OpenRaiser/Intern-Atlas huggingface dataset:
AI-powered skin spectral imaging enables instant sepsis diagnosis and outcome prediction in critically ill patients
Venue: arXiv cs.LG 2025
Year: 2025

With sepsis remaining a leading cause of mortality, early identification of patients with sepsis and those at high risk of death is a challenge of high socioeconomic importance. Given the potential of hyperspectral imaging (HSI) to monitor microcirculatory alterations, we propose a deep learning approach to automated sepsis diagnosis and mortality prediction using a single HSI cube acquired within seconds. In a prospective observational study, we collected HSI data from the palms and fingers of more than 480 intensive care unit patients. Neural networks applied to HSI measurements predicted sepsis and mortality with areas under the receiver operating characteristic curve (AUROCs) of 0.80 and 0.72, respectively. Performance improved substantially with additional clinical data, reaching AUROCs of 0.94 for sepsis and 0.83 for mortality. We conclude that deep learning-based HSI analysis enables rapid and noninvasive prediction of sepsis and mortality, with a potential clinical value for enhancing diagnosis and treatment.
Enforcing View-Consistency in Class-Agnostic 3D Segmentation Fields
Venue: arXiv cs.CV 2025
Year: 2025

Radiance Fields have become a powerful tool for modeling 3D scenes from multiple images. However, they remain difficult to segment into semantically meaningful regions. Some methods work well using 2D semantic masks, but they generalize poorly to class-agnostic segmentations. More recent methods circumvent this issue by using contrastive learning to optimize a high-dimensional 3D feature field instead. However, recovering a segmentation then requires clustering and fine-tuning the associated hyperparameters. In contrast, we aim to identify the necessary changes in segmentation field methods to directly learn a segmentation field while being robust to inconsistent class-agnostic masks, successfully decomposing the scene into a set of objects of any class. By introducing an additional spatial regularization term and restricting the field to a limited number of competing object slots against which masks are matched, a meaningful object representation emerges that best explains the 2D supervision. Our experiments demonstrate the ability of our method to generate 3D panoptic segmentations on complex scenes, and extract high-quality 3D assets from radiance fields that can then be used in virtual 3D environments.
LNQ 2023 challenge: Benchmark of weakly-supervised techniques for mediastinal lymph node quantification
Venue: arXiv cs.CV 2025
Year: 2025

Accurate assessment of lymph node size in 3D CT scans is crucial for cancer staging, therapeutic management, and monitoring treatment response. Existing state-of-the-art segmentation frameworks in medical imaging often rely on fully annotated datasets. However, for lymph node segmentation, these datasets are typically small due to the extensive time and expertise required to annotate the numerous lymph nodes in 3D CT scans. Weakly-supervised learning, which leverages incomplete or noisy annotations, has recently gained interest in the medical imaging community as a potential solution. Despite the variety of weakly-supervised techniques proposed, most have been validated only on private datasets or small publicly available datasets. To address this limitation, the Mediastinal Lymph Node Quantification (LNQ) challenge was organized in conjunction with the 26th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2023). This challenge aimed to advance weakly-supervised segmentation methods by providing a new, partially annotated dataset and a robust evaluation framework. A total of 16 teams from 5 countries submitted predictions to the validation leaderboard, and 6 teams from 3 countries participated in the evaluation phase. The results highlighted both the potential and the current limitations of weakly-supervised approaches. On one hand, weakly-supervised approaches obtained relatively good performance with a median Dice score of $61.0\%$. On the other hand, top-ranked teams, with a median Dice score exceeding $70\%$, boosted their performance by leveraging smaller but fully annotated datasets to combine weak supervision and full supervision. This highlights both the promise of weakly-supervised methods and the ongoing need for high-quality, fully annotated data to achieve higher segmentation performance.
FEDKIM: Adaptive Federated Knowledge Injection into Medical Foundation Models
Venue: arXiv cs.LG 2025
Year: 2025

