OpenRaiser/Intern-Atlas huggingface dataset:
Evaluation of LLMs in Medical Text Summarization: The Role of Vocabulary Adaptation in High OOV Settings
Venue: arXiv cs.CL 2025
Year: 2025

Large Language Models (LLMs) recently achieved great success in medical text summarization by simply using in-context learning. However, these recent efforts do not perform fine-grained evaluations under difficult settings where LLMs might fail. They typically report performance scores over the entire dataset. Through our benchmarking study, we show that LLMs show a significant performance drop for data points with high concentration of out-of-vocabulary (OOV) words or with high novelty. Vocabulary adaptation is an intuitive solution to this vocabulary mismatch issue where the LLM vocabulary gets updated with certain expert domain (here, medical) words or subwords. An interesting finding from our study is that Llama-3.1, even with a vocabulary size of around 128K tokens, still faces over-fragmentation issue with medical words. To that end, we show vocabulary adaptation helps improve the LLM summarization performance even in difficult settings. Through extensive experimentation of multiple vocabulary adaptation strategies, two continual pretraining strategies, and three benchmark medical summarization datasets, we gain valuable insights into the role of vocabulary adaptation strategies for customizing LLMs to the medical domain. We also performed a human evaluation study with medical experts where they found that vocabulary adaptation results in more relevant and faithful summaries. Our codebase is made publicly available at https://github.com/gb-kgp/LLM-MedicalSummarization-Benchmark.
When to Deceive: A Cross-Layer Stackelberg Game Framework for Strategic Timing of Cyber Deception
Venue: arXiv cs.GT 2025
Year: 2025

Cyber deception is an emerging proactive defense strategy to counter increasingly sophisticated attacks such as Advanced Persistent Threats (APTs) by misleading and distracting attackers from critical assets. However, since deception techniques incur costs and may lose effectiveness over time, defenders must strategically time and select them to adapt to the dynamic system and the attacker's responses. In this study, we propose a Stackelberg game-based framework to design strategic timing for cyber deception: the lower tactical layer (follower) captures the evolving attacker-defender dynamics under a given deception through a one-sided information Markov game, while the upper strategic layer (leader) employs a stopping-time decision process to optimize the timing and selection of deception techniques. We also introduce a computational algorithm that integrates dynamic programming and belief-state updates to account for the attacker's adaptive behavior and limited deception resources. Numerical experiments validate the framework, showing that strategically timed deceptions can enhance the defender's expected utility and reduce the risk of asset compromise compared to baseline strategies.
Distributed Discrete Morse Sandwich: Efficient Computation of Persistence Diagrams for Massive Scalar Data
Venue: arXiv cs.DC 2025
Year: 2025

The persistence diagram, which describes the topological features of a dataset, is a key descriptor in Topological Data Analysis. The "Discrete Morse Sandwich" (DMS) method has been reported to be the most efficient algorithm for computing persistence diagrams of 3D scalar fields on a single node, using shared-memory parallelism. In this work, we extend DMS to distributed-memory parallelism for the efficient and scalable computation of persistence diagrams for massive datasets across multiple compute nodes. On the one hand, we can leverage the embarrassingly parallel procedure of the first and most time-consuming step of DMS (namely the discrete gradient computation). On the other hand, the efficient distributed computations of the subsequent DMS steps are much more challenging. To address this, we have extensively revised the DMS routines by contributing a new self-correcting distributed pairing algorithm, redesigning key data structures and introducing computation tokens to coordinate distributed computations. We have also introduced a dedicated communication thread to overlap communication and computation. Detailed performance analyses show the scalability of our hybrid MPI+thread approach for strong and weak scaling using up to 16 nodes of 32 cores (512 cores total). Our algorithm outperforms DIPHA, a reference method for the distributed computation of persistence diagrams, with an average speedup of x8 on 512 cores. We show the practical capabilities of our approach by computing the persistence diagram of a public 3D scalar field of 6 billion vertices in 174 seconds on 512 cores. Finally, we provide a usage example of our open-source implementation at https://github.com/eve-le-guillou/DDMS-example.
A Cross Modal Knowledge Distillation & Data Augmentation Recipe for Improving Transcriptomics Representations through Morphological Features
Venue: arXiv cs.LG 2025
Year: 2025

