Lian Zhang

Huang Huang, Fei Yu, Jianqing Zhu et al.

This paper is devoted to the development of a localized Large Language Model (LLM) specifically for Arabic, a language imbued with unique cultural characteristics inadequately addressed by current mainstream models. Significant concerns emerge when addressing cultural sensitivity and local values. To address this, the paper proposes a comprehensive solution that includes further pre-training with Arabic texts, Supervised Fine-Tuning (SFT) utilizing native Arabic instructions, and GPT-4 responses in Arabic, alongside Reinforcement Learning with AI Feedback (RLAIF) employing a reward model attuned to local culture and values. The goal is to cultivate culturally cognizant and value-aligned Arabic LLMs capable of accommodating the diverse, application-specific needs of Arabic-speaking communities. Comprehensive evaluations reveal that the resulting model, dubbed `AceGPT', sets the state-of-the-art standard for open Arabic LLMs across various benchmarks. Codes, data, and models are in https://github.com/FreedomIntelligence/AceGPT.

Jason Holmes, Zhengliang Liu, Lian Zhang et al.

We present the first study to investigate Large Language Models (LLMs) in answering radiation oncology physics questions. Because popular exams like AP Physics, LSAT, and GRE have large test-taker populations and ample test preparation resources in circulation, they may not allow for accurately assessing the true potential of LLMs. This paper proposes evaluating LLMs on a highly-specialized topic, radiation oncology physics, which may be more pertinent to scientific and medical communities in addition to being a valuable benchmark of LLMs. We developed an exam consisting of 100 radiation oncology physics questions based on our expertise at Mayo Clinic. Four LLMs, ChatGPT (GPT-3.5), ChatGPT (GPT-4), Bard (LaMDA), and BLOOMZ, were evaluated against medical physicists and non-experts. ChatGPT (GPT-4) outperformed all other LLMs as well as medical physicists, on average. The performance of ChatGPT (GPT-4) was further improved when prompted to explain first, then answer. ChatGPT (GPT-3.5 and GPT-4) showed a high level of consistency in its answer choices across a number of trials, whether correct or incorrect, a characteristic that was not observed in the human test groups. In evaluating ChatGPTs (GPT-4) deductive reasoning ability using a novel approach (substituting the correct answer with "None of the above choices is the correct answer."), ChatGPT (GPT-4) demonstrated surprising accuracy, suggesting the potential presence of an emergent ability. Finally, although ChatGPT (GPT-4) performed well overall, its intrinsic properties did not allow for further improvement when scoring based on a majority vote across trials. In contrast, a team of medical physicists were able to greatly outperform ChatGPT (GPT-4) using a majority vote. This study suggests a great potential for LLMs to work alongside radiation oncology experts as highly knowledgeable assistants.

Xing Hu, Xiangcheng Liu, Qianqian Duan et al.

Hyperspectral image (HSI) analysis plays a critical role in remote sensing, agriculture, and environmental monitoring. However, traditional methods often struggle to handle the high dimensionality, spectral redundancy, and noise inherent in HSI data, limiting their accuracy and scalability. Recently, diffusion models including denoising diffusion probabilistic models and other generative frameworks based on stochastic differential equations have shown strong potential in capturing complex spectral spatial structures and generating high fidelity HSI data. These models offer effective solutions for tasks such as noise supression, data augmentation, classification, and anomaly detection. This review presents a systematic summary of recent advances in diffusion models for HSI processing. We categorize existing methods, highlight their strengths in handling high dimensional data, and compare their performance with conventional approaches. Special attention is given to critical applications such as change detection and post disaster anomaly identification. The review also discusses current limitations, such as computational cost and training stability, and outlines potential research directions. Our main contributions can be summarized as follows: we provide a systematic taxonomy of diffusion based HSI methods, examine their applications across major remote sensing tasks, and offer perspectives on potential directions for future research. With these efforts, this review seeks to support the community in harnessing deep learning models to achieve more effective and efficient hyperspectral image analysis.

Zhengliang Liu, Peilong Wang, Yiwei Li et al.

This paper presents RadOnc-GPT, a large language model specialized for radiation oncology through advanced tuning methods. RadOnc-GPT was finetuned on a large dataset of radiation oncology patient records from the Mayo Clinic in Arizona. The model employs instruction tuning on three key tasks - generating radiotherapy treatment regimens, determining optimal radiation modalities, and providing diagnostic descriptions/ICD codes based on patient diagnostic details. Evaluations conducted by comparing RadOnc-GPT outputs to general large language model outputs showed higher ROUGE scores in these three tasks. The study demonstrated the potential of using large language models fine-tuned using domain-specific knowledge like RadOnc-GPT to achieve transformational capabilities in highly specialized healthcare fields such as radiation oncology. However, our model's clinical relevance requires confirmation, and it specializes in only the aforementioned three specific tasks and lacks broader applicability. Furthermore, its evaluation through ROUGE scores might not reflect the true semantic and clinical accuracy - challenges we intend to address in future research.

