Classification and mutation prediction from non-small cell lung cancer histopathology images using deep learning

The value of MRI radiomics in distinguishing different types of spinal infections

BACKGROUND

In clinical practice, the three most prevalent forms of infectious spondylitis are tuberculous spondylitis (TS), brucellosis spondylitis (BS), and pyogenic spondylitis (PS). It is possible to successfully lessen neurological and spinal damage by detecting them early. In the medical field, radiomics has been applied extensively. It is crucial to find out if MRI imaging can be used to diagnose spinal infections early.

PURPOSE

To explore the diagnostic value of establishing models based on MRI radiomics for different spinal infections.

METHODS

This retrospective study collected clinical and magnetic resonance imaging information on a total of 136 patients diagnosed with spondylitis in April 2019 and August 2023, who were classified into specific spinal infections (TS or BS) and non-specific spinal infections (PS) based on treatment. 3D Slicer software was used to outline the region of interest (ROI) and extracted ROI features. All patients were randomly divided into a training set and a test set (7:3), and after standardized, the t-test and LASSO were sequentially performed in the training set to extract the optimal radiomic features. These features were used to calculate the Radscore and construct the features classifier model and evaluated by test set. Univariate and multivariate logistic regression of Radscore and clinical features to identify predictors contributing to the diagnosis were used to plot nomograms, the area under the receiver operating characteristic curve (AUC), calibration curves, and decision curve analysis (DCA) to assess the nomogram. The same approach described above was used to diagnose both subgroups of BS and TS in SSI.

RESULTS

321 radiological features were extracted from the three different sequences. The remaining 7 optimal radiomics features were used to calculate the Radscore and establish three feature classifier models, with RF having the best performance (AUC=1 and 0.86). And after univariate and multivariate logistic regression, the final nomogram constructed by Radscore and had good discriminatory performance in the training set and the test set (AUC =0.924 and 0.868), and the calibration curve and DCA showed good clinical efficacy. In the subgroup, the AUC of the training and test sets was 0.929and0.863.

CONCLUSION

The diagnostic model based on MR radiomics can gradually differentiate tuberculous spondylitis, brucellosis spondylitis, and pyogenic spondylitis.

Joint modeling histology and molecular markers for cancer classification

Cancers are characterized by remarkable heterogeneity and diverse prognosis. Accurate cancer classification is essential for patient stratification and clinical decision-making. Although digital pathology has been advancing cancer diagnosis and prognosis, the paradigm in cancer pathology has shifted from purely relying on histology features to incorporating molecular markers. There is an urgent need for digital pathology methods to meet the needs of the new paradigm. We introduce a novel digital pathology approach to jointly predict molecular markers and histology features and model their interactions for cancer classification. Firstly, to mitigate the challenge of cross-magnification information propagation, we propose a multi-scale disentangling module, enabling the extraction of multi-scale features from high-magnification (cellular-level) to low-magnification (tissue-level) whole slide images. Further, based on the multi-scale features, we propose an attention-based hierarchical multi-task multi-instance learning framework to simultaneously predict histology and molecular markers. Moreover, we propose a co-occurrence probability-based label correlation graph network to model the co-occurrence of molecular markers. Lastly, we design a cross-modal interaction module with the dynamic confidence constrain loss and a cross-modal gradient modulation strategy, to model the interactions of histology and molecular markers. Our experiments demonstrate that our method outperforms other state-of-the-art methods in classifying glioma, histology features and molecular markers. Our method promises to promote precise oncology with the potential to advance biomedical research and clinical applications. The code is available at github.

Navigating Through Whole Slide Images With Hierarchy, Multi-Object, and Multi-Scale Data

Building deep learning models that can rapidly segment whole slide images (WSIs) using only a handful of training samples remains an open challenge in computational pathology. The difficulty lies in the histological images themselves: many morphological structures within a slide are closely related and very similar in appearance, making it difficult to distinguish between them. However, a skilled pathologist can quickly identify the relevant phenotypes. Through years of training, they have learned to organize visual features into a hierarchical taxonomy (e.g., identifying carcinoma versus healthy tissue, or distinguishing regions within a tumor as cancer cells, the microenvironment, …). Thus, each region is associated with multiple labels representing different tissue types. Pathologists typically deal with this by analyzing the specimen at multiple scales and comparing visual features between different magnifications. Inspired by this multi-scale diagnostic workflow, we introduce the Navigator, a vision model that navigates through WSIs like a domain expert: it searches for the region of interest at a low scale, zooms in gradually, and localizes ever finer microanatomical classes. As a result, the Navigator can detect coarse-grained patterns at lower resolution and fine-grained features at higher resolution. In addition, to deal with sparsely annotated samples, we train the Navigator with a novel semi-supervised framework called S5CL v2. The proposed model improves the F1 score by up to 8% on various datasets including our challenging new TCGA-COAD-30CLS and Erlangen cohorts.

[Foundation models in pathology]

Foundation models prepare neural networks for applications in specific domains, such as speech applications or image analysis, through self-supervised pretraining. These models can be adapted for specific applications, such as histopathological diagnostics. While adaptation still requires supervised training, AI applications based on foundation models achieve significantly better prediction accuracy with fewer training data compared to conventional approaches. This article introduces the topic and provides an overview of foundation models in pathology.

CellOMaps: A compact representation for robust classification of lung adenocarcinoma growth patterns

Lung adenocarcinoma (LUAD) is a morphologically heterogeneous disease, characterized by five primary histological growth patterns. The classification of such patterns is crucial due to their direct relation to prognosis but the high subjectivity and observer variability pose a major challenge. Related studies in the literature focus on machine learning methods for growth pattern classification, often formulating the problem as a slide-level predominant pattern classification problem. We propose a generalizable machine learning pipeline capable of classifying lung tissue into one of the five patterns or as non-tumor. The proposed pipeline's strength lies in a novel compact Cell Organization Maps (cellOMaps) representation that captures the cellular spatial patterns from Hematoxylin and Eosin (H&E) whole slide images (WSIs). The proposed pipeline provides state-of-the-art performance on LUAD growth pattern classification when evaluated on both internal unseen slides and external datasets, comparing favorably with the current approaches. In addition, our preliminary results show that the model's outputs can be used to predict patients Tumor Mutational Burden (TMB) levels.

Deep learning radiopathomics predicts targeted therapy sensitivity in EGFR-mutant lung adenocarcinoma

BACKGROUND

Ttyrosine kinase inhibitors (TKIs) represent the standard first-line treatment for patients with epidermal growth factor receptor (EGFR)-mutant lung adenocarcinoma. However, not all patients with EGFR mutations respond to TKIs. This study aims to develop a deep learning radiological-pathological-clinical (DLRPC) model that integrates computed tomography (CT) images, hematoxylin and eosin (H&E)-stained aspiration biopsy samples, and clinical data to predict the response in EGFR-mutant lung adenocarcinoma patients undergoing TKIs treatment.

METHODS

We retrospectively analyzed data from 214 lung adenocarcinoma patients who received TKIs treatment from two medical centers between September 2013 and June 2023. The DLRPC model leverages paired CT, pathological images and clinical data, incorporating a clinical-based attention mask to further explore the cross-modality associations. To evaluate its diagnostic performance, we compared the DLRPC model against single-modality models and a decision level fusion model based on Dempster-Shafer theory. Model performances metrics, including area under the curve (AUC), accuracy, sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV), were used for evaluation. The Delong test assessed statistically significantly differences in AUC among models.

RESULTS

The DLRPC model demonstrated strong performance, achieving an AUC value of 0.8424. It outperformed the single-modality models (AUC = 0.6894, 0.7753, 0.8052 for CT model, pathology model and clinical model, respectively. P < 0.05). Additionally, the DLRPC model surpassed the decision level fusion model (AUC = 0.8132, P < 0.05).

CONCLUSION

The DLRPC model effectively predicts the response of EGFR-mutant lung adenocarcinoma patients to TKIs, providing a promising tool for personalized treatment decisions in lung cancer management.

Artificial intelligence entering the pathology arena in oncology: current applications and future perspectives

BACKGROUND

Artificial intelligence (AI) is rapidly transforming the fields of pathology and oncology, offering novel opportunities for advancing diagnosis, prognosis, and treatment of cancer.

METHODS

Through a systematic review-based approach, the representatives from the European Society for Medical Oncology (ESMO) Precision Oncology Working Group (POWG) and international experts identified studies in pathology and oncology that applied AI-based algorithms for tumour diagnosis, molecular biomarker detection, and cancer prognosis assessment. These findings were synthesised to provide a comprehensive overview of current AI applications and future directions in cancer pathology.