Foundation models have demonstrated remarkable capabilities in handling diverse modalities and tasks, outperforming conventional artificial intelligence (AI) approaches that are highly task-specific and modality-reliant. In the medical domain, however, the development of comprehensive foundation models is constrained by limited access to diverse modalities and stringent privacy regulations. To address these constraints, this study introduces a novel knowledge injection approach, FedKIM, designed to scale the medical foundation model within a federated learning framework. FedKIM leverages lightweight local models to extract healthcare knowledge from private data and integrates this knowledge into a centralized foundation model using a designed adaptive Multitask Multimodal Mixture Of Experts (M3OE) module. This method not only preserves privacy but also enhances the model's ability to handle complex medical tasks involving multiple modalities. Our extensive experiments across twelve tasks in seven modalities demonstrate the effectiveness of FedKIM in various settings, highlighting its potential to scale medical foundation models without direct access to sensitive data.
Deep-MacroFin: Informed Equilibrium Neural Network for Continuous Time Economic Models
Venue: arXiv cs.LG 2025
Year: 2025

In this paper, we present Deep-MacroFin, a comprehensive framework designed to solve partial differential equations, with a particular focus on models in continuous time economics. This framework leverages deep learning methodologies, including Multi-Layer Perceptrons and the newly developed Kolmogorov-Arnold Networks. It is optimized using economic information encapsulated by Hamilton-Jacobi-Bellman (HJB) equations and coupled algebraic equations. The application of neural networks holds the promise of accurately resolving high-dimensional problems with fewer computational demands and limitations compared to other numerical methods. This framework can be readily adapted for systems of partial differential equations in high dimensions. Importantly, it offers a more efficient (5$\times$ less CUDA memory and 40$\times$ fewer FLOPs in 100D problems) and user-friendly implementation than existing libraries. We also incorporate a time-stepping scheme to enhance training stability for nonlinear HJB equations, enabling the solution of 50D economic models.
Boolean Matrix Logic Programming on the GPU
Venue: arXiv cs.SC 2025
Year: 2025

Traditional logic programming relies on symbolic computation on the CPU, which can limit performance for large-scale inference tasks. Recent advances in GPU hardware enable high-throughput matrix operations, motivating a shift toward parallel logic inference. Boolean Matrix Logic Programming (BMLP) introduces a novel approach to datalog query evaluation using Boolean matrix algebra, well-suited to GPU acceleration. Building on this paradigm, we present two GPU-accelerated BMLP algorithms for bottom-up inference over linear dyadic recursive datalog programs. We further extend the BMLP theoretical framework to support general linear recursion with binary predicates. Empirical evaluations on reachability queries in large directed graphs and the Freebase 15K dataset show that our methods achieve 1-4 orders of magnitude speed up over state-of-the-art systems. These results demonstrate that Boolean matrix-based reasoning can significantly advance the scalability and efficiency of logic programming on modern hardware. Source code is available on https://github.com/lun-ai/BMLP.git.
Putting People in LLMs' Shoes: Generating Better Answers via Question Rewriter
Venue: arXiv cs.CL 2025
Year: 2025

Large Language Models (LLMs) have demonstrated significant capabilities, particularly in the domain of question answering (QA). However, their effectiveness in QA is often undermined by the vagueness of user questions. To address this issue, we introduce single-round instance-level prompt optimization, referred to as question rewriter. By enhancing the intelligibility of human questions for black-box LLMs, our question rewriter improves the quality of generated answers. The rewriter is optimized using direct preference optimization based on feedback collected from automatic criteria for evaluating generated answers; therefore, its training does not require costly human annotations. The experiments across multiple black-box LLMs and long-form question answering (LFQA) datasets demonstrate the efficacy of our method. This paper provides a practical framework for training question rewriters and sets a precedent for future explorations in prompt optimization within LFQA tasks. Code is available at https://github.com/3244we/Question-Rewriter.
Vocabulary-Free 3D Instance Segmentation with Vision and Language Assistant
Venue: arXiv cs.CV 2025
Year: 2025