Understanding cellular responses to stimuli is crucial for biological discovery and drug development. Transcriptomics provides interpretable, gene-level insights, while microscopy imaging offers rich predictive features but is harder to interpret. Weakly paired datasets, where samples share biological states, enable multimodal learning but are scarce, limiting their utility for training and multimodal inference. We propose a framework to enhance transcriptomics by distilling knowledge from microscopy images. Using weakly paired data, our method aligns and binds modalities, enriching gene expression representations with morphological information. To address data scarcity, we introduce (1) Semi-Clipped, an adaptation of CLIP for cross-modal distillation using pretrained foundation models, achieving state-of-the-art results, and (2) PEA (Perturbation Embedding Augmentation), a novel augmentation technique that enhances transcriptomics data while preserving inherent biological information. These strategies improve the predictive power and retain the interpretability of transcriptomics, enabling rich unimodal representations for complex biological tasks.
MME-Reasoning: A Comprehensive Benchmark for Logical Reasoning in MLLMs
Venue: arXiv cs.AI 2025
Year: 2025

Logical reasoning is a fundamental aspect of human intelligence and an essential capability for multimodal large language models (MLLMs). Despite the significant advancement in multimodal reasoning, existing benchmarks fail to comprehensively evaluate their reasoning abilities due to the lack of explicit categorization for logical reasoning types and an unclear understanding of reasoning. To address these issues, we introduce MME-Reasoning, a comprehensive benchmark designed to evaluate the reasoning ability of MLLMs, which covers all three types of reasoning (i.e., inductive, deductive, and abductive) in its questions. We carefully curate the data to ensure that each question effectively evaluates reasoning ability rather than perceptual skills or knowledge breadth, and extend the evaluation protocols to cover the evaluation of diverse questions. Our evaluation reveals substantial limitations of state-of-the-art MLLMs when subjected to holistic assessments of logical reasoning capabilities. Even the most advanced MLLMs show limited performance in comprehensive logical reasoning, with notable performance imbalances across reasoning types. In addition, we conducted an in-depth analysis of approaches such as ``thinking mode'' and Rule-based RL, which are commonly believed to enhance reasoning abilities. These findings highlight the critical limitations and performance imbalances of current MLLMs in diverse logical reasoning scenarios, providing comprehensive and systematic insights into the understanding and evaluation of reasoning capabilities.
Out of the Past: An AI-Enabled Pipeline for Traffic Simulation from Noisy, Multimodal Detector Data and Stakeholder Feedback
Venue: arXiv cs.CE 2025
Year: 2025

How can a traffic simulation be designed to faithfully reflect real-world traffic conditions? One crucial step is modeling the volume of traffic demand. But past demand modeling approaches have relied on unrealistic or suboptimal heuristics, and they have failed to adequately account for the effects of noisy and multimodal data on simulation outcomes. In this work, we integrate advances in AI to construct a three-step, end-to-end pipeline for systematically modeling traffic demand from detector data: computer vision for vehicle counting from noisy camera footage, combinatorial optimization for vehicle route generation from multimodal data, and large language models for iterative simulation refinement from natural language feedback. Using a road network from Strongsville, Ohio as a testbed, we show that our pipeline accurately captures the city's traffic patterns in a granular simulation. Beyond Strongsville, incorporating noise and multimodality makes our framework generalizable to municipalities with different levels of data and infrastructure availability.
EquAct: An SE(3)-Equivariant Multi-Task Transformer for Open-Loop Robotic Manipulation
Venue: arXiv cs.RO 2025
Year: 2025