RESULTS

The integration of AI tools in digital pathology is markedly improving the accuracy and efficiency of image analysis, allowing for automated tumour detection and classification, identification of prognostic molecular biomarkers, and prediction of treatment response and patient outcomes. Several barriers for the adoption of AI in clinical workflows, such as data availability, explainability, and regulatory considerations, still persist. There are currently no prognostic or predictive AI-based biomarkers supported by level IA or IB evidence. The ongoing advancements in AI algorithms, particularly foundation models, generalist models and transformer-based deep learning, offer immense promise for the future of cancer research and care. AI is also facilitating the integration of multi-omics data, leading to more precise patient stratification and personalised treatment strategies.

CONCLUSIONS

The application of AI in pathology is poised to not only enhance the accuracy and efficiency of cancer diagnosis and prognosis but also facilitate the development of personalised treatment strategies. Although barriers to implementation remain, ongoing research and development in this field coupled with addressing ethical and regulatory considerations will likely lead to a future where AI plays an integral role in cancer management and precision medicine. The continued evolution and adoption of AI in pathology and oncology are anticipated to reshape the landscape of cancer care, heralding a new era of precision medicine and improved patient outcomes.

A clinical benchmark of public self-supervised pathology foundation models

The use of self-supervised learning to train pathology foundation models has increased substantially in the past few years. Notably, several models trained on large quantities of clinical data have been made publicly available in recent months. This will significantly enhance scientific research in computational pathology and help bridge the gap between research and clinical deployment. With the increase in availability of public foundation models of different sizes, trained using different algorithms on different datasets, it becomes important to establish a benchmark to compare the performance of such models on a variety of clinically relevant tasks spanning multiple organs and diseases. In this work, we present a collection of pathology datasets comprising clinical slides associated with clinically relevant endpoints including cancer diagnoses and a variety of biomarkers generated during standard hospital operation from three medical centers. We leverage these datasets to systematically assess the performance of public pathology foundation models and provide insights into best practices for training foundation models and selecting appropriate pretrained models. To enable the community to evaluate their models on our clinical datasets, we make available an automated benchmarking pipeline for external use.

AI-assisted SERS imaging method for label-free and rapid discrimination of clinical lymphoma

BACKGROUND

Lymphoma is a malignant tumor of the immune system and its incidence is increasing year after year, causing a major threat to people's health. Conventional diagnosis of lymphoma basically depends on histological images consuming long-time and tedious manipulations (e.g., 7-15 days) and large-field view (e.g., > 1000 × 1000 μm2). Artificial intelligence has recently revolutionized cancer diagnosis by training pathological image databases via deep learning. Current approaches, however, remain dependent on analyzing wide-field pathological images to detect distinct nuclear, cytologic, and histomorphologic traits for diagnostic categorization, limiting their applicability to minimally invasive lesion.

RESULTS

Herein, we develop a molecular imaging strategy for minimally invasive lymphoma diagnosis. By spreading lymphoma tissue sections tightly on a surface-enhanced Raman scattering (SERS) chip, label-free images of DNA double strand breaks (DSBs) in 30 × 30 μm2 tissue sections could be achieved in ~ 15 min. To establish a proof of concept, the Raman image datasets collected from clinical samples of normal lymphatic tissues and non-Hodgkin's lymphoma (NHL) tissues were well organized and trained in a deep convolutional neural network model, finally achieving a recognition rate of ~ 91.7 ± 2.1%.

CONCLUSIONS

The molecular imaging strategy for minimally invasive lymphoma diagnosis that can achieve a recognition rate of ~ 91.7 ± 2.1%. We anticipate that these results will catalyze the development of a series of histological SERS-AI technologies for diagnosing various diseases, including other types of cancer. In this work, we present a reliable tool to facilitate clinicians in the diagnosis of lymphoma.

Artificial Intelligence-Powered Quality Assurance: Transforming Diagnostics, Surgery, and Patient Care-Innovations, Limitations, and Future Directions

Artificial intelligence is rapidly transforming quality assurance in healthcare, driving advancements in diagnostics, surgery, and patient care. This review presents a comprehensive analysis of artificial intelligence integration-particularly convolutional and recurrent neural networks-across key clinical domains, significantly enhancing diagnostic accuracy, surgical performance, and pathology evaluation. Artificial intelligence-based approaches have demonstrated clear superiority over conventional methods: convolutional neural networks achieved 91.56% accuracy in scanner fault detection, surpassing manual inspections; endoscopic lesion detection sensitivity rose from 2.3% to 6.1% with artificial intelligence assistance; and gastric cancer invasion depth classification reached 89.16% accuracy, outperforming human endoscopists by 17.25%. In pathology, artificial intelligence achieved 93.2% accuracy in identifying out-of-focus regions and an F1 score of 0.94 in lymphocyte quantification, promoting faster and more reliable diagnostics. Similarly, artificial intelligence improved surgical workflow recognition with over 81% accuracy and exceeded 95% accuracy in skill assessment classification. Beyond traditional diagnostics and surgical support, AI-powered wearable sensors, drug delivery systems, and biointegrated devices are advancing personalized treatment by optimizing physiological monitoring, automating care protocols, and enhancing therapeutic precision. Despite these achievements, challenges remain in areas such as data standardization, ethical governance, and model generalizability. Overall, the findings underscore artificial intelligence's potential to outperform traditional techniques across multiple parameters, emphasizing the need for continued development, rigorous clinical validation, and interdisciplinary collaboration to fully realize its role in precision medicine and patient safety.

Using pathology images and artificial intelligence to identify bacterial infections and their types

Bacterial infections pose a significant biosafety concern, making early and accurate diagnosis essential for effective treatment and prognosis. Traditional diagnostic methods, while reliable, are often slow and fail to meet urgent clinical demands. In contrast, emerging technologies offer greater efficiency but are often costly and inaccessible. In this study, we utilized easily accessible pathology images to diagnose bacterial infections. Our initial findings indicate that, in the absence of postmortem phenomena, microscopic examination of pathological images can confirm the presence of a bacterial infection. However, distinguishing between different types of bacterial infections remains challenging due to similarities in pathological changes. To address this limitation, we applied a computational pathology approach by integrating pathology images with artificial intelligence (AI) algorithms. Our model classified bacterial infections at both the patch-level and whole slide image (WSI)-level. The results demonstrated strong performance, with an overall AUC consistently above 0.950 across training, testing, and external validation datasets, indicating high accuracy, robustness, and generalizability. This study highlights AI's potential in identifying bacterial infection types and provides valuable technical support for clinical diagnostics, paving the way for faster and more precise infection management.

Recent Advances in Artificial Intelligence for Precision Diagnosis and Treatment of Bladder Cancer: A Review

BACKGROUND

Bladder cancer is one of the top ten cancers globally, with its incidence steadily rising in China. Early detection and prognosis risk assessment play a crucial role in guiding subsequent treatment decisions for bladder cancer. However, traditional diagnostic methods such as bladder endoscopy, imaging, or pathology examinations heavily rely on the clinical expertise and experience of clinicians, exhibiting subjectivity and poor reproducibility.

MATERIALS AND METHODS

With the rise of artificial intelligence, novel approaches, particularly those employing deep learning technology, have shown significant advancements in clinical tasks related to bladder cancer, including tumor detection, molecular subtyping identification, tumor staging and grading, prognosis prediction, and recurrence assessment.

RESULTS

Artificial intelligence, with its robust data mining capabilities, enhances diagnostic efficiency and reproducibility when assisting clinicians in decision-making, thereby reducing the risks of misdiagnosis and underdiagnosis. This not only helps alleviate the current challenges of talent shortages and uneven distribution of medical resources but also fosters the development of precision medicine.

CONCLUSIONS

This study provides a comprehensive review of the latest research advances and prospects of artificial intelligence technology in the precise diagnosis and treatment of bladder cancer.

Autonomous learning of pathologists' cancer grading rules

Deep learning (DL) algorithms have demonstrated remarkable proficiency in histopathology classification tasks, presenting an opportunity to discover disease-related features escaping visual inspection. However, the "black box" nature of DL obfuscates the basis of the classification. Here, we develop an algorithm for interpretable Deep Learning (IDL) that sheds light on the links between tissue morphology and cancer biology. We make use of a generative model trained to represent images via a combination of a semantic latent space and a noise vector to capture low level image details. We traversed the latent space so as to induce prototypical image changes associated with the disease state, which we identified via a second DL model. Applied to a dataset of clear cell renal cell carcinoma (ccRCC) tissue images the AI system pinpoints nuclear size and nucleolus density in tumor cells (but not other cell types) as the decisive features of tumor progression from grade 1 to grade 4 - mirroring the rules that have been used for decades in the clinic and are taught in textbooks. Moreover, the AI system posits a decrease in vasculature with increasing grade. While the association has been illustrated by some previous reports, the correlation is not part of currently implemented grading systems. These results indicate the potential of IDL to autonomously formalize the connection between the histopathological presentation of a disease and the underlying tissue architectural drivers.

