OpenRaiser/Intern-Atlas huggingface dataset:
Twilight: Adaptive Attention Sparsity with Hierarchical Top-$p$  Pruning
Venue: Conference NeurIPS 2025
Year: 2025

Leveraging attention sparsity to accelerate long-context large language models (LLMs) has been a hot research topic. However, current algorithms such as sparse attention or key-value (KV) cache compression tend to use a fixed budget, which presents a significant challenge during deployment because it fails to account for the dynamic nature of real-world scenarios, where the optimal balance between accuracy and efficiency can vary greatly. In this paper, we find that borrowing top-$p$ sampling (nucleus sampling) to sparse attention can surprisingly achieve adaptive budgeting. Based on this, we propose Twilight, a framework to bring adaptive sparsity to any existing sparse attention algorithm without sacrificing their accuracy. Empirical results show that Twilight can adaptively prune at most 98% of redundant tokens, leading to $15.4\times$ acceleration in self-attention operations and $3.9\times$ acceleration in end-to-end per token latency in long context LLM decoding.
MASTER: Enhancing Large Language Model via Multi-Agent Simulated Teaching
Venue: Conference NeurIPS 2025
Year: 2025

Instruction fine-tuning is crucial in NLP tasks, enhancing pretrained models' instruction-following capabilities and task-specific performance. However, obtaining high-quality fine-tuning data for large models is challenging due to data collection difficulties and high production costs. To address this, we propose MASTER, a novel data augmentation method that enriches original data through interactions among multiple agents with varying cognitive levels. We simulate three pedagogically grounded teaching scenarios, leveraging multi-agent conversations to generate high-quality teacher-student interaction data. Utilizing MASTER, we construct BOOST-QA, a fine-tuning dataset augmented from existing datasets like Orca-Math-200k, ProcQA, and OpenHermes2.5. Experiments show that models fine-tuned with BOOST-QA perform excellently across multiple benchmarks, demonstrating strong multitask generalization. Notably, MASTER significantly improves models' reasoning abilities in complex tasks, providing valuable insights for future research.
Self-Supervised Learning of Graph Representations for Network Intrusion Detection
Venue: Conference NeurIPS 2025
Year: 2025

Detecting intrusions in network traffic is a challenging task, particularly under limited supervision and constantly evolving attack patterns. While recent works have leveraged graph neural networks for network intrusion detection, they often decouple representation learning from anomaly detection, limiting the utility of the embeddings for identifying attacks. We propose GraphIDS, a self-supervised intrusion detection model that unifies these two stages by learning local graph representations of normal communication patterns through a masked autoencoder. An inductive graph neural network embeds each flow with its local topological context to capture typical network behavior, while a Transformer-based encoder-decoder reconstructs these embeddings, implicitly learning global co-occurrence patterns via self-attention without requiring explicit positional information. During inference, flows with unusually high reconstruction errors are flagged as potential intrusions. This end-to-end framework ensures that embeddings are directly optimized for the downstream task, facilitating the recognition of malicious traffic. On diverse NetFlow benchmarks, GraphIDS achieves up to 99.98% PR-AUC and 99.61% macro F1-score, outperforming baselines by 5-25 percentage points.
Kernel conditional tests from learning-theoretic bounds
Venue: Conference NeurIPS 2025
Year: 2025

We propose a framework for hypothesis testing on conditional probability distributions, which we then use to construct statistical tests of functionals of conditional distributions. These tests identify the inputs where the functionals differ with high probability, and include tests of conditional moments or two-sample tests. Our key idea is to transform confidence bounds of a learning method into a test of conditional expectations. We instantiate this principle for kernel ridge regression (KRR) with subgaussian noise. An intermediate data embedding then enables more general tests -- including conditional two-sample tests -- via kernel mean embeddings of distributions. To have guarantees in this setting, we generalize existing pointwise-in-time or time-uniform confidence bounds for KRR to previously-inaccessible yet essential cases such as infinite-dimensional outputs with non-trace-class kernels. These bounds also circumvent the need for independent data, allowing for instance online sampling. To make our tests readily applicable in practice, we introduce bootstrapping schemes leveraging the parametric form of testing thresholds identified in theory to avoid tuning inaccessible parameters. We illustrate the tests on examples, including one in process monitoring and comparison of dynamical systems. Overall, our results establish a comprehensive foundation for conditional testing on functionals, from theoretical guarantees to an algorithmic implementation, and advance the state of the art on confidence bounds for vector-valued least squares estimation.
SPOT: Scalable Policy Optimization with Trees for Markov Decision Processes
Venue: Conference NeurIPS 2025
Year: 2025

