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Simple Summary: Automatic segmentation of organs and other regions of interest is a promising approach for reducing the workload of doctors in radiotherapeutic planning, but it can be hard for doctors and researchers to keep up with current developments. This review evaluates 807 papers and reveals trends, commonalities, and gaps in the existing corpus. A set of recommendations for conducting effective segmentation studies is also provided. This review provides a formal overview of current automatic segmentation studies that use deep learning in radiotherapy. It covers 807 published papers and includes multiple cancer sites, image types (CT/MRI/PET), and segmentation methods. We collect key statistics about the papers to uncover commonalities, trends, and methods, and identify areas where more research might be needed. Moreover, we analyzed the corpus by posing explicit questions aimed at providing high-quality and actionable insights, including: "What should researchers think about when starting a segmentation study?", "How can research practices in medical image segmentation be improved?", "What is missing from the current corpus?", and more. This allowed us to provide practical guidelines on how to conduct a good segmentation study in today's competitive environment that will be useful for future research within the field, regardless of the specific radiotherapeutic subfield. To aid in our analysis, we used the large language model ChatGPT to condense information. [ABSTRACT FROM AUTHOR]

Simple Summary: To investigate the adoption of machine learning in palliative care research and clinical practice, we systematically searched for published research papers on the topic. We found several publications that used different kinds of machine learning in palliative care for different use cases. However, on average, there needs to be more rigorous testing of the models to ensure that they work well in different settings. Objective: To summarize the available literature on using machine learning (ML) for palliative care practice as well as research and to assess the adherence of the published studies to the most important ML best practices. Methods: The MEDLINE database was searched for the use of ML in palliative care practice or research, and the records were screened according to PRISMA guidelines. Results: In total, 22 publications using machine learning for mortality prediction (n = 15), data annotation (n = 5), predicting morbidity under palliative therapy (n = 1), and predicting response to palliative therapy (n = 1) were included. Publications used a variety of supervised or unsupervised models, but mostly tree-based classifiers and neural networks. Two publications had code uploaded to a public repository, and one publication uploaded the dataset. Conclusions: Machine learning in palliative care is mainly used to predict mortality. Similarly to other applications of ML, external test sets and prospective validations are the exception. [ABSTRACT FROM AUTHOR]

Simple Summary: The classification is performed later by an interactively learning Swin Transformer block, the core unit for feature representation and long-range semantic information. In particular, the proposed strategy improved significantly and was very resilient while dealing with small liver pieces, discontinuous liver regions, and fuzzy liver boundaries. The experimental results confirm that the proposed APESTNet is more effective in classifying liver tumours than the current state-of-the-art models. Without compromising accuracy, the proposed method conserved resources. However, the proposed method is prone to slight over-segmentation or under-segmentation errors when dealing with lesions or tumours at the liver boundary. Therefore, our future work will concentrate on completely utilizing the z-axis information in 3D to reduce errors. Diagnosis and treatment of hepatocellular carcinoma or metastases rely heavily on accurate segmentation and classification of liver tumours. However, due to the liver tumor's hazy borders and wide range of possible shapes, sizes, and positions, accurate and automatic tumour segmentation and classification remains a difficult challenge. With the advancement of computing, new models in artificial intelligence have evolved. Following its success in Natural language processing (NLP), the transformer paradigm has been adopted by the computer vision (CV) community of the NLP. While there are already accepted approaches to classifying the liver, especially in clinical settings, there is room for advancement in terms of their precision. This paper makes an effort to apply a novel model for segmenting and classifying liver tumours built on deep learning. In order to accomplish this, the created model follows a three-stage procedure consisting of (a) pre-processing, (b) liver segmentation, and (c) classification. In the first phase, the collected Computed Tomography (CT) images undergo three stages of pre-processing, including contrast improvement via histogram equalization and noise reduction via the median filter. Next, an enhanced mask region-based convolutional neural networks (Mask R-CNN) model is used to separate the liver from the CT abdominal image. To prevent overfitting, the segmented picture is fed onto an Enhanced Swin Transformer Network with Adversarial Propagation (APESTNet). The experimental results prove the superior performance of the proposed perfect on a wide variety of CT images, as well as its efficiency and low sensitivity to noise. [ABSTRACT FROM AUTHOR]

