High-dimensional role of AI and machine learning in cancer research

Deep learning-based multimodal spatial transcriptomics analysis for cancer

The advent of deep learning (DL) and multimodal spatial transcriptomics (ST) has revolutionized cancer research, offering unprecedented insights into tumor biology. This book chapter explores the integration of DL with ST to advance cancer diagnostics, treatment planning, and precision medicine. DL, a subset of artificial intelligence, employs neural networks to model complex patterns in vast datasets, significantly enhancing diagnostic and treatment applications. In oncology, convolutional neural networks excel in image classification, segmentation, and tumor volume analysis, essential for identifying tumors and optimizing radiotherapy. The chapter also delves into multimodal data analysis, which integrates genomic, proteomic, imaging, and clinical data to offer a holistic understanding of cancer biology. Leveraging diverse data sources, researchers can uncover intricate details of tumor heterogeneity, microenvironment interactions, and treatment responses. Examples include integrating MRI data with genomic profiles for accurate glioma grading and combining proteomic and clinical data to uncover drug resistance mechanisms. DL's integration with multimodal data enables comprehensive and actionable insights for cancer diagnosis and treatment. The synergy between DL models and multimodal data analysis enhances diagnostic accuracy, personalized treatment planning, and prognostic modeling. Notable applications include ST, which maps gene expression patterns within tissue contexts, providing critical insights into tumor heterogeneity and potential therapeutic targets. In summary, the integration of DL and multimodal ST represents a paradigm shift towards more precise and personalized oncology. This chapter elucidates the methodologies and applications of these advanced technologies, highlighting their transformative potential in cancer research and clinical practice.

Early 2-Factor Transcription Factors Associated with Progression and Recurrence in Bevacizumab-Responsive Subtypes of Glioblastoma

The early 2-factor (E2F) family of transcription factors, including E2F1 through 8, plays a critical role in apoptosis, metabolism, proliferation, and angiogenesis within glioblastoma (GBM). However, the specific functions of E2F transcription factors (E2Fs) and their impact on the malignancy of Bevacizumab (BVZ)-responsive GBM subtypes remain unclear. This study used data from The Cancer Genome Atlas (TCGA), Chinese Glioma Genome Atlas (CGGA), European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI), and Gene Expression Omnibus (GEO) to explore the impact of eight E2F family members on the clinical characteristics of BVZ-responsive GBM subtypes and possible mechanisms of recurrence after BVZ treatment. Using machine learning algorithms, including TreeBagger and deep neural networks, we systematically predicted and validated GBM patient survival terms based on the expression profiles of E2Fs across BVZ-responsive GBM subtypes. Our bioinformatics analyses suggested that a significant increase in E2F8 post-BVZ treatment may enhance the function of angiogenesis and stem cell proliferation, implicating this factor as a candidate mechanism of GBM recurrence after treatment. In addition, BVZ treatment in unresponsive GBM patients may potentially worsen disease progression. These insights underscore that E2F family members play important roles in GBM malignancy and BVZ treatment response, highlighting their potential as prognostic biomarkers, therapeutic targets, and recommending precision BVZ treatment to individual GBM patients.

UK Stakeholder Perspectives on Surrogate Endpoints in Cancer, and the Potential for UK Real-World Datasets to Validate Their Use in Decision-Making

Duration of overall survival in patients with cancer has lengthened due to earlier detection and improved treatments. However, these improvements have created challenges in assessing the impact of newer treatments, particularly those used early in the treatment pathway. As overall survival remains most decision-makers' preferred primary endpoint, therapeutic innovations may take a long time to be introduced into clinical practice. Moreover, it is difficult to extrapolate findings to heterogeneous populations and address the concerns of patients wishing to evaluate everyday quality and extension of life. There is growing interest in the use of surrogate or interim endpoints to demonstrate robust treatment effects sooner than is possible with measurement of overall survival. It is hoped that they could speed up patients' access to new drugs, combinations, and sequences, and inform treatment decision-making. However, while surrogate endpoints have been used by regulators for drug approvals, this has occurred on a case-by-case basis. Evidence standards are yet to be clearly defined for acceptability in health technology appraisals or to shape clinical practice. This article considers the relevance of the use of surrogate endpoints in cancer in the UK context, and explores whether collection and analysis of real-world UK data and evidence might contribute to validation.

