Using a single abdominal computed tomography image to differentiate five contrast-enhancement phases: A machine-learning algorithm for radiomics-based precision medicine

Machine learning-based identification of contrast-enhancement phase of computed tomography scans

Contrast-enhanced computed tomography scans (CECT) are routinely used in the evaluation of different clinical scenarios, including the detection and characterization of hepatocellular carcinoma (HCC). Quantitative medical image analysis has been an exponentially growing scientific field. A number of studies reported on the effects of variations in the contrast enhancement phase on the reproducibility of quantitative imaging features extracted from CT scans. The identification and labeling of phase enhancement is a time-consuming task, with a current need for an accurate automated labeling algorithm to identify the enhancement phase of CT scans. In this study, we investigated the ability of machine learning algorithms to label the phases in a dataset of 59 HCC patients scanned with a dynamic contrast-enhanced CT protocol. The ground truth labels were provided by expert radiologists. Regions of interest were defined within the aorta, the portal vein, and the liver. Mean density values were extracted from those regions of interest and used for machine learning modeling. Models were evaluated using accuracy, the area under the curve (AUC), and Matthew's correlation coefficient (MCC). We tested the algorithms on an external dataset (76 patients). Our results indicate that several supervised learning algorithms (logistic regression, random forest, etc.) performed similarly, and our developed algorithms can accurately classify the phase of contrast enhancement.

Image-Guided Precision Medicine in the Diagnosis and Treatment of Pheochromocytomas and Paragangliomas

In this comprehensive review, we aimed to discuss the current state-of-the-art medical imaging for pheochromocytomas and paragangliomas (PPGLs) diagnosis and treatment. Despite major medical improvements, PPGLs, as with other neuroendocrine tumors (NETs), leave clinicians facing several challenges; their inherent particularities and their diagnosis and treatment pose several challenges for clinicians due to their inherent complexity, and they require management by multidisciplinary teams. The conventional concepts of medical imaging are currently undergoing a paradigm shift, thanks to developments in radiomic and metabolic imaging. However, despite active research, clinical relevance of these new parameters remains unclear, and further multicentric studies are needed in order to validate and increase widespread use and integration in clinical routine. Use of AI in PPGLs may detect changes in tumor phenotype that precede classical medical imaging biomarkers, such as shape, texture, and size. Since PPGLs are rare, slow-growing, and heterogeneous, multicentric collaboration will be necessary to have enough data in order to develop new PPGL biomarkers. In this nonsystematic review, our aim is to present an exhaustive pedagogical tool based on real-world cases, dedicated to physicians dealing with PPGLs, augmented by perspectives of artificial intelligence and big data.

Contrast phase recognition in liver computer tomography using deep learning

Hepatocellular carcinoma (HCC) has become the 4th leading cause of cancer-related deaths, with high social, economical and health implications. Imaging techniques such as multiphase computed tomography (CT) have been successfully used for diagnosis of liver tumors such as HCC in a feasible and accurate way and its interpretation relies mainly on comparing the appearance of the lesions in the different contrast phases of the exam. Recently, some researchers have been dedicated to the development of tools based on machine learning (ML) algorithms, especially by deep learning techniques, to improve the diagnosis of liver lesions in imaging exams. However, the lack of standardization in the naming of the CT contrast phases in the DICOM metadata is a problem for real-life deployment of machine learning tools. Therefore, it is important to correctly identify the exam phase based only on the image and not on the exam metadata, which is unreliable. Motivated by this problem, we successfully created an annotation platform and implemented a convolutional neural network (CNN) to automatically identify the CT scan phases in the HCFMUSP database in the city of São Paulo, Brazil. We improved this algorithm with hyperparameter tuning and evaluated it with cross validation methods. Comparing its predictions with the radiologists annotation, it achieved an accuracy of 94.6%, 98% and 100% in the testing dataset for the slice, volume and exam evaluation, respectively.

Effectiveness of Artificial Intelligence for Personalized Medicine in Neoplasms: A Systematic Review

Purpose

Artificial intelligence (AI) techniques are used in precision medicine to explore novel genotypes and phenotypes data. The main aims of precision medicine include early diagnosis, screening, and personalized treatment regime for a patient based on genetic-oriented features and characteristics. The main objective of this study was to review AI techniques and their effectiveness in neoplasm precision medicine.

