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Rethinking Mitosis Detection: Towards Diverse Data and Feature Representation for Better Domain Generalization

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SSRN

SSRN 2024年

作者： Wang, Hao Lin, Jiatai Li, Danyi Wang, Jing Zhao, Bingchao Shi, Zhenwei Liang, Changhong Han, Guoqiang Liang, Li Han, Chu Liu, Zaiyi The School of Computer Science and Engineering South China University of Technology Guangzhou510006 China Department of Radiology Guangdong Provincial People’s Hospital Guangdong Academy of Medical Sciences Southern Medical University Guangzhou510080 China Guangdong Provincial Key Laboratory of Artificial Intelligence in Medical Image Analysis and Application Guangzhou510080 China The Department of Pathology Nanfang Hospital Basic Medical College Southern Medical University Guangdong Guangzhou China Guangdong Province Key Laboratory of Molecular Tumor Pathology Guangdong Guangzhou China

Mitosis detection is one of the fundamental tasks in computational pathology, which is extremely challenging due to the heterogeneity of mitotic cell. Most of the current studies solve the heterogeneity in the technical aspect by increasing the model complexity. However, lacking consideration of the biological knowledge and the complex model design may lead to the overfitting problem while limited the generalizability of the detection model. In this paper, we systematically study the morphological appearances in different mitotic phases as well as the ambiguous non-mitotic cells and identify that balancing the data and feature diversity can achieve better generalizability. Based on this observation, we propose a novel generalizable framework (MitDet) for mitosis detection. The data diversity is considered by the proposed diversity-guided sample balancing (DGSB). And the feature diversity is preserved by inter- and intra- class feature diversity-preserved module (InCDP). Stain enhancement (SE) module is introduced to enhance the domain-relevant diversity of both data and features simultaneously. Extensive experiments have demonstrated that our proposed model outperforms all the state-of-the-art (SOTA) approaches in several popular mitosis detection datasets in both internal and unseen test sets using point annotations only. Comprehensive ablation studies have also proven the effectiveness of the rethinking of data and feature diversity balancing. By analyzing the results quantitatively and qualitatively, we believe that our proposed model not only achieves SOTA performance but also might inspire the future studies in new perspectives. © 2024, The Authors. All rights reserved.

关键词： Pathology

An artificially intelligent magnetic resonance spectroscopy quantification method: Comparison between QNet and LCModel on the cloud computing platform CloudBrain-MRS

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arXiv 2025年

作者： Lin, Meijin Guo, Lin Chen, Dicheng Chen, Jianshu Tu, Zhangren Huang, Xu Wang, Jianhua Qi, Ji Long, Yuan Huang, Zhiguo Guo, Di Qu, Xiaobo Han, Haiwei College of Ocean & Earth Sciences Xiamen University Xiamen361102 China Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance Xiamen University Xiamen361102 China National Integrated Circuit Industry Education Integration Innovation Platform Xiamen University Xiamen361100 China Department of Electronic Science Xiamen University Xiamen361102 China Department of Radiology the First Affiliated Hospital of Xiamen University School of Medicine Xiamen University Xiamen361100 China Software Technology Company Limited Suzhou215163 China School of Computer and Information Engineering Fujian Engineering Research Center for Medical Data Mining and Application Xiamen University of Technology Xiamen361024 China

Objctives: This work aimed to statistically compare the metabolite quantification of human brain magnetic resonance spectroscopy (MRS) between the deep learning method QNet and the classical method LCModel through an easy-to-use intelligent cloud computing platform CloudBrain-MRS. Materials and Methods: In this retrospective study, two 3 T MRI scanners Philips Ingenia and Achieva collected 61 and 46 in vivo 1H magnetic resonance (MR) spectra of healthy participants, respectively, from the brain region of pregenual anterior cingulate cortex from September to October 2021. The analyses of Bland-Altman, Pearson correlation and reasonability were performed to assess the degree of agreement, linear correlation and reasonability between the two quantification methods. Results: Fifteen healthy volunteers (12 females and 3 males, age range: 21-35 years, mean age ± standard deviation = 27.4 ± 3.9 years) were recruited. The analyses of Bland-Altman, Pearson correlation and reasonability showed high to good consistency and very strong to moderate correlation between the two methods for quantification of total N-acetylaspartate (tNAA), total choline (tCho), and inositol (Ins) (relative half interval of limits of agreement = 3.04%, 9.3%, and 18.5%, respectively;Pearson correlation coefficient r = 0.775, 0.927, and 0.469, respectively). In addition, quantification results of QNet are more likely to be closer to the previous reported average values than those of LCModel. Conclusion: There were high or good degrees of consistency between the quantification results of QNet and LCModel for tNAA, tCho, and Ins, and QNet generally has more reasonable quantification than LCModel. © 2025, CC BY.