A review of big data technology and its application in cancer care

The development of modern medical devices and information technology has led to a rapid growth in the amount of data available for health protection information, with the concept of medical big data emerging globally, along with significant advances in cancer care relying on data-driven approaches. However, outstanding issues such as fragmented data governance, low-quality data specification, and data lock-in still make sharing challenging. Big data technology provides solutions for managing massive heterogeneous data while combining artificial intelligence (AI) techniques such as machine learning (ML) and deep learning (DL) to better mine the intrinsic connections between data. This paper surveys and organizes recent articles on big data technology and its applications in cancer, dividing them into three different types to outline their primary content and summarize their critical role in assisting cancer care. It then examines the latest research directions in big data technology in cancer and evaluates the current state of development of each type of application. Finally, current challenges and opportunities are discussed, and recommendations are made for the further integration of big data technology into the medical industry in the future.

Identification of prognostic signatures in remnant gastric cancer through an interpretable risk model based on machine learning: a multicenter cohort study

OBJECTIVE

The purpose of this study was to develop an individual survival prediction model based on multiple machine learning (ML) algorithms to predict survival probability for remnant gastric cancer (RGC).

METHODS

Clinicopathologic data of 286 patients with RGC undergoing operation (radical resection and palliative resection) from a multi-institution database were enrolled and analyzed retrospectively. These individuals were split into training (80%) and test cohort (20%) by using random allocation. Nine commonly used ML methods were employed to construct survival prediction models. Algorithm performance was estimated by analyzing accuracy, precision, recall, F1-score, area under the receiver operating characteristic curve (AUC), confusion matrices, five-fold cross-validation, decision curve analysis (DCA), and calibration curve. The best model was selected through appropriate verification and validation and was suitably explained by the SHapley Additive exPlanations (SHAP) approach.

RESULTS

Compared with the traditional methods, the RGC survival prediction models employing ML exhibited good performance. Except for the decision tree model, all other models performed well, with a mean ROC AUC above 0.7. The DCA findings suggest that the developed models have the potential to enhance clinical decision-making processes, thereby improving patient outcomes. The calibration curve reveals that all models except the decision tree model displayed commendable predictive performance. Through CatBoost-based modeling and SHAP analysis, the five-year survival probability is significantly influenced by several factors: the lymph node ratio (LNR), T stage, tumor size, resection margins, perineural invasion, and distant metastasis.

CONCLUSIONS

This study established predictive models for survival probability at five years in RGC patients based on ML algorithms which showed high accuracy and applicative value.

Just how transformative will AI/ML be for immuno-oncology?

Immuno-oncology involves the study of approaches which harness the patient's immune system to fight malignancies. Immuno-oncology, as with every other biomedical and clinical research field as well as clinical operations, is in the midst of technological revolutions, which vastly increase the amount of available data. Recent advances in artificial intelligence and machine learning (AI/ML) have received much attention in terms of their potential to harness available data to improve insights and outcomes in many areas including immuno-oncology. In this review, we discuss important aspects to consider when evaluating the potential impact of AI/ML applications in the clinic. We highlight four clinical/biomedical challenges relevant to immuno-oncology and how they may be able to be addressed by the latest advancements in AI/ML. These challenges include (1) efficiency in clinical workflows, (2) curation of high-quality image data, (3) finding, extracting and synthesizing text knowledge as well as addressing, and (4) small cohort size in immunotherapeutic evaluation cohorts. Finally, we outline how advancements in reinforcement and federated learning, as well as the development of best practices for ethical and unbiased data generation, are likely to drive future innovations.

