OpenRaiser/Intern-Atlas huggingface dataset:
From Style to Facts: Mapping the Boundaries of Knowledge Injection with Finetuning
Venue: Conference NeurIPS 2025
Year: 2025

Finetuning provides a scalable and cost-effective means of customizing language models for specific tasks or response styles, with greater reliability than prompting or in-context learning. In contrast, the conventional wisdom is that injecting knowledge via finetuning results in brittle performance and poor generalization. We argue that the dichotomy of "task customization" (e.g., instruction tuning) and "knowledge injection" (e.g., teaching new facts) is a distinction without a difference. We instead identify concrete factors that explain the heterogeneous effectiveness observed with finetuning. To this end, we conduct a large-scale experimental study of finetuning the frontier Gemini v1.5 model family on a spectrum of datasets that are artificially engineered to interpolate between the strengths and failure modes of finetuning. Our findings indicate that question-answer training data formats provide much stronger knowledge generalization than document/article-style training data, numerical information can be harder for finetuning to retain than categorical information, and models struggle to apply finetuned knowledge during multi-step reasoning even when trained on similar examples -- all factors that render "knowledge injection" to be especially difficult, even after controlling for considerations like data augmentation and information volume. On the other hand, our findings also indicate that it is not fundamentally more difficult to finetune information about a real-world event than information about what a model's writing style should be.
Multi-Modal View Enhanced Large Vision Models for Long-Term Time Series Forecasting
Venue: Conference NeurIPS 2025
Year: 2025

Time series, typically represented as numerical sequences, can also be transformed into images and texts, offering multi-modal views (MMVs) of the same underlying signal. These MMVs can reveal complementary patterns and enable the use of powerful pre-trained large models, such as large vision models (LVMs), for long-term time series forecasting (LTSF). However, as we identified in this work, the state-of-the-art (SOTA) LVM-based forecaster poses an inductive bias towards "forecasting periods". To harness this bias, we propose DMMV, a novel decomposition-based multi-modal view framework that leverages trend-seasonal decomposition and a novel backcast-residual based adaptive decomposition to integrate MMVs for LTSF. Comparative evaluations against 14 SOTA models across diverse datasets show that DMMV outperforms single-view and existing multi-modal baselines, achieving the best mean squared error (MSE) on 6 out of 8 benchmark datasets. The code for this paper is available at: https://github.com/D2I-Group/dmmv.
Learning to Watermark: A Selective Watermarking Framework for Large Language Models via Multi-Objective Optimization
Venue: Conference NeurIPS 2025
Year: 2025

The rapid development of LLMs has raised concerns about their potential misuse, leading to various watermarking schemes that typically offer high detectability. However, existing watermarking techniques often face trade-off between watermark detectability and generated text quality. In this paper, we introduce Learning to Watermark (LTW), a novel selective watermarking framework that leverages multi-objective optimization to effectively balance these competing goals. LTW features a lightweight network that adaptively decides when to apply the watermark by analyzing sentence embeddings, token entropy, and current watermarking ratio. Training of the network involves two specifically constructed loss functions that guide the model toward Pareto-optimal solutions, thereby harmonizing watermark detectability and text quality. By integrating LTW with two baseline watermarking methods, our experimental evaluations demonstrate that LTW significantly enhances text quality without compromising detectability. Our selective watermarking approach offers a new perspective for designing watermarks for LLMs and a way to preserve high text quality for watermarks. The code is publicly available at: https://github.com/fattyray/learning-to-watermark
BlockScan: Detecting Anomalies in Blockchain Transactions
Venue: Conference NeurIPS 2025
Year: 2025