关键词： Metabolites

Analyzing Diversity in Healthcare LLM Research: A Scientometric Perspective

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arXiv 2024年

作者： Restrepo, David Wu, Chenwei Vásquez-Venegas, Constanza Matos, João Gallifant, Jack Celi, Leo Anthony Bitterman, Danielle S. Nakayama, Luis Filipe Laboratory for Computational Physiology Massachusetts Institute of Technology CambridgeMA United States Departamento de Telematica Universidad del Cauca Cauca Popayán Colombia Department of Electrical Engineering and Computer Science University of Michigan Ann ArborMI United States Scientific Image Analysis Lab Faculty of Medicine Universidad de Chile RM Santiago Chile Department of Computer Science Faculty of Engineering Universidad de Concepción Biobio Concepción Chile Department of Biostatistics Harvard TH Chan School of Public Health BostonMA United States Department of Medicine Beth Israel Deaconess Medical Center BostonMA United States Artificial Intelligence in Medicine Program Mass General Brigham Harvard Medical School BostonMA United States Department of Ophthalmology São Paulo Federal University São Paulo São Paulo Brazil

The deployment of large language models (LLMs) in healthcare has demonstrated substantial potential for enhancing clinical decision-making, administrative efficiency, and patient outcomes. However, the underrepresentation of diverse groups in the development and application of these models can perpetuate biases, leading to inequitable healthcare delivery. This paper presents a comprehensive scientometric analysis of LLM research for healthcare, including data from January 1, 2021, to July 1, 2024. By analyzing metadata from PubMed and Dimensions, including author affiliations, countries, and funding sources, we assess the diversity of contributors to LLM research. Our findings highlight significant gender and geographic disparities, with a predominance of male authors and contributions primarily from high-income countries (HICs). We introduce a novel journal diversity index based on Gini diversity to measure the inclusiveness of scientific publications. Our results underscore the necessity for greater representation in order to ensure the equitable application of LLMs in healthcare. We propose actionable strategies to enhance diversity and inclusivity in artificial intelligence research, with the ultimate goal of fostering a more inclusive and equitable future in healthcare innovation. © 2024, CC BY.

关键词： Decision making

A Dynamics Theory of Implicit Regularization in Deep Low-Rank Matrix Factorization

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arXiv 2022年

作者： Cao, Jian Qian, Chen Huang, Yihui Chen, Dicheng Gao, Yuncheng Dong, Jiyang Guo, Di Qu, Xiaobo Department of Electronic Science Biomedical Intelligent Cloud R&D Center Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance Xiamen University Xiamen361005 China School of Computer and Information Engineering Fujian Engineering Research Center for Medical Data Mining and Application Xiamen University of Technology Xiamen361024 China

Implicit regularization is an important way to interpret neural networks. Recent theory starts to explain implicit regularization with the model of deep matrix factorization (DMF) and analyze the trajectory of discrete gradient dynamics in the optimization process. These discrete gradient dynamics are relatively small but not infinitesimal, thus fitting well with the practical implementation of neural networks. Currently, discrete gradient dynamics analysis has been successfully applied to shallow networks but encounters the difficulty of complex computation for deep networks. In this work, we introduce another discrete gradient dynamics approach to explain implicit regularization, i.e. landscape analysis. It mainly focuses on gradient regions, such as saddle points and local minima. We theoretically establish the connection between saddle point escaping (SPE) stages and the matrix rank in DMF. We prove that, for a rank-R matrix reconstruction, DMF will converge to a second-order critical point after R stages of SPE. This conclusion is further experimentally verified on a low-rank matrix reconstruction problem. This work provides a new theory to analyze implicit regularization in deep learning. Copyright © 2022, The Authors. All rights reserved.