Simple Summary: Cancer stands as a leading cause of death globally and remains a significant threat to public health in developed nations. With an anticipated rise in cancer cases, the number of survivors is also expected to increase, many of whom grapple with distorted body image perception. Addressing the common poor quality of life among cancer patients and survivors necessitates monitoring emotions and body perception to mitigate psychological burdens. Given the strain on healthcare resources, exploring automated screening methods for cancer patients is crucial. This article proposes leveraging Natural Language Processing for monitoring body image perception in enterally fed patients with head and neck or upper gastrointestinal tract cancers, offering potential advancements in care delivery and patient support within oncology settings. Background: Psycho-oncology care has emerged as a significant concern in contemporary oncology practice, given its profound impact on patient psychological well-being. Patients undergoing treatment for head–neck or upper gastrointestinal tract cancers often experience complex emotional and psychological challenges, necessitating specialized support and intervention. Traditional approaches to psycho-oncological care may be limited in their ability to comprehensively assess and address patients' needs. Therefore, exploring innovative methodologies, such as leveraging natural language processing (NLP) elements, is crucial to enhancing the effectiveness of psycho-oncological interventions. Methods: In this study, we developed a method utilizing natural language processing (NLP) elements to augment psycho-oncological care for patients with head–neck or upper gastrointestinal tract cancers. The method aimed to facilitate vocabulary, sentiment, and intensity analysis of five basic emotions (happiness, sadness, anger, disgust, and fear), as well as to explore potential areas of difficulty such as body image, pain, and self-esteem. We conducted research involving 50 patients across three treatment stages. Results: Our method facilitated the identification of characteristic features at each treatment stage, aiding in the tailoring of appropriate therapies to individual patient needs. The results offer insights valuable to psychologists and psychiatrists for expedited diagnosis and intervention, potentially influencing therapy outcomes. Additionally, the data may inform treatment decisions by addressing patient-specific concerns. Furthermore, our method holds promise for optimizing the allocation of psychological care resources, particularly at the initial stages of patient contact. Limitations: The main problem in the research was the fairly wide age range of participants, which explains the potential diversity of vocabulary. Conclusion: In conclusion, our study demonstrates the potential utility of integrating natural language processing (NLP) elements into psycho-oncological care for patients with head–neck or upper gastrointestinal tract cancers. The developed method offers a novel approach to comprehensively assessing patients' emotional states and areas of difficulty, thereby facilitating tailored interventions and treatment planning. These findings underscore the importance of continued research and innovation in psycho-oncology to enhance patient care and outcomes. [ABSTRACT FROM AUTHOR]