We propose BlockScan, a customized Transformer for anomaly detection in blockchain transactions. Unlike existing methods that rely on rule-based systems or directly apply off-the-shelf large language models (LLMs), BlockScan introduces a series of customized designs to effectively model the unique data structure of blockchain transactions. First, a blockchain transaction is multi-modal, containing blockchain-specific tokens, texts, and numbers. We design a novel modularized tokenizer to handle these multi-modal inputs, balancing the information across different modalities. Second, we design a customized masked language modeling mechanism for pretraining the Transformer architecture, incorporating RoPE embedding and FlashAttention for handling longer sequences. Finally, we design a novel anomaly detection method based on the model outputs. We further provide theoretical analysis for the detection method of our system. Extensive evaluations on Ethereum and Solana transactions demonstrate BlockScan's exceptional capability in anomaly detection while maintaining a low false positive rate. Remarkably, BlockScan is the only method that successfully detects anomalous transactions on Solana with high accuracy, whereas all other approaches achieved very low or zero detection recall scores. This work sets a new benchmark for applying Transformer-based approaches in blockchain data analysis.
Orochi: Versatile Biomedical Image Processor
Venue: Conference NeurIPS 2025
Year: 2025

Deep learning has emerged as a pivotal tool for accelerating research in the life sciences, with the low-level processing of biomedical images (e.g., registration, fusion, restoration, super-resolution) being one of its most critical applications. Platforms such as ImageJ (Fiji) and napari have enabled the development of customized plugins for various models. However, these plugins are typically based on models that are limited to specific tasks and datasets, making them less practical for biologists. To address this challenge, we introduce Orochi, the first application-oriented, efficient, and versatile image processor designed to overcome these limitations. Orochi is pre-trained on patches/volumes extracted from the raw data of over 100 publicly available studies using our Random Multi-scale Sampling strategy. We further propose Task-related Joint-embedding Pre-Training (TJP), which employs biomedical task-related degradation for self-supervision rather than relying on Masked Image Modelling (MIM), which performs poorly in downstream tasks such as registration. To ensure computational efficiency, we leverage Mamba's linear computational complexity and construct Multi-head Hierarchy Mamba. Additionally, we provide a three-tier fine-tuning framework (Full, Normal, and Light) and demonstrate that Orochi achieves comparable or superior performance to current state-of-the-art specialist models, even with lightweight parameter-efficient options. We hope that our study contributes to the development of an all-in-one workflow, thereby relieving biologists from the overwhelming task of selecting among numerous models.
GPO: Learning from Critical Steps to Improve LLM Reasoning
Venue: Conference NeurIPS 2025
Year: 2025

Large language models (LLMs) are increasingly used in various domains, showing impressive potential on different tasks. Recently, reasoning LLMs have been proposed to improve the \textit{reasoning} or \textit{thinking} capabilities of LLMs to solve complex problems. Despite the promising results of reasoning LLMs, enhancing the multi-step reasoning capabilities of LLMs still remains a significant challenge. While existing optimization methods have advanced the LLM reasoning capabilities, they often treat reasoning trajectories as a whole, without considering the underlying critical steps within the trajectory. In this paper, we introduce \textbf{G}uided \textbf{P}ivotal \textbf{O}ptimization (GPO), a novel fine-tuning strategy that dives into the reasoning process to enable more effective improvements. GPO first identifies the `critical step' within a reasoning trajectory - a point that the model must carefully proceed to succeed at the problem. We locate the critical step by estimating the advantage function. GPO then resets the policy to the critical step, samples the new rollout and prioritizes the learning process on those rollouts. This focus allows the model to learn more effectively from pivotal moments within the reasoning process to improve the reasoning performance. We demonstrate that GPO is a general strategy that can be integrated with various optimization methods to improve reasoning performance. Besides theoretical analysis, our experiments across challenging reasoning benchmarks show that GPO can consistently and significantly enhance the performance of existing optimization methods, showcasing its effectiveness and generalizability in improving LLM reasoning by concentrating on pivotal moments within the generation process.
IDOL: Meeting Diverse Distribution Shifts with Prior Physics for Tropical Cyclone Multi-Task Estimation
Venue: Conference NeurIPS 2025
Year: 2025

