{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/mag-a-simple-learning-based-patient-level","title":"MAg: a simple learning-based patient-level aggregation method for detecting microsatellite instability from whole-slide images","arxiv_id":"2201.04769","date":"2022-01-13","proceeding":null,"authors":["Kaifeng Pang","Zuhayr Asad","Shilin Zhao","Yuankai Huo"],"abstract":"The prediction of microsatellite instability (MSI) and microsatellite stability (MSS) is essential in predicting both the treatment response and prognosis of gastrointestinal cancer. In clinical practice, a universal MSI testing is recommended, but the accessibility of such a test is limited. Thus, a more cost-efficient and broadly accessible tool is desired to cover the traditionally untested patients. In the past few years, deep-learning-based algorithms have been proposed to predict MSI directly from haematoxylin and eosin (H&E)-stained whole-slide images (WSIs). Such algorithms can be summarized as (1) patch-level MSI/MSS prediction, and (2) patient-level aggregation. Compared with the advanced deep learning approaches that have been employed for the first stage, only the na\\\"ive first-order statistics (e.g., averaging and counting) were employed in the second stage. In this paper, we propose a simple yet broadly generalizable patient-level MSI aggregation (MAg) method to effectively integrate the precious patch-level information. Briefly, the entire probabilistic distribution in the first stage is modeled as histogram-based features to be fused as the final outcome with machine learning (e.g., SVM). The proposed MAg method can be easily used in a plug-and-play manner, which has been evaluated upon five broadly used deep neural networks: ResNet, MobileNetV2, EfficientNet, Dpn and ResNext. From the results, the proposed MAg method consistently improves the accuracy of patient-level aggregation for two publicly available datasets. It is our hope that the proposed method could potentially leverage the low-cost H&E based MSI detection method. The code of our work has been made publicly available at https://github.com/Calvin-Pang/MAg.","url_abs":"https://arxiv.org/abs/2201.04769v1","url_pdf":"https://arxiv.org/pdf/2201.04769v1.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"mag-a-simple-learning-based-patient-level","repo_url":"https://github.com/Calvin-Pang/MAg","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":null}],"tasks":[{"task_slug":"prognosis","task_name":"Prognosis"},{"task_slug":"whole-slide-images","task_name":"whole slide images"}],"methods":[{"method_slug":"1x1-convolution","method_name":"1x1 Convolution"},{"method_slug":"average-pooling","method_name":"Average Pooling"},{"method_slug":"batch-normalization","method_name":"Batch Normalization"},{"method_slug":"bottleneck-residual-block","method_name":"Bottleneck Residual Block"},{"method_slug":"concatenated-skip-connection","method_name":"Concatenated Skip Connection"},{"method_slug":"convolution","method_name":"Convolution"},{"method_slug":"dpn","method_name":"DPN"},{"method_slug":"dpn-block","method_name":"DPN Block"},{"method_slug":"dense-connections","method_name":"Dense Connections"},{"method_slug":"depthwise-convolution","method_name":"Depthwise Convolution"},{"method_slug":"depthwise-separable-convolution","method_name":"Depthwise Separable Convolution"},{"method_slug":"dropout","method_name":"Dropout"},{"method_slug":"global-average-pooling","method_name":"Global Average Pooling"},{"method_slug":"grouped-convolution","method_name":"Grouped Convolution"},{"method_slug":"inverted-residual-block","method_name":"Inverted Residual Block"},{"method_slug":"kaiming-initialization","method_name":"Kaiming Initialization"},{"method_slug":"max-pooling","method_name":"Max Pooling"},{"method_slug":"pointwise-convolution","method_name":"Pointwise Convolution"},{"method_slug":"rmsprop","method_name":"RMSProp"},{"method_slug":"relu","method_name":"ReLU"},{"method_slug":"residual-block","method_name":"Residual Block"},{"method_slug":"residual-connection","method_name":"Residual Connection"},{"method_slug":"sigmoid-activation","method_name":"Sigmoid Activation"},{"method_slug":"softmax","method_name":"Softmax"},{"method_slug":"squeeze-and-excitation-block","method_name":"Squeeze-and-Excitation Block"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}