Most recent 3D instance segmentation methods are open vocabulary, offering a greater flexibility than closed-vocabulary methods. Yet, they are limited to reasoning within a specific set of concepts, \ie the vocabulary, prompted by the user at test time. In essence, these models cannot reason in an open-ended fashion, i.e., answering "List the objects in the scene.''. We introduce the first method to address 3D instance segmentation in a setting that is void of any vocabulary prior, namely a vocabulary-free setting. We leverage a large vision-language assistant and an open-vocabulary 2D instance segmenter to discover and ground semantic categories on the posed images. To form 3D instance mask, we first partition the input point cloud into dense superpoints, which are then merged into 3D instance masks. We propose a novel superpoint merging strategy via spectral clustering, accounting for both mask coherence and semantic coherence that are estimated from the 2D object instance masks. We evaluate our method using ScanNet200 and Replica, outperforming existing methods in both vocabulary-free and open-vocabulary settings. Code will be made available. Project page: https://gfmei.github.io/PoVo
Tensor tree learns hidden relational structures in data to construct generative models
Venue: arXiv cs.LG 2025
Year: 2025

Based on the tensor tree network with the Born machine framework, we propose a general method for constructing a generative model by expressing the target distribution function as the amplitude of the quantum wave function represented by a tensor tree. The key idea is dynamically optimizing the tree structure that minimizes the bond mutual information. The proposed method offers enhanced performance and uncovers hidden relational structures in the target data. We illustrate potential practical applications with four examples: (i) random patterns, (ii) QMNIST handwritten digits, (iii) Bayesian networks, and (iv) the pattern of stock price fluctuation pattern in S&P500. In (i) and (ii), the strongly correlated variables were concentrated near the center of the network; in (iii), the causality pattern was identified; and in (iv), a structure corresponding to the eleven sectors emerged.
Performance Analysis of Physical Layer Security: From Far-Field to Near-Field
Venue: arXiv cs.IT 2025
Year: 2025

The secrecy performance in both near-field and far-field communications is analyzed using two fundamental metrics: the secrecy capacity under a power constraint and the minimum power requirement to achieve a specified secrecy rate target. 1) For the secrecy capacity, a closed-form expression is derived under a discrete-time memoryless setup. This expression is further analyzed under several far-field and near-field channel models, and the capacity scaling law is revealed by assuming an infinitely large transmit array and an infinitely high power. A novel concept of "depth of insecurity" is proposed to evaluate the secrecy performance achieved by near-field beamfocusing. It is demonstrated that increasing the number of transmit antennas reduces this depth and thus improves the secrecy performance. 2) Regarding the minimum required power, a closed-form expression is derived and analyzed within far-field and near-field scenarios. Asymptotic analyses are performed by setting the number of transmit antennas to infinity to unveil the power scaling law. Numerical results are provided to demonstrate that: i) compared to far-field communications, near-field communications expand the areas where secure transmission is feasible, specifically when the eavesdropper is located in the same direction as the intended receiver; ii) as the number of transmit antennas increases, neither the secrecy capacity nor the minimum required power scales or vanishes unboundedly, adhering to the principle of energy conservation.
On Learning Action Costs from Input Plans
Venue: arXiv cs.AI 2025
Year: 2025

Most of the work on learning action models focus on learning the actions' dynamics from input plans. This allows us to specify the valid plans of a planning task. However, very little work focuses on learning action costs, which in turn allows us to rank the different plans. In this paper we introduce a new problem: that of learning the costs of a set of actions such that a set of input plans are optimal under the resulting planning model. To solve this problem we present $LACFIP^k$, an algorithm to learn action's costs from unlabeled input plans. We provide theoretical and empirical results showing how $LACFIP^k$ can successfully solve this task.
Near, far: Patch-ordering enhances vision foundation models' scene understanding
Venue: arXiv cs.CV 2025
Year: 2025

