Yi Guo

Zehao Yu, Xi Yang, Chong Dang et al.

Objective: We aim to develop an open-source natural language processing (NLP) package, SODA (i.e., SOcial DeterminAnts), with pre-trained transformer models to extract social determinants of health (SDoH) for cancer patients, examine the generalizability of SODA to a new disease domain (i.e., opioid use), and evaluate the extraction rate of SDoH using cancer populations. Methods: We identified SDoH categories and attributes and developed an SDoH corpus using clinical notes from a general cancer cohort. We compared four transformer-based NLP models to extract SDoH, examined the generalizability of NLP models to a cohort of patients prescribed with opioids, and explored customization strategies to improve performance. We applied the best NLP model to extract 19 categories of SDoH from the breast (n=7,971), lung (n=11,804), and colorectal cancer (n=6,240) cohorts. Results and Conclusion: We developed a corpus of 629 cancer patients notes with annotations of 13,193 SDoH concepts/attributes from 19 categories of SDoH. The Bidirectional Encoder Representations from Transformers (BERT) model achieved the best strict/lenient F1 scores of 0.9216 and 0.9441 for SDoH concept extraction, 0.9617 and 0.9626 for linking attributes to SDoH concepts. Fine-tuning the NLP models using new annotations from opioid use patients improved the strict/lenient F1 scores from 0.8172/0.8502 to 0.8312/0.8679. The extraction rates among 19 categories of SDoH varied greatly, where 10 SDoH could be extracted from >70% of cancer patients, but 9 SDoH had a low extraction rate (<70% of cancer patients). The SODA package with pre-trained transformer models is publicly available at https://github.com/uf-hobiinformatics-lab/SDoH_SODA.

Mengyun Qiao, Berke Doga Basaran, Huaqi Qiu et al.

Cardiovascular disease, the leading cause of death globally, is an age-related disease. Understanding the morphological and functional changes of the heart during ageing is a key scientific question, the answer to which will help us define important risk factors of cardiovascular disease and monitor disease progression. In this work, we propose a novel conditional generative model to describe the changes of 3D anatomy of the heart during ageing. The proposed model is flexible and allows integration of multiple clinical factors (e.g. age, gender) into the generating process. We train the model on a large-scale cross-sectional dataset of cardiac anatomies and evaluate on both cross-sectional and longitudinal datasets. The model demonstrates excellent performance in predicting the longitudinal evolution of the ageing heart and modelling its data distribution. The codes are available at https://github.com/MengyunQ/AgeHeart.

Zhiqi Shao, Dai Shi, Andi Han et al. · tsinghua

Graph Neural Networks (GNNs) have emerged as one of the leading approaches for machine learning on graph-structured data. Despite their great success, critical computational challenges such as over-smoothing, over-squashing, and limited expressive power continue to impact the performance of GNNs. In this study, inspired from the time-reversal principle commonly utilized in classical and quantum physics, we reverse the time direction of the graph heat equation. The resulted reversing process yields a class of high pass filtering functions that enhance the sharpness of graph node features. Leveraging this concept, we introduce the Multi-Scaled Heat Kernel based GNN (MHKG) by amalgamating diverse filtering functions' effects on node features. To explore more flexible filtering conditions, we further generalize MHKG into a model termed G-MHKG and thoroughly show the roles of each element in controlling over-smoothing, over-squashing and expressive power. Notably, we illustrate that all aforementioned issues can be characterized and analyzed via the properties of the filtering functions, and uncover a trade-off between over-smoothing and over-squashing: enhancing node feature sharpness will make model suffer more from over-squashing, and vice versa. Furthermore, we manipulate the time again to show how G-MHKG can handle both two issues under mild conditions. Our conclusive experiments highlight the effectiveness of proposed models. It surpasses several GNN baseline models in performance across graph datasets characterized by both homophily and heterophily.

Yi Guo, Kyri Baker, Emiliano Dall'Anese et al.

We propose a data-based method to solve a multi-stage stochastic optimal power flow (OPF) problem based on limited information about forecast error distributions. The framework explicitly combines multi-stage feedback policies with any forecasting method and historical forecast error data. The objective is to determine power scheduling policies for controllable devices in a power network to balance operational cost and conditional value-at-risk (CVaR) of device and network constraint violations. These decisions include both nominal power schedules and reserve policies, which specify planned reactions to forecast errors in order to accommodate fluctuating renewable energy sources. Instead of assuming the uncertainties across the networks follow prescribed probability distributions, we consider ambiguity sets of distributions centered around a finite training dataset. By utilizing the Wasserstein metric to quantify differences between the empirical data-based distribution and the real unknown data-generating distribution, we formulate a multi-stage distributionally robust OPF problem to compute optimal control policies that are robust to both forecast errors and sampling errors inherent in the dataset. Two specific data-based distributionally robust stochastic OPF problems are proposed for distribution networks and transmission systems.

Yi Guo, Kyri Baker, Emiliano Dall'Anese et al.

This is the second part of a two-part paper on data-based distributionally robust stochastic optimal power flow (OPF). The general problem formulation and methodology have been presented in Part I [1]. Here, we present extensive numerical experiments in both distribution and transmission networks to illustrate the effectiveness and flexibility of the proposed methodology for balancing efficiency, constraint violation risk, and out-of-sample performance. On the distribution side, the method mitigates overvoltages due to high photovoltaic penetration using local energy storage devices. On the transmission side, the method reduces N-1 security line flow constraint risks due to high wind penetration using reserve policies for controllable generators. In both cases, the data-based distributionally robust model predictive control (MPC) algorithm explicitly utilizes forecast error training datasets, which can be updated online. The numerical results illustrate inherent tradeoffs between the operational costs, risks of constraints violations, and out-of-sample performance, offering systematic techniques for system operators to balance these objectives.

Yi Guo, Kyri Baker, Emiliano Dall'Anese et al.

We propose a data-driven method to solve a stochastic optimal power flow (OPF) problem based on limited information about forecast error distributions. The objective is to determine power schedules for controllable devices in a power network to balance operation cost and conditional value-at-risk (CVaR) of device and network constraint violations. These decisions include scheduled power output adjustments and reserve policies, which specify planned reactions to forecast errors in order to accommodate fluctuating renewable energy sources. Instead of assuming the uncertainties across the networks follow prescribed probability distributions, we assume the distributions are only observable through a finite training dataset. By utilizing the Wasserstein metric to quantify differences between the empirical data-based distribution and the real data-generating distribution, we formulate a distributionally robust optimization OPF problem to search for power schedules and reserve policies that are robust to sampling errors inherent in the dataset. A simple numerical example illustrates inherent tradeoffs between operation cost and risk of constraint violation, and we show how our proposed method offers a data-driven framework to balance these objectives.

Aokun Chen, Zehao Yu, Xi Yang et al.

Objective: To develop a natural language processing (NLP) system to extract medications and contextual information that help understand drug changes. This project is part of the 2022 n2c2 challenge. Materials and methods: We developed NLP systems for medication mention extraction, event classification (indicating medication changes discussed or not), and context classification to classify medication changes context into 5 orthogonal dimensions related to drug changes. We explored 6 state-of-the-art pretrained transformer models for the three subtasks, including GatorTron, a large language model pretrained using >90 billion words of text (including >80 billion words from >290 million clinical notes identified at the University of Florida Health). We evaluated our NLP systems using annotated data and evaluation scripts provided by the 2022 n2c2 organizers. Results:Our GatorTron models achieved the best F1-scores of 0.9828 for medication extraction (ranked 3rd), 0.9379 for event classification (ranked 2nd), and the best micro-average accuracy of 0.9126 for context classification. GatorTron outperformed existing transformer models pretrained using smaller general English text and clinical text corpora, indicating the advantage of large language models. Conclusion: This study demonstrated the advantage of using large transformer models for contextual medication information extraction from clinical narratives.