关键词： Deep learning

Selective Fairness in Recommendation via Prompts

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arXiv 2022年

作者： Wu, Yiqing Xie, Ruobing Zhu, Yongchun Zhuang, Fuzhen Ao, Xiang Zhang, Xu Lin, Leyu He, Qing Institute of Computing Technology Cas Beijing100190 China University of Chinese Academy of Sciences Beijing100049 China WeChat Search Application Department Tencent China Institute of Artificial Intelligence Beihang University Beijing100191 China Sklsde School of Computer Science Beihang University Beijing100191 China Institute of Intelligent Computing Technology Suzhou Cas China

Recommendation fairness has attracted great attention recently. In real-world systems, users usually have multiple sensitive attributes (e.g. age, gender, and occupation), and users may not want their recommendation results influenced by those attributes. Moreover, which of and when these user attributes should be considered in fairness-aware modeling should depend on users' specific demands. In this work, we define the selective fairness task, where users can flexibly choose which sensitive attributes should the recommendation model be bias-free. We propose a novel parameter-efficient prompt-based fairness-aware recommendation (PFRec) framework, which relies on attribute-specific prompt-based bias eliminators with adversarial training, enabling selective fairness with different attribute combinations on sequential recommendation. Both task-specific and user-specific prompts are considered. We conduct extensive evaluations to verify PFRec's superiority in selective fairness. The source codes are released in https://***/wyqing20/PFRec. Copyright © 2022, The Authors. All rights reserved.

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Current Progress and Challenges in Large-scale 3D Mitochondria Instance Segmentation

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TechRxiv

TechRxiv 2023年

作者： Franco-Barranco, Daniel Lin, Zudi Jang, Won-Dong Wang, Xueying Shen, Qijia Yin, Wenjie Fan, Yutian Li, Mingxing Chen, Chang Xiong, Zhiwei Xin, Rui Liu, Hao Chen, Huai Li, Zhili Zhao, Jie Chen, Xuejin Pape, Constantin Conrad, Ryan De Folter, Jozefus Nightingale, Luke Jones, Martin L. Liu, Yanling Ziaei, Dorsa Huschauer, Stephan Arganda-Carreras, Ignacio Pfister, Hanspeter Wei, Donglai The Department of Computer Science and Artificial Intelligence University of the Basque Country Donostia-San Sebastian Spain San Sebastian Spain Ikerbasque Basque Foundation for Science Bilbao Spain Biofisika Institute CSIC UPV/EHU Bilbao Spain Harvard University All-ston MA United States The Department of Molecular and Cellular Biology Harvard University CambridgeMA United States The Wellcome Centre for Integrative Neuroimaging FMRIB Nuffield Department of Clinical Neurosciences University of Oxford Oxford United Kingdom University of Science and Technology of China Anhui China The Institute of Image Processing and Pattern Recognition Department of Automation Shanghai Jiao Tong University Shanghai China The National Engineering Laboratory for Brain-inspired Intelligence Technology and Application University of Science and Technology of China Anhui China The Georg-August University Goettingen Germany The Center for Molecular Microscopy Center for Cancer Research National Cancer Institute National Institutes of Health Bethesda United States The Cancer Research Technology Program Frederick National Laboratory for Cancer Research Frederick United States The Francis Crick Institute London United Kingdom The Advanced Biomedical Computational Science Group Frederick National Laboratory for Cancer Research FrederickMD United States The Computer Science Department Boston College Chestnut Hill MA United States

In this paper, we present the results of the MitoEM challenge on mitochondria 3D instance segmentation from electron microscopy images, organized in conjunction with the IEEE-ISBI 2021 conference. Our benchmark dataset consists of two large-scale 3D volumes, one from human and one from rat cortex tissue, which are 3,600 times larger than previously used datasets. At the time of paper submission, 257 participants had registered for the challenge, 14 teams had submitted their results, and six teams participated in the challenge workshop. Here, we present eight top-performing approaches from the challenge participants, along with our own baseline strategies. Posterior to the challenge, annotation errors in the ground truth were corrected without altering the final ranking. Additionally, we present a retrospective evaluation of the scoring system which revealed that (1) the challenge metric was permissive with the false positive predictions and (2) the size-based grouping of instances did not correctly categorize mitochondria of interest. Thus, we propose a new scoring system that better reflects the correctness of the segmentation results. Although several of the top methods are compared favorably to our own baselines, substantial errors remain unsolved for mitochondria with challenging morphologies. Thus, the challenge remains open for submission and automatic evaluation, with all volumes available for download. © 2023, CC BY.

