Generalizing AI-driven Assessment of Immunohistochemistry across Immunostains and Cancer Types: A Universal Immunohistochemistry Analyzer
- URL: http://arxiv.org/abs/2407.20643v1
- Date: Tue, 30 Jul 2024 08:39:30 GMT
- Title: Generalizing AI-driven Assessment of Immunohistochemistry across Immunostains and Cancer Types: A Universal Immunohistochemistry Analyzer
- Authors: Biagio Brattoli, Mohammad Mostafavi, Taebum Lee, Wonkyung Jung, Jeongun Ryu, Seonwook Park, Jongchan Park, Sergio Pereira, Seunghwan Shin, Sangjoon Choi, Hyojin Kim, Donggeun Yoo, Siraj M. Ali, Kyunghyun Paeng, Chan-Young Ock, Soo Ick Cho, Seokhwi Kim,
- Abstract summary: We developed a Universal IHC (UIHC) analyzer, an AI model for interpreting IHC images regardless of tumor or IHC types.
This multi-cohort trained model outperforms conventional single-cohort models in interpreting unseen IHCs.
- Score: 12.164507399614347
- License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/
- Abstract: Despite advancements in methodologies, immunohistochemistry (IHC) remains the most utilized ancillary test for histopathologic and companion diagnostics in targeted therapies. However, objective IHC assessment poses challenges. Artificial intelligence (AI) has emerged as a potential solution, yet its development requires extensive training for each cancer and IHC type, limiting versatility. We developed a Universal IHC (UIHC) analyzer, an AI model for interpreting IHC images regardless of tumor or IHC types, using training datasets from various cancers stained for PD-L1 and/or HER2. This multi-cohort trained model outperforms conventional single-cohort models in interpreting unseen IHCs (Kappa score 0.578 vs. up to 0.509) and consistently shows superior performance across different positive staining cutoff values. Qualitative analysis reveals that UIHC effectively clusters patches based on expression levels. The UIHC model also quantitatively assesses c-MET expression with MET mutations, representing a significant advancement in AI application in the era of personalized medicine and accumulating novel biomarkers.
Related papers
- Deep learning-based classification of breast cancer molecular subtypes from H&E whole-slide images [0.0]
We investigated whether H&E-stained whole slide images could be leveraged to predict breast cancer molecular subtypes.
We used 1,433 WSIs of breast cancer in a two-step pipeline: first, classifying tumor and non-tumor tiles to use only the tumor regions for molecular subtyping.
The pipeline was tested on 221 hold-out WSIs, achieving an overall macro F1 score of 0.95 for tumor detection and 0.73 for molecular subtyping.
arXiv Detail & Related papers (2024-08-30T13:57:33Z) - Screen Them All: High-Throughput Pan-Cancer Genetic and Phenotypic Biomarker Screening from H&E Whole Slide Images [3.119559770601732]
Using AI on routine H&E slides offers a fast and economical approach to screen for multiple molecular biomarkers.
We present a high- throughput AI-based system leveraging Virchow2, a foundation model pre-trained on 3 million slides.
Unlike traditional methods that train individual models for each biomarker or cancer type, our system employs a unified model to simultaneously predict a wide range of clinically relevant molecular biomarkers.
arXiv Detail & Related papers (2024-08-18T17:44:00Z) - Lymphoid Infiltration Assessment of the Tumor Margins in H&E Slides [1.715270928578365]
Lymphoid infiltration at tumor margins is a key prognostic marker in solid tumors.
Current assessment methods, heavily reliant onchemistry, face challenges in tumor margin delineation.
We propose a Hematoxylin and Eosin (H&E) staining-based approach, underpinned by an advanced lymphocyte segmentation model.
arXiv Detail & Related papers (2024-07-23T13:27:44Z) - TACCO: Task-guided Co-clustering of Clinical Concepts and Patient Visits for Disease Subtyping based on EHR Data [42.96821770394798]
TACCO is a novel framework that jointly discovers clusters of clinical concepts and patient visits based on a hypergraph modeling of EHR data.
