Multi-modality artificial intelligence in digital pathology

Nongenerative Artificial Intelligence in Medicine: Advancements and Applications in Supervised and Unsupervised Machine Learning

The use of artificial intelligence (AI) within pathology and health care has advanced extensively. We have accordingly witnessed an increased adoption of various AI tools that are transforming our approach to clinical decision support, personalized medicine, predictive analytics, automation, and discovery. The familiar and more reliable AI tools that have been incorporated within health care thus far fall mostly under the nongenerative AI domain, which includes supervised and unsupervised machine learning (ML) techniques. This review article explores how such nongenerative AI methods, rooted in traditional rules-based systems, enhance diagnostic accuracy, efficiency, and consistency within medicine. Key concepts and the application of supervised learning models (ie, classification and regression) such as decision trees, support vector machines, linear and logistic regression, K-nearest neighbor, and neural networks are explained along with the newer landscape of neural network-based nongenerative foundation models. Unsupervised learning techniques, including clustering, dimensionality reduction, and anomaly detection, are also discussed for their roles in uncovering novel disease subtypes or identifying outliers. Technical details related to the application of nongenerative AI algorithms for analyzing whole slide images are also highlighted. The performance, explainability, and reliability of nongenerative AI models essential for clinical decision-making is also reviewed, as well as challenges related to data quality, model interpretability, and risk of data drift. An understanding of which AI-ML models to employ and which shortcomings need to be addressed is imperative to safely and efficiently leverage, integrate, and monitor these traditional AI tools in clinical practice and research.

Artificial Intelligence in Lymphoma Histopathology: Systematic Review

BACKGROUND

Artificial intelligence (AI) shows considerable promise in the areas of lymphoma diagnosis, prognosis, and gene prediction. However, a comprehensive assessment of potential biases and the clinical utility of AI models is still needed.

OBJECTIVE

Our goal was to evaluate the biases of published studies using AI models for lymphoma histopathology and assess the clinical utility of comprehensive AI models for diagnosis or prognosis.

METHODS

This study adhered to the Systematic Review Reporting Standards. A comprehensive literature search was conducted across PubMed, Cochrane Library, and Web of Science from their inception until August 30, 2024. The search criteria included the use of AI for prognosis involving human lymphoma tissue pathology images, diagnosis, gene mutation prediction, etc. The risk of bias was evaluated using the Prediction Model Risk of Bias Assessment Tool (PROBAST). Information for each AI model was systematically tabulated, and summary statistics were reported. The study is registered with PROSPERO (CRD42024537394) and follows the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) 2020 reporting guidelines.

RESULTS

The search identified 3565 records, with 41 articles ultimately meeting the inclusion criteria. A total of 41 AI models were included in the analysis, comprising 17 diagnostic models, 10 prognostic models, 2 models for detecting ectopic gene expression, and 12 additional models related to diagnosis. All studies exhibited a high or unclear risk of bias, primarily due to limited analysis and incomplete reporting of participant recruitment. Most high-risk models (10/41) predominantly assigned high-risk classifications to participants. Almost all the articles presented an unclear risk of bias in at least one domain, with the most frequent being participant selection (16/41) and statistical analysis (37/41). The primary reasons for this were insufficient analysis of participant recruitment and a lack of interpretability in outcome analyses. In the diagnostic models, the most frequently studied lymphoma subtypes were diffuse large B-cell lymphoma, follicular lymphoma, chronic lymphocytic leukemia, and mantle cell lymphoma, while in the prognostic models, the most common subtypes were diffuse large B-cell lymphoma, follicular lymphoma, chronic lymphocytic leukemia, and Hodgkin lymphoma. In the internal validation results of all models, the area under the receiver operating characteristic curve (AUC) ranged from 0.75 to 0.99 and accuracy ranged from 68.3% to 100%. In models with external validation results, the AUC ranged from 0.93 to 0.99.

CONCLUSIONS

From a methodological perspective, all models exhibited biases. The enhancement of the accuracy of AI models and the acceleration of their clinical translation hinge on several critical aspects. These include the comprehensive reporting of data sources, the diversity of datasets, the study design, the transparency and interpretability of AI models, the use of cross-validation and external validation, and adherence to regulatory guidance and standardized processes in the field of medical AI.

