Predicting breast cancer types on and beyond molecular level in a multi-modal fashion

Frozen Large-Scale Pretrained Vision-Language Models are the Effective Foundational Backbone for Multimodal Breast Cancer Prediction

Breast cancer is a pervasive global health concern among women. Leveraging multimodal data from enterprise patient databases-including Picture Archiving and Communication Systems (PACS) and Electronic Health Records (EHRs)-holds promise for improving prediction. This study introduces a multimodal deep-learning model leveraging mammogram datasets to evaluate breast cancer prediction. Our approach integrates frozen large-scale pretrained vision-language models, showcasing superior performance and stability compared to traditional image-tabular models across two public breast cancer datasets. The model consistently outperforms conventional full fine-tuning methods by using frozen pretrained vision-language models alongside a lightweight trainable classifier. The observed improvements are significant. In the CBIS-DDSM dataset, the Area Under the Curve (AUC) increases from 0.867 to 0.902 during validation and from 0.803 to 0.830 for the official test set. Within the EMBED dataset, AUC improves from 0.780 to 0.805 during validation. In scenarios with limited data, using Breast Imaging-Reporting and Data System category three (BI-RADS 3) cases, AUC improves from 0.91 to 0.96 on the official CBIS-DDSM test set and from 0.79 to 0.83 on a challenging validation set. This study underscores the benefits of vision-language models in jointly training diverse image-clinical datasets from multiple healthcare institutions, effectively addressing challenges related to non-aligned tabular features. Combining training data enhances breast cancer prediction on the EMBED dataset, outperforming all other experiments. In summary, our research emphasizes the efficacy of frozen large-scale pretrained vision-language models in multimodal breast cancer prediction, offering superior performance and stability over conventional methods, reinforcing their potential for breast cancer prediction.

A large model for non-invasive and personalized management of breast cancer from multiparametric MRI

Breast Magnetic Resonance Imaging (MRI) demonstrates the highest sensitivity for breast cancer detection among imaging modalities and is standard practice for high-risk women. Interpreting the multi-sequence MRI is time-consuming and prone to subjective variation. We develop a large mixture-of-modality-experts model (MOME) that integrates multiparametric MRI information within a unified structure, leveraging breast MRI scans from 5205 female patients in China for model development and validation. MOME matches four senior radiologists' performance in identifying breast cancer and outperforms a junior radiologist. The model is able to reduce unnecessary biopsies in Breast Imaging-Reporting and Data System (BI-RADS) 4 patients, classify triple-negative breast cancer, and predict pathological complete response to neoadjuvant chemotherapy. MOME further supports inference with missing modalities and provides decision explanations by highlighting lesions and measuring modality contributions. To summarize, MOME exemplifies an accurate and robust multimodal model for noninvasive, personalized management of breast cancer patients via multiparametric MRI.

Artificial intelligence-assisted multimodal imaging for the clinical applications of breast cancer: a bibliometric analysis

BACKGROUND

Breast cancer (BC) remains a leading cause of cancer-related mortality among women globally, with increasing incidence rates posing significant public health challenges. Recent advancements in artificial intelligence (AI) have revolutionized medical imaging, particularly in enhancing diagnostic accuracy and prognostic capabilities for BC. While multimodal imaging combined with AI has shown remarkable potential, a comprehensive analysis is needed to synthesize current research and identify emerging trends and hotspots in AI-assisted multimodal imaging for BC.

METHODS

This study analyzed literature on AI-assisted multimodal imaging in BC from January 2010 to November 2024 in Web of Science Core Collection (WoSCC). Bibliometric and visualization tools, including VOSviewer, CiteSpace, and the Bibliometrix R package, were employed to assess countries, institutions, authors, journals, and keywords.

RESULTS

A total of 80 publications were included, revealing a steady increase in annual publications and citations, with a notable surge post-2021. China led in productivity and citations, while Germany exhibited the highest citation average. The United States demonstrated the strongest international collaboration. The most productive institution and author are Radboud University Nijmegen and Xi, Xiaoming. Publications were predominantly published in Computerized Medical Imaging and Graphics, with Qian, XJ's 2021 study on BC risk prediction under deep learning frameworks being the most influential. Keyword analysis highlighted themes such as "breast cancer", "classification", and "deep learning".