Lian Zhang, Zhengliang Liu, Lu Zhang et al.

In this study, we evaluate the performance of the Segment Anything Model (SAM) in clinical radiotherapy. Our results indicate that SAM's 'segment anything' mode can achieve clinically acceptable segmentation results in most organs-at-risk (OARs) with Dice scores higher than 0.7. SAM's 'box prompt' mode further improves the Dice scores by 0.1 to 0.5. Considering the size of the organ and the clarity of its boundary, SAM displays better performance for large organs with clear boundaries but performs worse for smaller organs with unclear boundaries. Given that SAM, a model pre-trained purely on natural images, can handle the delineation of OARs from medical images with clinically acceptable accuracy, these results highlight SAM's robust generalization capabilities with consistent accuracy in automatic segmentation for radiotherapy. In other words, SAM can achieve delineation of different OARs at different sites using a generic automatic segmentation model. SAM's generalization capabilities across different disease sites suggest that it is technically feasible to develop a generic model for automatic segmentation in radiotherapy.

Tianyang Zhong, Zhengliang Liu, Yi Pan et al.

This comprehensive study evaluates the performance of OpenAI's o1-preview large language model across a diverse array of complex reasoning tasks, spanning multiple domains, including computer science, mathematics, natural sciences, medicine, linguistics, and social sciences. Through rigorous testing, o1-preview demonstrated remarkable capabilities, often achieving human-level or superior performance in areas ranging from coding challenges to scientific reasoning and from language processing to creative problem-solving. Key findings include: -83.3% success rate in solving complex competitive programming problems, surpassing many human experts. -Superior ability in generating coherent and accurate radiology reports, outperforming other evaluated models. -100% accuracy in high school-level mathematical reasoning tasks, providing detailed step-by-step solutions. -Advanced natural language inference capabilities across general and specialized domains like medicine. -Impressive performance in chip design tasks, outperforming specialized models in areas such as EDA script generation and bug analysis. -Remarkable proficiency in anthropology and geology, demonstrating deep understanding and reasoning in these specialized fields. -Strong capabilities in quantitative investing. O1 has comprehensive financial knowledge and statistical modeling skills. -Effective performance in social media analysis, including sentiment analysis and emotion recognition. The model excelled particularly in tasks requiring intricate reasoning and knowledge integration across various fields. While some limitations were observed, including occasional errors on simpler problems and challenges with certain highly specialized concepts, the overall results indicate significant progress towards artificial general intelligence.

Jianqing Zhu, Juncai He, Lian Zhang et al.

By investigating iterative methods for a constrained linear model, we propose a new class of fully connected V-cycle MgNet for long-term time series forecasting, which is one of the most difficult tasks in forecasting. MgNet is a CNN model that was proposed for image classification based on the multigrid (MG) methods for solving discretized partial differential equations (PDEs). We replace the convolutional operations with fully connected operations in the existing MgNet and then apply them to forecasting problems. Motivated by the V-cycle structure in MG, we further propose the FV-MgNet, a V-cycle version of the fully connected MgNet, to extract features hierarchically. By evaluating the performance of FV-MgNet on popular data sets and comparing it with state-of-the-art models, we show that the FV-MgNet achieves better results with less memory usage and faster inference speed. In addition, we develop ablation experiments to demonstrate that the structure of FV-MgNet is the best choice among the many variants.

Jason Holmes, Lian Zhang, Yuzhen Ding et al.

Purpose: To introduce the concept of using large language models (LLMs) to re-label structure names in accordance with the American Association of Physicists in Medicine (AAPM) Task Group (TG)-263 standard, and to establish a benchmark for future studies to reference. Methods and Materials: The Generative Pre-trained Transformer (GPT)-4 application programming interface (API) was implemented as a Digital Imaging and Communications in Medicine (DICOM) storage server, which upon receiving a structure set DICOM file, prompts GPT-4 to re-label the structure names of both target volumes and normal tissues according to the AAPM TG-263. Three disease sites, prostate, head and neck, and thorax were selected for evaluation. For each disease site category, 150 patients were randomly selected for manually tuning the instructions prompt (in batches of 50) and 50 patients were randomly selected for evaluation. Structure names that were considered were those that were most likely to be relevant for studies utilizing structure contours for many patients. Results: The overall re-labeling accuracy of both target volumes and normal tissues for prostate, head and neck, and thorax cases was 96.0%, 98.5%, and 96.9% respectively. Re-labeling of target volumes was less accurate on average except for prostate - 100%, 93.1%, and 91.1% respectively. Conclusions: Given the accuracy of GPT-4 in re-labeling structure names of both target volumes and normal tissues as presented in this work, LLMs are poised to be the preferred method for standardizing structure names in radiation oncology, especially considering the rapid advancements in LLM capabilities that are likely to continue.