Yi Guo, Tyler H. Summers

Traditional synchronous generators with rotational inertia are being replaced by low-inertia renewable energy resources (RESs) in many power grids and operational scenarios. Due to emerging market mechanisms, inherent variability of RESs, and existing control schemes, the resulting system inertia levels can not only be low but also markedly time-varying. In this paper, we investigate performance and stability of low-inertia power systems with stochastic system inertia. In particular, we consider system dynamics modelled by a linearized stochastic swing equation, where stochastic system inertia is regarded as multiplicative noise. The $\mathcal{H}_2$ norm is used to quantify the performance of the system in the presence of persistent disturbances or transient faults. The performance metric can be computed by solving a generalized Lyapunov equation, which has fundamentally different characteristics from systems with only additive noise. For grids with uniform inertia and damping parameters, we derive closed-form expressions for the $\mathcal{H}_2$ norm of the proposed stochastic swing equation. The analysis gives insights into how the $\mathcal{H}_2$ norm of the stochastic swing equation depends on 1) network topology; 2) system parameters; and 3) distribution parameters of disturbances. A mean-square stability condition is also derived. Numerical results provide additional insights for performance and stability of the stochastic swing equation.

Yi Guo, Che Sun, Yunde Jia et al.

Neural 3D scene reconstruction methods have achieved impressive performance when reconstructing complex geometry and low-textured regions in indoor scenes. However, these methods heavily rely on 3D data which is costly and time-consuming to obtain in real world. In this paper, we propose a novel neural reconstruction method that reconstructs scenes using sparse depth under the plane constraints without 3D supervision. We introduce a signed distance function field, a color field, and a probability field to represent a scene. We optimize these fields to reconstruct the scene by using differentiable ray marching with accessible 2D images as supervision. We improve the reconstruction quality of complex geometry scene regions with sparse depth obtained by using the geometric constraints. The geometric constraints project 3D points on the surface to similar-looking regions with similar features in different 2D images. We impose the plane constraints to make large planes parallel or vertical to the indoor floor. Both two constraints help reconstruct accurate and smooth geometry structures of the scene. Without 3D supervision, our method achieves competitive performance compared with existing methods that use 3D supervision on the ScanNet dataset.

Dai Shi, Andi Han, Lequan Lin et al.

Graph-based message-passing neural networks (MPNNs) have achieved remarkable success in both node and graph-level learning tasks. However, several identified problems, including over-smoothing (OSM), limited expressive power, and over-squashing (OSQ), still limit the performance of MPNNs. In particular, OSQ serves as the latest identified problem, where MPNNs gradually lose their learning accuracy when long-range dependencies between graph nodes are required. In this work, we provide an exposition on the OSQ problem by summarizing different formulations of OSQ from current literature, as well as the three different categories of approaches for addressing the OSQ problem. In addition, we also discuss the alignment between OSQ and expressive power and the trade-off between OSQ and OSM. Furthermore, we summarize the empirical methods leveraged from existing works to verify the efficiency of OSQ mitigation approaches, with illustrations of their computational complexities. Lastly, we list some open questions that are of interest for further exploration of the OSQ problem along with potential directions from the best of our knowledge.

Dai Shi, Yi Guo, Zhiqi Shao et al.

Graph neural network (GNN) has been demonstrated powerful in modeling graph-structured data. However, despite many successful cases of applying GNNs to various graph classification and prediction tasks, whether the graph geometrical information has been fully exploited to enhance the learning performance of GNNs is not yet well understood. This paper introduces a new approach to enhance GNN by discrete graph Ricci curvature. Specifically, the graph Ricci curvature defined on the edges of a graph measures how difficult the information transits on one edge from one node to another based on their neighborhoods. Motivated by the geometric analogy of Ricci curvature in the graph setting, we prove that by inserting the curvature information with different carefully designed transformation function $ζ$, several known computational issues in GNN such as over-smoothing can be alleviated in our proposed model. Furthermore, we verified that edges with very positive Ricci curvature (i.e., $κ_{i,j} \approx 1$) are preferred to be dropped to enhance model's adaption to heterophily graph and one curvature based graph edge drop algorithm is proposed. Comprehensive experiments show that our curvature-based GNN model outperforms the state-of-the-art baselines in both homophily and heterophily graph datasets, indicating the effectiveness of involving graph geometric information in GNNs.

Chen Qian, Haoyu Zhang, Yuncheng Gao et al.

Diffusion magnetic resonance imaging (MRI) is the only imaging modality for non-invasive movement detection of in vivo water molecules, with significant clinical and research applications. Diffusion weighted imaging (DWI) MRI acquired by multi-shot techniques can achieve higher resolution, better signal-to-noise ratio, and lower geometric distortion than single-shot, but suffers from inter-shot motion-induced artifacts. These artifacts cannot be removed prospectively, leading to the absence of artifact-free training labels. Thus, the potential of deep learning in multi-shot DWI reconstruction remains largely untapped. To break the training data bottleneck, here, we propose a Physics-Informed Deep DWI reconstruction method (PIDD) to synthesize high-quality paired training data by leveraging the physical diffusion model (magnitude synthesis) and inter-shot motion-induced phase model (motion phase synthesis). The network is trained only once with 100,000 synthetic samples, achieving encouraging results on multiple realistic in vivo data reconstructions. Advantages over conventional methods include: (a) Better motion artifact suppression and reconstruction stability; (b) Outstanding generalization to multi-scenario reconstructions, including multi-resolution, multi-b-value, multi-under-sampling, multi-vendor, and multi-center; (c) Excellent clinical adaptability to patients with verifications by seven experienced doctors (p<0.001). In conclusion, PIDD presents a novel deep learning framework by exploiting the power of MRI physics, providing a cost-effective and explainable way to break the data bottleneck in deep learning medical imaging.

Dai Shi, Zhiqi Shao, Yi Guo et al.

Knowledge distillation (KD) has shown great potential for transferring knowledge from a complex teacher model to a simple student model in which the heavy learning task can be accomplished efficiently and without losing too much prediction accuracy. Recently, many attempts have been made by applying the KD mechanism to the graph representation learning models such as graph neural networks (GNNs) to accelerate the model's inference speed via student models. However, many existing KD-based GNNs utilize MLP as a universal approximator in the student model to imitate the teacher model's process without considering the graph knowledge from the teacher model. In this work, we provide a KD-based framework on multi-scaled GNNs, known as graph framelet, and prove that by adequately utilizing the graph knowledge in a multi-scaled manner provided by graph framelet decomposition, the student model is capable of adapting both homophilic and heterophilic graphs and has the potential of alleviating the over-squashing issue with a simple yet effectively graph surgery. Furthermore, we show how the graph knowledge supplied by the teacher is learned and digested by the student model via both algebra and geometry. Comprehensive experiments show that our proposed model can generate learning accuracy identical to or even surpass the teacher model while maintaining the high speed of inference.

Manu, Yi Guo, Kanchana Thilakarathna et al.

