matrices over random rotation matrices to push the boundaries of quantization in LLMs. We demonstrate that Hadamard matrices are more effective in reducing outliers, which are a significant obstacle in achieving low-bit quantization. Our method based on a gradual binary search enables 3-bit quantization for weights, activations, and key-value (KV) caches, resulting in a 40% increase in accuracy on common benchmarks compared to SoTA methods. We extend the use of rotation matrices to support non-power-of-2 embedding dimensions, similar to the Qwen architecture, by employing the Paley algorithm. We theoretically demonstrates the superiority of Hadamard matrices in reducing outliers.We achieved 3-bit quantization for weights, activations, and KV cache, significantly enhancing model performance. Our experimental results on multiple models family like Mistral, LLaMA, and Qwen demonstrate the effectiveness of our approach, outperforming existing methods and enabling practical 3-bit quantization.
Continuous Subspace Optimization for Continual Learning
Venue: Conference NeurIPS 2025
Year: 2025

Continual learning aims to learn multiple tasks sequentially while preserving prior knowledge, but faces the challenge of catastrophic forgetting when adapting to new tasks. Recently, approaches leveraging pre-trained models have gained increasing popularity in mitigating this issue, due to the strong generalization ability of foundation models. To adjust pre-trained models for new tasks, existing methods usually employ low-rank adaptation, which restricts parameter updates to a fixed low-rank subspace. However, constraining the optimization space inherently compromises the model's learning capacity, resulting in inferior performance. To address this limitation, we propose Continuous Subspace Optimization for Continual Learning (CoSO) to fine-tune the model in a series of subspaces rather than a single one. These sequential subspaces are dynamically determined through the singular value decomposition of the gradients. CoSO updates the model by projecting gradients onto these subspaces, ensuring memory-efficient optimization. To mitigate forgetting, the optimization subspace of each task is constrained to be orthogonal to the historical task subspace. During task learning, CoSO maintains a task-specific component that captures the critical update directions for the current task. Upon completing a task, this component is used to update the historical task subspace, laying the groundwork for subsequent learning. Extensive experiments on multiple datasets demonstrate that CoSO significantly outperforms state-of-the-art methods, especially in challenging scenarios with long task sequences.