CONCLUSIONS

AI-assisted multimodal imaging has significantly advanced BC diagnosis and management, with promising future developments. This study offers researchers a comprehensive overview of current frameworks and emerging research directions. Future efforts are expected to focus on improving diagnostic precision and refining therapeutic strategies through optimized imaging techniques and AI algorithms, emphasizing international collaboration to drive innovation and clinical translation.

Multimodal diagnostic models and subtype analysis for neoadjuvant therapy in breast cancer

Background

Breast cancer, a heterogeneous malignancy, comprises multiple subtypes and poses a substantial threat to women's health globally. Neoadjuvant therapy (NAT), administered prior to surgery, is integral to breast cancer treatment strategies. It aims to downsize tumors, optimize surgical outcomes, and evaluate tumor responsiveness to treatment. However, accurately predicting NAT efficacy remains challenging due to the disease's complexity and the diverse responses across different molecular subtypes.

Methods

In this study, we harnessed multimodal data, including proteomic, genomic, MRI imaging, and clinical information, sourced from multiple cohorts such as I-SPY2, TCGA-BRCA, GSE161529, and METABRIC. Post data preprocessing, Lasso regression was utilized for feature extraction and selection. Five machine learning algorithms were employed to construct diagnostic models, with pathological complete response (pCR) as the predictive endpoint.

Results

Our results revealed that the multi-omics Ridge regression model achieved the optimal performance in predicting pCR, with an AUC of 0.917. Through unsupervised clustering using the R package MOVICS and nine clustering algorithms, we identified four distinct multimodal breast cancer subtypes associated with NAT. These subtypes exhibited significant differences in proteomic profiles, hallmark cancer gene sets, pathway activities, tumor immune microenvironments, transcription factor activities, and clinical characteristics. For instance, CS1 subtype, predominantly ER-positive, had a low pCR rate and poor response to chemotherapy drugs, while CS4 subtype, characterized by high immune infiltration, showed a better response to immunotherapy. At the single-cell level, we detected significant heterogeneity in the tumor microenvironment among the four subtypes. Malignant cells in different subtypes displayed distinct copy number variations, differentiation levels, and evolutionary trajectories. Cell-cell communication analysis further highlighted differential interaction patterns among the subtypes, with implications for tumor progression and treatment response.

Conclusion

Our multimodal diagnostic model and subtype analysis provide novel insights into predicting NAT efficacy in breast cancer. These findings hold promise for guiding personalized treatment strategies. Future research should focus on experimental validation, in-depth exploration of the underlying mechanisms, and extension of these methods to other cancers and treatment modalities.

Enhanced Multi-Class Breast Cancer Classification from Whole-Slide Histopathology Images Using a Proposed Deep Learning Model

Background/Objectives: Breast cancer is among the most frequently diagnosed cancers and leading cause of mortality worldwide. The accurate classification of breast cancer from the histology photographs is very important for the diagnosis and effective treatment planning. Methods: In this article, we propose a DenseNet121-based deep learning model for breast cancer detection and multi-class classification. The experiments were performed using whole-slide histopathology images collected from the BreakHis dataset. Results: The proposed method attained state-of-the-art performance with a 98.50% accuracy and an AUC of 0.98 for the binary classification. In multi-class classification, it obtained competitive results with 92.50% accuracy and an AUC of 0.94. Conclusions: The proposed model outperforms state-of-the-art methods in distinguishing between benign and malignant tumors as well as in classifying specific malignancy subtypes. This study highlights the potential of deep learning in breast cancer diagnosis and establishes the foundation for developing advanced diagnostic tools.