We introduce NeCo: Patch Neighbor Consistency, a novel self-supervised training loss that enforces patch-level nearest neighbor consistency across a student and teacher model. Compared to contrastive approaches that only yield binary learning signals, i.e., 'attract' and 'repel', this approach benefits from the more fine-grained learning signal of sorting spatially dense features relative to reference patches. Our method leverages differentiable sorting applied on top of pretrained representations, such as DINOv2-registers to bootstrap the learning signal and further improve upon them. This dense post-pretraining leads to superior performance across various models and datasets, despite requiring only 19 hours on a single GPU. This method generates high-quality dense feature encoders and establishes several new state-of-the-art results such as +5.5% and +6% for non-parametric in-context semantic segmentation on ADE20k and Pascal VOC, +7.2% and +5.7% for linear segmentation evaluations on COCO-Things and -Stuff and improvements in the 3D understanding of multi-view consistency on SPair-71k, by more than 1.5%.
ISLES'24 -- A Real-World Longitudinal Multimodal Stroke Dataset
Venue: arXiv cs.CV 2025
Year: 2025

Stroke remains a leading cause of global morbidity and mortality, imposing a heavy socioeconomic burden. Advances in endovascular reperfusion therapy and CT and MR imaging for treatment guidance have significantly improved patient outcomes. Developing machine learning algorithms that can create accurate models of brain function from stroke images for tasks like lesion identification and tissue survival prediction requires large, diverse, and well annotated public datasets. While several high-quality image datasets in stroke exist, they include only single time point data. Data over different time points are essential to accurately identify lesions and predict prognosis. Here, we provide comprehensive longitudinal stroke data, including (sub-)acute CT imaging with angiography and perfusion, follow-up MRI after 2-9 days, and acute and longitudinal clinical data up to a three-month outcome. The dataset also includes vessel occlusion masks from acute CT angiography and delineated infarction masks in follow-up MRI. This multicenter dataset consists of 245 cases and is a solid basis for developing powerful machine-learning algorithms to facilitate clinical decision-making.
Hide Your Malicious Goal Into Benign Narratives: Jailbreak Large Language Models through Carrier Articles
Venue: arXiv cs.CR 2025
Year: 2025

Large Language Model (LLM) jailbreak refers to a type of attack aimed to bypass the safeguard of an LLM to generate contents that are inconsistent with the safe usage guidelines. Based on the insights from the self-attention computation process, this paper proposes a novel blackbox jailbreak approach, which involves crafting the payload prompt by strategically injecting the prohibited query into a carrier article. The carrier article maintains the semantic proximity to the prohibited query, which is automatically produced by combining a hypernymy article and a context, both of which are generated from the prohibited query. The intuition behind the usage of carrier article is to activate the neurons in the model related to the semantics of the prohibited query while suppressing the neurons that will trigger the objectionable text. Carrier article itself is benign, and we leveraged prompt injection techniques to produce the payload prompt. We evaluate our approach using JailbreakBench, testing against four target models across 100 distinct jailbreak objectives. The experimental results demonstrate our method's superior effectiveness, achieving an average success rate of 63% across all target models, significantly outperforming existing blackbox jailbreak methods.
Emotional RAG LLMs: Reading Comprehension for the Open Internet
Venue: arXiv cs.CL 2025
Year: 2025

Queries to large language models (LLMs) can be divided into two parts: the instruction/question and the accompanying context. The context for retrieval-augmented generation (RAG) systems in most benchmarks comes from Wikipedia-like texts written in a neutral and factual tone. However, real-world RAG applications often retrieve internet-based text with diverse tones and linguistic styles, posing challenges for downstream tasks. This paper introduces (a) a dataset that transforms RAG-retrieved passages into emotionally inflected and sarcastic text, (b) an emotion translation model for adapting text to different tones, and (c) a prompt-based method to improve LLMs' pragmatic interpretation of retrieved text.
Automated Prompt Engineering for Cost-Effective Code Generation Using Evolutionary Algorithm
Venue: arXiv cs.SE 2025
Year: 2025