Advancing precision medicine: the transformative role of artificial intelligence in immunogenomics, radiomics, and pathomics for biomarker discovery and immunotherapy optimization

Artificial intelligence (AI) is significantly advancing precision medicine, particularly in the fields of immunogenomics, radiomics, and pathomics. In immunogenomics, AI can process vast amounts of genomic and multi-omic data to identify biomarkers associated with immunotherapy responses and disease prognosis, thus providing strong support for personalized treatments. In radiomics, AI can analyze high-dimensional features from computed tomography (CT), magnetic resonance imaging (MRI), and positron emission tomography/computed tomography (PET/CT) images to discover imaging biomarkers associated with tumor heterogeneity, treatment response, and disease progression, thereby enabling non-invasive, real-time assessments for personalized therapy. Pathomics leverages AI for deep analysis of digital pathology images, and can uncover subtle changes in tissue microenvironments, cellular characteristics, and morphological features, and offer unique insights into immunotherapy response prediction and biomarker discovery. These AI-driven technologies not only enhance the speed, accuracy, and robustness of biomarker discovery but also significantly improve the precision, personalization, and effectiveness of clinical treatments, and are driving a shift from empirical to precision medicine. Despite challenges such as data quality, model interpretability, integration of multi-modal data, and privacy protection, the ongoing advancements in AI, coupled with interdisciplinary collaboration, are poised to further enhance AI's roles in biomarker discovery and immunotherapy response prediction. These improvements are expected to lead to more accurate, personalized treatment strategies and ultimately better patient outcomes, marking a significant step forward in the evolution of precision medicine.

Relationship between EZH2 expression and prognosis of patients with hepatocellular carcinoma using a pathomics predictive model

Background

Enhancer of zeste 2 polycomb repressive complex 2 subunit (EZH2) is overexpressed in hepatocellular carcinoma, promoting tumorigenesis and correlating with poor prognosis. Traditional histopathological examinations are insufficient to accurately predict hepatocellular carcinoma (HCC) survival; however, pathomics models can predict EZH2 expression and HCC prognosis. This study aimed to investigate the relationship between pathomics features and EZH2 expression for predicting overall survival of patients with HCC.

Methods

We analyzed 267 patients with HCC from the Cancer Genome Atlas database, with available pathological images and gene expression data. RNA sequencing data were divided into high and low EZH2 expression groups for prognosis and survival analysis. Pathological image features were screened using mRMR_RFE. A pathological model was constructed using a gradient boosting machine (GBM) algorithm, and efficiency evaluation and survival analysis of the model were performed. The R package "survminer" took the pathomics score (PS) cutoff value of 0.4628 to divide the patients into two groups: high and low PS expression. Survival analyses included Kaplan-Meier curve analysis, univariate and multivariate Cox regression analyses, and interaction tests. Potential pathomechanisms were explored through enrichment, differential, immune cell infiltration abundance, and gene mutation analyses.

Result

EZH2 was highly expressed in tumor samples but poorly expressed in normal tissue samples. Univariate and multivariate Cox regression analyses revealed that EZH2 was an independent risk factor for HCC (hazard ratio [HR], 2.792 and 3.042, respectively). Seven imaging features were selected to construct a pathomics model to predict EZH2. Decision curve analysis showed that the model had high clinical utility. Multivariate Cox regression analysis showed that high PS expression was an independent risk factor for HCC prognosis (HR, 2.446). The Kaplan-Meier curve showed that high PS expression was a risk factor for overall survival.

Conclusion

EZH2 expression can affect the prognosis of patients with liver cancer. Our pathological model could predict EZH2 expression and prognosis of patients with HCC with high accuracy and robustness, making it a new and potentially valuable tool.