A diagnostic test of two-dimensional ultrasonic feature extraction based on artificial intelligence combined with blood flow Adler classification and contrast-enhanced ultrasound for predicting HER-2-positive breast cancer

Background

Human epidermal growth factor receptor 2 (HER-2) was an important driver gene for breast cancer which had high degree of malignancy and poor prognosis. Ultrasonography was an important imaging method for the diagnosis of breast cancer, but its diagnostic efficacy of HER-2-positive breast cancer was not satisfactory. To assess the predictive value of two-dimensional ultrasonic feature extraction based on artificial intelligence (AI) combined with blood flow Adler classification and contrast-enhanced ultrasound (CEUS) for HER-2-positive breast cancer, we compared the value of the area under the receiver operating characteristic (ROC) curve (AUC) of the combined diagnosis model and single-factor models.

Methods

A retrospective analysis was performed on 140 patients (88 HER-2-positive and 52 HER-2-negative). These patients were divided into internal test samples and external validation samples in a ratio of 7:3 randomly. The two samples were divided into HER-2-positive group and HER-2-negative group. All the patients were examined by two-dimensional ultrasound, color Doppler ultrasound, and CEUS, and AI was used to extract two-dimensional ultrasonic image features. Features of two-dimensional ultrasound included not parallel to the skin, irregular shape, unclear boundary, posterior echo attenuated, solid or cystic-solid mixed, microcalcification or coarse calcification were treated as HER-2-positive. Levels of Doppler ultrasound included level 3 and level 4 were treated as HER-2-positive. Features of CEUS included high enhancement, fast forward, centrifugal or diffuse, uneven, lesion range increased after CEUS, with perforating branches, unclear nodule boundary after CEUS were treated as HER-2-positive. The ultrasonography characteristics in different ultrasonography methods were analyzed, the parameters with statistically significant differences between groups of internal test samples were incorporated to establish a joint diagnosis model. The sensitivity, specificity and accuracy of the combined diagnosis model and single-factor models were calculated, the ROC curve was drawn to evaluate the diagnostic efficacy of the combined diagnosis model.

Results

Long diameter direction, Adler grade of blood flow, contrast agent distribution characteristics, and nodule boundary after CEUS were statistically significant different between the positive and negative groups in internal test and external validation samples (P<0.05). The sensitivity, specificity, accuracy of the combined diagnosis model were significantly higher than single-parameter diagnosis method both in internal test and external validation samples, and the kappa values of combined diagnosis model were highest. The AUC of the combined diagnosis model of internal test and external validation samples was 0.861 and 0.969, which was significantly higher (P<0.05) than that in the long diameter direction (0.717 and 0.732), blood flow Adler grade (0.674 and 0.786), CEUS distribution characteristics (0.666 and 0.750), and the nodule boundary after CEUS (0.684 and 0.786).

Conclusions

The combined diagnosis model based on two-dimensional ultrasonic feature extraction, blood flow, and CEUS can effectively predict the expression of HER-2 in breast cancer.

Preoperative Prediction of Axillary Lymph Node Metastasis in Patients With Breast Cancer Through Multimodal Deep Learning Based on Ultrasound and Magnetic Resonance Imaging Images

RATIONALE AND OBJECTIVES

Deep learning can enhance the performance of multimodal image analysis, which is known for its noninvasive attributes and complementary efficacy, in predicting axillary lymph node (ALN) metastasis. Therefore, we established a multimodal deep learning model incorporating ultrasound (US) and magnetic resonance imaging (MRI) images to predict ALN metastasis in patients with breast cancer.

MATERIALS AND METHODS

A retrospective cohort of patients with histologically confirmed breast cancer from two hospitals composed of the primary cohort (n = 465) and the external validation cohort (n = 123). All patients had undergone both preoperative US and MRI scans. After data preprocessing, three convolutional neural network models were used to analyze the US and MRI images, respectively. After integrating the US and MRI deep learning prediction results (DLUS and DLMRI, respectively), a multimodal deep learning (DLMRI+US+Clinical parameter) model was constructed. The predictive ability of the proposed model was compared to that of the DLUS, DLMRI, combined bimodal (DLMRI+US), and clinical parameter models. Evaluation was performed using the area under the receiver operating characteristic curves (AUCs) and decision curves.

