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Xiang Wan

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HuatuoGPT-II, One-stage Training for Medical Adaption of LLMs

Nov 16, 2023
Junying Chen, Xidong Wang, Anningzhe Gao, Feng Jiang, Shunian Chen, Hongbo Zhang, Dingjie Song, Wenya Xie, Chuyi Kong, Jianquan Li, Xiang Wan, Haizhou Li, Benyou Wang

Adapting a language model into a specific domain, a.k.a `domain adaption', is a common practice when specialized knowledge, e.g. medicine, is not encapsulated in a general language model like Llama2. The challenge lies in the heterogeneity of data across the two training stages, as it varies in languages, genres, or formats. To tackle this and simplify the learning protocol, we propose to transform heterogeneous data, from the both pre-training and supervised stages, into a unified, simple input-output pair format. We validate the new protocol in the domains where proprietary LLMs like ChatGPT perform relatively poorly, such as Traditional Chinese Medicine. The developed model, HuatuoGPT-II, has shown state-of-the-art performance in Chinese medicine domain on a number of benchmarks, e.g. medical licensing exams. It even outperforms proprietary models like ChatGPT and GPT-4 in some aspects, especially in Traditional Chinese Medicine. Expert manual evaluations further validate HuatuoGPT-II's advantages over existing LLMs. Notably, HuatuoGPT-II was benchmarked in a fresh Chinese National Medical Licensing Examination where it achieved the best performance, showcasing not only its effectiveness but also its generalization capabilities.

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GCS-ICHNet: Assessment of Intracerebral Hemorrhage Prognosis using Self-Attention with Domain Knowledge Integration

Nov 08, 2023
Xuhao Shan, Xinyang Li, Ruiquan Ge, Shibin Wu, Ahmed Elazab, Jichao Zhu, Lingyan Zhang, Gangyong Jia, Qingying Xiao, Xiang Wan, Changmiao Wang

Intracerebral Hemorrhage (ICH) is a severe condition resulting from damaged brain blood vessel ruptures, often leading to complications and fatalities. Timely and accurate prognosis and management are essential due to its high mortality rate. However, conventional methods heavily rely on subjective clinician expertise, which can lead to inaccurate diagnoses and delays in treatment. Artificial intelligence (AI) models have been explored to assist clinicians, but many prior studies focused on model modification without considering domain knowledge. This paper introduces a novel deep learning algorithm, GCS-ICHNet, which integrates multimodal brain CT image data and the Glasgow Coma Scale (GCS) score to improve ICH prognosis. The algorithm utilizes a transformer-based fusion module for assessment. GCS-ICHNet demonstrates high sensitivity 81.03% and specificity 91.59%, outperforming average clinicians and other state-of-the-art methods.

* 6 pages, 3 figures, 5 tables, published to BIBM 2023 
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Multi-stream Cell Segmentation with Low-level Cues for Multi-modality Images

Oct 22, 2023
Wei Lou, Xinyi Yu, Chenyu Liu, Xiang Wan, Guanbin Li, Siqi Liu, Haofeng Li

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Cell segmentation for multi-modal microscopy images remains a challenge due to the complex textures, patterns, and cell shapes in these images. To tackle the problem, we first develop an automatic cell classification pipeline to label the microscopy images based on their low-level image characteristics, and then train a classification model based on the category labels. Afterward, we train a separate segmentation model for each category using the images in the corresponding category. Besides, we further deploy two types of segmentation models to segment cells with roundish and irregular shapes respectively. Moreover, an efficient and powerful backbone model is utilized to enhance the efficiency of our segmentation model. Evaluated on the Tuning Set of NeurIPS 2022 Cell Segmentation Challenge, our method achieves an F1-score of 0.8795 and the running time for all cases is within the time tolerance.

* The second place in NeurIPS 2022 cell segmentation challenge (, released code: 
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Diffusion-based Data Augmentation for Nuclei Image Segmentation

Oct 22, 2023
Xinyi Yu, Guanbin Li, Wei Lou, Siqi Liu, Xiang Wan, Yan Chen, Haofeng Li