Computational pathology: an evolving concept

The initial enthusiasm about computational pathology (CP) and artificial intelligence (AI) was that they will replace pathologists entirely on the way to fully automated diagnostics. It is becoming clear that currently this is not the immediate model to pursue. On top of the legal and regulatory complexities surrounding its implementation, the majority of tested machine learning (ML)-based predictive algorithms do not display the exquisite performance needed to render them unequivocal, standalone decision makers for matters with direct implications to human health. We are thus moving into a different model of "computer-assisted diagnostics", where AI is there to provide support, rather than replacing, the pathologist. Herein we focus on the practical aspects of CP, from a pathologist perspective. There is a wide range of potential applications where CP can enhance precision of pathology diagnosis, tailor prognostic and predictive information, as well as save time. There are, however, a number of potential limitations for CP that currently hinder their wider adoption in the clinical setting. We address the key necessary steps towards clinical implementation of computational pathology, discuss the significant obstacles that hinders its adoption in the clinical context and summarize some proposed solutions. We conclude that the advancement of CP in the clinic is a promising resource-intensive endeavour that requires broad and inclusive collaborations between academia, industry, and regulatory bodies.

Interactivity, humanness, and trust: a psychological approach to AI chatbot adoption in e-commerce

This study aims to investigate the impact of interactivity and perceived humanness on trust toward AI chatbots in the e-commerce setting. Moreover, this study also aims to examine the mediation effect of trust toward AI chatbots in the relationship between interactivity and intention to adopt AI chatbots for e-commerce as well as in the relationship between perceived humanness and intention to adopt chatbots for e-commerce. This study used a time lag approach to collect the data from 343 customers from the southern region of China. The data were collected online through a questionnaire designed in Chinese language using a survey firm. The findings of this study indicated that there is a significant impact of interactivity and humanness on the trust toward chatbots. Moreover, the findings of this study indicated that there is a significant mediating effect of trust toward chatbots in the relationships of interactivity and perceived humanness to adopt chatbots for e-commerce. In addition, this study found a significant moderating influence on the perceived enjoyment of using chatbots in e-commerce settings. This study provides a unique perspective of expectation-confirmation theory for adopting emerging technologies for online shopping and also provides insights for designers and business firms to develop businesses to facilitate the AI chatbot feature for e-commerce.

Predicting lymph node recurrence in cT1-2N0 tongue squamous cell carcinoma: collaboration between artificial intelligence and pathologists

Researchers have attempted to identify the factors involved in lymph node recurrence in cT1-2N0 tongue squamous cell carcinoma (SCC). However, studies combining histopathological and clinicopathological information in prediction models are limited. We aimed to develop a highly accurate lymph node recurrence prediction model for clinical stage T1-2, N0 (cT1-2N0) tongue SCC by integrating histopathological artificial intelligence (AI) with clinicopathological information. A dataset from 148 patients with cT1-2N0 tongue SCC was divided into training and test sets. The prediction models were constructed using AI-extracted information from whole slide images (WSIs), human-assessed clinicopathological information, and both combined. Weakly supervised learning and machine learning algorithms were used for WSIs and clinicopathological information, respectively. The combination model utilised both algorithms. Highly predictive patches from the model were analysed for histopathological features. In the test set, the areas under the receiver operating characteristic (ROC) curve for the model using WSI, clinicopathological information, and both combined were 0.826, 0.835, and 0.991, respectively. The highest area under the ROC curve was achieved with the model combining WSI and clinicopathological factors. Histopathological feature analysis showed that highly predicted patches extracted from recurrence cases exhibited significantly more tumour cells, inflammatory cells, and muscle content compared with non-recurrence cases. Moreover, patches with mixed inflammatory cells, tumour cells, and muscle were significantly more prevalent in recurrence versus non-recurrence cases. The model integrating AI-extracted histopathological and human-assessed clinicopathological information demonstrated high accuracy in predicting lymph node recurrence in patients with cT1-2N0 tongue SCC.

DLCNBC-SA: a model for assessing axillary lymph node metastasis status in early breast cancer patients

Background

Axillary lymph node (ALN) status is a crucial prognostic indicator for breast cancer metastasis, with manual interpretation of whole slide images (WSIs) being the current standard practice. However, this method is subjective and time-consuming. Recent advancements in deep learning-based methods for medical image analysis have shown promise in improving clinical diagnosis. This study aims to leverage these technological advancements to develop a deep learning model based on features extracted from primary tumor biopsies for preoperatively identifying ALN metastasis in early-stage breast cancer patients with negative nodes.