Labor-Efficient Pathological Auxiliary Diagnostic Model for Primary and Metastatic Tumor Tissue Detection in Pancreatic Ductal Adenocarcinoma

Accurate histopathological evaluation of pancreatic ductal adenocarcinoma (PDAC), including primary tumor lesions and lymph node metastases, is critical for prognostic evaluation and personalized therapeutic strategies. Distinct from other solid tumors, PDAC presents unique diagnostic challenges owing to its extensive desmoplasia, unclear tumor boundary, and difficulty in differentiating from chronic pancreatitis. These characteristics not only complicate pathological diagnosis but also hinder the acquisition of pixel-level annotations required for training computational pathology models. In this study, we present PANseg, a multiscale weakly supervised deep learning framework for PDAC segmentation, trained and tested on 368 whole-slide images (WSIs) from 208 patients across 2 independent centers. Using only image-level labels (2048 × 2048 pixels), PANseg achieved comparable performance with fully supervised baseline (FSB) across the internal test set 1 (17 patients/58 WSIs; PANseg area under the receiver operating characteristic curve [AUROC]: 0.969 vs FSB AUROC: 0.968), internal test set 2 (40 patients/44 WSIs; PANseg AUROC: 0.991 vs FSB AUROC: 0.980), and external test set (20 patients/20 WSIs; PANseg AUROC: 0.950 vs FSB AUROC: 0.958). Moreover, the model demonstrated considerable generalizability with previously unseen sample types, attaining AUROCs of 0.878 on fresh-frozen specimens (20 patients/20 WSIs) and 0.821 on biopsy sections (20 patients/20 WSIs). In lymph node metastasis detection, PANseg augmented the diagnostic accuracy of 6 pathologists from 0.888 to 0.961, while reducing the average diagnostic time by 32.6% (72.0 vs 48.5 minutes). This study demonstrates that our weakly supervised model can achieve expert-level segmentation performance and substantially reduce annotation burden. The clinical implementation of PANseg holds great potential in enhancing diagnostic precision and workflow efficiency in the routine histopathological assessment of PDAC.

Public Awareness of and Attitudes Toward the Use of AI in Pathology Research and Practice: Mixed Methods Study

BACKGROUND

The last decade has witnessed major advances in the development of artificial intelligence (AI) technologies for use in health care. One of the most promising areas of research that has potential clinical utility is the use of AI in pathology to aid cancer diagnosis and management. While the value of using AI to improve the efficiency and accuracy of diagnosis cannot be underestimated, there are challenges in the development and implementation of such technologies. Notably, questions remain about public support for the use of AI to assist in pathological diagnosis and for the use of health care data, including data obtained from tissue samples, to train algorithms.

OBJECTIVE

This study aimed to investigate public awareness of and attitudes toward AI in pathology research and practice.

METHODS

A nationally representative, cross-sectional, web-based mixed methods survey (N=1518) was conducted to assess the UK public's awareness of and views on the use of AI in pathology research and practice. Respondents were recruited via Prolific, an online research platform. To be eligible for the study, participants had to be aged >18 years, be UK residents, and have the capacity to express their own opinion. Respondents answered 30 closed-ended questions and 2 open-ended questions. Sociodemographic information and previous experience with cancer were collected. Descriptive and inferential statistics were used to analyze quantitative data; qualitative data were analyzed thematically.

RESULTS

Awareness was low, with only 23.19% (352/1518) of the respondents somewhat or moderately aware of AI being developed for use in pathology. Most did not support a diagnosis of cancer (908/1518, 59.82%) or a diagnosis based on biomarkers (694/1518, 45.72%) being made using AI only. However, most (1478/1518, 97.36%) supported diagnoses made by pathologists with AI assistance. The adjusted odds ratio (aOR) for supporting AI in cancer diagnosis and management was higher for men (aOR 1.34, 95% CI 1.02-1.75). Greater awareness (aOR 1.25, 95% CI 1.10-1.42), greater trust in data security and privacy protocols (aOR 1.04, 95% CI 1.01-1.07), and more positive beliefs (aOR 1.27, 95% CI 1.20-1.36) also increased support, whereas identifying more risks reduced the likelihood of support (aOR 0.80, 95% CI 0.73-0.89). In total, 3 main themes emerged from the qualitative data: bringing the public along, the human in the loop, and more hard evidence needed, indicating conditional support for AI in pathology with human decision-making oversight, robust measures for data handling and protection, and evidence for AI benefit and effectiveness.

CONCLUSIONS

Awareness of AI's potential use in pathology was low, but attitudes were positive, with high but conditional support. Challenges remain, particularly among women, regarding AI use in cancer diagnosis and management. Apprehension persists about the access to and use of health care data by private organizations.

Predicting the Evolution of Lung Squamous Cell Carcinoma In Situ Using Computational Pathology

Lung squamous cell carcinoma in situ (SCIS) is the preinvasive precursor lesion of lung squamous cell carcinoma (SCC). Only around two-thirds of these lesions progress to invasive cancer, while one-third undergo spontaneous regression, which presents a significant clinical challenge due to the risk of overtreatment. The ability to predict the evolution of SCIS lesions can significantly impact patient management. Our study explores the use of computational pathology in predicting the evolution of SCIS. We used a dataset consisting of 112 H&E-stained whole slide images (WSIs) that were obtained from the Image Data Resource public repository. The dataset corresponded to tumors of patients who underwent biopsies of SCIS lesions and were subsequently followed up by bronchoscopy and CT scans to monitor for progression to SCC. We used this dataset to train two models: a pathomics-based ridge classifier trained on 80 principal components derived from almost 2000 extracted features and a deep convolutional neural network with a modified ResNet18 architecture. The performance of both approaches in predicting progression was assessed. The pathomics-based ridge classifier model obtained an F1-score of 0.77, precision of 0.80, and recall of 0.77. The deep learning model performance was similar, with a WSI-level F1-score of 0.80, precision of 0.71, and recall of 0.90. These findings highlight the potential of computational pathology approaches in providing insights into the evolution of SCIS. Larger datasets will be required in order to train highly accurate models. In the future, computational pathology could be used in predicting outcomes in other preinvasive lesions.

Increasing use of artificial intelligence in genomic medicine for cancer care- the promise and potential pitfalls

The field of genomic medicine produces large datasets, which need to be rapidly analysed to produce clinically actionable insights in cancer care. Artificial intelligence thrives on data, processing and learning from datasets with a degree of accuracy and efficiency that traditional computing algorithms can not achieve. Based on a patient's genome sequence, AI could allow earlier detection of cancer, inform personalised treatment plans and provide insights into prognostication. However, this valuable tool is met with skepticism, with stakeholders concerned over data security, liability for AI's mistakes due to hallucination and the threat to clinical jobs. This review highlights both the benefits and potential problems of using AI in genomic medicine for cancer care, with the aim to lessen the knowledge gap between clinicians and data scientists and facilitate the future deployment of AI in cancer care.

Defining a 'cells to society' research framework for appendiceal tumours

Tumours of the appendix - a vestigial digestive organ attached to the colon - are rare. Although we estimate that around 3,000 new appendiceal cancer cases are diagnosed annually in the USA, the challenges of accurately diagnosing and identifying this tumour type suggest that this number may underestimate true population incidence. In the current absence of disease-specific screening and diagnostic imaging modalities, or well-established risk factors, the incidental discovery of appendix tumours is often prompted by acute presentations mimicking appendicitis or when the tumour has already spread into the abdominal cavity - wherein the potential misclassification of appendiceal tumours as malignancies of the colon and ovaries also increases. Notwithstanding these diagnostic difficulties, our understanding of appendix carcinogenesis has advanced in recent years. However, there persist considerable challenges to accelerating the pace of research discoveries towards the path to improved treatments and cures for patients with this group of orphan malignancies. The premise of this Expert Recommendation article is to discuss the current state of the field, to delineate unique challenges for the study of appendiceal tumours, and to propose key priority research areas that will deliver a more complete picture of appendix carcinogenesis and metastasis. The Appendix Cancer Pseudomyxoma Peritonei (ACPMP) Research Foundation Scientific Think Tank delivered a consensus of core research priorities for appendiceal tumours that are poised to be ground-breaking and transformative for scientific discovery and innovation. On the basis of these six research areas, here, we define the first 'cells to society' research framework for appendix tumours.