The Psychedelic Future of Post-Traumatic Stress Disorder Treatment

Post-traumatic stress disorder (PTSD) is a mental health condition that can occur following exposure to a traumatic experience. An estimated 12 million U.S. adults are presently affected by this disorder. Current treatments include psychological therapies (e.g., exposure-based interventions) and pharmacological treatments (e.g., selective serotonin reuptake inhibitors (SSRIs)). However, a significant proportion of patients receiving standard-of-care therapies for PTSD remain symptomatic, and new approaches for this and other trauma-related mental health conditions are greatly needed. Psychedelic compounds that alter cognition, perception, and mood are currently being examined for their efficacy in treating PTSD despite their current status as Drug Enforcement Administration (DEA)- scheduled substances. Initial clinical trials have demonstrated the potential value of psychedelicassisted therapy to treat PTSD and other psychiatric disorders. In this comprehensive review, we summarize the state of the science of PTSD clinical care, including current treatments and their shortcomings. We review clinical studies of psychedelic interventions to treat PTSD, trauma-related disorders, and common comorbidities. The classic psychedelics psilocybin, lysergic acid diethylamide (LSD), and N,N-dimethyltryptamine (DMT) and DMT-containing ayahuasca, as well as the entactogen 3,4-methylenedioxymethamphetamine (MDMA) and the dissociative anesthetic ketamine, are reviewed. For each drug, we present the history of use, psychological and somatic effects, pharmacology, and safety profile. The rationale and proposed mechanisms for use in treating PTSD and traumarelated disorders are discussed. This review concludes with an in-depth consideration of future directions for the psychiatric applications of psychedelics to maximize therapeutic benefit and minimize risk in individuals and communities impacted by trauma-related conditions.

Wavelet scattering networks in deep learning for discovering protein markers in a cohort of Swedish rectal cancer patients

BACKGROUND

Cancer biomarkers play a pivotal role in the diagnosis, prognosis, and treatment response prediction of the disease. In this study, we analyzed the expression levels of RhoB and DNp73 proteins in rectal cancer, as captured in immunohistochemical images, to predict the 5-year survival time of two patient groups: one with preoperative radiotherapy and one without.

METHODS

The utilization of deep convolutional neural networks in medical research, particularly in clinical cancer studies, has been gaining substantial attention. This success primarily stems from their ability to extract intricate image features that prove invaluable in machine learning. Another innovative method for extracting features at multiple levels is the wavelet-scattering network. Our study combines the strengths of these two convolution-based approaches to robustly extract image features related to protein expression.

RESULTS

The efficacy of our approach was evaluated across various tissue types, including tumor, biopsy, metastasis, and adjacent normal tissue. Statistical assessments demonstrated exceptional performance across a range of metrics, including prediction accuracy, classification accuracy, precision, and the area under the receiver operating characteristic curve.

CONCLUSION

These results underscore the potential of dual convolutional learning to assist clinical researchers in the timely validation and discovery of cancer biomarkers.

Deep neural network based tissue deconvolution of circulating tumor cell RNA

Prior research has shown that the deconvolution of cell-free RNA can uncover the tissue origin. The conventional deconvolution approaches rely on constructing a reference tissue-specific gene panel, which cannot capture the inherent variation present in actual data. To address this, we have developed a novel method that utilizes a neural network framework to leverage the entire training dataset. Our approach involved training a model that incorporated 15 distinct tissue types. Through one semi-independent and two complete independent validations, including deconvolution using a semi in silico dataset, deconvolution with a custom normal tissue mixture RNA-seq data, and deconvolution of longitudinal circulating tumor cell RNA-seq (ctcRNA) data from a cancer patient with metastatic tumors, we demonstrate the efficacy and advantages of the deep-learning approach which were exerted by effectively capturing the inherent variability present in the dataset, thus leading to enhanced accuracy. Sensitivity analyses reveal that neural network models are less susceptible to the presence of missing data, making them more suitable for real-world applications. Moreover, by leveraging the concept of organotropism, we applied our approach to trace the migration of circulating tumor cell-derived RNA (ctcRNA) in a cancer patient with metastatic tumors, thereby highlighting the potential clinical significance of early detection of cancer metastasis.