Methods

We present DLCNBC-SA, a deep learning-based network specifically tailored for core needle biopsy and clinical data feature extraction, which integrates a self-attention mechanism (CNBC-SA). The proposed model consists of a feature extractor based on convolutional neural network (CNN) and an improved self-attention mechanism module, which can preserve the independence of features in WSIs for analysis and enhancement to provide rich feature representation. To validate the performance of the proposed model, we conducted comparative experiments and ablation studies using publicly available datasets, and verification was performed through quantitative analysis.

Results

The comparative experiment illustrates the superior performance of the proposed model in the task of binary classification of ALNs, as compared to alternative methods. Our method achieved outstanding performance [area under the curve (AUC): 0.882] in this task, significantly surpassing the state-of-the-art (SOTA) method on the same dataset (AUC: 0.862). The ablation experiment reveals that incorporating RandomRotation data augmentation technology and utilizing Adadelta optimizer can effectively enhance the performance of the proposed model.

Conclusions

The experimental results demonstrate that the model proposed in this paper outperforms the SOTA model on the same dataset, thereby establishing its reliability as an assistant for pathologists in analyzing WSIs of breast cancer. Consequently, it significantly enhances both the efficiency and accuracy of doctors during the diagnostic process.

Perspective on quantitative phase imaging to improve precision cancer medicine

Significance

Quantitative phase imaging (QPI) offers a label-free approach to non-invasively characterize cellular processes by exploiting their refractive index based intrinsic contrast. QPI captures this contrast by translating refractive index associated phase shifts into intensity-based quantifiable data with nanoscale sensitivity. It holds significant potential for advancing precision cancer medicine by providing quantitative characterization of the biophysical properties of cells and tissue in their natural states.

Aim

This perspective aims to discuss the potential of QPI to increase our understanding of cancer development and its response to therapeutics. It also explores new developments in QPI methods towards advancing personalized cancer therapy and early detection.

Approach

We begin by detailing the technical advancements of QPI, examining its implementations across transmission and reflection geometries and phase retrieval methods, both interferometric and non-interferometric. The focus then shifts to QPI's applications in cancer research, including dynamic cell mass imaging for drug response assessment, cancer risk stratification, and in-vivo tissue imaging.

Results

QPI has emerged as a crucial tool in precision cancer medicine, offering insights into tumor biology and treatment efficacy. Its sensitivity to detecting nanoscale changes holds promise for enhancing cancer diagnostics, risk assessment, and prognostication. The future of QPI is envisioned in its integration with artificial intelligence, morpho-dynamics, and spatial biology, broadening its impact in cancer research.

Conclusions

QPI presents significant potential in advancing precision cancer medicine and redefining our approach to cancer diagnosis, monitoring, and treatment. Future directions include harnessing high-throughput dynamic imaging, 3D QPI for realistic tumor models, and combining artificial intelligence with multi-omics data to extend QPI's capabilities. As a result, QPI stands at the forefront of cancer research and clinical application in cancer care.

Physician Versus Large Language Model Chatbot Responses to Web-Based Questions From Autistic Patients in Chinese: Cross-Sectional Comparative Analysis

BACKGROUND

There is a dearth of feasibility assessments regarding using large language models (LLMs) for responding to inquiries from autistic patients within a Chinese-language context. Despite Chinese being one of the most widely spoken languages globally, the predominant research focus on applying these models in the medical field has been on English-speaking populations.

OBJECTIVE

This study aims to assess the effectiveness of LLM chatbots, specifically ChatGPT-4 (OpenAI) and ERNIE Bot (version 2.2.3; Baidu, Inc), one of the most advanced LLMs in China, in addressing inquiries from autistic individuals in a Chinese setting.

METHODS

For this study, we gathered data from DXY-a widely acknowledged, web-based, medical consultation platform in China with a user base of over 100 million individuals. A total of 100 patient consultation samples were rigorously selected from January 2018 to August 2023, amounting to 239 questions extracted from publicly available autism-related documents on the platform. To maintain objectivity, both the original questions and responses were anonymized and randomized. An evaluation team of 3 chief physicians assessed the responses across 4 dimensions: relevance, accuracy, usefulness, and empathy. The team completed 717 evaluations. The team initially identified the best response and then used a Likert scale with 5 response categories to gauge the responses, each representing a distinct level of quality. Finally, we compared the responses collected from different sources.