Interpretable reinforcement learning policies are essential for high-stakes decision-making, yet optimizing decision tree policies in Markov Decision Processes (MDPs) remains challenging. We propose SPOT, a novel method for computing decision tree policies, which formulates the optimization problem as a mixed-integer linear program (MILP). To enhance efficiency, we employ a reduced-space branch-and-bound approach that decouples the MDP dynamics from tree-structure constraints, enabling efficient parallel search. This significantly improves runtime and scalability compared to previous methods. Our approach ensures that each iteration yields the optimal decision tree. Experimental results on standard benchmarks demonstrate that SPOT achieves substantial speedup and scales to larger MDPs with a significantly higher number of states. The resulting decision tree policies are interpretable and compact, maintaining transparency without compromising performance. These results demonstrate that our approach simultaneously achieves interpretability and scalability, delivering high-quality policies an order of magnitude faster than existing approaches.
Thinking in Character: Advancing Role-Playing Agents with Role-Aware Reasoning
Venue: Conference NeurIPS 2025
Year: 2025

The advancement of Large Language Models (LLMs) has spurred significant interest in Role-Playing Agents (RPAs) for applications such as emotional companionship and virtual interaction. However, recent RPAs are often built on explicit dialogue data, lacking deep, human-like internal thought processes, resulting in superficial knowledge and style expression. While Large Reasoning Models (LRMs) can be employed to simulate character thought, their direct application is hindered by attention diversion (i.e., RPAs forget their role) and style drift (i.e., overly formal and rigid reasoning rather than character-consistent reasoning). To address these challenges, this paper introduces a novel Role-Aware Reasoning (RAR) method, which consists of two important stages: Role Identity Activation (RIA) and Reasoning Style Optimization (RSO). RIA explicitly guides the model with character profiles during reasoning to counteract attention diversion, and then RSO aligns reasoning style with the character and scene via LRM distillation to mitigate style drift. Extensive experiments demonstrate that the proposed RAR significantly enhances the performance of RPAs by effectively addressing attention diversion and style drift.
SAFEx: Analyzing Vulnerabilities of MoE-Based LLMs via Stable Safety-critical Expert Identification
Venue: Conference NeurIPS 2025
Year: 2025

Large language models with Mixture-of-Experts (MoE) architectures achieve efficiency and scalability, yet their routing mechanisms introduce safety alignment challenges insufficiently addressed by techniques developed for dense models. In this work, the MoE-specific safety risk of positional vulnerability-that safety-aligned behaviors rely on specific expert modules-is formalized and systematically analyzed. An analytical framework, SAFEx, is presented to robustly identify, characterize, and validate safety-critical experts via a stability-based expert selection procedure, and to decompose them into two functional groups: the Harmful Content Detection Group (HCDG), which specializes in identifying and recognizing harmful content within user inputs, and the Harmful Response Control Group (HRCG), which specializes in controlling and enforcing model behaviors to generate appropriate safety responses. Expert-level interventions are conducted to probe causality and to test mitigation. Targeted masking of SAFEx-selected experts reveals that safety behavior is highly concentrated. On Qwen3-30B-A3B, configured with 48 MoE-FFN layers and 128 experts per layer under top-8 routing (48x128=6,144 experts in total), disabling 12 selected experts reduces the refusal rate by 22%. In addition, lightweight adaptation is performed using LoRA under three configurations-the HRCG, the union of HCDG and HRCG, and all experts-and the resulting updates are composed through negative weight merging targeted at the HRCG, leading to improved refusal under adversarial prompts without full-model retraining. These results establish positional vulnerability as a distinct MoE-specific safety challenge and provide a practical, compute-efficient pathway for expert-level safety interventions within routed architectures.
A geometric framework for momentum-based optimizers for low-rank training
Venue: Conference NeurIPS 2025
Year: 2025

Low-rank pre-training and fine-tuning have recently emerged as promising techniques for reducing the computational and storage costs of large neural networks. Training low-rank parameterizations typically relies on conventional optimizers such as heavy ball momentum methods or Adam. In this work, we identify and analyze potential difficulties that these training methods encounter when used to train low-rank parameterizations of weights. In particular, we show that classical momentum methods can struggle to converge to a local optimum due to the geometry of the underlying optimization landscape. To address this, we introduce novel training strategies derived from dynamical low-rank approximation, which explicitly account for the underlying geometric structure. Our approach leverages and combines tools from dynamical low-rank approximation and momentum-based optimization to design optimizers that respect the intrinsic geometry of the parameter space. We validate our methods through numerical experiments, demonstrating faster convergence, and stronger validation metrics at given parameter budgets.
Atomic Thinking of LLMs: Decoupling and Exploring Mathematical Reasoning Abilities
Venue: Conference NeurIPS 2025
Year: 2025