Large Language Models (LLMs) can be driven into over-generation, emitting thousands of tokens before producing an end-of-sequence (EOS) token. This degrades answer quality, inflates latency and cost, and can be weaponized as a denial-of-service (DoS) attack. Recent work has begun to study DoS-style prompt attacks, but typically focuses on a single attack algorithm or assumes white-box access, without an attack-side benchmark that compares prompt-based attackers in a black-box, query-only regime with a known tokenizer. We introduce such a benchmark and study two prompt-only attackers. The first is an Evolutionary Over-Generation Prompt Search (EOGen) that searches the token space for prefixes that suppress EOS and induce long continuations. The second is a goal-conditioned reinforcement learning attacker (RL-GOAL) that trains a network to generate prefixes conditioned on a target length. To characterize behavior, we introduce Over-Generation Factor (OGF): the ratio of produced tokens to a model's context window, along with stall and latency summaries. EOGen discovers short-prefix attacks that raise Phi-3 to OGF = 1.39 +/- 1.14 (Success@>=2: 25.2%); RL-GOAL nearly doubles severity to OGF = 2.70 +/- 1.43 (Success@>=2: 64.3%) and drives budget-hit non-termination in 46% of trials.

Xiaosong Wang, Xiaofan Zhang, Guotai Wang et al.

The emerging trend of advancing generalist artificial intelligence, such as GPTv4 and Gemini, has reshaped the landscape of research (academia and industry) in machine learning and many other research areas. However, domain-specific applications of such foundation models (e.g., in medicine) remain untouched or often at their very early stages. It will require an individual set of transfer learning and model adaptation techniques by further expanding and injecting these models with domain knowledge and data. The development of such technologies could be largely accelerated if the bundle of data, algorithms, and pre-trained foundation models were gathered together and open-sourced in an organized manner. In this work, we present OpenMEDLab, an open-source platform for multi-modality foundation models. It encapsulates not only solutions of pioneering attempts in prompting and fine-tuning large language and vision models for frontline clinical and bioinformatic applications but also building domain-specific foundation models with large-scale multi-modal medical data. Importantly, it opens access to a group of pre-trained foundation models for various medical image modalities, clinical text, protein engineering, etc. Inspiring and competitive results are also demonstrated for each collected approach and model in a variety of benchmarks for downstream tasks. We welcome researchers in the field of medical artificial intelligence to continuously contribute cutting-edge methods and models to OpenMEDLab, which can be accessed via https://github.com/openmedlab.

Yi Guo, Feng Li, Zhuo Wang

Cloud removal is an essential task in remote sensing data analysis. As the image sensors are distant from the earth ground, it is likely that part of the area of interests is covered by cloud. Moreover, the atmosphere in between creates a constant haze layer upon the acquired images. To recover the ground image, we propose to use scattering model for temporal sequence of images of any scene in the framework of low rank and sparse models. We further develop its variant, which is much faster and yet more accurate. To measure the performance of different methods {\em objectively}, we develop a semi-realistic simulation method to produce cloud cover so that various methods can be quantitatively analysed, which enables detailed study of many aspects of cloud removal algorithms, including verifying the effectiveness of proposed models in comparison with the state-of-the-arts, including deep learning models, and addressing the long standing problem of the determination of regularisation parameters. The latter is companioned with theoretic analysis on the range of the sparsity regularisation parameter and verified numerically.

Yi Guo, Fanliu Kong, Xiaoyang Li et al.

Quantization emerges as one of the most promising compression technologies for deploying efficient large models for various real time application in recent years. Considering that the storage and IO of weights take up the vast majority of the overhead inside a large model, weight only quantization can lead to large gains. However, existing quantization schemes suffer from significant accuracy degradation at very low bits, or require some additional computational overhead when deployed, making it difficult to be applied to large-scale applications in industry. In this paper, we propose decoupleQ, achieving a substantial increase in model accuracy, especially at very low bits. decoupleQ abandons the traditional heuristic quantization paradigm and decouples the model parameters into integer and floating-point parts, thus transforming the quantization problem into a traditional mathematical optimization problem with constraints, which is then solved alternatively by off-the-shelf optimization methods. Quantization via decoupleQ is linear and uniform, making it hardware-friendlier than non-uniform counterpart, and enabling the idea to be migrated to high-bit quantization to enhance its robustness. Our method has achieved well on-line accuracy near fp16/bf16 on the 2-bit quantization of large speech models in ByteDance. The code is available at https://github.com/bytedance/decoupleQ

Colin Jüni, Mina Montazeri, Yi Guo et al.

Buildings account for approximately 40% of global energy consumption, and with the growing share of intermittent renewable energy sources, enabling demand-side flexibility, particularly in heating, ventilation and air conditioning systems, is essential for grid stability and energy efficiency. This paper presents a safe deep reinforcement learning-based control framework to optimize building space heating while enabling demand-side flexibility provision for power system operators. A deep deterministic policy gradient algorithm is used as the core deep reinforcement learning method, enabling the controller to learn an optimal heating strategy through interaction with the building thermal model while maintaining occupant comfort, minimizing energy cost, and providing flexibility. To address safety concerns with reinforcement learning, particularly regarding compliance with flexibility requests, we propose a real-time adaptive safety-filter to ensure that the system operates within predefined constraints during demand-side flexibility provision. The proposed real-time adaptive safety filter guarantees full compliance with flexibility requests from system operators and improves energy and cost efficiency -- achieving up to 50% savings compared to a rule-based controller -- while outperforming a standalone deep reinforcement learning-based controller in energy and cost metrics, with only a slight increase in comfort temperature violations.

Qing He, Dongsheng Bi, Jianrong Lu et al.

The proliferation of Large Language Models (LLMs) presents transformative potential for healthcare, yet practical deployment is hindered by the absence of frameworks that assess real-world clinical utility. Existing benchmarks test static knowledge, failing to capture the dynamic, application-oriented capabilities required in clinical practice. To bridge this gap, we introduce a Medical LLM Benchmark MLB, a comprehensive benchmark evaluating LLMs on both foundational knowledge and scenario-based reasoning. MLB is structured around five core dimensions: Medical Knowledge (MedKQA), Safety and Ethics (MedSE), Medical Record Understanding (MedRU), Smart Services (SmartServ), and Smart Healthcare (SmartCare). The benchmark integrates 22 datasets (17 newly curated) from diverse Chinese clinical sources, covering 64 clinical specialties. Its design features a rigorous curation pipeline involving 300 licensed physicians. Besides, we provide a scalable evaluation methodology, centered on a specialized judge model trained via Supervised Fine-Tuning (SFT) on expert annotations. Our comprehensive evaluation of 10 leading models reveals a critical translational gap: while the top-ranked model, Kimi-K2-Instruct (77.3% accuracy overall), excels in structured tasks like information extraction (87.8% accuracy in MedRU), performance plummets in patient-facing scenarios (61.3% in SmartServ). Moreover, the exceptional safety score (90.6% in MedSE) of the much smaller Baichuan-M2-32B highlights that targeted training is equally critical. Our specialized judge model, trained via SFT on a 19k expert-annotated medical dataset, achieves 92.1% accuracy, an F1-score of 94.37%, and a Cohen's Kappa of 81.3% for human-AI consistency, validating a reproducible and expert-aligned evaluation protocol. MLB thus provides a rigorous framework to guide the development of clinically viable LLMs.

Fengcheng Wu, Zhenxi Song, Guoyang Xu et al.