RESULTS

Among the 717 evaluations conducted, 46.86% (95% CI 43.21%-50.51%) of assessors displayed varying preferences for responses from physicians, with 34.87% (95% CI 31.38%-38.36%) of assessors favoring ChatGPT and 18.27% (95% CI 15.44%-21.10%) of assessors favoring ERNIE Bot. The average relevance scores for physicians, ChatGPT, and ERNIE Bot were 3.75 (95% CI 3.69-3.82), 3.69 (95% CI 3.63-3.74), and 3.41 (95% CI 3.35-3.46), respectively. Physicians (3.66, 95% CI 3.60-3.73) and ChatGPT (3.73, 95% CI 3.69-3.77) demonstrated higher accuracy ratings compared to ERNIE Bot (3.52, 95% CI 3.47-3.57). In terms of usefulness scores, physicians (3.54, 95% CI 3.47-3.62) received higher ratings than ChatGPT (3.40, 95% CI 3.34-3.47) and ERNIE Bot (3.05, 95% CI 2.99-3.12). Finally, concerning the empathy dimension, ChatGPT (3.64, 95% CI 3.57-3.71) outperformed physicians (3.13, 95% CI 3.04-3.21) and ERNIE Bot (3.11, 95% CI 3.04-3.18).

CONCLUSIONS

In this cross-sectional study, physicians' responses exhibited superiority in the present Chinese-language context. Nonetheless, LLMs can provide valuable medical guidance to autistic patients and may even surpass physicians in demonstrating empathy. However, it is crucial to acknowledge that further optimization and research are imperative prerequisites before the effective integration of LLMs in clinical settings across diverse linguistic environments can be realized.

TRIAL REGISTRATION

Chinese Clinical Trial Registry ChiCTR2300074655; https://www.chictr.org.cn/bin/project/edit?pid=199432.

Bringing CAM photosynthesis to the table: Paving the way for resilient and productive agricultural systems in a changing climate

Modern agricultural systems are directly threatened by global climate change and the resulting freshwater crisis. A considerable challenge in the coming years will be to develop crops that can cope with the consequences of declining freshwater resources and changing temperatures. One approach to meeting this challenge may lie in our understanding of plant photosynthetic adaptations and water use efficiency. Plants from various taxa have evolved crassulacean acid metabolism (CAM), a water-conserving adaptation of photosynthetic carbon dioxide fixation that enables plants to thrive under semi-arid or seasonally drought-prone conditions. Although past research on CAM has led to a better understanding of the inner workings of plant resilience and adaptation to stress, successful introduction of this pathway into C3 or C4 plants has not been reported. The recent revolution in molecular, systems, and synthetic biology, as well as innovations in high-throughput data generation and mining, creates new opportunities to uncover the minimum genetic tool kit required to introduce CAM traits into drought-sensitive crops. Here, we propose four complementary research avenues to uncover this tool kit. First, genomes and computational methods should be used to improve understanding of the nature of variations that drive CAM evolution. Second, single-cell 'omics technologies offer the possibility for in-depth characterization of the mechanisms that trigger environmentally controlled CAM induction. Third, the rapid increase in new 'omics data enables a comprehensive, multimodal exploration of CAM. Finally, the expansion of functional genomics methods is paving the way for integration of CAM into farming systems.

Computer Vision in Digital Neuropathology

Digital pathology has revolutionized the field of neuropathology, enabling rapid and precise analysis of tissue samples. As neuropathologists and neurosurgeons increasingly embrace digital platforms, computer vision techniques and computerized quantitative analyses (i.e., pathomics) play a pivotal role in automating and enhancing diagnostic processes, as well as in unlocking new insights from neuropathological images. This chapter explores the role of computer vision in bridging the gap between traditional and digital neuropathology, providing a comprehensive overview of computer vision applications in neuropathology, covering image preprocessing, and decision support for clinical tasks, such as early detection of neurological disorders, classification of brain tumors, and quantitative assessment of tissue biomarkers. In addition, we further delve into the challenges and opportunities presented by large-scale image datasets and the integration of digital pathology into neurosurgical practice.

Human-Machine Collaboration in Diagnostics: Exploring the Synergy in Clinical Imaging with Artificial Intelligence

Advancements in artificial intelligence (AI), thanks to IT developments during the COVID-19 pandemic, have revolutionized the field of diagnostics, particularly in clinical imaging [...].