Large Language Models (LLMs) have demonstrated outstanding performance in mathematical reasoning capabilities. However, we argue that current large-scale reasoning models primarily rely on scaling up training datasets with diverse mathematical problems and long thinking chains, which raises questions about whether LLMs genuinely acquire mathematical concepts and reasoning principles or merely remember the training data. In contrast, humans tend to break down complex problems into multiple fundamental atomic capabilities. Inspired by this, we propose a new paradigm for evaluating mathematical atomic capabilities. Our work categorizes atomic abilities into two dimensions: (1) field-specific abilities across four major mathematical fields, algebra, geometry, analysis, and topology, and (2) logical abilities at different levels, including conceptual understanding, forward multi-step reasoning with formal math language, and counterexample-driven backward reasoning. We propose corresponding training and evaluation datasets for each atomic capability unit, and conduct extensive experiments about how different atomic capabilities influence others, to explore the strategies to elicit the required specific atomic capability. Evaluation and experimental results on advanced models show many interesting discoveries and inspirations about the different performances of models on various atomic capabilities and the interactions between atomic capabilities. Our findings highlight the importance of decoupling mathematical intelligence into atomic components, providing new insights into model cognition and guiding the development of training strategies toward a more efficient, transferable, and cognitively grounded paradigm of "atomic thinking".
Reasoning Models Sometimes Output Illegible Chains of Thought
Venue: Conference NeurIPS 2025
Year: 2025

Language models trained via outcome-based reinforcement learning (RL) to reason using chain-of-thought (CoT) have shown remarkable performance. Monitoring such a model's CoT may allow us to understand its intentions and detect potential malicious behavior. However, to be effective, this requires that CoTs are legible and faithful. We study CoT legibility across 14 reasoning models, finding that RL often causes reasoning to become illegible to both humans and AI monitors, with reasoning models (except Claude) generating illegible CoTs while returning to perfectly readable final answers. We show that models use illegible reasoning to reach correct answers (accuracy dropping by 53\% when forced to use only legible portions), yet find no correlation between legibility and performance when resampling - suggesting the relationship is more nuanced. We also find that legibility degrades on harder questions. We discuss potential hypotheses for these results, including steganography, training artifacts, and vestigial tokens. These results suggest that without explicit optimization for legibility, outcome-based RL naturally produces models with increasingly opaque reasoning processes, potentially undermining monitoring approaches.
JanusDNA: A Powerful Bi-directional Hybrid DNA Foundation Model
Venue: Conference NeurIPS 2025
Year: 2025

Large language models (LLMs) have revolutionized natural language processing and are increasingly applied to other sequential data types, including genetic sequences. However, adapting LLMs to genomics presents significant challenges. Capturing complex genomic interactions requires modeling long-range dependencies within DNA sequences, where interactions often span over 10,000 base pairs, even within a single gene, posing substantial computational burdens under conventional model architectures and training paradigms. Moreover, standard LLM training approaches are suboptimal for DNA: autoregressive training, while efficient, supports only unidirectional understanding. However, DNA is inherently bidirectional, e.g., bidirectional promoters regulate transcription in both directions and account for nearly 11% of human gene expression. Masked language models (MLMs) allow bidirectional understanding but are inefficient, as only masked tokens contribute to the loss per step. To address these limitations, we introduce JanusDNA, the first bidirectional DNA foundation model built upon a novel pretraining paradigm that combines the optimization efficiency of autoregressive modeling with the bidirectional comprehension of masked modeling. JanusDNA adopts a hybrid Mamba, Attention and Mixture of Experts (MoE) architecture, combining long-range modeling of Attention with efficient sequential learning of Mamba. MoE layers further scale model capacity via sparse activation while keeping computational cost low. Notably, JanusDNA processes up to 1 million base pairs at single nucleotide resolution on a single 80GB GPU. Extensive experiments and ablations show JanusDNA achieves new SOTA results on three genomic representation benchmarks, outperforming models with 250x more activated parameters. Code: https://github.com/Qihao-Duan/JanusDNA
PubSub-VFL: Towards Efficient Two-Party Split Learning in Heterogeneous Environments via Publisher/Subscriber Architecture
Venue: Conference NeurIPS 2025
Year: 2025