Juhao Liang, Zhenyang Cai, Jianqing Zhu et al.

The alignment of large language models (LLMs) is critical for developing effective and safe language models. Traditional approaches focus on aligning models during the instruction tuning or reinforcement learning stages, referred to in this paper as `post alignment'. We argue that alignment during the pre-training phase, which we term `native alignment', warrants investigation. Native alignment aims to prevent unaligned content from the beginning, rather than relying on post-hoc processing. This approach leverages extensively aligned pre-training data to enhance the effectiveness and usability of pre-trained models. Our study specifically explores the application of native alignment in the context of Arabic LLMs. We conduct comprehensive experiments and ablation studies to evaluate the impact of native alignment on model performance and alignment stability. Additionally, we release open-source Arabic LLMs that demonstrate state-of-the-art performance on various benchmarks, providing significant benefits to the Arabic LLM community.

Jianqing Zhu, Huang Huang, Zhihang Lin et al.

This paper addresses the critical need for democratizing large language models (LLM) in the Arab world, a region that has seen slower progress in developing models comparable to state-of-the-art offerings like GPT-4 or ChatGPT 3.5, due to a predominant focus on mainstream languages (e.g., English and Chinese). One practical objective for an Arabic LLM is to utilize an Arabic-specific vocabulary for the tokenizer that could speed up decoding. However, using a different vocabulary often leads to a degradation of learned knowledge since many words are initially out-of-vocabulary (OOV) when training starts. Inspired by the vocabulary learning during Second Language (Arabic) Acquisition for humans, the released AraLLaMA employs progressive vocabulary expansion, which is implemented by a modified BPE algorithm that progressively extends the Arabic subwords in its dynamic vocabulary during training, thereby balancing the OOV ratio at every stage. The ablation study demonstrated the effectiveness of Progressive Vocabulary Expansion. Moreover, AraLLaMA achieves decent performance comparable to the best Arabic LLMs across a variety of Arabic benchmarks. Models, training data, benchmarks, and codes will be all open-sourced.

Peilong Wang, Zhengliang Liu, Yiwei Li et al.

Background: The radiation oncology clinical practice involves many steps relying on the dynamic interplay of abundant text data. Large language models have displayed remarkable capabilities in processing complex text information. But their direct applications in specific fields like radiation oncology remain underexplored. Purpose: This study aims to investigate whether fine-tuning LLMs with domain knowledge can improve the performance on Task (1) treatment regimen generation, Task (2) treatment modality selection (photon, proton, electron, or brachytherapy), and Task (3) ICD-10 code prediction in radiation oncology. Methods: Data for 15,724 patient cases were extracted. Cases where patients had a single diagnostic record, and a clearly identifiable primary treatment plan were selected for preprocessing and manual annotation to have 7,903 cases of the patient diagnosis, treatment plan, treatment modality, and ICD-10 code. Each case was used to construct a pair consisting of patient diagnostics details and an answer (treatment regimen, treatment modality, or ICD-10 code respectively) for the supervised fine-tuning of these three tasks. Open source LLaMA2-7B and Mistral-7B models were utilized for the fine-tuning with the Low-Rank Approximations method. Accuracy and ROUGE-1 score were reported for the fine-tuned models and original models. Clinical evaluation was performed on Task (1) by radiation oncologists, while precision, recall, and F-1 score were evaluated for Task (2) and (3). One-sided Wilcoxon signed-rank tests were used to statistically analyze the results. Results: Fine-tuned LLMs outperformed original LLMs across all tasks with p-value <= 0.001. Clinical evaluation demonstrated that over 60% of the fine-tuned LLMs-generated treatment regimens were clinically acceptable. Precision, recall, and F1-score showed improved performance of fine-tuned LLMs.

Joongwon Chae, Runming Wang, Chen Xiong et al.