Tropical Cyclone (TC) estimation aims to accurately estimate various TC attributes in real time. However, distribution shifts arising from the complex and dynamic nature of TC environmental fields, such as varying geographical conditions and seasonal changes, present significant challenges to reliable estimation. Most existing methods rely on multi-modal fusion for feature extraction but overlook the intrinsic distribution of feature representations, leading to poor generalization under out-of-distribution (OOD) scenarios. To address this, we propose an effective Identity Distribution-Oriented Physical Invariant Learning framework (IDOL), which imposes identity-oriented constraints to regulate the feature space under the guidance of prior physical knowledge, thereby dealing distribution variability with physical invariance. Specifically, the proposed IDOL employs the wind field model and dark correlation knowledge of TC to model task-shared and task-specific identity tokens. These tokens capture task dependencies and intrinsic physical invariances of TC, enabling robust estimation of TC wind speed, pressure, inner-core, and outer-core size under distribution shifts. Extensive experiments conducted on multiple datasets and tasks demonstrate the outperformance of the proposed IDOL, verifying that imposing identity-oriented constraints based on prior physical knowledge can effectively mitigates diverse distribution shifts in TC estimation.Code is available at https://github.com/Zjut-MultimediaPlus/IDOL.
Memory-Augmented Potential Field Theory: A Framework for Adaptive Control in Non-Convex Domains
Venue: Conference NeurIPS 2025
Year: 2025

Stochastic optimal control methods often struggle in complex non-convex landscapes, frequently becoming trapped in local optima due to their inability to learn from historical trajectory data. This paper introduces Memory-Augmented Potential Field Theory, a unified mathematical framework that integrates historical experience into stochastic optimal control. Our approach dynamically constructs memory-based potential fields that identify and encode key topological features of the state space, enabling controllers to automatically learn from past experiences and adapt their optimization strategy. We provide a theoretical analysis showing that memory-augmented potential fields possess non-convex escape properties, asymptotic convergence characteristics, and computational efficiency. We implement this theoretical framework in a Memory-Augmented Model Predictive Path Integral (MPPI) controller that demonstrates significantly improved performance in challenging non-convex environments. The framework represents a generalizable approach to experience-based learning within control systems (especially robotic dynamics), enhancing their ability to navigate complex state spaces without requiring specialized domain knowledge or extensive offline training.
Multimodal 3D Genome Pre-training
Venue: Conference NeurIPS 2025
Year: 2025

Deep learning techniques have driven significant progress in various analytical tasks within 3D genomics in computational biology. However, a holistic understanding of 3D genomics knowledge remains underexplored. Here, we propose MIX-HIC, the first multimodal foundation model of 3D genome that integrates both 3D genome structure and epigenomic tracks, which obtains unified and comprehensive semantics. For accurate heterogeneous semantic fusion, we design the cross-modal interaction and mapping blocks for robust unified representation, yielding the accurate aggregation of 3D genome knowledge. Besides, we introduce the first large-scale dataset comprising over 1 million pairwise samples of Hi-C contact maps and epigenomic tracks for high-quality pre-training, enabling the exploration of functional implications in 3D genomics. Extensive experiments show that MIX-HIC can significantly surpass existing state-of-the-art methods in diverse downstream tasks. This work provides a valuable resource for advancing 3D genomics research.
DAPO: An Open-Source LLM Reinforcement Learning System at Scale
Venue: Conference NeurIPS 2025
Year: 2025

Inference scaling empowers LLMs with unprecedented reasoning ability, with reinforcement learning as the core technique to elicit complex reasoning. However, key technical details of state-of-the-art reasoning LLMs are concealed (such as in OpenAI o1 blog and DeepSeek R1 technical report), thus the community still struggles to reproduce their RL training results. We propose the $\textbf{D}$ecoupled Clip and $\textbf{D}$ynamic s$\textbf{A}$mpling $\textbf{P}$olicy $\textbf{O}$ptimization ($\textbf{DAPO}$) algorithm, and fully open-source a state-of-the-art large-scale RL system that achieves 50 points on AIME 2024 using Qwen2.5-32B base model. Unlike previous works that withhold training details, we introduce four key techniques of our algorithm that make large-scale LLM RL a success. In addition, we open-source our training code, which is built on the verl framework, along with a carefully curated and processed dataset. These components of our open-source system enhance reproducibility and support future research in large-scale LLM RL.
Clip-and-Verify: Linear Constraint-Driven Domain Clipping for Accelerating Neural Network Verification
Venue: Conference NeurIPS 2025
Year: 2025