Nuclei segmentation is a fundamental but challenging task in the quantitative analysis of histopathology images. Although fully-supervised deep learning-based methods have made significant progress, a large number of labeled images are required to achieve great segmentation performance. Considering that manually labeling all nuclei instances for a dataset is inefficient, obtaining a large-scale human-annotated dataset is time-consuming and labor-intensive. Therefore, augmenting a dataset with only a few labeled images to improve the segmentation performance is of significant research and application value. In this paper, we introduce the first diffusion-based augmentation method for nuclei segmentation. The idea is to synthesize a large number of labeled images to facilitate training the segmentation model. To achieve this, we propose a two-step strategy. In the first step, we train an unconditional diffusion model to synthesize the Nuclei Structure that is defined as the representation of pixel-level semantic and distance transform. Each synthetic nuclei structure will serve as a constraint on histopathology image synthesis and is further post-processed to be an instance map. In the second step, we train a conditioned diffusion model to synthesize histopathology images based on nuclei structures. The synthetic histopathology images paired with synthetic instance maps will be added to the real dataset for training the segmentation model. The experimental results show that by augmenting 10% labeled real dataset with synthetic samples, one can achieve comparable segmentation results with the fully-supervised baseline.

* MICCAI 2023, released code: 
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Prompt-based Grouping Transformer for Nucleus Detection and Classification

Oct 22, 2023
Junjia Huang, Haofeng Li, Weijun Sun, Xiang Wan, Guanbin Li

Automatic nuclei detection and classification can produce effective information for disease diagnosis. Most existing methods classify nuclei independently or do not make full use of the semantic similarity between nuclei and their grouping features. In this paper, we propose a novel end-to-end nuclei detection and classification framework based on a grouping transformer-based classifier. The nuclei classifier learns and updates the representations of nuclei groups and categories via hierarchically grouping the nucleus embeddings. Then the cell types are predicted with the pairwise correlations between categorical embeddings and nucleus features. For the efficiency of the fully transformer-based framework, we take the nucleus group embeddings as the input prompts of backbone, which helps harvest grouping guided features by tuning only the prompts instead of the whole backbone. Experimental results show that the proposed method significantly outperforms the existing models on three datasets.

* MICCAI 2023, released code: 
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ASC: Appearance and Structure Consistency for Unsupervised Domain Adaptation in Fetal Brain MRI Segmentation

Oct 22, 2023
Zihang Xu, Haifan Gong, Xiang Wan, Haofeng Li

Automatic tissue segmentation of fetal brain images is essential for the quantitative analysis of prenatal neurodevelopment. However, producing voxel-level annotations of fetal brain imaging is time-consuming and expensive. To reduce labeling costs, we propose a practical unsupervised domain adaptation (UDA) setting that adapts the segmentation labels of high-quality fetal brain atlases to unlabeled fetal brain MRI data from another domain. To address the task, we propose a new UDA framework based on Appearance and Structure Consistency, named ASC. We adapt the segmentation model to the appearances of different domains by constraining the consistency before and after a frequency-based image transformation, which is to swap the appearance between brain MRI data and atlases. Consider that even in the same domain, the fetal brain images of different gestational ages could have significant variations in the anatomical structures. To make the model adapt to the structural variations in the target domain, we further encourage prediction consistency under different structural perturbations. Extensive experiments on FeTA 2021 benchmark demonstrate the effectiveness of our ASC in comparison to registration-based, semi-supervised learning-based, and existing UDA-based methods.

* MICCAI 2023, released code: 
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Visual-Attribute Prompt Learning for Progressive Mild Cognitive Impairment Prediction

Oct 22, 2023
Luoyao Kang, Haifan Gong, Xiang Wan, Haofeng Li

Deep learning (DL) has been used in the automatic diagnosis of Mild Cognitive Impairment (MCI) and Alzheimer's Disease (AD) with brain imaging data. However, previous methods have not fully exploited the relation between brain image and clinical information that is widely adopted by experts in practice. To exploit the heterogeneous features from imaging and tabular data simultaneously, we propose the Visual-Attribute Prompt Learning-based Transformer (VAP-Former), a transformer-based network that efficiently extracts and fuses the multi-modal features with prompt fine-tuning. Furthermore, we propose a Prompt fine-Tuning (PT) scheme to transfer the knowledge from AD prediction task for progressive MCI (pMCI) diagnosis. In details, we first pre-train the VAP-Former without prompts on the AD diagnosis task and then fine-tune the model on the pMCI detection task with PT, which only needs to optimize a small amount of parameters while keeping the backbone frozen. Next, we propose a novel global prompt token for the visual prompts to provide global guidance to the multi-modal representations. Extensive experiments not only show the superiority of our method compared with the state-of-the-art methods in pMCI prediction but also demonstrate that the global prompt can make the prompt learning process more effective and stable. Interestingly, the proposed prompt learning model even outperforms the fully fine-tuning baseline on transferring the knowledge from AD to pMCI.