Transformer architectures can effectively learn language-conditioned, multi-task 3D open-loop manipulation policies from demonstrations by jointly processing natural language instructions and 3D observations. However, although both the robot policy and language instructions inherently encode rich 3D geometric structures, standard transformers lack built-in guarantees of geometric consistency, often resulting in unpredictable behavior under SE(3) transformations of the scene. In this paper, we leverage SE(3) equivariance as a key structural property shared by both policy and language, and propose EquAct-a novel SE(3)-equivariant multi-task transformer. EquAct is theoretically guaranteed to be SE(3) equivariant and consists of two key components: (1) an efficient SE(3)-equivariant point cloud-based U-net with spherical Fourier features for policy reasoning, and (2) SE(3)-invariant Feature-wise Linear Modulation (iFiLM) layers for language conditioning. To evaluate its spatial generalization ability, we benchmark EquAct on 18 RLBench simulation tasks with both SE(3) and SE(2) scene perturbations, and on 4 physical tasks. EquAct performs state-of-the-art across these simulation and physical tasks.
CRISP-NAM: Competing Risks Interpretable Survival Prediction with Neural Additive Models
Venue: arXiv cs.LG 2025
Year: 2025

Competing risks are crucial considerations in survival modelling, particularly in healthcare domains where patients may experience multiple distinct event types. We propose CRISP-NAM (Competing Risks Interpretable Survival Prediction with Neural Additive Models), an interpretable neural additive model for competing risks survival analysis which extends the neural additive architecture to model cause-specific hazards while preserving feature-level interpretability. Each feature contributes independently to risk estimation through dedicated neural networks, allowing for visualization of complex non-linear relationships between covariates and each competing risk. We demonstrate competitive performance on multiple datasets compared to existing approaches.
YOLO-SPCI: Enhancing Remote Sensing Object Detection via Selective-Perspective-Class Integration
Venue: arXiv cs.CV 2025
Year: 2025

Object detection in remote sensing imagery remains a challenging task due to extreme scale variation, dense object distributions, and cluttered backgrounds. While recent detectors such as YOLOv8 have shown promising results, their backbone architectures lack explicit mechanisms to guide multi-scale feature refinement, limiting performance on high-resolution aerial data. In this work, we propose YOLO-SPCI, an attention-enhanced detection framework that introduces a lightweight Selective-Perspective-Class Integration (SPCI) module to improve feature representation. The SPCI module integrates three components: a Selective Stream Gate (SSG) for adaptive regulation of global feature flow, a Perspective Fusion Module (PFM) for context-aware multi-scale integration, and a Class Discrimination Module (CDM) to enhance inter-class separability. We embed two SPCI blocks into the P3 and P5 stages of the YOLOv8 backbone, enabling effective refinement while preserving compatibility with the original neck and head. Experiments on the NWPU VHR-10 dataset demonstrate that YOLO-SPCI achieves superior performance compared to state-of-the-art detectors.
AutoJudger: An Agent-Driven Framework for Efficient Benchmarking of MLLMs
Venue: arXiv cs.CL 2025
Year: 2025

Evaluating multimodal large language models (MLLMs) is increasingly expensive, as the growing size and cross-modality complexity of benchmarks demand significant scoring efforts. To tackle with this difficulty, we introduce AutoJudger, an agent-driven framework for efficient and adaptive benchmarking of MLLMs that tackles this escalating cost. AutoJudger employs the Item Response Theory (IRT) to estimate the question difficulty and an autonomous evaluation agent to dynamically select the most informative test questions based on the model's real-time performance. Specifically, AutoJudger incorporates two pivotal components: a semantic-aware retrieval mechanism to ensure that selected questions cover diverse and challenging scenarios across both vision and language modalities, and a dynamic memory that maintains contextual statistics of previously evaluated questions to guide coherent and globally informed question selection throughout the evaluation process. Extensive experiments on four representative multimodal benchmarks demonstrate that our adaptive framework dramatically reduces evaluation expenses, i.e. AutoJudger uses only 4% of the data to achieve over 90% ranking accuracy with the full benchmark evaluation on MMT-Bench.
Leveraging the Power of Conversations: Optimal Key Term Selection in Conversational Contextual Bandits
Venue: arXiv cs.LG 2025
Year: 2025