Simple Summary: Topic modeling, widely used in natural language processing, categorizes text documents into themes based on word frequency analysis. It has found success in various biological data analyses, including the accurate prediction of cancer subtypes and the simultaneous identification of genes, enhancers, and cell types from sparse single-cell data. Our study introduces a novel topic modeling approach for clustering single cells and detecting gene signatures in multi-omics single-cell datasets. Applied to study transcriptional heterogeneity in breast cancer cells resistant to chemotherapy and targeted therapy, it identifies protein-coding genes and long non-coding RNAs grouping cells into biologically similar clusters, effectively distinguishing between drug-sensitive and -resistant cancer types. Previous studies have interrogated long non-coding RNA (lncRNA) expression in single-cell data within breast cancer subtypes. Yet, the combined analysis of both lncRNA and mRNA expression in a cell type-specific manner remains to be explored. Compared to standard clustering methods, our approach offers a simultaneous optimal partitioning of genes and cells into topics and clusters, yielding easily interpretable results. Integrating mRNA and lncRNA data enhances cell classification accuracy. Topic modeling is a popular technique in machine learning and natural language processing, where a corpus of text documents is classified into themes or topics using word frequency analysis. This approach has proven successful in various biological data analysis applications, such as predicting cancer subtypes with high accuracy and identifying genes, enhancers, and stable cell types simultaneously from sparse single-cell epigenomics data. The advantage of using a topic model is that it not only serves as a clustering algorithm, but it can also explain clustering results by providing word probability distributions over topics. Our study proposes a novel topic modeling approach for clustering single cells and detecting topics (gene signatures) in single-cell datasets that measure multiple omics simultaneously. We applied this approach to examine the transcriptional heterogeneity of luminal and triple-negative breast cancer cells using patient-derived xenograft models with acquired resistance to chemotherapy and targeted therapy. Through this approach, we identified protein-coding genes and long non-coding RNAs (lncRNAs) that group thousands of cells into biologically similar clusters, accurately distinguishing drug-sensitive and -resistant breast cancer types. In comparison to standard state-of-the-art clustering analyses, our approach offers an optimal partitioning of genes into topics and cells into clusters simultaneously, producing easily interpretable clustering outcomes. Additionally, we demonstrate that an integrative clustering approach, which combines the information from mRNAs and lncRNAs treated as disjoint omics layers, enhances the accuracy of cell classification. [ABSTRACT FROM AUTHOR]

Simple Summary: Transformer models, originally successful in natural language processing, have found application in computer vision, demonstrating promising results in tasks related to cancer image analysis. Despite being one of the prevalent and swiftly spreading cancers globally, there is a pressing need for accurate automated analysis methods for oral cancer. This need is particularly critical for high-risk populations residing in low- and middle-income countries. In this study, we evaluated the performance of the Vision Transformer (ViT) and the Swin Transformer in the classification of mobile-based oral cancer images we collected from high-risk populations. The results showed that the Swin Transformer model achieved higher accuracy than the ViT model, and both transformer models work better than the conventional convolution model VGG19. Oral cancer, a pervasive and rapidly growing malignant disease, poses a significant global health concern. Early and accurate diagnosis is pivotal for improving patient outcomes. Automatic diagnosis methods based on artificial intelligence have shown promising results in the oral cancer field, but the accuracy still needs to be improved for realistic diagnostic scenarios. Vision Transformers (ViT) have outperformed learning CNN models recently in many computer vision benchmark tasks. This study explores the effectiveness of the Vision Transformer and the Swin Transformer, two cutting-edge variants of the transformer architecture, for the mobile-based oral cancer image classification application. The pre-trained Swin transformer model achieved 88.7% accuracy in the binary classification task, outperforming the ViT model by 2.3%, while the conventional convolutional network model VGG19 and ResNet50 achieved 85.2% and 84.5% accuracy. Our experiments demonstrate that these transformer-based architectures outperform traditional convolutional neural networks in terms of oral cancer image classification, and underscore the potential of the ViT and the Swin Transformer in advancing the state of the art in oral cancer image analysis. [ABSTRACT FROM AUTHOR]