Effective surveillance of hand, foot and mouth disease (HFMD) requires forecasts accounting for epidemiological patterns and contextual drivers like school calendars and weather. While classical models and recent foundation models (e.g., Chronos, TimesFM) incorporate covariates, they often lack the semantic reasoning to interpret the causal interplay between conflicting drivers. In this work, we propose a two-agent framework decoupling contextual interpretation from probabilistic forecasting. An LLM "event interpreter" processes heterogeneous signals-including school schedules, meteorological summaries, and reports-into a scalar transmission-impact signal. A neuro-symbolic core then combines this with historical case counts to produce calibrated probabilistic forecasts. We evaluate the framework on real-world HFMD datasets from Hong Kong (2023-2024) and Lishui, China (2024). Compared to traditional and foundation-model baselines, our approach achieves competitive point forecasting accuracy while providing robust 90% prediction intervals (coverage 0.85-1.00) and human-interpretable rationales. Our results suggest that structurally integrating domain knowledge through LLMs can match state-of-the-art performance while yielding context-aware forecasts that align with public health workflows. Code is available at https://github.com/jw-chae/forecast_MED .

Joongwon Chae, Lihui Luo, Xi Yuan et al.

Accurate tongue segmentation is crucial for reliable TCM analysis. Supervised models require large annotated datasets, while SAM-family models remain prompt-driven. We present Memory-SAM, a training-free, human-prompt-free pipeline that automatically generates effective prompts from a small memory of prior cases via dense DINOv3 features and FAISS retrieval. Given a query image, mask-constrained correspondences to the retrieved exemplar are distilled into foreground/background point prompts that guide SAM2 without manual clicks or model fine-tuning. We evaluate on 600 expert-annotated images (300 controlled, 300 in-the-wild). On the mixed test split, Memory-SAM achieves mIoU 0.9863, surpassing FCN (0.8188) and a detector-to-box SAM baseline (0.1839). On controlled data, ceiling effects above 0.98 make small differences less meaningful given annotation variability, while our method shows clear gains under real-world conditions. Results indicate that retrieval-to-prompt enables data-efficient, robust segmentation of irregular boundaries in tongue imaging. The code is publicly available at https://github.com/jw-chae/memory-sam.

Zhengliang Liu, Jason Holmes, Wenxiong Liao et al.

We present the Radiation Oncology NLP Database (ROND), the first dedicated Natural Language Processing (NLP) dataset for radiation oncology, an important medical specialty that has received limited attention from the NLP community in the past. With the advent of Artificial General Intelligence (AGI), there is an increasing need for specialized datasets and benchmarks to facilitate research and development. ROND is specifically designed to address this gap in the domain of radiation oncology, a field that offers many opportunities for NLP exploration. It encompasses various NLP tasks including Logic Reasoning, Text Classification, Named Entity Recognition (NER), Question Answering (QA), Text Summarization, and Patient-Clinician Conversations, each with a distinct focus on radiation oncology concepts and application cases. In addition, we have developed an instruction-tuning dataset consisting of over 20k instruction pairs (based on ROND) and trained a large language model, CancerChat. This serves to demonstrate the potential of instruction-tuning large language models within a highly-specialized medical domain. The evaluation results in this study could serve as baseline results for future research. ROND aims to stimulate advancements in radiation oncology and clinical NLP by offering a platform for testing and improving algorithms and models in a domain-specific context. The ROND dataset is a joint effort of multiple U.S. health institutions. The data is available at https://github.com/zl-liu/Radiation-Oncology-NLP-Database.

Bingyu Yan, Zhibo Zhou, Litian Zhang et al.

Large language model-based multi-agent systems have recently gained significant attention due to their potential for complex, collaborative, and intelligent problem-solving capabilities. Existing surveys typically categorize LLM-based multi-agent systems (LLM-MAS) according to their application domains or architectures, overlooking the central role of communication in coordinating agent behaviors and interactions. To address this gap, this paper presents a comprehensive survey of LLM-MAS from a communication-centric perspective. Specifically, we propose a structured framework that integrates system-level communication (architecture, goals, and protocols) with system internal communication (strategies, paradigms, objects, and content), enabling a detailed exploration of how agents interact, negotiate, and achieve collective intelligence. Through an extensive analysis of recent literature, we identify key components in multiple dimensions and summarize their strengths and limitations. In addition, we highlight current challenges, including communication efficiency, security vulnerabilities, inadequate benchmarking, and scalability issues, and outline promising future research directions. This review aims to help researchers and practitioners gain a clear understanding of the communication mechanisms in LLM-MAS, thereby facilitating the design and deployment of robust, scalable, and secure multi-agent systems.

Joongwon Chae, Zhenyu Wang, Lian Zhang et al.