Artificial intelligence in digital pathology - time for a reality check

The past decade has seen the introduction of artificial intelligence (AI)-based approaches aimed at optimizing several workflows across many medical specialties. In clinical oncology, the most promising applications include those involving image analysis, such as digital pathology. In this Perspective, we provide a comprehensive examination of the developments in AI in digital pathology between 2019 and 2024. We evaluate the current landscape from the lens of technological innovations, regulatory trends, deployment and implementation, reimbursement and commercial implications. We assess the technological advances that have driven improvements in AI, enabling more robust and scalable solutions for digital pathology. We also examine regulatory developments, in particular those affecting in-house devices and laboratory-developed tests, which are shaping the landscape of AI-based tools in digital pathology. Finally, we discuss the role of reimbursement frameworks and commercial investment in the clinical adoption of AI-based technologies. In this Perspective, we highlight both the progress and challenges in AI-driven digital pathology over the past 5 years, outlining the path forward for its adoption into routine practice in clinical oncology.

A deep-learning model for predicting tyrosine kinase inhibitor response from histology in gastrointestinal stromal tumor

Over 90% of gastrointestinal stromal tumors (GISTs) harbor mutations in KIT or PDGFRA that can predict response to tyrosine kinase inhibitor (TKI) therapies, as recommended by NCCN (National Comprehensive Cancer Network) guidelines. However, gene sequencing for mutation testing is expensive and time-consuming and is susceptible to a variety of preanalytical factors. To overcome the challenges associated with genetic screening by sequencing, in the current study we developed an artificial intelligence-based deep-learning （DL） model that uses convolutional neural networks (CNN) to analyze digitized hematoxylin and eosin staining in tumor histological sections to predict potential response to imatinib or avapritinib treatment in GIST patients. Assessment with an independent testing set showed that our DL  model could predict imatinib sensitivity with an area under the curve (AUC) of 0.902 in case-wise analysis and 0.807 in slide-wise analysis. Case-level AUCs for predicting imatinib-dose-adjustment cases, avapritinib-sensitive cases, and wildtype GISTs were 0.920, 0.958, and 0.776, respectively, while slide-level AUCs for these respective groups were 0.714, 0.922, and 0.886, respectively. Our model showed comparable or better prediction of actual response to TKI than sequencing-based screening (accuracy 0.9286 versus 0.8929; DL model versus sequencing), while predictions of nonresponse to imatinib/avapritinib showed markedly higher accuracy than sequencing (0.7143 versus 0.4286). These results demonstrate the potential of a DL model to improve predictions of treatment response to TKI therapy from histology in GIST patients. © 2025 The Pathological Society of Great Britain and Ireland.

Decoding pathology: the role of computational pathology in research and diagnostics

Traditional histopathology, characterized by manual quantifications and assessments, faces challenges such as low-throughput and inter-observer variability that hinder the introduction of precision medicine in pathology diagnostics and research. The advent of digital pathology allowed the introduction of computational pathology, a discipline that leverages computational methods, especially based on deep learning (DL) techniques, to analyze histopathology specimens. A growing body of research shows impressive performances of DL-based models in pathology for a multitude of tasks, such as mutation prediction, large-scale pathomics analyses, or prognosis prediction. New approaches integrate multimodal data sources and increasingly rely on multi-purpose foundation models. This review provides an introductory overview of advancements in computational pathology and discusses their implications for the future of histopathology in research and diagnostics.

Self-interactive learning: Fusion and evolution of multi-scale histomorphology features for molecular traits prediction in computational pathology

Predicting disease-related molecular traits from histomorphology brings great opportunities for precision medicine. Despite the rich information present in histopathological images, extracting fine-grained molecular features from standard whole slide images (WSI) is non-trivial. The task is further complicated by the lack of annotations for subtyping and contextual histomorphological features that might span multiple scales. This work proposes a novel multiple-instance learning (MIL) framework capable of WSI-based cancer morpho-molecular subtyping by fusion of different-scale features. Our method, debuting as Inter-MIL, follows a weakly-supervised scheme. It enables the training of the patch-level encoder for WSI in a task-aware optimisation procedure, a step normally not modelled in most existing MIL-based WSI analysis frameworks. We demonstrate that optimising the patch-level encoder is crucial to achieving high-quality fine-grained and tissue-level subtyping results and offers a significant improvement over task-agnostic encoders. Our approach deploys a pseudo-label propagation strategy to update the patch encoder iteratively, allowing discriminative subtype features to be learned. This mechanism also empowers extracting fine-grained attention within image tiles (the small patches), a task largely ignored in most existing weakly supervised-based frameworks. With Inter-MIL, we carried out four challenging cancer molecular subtyping tasks in the context of ovarian, colorectal, lung, and breast cancer. Extensive evaluation results show that Inter-MIL is a robust framework for cancer morpho-molecular subtyping with superior performance compared to several recently proposed methods, in small dataset scenarios where the number of available training slides is less than 100. The iterative optimisation mechanism of Inter-MIL significantly improves the quality of the image features learned by the patch embedded and generally directs the attention map to areas that better align with experts' interpretation, leading to the identification of more reliable histopathology biomarkers. Moreover, an external validation cohort is used to verify the robustness of Inter-MIL on molecular trait prediction.

General Applicability of Existing College of American Pathologists Accreditation Requirements to Clinical Implementation of Machine Learning-Based Methods in Molecular Oncology Testing

CONTEXT.—

The College of American Pathologists (CAP) accreditation requirements for clinical laboratory testing help ensure laboratories implement and maintain systems and processes that are associated with quality. Machine learning (ML)-based models share some features of conventional laboratory testing methods. Accreditation requirements that specifically address clinical laboratories' use of ML remain in the early stages of development.

OBJECTIVE.—

To identify relevant CAP accreditation requirements that may be applied to the clinical adoption of ML-based molecular oncology assays, and to provide examples of current and emerging ML applications in molecular oncology testing.

DESIGN.—

CAP accreditation checklists related to molecular pathology and general laboratory practices (Molecular Pathology, All Common and Laboratory General) were reviewed. Examples of checklist requirements that are generally applicable to validation, revalidation, quality management, infrastructure, and analytical procedures of ML-based molecular oncology assays were summarized. Instances of ML use in molecular oncology testing were assessed from literature review.

RESULTS.—

Components of the general CAP accreditation framework that exist for traditional molecular oncology assay validation and maintenance are also relevant for implementing ML-based tests in a clinical laboratory. Current and emerging applications of ML in molecular oncology testing include DNA methylation profiling for central nervous system tumor classification, variant calling, microsatellite instability testing, mutational signature analysis, and variant prediction from histopathology images.

CONCLUSIONS.—

Currently, much of the ML activity in molecular oncology is within early clinical implementation. Despite specific considerations that apply to the adoption of ML-based methods, existing CAP requirements can serve as general guidelines for the clinical implementation of ML-based assays in molecular oncology testing.

Implementing Trust in Non-Small Cell Lung Cancer Diagnosis with a Conformalized Uncertainty-Aware AI Framework in Whole-Slide Images

Ensuring trustworthiness is fundamental to the development of artificial intelligence (AI) that is considered societally responsible, particularly in cancer diagnostics, where a misdiagnosis can have dire consequences. Current digital pathology AI models lack systematic solutions to address trustworthiness concerns arising from model limitations and data discrepancies between model deployment and development environments. To address this issue, we developed TRUECAM, a framework designed to ensure both data and model trustworthiness in non-small cell lung cancer subtyping with whole-slide images. TRUECAM integrates 1) a spectral-normalized neural Gaussian process for identifying out-of-scope inputs and 2) an ambiguity-guided elimination of tiles to filter out highly ambiguous regions, addressing data trustworthiness, as well as 3) conformal prediction to ensure controlled error rates. We systematically evaluated the framework across multiple large-scale cancer datasets, leveraging both task-specific and foundation models, illustrate that an AI model wrapped with TRUECAM significantly outperforms models that lack such guidance, in terms of classification accuracy, robustness, interpretability, and data efficiency, while also achieving improvements in fairness. These findings highlight TRUECAM as a versatile wrapper framework for digital pathology AI models with diverse architectural designs, promoting their responsible and effective applications in real-world settings.