Artificial Intelligence in Oncological Hybrid Imaging

BACKGROUND

 Artificial intelligence (AI) applications have become increasingly relevant across a broad spectrum of settings in medical imaging. Due to the large amount of imaging data that is generated in oncological hybrid imaging, AI applications are desirable for lesion detection and characterization in primary staging, therapy monitoring, and recurrence detection. Given the rapid developments in machine learning (ML) and deep learning (DL) methods, the role of AI will have significant impact on the imaging workflow and will eventually improve clinical decision making and outcomes.

METHODS AND RESULTS

 The first part of this narrative review discusses current research with an introduction to artificial intelligence in oncological hybrid imaging and key concepts in data science. The second part reviews relevant examples with a focus on applications in oncology as well as discussion of challenges and current limitations.

CONCLUSION

 AI applications have the potential to leverage the diagnostic data stream with high efficiency and depth to facilitate automated lesion detection, characterization, and therapy monitoring to ultimately improve quality and efficiency throughout the medical imaging workflow. The goal is to generate reproducible, structured, quantitative diagnostic data for evidence-based therapy guidance in oncology. However, significant challenges remain regarding application development, benchmarking, and clinical implementation.

KEY POINTS

  · Hybrid imaging generates a large amount of multimodality medical imaging data with high complexity and depth.. · Advanced tools are required to enable fast and cost-efficient processing along the whole radiology value chain.. · AI applications promise to facilitate the assessment of oncological disease in hybrid imaging with high quality and efficiency for lesion detection, characterization, and response assessment. The goal is to generate reproducible, structured, quantitative diagnostic data for evidence-based oncological therapy guidance.. · Selected applications in three oncological entities (lung, prostate, and neuroendocrine tumors) demonstrate how AI algorithms may impact imaging-based tasks in hybrid imaging and potentially guide clinical decision making..

Model-based prediction of progression-free survival for combination therapies in oncology

Progression-free survival (PFS) is an important clinical metric for comparing and evaluating similar treatments for the same disease within oncology. After the completion of a clinical trial, a descriptive analysis of the patients' PFS is often performed post hoc using the Kaplan-Meier estimator. However, to perform predictions, more sophisticated quantitative methods are needed. Tumor growth inhibition models are commonly used to describe and predict the dynamics of preclinical and clinical tumor size data. Moreover, frameworks also exist for describing the probability of different types of events, such as tumor metastasis or patient dropout. Combining these two types of models into a so-called joint model enables model-based prediction of PFS. In this paper, we have constructed a joint model from clinical data comparing the efficacy of FOLFOX against FOLFOX + panitumumab in patients with metastatic colorectal cancer. The nonlinear mixed effects framework was used to quantify interindividual variability (IIV). The model describes tumor size and PFS data well, and showed good predictive capabilities using truncated as well as external data. A machine-learning guided analysis was performed to reduce unexplained IIV by incorporating patient covariates. The model-based approach illustrated in this paper could be useful to help design clinical trials or to determine new promising drug candidates for combination therapy trials.

Expression patterns and immunological characterization of PANoptosis -related genes in gastric cancer

Background

Accumulative studies have demonstrated the close relationship between tumor immunity and pyroptosis, apoptosis, and necroptosis. However, the role of PANoptosis in gastric cancer (GC) is yet to be fully understood.

Methods

This research attempted to identify the expression patterns of PANoptosis regulators and the immune landscape in GC by integrating the GSE54129 and GSE65801 datasets. We analyzed GC specimens and established molecular clusters associated with PANoptosis-related genes (PRGs) and corresponding immune characteristics. The differentially expressed genes were determined with the WGCNA method. Afterward, we employed four machine learning algorithms (Random Forest, Support Vector Machine, Generalized linear Model, and eXtreme Gradient Boosting) to select the optimal model, which was validated using nomogram, calibration curve, decision curve analysis (DCA), and two validation cohorts. Additionally, this study discussed the relationship between infiltrating immune cells and variables in the selected model.

