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The surge in high-throughput omics data has reshaped the landscape of biological research, underlining the need for powerful, user-friendly data analysis and interpretation tools. This paper presents GenoCraft, a web-based comprehensive…

Motivation: Many researchers with domain expertise are unable to easily apply machine learning to their bioinformatics data due to a lack of machine learning and/or coding expertise. Methods that have been proposed thus far to automate…

Machine Learning · Computer Science 2020-04-29 William La Cava , Heather Williams , Weixuan Fu , Steve Vitale , Durga Srivatsan , Jason H. Moore

As a future trend of healthcare, personalized medicine tailors medical treatments to individual patients. It requires to identify a subset of patients with the best response to treatment. The subset can be defined by a biomarker (e.g.…

Methodology · Statistics 2021-08-16 Yitao Lu , Julie Zhou , Li Xing , Xuekui Zhang

Cell detection is a fundamental task in computational pathology that can be used for extracting high-level medical information from whole-slide images. For accurate cell detection, pathologists often zoom out to understand the tissue-level…

Deep intracranial tumors situated in eloquent brain regions controlling vital functions present critical diagnostic challenges. Clinical practice has shifted toward stereotactic biopsy for pathological confirmation before treatment. Yet…

Computer Vision and Pattern Recognition · Computer Science 2026-02-26 Xinzhe Luo , Shuai Shao , Yan Wang , Jiangtao Wang , Yutong Bai , Jianguo Zhang

Non-small cell lung cancer (NSCLC) remains a major global health challenge, with high post-surgical recurrence rates underscoring the need for accurate pathological response predictions to guide personalized treatments. Although artificial…

Optical coherence tomography angiography (OCTA) is a non-invasive imaging modality that can acquire high-resolution volumes of the retinal vasculature and aid the diagnosis of ocular, neurological and cardiac diseases. Segmenting the…

Deep learning has recently gained popularity in digital pathology due to its high prediction quality. However, the medical domain requires explanation and insight for a better understanding beyond standard quantitative performance…

Image and Video Processing · Electrical Eng. & Systems 2020-04-28 Miriam Hägele , Philipp Seegerer , Sebastian Lapuschkin , Michael Bockmayr , Wojciech Samek , Frederick Klauschen , Klaus-Robert Müller , Alexander Binder

Clinical diagnosis is a highly specialized discipline requiring both domain expertise and strict adherence to rigorous guidelines. While current AI-driven medical research predominantly focuses on knowledge graphs or natural text…

Machine Learning · Computer Science 2025-12-12 Haolin Li , Tianjie Dai , Zhe Chen , Siyuan Du , Jiangchao Yao , Ya Zhang , Yanfeng Wang

In recent years, the diagnosis of gliomas has become increasingly complex. Analysis of glioma histopathology images using artificial intelligence (AI) offers new opportunities to support diagnosis and outcome prediction. To give an overview…

With the rapid development of high-throughput sequencing platforms, an increasing number of omics technologies, such as genomics, metabolomics, and transcriptomics, are being applied to disease genetics research. However, biological data…

Genomics · Quantitative Biology 2024-12-18 Lei Xin , Caiyun Huang , Hao Li , Shihong Huang , Yuling Feng , Zhenglun Kong , Zicheng Liu , Siyuan Li , Chang Yu , Fei Shen , Hao Tang

Image based biomarker discovery typically requires an accurate segmentation of histologic structures (e.g., cell nuclei, tubules, epithelial regions) in digital pathology Whole Slide Images (WSI). Unfortunately, annotating each structure of…

Image and Video Processing · Electrical Eng. & Systems 2021-01-07 Runtian Miao , Robert Toth , Yu Zhou , Anant Madabhushi , Andrew Janowczyk

Driven by the recent advances in deep learning methods and, in particular, by the development of modern self-supervised learning algorithms, increased interest and efforts have been devoted to build foundation models (FMs) for medical…

Computer Vision and Pattern Recognition · Computer Science 2024-04-24 kaiko. ai , Nanne Aben , Edwin D. de Jong , Ioannis Gatopoulos , Nicolas Känzig , Mikhail Karasikov , Axel Lagré , Roman Moser , Joost van Doorn , Fei Tang

Thyroid cancer, the most prevalent endocrine cancer, has gained significant global attention due to its impact on public health. Extensive research efforts have been dedicated to leveraging artificial intelligence (AI) methods for the early…

Machine Learning · Computer Science 2024-01-09 Xinyu Zhang , Vincent CS Lee , Feng Liu

Pathology image analysis plays a pivotal role in medical diagnosis, with deep learning techniques significantly advancing diagnostic accuracy and research. While numerous studies have been conducted to address specific pathological tasks,…

Image and Video Processing · Electrical Eng. & Systems 2025-03-31 Dankai Liao , Sicheng Chen , Nuwa Xi , Qiaochu Xue , Jieyu Li , Lingxuan Hou , Zeyu Liu , Chang Han Low , Yufeng Wu , Yiling Liu , Yanqin Jiang , Dandan Li , Shangqing Lyu

Bone marrow cytology is required to make a hematological diagnosis, influencing critical clinical decision points in hematology. However, bone marrow cytology is tedious, limited to experienced reference centers and associated with high…

Image and Video Processing · Electrical Eng. & Systems 2021-07-09 Rohollah Moosavi Tayebi , Youqing Mu , Taher Dehkharghanian , Catherine Ross , Monalisa Sur , Ronan Foley , Hamid R. Tizhoosh , Clinton JV Campbell

In pathological research, education, and clinical practice, the decision-making process based on pathological images is critically important. This significance extends to digital pathology image analysis: its adequacy is demonstrated by the…

Image and Video Processing · Electrical Eng. & Systems 2024-08-19 Zhi-Bo Liu , Xiaobo Pang , Jizhao Wang , Shuai Liu , Chen Li

Breast cancer (BC) stands as one of the most common malignancies affecting women worldwide, necessitating advancements in diagnostic methodologies for better clinical outcomes. This article provides a comprehensive exploration of the…

Artificial Intelligence · Computer Science 2025-12-11 Samita Bai , Sidra Nasir , Rizwan Ahmed Khan , Alexandre Meyer , Hubert Konik

Artificial Intelligence (AI) is poised to transform healthcare delivery through revolutionary advances in clinical decision support and diagnostic capabilities. While human expertise remains foundational to medical practice, AI-powered…

Cancer has relational information residing at varying scales, modalities, and resolutions of the acquired data, such as radiology, pathology, genomics, proteomics, and clinical records. Integrating diverse data types can improve the…

Machine Learning · Computer Science 2024-07-29 Asim Waqas , Aakash Tripathi , Ravi P. Ramachandran , Paul Stewart , Ghulam Rasool