Robust and interpretable dementia diagnosis from noisy, non-stationary electroencephalography (EEG) is clinically essential yet remains challenging. To this end, we propose SeeGraph, a Sparse-Explanatory dynamic EEG-graph network that models time-evolving functional connectivity and employs a node-guided sparse edge mask to reveal the connections that drive diagnostic decisions, while remaining robust to noise and cross-site variability. SeeGraph comprises four components: (1) a dual-trajectory temporal encoder that models dynamic EEG with two streams, where node signals capture regional oscillations and edge signals capture interregional coupling; (2) a topology-aware positional encoder that derives graph-spectral Laplacian coordinates from the fused connectivity and augments node embeddings; (3) a node-guided sparse explanatory edge mask that gates the connectivity into a compact subgraph; and (4) a gated graph predictor that operates on the sparsified graph. The framework is trained using cross-entropy loss together with a sparsity regularizer on the mask, yielding noise-robust and interpretable diagnoses. The effectiveness of SeeGraph is validated on public and in-house EEG cohorts, including patients with neurodegenerative dementias and healthy controls, under both raw and noise-perturbed conditions. Its sparse, node-guided explanations highlight disease-relevant connections and align with established clinical findings on functional connectivity alterations, thereby offering transparent cues for neurological evaluation.

Nirhoshan Sivaroopan, Kanchana Thilakarathna, Albert Zomaya et al.

Sponge attacks increasingly threaten LLM systems by inducing excessive computation and DoS. Existing defenses either rely on statistical filters that fail on semantically meaningful attacks or use static LLM-based detectors that struggle to adapt as attack strategies evolve. We introduce SHIELD, a multi-agent, auto-healing defense framework centered on a three-stage Defense Agent that integrates semantic similarity retrieval, pattern matching, and LLM-based reasoning. Two auxiliary agents, a Knowledge Updating Agent and a Prompt Optimization Agent, form a closed self-healing loop, when an attack bypasses detection, the system updates an evolving knowledgebase, and refines defense instructions. Extensive experiments show that SHIELD consistently outperforms perplexity-based and standalone LLM defenses, achieving high F1 scores across both non-semantic and semantic sponge attacks, demonstrating the effectiveness of agentic self-healing against evolving resource-exhaustion threats.

Chen Ma, Yunshu Li, Junhu Fu et al.

Clinical ultrasound analysis demands models that generalize across heterogeneous organs, views, and devices, while supporting interpretable workflow-level analysis. Existing methods often rely on task-wise adaptation, and joint learning may be unstable due to cross-task interference, making it hard to deliver workflow-level outputs in practice. To address these challenges, we present USTri, a tri-stage ultrasound intelligence pipeline for unified multi-organ, multi-task analysis. Stage I trains a universal generalist USGen on different domains to learn broad, transferable priors that are robust to device and protocol variability. To better handle domain shifts and reach task-aligned performance while preserving ultrasound shared knowledge, Stage II builds USpec by keeping USGen frozen and finetuning dataset-specific heads. Stage III introduces USAgent, which mimics clinician workflows by orchestrating USpec specialists for multi-step inference and deterministic structured reports. On the FMC\_UIA validation set, our model achieves the best overall performance across 4 task types and 27 datasets, outperforming state-of-the-art methods. Moreover, qualitative results show that USAgent produces clinically structured reports with high accuracy and interpretability. Our study suggests a scalable path to ultrasound intelligence that generalizes across heterogeneous ultrasound tasks and supports consistent end-to-end clinical workflows.

Junhu Fu, Shuyu Liang, Wutong Li et al.

Colonoscopy video generation delivers dynamic, information-rich data critical for diagnosing intestinal diseases, particularly in data-scarce scenarios. High-quality video generation demands temporal consistency and precise control over clinical attributes, but faces challenges from irregular intestinal structures, diverse disease representations, and various imaging modalities. To this end, we propose ColoDiff, a diffusion-based framework that generates dynamic-consistent and content-aware colonoscopy videos, aiming to alleviate data shortage and assist clinical analysis. At the inter-frame level, our TimeStream module decouples temporal dependency from video sequences through a cross-frame tokenization mechanism, enabling intricate dynamic modeling despite irregular intestinal structures. At the intra-frame level, our Content-Aware module incorporates noise-injected embeddings and learnable prototypes to realize precise control over clinical attributes, breaking through the coarse guidance of diffusion models. Additionally, ColoDiff employs a non-Markovian sampling strategy that cuts steps by over 90% for real-time generation. ColoDiff is evaluated across three public datasets and one hospital database, based on both generation metrics and downstream tasks including disease diagnosis, modality discrimination, bowel preparation scoring, and lesion segmentation. Extensive experiments show ColoDiff generates videos with smooth transitions and rich dynamics. ColoDiff presents an effort in controllable colonoscopy video generation, revealing the potential of synthetic videos in complementing authentic representation and mitigating data scarcity in clinical settings.

Tao Song, Yicheng Wu, Minhao Hu et al.

Multimodal MR image synthesis aims to generate missing modality images by effectively fusing and mapping from a subset of available MRI modalities. Most existing methods adopt an image-to-image translation paradigm, treating multiple modalities as input channels. However, these approaches often yield sub-optimal results due to the inherent difficulty in achieving precise feature- or semantic-level alignment across modalities. To address these challenges, we propose an Adaptive Group-wise Interaction Network (AGI-Net) that explicitly models both inter-modality and intra-modality relationships for multimodal MR image synthesis. Specifically, feature channels are first partitioned into predefined groups, after which an adaptive rolling mechanism is applied to conventional convolutional kernels to better capture feature and semantic correspondences between different modalities. In parallel, a cross-group attention module is introduced to enable effective feature fusion across groups, thereby enhancing the network's representational capacity. We validate the proposed AGI-Net on the publicly available IXI and BraTS2023 datasets. Experimental results demonstrate that AGI-Net achieves state-of-the-art performance in multimodal MR image synthesis tasks, confirming the effectiveness of its modality-aware interaction design. We release the relevant code at: https://github.com/zunzhumu/Adaptive-Group-wise-Interaction-Network-for-Multimodal-MRI-Synthesis.git.

Xi Yang, Zehao Yu, Yi Guo et al.

The newly emerged transformer technology has a tremendous impact on NLP research. In the general English domain, transformer-based models have achieved state-of-the-art performances on various NLP benchmarks. In the clinical domain, researchers also have investigated transformer models for clinical applications. The goal of this study is to systematically explore three widely used transformer-based models (i.e., BERT, RoBERTa, and XLNet) for clinical relation extraction and develop an open-source package with clinical pre-trained transformer-based models to facilitate information extraction in the clinical domain. We developed a series of clinical RE models based on three transformer architectures, namely BERT, RoBERTa, and XLNet. We evaluated these models using 2 publicly available datasets from 2018 MADE1.0 and 2018 n2c2 challenges. We compared two classification strategies (binary vs. multi-class classification) and investigated two approaches to generate candidate relations in different experimental settings. In this study, we compared three transformer-based (BERT, RoBERTa, and XLNet) models for relation extraction. We demonstrated that the RoBERTa-clinical RE model achieved the best performance on the 2018 MADE1.0 dataset with an F1-score of 0.8958. On the 2018 n2c2 dataset, the XLNet-clinical model achieved the best F1-score of 0.9610. Our results indicated that the binary classification strategy consistently outperformed the multi-class classification strategy for clinical relation extraction. Our methods and models are publicly available at https://github.com/uf-hobi-informatics-lab/ClinicalTransformerRelationExtraction. We believe this work will improve current practice on clinical relation extraction and other related NLP tasks in the biomedical domain.

Runsheng Xu, Yi Guo, Xu Han et al.