Results

This study identified dysregulated PRGs and differential immune activities between GC and normal samples, and further identified two PANoptosis-related molecular clusters in GC. These clusters demonstrated remarkable immunological heterogeneity, with Cluster1 exhibiting abundant immune infiltration. The Support Vector Machine signature was found to have the best discriminative ability, and a 5-gene-based SVM signature was established. This model showed excellent performance in the external validation cohorts, and the nomogram, calibration curve, and DCA indicated its reliability in predicting GC patterns. Further analysis confirmed that the 5 selected variables were remarkably related to infiltrating immune cells and immune-related pathways.

Conclusion

Taken together, this work demonstrates that the PANoptosis pattern has the potential as a stratification tool for patient risk assessment and a reflection of the immune microenvironment in GC.

Profiling of patients with type 2 diabetes based on medication adherence data

Introduction

Type 2 diabetes mellitus (T2DM) is a complex, chronic disease affecting multiple organs with varying symptoms and comorbidities. Profiling patients helps identify those with unfavorable disease progression, allowing for tailored therapy and addressing special needs. This study aims to uncover different T2DM profiles based on medication intake records and laboratory measurements, with a focus on how individuals with diabetes move through disease phases.

Methods

We use medical records from databases of the last 20 years from the Department of Endocrinology and Diabetology of the University Medical Center in Maribor. Using the standard ATC medication classification system, we created a patient-specific drug profile, created using advanced natural language processing methods combined with data mining and hierarchical clustering.

Results

Our results show a well-structured profile distribution characterizing different age groups of individuals with diabetes. Interestingly, only two main profiles characterize the early 40-50 age group, and the same is true for the last 80+ age group. One of these profiles includes individuals with diabetes with very low use of various medications, while the other profile includes individuals with diabetes with much higher use. The number in both groups is reciprocal. Conversely, the middle-aged groups are characterized by several distinct profiles with a wide range of medications that are associated with the distinct concomitant complications of T2DM. It is intuitive that the number of profiles increases in the later age groups, but it is not obvious why it is reduced later in the 80+ age group. In this context, further studies are needed to evaluate the contributions of a range of factors, such as drug development, drug adoption, and the impact of mortality associated with all T2DM-related diseases, which characterize these middle-aged groups, particularly those aged 55-75.

Conclusion

Our approach aligns with existing studies and can be widely implemented without complex or expensive analyses. Treatment and drug use data are readily available in healthcare facilities worldwide, allowing for profiling insights into individuals with diabetes. Integrating data from other departments, such as cardiology and renal disease, may provide a more sophisticated understanding of T2DM patient profiles.

UK Biobank: a globally important resource for cancer research

UK Biobank is a large-scale prospective study with deep phenotyping and genomic data. Its open-access policy allows researchers worldwide, from academia or industry, to perform health research in the public interest. Between 2006 and 2010, the study recruited 502,000 adults aged 40-69 years from the general population of the United Kingdom. At enrolment, participants provided information on a wide range of factors, physical measurements were taken, and biological samples (blood, urine and saliva) were collected for long-term storage. Participants have now been followed up for over a decade with more than 52,000 incident cancer cases recorded. The study continues to be enhanced with repeat assessments, web-based questionnaires, multi-modal imaging, and conversion of the stored biological samples to genomic and other '-omic' data. The study has already demonstrated its value in enabling research into the determinants of cancer, and future planned enhancements will make the resource even more valuable to cancer researchers. Over 26,000 researchers worldwide are currently using the data, performing a wide range of cancer research. UK Biobank is uniquely placed to transform our understanding of the causes of cancer development and progression, and drive improvements in cancer treatment and prevention over the coming decades.

Artificial Intelligence in Oncological Hybrid Imaging

BACKGROUND

Artificial intelligence (AI) applications have become increasingly relevant across a broad spectrum of settings in medical imaging. Due to the large amount of imaging data that is generated in oncological hybrid imaging, AI applications are desirable for lesion detection and characterization in primary staging, therapy monitoring, and recurrence detection. Given the rapid developments in machine learning (ML) and deep learning (DL) methods, the role of AI will have significant impact on the imaging workflow and will eventually improve clinical decision making and outcomes.