State-of-the-art neural network (NN) verifiers demonstrate that applying the branch-and-bound (BaB) procedure with fast bounding techniques plays a key role in tackling many challenging verification properties. In this work, we introduce the linear constraint-driven clipping framework, a class of scalable and efficient methods designed to enhance the efficacy of NN verifiers. Under this framework, we develop two novel algorithms that efficiently utilize linear constraints to 1) reduce portions of the input space that are either verified or irrelevant to a subproblem in the context of branch-and-bound, and 2) directly improve intermediate bounds throughout the network. The process novelly leverages linear constraints that often arise from bound propagation methods and is general enough to also incorporate constraints from other sources. It efficiently handles linear constraints using a specialized GPU procedure that can scale to large neural networks without the use of expensive external solvers. Our verification procedure, Clip-and-Verify, consistently tightens bounds across multiple benchmarks and can significantly reduce the number of subproblems handled during BaB. We show that our clipping algorithms can be integrated with BaB-based verifiers such as $α,β$-CROWN, utilizing either the split constraints in activation-space BaB or the output constraints that denote the unverified input space. We demonstrate the effectiveness of our procedure on a broad range of benchmarks where, in some instances, we witness a 96% reduction in the number of subproblems during branch-and-bound, and also achieve state-of-the-art verified accuracy across multiple benchmarks. Clip-and-Verify is part of the $α,β$-CROWN verifier (http://abcrown.org), the VNN-COMP 2025 winner. Code available at https://github.com/Verified-Intelligence/Clip_and_Verify.
Jasmine: Harnessing Diffusion Prior for Self-supervised Depth Estimation
Venue: Conference NeurIPS 2025
Year: 2025

In this paper, we propose Jasmine, the first Stable Diffusion (SD)-based self-supervised framework for monocular depth estimation, which effectively harnesses SD's visual priors to enhance the sharpness and generalization of unsupervised prediction. Previous SD-based methods are all supervised since adapting diffusion models for dense prediction requires high-precision supervision. In contrast, self-supervised reprojection suffers from inherent challenges (e.g., occlusions, texture-less regions, illumination variance), and the predictions exhibit blurs and artifacts that severely compromise SD's latent priors. To resolve this, we construct a novel surrogate task of hybrid image reconstruction. Without any additional supervision, it preserves the detail priors of SD models by reconstructing the images themselves while preventing depth estimation from degradation. Furthermore, to address the inherent misalignment between SD's scale and shift invariant estimation and self-supervised scale-invariant depth estimation, we build the Scale-Shift GRU. It not only bridges this distribution gap but also isolates the fine-grained texture of SD output against the interference of reprojection loss. Extensive experiments demonstrate that Jasmine achieves SoTA performance on the KITTI benchmark and exhibits superior zero-shot generalization across multiple datasets.
WISA: World simulator assistant for physics-aware text-to-video generation
Venue: Conference NeurIPS 2025
Year: 2025

Recent rapid advancements in text-to-video (T2V) generation, such as SoRA and Kling, have shown great potential for building world simulators. However, current T2V models struggle to grasp abstract physical principles and generate videos that adhere to physical laws. This challenge arises primarily from a lack of clear guidance on physical information due to a significant gap between abstract physical principles and generation models. To this end, we introduce the World Simulator Assistant (WISA), an effective framework for decomposing and incorporating physical principles into T2V models. Specifically, WISA decomposes physical principles into textual physical descriptions, qualitative physical categories, and quantitative physical properties. To effectively embed these physical attributes into the generation process, WISA incorporates several key designs, including Mixture-of-Physical-Experts Attention (MoPA) and a Physical Classifier, enhancing the model's physics awareness. Furthermore, most existing datasets feature videos where physical phenomena are either weakly represented or entangled with multiple co-occurring processes, limiting their suitability as dedicated resources for learning explicit physical principles. We propose a novel video dataset, WISA-32K, collected based on qualitative physical categories. It consists of 32,000 videos, representing 17 physical laws across three domains of physics: dynamics, thermodynamics, and optics. Experimental results demonstrate that WISA can effectively enhance the compatibility of T2V models with real-world physical laws, achieving a considerable improvement on the VideoPhy benchmark. The visual exhibitions of WISA and WISA-32K are available in the https://360cvgroup.github.io/WISA/.
U-CAN: Unsupervised Point Cloud Denoising with Consistency-Aware Noise2Noise Matching
Venue: Conference NeurIPS 2025
Year: 2025

