OpenRaiser/Intern-Atlas huggingface dataset:
LLMs are not Zero-Shot Reasoners for Biomedical Information Extraction
Venue: arXiv cs.CL 2025
Year: 2025

Large Language Models (LLMs) are increasingly adopted for applications in healthcare, reaching the performance of domain experts on tasks such as question answering and document summarisation. Despite their success on these tasks, it is unclear how well LLMs perform on tasks that are traditionally pursued in the biomedical domain, such as structured information extraction. To bridge this gap, in this paper, we systematically benchmark LLM performance in Medical Classification and Named Entity Recognition (NER) tasks. We aim to disentangle the contribution of different factors to the performance, particularly the impact of LLMs' task knowledge and reasoning capabilities, their (parametric) domain knowledge, and addition of external knowledge. To this end, we evaluate various open LLMs - including BioMistral and Llama-2 models - on a diverse set of biomedical datasets, using standard prompting, Chain of-Thought (CoT) and Self Consistency based reasoning as well as Retrieval-Augmented Generation (RAG) with PubMed and Wikipedia corpora. Counter intuitively, our results reveal that standard prompting consistently outperforms more complex techniques across both tasks, laying bare the limitations in the current application of CoT, self-consistency and RAG in the biomedical domain. Our findings suggest that advanced prompting methods developed for knowledge- or reasoning-intensive tasks, such as CoT or RAG, are not easily portable to biomedical tasks where precise structured outputs are required. This highlights the need for more effective integration of external knowledge and reasoning mechanisms in LLMs to enhance their performance in real-world biomedical applications.
GRATR: Zero-Shot Evidence Graph Retrieval-Augmented Trustworthiness Reasoning
Venue: arXiv cs.AI 2025
Year: 2025

Trustworthiness reasoning aims to enable agents in multiplayer games with incomplete information to identify potential allies and adversaries, thereby enhancing decision-making. In this paper, we introduce the graph retrieval-augmented trustworthiness reasoning (GRATR) framework, which retrieves observable evidence from the game environment to inform decision-making by large language models (LLMs) without requiring additional training, making it a zero-shot approach. Within the GRATR framework, agents first observe the actions of other players and evaluate the resulting shifts in inter-player trust, constructing a corresponding trustworthiness graph. During decision-making, the agent performs multi-hop retrieval to evaluate trustworthiness toward a specific target, where evidence chains are retrieved from multiple trusted sources to form a comprehensive assessment. Experiments in the multiplayer game \emph{Werewolf} demonstrate that GRATR outperforms the alternatives, improving reasoning accuracy by 50.5\% and reducing hallucination by 30.6\% compared to the baseline method. Additionally, when tested on a dataset of Twitter tweets during the U.S. election period, GRATR surpasses the baseline method by 10.4\% in accuracy, highlighting its potential in real-world applications such as intent analysis.
FlexEdit: Marrying Free-Shape Masks to VLLM for Flexible Image Editing
Venue: arXiv cs.CV 2025
Year: 2025

Combining Vision Large Language Models (VLLMs) with diffusion models offers a powerful method for executing image editing tasks based on human language instructions. However, language instructions alone often fall short in accurately conveying user requirements, particularly when users want to add, replace elements in specific areas of an image. Luckily, masks can effectively indicate the exact locations or elements to be edited, while they require users to precisely draw the shapes at the desired locations, which is highly user-unfriendly. To address this, we propose FlexEdit, an end-to-end image editing method that leverages both free-shape masks and language instructions for Flexible Editing. Our approach employs a VLLM in comprehending the image content, mask, and user instructions. Additionally, we introduce the Mask Enhance Adapter (MEA) that fuses the embeddings of the VLLM with the image data, ensuring a seamless integration of mask information and model output embeddings. Furthermore, we construct FSMI-Edit, a benchmark specifically tailored for free-shape mask, including 8 types of free-shape mask. Extensive experiments show that our method achieves state-of-the-art (SOTA) performance in LLM-based image editing, and our simple prompting technique stands out in its effectiveness. The code and data can be found at https://github.com/A-new-b/flex_edit.
Dynamics of Meta-learning Representation in the Teacher-student Scenario
Venue: arXiv cs.LG 2025
Year: 2025

Gradient-based meta-learning algorithms have gained popularity for their ability to train models on new tasks using limited data. Empirical observations indicate that such algorithms are able to learn a shared representation across tasks, which is regarded as a key factor in their success. However, the in-depth theoretical understanding of the learning dynamics and the origin of the shared representation remains underdeveloped. In this work, we investigate the meta-learning dynamics of nonlinear two-layer neural networks trained on streaming tasks in the teacher-student scenario. Through the lens of statistical physics analysis, we characterize the macroscopic behavior of the meta-training processes, the formation of the shared representation, and the generalization ability of the model on new tasks. The analysis also points to the importance of the choice of certain hyperparameters of the learning algorithms.
A Large Model for Non-invasive and Personalized Management of Breast Cancer from Multiparametric MRI
Venue: arXiv cs.CV 2025
Year: 2025