METHODS AND RESULTS

The first part of this narrative review discusses current research with an introduction to artificial intelligence in oncological hybrid imaging and key concepts in data science. The second part reviews relevant examples with a focus on applications in oncology as well as discussion of challenges and current limitations.

CONCLUSION

AI applications have the potential to leverage the diagnostic data stream with high efficiency and depth to facilitate automated lesion detection, characterization, and therapy monitoring to ultimately improve quality and efficiency throughout the medical imaging workflow. The goal is to generate reproducible, structured, quantitative diagnostic data for evidence-based therapy guidance in oncology. However, significant challenges remain regarding application development, benchmarking, and clinical implementation.

KEY POINTS

· Hybrid imaging generates a large amount of multimodality medical imaging data with high complexity and depth.. · Advanced tools are required to enable fast and cost-efficient processing along the whole radiology value chain.. · AI applications promise to facilitate the assessment of oncological disease in hybrid imaging with high quality and efficiency for lesion detection, characterization, and response assessment. The goal is to generate reproducible, structured, quantitative diagnostic data for evidence-based oncological therapy guidance.. · Selected applications in three oncological entities (lung, prostate, and neuroendocrine tumors) demonstrate how AI algorithms may impact imaging-based tasks in hybrid imaging and potentially guide clinical decision making..

CITATION FORMAT

· Feuerecker B, Heimer M, Geyer T et al. Artificial Intelligence in Oncological Hybrid Imaging. Fortschr Röntgenstr 2023; 195: 105 - 114.

Artificial Intelligence Implementation in Healthcare: A Theory-Based Scoping Review of Barriers and Facilitators

There is a large proliferation of complex data-driven artificial intelligence (AI) applications in many aspects of our daily lives, but their implementation in healthcare is still limited. This scoping review takes a theoretical approach to examine the barriers and facilitators based on empirical data from existing implementations. We searched the major databases of relevant scientific publications for articles related to AI in clinical settings, published between 2015 and 2021. Based on the theoretical constructs of the Consolidated Framework for Implementation Research (CFIR), we used a deductive, followed by an inductive, approach to extract facilitators and barriers. After screening 2784 studies, 19 studies were included in this review. Most of the cited facilitators were related to engagement with and management of the implementation process, while the most cited barriers dealt with the intervention's generalizability and interoperability with existing systems, as well as the inner settings' data quality and availability. We noted per-study imbalances related to the reporting of the theoretic domains. Our findings suggest a greater need for implementation science expertise in AI implementation projects, to improve both the implementation process and the quality of scientific reporting.

Artificial Intelligence-Driven Diagnosis of Pancreatic Cancer

Pancreatic cancer is among the most challenging forms of cancer to treat, owing to its late diagnosis and aggressive nature that reduces the survival rate drastically. Pancreatic cancer diagnosis has been primarily based on imaging, but the current state-of-the-art imaging provides a poor prognosis, thus limiting clinicians' treatment options. The advancement of a cancer diagnosis has been enhanced through the integration of artificial intelligence and imaging modalities to make better clinical decisions. In this review, we examine how AI models can improve the diagnosis of pancreatic cancer using different imaging modalities along with a discussion on the emerging trends in an AI-driven diagnosis, based on cytopathology and serological markers. Ethical concerns regarding the use of these tools have also been discussed.

Application of non-negative matrix factorization in oncology: one approach for establishing precision medicine

The increase in the expectations of artificial intelligence (AI) technology has led to machine learning technology being actively used in the medical field. Non-negative matrix factorization (NMF) is a machine learning technique used for image analysis, speech recognition, and language processing; recently, it is being applied to medical research. Precision medicine, wherein important information is extracted from large-scale medical data to provide optimal medical care for every individual, is considered important in medical policies globally, and the application of machine learning techniques to this end is being handled in several ways. NMF is also introduced differently because of the characteristics of its algorithms. In this review, the importance of NMF in the field of medicine, with a focus on the field of oncology, is described by explaining the mathematical science of NMF and the characteristics of the algorithm, providing examples of how NMF can be used to establish precision medicine, and presenting the challenges of NMF. Finally, the direction regarding the effective use of NMF in the field of oncology is also discussed.