With the rapid advancement of the digital economy, data collaboration between organizations has become a well-established business model, driving the growth of various industries. However, privacy concerns make direct data sharing impractical. To address this, Two-Party Split Learning (a.k.a. Vertical Federated Learning (VFL)) has emerged as a promising solution for secure collaborative learning. Despite its advantages, this architecture still suffers from low computational resource utilization and training efficiency. Specifically, its synchronous dependency design increases training latency, while resource and data heterogeneity among participants further hinder efficient computation. To overcome these challenges, we propose PubSub-VFL, a novel VFL paradigm with a Publisher/Subscriber architecture optimized for two-party collaborative learning with high computational efficiency. PubSub-VFL leverages the decoupling capabilities of the Pub/Sub architecture and the data parallelism of the parameter server architecture to design a hierarchical asynchronous mechanism, reducing training latency and improving system efficiency. Additionally, to mitigate the training imbalance caused by resource and data heterogeneity, we formalize an optimization problem based on participants' system profiles, enabling the selection of optimal hyperparameters while preserving privacy. We conduct a theoretical analysis to demonstrate that PubSub-VFL achieves stable convergence and is compatible with security protocols such as differential privacy. Extensive case studies on five benchmark datasets further validate its effectiveness, showing that, compared to state-of-the-art baselines, PubSub-VFL not only accelerates training by $2 \sim 7\times$ without compromising accuracy, but also achieves a computational resource utilization rate of up to 91.07%.
Bohdi: Heterogeneous LLM Fusion with Automatic Data Exploration
Venue: Conference NeurIPS 2025
Year: 2025

Heterogeneous Large Language Model (LLM) fusion integrates the strengths of multiple source LLMs with different architectures into a target LLM with low computational overhead. While promising, existing methods suffer from two major limitations: 1) reliance on real data from limited domain for knowledge fusion, preventing the target LLM from fully acquiring knowledge across diverse domains, and 2) fixed data allocation proportions across domains, failing to dynamically adjust according to the target LLM's varying capabilities across domains, leading to a capability imbalance. To overcome these limitations, we propose Bohdi, a synthetic-data-only heterogeneous LLM fusion framework. Through the organization of knowledge domains into a hierarchical tree structure, Bohdi enables automatic domain exploration and multi-domain data generation through multi-model collaboration, thereby comprehensively extracting knowledge from source LLMs. By formalizing domain expansion and data sampling proportion allocation on the knowledge tree as a Hierarchical Multi-Armed Bandit problem, Bohdi leverages the designed DynaBranches mechanism to adaptively adjust sampling proportions based on the target LLM's performance feedback across domains. Integrated with our proposed Introspection-Rebirth (IR) mechanism, DynaBranches dynamically tracks capability shifts during target LLM's updates via Sliding Window Binomial Likelihood Ratio Testing (SWBLRT), further enhancing its online adaptation capability. Comparative experimental results on a comprehensive suite of benchmarks demonstrate that Bohdi significantly outperforms existing baselines on multiple target LLMs, exhibits higher data efficiency, and virtually eliminates the imbalance in the target LLM's capabilities. Our code is available at https://github.com/gjq100/Bohdi.git.
How Does Sequence Modeling Architecture Influence Base Capabilities of Pre-trained Language Models? Exploring Key Architecture Design Principles to Avoid Base Capabilities Degradation
Venue: Conference NeurIPS 2025
Year: 2025

Pre-trained language models represented by the Transformer have been proven to possess strong base capabilities, and the representative self-attention mechanism in the Transformer has become a classic in sequence modeling architectures. Different from the work of proposing sequence modeling architecture to improve the efficiency of attention mechanism, this work focuses on the impact of sequence modeling architectures on base capabilities. Specifically, our concern is: How exactly do sequence modeling architectures affect the base capabilities of pre-trained language models? In this work, we first point out that the mixed domain pre-training setting commonly adopted in existing architecture design works fails to adequately reveal the differences in base capabilities among various architectures. To address this, we propose a limited domain pre-training setting with out-of-distribution testing, which successfully uncovers significant differences in base capabilities among architectures at an early stage. Next, we analyze the base capabilities of stateful sequence modeling architectures, and find that they exhibit significant degradation in base capabilities compared to the Transformer. Then, through a series of architecture component analysis, we summarize a key architecture design principle: A sequence modeling architecture need possess full-sequence arbitrary selection capability to avoid degradation in base capabilities. Finally, we empirically validate this principle using an extremely simple Top-1 element selection architecture and further generalize it to a more practical Top-1 chunk selection architecture. Experimental results demonstrate our proposed sequence modeling architecture design principle and suggest that our work can serve as a valuable reference for future architecture improvements and novel designs.
Curse of Slicing: Why Sliced Mutual Information is a Deceptive Measure of Statistical Dependence
Venue: Conference NeurIPS 2025
Year: 2025

Sliced Mutual Information (SMI) is widely used as a scalable alternative to mutual information for measuring non-linear statistical dependence. Despite its advantages, such as faster convergence, robustness to high dimensionality, and nullification only under statistical independence, we demonstrate that SMI is highly susceptible to data manipulation and exhibits counterintuitive behavior. Through extensive benchmarking and theoretical analysis, we show that SMI saturates easily, fails to detect increases in statistical dependence, prioritizes redundancy over informative content, and in some cases, performs worse than correlation coefficient.