Double-Multiplex Immunostainings for Immune Profiling of Invasive Breast Carcinoma: Emerging Novel Immune-Based Biomarkers

The role of tumor microenvironment in invasive breast cancer prognosis and treatment is highly appreciated. With the advent of immunotherapy, immunophenotypic characterization in primary tumors is gaining attention as it can improve patient stratification. Here, we discuss the benefits of spatial analysis employing double and multiplex immunostaining, allowing the simultaneous detection of more than one protein on the same tissue section, which in turn helps us provide functional insight into infiltrating immune cells within tumors. We focus on studies demonstrating the prognostic and predictive impact of distinct tumor-infiltrating lymphocyte subpopulations including different CD8(+) T subsets as well as CD4(+) T cells and tumor-associated macrophages in invasive breast carcinoma. The clinical value of immune cell topography is also appreciated. We further refer to how the integration of digital pathology and artificial intelligence in routine practice could enhance the accuracy of multiplex immunostainings evaluation within the tumor microenvironment, maximizing our perception of host immune response, improving in turn decision-making towards more precise immune-associated therapies.

Assessments of lung nodules by an artificial intelligence chatbot using longitudinal CT images

Large language models have shown efficacy across multiple medical tasks. However, their value in the assessment of longitudinal follow-up computed tomography (CT) images of patients with lung nodules is unclear. In this study, we evaluate the ability of the latest generative pre-trained transformer (GPT)-4o model to assess changes in malignancy probability, size, and features of lung nodules on longitudinal CT scans from 647 patients (547 from two local centers and 100 from a public dataset). GPT-4o achieves an average accuracy of 0.88 in predicting lung nodule malignancy compared to pathological results and an average intraclass correlation coefficient of 0.91 in measuring nodule size compared with manual measurements by radiologists. Six radiologists' evaluations demonstrate GPT-4o's ability to capture changes in nodule features with a median Likert score of 4.17 (out of 5.00). In summary, GPT-4o could capture dynamic changes in lung nodules across longitudinal follow-up CT images, thus providing high-quality radiological evidence to assist in clinical management.

Translational Advances in Oncogene and Tumor-Suppressor Gene Research

Cancer, characterized by the uncontrolled proliferation of cells, is one of the leading causes of death globally, with approximately one in five people developing the disease in their lifetime. While many driver genes were identified decades ago, and most cancers can be classified based on morphology and progression, there is still a significant gap in knowledge about genetic aberrations and nuclear DNA damage. The study of two critical groups of genes-tumor suppressors, which inhibit proliferation and promote apoptosis, and oncogenes, which regulate proliferation and survival-can help to understand the genomic causes behind tumorigenesis, leading to more personalized approaches to diagnosis and treatment. Aberration of tumor suppressors, which undergo two-hit and loss-of-function mutations, and oncogenes, activated forms of proto-oncogenes that experience one-hit and gain-of-function mutations, are responsible for the dysregulation of key signaling pathways that regulate cell division, such as p53, Rb, Ras/Raf/ERK/MAPK, PI3K/AKT, and Wnt/β-catenin. Modern breakthroughs in genomics research, like next-generation sequencing, have provided efficient strategies for mapping unique genomic changes that contribute to tumor heterogeneity. Novel therapeutic approaches have enabled personalized medicine, helping address genetic variability in tumor suppressors and oncogenes. This comprehensive review examines the molecular mechanisms behind tumor-suppressor genes and oncogenes, the key signaling pathways they regulate, epigenetic modifications, tumor heterogeneity, and the drug resistance mechanisms that drive carcinogenesis. Moreover, the review explores the clinical application of sequencing techniques, multiomics, diagnostic procedures, pharmacogenomics, and personalized treatment and prevention options, discussing future directions for emerging technologies.

Artificial intelligence based classification and prediction of medical imaging using a novel framework of inverted and self-attention deep neural network architecture

Classifying medical images is essential in computer-aided diagnosis (CAD). Although the recent success of deep learning in the classification tasks has proven advantages over the traditional feature extraction techniques, it remains challenging due to the inter and intra-class similarity caused by the diversity of imaging modalities (i.e., dermoscopy, mammography, wireless capsule endoscopy, and CT). In this work, we proposed a novel deep-learning framework for classifying several medical imaging modalities. In the training phase of the deep learning models, data augmentation is performed at the first stage on all selected datasets. After that, two novel custom deep learning architectures were introduced, called the Inverted Residual Convolutional Neural Network (IRCNN) and Self Attention CNN (SACNN). Both models are trained on the augmented datasets with manual hyperparameter selection. Each dataset's testing images are used to extract features during the testing stage. The extracted features are fused using a modified serial fusion with a strong correlation approach. An optimization algorithm- slap swarm controlled standard Error mean (SScSEM) has been employed, and the best features that passed to the shallow wide neural network (SWNN) classifier for the final classification have been selected. GradCAM, an explainable artificial intelligence (XAI) approach, analyzes custom models. The proposed architecture was tested on five publically available datasets of different imaging modalities and obtained improved accuracy of 98.6 (INBreast), 95.3 (KVASIR), 94.3 (ISIC2018), 95.0 (Lung Cancer), and 98.8% (Oral Cancer), respectively. A detailed comparison is conducted based on precision and accuracy, showing that the proposed architecture performs better. The implemented models are available on GitHub ( https://github.com/ComputerVisionLabPMU/ScientificImagingPaper.git ).

SNUH methylation classifier for CNS tumors

BACKGROUND

Methylation profiling of central nervous system (CNS) tumors, pioneered by the German Cancer Research Center, has significantly improved diagnostic accuracy. This study aimed to further enhance the performance of methylation classifiers by leveraging publicly available data and innovative machine-learning techniques.

RESULTS

Seoul National University Hospital Methylation Classifier (SNUH-MC) addressed data imbalance using the Synthetic Minority Over-sampling Technique (SMOTE) algorithm and incorporated OpenMax within a Multi-Layer Perceptron to prevent labeling errors in low-confidence diagnoses. Compared to two published CNS tumor methylation classification models (DKFZ-MC: Deutsches Krebsforschungszentrum Methylation Classifier v11b4: RandomForest, 767-MC: Multi-Layer Perceptron), our SNUH-MC showed improved performance in F1-score. For 'Filtered Test Data Set 1,' the SNUH-MC achieved higher F1-micro (0.932) and F1-macro (0.919) scores compared to DKFZ-MC v11b4 (F1-micro: 0.907, F1-macro: 0.627). We evaluated the performance of three classifiers; SNUH-MC, DKFZ-MC v11b4, and DKFZ-MC v12.5, using specific criteria. We set established 'Decisions' categories based on histopathology, clinical information, and next-generation sequencing to assess the classification results. When applied to 193 unknown SNUH methylation data samples, SNUH-MC notably improved diagnosis compared to DKFZ-MC v11b4. Specifically, 17 cases were reclassified as 'Match' and 34 cases as 'Likely Match' when transitioning from DKFZ-MC v11b4 to SNUH-MC. Additionally, SNUH-MC demonstrated similar results to DKFZ-MC v12.5 for 23 cases that were unclassified by v11b4.

CONCLUSIONS

This study presents SNUH-MC, an innovative methylation-based classification tool that significantly advances the field of neuropathology and bioinformatics. Our classifier incorporates cutting-edge techniques such as the SMOTE and OpenMax resulting in improved diagnostic accuracy and robustness, particularly when dealing with unknown or noisy data.

A foundation model for generalizable cancer diagnosis and survival prediction from histopathological images

Computational pathology, utilizing whole slide images (WSIs) for pathological diagnosis, has advanced the development of intelligent healthcare. However, the scarcity of annotated data and histological differences hinder the general application of existing methods. Extensive histopathological data and the robustness of self-supervised models in small-scale data demonstrate promising prospects for developing foundation pathology models. Here we show BEPH (BEiT-based model Pre-training on Histopathological image), a foundation model that leverages self-supervised learning to learn meaningful representations from 11 million unlabeled histopathological images. These representations are then efficiently adapted to various tasks, including patch-level cancer diagnosis, WSI-level cancer classification, and survival prediction for multiple cancer subtypes. By leveraging the masked image modeling (MIM) pre-training approach, BEPH offers an efficient solution to enhance model performance, reduce the reliance on expert annotations, and facilitate the broader application of artificial intelligence in clinical settings. The pre-trained model is available at https://github.com/Zhcyoung/BEPH .