Conversational recommender systems proactively query users with relevant "key terms" and leverage the feedback to elicit users' preferences for personalized recommendations. Conversational contextual bandits, a prevalent approach in this domain, aim to optimize preference learning by balancing exploitation and exploration. However, several limitations hinder their effectiveness in real-world scenarios. First, existing algorithms employ key term selection strategies with insufficient exploration, often failing to thoroughly probe users' preferences and resulting in suboptimal preference estimation. Second, current algorithms typically rely on deterministic rules to initiate conversations, causing unnecessary interactions when preferences are well-understood and missed opportunities when preferences are uncertain. To address these limitations, we propose three novel algorithms: CLiSK, CLiME, and CLiSK-ME. CLiSK introduces smoothed key term contexts to enhance exploration in preference learning, CLiME adaptively initiates conversations based on preference uncertainty, and CLiSK-ME integrates both techniques. We theoretically prove that all three algorithms achieve a tighter regret upper bound of $O(\sqrt{dT\log{T}})$ with respect to the time horizon $T$, improving upon existing methods. Additionally, we provide a matching lower bound $Ω(\sqrt{dT})$ for conversational bandits, demonstrating that our algorithms are nearly minimax optimal. Extensive evaluations on both synthetic and real-world datasets show that our approaches achieve at least a 14.6% improvement in cumulative regret.
GUARD:Dual-Agent based Backdoor Defense on Chain-of-Thought in Neural Code Generation
Venue: arXiv cs.SE 2025
Year: 2025

With the widespread application of large language models in code generation, recent studies demonstrate that employing additional Chain-of-Thought generation models can significantly enhance code generation performance by providing explicit reasoning steps. However, as external components, CoT models are particularly vulnerable to backdoor attacks, which existing defense mechanisms often fail to detect effectively. To address this challenge, we propose GUARD, a novel dual-agent defense framework specifically designed to counter CoT backdoor attacks in neural code generation. GUARD integrates two core components: GUARD-Judge, which identifies suspicious CoT steps and potential triggers through comprehensive analysis, and GUARD-Repair, which employs a retrieval-augmented generation approach to regenerate secure CoT steps for identified anomalies. Experimental results show that GUARD effectively mitigates attacks while maintaining generation quality, advancing secure code generation systems.
Hume: Introducing System-2 Thinking in Visual-Language-Action Model
Venue: arXiv cs.RO 2025
Year: 2025

Humans practice slow thinking before performing actual actions when handling complex tasks in the physical world. This thinking paradigm, recently, has achieved remarkable advancement in boosting Large Language Models (LLMs) to solve complex tasks in digital domains. However, the potential of slow thinking remains largely unexplored for robotic foundation models interacting with the physical world. In this work, we propose Hume: a dual-system Vision-Language-Action (VLA) model with value-guided System-2 thinking and cascaded action denoising, exploring human-like thinking capabilities of Vision-Language-Action models for dexterous robot control. System 2 of Hume implements value-Guided thinking by extending a Vision-Language-Action Model backbone with a novel value-query head to estimate the state-action value of predicted actions. The value-guided thinking is conducted by repeat sampling multiple action candidates and selecting one according to state-action value. System 1 of Hume is a lightweight reactive visuomotor policy that takes System 2 selected action and performs cascaded action denoising for dexterous robot control. At deployment time, System 2 performs value-guided thinking at a low frequency while System 1 asynchronously receives the System 2 selected action candidate and predicts fluid actions in real time. We show that Hume outperforms the existing state-of-the-art Vision-Language-Action models across multiple simulation benchmark and real-robot deployments.
Be Decisive: Noise-Induced Layouts for Multi-Subject Generation
Venue: arXiv cs.CV 2025
Year: 2025