关键词： Electron microscopy

Computational prediction and validation of specific EmbR binding site on PknH

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Synthetic and Systems Biotechnology 2021年第4期6卷 429-436页

作者： Insung Na Huanqin Dai Hantian Li Anvita Gupta David Kreda Powell Zhang Xiangyin Chen Lixin Zhang Gil Alterovitz Computational Health Informatics Program Boston Children’s Hospital/Harvard Medical SchoolBostonMA 02115USA Department of Medicine Brigham and Women’s Hospital/Harvard Medical SchoolBostonMA 02115USA State Key Laboratory of Mycology Institute of MicrobiologyBeijing100101 China Department of Computer Sciences Stanford UniversityStanford CA 94305USA Center for Biomedical Informatics Harvard Medical SchoolBostonMA 02115USA State Key Laboratory of Bioreactor Engineering East China University of Science and TechnologyShanghaiChina Department of Biology The Johns Hopkins UniversityBaltimoreMD 21218USA Lexington High School BostonMA 02115USA

Tuberculosis drug resistance continues to threaten global health but the underline molecular mechanisms are not ***(EMB),one of the well-known first-line drugs in tuberculosis treatment is,unfortunately,not free from drug resistance *** studies have shown that some genetic mutations in Mycobacterium tuberculosis(Mtb)EmbR,and EmbC/A/B genes cause EMB ***-PknH pair controls embC/A/B operon,which encodes EmbC/A/B genes,and EMB interacts with EmbA/B ***,the EmbR binding site on PknH was *** conducted molecular simulation on the EmbR-peptides binding structures and discovered phosphorylated PknH 273-280(N′-HEALS^(P)DPD-C′)makesβstrand with the EmbR FHA domain,asβ-MoRF(MoRF;molecular recognition feature)does at its binding *** bond number analysis also supported the peptides’β-MoRF forming activity at the EmbR FHA ***,we discovered that previously known phosphorylation residues might have their chronological order according to the phosphorylation *** discovery validated that Mtb PknH 273-280(N′-HEALSDPD-C′)has reliable EmbR binding *** approach is revolutionary in the computer-aided drug discovery field,because it is the first trial to discover the protein-protein interaction site,and find binding partner in nature from this site.

关键词： Disorder-to-order transition Protein intrinsic disorder Binding site prediction Drug resistance Molecular simulation

WSSS4LUAD: Grand Challenge on Weakly-supervised Tissue Semantic Segmentation for Lung Adenocarcinoma

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arXiv 2022年

作者： Han, Chu Pan, Xipeng Yan, Lixu Lin, Huan Li, Bingbing Yao, Su Lv, Shanshan Shi, Zhenwei Mai, Jinhai Lin, Jiatai Zhao, Bingchao Xu, Zeyan Wang, Zhizhen Wang, Yumeng Zhang, Yuan Wang, Huihui Zhu, Chao Lin, Chunhui Mao, Lijian Wu, Min Duan, Luwen Zhu, Jingsong Hu, Dong Fang, Zijie Chen, Yang Zhang, Yongbing Li, Yi Zou, Yiwen Yu, Yiduo Li, Xiaomeng Li, Haiming Cui, Yanfen Han, Guoqiang Xu, Yan Xu, Jun Yang, Huihua Li, Chunming Liu, Zhenbing Lu, Cheng Chen, Xin Liang, Changhong Zhang, Qingling Liu, Zaiyi The Department of Radiology Guangdong Provincial People's Hospital Guangdong Academy of Medical Sciences Guangzhou510080 China Guangdong Prov. Key Laboratory of Artificial Intelligence in Medical Image Analysis and Application Guangdong Provincial People's Hospital Guangdong Academy of Medical Sciences Guangzhou510080 China The Department of Pathology Guangdong Provincial People's Hospital Guangdong Academy of Medical Sciences Guangzhou510080 China The School of Computer Science and Information Security Guilin University of Electronic Technology Guangxi541004 China The Department of Pathology Guangdong Provicial People's Hospital Ganzhou Hospital Ganzhou China The College of Artificial Intelligence Beijing University of Posts and Telecommunications Beijing100876 China The School of Computer Science and Engineering South China University of Technology Guangzhou510640 China The Institute for AI in Medicine School of Artificial Intelligence Nanjing University of Information Science and Technology Nanjing210044 China The School of Biological Science and Medical Engineering State Key Laboratory of Software Development Environment Key Laboratory of Biomechanics and Mechanobiology of Ministry of Education Research Institute of Beihang University in Shenzhen Beijing Advanced Innovation Center for Biomedical Engineering Beihang University Beijing100191 China The Department of Radiology Guangzhou First People's Hospital Hospital of South China University of Technology Guangzhou510180 China The Zhejiang Dahua Technology Co. Ltd Zhejiang310053 China The School of Biomedical Engineering University of Science and Technology of China Hefei230022 China The Tsinghua Shenzhen International Graduate School Tsinghua University Shenzhen China Electronic and Computer Engineering & Computer Science and Engineering The Hong Kong University of Science and Technology Hong Kong Hong Kong The School of Automation Science and Engineering Xi'An Jiaotong University Xian710049 Chi