Emerging molecular testing paradigms in non-small cell lung cancer management-current perspectives and recommendations

Advances in molecular testing and precision oncology have transformed the clinical management of lung cancer, especially non-small cell lung cancer, enhancing diagnosis, treatment, and outcomes. Practical guidelines offer insights into selecting appropriate biomarkers and assays, emphasizing the importance of comprehensive testing. However, real-world data reveal the underutilization of biomarker testing and consequently targeted therapies. Molecular testing often occurs late in diagnosis or not at all in clinical practice, leading to delayed or inadequate treatment. Enhancing precision requires adherence to best practices by all health care professionals involved, which can ultimately improve lung cancer patient outcomes. The future of precision oncology for lung cancer will likely involve a more personalized approach, starting increasingly from earlier disease settings, with novel and more complex targeted therapies, immunotherapies, and combination regimens, and relying on liquid biopsies, muti-detection advanced genomic technologies and data integration, with artificial intelligence as a central orchestrator. This review presents the currently known actionable mutations in lung cancer and new upcoming ones that are likely to enter clinical practice soon and provides an overview of established and emerging concepts in testing methodologies. Challenges are discussed and best practice recommendations are made that are relevant today, will continue to be relevant in the future, and are likely to be relevant for other cancer types too.

Implementing digital pathology: qualitative and financial insights from eight leading European laboratories

Digital Pathology (DP) revolutionizes the diagnostic workflow. Digitized scanned slides enhance operational efficiency by facilitating remote access, slide storage, reporting and automated AI image analysis, and enabling collaboration and research. However, substantial upfront and maintenance costs remain significant barriers to adoption. This study evaluates DP's financial and qualitative value, exploring whether the long-term financial benefits justify investments and addressing implementation challenges in large public and private European laboratory settings. A targeted literature review, semi-structured interviews, surveys, and a net present value (NPV) model were employed to assess DP's impact on clinical practice and laboratory financials. Qualitative findings validate the key benefits of DP, including optimized workflow, enhanced logistics, and improved laboratory organization. Pathologists reported a smooth integration, improved training, teaching, and research capabilities, and increased flexibility through remote work. Collaboration within multidisciplinary teams was strengthened, while case examination efficiency and access to archival slides were notably improved. Quantitative results indicate that DP demonstrates strong financial potential, achieving cost recovery within 6 years. DP investment results in a 7-year NPV of + €0.21 million (m) driven by increased productivity and diagnosis volumes. Although the high upfront costs for scanners, training, and system integration pose a significant barrier to the adoption of DP, larger institutions are better positioned to leverage economies of scale. This study underscores the importance of sustained financial support to cope with the initial investment and regional collaboration in driving widespread adoption of DP. Expanding reimbursement policies for pathology procedures could significantly reduce financial barriers.

Role of AI in empowering and redefining the oncology care landscape: perspective from a developing nation

Early diagnosis and accurate prognosis play a pivotal role in the clinical management of cancer and in preventing cancer-related mortalities. The burgeoning population of Asia in general and South Asian countries like India in particular pose significant challenges to the healthcare system. Regrettably, the demand for healthcare services in India far exceeds the available resources, resulting in overcrowded hospitals, prolonged wait times, and inadequate facilities. The scarcity of trained manpower in rural settings, lack of awareness and low penetrance of screening programs further compounded the problem. Artificial Intelligence (AI), driven by advancements in machine learning, deep learning, and natural language processing, can profoundly transform the underlying shortcomings in the healthcare industry, more for populous nations like India. With about 1.4 million cancer cases reported annually and 0.9 million deaths, India has a significant cancer burden that surpassed several nations. Further, India's diverse and large ethnic population is a data goldmine for healthcare research. Under these circumstances, AI-assisted technology, coupled with digital health solutions, could support effective oncology care and reduce the economic burden of GDP loss in terms of years of potential productive life lost (YPPLL) due to India's stupendous cancer burden. This review explores different aspects of cancer management, such as prevention, diagnosis, precision treatment, prognosis, and drug discovery, where AI has demonstrated promising clinical results. By harnessing the capabilities of AI in oncology research, healthcare professionals can enhance their ability to diagnose cancers at earlier stages, leading to more effective treatments and improved patient outcomes. With continued research and development, AI and digital health can play a transformative role in mitigating the challenges posed by the growing population and advancing the fight against cancer in India. Moreover, AI-driven technologies can assist in tailoring personalized treatment plans, optimizing therapeutic strategies, and supporting oncologists in making well-informed decisions. However, it is essential to ensure responsible implementation and address potential ethical and privacy concerns associated with using AI in healthcare.

Association between intraoperative electroencephalograph complexity index and postoperative delirium in elderly patients undergoing orthopedic surgery: a prospective cohort study

PURPOSE

The primary method for predicting POD (postoperative confusion) relies on the analysis of clinical features. Brain activity complexity is a promising factor associated with the state of consciousness. The aim of this study was to investigate the role of EEG (electroencephalography) complexity changes in predicting POD in elderly patients undergoing orthopedic surgery.

METHODS

From January 2024 to August 2024, 289 elderly patients undergoing orthopedic surgery were recruited at the Second Affiliated Hospital of Nanjing Medical University. Intraoperative EEG data from patients were collected and then EEG nonlinear features were extracted by MATLAB custom scripts. The logistic regression and CNN (convolutional neural networks) were used to explore the predictive effect of nonlinear features on POD from both static and dynamic perspectives.

RESULTS

Low permutation Lempel-Ziv complexity (PLZC) among the EEG nonlinear features emerged as an independent risk factor for POD [OR = 0.210; 95% CI (0.050-0.850); p = 0.029]. Receiver operating characteristic curve (ROC) analysis revealed a poor area under the curve of 0.615 (95% CI 0.517-0.711) for PLZC in predicting POD. After the inclusion of temporal factors, the ROC analysis indicated that the EEG nonlinear indices had a moderate predictive effect on POD [AUC = 0.701; (95% CI 0.541-0.862)].

CONCLUSIONS

EEG nonlinear feature indices may be effective biomarkers for POD and could help predict POD in elderly patients undergoing orthopedic surgery.

A Thorough Review of the Clinical Applications of Artificial Intelligence in Lung Cancer

According to data from the World Health Organization (WHO), lung cancer is becoming a global epidemic. It is particularly high in the list of the leading causes of death not only in developed countries, but also worldwide; furthermore, it holds the leading place in terms of cancer-related mortality. Nevertheless, many breakthroughs have been made the last two decades regarding its management, with one of the most prominent being the implementation of artificial intelligence (AI) in various aspects of disease management. We included 473 papers in this thorough review, most of which have been published during the last 5-10 years, in order to describe these breakthroughs. In screening programs, AI is capable of not only detecting suspicious lung nodules in different imaging modalities-such as chest X-rays, computed tomography (CT), and positron emission tomography (PET) scans-but also discriminating between benign and malignant nodules as well, with success rates comparable to or even better than those of experienced radiologists. Furthermore, AI seems to be able to recognize biomarkers that appear in patients who may develop lung cancer, even years before this event. Moreover, it can also assist pathologists and cytologists in recognizing the type of lung tumor, as well as specific histologic or genetic markers that play a key role in treating the disease. Finally, in the treatment field, AI can guide in the development of personalized options for lung cancer patients, possibly improving their prognosis.

Transformer-Based Multilabel Deep Learning Model Is Efficient for Detecting Ankle Lateral and Medial Ligament Injuries on Magnetic Resonance Imaging and Improving Clinicians' Diagnostic Accuracy for Rotational Chronic Ankle Instability

PURPOSE

To develop a deep learning (DL) model that can simultaneously detect lateral and medial collateral ligament injuries of the ankle, aiding in the diagnosis of chronic ankle instability (CAI), and assess its impact on clinicians' diagnostic performance.

METHODS

DL models were developed and externally validated on retrospectively collected ankle magnetic resonance imaging (MRI) between April 2016 and March 2022 respectively at 3 centers. Included patients had confirmed diagnoses of CAI through arthroscopy, as well as individuals who had undergone MRI and physical examinations that ruled out ligament injuries. DL models were constructed based on a multilabel paradigm. A transformer-based multilabel DL model (AnkleNet) was developed and compared with 4 convolution neural network (CNN) models. Subsequently, a reader study was conducted to evaluate the impact of model assistance on clinicians when diagnosing challenging cases: identifying rotational CAI (RCAI). Diagnostic performance was assessed using area under the receiver operating characteristic curve (AUC).

RESULTS

Our transformer-based model achieved AUCs of 0.910 and 0.892 for detecting lateral and medial collateral ligament injury, respectively, both of which were significantly higher than those of CNN-based models (all P < .001). In terms of further CAI diagnosis, there was a macro-average AUC of 0.870 and a balanced accuracy of 0.805. The reader study indicated that incorporation with our model significantly enhanced the diagnostic accuracy of clinicians (P = .042), particularly junior clinicians, and led to a reduction in diagnostic variability. The code of the model can be accessed at https://github.com/ChiariRay/AnkleNet.