Although Cooperative Driving Automation (CDA) has attracted considerable attention in recent years, there remain numerous open challenges in this field. The gap between existing simulation platforms that mainly concentrate on single-vehicle intelligence and CDA development is one of the critical barriers, as it inhibits researchers from validating and comparing different CDA algorithms conveniently. To this end, we propose OpenCDA, a generalized framework and tool for developing and testing CDA systems. Specifically, OpenCDA is composed of three major components: a co-simulation platform with simulators of different purposes and resolutions, a full-stack cooperative driving system, and a scenario manager. Through the interactions of these three components, our framework offers a straightforward way for researchers to test different CDA algorithms at both levels of traffic and individual autonomy. More importantly, OpenCDA is highly modularized and installed with benchmark algorithms and test cases. Users can conveniently replace any default module with customized algorithms and use other default modules of the CDA platform to perform evaluations of the effectiveness of new functionalities in enhancing the overall CDA performance. An example of platooning implementation is used to illustrate the framework's capability for CDA research. The codes of OpenCDA are available in the https://github.com/ucla-mobility/OpenCDA.

Haocong Rao, Siqi Wang, Xiping Hu et al.

Person re-identification (Re-ID) via gait features within 3D skeleton sequences is a newly-emerging topic with several advantages. Existing solutions either rely on hand-crafted descriptors or supervised gait representation learning. This paper proposes a self-supervised gait encoding approach that can leverage unlabeled skeleton data to learn gait representations for person Re-ID. Specifically, we first create self-supervision by learning to reconstruct unlabeled skeleton sequences reversely, which involves richer high-level semantics to obtain better gait representations. Other pretext tasks are also explored to further improve self-supervised learning. Second, inspired by the fact that motion's continuity endows adjacent skeletons in one skeleton sequence and temporally consecutive skeleton sequences with higher correlations (referred as locality in 3D skeleton data), we propose a locality-aware attention mechanism and a locality-aware contrastive learning scheme, which aim to preserve locality-awareness on intra-sequence level and inter-sequence level respectively during self-supervised learning. Last, with context vectors learned by our locality-aware attention mechanism and contrastive learning scheme, a novel feature named Constrastive Attention-based Gait Encodings (CAGEs) is designed to represent gait effectively. Empirical evaluations show that our approach significantly outperforms skeleton-based counterparts by 15-40% Rank-1 accuracy, and it even achieves superior performance to numerous multi-modal methods with extra RGB or depth information. Our codes are available at https://github.com/Kali-Hac/Locality-Awareness-SGE.

Qin Wang, Zhiqing He, Yu Liu et al.

Reliable interpretation of echocardiography (Echo) is crucial for assessing cardiac function, which demands clinicians to synchronously orchestrate multiple capabilities, including visual observation (eyes), manual measurement (hands), and expert knowledge learning and reasoning (minds). While current task-specific deep-learning approaches and multimodal large language models have demonstrated promise in assisting Echo analysis through automated segmentation or reasoning, they remain focused on restricted skills, i.e., eyes-hands or eyes-minds, thereby limiting clinical reliability and utility. To address these issues, we propose EchoAgent, an agentic system tailored for end-to-end Echo interpretation, which achieves a fully coordinated eyes-hands-minds workflow that learns, observes, operates, and reasons like a cardiac sonographer. First, we introduce an expertise-driven cognition engine where our agent can automatically assimilate credible Echo guidelines into a structured knowledge base, thus constructing an Echo-customized mind. Second, we devise a hierarchical collaboration toolkit to endow EchoAgent with eyes-hands, which can automatically parse Echo video streams, identify cardiac views, perform anatomical segmentation, and quantitative measurement. Third, we integrate the perceived multimodal evidence with the exclusive knowledge base into an orchestrated reasoning hub to conduct explainable inferences. We evaluate EchoAgent on CAMUS and MIMIC-EchoQA datasets, which cover 48 distinct echocardiographic views spanning 14 cardiac anatomical regions. Experimental results show that EchoAgent achieves optimal performance across diverse structure analyses, yielding overall accuracy of up to 80.00%. Importantly, EchoAgent empowers a single system with abilities to learn, observe, operate and reason like an echocardiologist, which holds great promise for reliable Echo interpretation.

Junhu Fu, Ke Chen, Weidong Guo et al.

Controllable medical video generation has achieved remarkable progress, but it still lacks interpretability, which requires the alignment of generated contents with physical priors and faithful clinical manifestations. To push the boundaries from mere controllability to interpretability, we propose DepthPilot, the first interpretable framework for colonoscopy video generation. This work takes a step toward trustworthy generation through two synergistic paradigms. To achieve explicit geometric grounding, DepthPilot devises a prior distribution alignment strategy, injecting depth constraints into the diffusion backbone via parameter-efficient fine-tuning to ensure anatomical fidelity. To enhance intrinsic nonlinear modeling under these geometric constraints, DepthPilot employs an adaptive spline denoising module, replacing fixed linear weights with learnable spline functions to capture complex spatio-temporal dynamics. Extensive evaluations across three public datasets and in-house clinical data confirm DepthPilot's robust ability to produce physically consistent videos. It achieves FID scores below 15 across all benchmarks and ranks first in clinician assessments, bridging the gap between "visually realistic" and "clinically interpretable". Moreover, DepthPilot-generated videos are expected to enable reliable 3D reconstruction, facilitating surgical navigation and blind region identification, and serve as a foundation toward the colorectal world model.

Jie Xu, Xiaokang Li, Chengyu Yue et al.

Medical image segmentation often faces the challenge of prohibitively expensive annotation costs. While few-shot learning offers a promising solution to alleviate this burden, conventional approaches still rely heavily on pre-training with large volumes of labeled data from known categories. To address this issue, we propose leveraging the Segment Anything Model (SAM), pre-trained on over 1 billion masks, thus circumventing the need for extensive domain-specific annotated data. In light of this, we developed SAM-MPA, an innovative SAM-based framework for few-shot medical image segmentation using Mask Propagation-based Auto-prompting. Initially, we employ k-centroid clustering to select the most representative examples for labelling to construct the support set. These annotated examples are registered to other images yielding deformation fields that facilitate the propagation of the mask knowledge to obtain coarse masks across the dataset. Subsequently, we automatically generate visual prompts based on the region and boundary expansion of the coarse mask, including points, box and a coarse mask. Finally, we can obtain the segmentation predictions by inputting these prompts into SAM and refine the results by post refinement module. We validate the performance of the proposed framework through extensive experiments conducted on two medical image datasets with different modalities. Our method achieves Dices of 74.53%, 94.36% on Breast US, Chest X-ray, respectively. Experimental results substantiate that SAM-MPA yields high-accuracy segmentations within 10 labeled examples, outperforming other state-of-the-art few-shot auto-segmentation methods. Our method enables the customization of SAM for any medical image dataset with a small number of labeled examples.

Ziyi Chen, Mengyuan Zhang, Mustafa Mohammed Ahmed et al.

Cancer treatments are known to introduce cardiotoxicity, negatively impacting outcomes and survivorship. Identifying cancer patients at risk of heart failure (HF) is critical to improving cancer treatment outcomes and safety. This study examined machine learning (ML) models to identify cancer patients at risk of HF using electronic health records (EHRs), including traditional ML, Time-Aware long short-term memory (T-LSTM), and large language models (LLMs) using novel narrative features derived from the structured medical codes. We identified a cancer cohort of 12,806 patients from the University of Florida Health, diagnosed with lung, breast, and colorectal cancers, among which 1,602 individuals developed HF after cancer. The LLM, GatorTron-3.9B, achieved the best F1 scores, outperforming the traditional support vector machines by 39%, the T-LSTM deep learning model by 7%, and a widely used transformer model, BERT, by 5.6%. The analysis shows that the proposed narrative features remarkably increased feature density and improved performance.

Zhenxi Song, Ruihan Qin, Huixia Ren et al.