Breast Magnetic Resonance Imaging (MRI) demonstrates the highest sensitivity for breast cancer detection among imaging modalities and is standard practice for high-risk women. Interpreting the multi-sequence MRI is time-consuming and prone to subjective variation. We develop a large mixture-of-modality-experts model (MOME) that integrates multiparametric MRI information within a unified structure, leveraging breast MRI scans from 5,205 female patients in China for model development and validation. MOME matches four senior radiologists' performance in identifying breast cancer and outperforms a junior radiologist. The model is able to reduce unnecessary biopsies in Breast Imaging-Reporting and Data System (BI-RADS) 4 patients, classify triple-negative breast cancer, and predict pathological complete response to neoadjuvant chemotherapy. MOME further supports inference with missing modalities and provides decision explanations by highlighting lesions and measuring modality contributions. To summarize, MOME exemplifies an accurate and robust multimodal model for noninvasive, personalized management of breast cancer patients via multiparametric MRI. Code is available at https://github.com/LLYXC/MOME/tree/main.
Continual Gesture Learning without Data via Synthetic Feature Sampling
Venue: arXiv cs.CV 2025
Year: 2025

Data-Free Class Incremental Learning (DFCIL) aims to enable models to continuously learn new classes while retraining knowledge of old classes, even when the training data for old classes is unavailable. Although explored primarily with image datasets by researchers, this study focuses on investigating DFCIL for skeleton-based gesture classification due to its significant real-world implications, particularly considering the growing prevalence of VR/AR headsets where gestures serve as the primary means of control and interaction. In this work, we made an intriguing observation: skeleton models trained with base classes(even very limited) demonstrate strong generalization capabilities to unseen classes without requiring additional training. Building on this insight, we developed Synthetic Feature Replay (SFR) that can sample synthetic features from class prototypes to replay for old classes and augment for new classes (under a few-shot setting). Our proposed method showcases significant advancements over the state-of-the-art, achieving up to 15% enhancements in mean accuracy across all steps and largely mitigating the accuracy imbalance between base classes and new classes.
Repeated and incontrovertible collective action failure leads to protester disengagement and radicalisation
Venue: arXiv cs.SI 2025
Year: 2025

Protest is ubiquitous in the 21st Century and the people who participate in such movements do so because they seek to bring about social change. However, social change takes time and involves repeated interactions between individual protesters, social movements and the authorities to whom they appeal for change. These complexities of time and scale have frustrated efforts to isolate the conditions that foster an enduring movement, on the one hand, and the adoption of more radical (unconventional, unacceptable) tactics on the other. Here, we present a novel, theoretically informed and empirically evidenced, agent-based model of collective action that provides a unified framework to address these dual challenges. We model ~10,000 iterations within a simulated society and show that where an authority is responsive, and protesters can (cognitively and/or socially) contest the failure of their movement, a moderate conventional movement prevails. Conversely, where an authority repeatedly and incontrovertibly fails the movement, the population disengages but becomes radicalised (latent radicalism). This latter finding, whereby the whole population is disengaged but prepared to use radical methods to bring about social change, likely reflects the febrile pre-cursor state to sudden, revolutionary change. Results highlight the potential for simulations to reveal emergent, as-yet under-theorized, phenomena.
BackdoorLLM: A Comprehensive Benchmark for Backdoor Attacks and Defenses on Large Language Models
Venue: arXiv cs.AI 2025
Year: 2025

Generative large language models (LLMs) have achieved state-of-the-art results on a wide range of tasks, yet they remain susceptible to backdoor attacks: carefully crafted triggers in the input can manipulate the model to produce adversary-specified outputs. While prior research has predominantly focused on backdoor risks in vision and classification settings, the vulnerability of LLMs in open-ended text generation remains underexplored. To fill this gap, we introduce BackdoorLLM (Our BackdoorLLM benchmark was awarded First Prize in the SafetyBench competition, https://www.mlsafety.org/safebench/winners, organized by the Center for AI Safety, https://safe.ai/.), the first comprehensive benchmark for systematically evaluating backdoor threats in text-generation LLMs. BackdoorLLM provides: (i) a unified repository of benchmarks with a standardized training and evaluation pipeline; (ii) a diverse suite of attack modalities, including data poisoning, weight poisoning, hidden-state manipulation, and chain-of-thought hijacking; (iii) over 200 experiments spanning 8 distinct attack strategies, 7 real-world scenarios, and 6 model architectures; (iv) key insights into the factors that govern backdoor effectiveness and failure modes in LLMs; and (v) a defense toolkit encompassing 7 representative mitigation techniques. Our code and datasets are available at https://github.com/bboylyg/BackdoorLLM. We will continuously incorporate emerging attack and defense methodologies to support the research in advancing the safety and reliability of LLMs.
Decentralized MIMO Systems with Imperfect CSI using LMMSE Receivers
Venue: arXiv cs.IT 2025
Year: 2025

