OpenRaiser/Intern-Atlas huggingface dataset:
nnMIL: A generalizable multiple instance learning framework for computational pathology
Venue: arXiv cs.CV 2025
Year: 2025

Computational pathology holds substantial promise for improving diagnosis and guiding treatment decisions. Recent pathology foundation models enable the extraction of rich patch-level representations from large-scale whole-slide images (WSIs), but current approaches for aggregating these features into slide-level predictions remain constrained by design limitations that hinder generalizability and reliability. Here, we developed nnMIL, a simple yet broadly applicable multiple-instance learning framework that connects patch-level foundation models to robust slide-level clinical inference. nnMIL introduces random sampling at both the patch and feature levels, enabling large-batch optimization, task-aware sampling strategies, and efficient and scalable training across datasets and model architectures. A lightweight aggregator performs sliding-window inference to generate ensemble slide-level predictions and supports principled uncertainty estimation. Across 40,000 WSIs encompassing 35 clinical tasks and four pathology foundation models, nnMIL consistently outperformed existing MIL methods for disease diagnosis, histologic subtyping, molecular biomarker detection, and pan- cancer prognosis prediction. It further demonstrated strong cross-model generalization, reliable uncertainty quantification, and robust survival stratification in multiple external cohorts. In conclusion, nnMIL offers a practical and generalizable solution for translating pathology foundation models into clinically meaningful predictions, advancing the development and deployment of reliable AI systems in real-world settings.
On-Premise SLMs vs. Commercial LLMs: Prompt Engineering and Incident Classification in SOCs and CSIRTs
Venue: arXiv cs.CR 2025
Year: 2025

In this study, we evaluate open-source models for security incident classification, comparing them with proprietary models. We utilize a dataset of anonymized real incidents, categorized according to the NIST SP 800-61r3 taxonomy and processed using five prompt-engineering techniques (PHP, SHP, HTP, PRP, and ZSL). The results indicate that, although proprietary models still exhibit higher accuracy, locally deployed open-source models provide advantages in privacy, cost-effectiveness, and data sovereignty.
A visual study of ICP variants for Lidar Odometry
Venue: arXiv cs.RO 2025
Year: 2025

Odometry with lidar sensors is a state-of-the-art method to estimate the ego pose of a moving vehicle. Many implementations of lidar odometry use variants of the Iterative Closest Point (ICP) algorithm. Real-world effects such as dynamic objects, non-overlapping areas, and sensor noise diminish the accuracy of ICP. We build on a recently proposed method that makes these effects visible by visualizing the multidimensional objective function of ICP in two dimensions. We use this method to study different ICP variants in the context of lidar odometry. In addition, we propose a novel method to filter out dynamic objects and to address the ego blind spot problem.
How to Train Private Clinical Language Models: A Comparative Study of Privacy-Preserving Pipelines for ICD-9 Coding
Venue: arXiv cs.LG 2025
Year: 2025

Large language models trained on clinical text risk exposing sensitive patient information, yet differential privacy (DP) methods often severely degrade the diagnostic accuracy needed for deployment. Despite rapid progress in DP optimisation and text generation, it remains unclear which privacy-preserving strategy actually works best for clinical language tasks. We present the first systematic head-to-head comparison of four training pipelines for automated diagnostic coding from hospital discharge summaries. All pipelines use identical 1B-parameter models and matched privacy budgets to predict ICD-9 codes. At moderate and relaxed privacy budgets ($\varepsilon \in \{4, 6\}$), knowledge distillation from DP-trained teachers outperforms both direct DP-SGD and DP-synthetic data training, recovering up to 63\% of the non-private performance whilst maintaining strong empirical privacy (membership-inference AUC $\approx$ 0.5). These findings expose large differences in the privacy-utility trade-off across architectures and identify knowledge distillation as the most practical route to privacy-preserving clinical NLP.
LFreeDA: Label-Free Drift Adaptation for Windows Malware Detection
Venue: arXiv cs.CR 2025
Year: 2025