Recent advances in multimodal models have demonstrated impressive capabilities in object recognition and scene understanding. However, these models often struggle with precise spatial localization - a critical capability for real-world applications. Inspired by how humans use grid-based references like chess boards and maps, we propose introducing explicit visual position encoding through a simple grid overlay approach. By adding a 9x9 black grid pattern onto input images, our method provides visual spatial guidance analogous to how positional encoding works in transformers, but in an explicit, visual form. Experiments on the COCO 2017 dataset demonstrate that our grid-based approach achieves significant improvements in localization accuracy, with a 107.4% increase in IoU (from 0.27 to 0.56) and a 194.4% improvement in GIoU (from 0.18 to 0.53) compared to baseline performance. Through attention visualization analysis, we show how this visual position encoding helps models better ground spatial relationships. Our method's simplicity and effectiveness make it particularly valuable for applications requiring accurate spatial reasoning, such as robotic manipulation, medical imaging, and autonomous navigation.

Xinliang Liu, Xia Yang, Chen-Song Zhang et al.

This research investigates the application of Multigrid Neural Operator (MgNO), a neural operator architecture inspired by multigrid methods, in the simulation for multiphase flow within porous media. The architecture is adjusted to manage a variety of crucial factors, such as permeability and porosity heterogeneity. The study extendes MgNO to time-dependent porous media flow problems and validate its accuracy in predicting essential aspects of multiphase flows. Furthermore, the research provides a detailed comparison between MgNO and Fourier Neural Opeartor (FNO), which is one of the most popular neural operator methods, on their performance regarding prediction error accumulation over time. This aspect provides valuable insights into the models' long-term predictive stability and reliability. The study demonstrates MgNO's capability to effectively simulate multiphase flow problems, offering considerable time savings compared to traditional simulation methods, marking an advancement in integrating data-driven methodologies in geoscience applications.

Yelu Gao, Huang Huang, Lian Zhang

Alzheimer's disease (AD) is an irreversible neurode generative disease of the brain.The disease may causes memory loss, difficulty communicating and disorientation. For the diagnosis of Alzheimer's disease, a series of scales are often needed to evaluate the diagnosis clinically, which not only increases the workload of doctors, but also makes the results of diagnosis highly subjective. Therefore, for Alzheimer's disease, imaging means to find early diagnostic markers has become a top priority. In this paper, we propose a novel 3DMgNet architecture which is a unified framework of multigrid and convolutional neural network to diagnose Alzheimer's disease (AD). The model is trained using an open dataset (ADNI dataset) and then test with a smaller dataset of ours. Finally, the model achieved 92.133% accuracy for AD vs NC classification and significantly reduced the model parameters.

Juncai He, Jinchao Xu, Lian Zhang et al.

We propose a constrained linear data-feature-mapping model as an interpretable mathematical model for image classification using a convolutional neural network (CNN). From this viewpoint, we establish detailed connections between the traditional iterative schemes for linear systems and the architectures of the basic blocks of ResNet- and MgNet-type models. Using these connections, we present some modified ResNet models that compared with the original models have fewer parameters and yet can produce more accurate results, thereby demonstrating the validity of this constrained learning data-feature-mapping assumption. Based on this assumption, we further propose a general data-feature iterative scheme to show the rationality of MgNet. We also provide a systematic numerical study on MgNet to show its success and advantages in image classification problems and demonstrate its advantages in comparison with established networks.

Juncai He, Yuyan Chen, Lian Zhang et al.

In this paper, we propose a constrained linear data-feature mapping model as an interpretable mathematical model for image classification using convolutional neural network (CNN) such as the ResNet. From this viewpoint, we establish the detailed connections in a technical level between the traditional iterative schemes for constrained linear system and the architecture for the basic blocks of ResNet. Under these connections, we propose some natural modifications of ResNet type models which will have less parameters but still maintain almost the same accuracy as these corresponding original models. Some numerical experiments are shown to demonstrate the validity of this constrained learning data-feature mapping assumption.

Juncai He, Xiaodong Jia, Jinchao Xu et al.

Compressed Sensing using $\ell_1$ regularization is among the most powerful and popular sparsification technique in many applications, but why has it not been used to obtain sparse deep learning model such as convolutional neural network (CNN)? This paper is aimed to provide an answer to this question and to show how to make it work. We first demonstrate that the commonly used stochastic gradient decent (SGD) and variants training algorithm is not an appropriate match with $\ell_1$ regularization and then replace it with a different training algorithm based on a regularized dual averaging (RDA) method. RDA was originally designed specifically for convex problem, but with new theoretical insight and algorithmic modifications (using proper initialization and adaptivity), we have made it an effective match with $\ell_1$ regularization to achieve a state-of-the-art sparsity for CNN compared to other weight pruning methods without compromising accuracy (achieving 95\% sparsity for ResNet18 on CIFAR-10, for example).