RESULTS

A total of 588 patients with breast cancer participated in this study. The DLMRI+US+Clinical parameter model outperformed the alternative models, achieving the highest AUCs of 0.819 (95% confidence interval [CI] 0.734-0.903) and 0.809 (95% CI 0.723-0.895) on the internal and external validation sets, respectively. The decision curve analysis confirmed its clinical usefulness.

CONCLUSION

The DLMRI+US＋Clinical parameter model demonstrates the feasibility and reliability of its performance for ALN metastasis prediction in patients with breast cancer.

Impact of Vitamin D Levels on Progression-Free Survival and Response to Neoadjuvant Chemotherapy in Breast Cancer Patients: A Systematic Review and Meta-Analysis

Background: Breast cancer remains the leading cause of cancer-related deaths among women despite advances in early detection. Neoadjuvant chemotherapy (NACT) is now standard for early-stage BC, with vitamin D (VD) emerging as a potential prognostic biomarker considering its positive pleiotropic effects. This review and meta-analysis assess the impact of baseline VD levels on outcomes in BC patients undergoing NACT. Methods: Inclusion criteria required patients to be over 18 years of age, have a pathologically confirmed BC diagnosis, and have their VD levels assessed prior to chemotherapy. Studies were included if they reported odds ratios (ORs) for response and/or hazard ratios (HRs) for PFS with 95% confidence intervals (CIs). A comprehensive literature search of PubMed/MEDLINE and Scopus/ELSEVIER (2014-2024) was conducted, and data were analyzed using fixed- and random-effects models, with Forest plots illustrating the results. Study quality and potential biases were assessed using the MINORS, NOS, and RoB2 scales, and statistical heterogeneity was evaluated with I2 statistics and funnel plots. Results: Six studies were included in the analysis. All studies addressed stages II and III, with three also including stage I. The meta-analysis covered data from 722 patients regarding NACT response and 1033 patients for PFS. The results revealed a 22% reduction in the likelihood of non-response to NACT associated with adequate VD levels (low/deficient VD vs. high/sufficient VD; OR: 0.78; 95% CI: 0.30-1.25; p = 0.001) and a 35% reduction in progression risk with sufficient baseline VD levels (low/deficient VD vs. high/sufficient VD; HR: 0.65; 95% CI: 0.33-0.97; p < 0.001). Conclusions: These findings highlight the significance of maintaining adequate vitamin D levels in BC treatment and encourage further studies to unravel the role of VD on cancer biology.

Imaging phenotype evaluation from digital breast tomosynthesis data: A preliminary study

BACKGROUND

Digital breast tomosynthesis (DBT) has been widely adopted as a supplemental imaging modality for diagnostic evaluation of breast cancer and confirmation studies. In this study, a deep learning-based method for characterizing breast tissue patterns in DBT data is presented.

METHODS

A set of 5388 2D image patches was produced from 230 right mediolateral oblique, 259 left mediolateral oblique, 18 right craniocaudal, and 15 left craniocaudal single-breast DBT studies, using slice-wise annotations of abnormalities and normal tissue. We implemented a patch classifier to predict samples according to two differing scenarios and train it using the patch dataset. First, tissue samples were classified into the following classes: malignant, benign, and normal breast tissue. Second, tissue samples were classified into the following classes: malignant mass, benign mass, benign architectural distortion, malignant architectural distortion, and normal breast tissue. We employed transfer learning and initialized the model base layers with existing pre-trained weights obtained from Globally-Aware Multiple Instance Classifier.

RESULTS

High class-wise recall values of 0.8906, 0.8541 and 0.7345 and specificities 0.9558, 0.9575 and 0.8830 were obtained for normal, benign, and malignant classification, respectively. More intricate classification yielded class-wise recall values of 0.8708, 0.8299, 0.9444 and 0.5723 and specificities 0.9406, 0.9833, 0.8943 and 0.9652 for benign mass, normal, malignant architectural distortion, and malignant mass, respectively. However, benign architectural distortion was confused with benign mass and malignant architectural distortion.

CONCLUSIONS

Combining the proposed phenotype classifier with the commonly used malignant-benign-normal classification enables a more detailed assessment of digital breast tomosynthesis images.