Cross-center data heterogeneity and annotation unreliability significantly challenge the intelligent diagnosis of diseases using brain signals. A notable example is the EEG-based diagnosis of neurodegenerative diseases, which features subtler abnormal neural dynamics typically observed in small-group settings. To advance this area, in this work, we introduce a transferable framework employing Manifold Attention and Confidence Stratification (MACS) to diagnose neurodegenerative disorders based on EEG signals sourced from four centers with unreliable annotations. The MACS framework's effectiveness stems from these features: 1) The Augmentor generates various EEG-represented brain variants to enrich the data space; 2) The Switcher enhances the feature space for trusted samples and reduces overfitting on incorrectly labeled samples; 3) The Encoder uses the Riemannian manifold and Euclidean metrics to capture spatiotemporal variations and dynamic synchronization in EEG; 4) The Projector, equipped with dual heads, monitors consistency across multiple brain variants and ensures diagnostic accuracy; 5) The Stratifier adaptively stratifies learned samples by confidence levels throughout the training process; 6) Forward and backpropagation in MACS are constrained by confidence stratification to stabilize the learning system amid unreliable annotations. Our subject-independent experiments, conducted on both neurocognitive and movement disorders using cross-center corpora, have demonstrated superior performance compared to existing related algorithms. This work not only improves EEG-based diagnostics for cross-center and small-setting brain diseases but also offers insights into extending MACS techniques to other data analyses, tackling data heterogeneity and annotation unreliability in multimedia and multimodal content understanding.

Hanmin Cai, Federica Bellizio, Yi Guo et al.

Harnessing the demand-side flexibility in building and mobility sectors can help to better integrate renewable energy into power systems and reduce global CO2 emissions. Enabling this sector coupling can be achieved with advances in energy management, business models, control technologies, and power grids. The study of demand-side flexibility extends beyond engineering, spanning social science, economics, and power and control systems, which present both challenges and opportunities to researchers and engineers in these fields. This Review outlines recent trends and studies in social, economic, and technological advancements in power systems that leverage demand-side flexibility. We first provide a concept of a socio-techno-economic system with an abstraction of end-users, building and mobility sectors, control systems, electricity markets, and power grids. We discuss the interconnections between these elements, highlighting the importance of bidirectional flows of information and coordinated decision-making. We then emphasize that fully realizing demand-side flexibility necessitates deep integration across stakeholders and systems, moving beyond siloed approaches. Finally, we discuss the future directions in renewable-based power systems and control engineering to address key challenges from both research and practitioners' perspectives. A holistic approach for identifying, measuring, and utilizing demand-side flexibility is key to successfully maximizing its multi-stakeholder benefits but requires further transdisciplinary collaboration and commercially viable solutions for broader implementation.

Yi Guo, Wei Wang, Zhihang Yuan et al.

Generative models like Flow Matching have achieved state-of-the-art performance but are often hindered by a computationally expensive iterative sampling process. To address this, recent work has focused on few-step or one-step generation by learning the average velocity field, which directly maps noise to data. MeanFlow, a leading method in this area, learns this field by enforcing a differential identity that connects the average and instantaneous velocities. In this work, we argue that this differential formulation is a limiting special case of a more fundamental principle. We return to the first principles of average velocity and leverage the additivity property of definite integrals. This leads us to derive a novel, purely algebraic identity we term Interval Splitting Consistency. This identity establishes a self-referential relationship for the average velocity field across different time intervals without resorting to any differential operators. Based on this principle, we introduce SplitMeanFlow, a new training framework that enforces this algebraic consistency directly as a learning objective. We formally prove that the differential identity at the core of MeanFlow is recovered by taking the limit of our algebraic consistency as the interval split becomes infinitesimal. This establishes SplitMeanFlow as a direct and more general foundation for learning average velocity fields. From a practical standpoint, our algebraic approach is significantly more efficient, as it eliminates the need for JVP computations, resulting in simpler implementation, more stable training, and broader hardware compatibility. One-step and two-step SplitMeanFlow models have been successfully deployed in large-scale speech synthesis products (such as Doubao), achieving speedups of 20x.

Yi Guo, Yihang Dong, Michael Kwok-Po Ng et al.

Brain-computer interfaces (BCIs) with speech decoding from brain recordings have broad application potential in fields such as clinical rehabilitation and cognitive neuroscience. However, current decoding methods remain limited to single-language, single-subject, and single neuroimaging modality settings, restricting their clinical applicability and generalizability. Here we propose a joint multilingual, multi-subject and multimodal decoding framework. It maps diverse brain recordings into a unified semantic space defined by a pre-trained multilingual model (PMM), enabling decoding across multiple languages, multiple subjects and multiple neuroimaging modalities. The proposed framework is validated using non-invasive brain recordings from 159 participants across four languages. Experimental results show that it exhibits strong generalization across multilingual, multi-subject, and multimodal settings. More importantly, the proposed framework can promote linguistic fairness, which is vital for underrepresented languages in BCI applications. The unified semantic space enables cross-lingual mapping enhancement, allowing the framework to boost the decoding performance of underrepresented languages, thereby promoting linguistic fairness. Overall, the proposed framework establishes a new potential paradigm for brain decoding, opening new paths for broader applications of BCI.

Yi Guo, Yiqian He, Xiaoyang Li et al.

Knowledge Distillation (KD) emerges as one of the most promising compression technologies to run advanced deep neural networks on resource-limited devices. In order to train a small network (student) under the guidance of a large network (teacher), the intuitive method is regularizing the feature maps or logits of the student using the teacher's information. However, existing methods either over-restrict the student to learn all information from the teacher, which lead to some bad local minimum, or use various fancy and elaborate modules to process and align features, which are complex and lack generality. In this work, we proposed an abstract and general paradigm for the KD task, referred to as DIMensionality Reduction KD (RdimKD), which solely relies on dimensionality reduction, with a very minor modification to naive L2 loss. RdimKD straightforwardly utilizes a projection matrix to project both the teacher's and student's feature maps onto a low-dimensional subspace, which are then optimized during training. RdimKD achieves the goal in the simplest way that not only does the student get valuable information from the teacher, but it also ensures sufficient flexibility to adapt to the student's low-capacity reality. Our extensive empirical findings indicate the effectiveness of RdimKD across various learning tasks and diverse network architectures.

Tao Song, Yicheng Wu, Minhao Hu et al.

Accelerated MRI reconstruction plays a vital role in reducing scan time while preserving image quality. While most existing methods rely on complex-valued image-space or k-space data, these formats are often inaccessible in clinical practice due to proprietary reconstruction pipelines, leaving only magnitude images stored in DICOM files. To address this gap, we focus on the underexplored task of magnitude-image-based MRI reconstruction. Recent advancements in diffusion models, particularly denoising diffusion probabilistic models (DDPMs), have demonstrated strong capabilities in modeling image priors. However, their task-agnostic denoising nature limits performance in source-to-target image translation tasks, such as MRI reconstruction. In this work, we propose a novel Self-Consistent Nested Diffusion Bridge (SC-NDB) framework that models accelerated MRI reconstruction as a bi-directional image translation process between under-sampled and fully-sampled magnitude MRI images. SC-NDB introduces a nested diffusion architecture with a self-consistency constraint and reverse bridge diffusion pathways to improve intermediate prediction fidelity and better capture the explicit priors of source images. Furthermore, we incorporate a Contour Decomposition Embedding Module (CDEM) to inject structural and textural knowledge by leveraging Laplacian pyramids and directional filter banks. Extensive experiments on the fastMRI and IXI datasets demonstrate that our method achieves state-of-the-art performance compared to both magnitude-based and non-magnitude-based diffusion models, confirming the effectiveness and clinical relevance of SC-NDB.