Machine learning (ML)-based malware detectors degrade over time as concept drift introduces new and evolving families unseen during training. Retraining is limited by the cost and time of manual labeling or sandbox analysis. Existing approaches mitigate this via drift detection and selective labeling, but fully label-free adaptation remains largely unexplored. Recent self-training methods use a previously trained model to generate pseudo-labels for unlabeled data and then train a new model on these labels. The unlabeled data are used only for inference and do not participate in training the earlier model. We argue that these unlabeled samples still carry valuable information that can be leveraged when incorporated appropriately into training. This paper introduces LFreeDA, an end-to-end framework that adapts malware classifiers to drift without manual labeling or drift detection. LFreeDA first performs unsupervised domain adaptation on malware images, jointly training on labeled and unlabeled samples to infer pseudo-labels and prune noisy ones. It then adapts a classifier on CFG representations using the labeled and selected pseudo-labeled data, leveraging the scalability of images for pseudo-labeling and the richer semantics of CFGs for final adaptation. Evaluations on the real-world MB-24+ dataset show that LFreeDA improves accuracy by up to 12.6% and F1 by 11.1% over no-adaptation lower bounds, and is only 4% and 3.4% below fully supervised upper bounds in accuracy and F1, respectively. It also matches the performance of state-of-the-art methods provided with ground truth labels for 300 target samples. Additional results on two controlled-drift benchmarks further confirm that LFreeDA maintains malware detection performance as malware evolves without human labeling.
Task Specific Sharpness Aware O-RAN Resource Management using Multi Agent Reinforcement Learning
Venue: arXiv cs.AI 2025
Year: 2025

Next-generation networks utilize the Open Radio Access Network (O-RAN) architecture to enable dynamic resource management, facilitated by the RAN Intelligent Controller (RIC). While deep reinforcement learning (DRL) models show promise in optimizing network resources, they often struggle with robustness and generalizability in dynamic environments. This paper introduces a novel resource management approach that enhances the Soft Actor Critic (SAC) algorithm with Sharpness-Aware Minimization (SAM) in a distributed Multi-Agent RL (MARL) framework. Our method introduces an adaptive and selective SAM mechanism, where regularization is explicitly driven by temporal-difference (TD)-error variance, ensuring that only agents facing high environmental complexity are regularized. This targeted strategy reduces unnecessary overhead, improves training stability, and enhances generalization without sacrificing learning efficiency. We further incorporate a dynamic $ρ$ scheduling scheme to refine the exploration-exploitation trade-off across agents. Experimental results show our method significantly outperforms conventional DRL approaches, yielding up to a $22\%$ improvement in resource allocation efficiency and ensuring superior QoS satisfaction across diverse O-RAN slices.
FRIENDS GUI: A graphical user interface for data collection and visualization of vaping behavior from a passive vaping monitor
Venue: arXiv cs.SE 2025
Year: 2025

Understanding puffing topography (PT), which includes puff duration, intra puff interval, and puff count per session, is critical for evaluating Electronic Nicotine Delivery Systems (ENDS) use, toxicant exposure, and informing regulatory decisions. We developed FRIENDS (Flexible Robust Instrumentation of ENDS), an open-source device that records puffing and touch events of ENDS by attaching to it. This paper introduces the FRIENDS GUI that improves accessibility and interpretability of data collected by FRIENDS. The GUI is a Python-based open-source tool that extracts, decodes, and visualizes 24-hour puffing data from the FRIENDS device. Validation using 24-hour experimental data confirmed accurate timestamp conversion, reliable event decoding, and effective behavioral visualization. The software is freely available on GitHub for public use.
CKDA: Cross-modality Knowledge Disentanglement and Alignment for Visible-Infrared Lifelong Person Re-identification
Venue: arXiv cs.CV 2025
Year: 2025