Centralized baseband processing (CBP) is required to achieve the full potential of massive multiple-input multiple-output (MIMO) systems. However, due to the large number of antennas, CBP suffers from two major issues: 1) Tremendous data interconnection between radio frequency (RF) circuitry and processing fabrics; and 2) high-dimensional computation. To this end, decentralized baseband processing (DBP) has been proposed, where the antennas at the BS are partitioned into clusters connected to separate RF circuits and equipped with separate computing units. Unfortunately, due to the decentralized structure, the optimal fusion scheme and performance analysis for DBP with general spatial correlation between clusters and imperfect channel state information (CSI) are not available in the literature. In this paper, we consider a decentralized MIMO system where all clusters adopt linear minimum mean-square error (LMMSE) receivers with imperfect CSI. Specifically, we first establish the optimal linear fusion scheme which has high computational and data input/output (I/O) costs. To reduce the costs, we further propose two sub-optimal fusion schemes with reduced complexity. For all three schemes, we derive the closed-form expressions for the signal-to-interference-and-noise ratio (SINR) by leveraging random matrix theory (RMT) and demonstrate the conditions under which the sub optimal schemes are optimal. Furthermore, we determine the optimal regularization parameter for decentralized LMMSE receivers, identify the best antenna partitioning strategy, and prove that the SINR will decrease as the number of clusters increases. Numerical simulations validate the accuracy of the theoretical results.
Keep Everyone Happy: Online Fair Division of Numerous Items with Few Copies
Venue: arXiv cs.LG 2025
Year: 2025

This paper considers a novel variant of the online fair division problem involving multiple agents in which a learner sequentially observes an indivisible item that has to be irrevocably allocated to one of the agents while satisfying a fairness and efficiency constraint. Existing algorithms assume a small number of items with a sufficiently large number of copies, which ensures a good utility estimation for all item-agent pairs from noisy bandit feedback. However, this assumption may not hold in many real-life applications, for example, an online platform that has a large number of users (items) who use the platform's service providers (agents) only a few times (a few copies of items), which makes it difficult to accurately estimate utilities for all item-agent pairs. To address this, we assume utility is an unknown function of item-agent features. We then propose algorithms that model online fair division as a contextual bandit problem, with sub-linear regret guarantees. Our experimental results further validate the effectiveness of the proposed algorithms.
Systematic Evaluation of LLM-as-a-Judge in LLM Alignment Tasks: Explainable Metrics and Diverse Prompt Templates
Venue: arXiv cs.CL 2025
Year: 2025

LLM-as-a-Judge has been widely applied to evaluate and compare different LLM alignmnet approaches (e.g., RLHF and DPO). However, concerns regarding its reliability have emerged, due to LLM judges' biases and inconsistent decision-making. Previous research has developed evaluation frameworks to assess reliability of LLM judges and their alignment with human preferences. However, the employed evaluation metrics often lack adequate explainability and fail to address LLM internal inconsistency. Additionally, existing studies inadequately explore the impact of various prompt templates when applying LLM-as-a-Judge methods, leading to potentially inconsistent comparisons between different alignment algorithms. In this work, we systematically evaluate LLM-as-a-Judge on alignment tasks by defining more theoretically interpretable evaluation metrics and explicitly mitigating LLM internal inconsistency from reliability metrics. We develop an open-source framework to evaluate, compare, and visualize the reliability and alignment of LLM judges, which facilitates practitioners to choose LLM judges for alignment tasks. In the experiments, we examine effects of diverse prompt templates on LLM-judge reliability and also demonstrate our developed framework by comparing various LLM judges on two common alignment datasets (i.e., TL;DR Summarization and HH-RLHF-Helpfulness). Our results indicate a significant impact of prompt templates on LLM judge performance, as well as a mediocre alignment level between the tested LLM judges and human evaluators.
Hierarchical Spatio-Temporal State-Space Modeling for fMRI Analysis
Venue: arXiv cs.LG 2025
Year: 2025