CONCLUSIONS

Our transformer-based model was able to detect lateral and medial collateral ligament injuries based on MRI and outperformed CNN-based models, demonstrating a promising performance in diagnosing CAI, especially patients with RCAI.

CLINICAL RELEVANCE

Developing such an algorithm can improve the diagnostic performance of clinicians, aiding in identifying patients who would benefit from arthroscopy, such as patients with RCAI.

Artificial intelligence can be trained to predict c-KIT-11 mutational status of canine mast cell tumors from hematoxylin and eosin-stained histological slides

Numerous prognostic factors are currently assessed histologically and immunohistochemically in canine mast cell tumors (MCTs) to evaluate clinical behavior. In addition, polymerase chain reaction (PCR) is often performed to detect internal tandem duplication (ITD) mutations in exon 11 of the c-KIT gene (c-KIT-11-ITD) to predict the therapeutic response to tyrosine kinase inhibitors. This project aimed at training deep learning models (DLMs) to identify MCTs with c-KIT-11-ITD solely based on morphology. Hematoxylin and eosin (HE) stained slides of 368 cutaneous, subcutaneous, and mucocutaneous MCTs (195 with ITD and 173 without) were stained consecutively in 2 different laboratories and scanned with 3 different slide scanners. This resulted in 6 data sets (stain-scanner variations representing diagnostic institutions) of whole-slide images. DLMs were trained with single and mixed data sets and their performances were assessed under stain-scanner variations (domain shifts). The DLM correctly classified HE slides according to their c-KIT-11-ITD status in up to 87% of cases with a 0.90 sensitivity and a 0.83 specificity. A relevant performance drop could be observed when the stain-scanner combination of training and test data set differed. Multi-institutional data sets improved the average accuracy but did not reach the maximum accuracy of algorithms trained and tested on the same stain-scanner variant (ie, intra-institutional). In summary, DLM-based morphological examination can predict c-KIT-11-ITD with high accuracy in canine MCTs in HE slides. However, staining protocol and scanner type influence accuracy. Larger data sets of scans from different laboratories and scanners may lead to more robust DLMs to identify c-KIT mutations in HE slides.

Artificial intelligence-based biomarkers for treatment decisions in oncology

The development of new therapeutic strategies such as immune checkpoint inhibitors (ICIs) and targeted therapies has increased the complexity of the treatment landscape for solid tumors. At the current rate of annual FDA approvals, the potential treatment options could increase by tenfold over the next 5 years. The cost of personalized medicine technologies limits its accessibility, thus increasing socioeconomic disparities in the treated population. In this review we describe artificial intelligence (AI)-based solutions - including deep learning (DL) methods for routine medical imaging and large language models (LLMs) for electronic health records (EHRs) - to support cancer treatment decisions with cost-effective biomarkers. We address the current limitations of these technologies and propose the next steps towards their adoption in routine clinical practice.

Generation of synthetic whole-slide image tiles of tumours from RNA-sequencing data via cascaded diffusion models

Training machine-learning models with synthetically generated data can alleviate the problem of data scarcity when acquiring diverse and sufficiently large datasets is costly and challenging. Here we show that cascaded diffusion models can be used to synthesize realistic whole-slide image tiles from latent representations of RNA-sequencing data from human tumours. Alterations in gene expression affected the composition of cell types in the generated synthetic image tiles, which accurately preserved the distribution of cell types and maintained the cell fraction observed in bulk RNA-sequencing data, as we show for lung adenocarcinoma, kidney renal papillary cell carcinoma, cervical squamous cell carcinoma, colon adenocarcinoma and glioblastoma. Machine-learning models pretrained with the generated synthetic data performed better than models trained from scratch. Synthetic data may accelerate the development of machine-learning models in scarce-data settings and allow for the imputation of missing data modalities.

Hallmarks of artificial intelligence contributions to precision oncology

The integration of artificial intelligence (AI) into oncology promises to revolutionize cancer care. In this Review, we discuss ten AI hallmarks in precision oncology, organized into three groups: (1) cancer prevention and diagnosis, encompassing cancer screening, detection and profiling; (2) optimizing current treatments, including patient outcome prediction, treatment planning and monitoring, clinical trial design and matching, and developing response biomarkers; and (3) advancing new treatments by identifying treatment combinations, discovering cancer vulnerabilities and designing drugs. We also survey AI applications in interventional clinical trials and address key challenges to broader clinical adoption of AI: data quality and quantity, model accuracy, clinical relevance and patient benefit, proposing actionable solutions for each.

Differentiating Separate Primary Lung Adenocarcinomas From Intrapulmonary Metastases With Emphasis on Pathological and Molecular Considerations: Recommendations From the International Association for the Study of Lung Cancer Pathology Committee

INTRODUCTION

With the implementation of low-dose computed tomography screening, multiple pulmonary tumor nodules are diagnosed with increasing frequency and the selection of surgical treatments versus systemic therapies has become challenging on a daily basis in clinical practice. In the presence of multiple carcinomas, especially adenocarcinomas, pathologically determined to be of pulmonary origin, the distinction between separate primary lung carcinomas (SPLCs) and intrapulmonary metastases (IPMs) is important for staging, management, and prognostication.

METHODS

We systemically reviewed various means that aid in the differentiation between SPLCs and IPMs explored by histopathologic evaluation and molecular profiling, the latter includes DNA microsatellite analysis, array comparative genomic hybridization, TP53 and oncogenic driver mutation testing and, more recently, with promising effectiveness, next-generation sequencing comprising small- or large-scale multi-gene panels.

RESULTS

Comprehensive histologic evaluation may suffice to differentiate between SPLCs and IPMs. Nevertheless, molecular profiling using larger-scale next-generation sequencing typically provides superior discriminatory power, allowing for more accurate classification. On the basis of the literature review and expert opinions, we proposed a combined four-step histologic and molecular classification algorithm for addressing multiple pulmonary tumor nodules of adenocarcinoma histology that encourages a multidisciplinary approach. It is also noteworthy that new technologies combining machine learning and digital pathology may develop into valuable diagnostic tools for distinguishing SPLCs from IPMs in the future.

CONCLUSIONS

Although histopathologic evaluation is often adequate to differentiate SPLCs from IPMs, molecular profiling should be performed when possible, especially in cases with tumors exhibiting similar morphology. This manuscript summarized the previous efforts in resolving the current challenges and highlighted the recent progress in the differentiation methods and algorithms used in categorizing multiple lung adenocarcinomas into SPLCs or IPMs, which are becoming more and more critical in precision lung cancer management.

Novel Computational Pipeline Enables Reliable Diagnosis of Inverted Urothelial Papilloma and Distinguishes It From Urothelial Carcinoma

PURPOSE

With the aid of ever-increasing computing resources, many deep learning algorithms have been proposed to aid in diagnostic workup for clinicians. However, existing studies usually selected informative patches from whole-slide images for the training of the deep learning model, requiring labor-intensive labeling efforts. This work aimed to improve diagnostic accuracy through the statistic features extracted from hematoxylin and eosin-stained slides.

METHODS

We designed a computational pipeline for the diagnosis of inverted urothelial papilloma (IUP) of the bladder from its cancer mimics using statistical features automatically extracted from whole-slide images. Whole-slide images from 225 cases of common and uncommon urothelial lesions (64 IUPs; 69 inverted urothelial carcinomas [UCInvs], and 92 low-grade urothelial carcinoma [UCLG]) were analyzed.

RESULTS

We identified 68 image features in total that were significantly different between IUP and UCInv and 42 image features significantly different between IUP and UCLG. Our method integrated multiple types of image features and achieved high AUCs (the AUCs) of 0.913 and 0.920 for classifying IUP from UCInv and conventional UC, respectively. Moreover, we constructed an ensemble classifier to test the prediction accuracy of IUP from an external validation cohort, which provided a new workflow to diagnose rare cancer subtypes and test the models with limited validation samples.

CONCLUSION

Our data suggest that the proposed computational pipeline can robustly and accurately capture histopathologic differences between IUP and other UC subtypes. The proposed workflow and related findings have the potential to expand the clinician's armamentarium for accurate diagnosis of urothelial malignancies and other rare tumors.