Lifelong person Re-IDentification (LReID) aims to match the same person employing continuously collected individual data from different scenarios. To achieve continuous all-day person matching across day and night, Visible-Infrared Lifelong person Re-IDentification (VI-LReID) focuses on sequential training on data from visible and infrared modalities and pursues average performance over all data. To this end, existing methods typically exploit cross-modal knowledge distillation to alleviate the catastrophic forgetting of old knowledge. However, these methods ignore the mutual interference of modality-specific knowledge acquisition and modality-common knowledge anti-forgetting, where conflicting knowledge leads to collaborative forgetting. To address the above problems, this paper proposes a Cross-modality Knowledge Disentanglement and Alignment method, called CKDA, which explicitly separates and preserves modality-specific knowledge and modality-common knowledge in a balanced way. Specifically, a Modality-Common Prompting (MCP) module and a Modality-Specific Prompting (MSP) module are proposed to explicitly disentangle and purify discriminative information that coexists and is specific to different modalities, avoiding the mutual interference between both knowledge. In addition, a Cross-modal Knowledge Alignment (CKA) module is designed to further align the disentangled new knowledge with the old one in two mutually independent inter- and intra-modality feature spaces based on dual-modality prototypes in a balanced manner. Extensive experiments on four benchmark datasets verify the effectiveness and superiority of our CKDA against state-of-the-art methods. The source code of this paper is available at https://github.com/PKU-ICST-MIPL/CKDA-AAAI2026.
Complex-Valued 2D Gaussian Representation for Computer-Generated Holography
Venue: arXiv cs.CV 2025
Year: 2025

We propose a new hologram representation based on structured complex-valued 2D Gaussian primitives, which replaces per-pixel information storage and reduces the parameter search space by up to 10:1. To enable end-to-end training, we develop a differentiable rasterizer for our representation, integrated with a GPU-optimized light propagation kernel in free space. Our extensive experiments show that our method achieves up to 2.5x lower VRAM usage and 50% faster optimization while producing higher-fidelity reconstructions than existing methods. We further introduce a conversion procedure that adapts our representation to practical hologram formats, including smooth and random phase-only holograms. Our experiments show that this procedure can effectively suppress noise artifacts observed in previous methods. By reducing the hologram parameter search space, our representation enables a more scalable hologram estimation in the next-generation computer-generated holography systems.
Oversampling techniques for predicting COVID-19 patient length of stay
Venue: arXiv cs.LG 2025
Year: 2025

COVID-19 is a respiratory disease that caused a global pandemic in 2019. It is highly infectious and has the following symptoms: fever or chills, cough, shortness of breath, fatigue, muscle or body aches, headache, the new loss of taste or smell, sore throat, congestion or runny nose, nausea or vomiting, and diarrhea. These symptoms vary in severity; some people with many risk factors have been known to have lengthy hospital stays or die from the disease. In this paper, we analyze patients' electronic health records (EHR) to predict the severity of their COVID-19 infection using the length of stay (LOS) as our measurement of severity. This is an imbalanced classification problem, as many people have a shorter LOS rather than a longer one. To combat this problem, we synthetically create alternate oversampled training data sets. Once we have this oversampled data, we run it through an Artificial Neural Network (ANN), which during training has its hyperparameters tuned using Bayesian optimization. We select the model with the best F1 score and then evaluate it and discuss it.
CellGenNet: A Knowledge-Distilled Framework for Robust Cell Segmentation in Cancer Tissues
Venue: arXiv cs.CV 2025
Year: 2025

Accurate nuclei segmentation in microscopy whole slide images (WSIs) remains challenging due to variability in staining, imaging conditions, and tissue morphology. We propose CellGenNet, a knowledge distillation framework for robust cross-tissue cell segmentation under limited supervision. CellGenNet adopts a student-teacher architecture, where a capacity teacher is trained on sparse annotations and generates soft pseudo-labels for unlabeled regions. The student is optimized using a joint objective that integrates ground-truth labels, teacher-derived probabilistic targets, and a hybrid loss function combining binary cross-entropy and Tversky loss, enabling asymmetric penalties to mitigate class imbalance and better preserve minority nuclear structures. Consistency regularization and layerwise dropout further stabilize feature representations and promote reliable feature transfer. Experiments across diverse cancer tissue WSIs show that CellGenNet improves segmentation accuracy and generalization over supervised and semi-supervised baselines, supporting scalable and reproducible histopathology analysis.
Beyond GeneGPT: A Multi-Agent Architecture with Open-Source LLMs for Enhanced Genomic Question Answering
Venue: arXiv cs.AI 2025
Year: 2025