Point clouds captured by scanning sensors are often perturbed by noise, which have a highly negative impact on downstream tasks (e.g. surface reconstruction and shape understanding). Previous works mostly focus on training neural networks with noisy-clean point cloud pairs for learning denoising priors, which requires extensively manual efforts. In this work, we introduce U-CAN, an Unsupervised framework for point cloud denoising with Consistency-Aware Noise2Noise matching. Specifically, we leverage a neural network to infer a multi-step denoising path for each point of a shape or scene with a noise to noise matching scheme. We achieve this by a novel loss which enables statistical reasoning on multiple noisy point cloud observations. We further introduce a novel constraint on the denoised geometry consistency for learning consistency-aware denoising patterns. We justify that the proposed constraint is a general term which is not limited to 3D domain and can also contribute to the area of 2D image denoising. Our evaluations under the widely used benchmarks in point cloud denoising, upsampling and image denoising show significant improvement over the state-of-the-art unsupervised methods, where U-CAN also produces comparable results with the supervised methods.
SAS: Simulated Attention Score
Venue: Conference NeurIPS 2025
Year: 2025

The attention mechanism is a core component of the Transformer architecture. Various methods have been developed to compute attention scores, including multi-head attention (MHA), multi-query attention, group-query attention and so on. We further analyze the MHA and observe that its performance improves as the number of attention heads increases, provided the hidden size per head remains sufficiently large. Therefore, increasing both the head count and hidden size per head with minimal parameter overhead can lead to significant performance gains at a low cost. Motivated by this insight, we introduce Simulated Attention Score (SAS), which maintains a compact model size while simulating a larger number of attention heads and hidden feature dimension per head. This is achieved by projecting a low-dimensional head representation into a higher-dimensional space, effectively increasing attention capacity without increasing parameter count. Beyond the head representations, we further extend the simulation approach to feature dimension of the key and query embeddings, enhancing expressiveness by mimicking the behavior of a larger model while preserving the original model size. To control the parameter cost, we also propose Parameter-Efficient Attention Aggregation (PEAA). Comprehensive experiments on a variety of datasets and tasks demonstrate the effectiveness of the proposed SAS method, achieving significant improvements over different attention variants.
Theoretical Benefit and Limitation of Diffusion Language Model
Venue: Conference NeurIPS 2025
Year: 2025

Diffusion language models have emerged as a promising approach for text generation. One would naturally expect this method to be an efficient replacement for autoregressive models since multiple tokens can be sampled in parallel during each diffusion step. However, its efficiency-accuracy trade-off is not yet well understood. In this paper, we present a rigorous theoretical analysis of a widely used type of diffusion language model, the Masked Diffusion Model (MDM), and find that its effectiveness heavily depends on the target evaluation metric. Under mild conditions, we prove that when using perplexity as the metric, MDMs can achieve near-optimal perplexity in sampling steps regardless of sequence length, demonstrating that efficiency can be achieved without sacrificing performance. However, when using the sequence error rate--which is important for understanding the "correctness" of a sequence, such as a reasoning chain--we show that the required sampling steps must scale linearly with sequence length to obtain "correct" sequences, thereby eliminating MDM's efficiency advantage over autoregressive models. Our analysis establishes the first theoretical foundation for understanding the benefits and limitations of MDMs. All theoretical findings are supported by empirical studies.