Identifying radiogenomic associations of breast cancer based on DCE-MRI by using Siamese Neural Network with manufacturer bias normalization

BACKGROUND AND PURPOSE

The immunohistochemical test (IHC) for Human Epidermal Growth Factor Receptor 2 (HER2) and hormone receptors (HR) provides prognostic information and guides treatment for patients with invasive breast cancer. The objective of this paper is to establish a non-invasive system for identifying HER2 and HR in breast cancer using dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI).

METHODS

In light of the absence of high-performance algorithms and external validation in previously published methods, this study utilizes 3D deep features and radiomics features to represent the information of the Region of Interest (ROI). A Siamese Neural Network was employed as the classifier, with 3D deep features and radiomics features serving as the network input. To neutralize manufacturer bias, a batch effect normalization method, ComBat, was introduced. To enhance the reliability of the study, two datasets, Predict Your Therapeutic Response with Imaging and moLecular Analysis (I-SPY 1) and I-SPY 2, were incorporated. I-SPY 2 was utilized for model training and validation, while I-SPY 1 was exclusively employed for external validation. Additionally, a breast tumor segmentation network was trained to improve radiomic feature extraction.

RESULTS

The results indicate that our approach achieved an average Area Under the Curve (AUC) of 0.632, with a Standard Error of the Mean (SEM) of 0.042 for HER2 prediction in the I-SPY 2 dataset. For HR prediction, our method attained an AUC of 0.635 (SEM 0.041), surpassing other published methods in the AUC metric. Moreover, the proposed method yielded competitive results in other metrics. In external validation using the I-SPY 1 dataset, our approach achieved an AUC of 0.567 (SEM 0.032) for HR prediction and 0.563 (SEM 0.033) for HER2 prediction.

CONCLUSION

This study proposes a non-invasive system for identifying HER2 and HR in breast cancer. Although the results do not conclusively demonstrate superiority in both tasks, they indicate that the proposed method achieved good performance and is a competitive classifier compared to other reference methods. Ablation studies demonstrate that both radiomics features and deep features for the Siamese Neural Network are beneficial for the model. The introduced manufacturer bias normalization method has been shown to enhance the method's performance. Furthermore, the external validation of the method enhances the reliability of this research. Source code, pre-trained segmentation network, Radiomics and deep features, data for statistical analysis, and Supporting Information of this article are online at: https://github.com/FORRESTHUACHEN/Siamese_Neural_Network_based_Brest_cancer_Radiogenomic.

Breast cancer prognosis through the use of multi-modal classifiers: current state of the art and the way forward

We present a survey of the current state-of-the-art in breast cancer detection and prognosis. We analyze the evolution of Artificial Intelligence-based approaches from using just uni-modal information to multi-modality for detection and how such paradigm shift facilitates the efficacy of detection, consistent with clinical observations. We conclude that interpretable AI-based predictions and ability to handle class imbalance should be considered priority.

Explainable breast cancer molecular expression prediction using multi-task deep-learning based on 3D whole breast ultrasound

OBJECTIVES

To noninvasively estimate three breast cancer biomarkers, estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) and enhance performance and interpretability via multi-task deep learning.

METHODS

The study included 388 breast cancer patients who received the 3D whole breast ultrasound system (3DWBUS) examinations at Xijing Hospital between October 2020 and September 2021. Two predictive models, a single-task and a multi-task, were developed; the former predicts biomarker expression, while the latter combines tumor segmentation with biomarker prediction to enhance interpretability. Performance evaluation included individual and overall prediction metrics, and Delong's test was used for performance comparison. The models' attention regions were visualized using Grad-CAM + + technology.

RESULTS

All patients were randomly split into a training set (n = 240, 62%), a validation set (n = 60, 15%), and a test set (n = 88, 23%). In the individual evaluation of ER, PR, and HER2 expression prediction, the single-task and multi-task models achieved respective AUCs of 0.809 and 0.735 for ER, 0.688 and 0.767 for PR, and 0.626 and 0.697 for HER2, as observed in the test set. In the overall evaluation, the multi-task model demonstrated superior performance in the test set, achieving a higher macro AUC of 0.733, in contrast to 0.708 for the single-task model. The Grad-CAM + + method revealed that the multi-task model exhibited a stronger focus on diseased tissue areas, improving the interpretability of how the model worked.