Peng Huang, Bowen Guo, Shuyu Liang et al.

Text-To-Image (TTI) generation is significant for controlled and diverse image generation with broad potential applications. Although current medical TTI methods have made some progress in report-to-Chest-Xray (CXR) generation, their generation performance may be limited due to the intrinsic characteristics of medical data. In this paper, we propose a novel disease-knowledge enhanced Diffusion-based TTI learning framework, named Diff-CXR, for medical report-to-CXR generation. First, to minimize the negative impacts of noisy data on generation, we devise a Latent Noise Filtering Strategy that gradually learns the general patterns of anomalies and removes them in the latent space. Then, an Adaptive Vision-Aware Textual Learning Strategy is designed to learn concise and important report embeddings in a domain-specific Vision-Language Model, providing textual guidance for Chest-Xray generation. Finally, by incorporating the general disease knowledge into the pretrained TTI model via a delicate control adapter, a disease-knowledge enhanced diffusion model is introduced to achieve realistic and precise report-to-CXR generation. Experimentally, our Diff-CXR outperforms previous SOTA medical TTI methods by 33.4\% / 8.0\% and 23.8\% / 56.4\% in the FID and mAUC score on MIMIC-CXR and IU-Xray, with the lowest computational complexity at 29.641 GFLOPs. Downstream experiments on three thorax disease classification benchmarks and one CXR-report generation benchmark demonstrate that Diff-CXR is effective in improving classical CXR analysis methods. Notably, models trained on the combination of 1\% real data and synthetic data can achieve a competitive mAUC score compared to models trained on all data, presenting promising clinical applications.

Aokun Chen, Qian Li, Yu Huang et al.

A comprehensive view of factors associated with AD/ADRD will significantly aid in studies to develop new treatments for AD/ADRD and identify high-risk populations and patients for prevention efforts. In our study, we summarized the risk factors for AD/ADRD by reviewing existing meta-analyses and review articles on risk and preventive factors for AD/ADRD. In total, we extracted 477 risk factors in 10 categories from 537 studies. We constructed an interactive knowledge map to disseminate our study results. Most of the risk factors are accessible from structured Electronic Health Records (EHRs), and clinical narratives show promise as information sources. However, evaluating genomic risk factors using RWD remains a challenge, as genetic testing for AD/ADRD is still not a common practice and is poorly documented in both structured and unstructured EHRs. Considering the constantly evolving research on AD/ADRD risk factors, literature mining via NLP methods offers a solution to automatically update our knowledge map.

Zixia Zhou, Junyan Liu, Wei Emma Wu et al.

Dynamic brain data, teeming with biological and functional insights, are becoming increasingly accessible through advanced measurements, providing a gateway to understanding the inner workings of the brain in living subjects. However, the vast size and intricate complexity of the data also pose a daunting challenge in reliably extracting meaningful information across various data sources. This paper introduces a generalizable unsupervised deep manifold learning for exploration of neurocognitive and behavioral patterns. Unlike existing methods that extract patterns directly from the input data as in the existing methods, the proposed Brain-dynamic Convolutional-Network-based Embedding (BCNE) seeks to capture the brain-state trajectories by deciphering the temporospatial correlations within the data and subsequently applying manifold learning to this correlative representation. The performance of BCNE is showcased through the analysis of several important dynamic brain datasets. The results, both visual and quantitative, reveal a diverse array of intriguing and interpretable patterns. BCNE effectively delineates scene transitions, underscores the involvement of different brain regions in memory and narrative processing, distinguishes various stages of dynamic learning processes, and identifies differences between active and passive behaviors. BCNE provides an effective tool for exploring general neuroscience inquiries or individual-specific patterns.

Peng Huang, Junhu Fu, Bowen Guo et al.

As the appearance of medical images is influenced by multiple underlying factors, generative models require rich attribute information beyond labels to produce realistic and diverse images. For instance, generating an image of skin lesion with specific patterns demands descriptions that go beyond diagnosis, such as shape, size, texture, and color. However, such detailed descriptions are not always accessible. To address this, we explore a framework, termed Visual Attribute Prompts (VAP)-Diffusion, to leverage external knowledge from pre-trained Multi-modal Large Language Models (MLLMs) to improve the quality and diversity of medical image generation. First, to derive descriptions from MLLMs without hallucination, we design a series of prompts following Chain-of-Thoughts for common medical imaging tasks, including dermatologic, colorectal, and chest X-ray images. Generated descriptions are utilized during training and stored across different categories. During testing, descriptions are randomly retrieved from the corresponding category for inference. Moreover, to make the generator robust to unseen combination of descriptions at the test time, we propose a Prototype Condition Mechanism that restricts test embeddings to be similar to those from training. Experiments on three common types of medical imaging across four datasets verify the effectiveness of VAP-Diffusion.

Junjie Yu, Wenxiao Ma, Jianyu Zhang et al.

Despite variations in architecture and pretraining strategies, recent studies indicate that large-scale AI models often converge toward similar internal representations that also align with neural activity. We propose that scale-invariance, a fundamental structural principle in natural systems, is a key driver of this convergence. In this work, we propose a multi-scale analytical framework to quantify two core aspects of scale-invariance in AI representations: dimensional stability and structural similarity across scales. We further investigate whether these properties can predict alignment performance with functional Magnetic Resonance Imaging (fMRI) responses in the visual cortex. Our analysis reveals that embeddings with more consistent dimension and higher structural similarity across scales align better with fMRI data. Furthermore, we find that the manifold structure of fMRI data is more concentrated, with most features dissipating at smaller scales. Embeddings with similar scale patterns align more closely with fMRI data. We also show that larger pretraining datasets and the inclusion of language modalities enhance the scale-invariance properties of embeddings, further improving neural alignment. Our findings indicate that scale-invariance is a fundamental structural principle that bridges artificial and biological representations, providing a new framework for evaluating the structural quality of human-like AI systems.

Ziyi Chen, Yiyang Liu, Mattia Prosperi et al.

Objective: To characterize stigma dimensions, social, and related behavioral circumstances in people living with HIV(PLWHs) seeking care, using NLP methods applied to a large collection of EHR clinical notes from a large integrated health system in the southeast United States. Methods: We identified a cohort of PLWHs from the UF Health IDR and performed topic modeling analysis using Latent Dirichlet Allocation to uncover stigma-related dimensions and related social and behavioral contexts. Domain experts created a seed list of HIV-related stigma keywords, then applied a snowball strategy to review notes for additional terms until saturation was reached iteratively. To identify more target topics, we tested three keyword-based filtering strategies. The detected topics were evaluated using three widely used metrics and manually reviewed by specialists. In addition, we conducted word frequency analysis and topic variation analysis among subgroups to examine differences across age and sex-specific demographics. Results: We identified 9140 PLWHs at UF Health and collected 2.9 million clinical notes. Through the iterative keyword approach, we generated a list of 91 keywords associated with HIV-related stigma. Topic modeling on sentences containing at least one keyword uncovered a wide range of topic themes, such as "Mental Health Concern, Stigma", "Treatment Refusal, Isolation", and "Substance Abuse". Topic variation analysis across age subgroups revealed substantial differences. Conclusion: Extracting and understanding the HIV-related stigma and associated social and behavioral circumstances from EHR clinical notes enables scalable, time-efficient assessment and overcoming the limitations of traditional questionnaires. Findings from this research provide actionable insights to inform patient care and interventions to improve HIV-care outcomes.