Lung cancer is the leading cause of cancer death worldwide, and adenocarcinoma (LUAD) is the most common subtype. Exploiting the potential value of the histopathology images can promote precision medicine in oncology. Tissue segmentation is the basic upstream task of histopathology image analysis. Existing deep learning models have achieved superior segmentation performance but require sufficient pixel-level annotations, which is time-consuming and expensive. To enrich the label resources of LUAD and to alleviate the annotation efforts, we organize this challenge WSSS4LUAD to call for the outstanding weakly-supervised semantic segmentation (WSSS) techniques for histopathology images of LUAD. Participants have to design the algorithm to segment tumor epithelial, tumor-associated stroma and normal tissue with only patch-level labels. This challenge includes 10,091 patch-level annotations (the training set) and over 130 million labeled pixels (the validation and test sets), from 87 WSIs (67 from GDPH, 20 from TCGA). All the labels were generated by a pathologist-in-the-loop pipeline with the help of AI models and checked by the label review board. Among 532 registrations, 28 teams submitted the results in the test phase with over 1,000 submissions. Finally, the first place team achieved mIoU of 0.8413 (tumor: 0.8389, stroma: 0.7931, normal: 0.8919). According to the technical reports of the top-tier teams, CAM is still the most popular approach in WSSS. Cutmix data augmentation has been widely adopted to generate more reliable samples. With the success of this challenge, we believe that WSSS approaches with patch-level annotations can be a complement to the traditional pixel annotations while reducing the annotation efforts. The entire dataset has been released to encourage more researches on computational pathology in LUAD and more novel WSSS techniques. © 2022, CC BY.

关键词： Semantic Segmentation

Improved diabetes disease prediction IWFO model using machine learning algorithms

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AIP Conference Proceedings 2024年第1期3161卷

作者： R. Gunavathi V. Sivakumar B. Senthil Kumar S. Vijayalakshmi Associate professor School of Science Department of Data Science Christ University Pune India Associate Professor & Program Leader School of Computing Asia Pacific University of Technology and Innovation Kuala Lumpur Malaysia Assistant Professor Department of Computer Science Sree Narayana Guru College Coimbatore India

Diabetic disease is the mostly affected and massive disease on a global level. Diagnosing the diabetic earlier will help the medicalist to give the improved and latest clinical treatment. The healthcare specialist unit uses many machine learning techniques, methodologies and tools for decision making in diabetic field. The machine learning techniques are utilized for the prediction of the diabetic diseases in the initial level. To eliminate such issues, optimized detection techniques are proposed. First of all, the training samples are increased using the sliding window protocol. Further, class imbalanced training data classes are balanced and resolved using the adaptive and gradient booster technique. Further, the diabetic feature selection process is improved by the Intensity Weighted Firefly Optimization firefly techniques (IWFO), in which irrelevant features are reduced based on the correlation between the features that deducts the unwanted features involved in the diabetic disease process. Then the feature transformation problem is faced by the PCA technique, which manages the several types of features. Finally, the improved and optimal hybrid random forest is applied into the normal and diabetes classes respectively. The proposed system predicts the diabetic disease efficiently and maximizes its precision of the prediction system. The present paper is compared with different classifiers to determine the efficiency of the work. Overall, the initiated system improved the present studies accuracy level.

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