Simple Summary: Pancreatic ductal adenocarcinoma (PDAC) is often diagnosed at advanced stages, resulting in limited treatment options and poor survival rates. To address this challenge, we conducted a comprehensive analysis of pyroptosis-related genes using advanced algorithms. Our study, involving 1273 PDAC cases, identified 357 pyroptosis-related genes. Notably, BHLHE40, IL18, BIRC3, and APOL1 were found to be related to unfavourable PDAC outcomes and were validated through experiments and multiple datasets. We developed a novel model and an accessible nomogram to predict PDAC prognosis. Our research enhances our understanding of PDAC and has significant implications for both research and clinical practice. Pancreatic ductal adenocarcinoma (PDAC) is often diagnosed at late stages, limiting treatment options and survival rates. Pyroptosis-related gene signatures hold promise as PDAC prognostic markers, but limited gene pools and small sample sizes hinder their utility. We aimed to enhance PDAC prognosis with a comprehensive multi-algorithm analysis. Using R, we employed natural language processing and latent Dirichlet allocation on PubMed publications to identify pyroptosis-related genes. We collected PDAC transcriptome data (n = 1273) from various databases, conducted a meta-analysis, and performed differential gene expression analysis on tumour and non-cancerous tissues. Cox and LASSO algorithms were used for survival modelling, resulting in a pyroptosis-related gene expression-based prognostic index. Laboratory and external validations were conducted. Bibliometric analysis revealed that pyroptosis publications focus on signalling pathways, disease correlation, and prognosis. We identified 357 pyroptosis-related genes, validating the significance of BHLHE40, IL18, BIRC3, and APOL1. Elevated expression of these genes strongly correlated with poor PDAC prognosis and guided treatment strategies. Our accessible nomogram model aids in PDAC prognosis and treatment decisions. We established an improved gene signature for pyroptosis-related genes, offering a novel model and nomogram for enhanced PDAC prognosis. [ABSTRACT FROM AUTHOR]

Simple Summary: Psychological assessment of a cancer patient is a challenge due to the difficulty of the issues raised and, additionally, the lack of a sufficient number of psycho-oncologists. The article proposes a minimally invasive automatic method of this assessment using a note prepared by the patient about his body image. The proposed method allows you to determine the general attitude, the intensity of the five basic emotions (happiness, fear, sadness, anger, disgust), and potential areas of difficulty in terms of: body image, self-esteem, and acceptance of the environment. The combination of the attributes of patient's condition determined by the method can indicate the direction of support for the patient, relatives, direct medical personnel, and psycho-oncologists. Background: Head and neck cancers (H&NCs) constitute a significant part of all cancer cases. H&NC patients experience unintentional weight loss, poor nutritional status, or speech disorders. Medical interventions affect appearance and interfere with patients' self-perception of their bodies. Psychological consultations are not affordable due to limited time. Methods: We used NLP to analyze the basic emotion intensity, sentiment about one's body, characteristic vocabulary, and potential areas of difficulty in free notes. The emotion intensity research uses the extended NAWL dictionary developed using word embedding. The sentiment analysis used a hybrid approach: a sentiment dictionary and a deep recursive network. The part-of-speech tagging and domain rules defined by a psycho-oncologist determine the distinct language traits. Potential areas of difficulty were analyzed using the dictionaries method with word polarity to define a given area and the presentation of a note using bag-of-words. Here, we applied the LSA method using SVD to reduce dimensionality. A total of 50 cancer patients requiring enteral nutrition participated in the study. Results: The results confirmed the complexity of emotions in patients with H&NC in relation to their body image. A negative attitude towards body image was detected in most of the patients. The method presented in the study appeared to be effective in assessing body image perception disturbances, but it cannot be used as the sole indicator of body image perception issues. Limitations: The main problem in the research was the fairly wide age range of participants, which explains the potential diversity of vocabulary. Conclusions: The combination of the attributes of a patient's condition, possible to determine using the method for a specific patient, can indicate the direction of support for the patient, relatives, direct medical personnel, and psycho-oncologists. [ABSTRACT FROM AUTHOR]