Large Language Models have seen increasing use in various software development tasks, especially in code generation. The most advanced recent methods attempt to incorporate feedback from code execution into prompts to help guide LLMs in generating correct code in an iterative process. While effective, these methods could be costly due to numerous interactions with the LLM and extensive token usage. To address this issue, we propose an alternative approach named Evolutionary Prompt Engineering for Code (EPiC), which leverages a lightweight evolutionary algorithm to refine the original prompts into improved versions that generate high quality code, with minimal interactions with the LLM. Our evaluation against state-of-the-art (SOTA) LLM based code generation agents shows that EPiC not only achieves up to 6% improvement in pass@k but is also 2-10 times more cost-effective than the baselines.
Counterfactuals As a Means for Evaluating Faithfulness of Attribution Methods in Autoregressive Language Models
Venue: arXiv cs.CL 2025
Year: 2025

Despite the widespread adoption of autoregressive language models, explainability evaluation research has predominantly focused on span infilling and masked language models. Evaluating the faithfulness of an explanation method -- how accurately it explains the inner workings and decision-making of the model -- is challenging because it is difficult to separate the model from its explanation. Most faithfulness evaluation techniques corrupt or remove input tokens deemed important by a particular attribution (feature importance) method and observe the resulting change in the model's output. However, for autoregressive language models, this approach creates out-of-distribution inputs due to their next-token prediction training objective. In this study, we propose a technique that leverages counterfactual generation to evaluate the faithfulness of attribution methods for autoregressive language models. Our technique generates fluent, in-distribution counterfactuals, making the evaluation protocol more reliable.
Optimizing Transmit Field Inhomogeneity of Parallel RF Transmit Design in 7T MRI using Deep Learning
Venue: arXiv cs.CV 2025
Year: 2025

Ultrahigh field (UHF) Magnetic Resonance Imaging (MRI) provides a higher signal-to-noise ratio and, thereby, higher spatial resolution. However, UHF MRI introduces challenges such as transmit radiofrequency (RF) field (B1+) inhomogeneities, leading to uneven flip angles and image intensity anomalies. These issues can significantly degrade imaging quality and its medical applications. This study addresses B1+ field homogeneity through a novel deep learning-based strategy. Traditional methods like Magnitude Least Squares (MLS) optimization have been effective but are time-consuming and dependent on the patient's presence. Recent machine learning approaches, such as RF Shim Prediction by Iteratively Projected Ridge Regression and deep learning frameworks, have shown promise but face limitations like extensive training times and oversimplified architectures. We propose a two-step deep learning strategy. First, we obtain the desired reference RF shimming weights from multi-channel B1+ fields using random-initialized Adaptive Moment Estimation. Then, we employ Residual Networks (ResNets) to train a model that maps B1+ fields to target RF shimming outputs. Our approach does not rely on pre-calculated reference optimizations for the testing process and efficiently learns residual functions. Comparative studies with traditional MLS optimization demonstrate our method's advantages in terms of speed and accuracy. The proposed strategy achieves a faster and more efficient RF shimming design, significantly improving imaging quality at UHF. This advancement holds potential for broader applications in medical imaging and diagnostics.
Political Bias in LLMs: Unaligned Moral Values in Agent-centric Simulations
Venue: arXiv cs.CL 2025
Year: 2025

Contemporary research in social sciences increasingly utilizes state-of-the-art generative language models to annotate or generate content. While these models achieve benchmark-leading performance on common language tasks, their application to novel out-of-domain tasks remains insufficiently explored. To address this gap, we investigate how personalized language models align with human responses on the Moral Foundation Theory Questionnaire. We adapt open-source generative language models to different political personas and repeatedly survey these models to generate synthetic data sets where model-persona combinations define our sub-populations. Our analysis reveals that models produce inconsistent results across multiple repetitions, yielding high response variance. Furthermore, the alignment between synthetic data and corresponding human data from psychological studies shows a weak correlation, with conservative persona-prompted models particularly failing to align with actual conservative populations. These results suggest that language models struggle to coherently represent ideologies through in-context prompting due to their alignment process. Thus, using language models to simulate social interactions requires measurable improvements in in-context optimization or parameter manipulation to align with psychological and sociological stereotypes properly.