Colorectal cancer classification using weakly annotated whole slide images: Multiple instance learning optimization study

Colorectal cancer (CRC) is considered one of the most deadly cancer types nowadays. It is rapidly increasing due to many factors, such as unhealthy lifestyles, water and food pollution, aging, and medical diagnosis development. Detecting CRC in its early stages can help stop its growth by providing the necessary treatments, thereby saving many people's lives. There are various tests that doctors can perform to diagnose CRC; however, biopsy using histopathological images is considered the "gold standard" for CRC diagnosis. Deep learning techniques can now be leveraged to build computer-aided diagnosis (CAD) systems that can affirm if an input sample shows any symptoms of cancer and determine its stage and location with an acceptable degree of confidence. In this research, we utilize deep learning to study the CRC classification problem using weakly annotated histopathological whole slide images (WSIs). We relax the constraints of the multiple instance learning (MIL) algorithm and primarily propose WSI-label prediction functions to be integrated with MIL, which significantly enhances the performance of WSI-level classification. We also applied efficient preprocessing techniques that output a computationally power-efficient dataset representation and performed multiple experiments to compose the most efficient CAD system. Our study introduces a notable improvement over the results obtained by the baseline research where we achieved an accuracy of 93.05% compared to 84.17%. Furthermore, our results using only the weakly annotated WSIs outperformed the baseline results that are based on performing initial pre-training using a strongly annotated part of the dataset.

A novel approach for estimating postmortem intervals under varying temperature conditions using pathology images and artificial intelligence models

Estimating the postmortem interval (PMI) is a critical yet complex task in forensic investigations, with accurate and timely determination playing a key role in case resolution and legal outcomes. Traditional methods often suffer from environmental variability and subjective biases, emphasizing the need for more reliable and objective approaches. In this study, we present a novel predictive model for PMI estimation, introduced here for the first time, that leverages pathological tissue images and artificial intelligence (AI). The model is designed to perform under three temperature conditions: 25 °C, 37 °C, and 4 °C. Using a ResNet50 neural network, patch-level images were analyzed to extract deep learning-derived features, which were integrated with machine learning algorithms for whole slide image (WSI) classification. The model achieved strong performance, with micro and macro AUC values of at least 0.949 at the patch-level and 0.800 at the WSI-level in both training and testing sets. In external validation, micro and macro AUC values at the patch-level exceeded 0.960. These results highlight the potential of AI to improve the accuracy and efficiency of PMI estimation. As AI technology continues to advance, this approach holds promise for enhancing forensic investigations and supporting more precise case resolutions.

Diagnosis of Lung Cancer Using Endobronchial Ultrasonography Image Based on Multi-Scale Image and Multi-Feature Fusion Framework

Lung cancer is the leading cause of cancer-related deaths globally and ranks among the most common cancer types. Given its low overall five-year survival rate, early diagnosis and timely treatment are essential to improving patient outcomes. In recent years, advances in computer technology have enabled artificial intelligence to make groundbreaking progress in imaging-based lung cancer diagnosis. The primary aim of this study is to develop a computer-aided diagnosis (CAD) system for lung cancer using endobronchial ultrasonography (EBUS) images and deep learning algorithms to facilitate early detection and improve patient survival rates. We propose M3-Net, which is a multi-branch framework that integrates multiple features through an attention-based mechanism, enhancing diagnostic performance by providing more comprehensive information for lung cancer assessment. The framework was validated on a dataset of 95 patient cases, including 13 benign and 82 malignant cases. The dataset comprises 1140 EBUS images, with 540 images used for training, and 300 images each for the validation and test sets. The evaluation yielded the following results: accuracy of 0.76, F1-score of 0.75, AUC of 0.83, PPV of 0.80, NPV of 0.75, sensitivity of 0.72, and specificity of 0.80. These findings indicate that the proposed attention-based multi-feature fusion framework holds significant potential in assisting with lung cancer diagnosis.

Realizing the promise of machine learning in precision oncology: expert perspectives on opportunities and challenges

BACKGROUND

The ability of machine learning (ML) to process and learn from large quantities of heterogeneous patient data is gaining attention in the precision oncology community. Some remarkable developments have taken place in the domain of image classification tasks in areas such as digital pathology and diagnostic radiology. The application of ML approaches to the analysis of DNA data, including tumor-derived genomic profiles, microRNAs, and cancer epigenetic signatures, while relatively more recent, has demonstrated some utility in identifying driver variants and molecular signatures with possible prognostic and therapeutic applications.

METHODS

We conducted semi-structured interviews with academic and clinical experts to capture the status quo, challenges, opportunities, ethical implications, and future directions.

RESULTS

Our participants agreed that machine learning in precision oncology is in infant stages, with clinical integration still rare. Overall, participants equated ongoing developments with better clinical workflows and improved treatment decisions for more cancer patients. They underscored the ability of machine learning to tackle the dynamic nature of cancer, break down the complexity of molecular data, and support decision-making. Our participants emphasized obstacles related to molecular data access, clinical utility, and guidelines. The availability of reliable and well-curated data to train and validate machine learning algorithms and integrate multiple data sources were described as constraints yet necessary for future clinical implementation. Frequently mentioned ethical challenges included privacy risks, equity, explainability, trust, and incidental findings, with privacy being the most polarizing. While participants recognized the issue of hype surrounding machine learning in precision oncology, they agreed that, in an assistive role, it represents the future of precision oncology.

CONCLUSIONS

Given the unique nature of medical AI, our findings highlight the field's potential and remaining challenges. ML will continue to advance cancer research and provide opportunities for patient-centric, personalized, and efficient precision oncology. Yet, the field must move beyond hype and toward concrete efforts to overcome key obstacles, such as ensuring access to molecular data, establishing clinical utility, developing guidelines and regulations, and meaningfully addressing ethical challenges.

A High-Resolution Digital Pathological Image Staining Style Transfer Model Based on Gradient Guidance

Digital pathology images have long been regarded as the gold standard for cancer diagnosis in clinical medicine. A highly generalized digital pathological image diagnosis system can provide strong support for cancer diagnosis, help to improve the diagnostic efficiency and accuracy of doctors, and has important research value. The whole slide image of different centers can lead to very large staining differences due to different scanners and dyes, which pose a challenge to the generalization performance of the model application in multi-center data testing. In order to achieve the normalization of multi-center data, this paper proposes a style transfer algorithm based on an adversarial generative network for high-resolution images. The gradient-guided dye migration model proposed in this paper introduces a gradient-enhanced regularized term in the loss function design of the algorithm. A style transfer algorithm was applied to the source data, and the diagnostic performance of the multi-example learning model based on the domain data was significantly improved by validation in the pathological image datasets of two centers. The proposed method improved the AUC of the best classification model from 0.8856 to 0.9243, and another set of experiments improved the AUC from 0.8012 to 0.8313.

Self supervised artificial intelligence predicts poor outcome from primary cutaneous squamous cell carcinoma at diagnosis

Primary cutaneous squamous cell carcinoma (cSCC) is responsible for ~10,000 deaths annually in the United States. Stratification of risk of poor outcome at initial biopsy would significantly impact clinical decision-making during the initial post operative period where intervention has been shown to be most effective. Using whole-slide images (WSI) from 163 patients from 3 institutions, we developed a self supervised deep-learning model to predict poor outcomes in cSCC patients from histopathological features at initial diagnosis, and validated it using WSI from 563 patients, collected from two other academic institutions. For disease-free survival prediction, the model attained a concordance index of 0.73 in the development cohort and 0.84 in the Mayo cohort. The model's interpretability revealed that features like poor differentiation and deep invasion were strongly associated with poor prognosis. Furthermore, the model is effective in stratifying risk among BWH T2a and AJCC T2, known for outcome heterogeneity.

Unraveling immune heterogeneity across pan-cancer and deep insights in lung adenocarcinoma based on alternative splicing

Alternative splicing (AS) participates in tumor development and tumor microenvironment formation. However, the landscape of immune-infiltrating AS events in pan-cancer and mechanisms of AS in lung adenocarcinoma (LUAD) have not been comprehensively characterized. We systematically profiled the immune-infiltrating AS event landscape of pan-cancer using data from The Cancer Genome Atlas, analyzing both commonalities and specific characteristics among different cancer types. We found that AS events tend to occur specifically in one cancer type rather than in multiple cancer types. AS events were used to classify 512 LUAD samples into 2 subtypes by unsupervised clustering: the aberrant splicing subtype and the immune-infiltrating subtype. The 2 subtypes showed significant differences in clinicopathology, prognosis, transcriptomics, genomics, and immune microenvironment. We constructed a classification signature comprising 10 genes involved in 14 AS events using logistic regression. The robustness of the signature was validated in 3 independent datasets using survival analysis. To explore AS mechanisms in LUAD, we constructed subtype-specific coexpression networks using Pearson correlation analysis. AS event of AKT3 regulated by splicing factor ENOX1 was associated with poor prognosis in LUAD. Overall, we outline AS events associated with immune infiltration in pan-cancer, and this study provides insights into AS mechanisms in LUAD patient classification.