Simple Summary: Lack of standardization among radiologists in writing radiological reports impacts the ability to interpret cancer response to treatment at a large-scale. This is an issue since large-scale data collection is necessary to generate Real World Evidence (RWE) towards understanding the effectiveness of cancer treatments and developing personalized patient treatment decisions. This study aims to examine the utility of applying natural language processing (NLP) for large-scale interpretation of disease response using the standardized oncologic response categories known as the OR-RADS to facilitate RWE collection. This study demonstrates the feasibility of applying NLP to predict disease response in cancer patients, exceeding human performance, thus encouraging use of the standardized OR-RADS categories among radiologists and researchers to improve large-scale response prediction accuracy. Generating Real World Evidence (RWE) on disease responses from radiological reports is important for understanding cancer treatment effectiveness and developing personalized treatment. A lack of standardization in reporting among radiologists impacts the feasibility of large-scale interpretation of disease response. This study examines the utility of applying natural language processing (NLP) to the large-scale interpretation of disease responses using a standardized oncologic response lexicon (OR-RADS) to facilitate RWE collection. Radiologists annotated 3503 retrospectively collected clinical impressions from radiological reports across several cancer types with one of seven OR-RADS categories. A Bidirectional Encoder Representations from Transformers (BERT) model was trained on this dataset with an 80–20% train/test split to perform multiclass and single-class classification tasks using the OR-RADS. Radiologists also performed the classification to compare human and model performance. The model achieved accuracies from 95 to 99% across all classification tasks, performing better in single-class tasks compared to the multiclass task and producing minimal misclassifications, which pertained mostly to overpredicting the equivocal and mixed OR-RADS labels. Human accuracy ranged from 74 to 93% across all classification tasks, performing better on single-class tasks. This study demonstrates the feasibility of the BERT NLP model in predicting disease response in cancer patients, exceeding human performance, and encourages the use of the standardized OR-RADS lexicon to improve large-scale prediction accuracy. [ABSTRACT FROM AUTHOR]

Simple Summary: Our study provides an overview of the current state of artificial intelligence applications in urooncology and explores potential future advancements in this field. With remarkable progress already achieved, artificial intelligence has revolutionized urooncology by facilitating image analysis, grading, biomarker research, and treatment planning. We also discuss types of artificial intelligence and their possible applications in the management of cancers such as prostate, kidney, bladder, and testicular. As artificial intelligence technology continues to evolve, it holds immense promise for further advancing urooncology and enhancing the care of patients with cancer. Introduction: Artificial intelligence is transforming healthcare by driving innovation, automation, and optimization across various fields of medicine. The aim of this study was to determine whether artificial intelligence (AI) techniques can be used in the diagnosis, treatment planning, and monitoring of urological cancers. Methodology: We conducted a thorough search for original and review articles published until 31 May 2022 in the PUBMED/Scopus database. Our search included several terms related to AI and urooncology. Articles were selected with the consensus of all authors. Results: Several types of AI can be used in the medical field. The most common forms of AI are machine learning (ML), deep learning (DL), neural networks (NNs), natural language processing (NLP) systems, and computer vision. AI can improve various domains related to the management of urologic cancers, such as imaging, grading, and nodal staging. AI can also help identify appropriate diagnoses, treatment options, and even biomarkers. In the majority of these instances, AI is as accurate as or sometimes even superior to medical doctors. Conclusions: AI techniques have the potential to revolutionize the diagnosis, treatment, and monitoring of urologic cancers. The use of AI in urooncology care is expected to increase in the future, leading to improved patient outcomes and better overall management of these tumors. [ABSTRACT FROM AUTHOR]

In this paper, we present a new deep learning model to classify hematoxylin–eosin-stained breast biopsy images into four classes (normal tissues, benign lesions, in situ carcinomas, and invasive carcinomas). Our model uses a parallel structure consist of a convolutional neural network (CNN) and a recurrent neural network (RNN) for image feature extraction, which is greatly different from the common existed serial method of extracting image features by CNN and then inputting them into RNN. Then, we introduce a special perceptron attention mechanism, which is derived from the natural language processing (NLP) field, to unify the features extracted by the two different neural network structures of the model. In the convolution layer, general batch normalization is replaced by the new switchable normalization method. And the latest regularization technology, targeted dropout, is used to substitute for the general dropout in the last three fully connected layers of the model. In the testing phase, we use the model fusion method and test time augmentation technology on three different datasets of hematoxylin–eosin-stained breast biopsy images. The results demonstrate that our model significantly outperforms state-of-the-art methods. [ABSTRACT FROM AUTHOR]