Genomic question answering often requires complex reasoning and integration across diverse biomedical sources. GeneGPT addressed this challenge by combining domain-specific APIs with OpenAI's code-davinci-002 large language model to enable natural language interaction with genomic databases. However, its reliance on a proprietary model limits scalability, increases operational costs, and raises concerns about data privacy and generalization. In this work, we revisit and reproduce GeneGPT in a pilot study using open source models, including Llama 3.1, Qwen2.5, and Qwen2.5 Coder, within a monolithic architecture; this allows us to identify the limitations of this approach. Building on this foundation, we then develop OpenBioLLM, a modular multi-agent framework that extends GeneGPT by introducing agent specialization for tool routing, query generation, and response validation. This enables coordinated reasoning and role-based task execution. OpenBioLLM matches or outperforms GeneGPT on over 90% of the benchmark tasks, achieving average scores of 0.849 on Gene-Turing and 0.830 on GeneHop, while using smaller open-source models without additional fine-tuning or tool-specific pretraining. OpenBioLLM's modular multi-agent design reduces latency by 40-50% across benchmark tasks, significantly improving efficiency without compromising model capability. The results of our comprehensive evaluation highlight the potential of open-source multi-agent systems for genomic question answering. Code and resources are available at https://github.com/ielab/OpenBioLLM.
Knowledge-Informed Automatic Feature Extraction via Collaborative Large Language Model Agents
Venue: arXiv cs.AI 2025
Year: 2025

The performance of machine learning models on tabular data is critically dependent on high-quality feature engineering. While Large Language Models (LLMs) have shown promise in automating feature extraction (AutoFE), existing methods are often limited by monolithic LLM architectures, simplistic quantitative feedback, and a failure to systematically integrate external domain knowledge. This paper introduces Rogue One, a novel, LLM-based multi-agent framework for knowledge-informed automatic feature extraction. Rogue One operationalizes a decentralized system of three specialized agents-Scientist, Extractor, and Tester-that collaborate iteratively to discover, generate, and validate predictive features. Crucially, the framework moves beyond primitive accuracy scores by introducing a rich, qualitative feedback mechanism and a "flooding-pruning" strategy, allowing it to dynamically balance feature exploration and exploitation. By actively incorporating external knowledge via an integrated retrieval-augmented (RAG) system, Rogue One generates features that are not only statistically powerful but also semantically meaningful and interpretable. We demonstrate that Rogue One significantly outperforms state-of-the-art methods on a comprehensive suite of 19 classification and 9 regression datasets. Furthermore, we show qualitatively that the system surfaces novel, testable hypotheses, such as identifying a new potential biomarker in the myocardial dataset, underscoring its utility as a tool for scientific discovery.
GPU-Initiated Networking for NCCL
Venue: arXiv cs.DC 2025
Year: 2025

Modern AI workloads, especially Mixture-of-Experts (MoE) architectures, increasingly demand low-latency, fine-grained GPU-to-GPU communication with device-side control. Traditional GPU communication follows a host-initiated model, where the CPU orchestrates all communication operations - a characteristic of the CUDA runtime. Although robust for collective operations, applications requiring tight integration of computation and communication can benefit from device-initiated communication that eliminates CPU coordination overhead. NCCL 2.28 introduces the Device API with three operation modes: Load/Store Accessible (LSA) for NVLink/PCIe, Multimem for NVLink SHARP, and GPU-Initiated Networking (GIN) for network RDMA. This paper presents the GIN architecture, design, semantics, and highlights its impact on MoE communication. GIN builds on a three-layer architecture: i) NCCL Core host-side APIs for device communicator setup and collective memory window registration; ii) Device-side APIs for remote memory operations callable from CUDA kernels; and iii) A network plugin architecture with dual semantics (GPUDirect Async Kernel-Initiated and Proxy) for broad hardware support. The GPUDirect Async Kernel-Initiated backend leverages DOCA GPUNetIO for direct GPU-to-NIC communication, while the Proxy backend provides equivalent functionality via lock-free GPU-to-CPU queues over standard RDMA networks. We demonstrate GIN's practicality through integration with DeepEP, an MoE communication library. Comprehensive benchmarking shows that GIN provides device-initiated communication within NCCL's unified runtime, combining low-latency operations with NCCL's collective algorithms and production infrastructure.
TiCAL:Typicality-Based Consistency-Aware Learning for Multimodal Emotion Recognition
Venue: arXiv cs.CV 2025
Year: 2025