Generating multiple distinct subjects remains a challenge for existing text-to-image diffusion models. Complex prompts often lead to subject leakage, causing inaccuracies in quantities, attributes, and visual features. Preventing leakage among subjects necessitates knowledge of each subject's spatial location. Recent methods provide these spatial locations via an external layout control. However, enforcing such a prescribed layout often conflicts with the innate layout dictated by the sampled initial noise, leading to misalignment with the model's prior. In this work, we introduce a new approach that predicts a spatial layout aligned with the prompt, derived from the initial noise, and refines it throughout the denoising process. By relying on this noise-induced layout, we avoid conflicts with externally imposed layouts and better preserve the model's prior. Our method employs a small neural network to predict and refine the evolving noise-induced layout at each denoising step, ensuring clear boundaries between subjects while maintaining consistency. Experimental results show that this noise-aligned strategy achieves improved text-image alignment and more stable multi-subject generation compared to existing layout-guided techniques, while preserving the rich diversity of the model's original distribution.
Reinforcing General Reasoning without Verifiers
Venue: arXiv cs.LG 2025
Year: 2025

The recent paradigm shift towards training large language models (LLMs) using DeepSeek-R1-Zero-style reinforcement learning (RL) on verifiable rewards has led to impressive advancements in code and mathematical reasoning. However, this methodology is limited to tasks where rule-based answer verification is possible and does not naturally extend to real-world domains such as chemistry, healthcare, engineering, law, biology, business, and economics. Current practical workarounds use an additional LLM as a model-based verifier; however, this introduces issues such as reliance on a strong verifier LLM, susceptibility to reward hacking, and the practical burden of maintaining the verifier model in memory during training. To address this and extend DeepSeek-R1-Zero-style training to general reasoning domains, we propose a verifier-free method (VeriFree) that bypasses answer verification and instead uses RL to directly maximize the probability of generating the reference answer. We compare VeriFree with verifier-based methods and demonstrate that, in addition to its significant practical benefits and reduced compute requirements, VeriFree matches and even surpasses verifier-based methods on extensive evaluations across MMLU-Pro, GPQA, SuperGPQA, and math-related benchmarks. Moreover, we provide insights into this method from multiple perspectives: as an elegant integration of training both the policy and implicit verifier in a unified model, and as a variational optimization approach. Code is available at https://github.com/sail-sg/VeriFree.
How does Alignment Enhance LLMs' Multilingual Capabilities? A Language Neurons Perspective
Venue: arXiv cs.CL 2025
Year: 2025

Multilingual Alignment is an effective and representative paradigm to enhance LLMs' multilingual capabilities, which transfers the capabilities from the high-resource languages to the low-resource languages. Meanwhile, some research on language-specific neurons provides a new perspective to analyze and understand LLMs' mechanisms. However, we find that there are many neurons that are shared by multiple but not all languages and cannot be correctly classified. In this work, we propose a ternary classification methodology that categorizes neurons into three types, including language-specific neurons, language-related neurons, and general neurons. And we propose a corresponding identification algorithm to distinguish these different types of neurons. Furthermore, based on the distributional characteristics of different types of neurons, we divide the LLMs' internal process for multilingual inference into four parts: (1) multilingual understanding, (2) shared semantic space reasoning, (3) multilingual output space transformation, and (4) vocabulary space outputting. Additionally, we systematically analyze the models before and after alignment with a focus on different types of neurons. We also analyze the phenomenon of ''Spontaneous Multilingual Alignment''. Overall, our work conducts a comprehensive investigation based on different types of neurons, providing empirical results and valuable insights to better understand multilingual alignment and multilingual capabilities of LLMs.