CONCLUSION

Both models demonstrated impressive performance, with the multi-task model excelling in accuracy and offering improved interpretability on noninvasive 3DWBUS images using Grad-CAM + + technology.

CRITICAL RELEVANCE STATEMENT

The multi-task deep learning model exhibits effective prediction for breast cancer biomarkers, offering direct biomarker identification and improved clinical interpretability, potentially boosting the efficiency of targeted drug screening.

KEY POINTS

Tumoral biomarkers are paramount for determining breast cancer treatment. The multi-task model can improve prediction performance, and improve interpretability in clinical practice. The 3D whole breast ultrasound system-based deep learning models excelled in predicting breast cancer biomarkers.

Evolutionary Mechanism Based Conserved Gene Expression Biclustering Module Analysis for Breast Cancer Genomics

The identification of significant gene biclusters with particular expression patterns and the elucidation of functionally related genes within gene expression data has become a critical concern due to the vast amount of gene expression data generated by RNA sequencing technology. In this paper, a Conserved Gene Expression Module based on Genetic Algorithm (CGEMGA) is proposed. Breast cancer data from the TCGA database is used as the subject of this study. The p-values from Fisher's exact test are used as evaluation metrics to demonstrate the significance of different algorithms, including the Cheng and Church algorithm, CGEM algorithm, etc. In addition, the F-test is used to investigate the difference between our method and the CGEM algorithm. The computational cost of the different algorithms is further investigated by calculating the running time of each algorithm. Finally, the established driver genes and cancer-related pathways are used to validate the process. The results of 10 independent runs demonstrate that CGEMGA has a superior average p-value of 1.54 × 10-4 ± 3.06 × 10-5 compared to all other algorithms. Furthermore, our approach exhibits consistent performance across all methods. The F-test yields a p-value of 0.039, indicating a significant difference between our approach and the CGEM. Computational cost statistics also demonstrate that our approach has a significantly shorter average runtime of 5.22 × 100 ± 1.65 × 10-1 s compared to the other algorithms. Enrichment analysis indicates that the genes in our approach are significantly enriched for driver genes. Our algorithm is fast and robust, efficiently extracting co-expressed genes and associated co-expression condition biclusters from RNA-seq data.

Radiogenomics: bridging the gap between imaging and genomics for precision oncology

Genomics allows the tracing of origin and evolution of cancer at molecular scale and underpin modern cancer diagnosis and treatment systems. Yet, molecular biomarker-guided clinical decision-making encounters major challenges in the realm of individualized medicine, consisting of the invasiveness of procedures and the sampling errors due to high tumor heterogeneity. By contrast, medical imaging enables noninvasive and global characterization of tumors at a low cost. In recent years, radiomics has overcomes the limitations of human visual evaluation by high-throughput quantitative analysis, enabling the comprehensive utilization of the vast amount of information underlying radiological images. The cross-scale integration of radiomics and genomics (hereafter radiogenomics) has the enormous potential to enhance cancer decoding and act as a catalyst for digital precision medicine. Herein, we provide a comprehensive overview of the current framework and potential clinical applications of radiogenomics in patient care. We also highlight recent research advances to illustrate how radiogenomics can address common clinical problems in solid tumors such as breast cancer, lung cancer, and glioma. Finally, we analyze existing literature to outline challenges and propose solutions, while also identifying future research pathways. We believe that the perspectives shared in this survey will provide a valuable guide for researchers in the realm of radiogenomics aiming to advance precision oncology.