Multimodal Emotion Recognition (MER) aims to accurately identify human emotional states by integrating heterogeneous modalities such as visual, auditory, and textual data. Existing approaches predominantly rely on unified emotion labels to supervise model training, often overlooking a critical challenge: inter-modal emotion conflicts, wherein different modalities within the same sample may express divergent emotional tendencies. In this work, we address this overlooked issue by proposing a novel framework, Typicality-based Consistent-aware Multimodal Emotion Recognition (TiCAL), inspired by the stage-wise nature of human emotion perception. TiCAL dynamically assesses the consistency of each training sample by leveraging pseudo unimodal emotion labels alongside a typicality estimation. To further enhance emotion representation, we embed features in a hyperbolic space, enabling the capture of fine-grained distinctions among emotional categories. By incorporating consistency estimates into the learning process, our method improves model performance, particularly on samples exhibiting high modality inconsistency. Extensive experiments on benchmark datasets, e.g, CMU-MOSEI and MER2023, validate the effectiveness of TiCAL in mitigating inter-modal emotional conflicts and enhancing overall recognition accuracy, e.g., with about 2.6% improvements over the state-of-the-art DMD.
DCL-SE: Dynamic Curriculum Learning for Spatiotemporal Encoding of Brain Imaging
Venue: arXiv cs.CV 2025
Year: 2025

High-dimensional neuroimaging analyses for clinical diagnosis are often constrained by compromises in spatiotemporal fidelity and by the limited adaptability of large-scale, general-purpose models. To address these challenges, we introduce Dynamic Curriculum Learning for Spatiotemporal Encoding (DCL-SE), an end-to-end framework centered on data-driven spatiotemporal encoding (DaSE). We leverage Approximate Rank Pooling (ARP) to efficiently encode three-dimensional volumetric brain data into information-rich, two-dimensional dynamic representations, and then employ a dynamic curriculum learning strategy, guided by a Dynamic Group Mechanism (DGM), to progressively train the decoder, refining feature extraction from global anatomical structures to fine pathological details. Evaluated across six publicly available datasets, including Alzheimer's disease and brain tumor classification, cerebral artery segmentation, and brain age prediction, DCL-SE consistently outperforms existing methods in accuracy, robustness, and interpretability. These findings underscore the critical importance of compact, task-specific architectures in the era of large-scale pretrained networks.
Multimodal Continual Instruction Tuning with Dynamic Gradient Guidance
Venue: arXiv cs.CV 2025
Year: 2025

Multimodal continual instruction tuning enables multimodal large language models to sequentially adapt to new tasks while building upon previously acquired knowledge. However, this continual learning paradigm faces the significant challenge of catastrophic forgetting, where learning new tasks leads to performance degradation on previous ones. In this paper, we introduce a novel insight into catastrophic forgetting by conceptualizing it as a problem of missing gradients from old tasks during new task learning. Our approach approximates these missing gradients by leveraging the geometric properties of the parameter space, specifically using the directional vector between current parameters and previously optimal parameters as gradient guidance. This approximated gradient can be further integrated with real gradients from a limited replay buffer and regulated by a Bernoulli sampling strategy that dynamically balances model stability and plasticity. Extensive experiments on multimodal continual instruction tuning datasets demonstrate that our method achieves state-of-the-art performance without model expansion, effectively mitigating catastrophic forgetting while maintaining a compact architecture.