Recent advances in deep learning structured state space models, especially the Mamba architecture, have demonstrated remarkable performance improvements while maintaining linear complexity. In this study, we introduce functional spatiotemporal Mamba (FST-Mamba), a Mamba-based model designed for discovering neurological biomarkers using functional magnetic resonance imaging (fMRI). We focus on dynamic functional network connectivity (dFNC) derived from fMRI and propose a hierarchical spatiotemporal Mamba-based network that processes spatial and temporal information separately using Mamba-based encoders. Leveraging the topological uniqueness of the FNC matrix, we introduce a component-wise varied-scale aggregation (CVA) mechanism to aggregate connectivity across individual components within brain networks, enabling the model to capture component-level and network-level information. Additionally, we propose symmetric rotary position encoding (SymRope) to encode the relative positions of each functional connection while considering the symmetric nature of the FNC matrix. Experimental results demonstrate significant improvements in the proposed FST-Mamba model on various brain-based classification and regression tasks. We further show brain connectivities and dynamics that are crucial for the prediction. Our work reveals the substantial potential of attention-free sequence modeling in brain discovery. The codes are publicly available here: https://github.com/yuxiangwei0808/FunctionalMamba/tree/main.
Detecting the Future: All-at-Once Event Sequence Forecasting with Horizon Matching
Venue: arXiv cs.LG 2025
Year: 2025

Long-horizon events forecasting is a crucial task across various domains, including retail, finance, healthcare, and social networks. Traditional models for event sequences often extend to forecasting on a horizon using an autoregressive (recursive) multi-step strategy, which has limited effectiveness due to typical convergence to constant or repetitive outputs. To address this limitation, we introduce DEF, a novel approach for simultaneous forecasting of multiple future events on a horizon with high accuracy and diversity. Our method optimally aligns predictions with ground truth events during training by using a novel matching-based loss function. We establish a new state-of-the-art in long-horizon event prediction, achieving up to a 50% relative improvement over existing temporal point processes and event prediction models. Furthermore, we achieve state-of-the-art performance in next-event prediction tasks while demonstrating high computational efficiency during inference.
An In-Depth Investigation of Data Collection in LLM App Ecosystems
Venue: arXiv cs.CR 2025
Year: 2025

LLM app (tool) ecosystems are rapidly evolving to support sophisticated use cases that often require extensive user data collection. Given that LLM apps are developed by third parties and anecdotal evidence indicating inconsistent enforcement of policies by LLM platforms, sharing user data with these apps presents significant privacy risks. In this paper, we aim to bring transparency in data practices of LLM app ecosystems. We examine OpenAI's GPT app ecosystem as a case study. We propose an LLM-based framework to analyze the natural language specifications of GPT Actions (custom tools) and assess their data collection practices. Our analysis reveals that Actions collect excessive data across 24 categories and 145 data types, with third-party Actions collecting 6.03% more data on average. We find that several Actions violate OpenAI's policies by collecting sensitive information, such as passwords, which is explicitly prohibited by OpenAI. Lastly, we develop an LLM-based privacy policy analysis framework to automatically check the consistency of data collection by Actions with disclosures in their privacy policies. Our measurements indicate that the disclosures for most of the collected data types are omitted, with only 5.8% of Actions clearly disclosing their data collection practices.
Explainable Concept Generation through Vision-Language Preference Learning for Understanding Neural Networks' Internal Representations
Venue: arXiv cs.CV 2025
Year: 2025

Understanding the inner representation of a neural network helps users improve models. Concept-based methods have become a popular choice for explaining deep neural networks post-hoc because, unlike most other explainable AI techniques, they can be used to test high-level visual "concepts" that are not directly related to feature attributes. For instance, the concept of "stripes" is important to classify an image as a zebra. Concept-based explanation methods, however, require practitioners to guess and manually collect multiple candidate concept image sets, making the process labor-intensive and prone to overlooking important concepts. Addressing this limitation, in this paper, we frame concept image set creation as an image generation problem. However, since naively using a standard generative model does not result in meaningful concepts, we devise a reinforcement learning-based preference optimization (RLPO) algorithm that fine-tunes a vision-language generative model from approximate textual descriptions of concepts. Through a series of experiments, we demonstrate our method's ability to efficiently and reliably articulate diverse concepts that are otherwise challenging to craft manually.
Reinforcement Learning for Causal Discovery without Acyclicity Constraints
Venue: arXiv cs.LG 2025
Year: 2025

Recently, reinforcement learning (RL) has proved a promising alternative for conventional local heuristics in score-based approaches to learning directed acyclic causal graphs (DAGs) from observational data. However, the intricate acyclicity constraint still challenges the efficient exploration of the vast space of DAGs in existing methods. In this study, we introduce ALIAS (reinforced dAg Learning wIthout Acyclicity conStraints), a novel approach to causal discovery powered by the RL machinery. Our method features an efficient policy for generating DAGs in just a single step with an optimal quadratic complexity, fueled by a novel parametrization of DAGs that directly translates a continuous space to the space of all DAGs, bypassing the need for explicitly enforcing acyclicity constraints. This approach enables us to navigate the search space more effectively by utilizing policy gradient methods and established scoring functions. In addition, we provide compelling empirical evidence for the strong performance of ALIAS in comparison with state-of-the-arts in causal discovery over increasingly difficult experiment conditions on both synthetic and real datasets.