Precision treatment in advanced hepatocellular carcinoma

The past decade has witnessed significant advances in the systemic treatment of advanced hepatocellular carcinoma (HCC). Nevertheless, the newly developed treatment strategies have not achieved universal success and HCC patients frequently exhibit therapeutic resistance to these therapies. Precision treatment represents a paradigm shift in cancer treatment in recent years. This approach utilizes the unique molecular characteristics of individual patient to personalize treatment modalities, aiming to maximize therapeutic efficacy while minimizing side effects. Although precision treatment has shown significant success in multiple cancer types, its application in HCC remains in its infancy. In this review, we discuss key aspects of precision treatment in HCC, including therapeutic biomarkers, molecular classifications, and the heterogeneity of the tumor microenvironment. We also propose future directions, ranging from revolutionizing current treatment methodologies to personalizing therapy through functional assays, which will accelerate the next phase of advancements in this area.

iCluF: an unsupervised iterative cluster-fusion method for patient stratification using multiomics data

Motivation

Patient stratification is crucial for the effective treatment or management of heterogeneous diseases, including cancers. Multiomic technologies facilitate molecular characterization of human diseases; however, the complexity of data warrants the need for the development of robust data integration tools for patient stratification using machine-learning approaches.

Results

iCluF iteratively integrates three types of multiomic data (mRNA, miRNA, and DNA methylation) using pairwise patient similarity matrices built from each omic data. The intermediate omic-specific neighborhood matrices implement iterative matrix fusion and message passing among the similarity matrices to derive a final integrated matrix representing all the omics profiles of a patient, which is used to further cluster patients into subtypes. iCluF outperforms other methods with significant differences in the survival profiles of 8581 patients belonging to 30 different cancers in TCGA. iCluF also predicted the four intrinsic subtypes of Breast Invasive Carcinomas with adjusted rand index and Fowlkes-Mallows scores of 0.72 and 0.83, respectively. The Gini importance score showed that methylation features were the primary decisive players, followed by mRNA and miRNA to identify disease subtypes. iCluF can be applied to stratify patients with any disease containing multiomic datasets.

Availability and implementation

Source code and datasets are available at https://github.com/GudaLab/iCluF_core.

Artificial Intelligence in Breast Cancer Diagnosis and Personalized Medicine

Breast cancer is a significant cause of cancer-related mortality in women worldwide. Early and precise diagnosis is crucial, and clinical outcomes can be markedly enhanced. The rise of artificial intelligence (AI) has ushered in a new era, notably in image analysis, paving the way for major advancements in breast cancer diagnosis and individualized treatment regimens. In the diagnostic workflow for patients with breast cancer, the role of AI encompasses screening, diagnosis, staging, biomarker evaluation, prognostication, and therapeutic response prediction. Although its potential is immense, its complete integration into clinical practice is challenging. Particularly, these challenges include the imperatives for extensive clinical validation, model generalizability, navigating the "black-box" conundrum, and pragmatic considerations of embedding AI into everyday clinical environments. In this review, we comprehensively explored the diverse applications of AI in breast cancer care, underlining its transformative promise and existing impediments. In radiology, we specifically address AI in mammography, tomosynthesis, risk prediction models, and supplementary imaging methods, including magnetic resonance imaging and ultrasound. In pathology, our focus is on AI applications for pathologic diagnosis, evaluation of biomarkers, and predictions related to genetic alterations, treatment response, and prognosis in the context of breast cancer diagnosis and treatment. Our discussion underscores the transformative potential of AI in breast cancer management and emphasizes the importance of focused research to realize the full spectrum of benefits of AI in patient care.

Molecular Classifiers in Skin Cancers: Challenges and Promises

Skin cancers are common and heterogenous malignancies affecting up to two in three Australians before age 70. Despite recent developments in diagnosis and therapeutic strategies, the mortality rate and costs associated with managing patients with skin cancers remain high. The lack of well-defined clinical and histopathological features makes their diagnosis and classification difficult in some cases and the prognostication difficult in most skin cancers. Recent advancements in large-scale "omics" studies, including genomics, transcriptomics, proteomics, metabolomics and imaging-omics, have provided invaluable information about the molecular and visual landscape of skin cancers. On many occasions, it has refined tumor classification and has improved prognostication and therapeutic stratification, leading to improved patient outcomes. Therefore, this paper reviews the recent advancements in omics approaches and appraises their limitations and potential for better classification and stratification of skin cancers.