We conduct experiments on the public MIMIC-III dataset and Emory internal CRADLE dataset over the downstream clinical tasks of phenotype classification and cardiovascular risk prediction.
In-depth model analysis, clustering results analysis, and clinical case studies further validate the improved utilities and insightful interpretations delivered by TACCO.
arXiv Detail & Related papers (2024-06-14T14:18:38Z) - IHC Matters: Incorporating IHC analysis to H&E Whole Slide Image Analysis for Improved Cancer Grading via Two-stage Multimodal Bilinear Pooling Fusion [19.813558168408047]
We show that IHC and H&E possess distinct advantages and disadvantages while possessing certain complementary qualities.
We develop a two-stage multi-modal bilinear model with a feature pooling module.
Experiments demonstrate that incorporating IHC data into machine learning models, alongside H&E stained images, leads to superior predictive results for cancer grading.
arXiv Detail & Related papers (2024-05-13T21:21:44Z) - CIMIL-CRC: a clinically-informed multiple instance learning framework for patient-level colorectal cancer molecular subtypes classification from H\&E stained images [42.771819949806655]
We introduce CIMIL-CRC', a framework that solves the MSI/MSS MIL problem by efficiently combining a pre-trained feature extraction model with principal component analysis (PCA) to aggregate information from all patches.
We assessed our CIMIL-CRC method using the average area under the curve (AUC) from a 5-fold cross-validation experimental setup for model development on the TCGA-CRC-DX cohort.
arXiv Detail & Related papers (2024-01-29T12:56:11Z) - COVID-Net Biochem: An Explainability-driven Framework to Building
Machine Learning Models for Predicting Survival and Kidney Injury of COVID-19
Patients from Clinical and Biochemistry Data [66.43957431843324]
We introduce COVID-Net Biochem, a versatile and explainable framework for constructing machine learning models.
We apply this framework to predict COVID-19 patient survival and the likelihood of developing Acute Kidney Injury during hospitalization.
arXiv Detail & Related papers (2022-04-24T07:38:37Z) - Multi-Scale Hybrid Vision Transformer for Learning Gastric Histology:
AI-Based Decision Support System for Gastric Cancer Treatment [50.89811515036067]
Gastric endoscopic screening is an effective way to decide appropriate gastric cancer (GC) treatment at an early stage, reducing GC-associated mortality rate.
We propose a practical AI system that enables five subclassifications of GC pathology, which can be directly matched to general GC treatment guidance.
arXiv Detail & Related papers (2022-02-17T08:33:52Z) - Lung Cancer Lesion Detection in Histopathology Images Using Graph-Based
Sparse PCA Network [93.22587316229954]
We propose a graph-based sparse principal component analysis (GS-PCA) network, for automated detection of cancerous lesions on histological lung slides stained by hematoxylin and eosin (H&E)
We evaluate the performance of the proposed algorithm on H&E slides obtained from an SVM K-rasG12D lung cancer mouse model using precision/recall rates, F-score, Tanimoto coefficient, and area under the curve (AUC) of the receiver operator characteristic (ROC)
arXiv Detail & Related papers (2021-10-27T19:28:36Z) - Bootstrapping Your Own Positive Sample: Contrastive Learning With
Electronic Health Record Data [62.29031007761901]
This paper proposes a novel contrastive regularized clinical classification model.
We introduce two unique positive sampling strategies specifically tailored for EHR data.
Our framework yields highly competitive experimental results in predicting the mortality risk on real-world COVID-19 EHR data.
arXiv Detail & Related papers (2021-04-07T06:02:04Z) - Multi-Phase Cross-modal Learning for Noninvasive Gene Mutation
Prediction in Hepatocellular Carcinoma [7.621860963237023]
We propose an end-to-end deep learning framework for mutation prediction in APOB, COL11A1 and ATRX genes using multiphasic CT scans.
arXiv Detail & Related papers (2020-05-08T14:36:59Z)
This list is automatically generated from the titles and abstracts of the papers in this site.
This site does not guarantee the quality of this site (including all information) and is not responsible for any consequences.