* MICCAI 2023, released code: 
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Affine-Consistent Transformer for Multi-Class Cell Nuclei Detection

Oct 22, 2023
Junjia Huang, Haofeng Li, Xiang Wan, Guanbin Li

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Multi-class cell nuclei detection is a fundamental prerequisite in the diagnosis of histopathology. It is critical to efficiently locate and identify cells with diverse morphology and distributions in digital pathological images. Most existing methods take complex intermediate representations as learning targets and rely on inflexible post-refinements while paying less attention to various cell density and fields of view. In this paper, we propose a novel Affine-Consistent Transformer (AC-Former), which directly yields a sequence of nucleus positions and is trained collaboratively through two sub-networks, a global and a local network. The local branch learns to infer distorted input images of smaller scales while the global network outputs the large-scale predictions as extra supervision signals. We further introduce an Adaptive Affine Transformer (AAT) module, which can automatically learn the key spatial transformations to warp original images for local network training. The AAT module works by learning to capture the transformed image regions that are more valuable for training the model. Experimental results demonstrate that the proposed method significantly outperforms existing state-of-the-art algorithms on various benchmarks.

* ICCV 2023, released code: 
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AceGPT, Localizing Large Language Models in Arabic

Sep 22, 2023
Huang Huang, Fei Yu, Jianqing Zhu, Xuening Sun, Hao Cheng, Dingjie Song, Zhihong Chen, Abdulmohsen Alharthi, Bang An, Ziche Liu, Zhiyi Zhang, Junying Chen, Jianquan Li, Benyou Wang, Lian Zhang, Ruoyu Sun, Xiang Wan, Haizhou Li, Jinchao Xu

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This paper explores the imperative need and methodology for developing a localized Large Language Model (LLM) tailored for Arabic, a language with unique cultural characteristics that are not adequately addressed by current mainstream models like ChatGPT. Key concerns additionally arise when considering cultural sensitivity and local values. To this end, the paper outlines a packaged solution, including further pre-training with Arabic texts, supervised fine-tuning (SFT) using native Arabic instructions and GPT-4 responses in Arabic, and reinforcement learning with AI feedback (RLAIF) using a reward model that is sensitive to local culture and values. The objective is to train culturally aware and value-aligned Arabic LLMs that can serve the diverse application-specific needs of Arabic-speaking communities. Extensive evaluations demonstrated that the resulting LLM called `AceGPT' is the SOTA open Arabic LLM in various benchmarks, including instruction-following benchmark (i.e., Arabic Vicuna-80 and Arabic AlpacaEval), knowledge benchmark (i.e., Arabic MMLU and EXAMs), as well as the newly-proposed Arabic cultural \& value alignment benchmark. Notably, AceGPT outperforms ChatGPT in the popular Vicuna-80 benchmark when evaluated with GPT-4, despite the benchmark's limited scale. % Natural Language Understanding (NLU) benchmark (i.e., ALUE) Codes, data, and models are in

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ArSDM: Colonoscopy Images Synthesis with Adaptive Refinement Semantic Diffusion Models

Sep 03, 2023
Yuhao Du, Yuncheng Jiang, Shuangyi Tan, Xusheng Wu, Qi Dou, Zhen Li, Guanbin Li, Xiang Wan

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Colonoscopy analysis, particularly automatic polyp segmentation and detection, is essential for assisting clinical diagnosis and treatment. However, as medical image annotation is labour- and resource-intensive, the scarcity of annotated data limits the effectiveness and generalization of existing methods. Although recent research has focused on data generation and augmentation to address this issue, the quality of the generated data remains a challenge, which limits the contribution to the performance of subsequent tasks. Inspired by the superiority of diffusion models in fitting data distributions and generating high-quality data, in this paper, we propose an Adaptive Refinement Semantic Diffusion Model (ArSDM) to generate colonoscopy images that benefit the downstream tasks. Specifically, ArSDM utilizes the ground-truth segmentation mask as a prior condition during training and adjusts the diffusion loss for each input according to the polyp/background size ratio. Furthermore, ArSDM incorporates a pre-trained segmentation model to refine the training process by reducing the difference between the ground-truth mask and the prediction mask. Extensive experiments on segmentation and detection tasks demonstrate the generated data by ArSDM could significantly boost the performance of baseline methods.

* Accepted by MICCAI-2023 
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