Progress in research on ultrasound radiomics for predicting the prognosis of breast cancer

Breast cancer is the most common malignant tumor and the leading cause of cancer-related deaths in women worldwide. Effective means of predicting the prognosis of breast cancer are very helpful in guiding treatment and improving patients' survival. Features extracted by radiomics reflect the genetic and molecular characteristics of a tumor and are related to its biological behavior and the patient's prognosis. Thus, radiomics provides a new approach to noninvasive assessment of breast cancer prognosis. Ultrasound is one of the commonest clinical means of examining breast cancer. In recent years, some results of research into ultrasound radiomics for diagnosing breast cancer, predicting lymph node status, treatment response, recurrence and survival times, and other aspects, have been published. In this article, we review the current research status and technical challenges of ultrasound radiomics for predicting breast cancer prognosis. We aim to provide a reference for radiomics researchers, promote the development of ultrasound radiomics, and advance its clinical application.

Ultrasound-based radiomics model for predicting molecular biomarkers in breast cancer

Background

Breast cancer (BC) is the most common cancer in women and is highly heterogeneous. BC can be classified into four molecular subtypes based on the status of estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2) and proliferation marker protein Ki-67. However, they can only be obtained by biopsy or surgery, which is invasive. Radiomics can noninvasively predict molecular expression via extracting the image features. Nevertheless, there is a scarcity of data available regarding the prediction of molecular biomarker expression using ultrasound (US) images in BC.

Objectives

To investigate the prediction performance of US radiomics for the assessment of molecular profiling in BC.

Methods

A total of 342 patients with BC who underwent preoperative US examination between January 2013 and December 2021 were retrospectively included. They were confirmed by pathology and molecular subtype analysis of ER, PR, HER2 and Ki-67. The radiomics features were extracted and four molecular models were constructed through support vector machine (SVM). Pearson correlation coefficient heatmaps are employed to analyze the relationship between selected features and their predictive power on molecular expression. The receiver operating characteristic curve was used for the prediction performance of US radiomics in the assessment of molecular profiling.

Results

359 lesions with 129 ER- and 230 ER+, 163 PR- and 196 PR+, 265 HER2- and 94 HER2+, 114 Ki-67- and 245 Ki-67+ expression were included. 1314 features were extracted from each ultrasound image. And there was a significant difference of some specific radiomics features between the molecule positive and negative groups. Multiple features demonstrated significant association with molecular biomarkers. The area under curves (AUCs) were 0.917, 0.835, 0.771, and 0.896 in the training set, while 0.868, 0.811, 0.722, and 0.706 in the validation set to predict ER, PR, HER2, and Ki-67 expression respectively.

Conclusion

Ultrasound-based radiomics provides a promising method for predicting molecular biomarker expression of ER, PR, HER2, and Ki-67 in BC.

Characterization of Breast Tumors from MR Images Using Radiomics and Machine Learning Approaches

Determining histological subtypes, such as invasive ductal and invasive lobular carcinomas (IDCs and ILCs) and immunohistochemical markers, such as estrogen response (ER), progesterone response (PR), and the HER2 protein status is important in planning breast cancer treatment. MRI-based radiomic analysis is emerging as a non-invasive substitute for biopsy to determine these signatures. We explore the effectiveness of radiomics-based and CNN (convolutional neural network)-based classification models to this end. T1-weighted dynamic contrast-enhanced, contrast-subtracted T1, and T2-weighted MR images of 429 breast cancer tumors from 323 patients are used. Various combinations of input data and classification schemes are applied for ER⁺ vs. ER^-, PR⁺ vs. PR^-, HER2⁺ vs. HER2^-, and IDC vs. ILC classification tasks. The best results were obtained for the ER⁺ vs. ER^- and IDC vs. ILC classification tasks, with their respective AUCs reaching 0.78 and 0.73 on test data. The results with multi-contrast input data were generally better than the mono-contrast alone. The radiomics and CNN-based approaches generally exhibited comparable results. ER and IDC/ILC classification results were promising. PR and HER2 classifications need further investigation through a larger dataset. Better results by using multi-contrast data might indicate that multi-parametric quantitative MRI could be used to achieve more reliable classifiers.