Namal Jayasuriya, Yi Guo, Wen Hu et al.

Estimation of a single leaf area can be a measure of crop growth and a phenotypic trait to breed new varieties. It has also been used to measure leaf area index and total leaf area. Some studies have used hand-held cameras, image processing 3D reconstruction and unsupervised learning-based methods to estimate the leaf area in plant images. Deep learning works well for object detection and segmentation tasks; however, direct area estimation of objects has not been explored. This work investigates deep learning-based leaf area estimation, for RGBD images taken using a mobile camera setup in real-world scenarios. A dataset for attached leaves captured with a top angle view and a dataset for detached single leaves were collected for model development and testing. First, image processing-based area estimation was tested on manually segmented leaves. Then a Mask R-CNN-based model was investigated, and modified to accept RGBD images and to estimate the leaf area. The detached-leaf data set was then mixed with the attached-leaf plant data set to estimate the single leaf area for plant images, and another network design with two backbones was proposed: one for segmentation and the other for area estimation. Instead of trying all possibilities or random values, an agile approach was used in hyperparameter tuning. The final model was cross-validated with 5-folds and tested with two unseen datasets: detached and attached leaves. The F1 score with 90% IoA for segmentation result on unseen detached-leaf data was 1.0, while R-squared of area estimation was 0.81. For unseen plant data segmentation, the F1 score with 90% IoA was 0.59, while the R-squared score was 0.57. The research suggests using attached leaves with ground truth area to improve the results.

Zirui Wang, Zhenxi Song, Yi Guo et al.

The development of EEG decoding algorithms confronts challenges such as data sparsity, subject variability, and the need for precise annotations, all of which are vital for advancing brain-computer interfaces and enhancing the diagnosis of diseases. To address these issues, we propose a novel two-stage approach named Self-Supervised State Reconstruction-Primed Riemannian Dynamics (EEG-ReMinD) , which mitigates reliance on supervised learning and integrates inherent geometric features. This approach efficiently handles EEG data corruptions and reduces the dependency on labels. EEG-ReMinD utilizes self-supervised and geometric learning techniques, along with an attention mechanism, to analyze the temporal dynamics of EEG features within the framework of Riemannian geometry, referred to as Riemannian dynamics. Comparative analyses on both intact and corrupted datasets from two different neurodegenerative disorders underscore the enhanced performance of EEG-ReMinD.

Wangli Yang, Jie Yang, Yi Guo et al.

The field of textual adversarial defenses has gained considerable attention in recent years due to the increasing vulnerability of natural language processing (NLP) models to adversarial attacks, which exploit subtle perturbations in input text to deceive models. This paper introduces the Defensive Dual Masking (DDM) algorithm, a novel approach designed to enhance model robustness against such attacks. DDM utilizes a unique adversarial training strategy where [MASK] tokens are strategically inserted into training samples to prepare the model to handle adversarial perturbations more effectively. During inference, potentially adversarial tokens are dynamically replaced with [MASK] tokens to neutralize potential threats while preserving the core semantics of the input. The theoretical foundation of our approach is explored, demonstrating how the selective masking mechanism strengthens the model's ability to identify and mitigate adversarial manipulations. Our empirical evaluation across a diverse set of benchmark datasets and attack mechanisms consistently shows that DDM outperforms state-of-the-art defense techniques, improving model accuracy and robustness. Moreover, when applied to Large Language Models (LLMs), DDM also enhances their resilience to adversarial attacks, providing a scalable defense mechanism for large-scale NLP applications.

Peng Huang, Xue Gao, Lihong Huang et al.

Text-to-image generation has important implications for generation of diverse and controllable images. Several attempts have been made to adapt Stable Diffusion (SD) to the medical domain. However, the large distribution difference between medical reports and natural texts, as well as high computational complexity in common stable diffusion limit the authenticity and feasibility of the generated medical images. To solve above problems, we propose a novel light-weight transformer-based diffusion model learning framework, Chest-Diffusion, for report-to-CXR generation. Chest-Diffusion employs a domain-specific text encoder to obtain accurate and expressive text features to guide image generation, improving the authenticity of the generated images. Meanwhile, we introduce a light-weight transformer architecture as the denoising model, reducing the computational complexity of the diffusion model. Experiments demonstrate that our Chest-Diffusion achieves the lowest FID score 24.456, under the computation budget of 118.918 GFLOPs, which is nearly one-third of the computational complexity of SD.

Dai Shi, Andi Han, Lequan Lin et al.

Physics-informed Graph Neural Networks have achieved remarkable performance in learning through graph-structured data by mitigating common GNN challenges such as over-smoothing, over-squashing, and heterophily adaption. Despite these advancements, the development of a simple yet effective paradigm that appropriately integrates previous methods for handling all these challenges is still underway. In this paper, we draw an analogy between the propagation of GNNs and particle systems in physics, proposing a model-agnostic enhancement framework. This framework enriches the graph structure by introducing additional nodes and rewiring connections with both positive and negative weights, guided by node labeling information. We theoretically verify that GNNs enhanced through our approach can effectively circumvent the over-smoothing issue and exhibit robustness against over-squashing. Moreover, we conduct a spectral analysis on the rewired graph to demonstrate that the corresponding GNNs can fit both homophilic and heterophilic graphs. Empirical validations on benchmarks for homophilic, heterophilic graphs, and long-term graph datasets show that GNNs enhanced by our method significantly outperform their original counterparts.

Dai Shi, Zhiqi Shao, Yi Guo et al.

This paper presents a comprehensive theoretical analysis of the graph p-Laplacian regularized framelet network (pL-UFG) to establish a solid understanding of its properties. We conduct a convergence analysis on pL-UFG, addressing the gap in the understanding of its asymptotic behaviors. Further by investigating the generalized Dirichlet energy of pL-UFG, we demonstrate that the Dirichlet energy remains non-zero throughout convergence, ensuring the avoidance of over-smoothing issues. Additionally, we elucidate the energy dynamic perspective, highlighting the synergistic relationship between the implicit layer in pL-UFG and graph framelets. This synergy enhances the model's adaptability to both homophilic and heterophilic data. Notably, we reveal that pL-UFG can be interpreted as a generalized non-linear diffusion process, thereby bridging the gap between pL-UFG and differential equations on the graph. Importantly, these multifaceted analyses lead to unified conclusions that offer novel insights for understanding and implementing pL-UFG, as well as other graph neural network (GNN) models. Finally, based on our dynamic analysis, we propose two novel pL-UFG models with manually controlled energy dynamics. We demonstrate empirically and theoretically that our proposed models not only inherit the advantages of pL-UFG but also significantly reduce computational costs for training on large-scale graph datasets.

Cheng Peng, Xi Yang, Aokun Chen et al.

There is enormous enthusiasm and concerns in using large language models (LLMs) in healthcare, yet current assumptions are all based on general-purpose LLMs such as ChatGPT. This study develops a clinical generative LLM, GatorTronGPT, using 277 billion words of mixed clinical and English text with a GPT-3 architecture of 20 billion parameters. GatorTronGPT improves biomedical natural language processing for medical research. Synthetic NLP models trained using GatorTronGPT generated text outperform NLP models trained using real-world clinical text. Physicians Turing test using 1 (worst) to 9 (best) scale shows that there is no significant difference in linguistic readability (p = 0.22; 6.57 of GatorTronGPT compared with 6.93 of human) and clinical relevance (p = 0.91; 7.0 of GatorTronGPT compared with 6.97 of human) and that physicians cannot differentiate them (p < 0.001). This study provides insights on the opportunities and challenges of LLMs for medical research and healthcare.