Materials and Methods

A comprehensive search was performed in Medline (through PubMed), Scopus, ISI Web of Science, IEEE Xplore, Embase, and Cochrane databases from inception to December 29, 2021, in order to identify the studies that used AI methods for cancer precision medicine and evaluate outcomes of the models.

Results

Sixty-three studies were included in this systematic review. The main AI approaches in 17 papers (26.9%) were linear and nonlinear categories (random forest or decision trees), and in 21 citations, rule-based systems and deep learning models were used. Notably, 62% of the articles were done in the United States and China. R package was the most frequent software, and breast and lung cancer were the most selected neoplasms in the papers. Out of 63 papers, in 34 articles, genomic data like gene expression, somatic mutation data, phenotype data, and proteomics with drug-response which is functional data was used as input in AI methods; in 16 papers' (25.3%) drug response, functional data was utilized in personalization of treatment. The maximum values of the assessment indicators such as accuracy, sensitivity, specificity, precision, recall, and area under the curve (AUC) in included studies were 0.99, 1.00, 0.96, 0.98, 0.99, and 0.9929, respectively.

Conclusion

The findings showed that in many cases, the use of artificial intelligence methods had effective application in personalized medicine.

Predicting death or recurrence of portal hypertension symptoms after TIPS procedures

BACKGROUND

Accurate prediction of portal hypertension recurrence after transjugular intrahepatic portosystemic shunt (TIPS) placement will improve clinical decision-making.

PURPOSE

To evaluate if perioperative variables could predict disease-free survival (DFS) in cirrhotic patients with portal hypertension (PHT) treated with TIPS.

MATERIALS AND METHODS

We recruited 206 cirrhotic patients with PHT treated with TIPS, randomly assigned to training (n = 138) and validation (n = 68) sets. We recorded 7 epidemiological, 4 clinical, and 9 radiological variables. TIPS-distal end positioning (TIPS-DEP) measured the distance between the distal end of the stent and the hepatocaval junction on contrast-enhanced CT scans. In the training set, the signature was defined as the random forest for survival algorithm achieving the lowest error rate for the prediction of DFS which was landmarked 4 weeks after the TIPS procedure. In the training set, a simple to use scoring system was derived from variables selected by the signature. The primary endpoint was to assess if TIPS-DEP was associated with DFS. The secondary endpoint was to validate the scoring system in the validation set.

RESULTS

Overall, patients with TIPS-DEP ≥ 6 mm (n = 49) had a median DFS of 24.5 months vs. 72.8 months otherwise (n = 157, p = 0.004). In the training set, the scoring system was calculated by adding age ≥ 60 years old, Child-Pugh B or C, and TIPS-DEP ≥ 6 mm (1 point each) since the signature showed high DFS probability at 6.5 months post-landmark in patients that did not meet these criteria: 86%, 80%, and 78%, respectively. The hazard ratio [95 CI] between patients determined to be low-risk (< 2 points) and high-risk (≥ 2 points) was 2.30 [1.35-3.93] (p = 0.002) in the training set and 2.01 [0.94-4.32] (p = 0.072) in the validation set.

CONCLUSION

TIPS-DEP is an actionable radiological biomarker which can be combined with age and Child-Pugh score to predict death or PHT symptom recurrence after TIPS procedure.

KEY POINTS

• TIPS-DEP measurement was the third most important but only actionable variable for predicting DFS. • TIPS-DEP < 6 mm was associated with a DFS probability of 78% at 6.5 months post-landmark. • A simple scoring system calculated using age, Child-Pugh score, and TIPS-DEP predicted DFS after TIPS.

Understanding Sources of Variation to Improve the Reproducibility of Radiomics

Radiomics is the method of choice for investigating the association between cancer imaging phenotype, cancer genotype and clinical outcome prediction in the era of precision medicine. The fast dispersal of this new methodology has benefited from the existing advances of the core technologies involved in radiomics workflow: image acquisition, tumor segmentation, feature extraction and machine learning. However, despite the rapidly increasing body of publications, there is no real clinical use of a developed radiomics signature so far. Reasons are multifaceted. One of the major challenges is the lack of reproducibility and generalizability of the reported radiomics signatures (features and models). Sources of variation exist in each step of the workflow; some are controllable or can be controlled to certain degrees, while others are uncontrollable or even unknown. Insufficient transparency in reporting radiomics studies further prevents translation of the developed radiomics signatures from the bench to the bedside. This review article first addresses sources of variation, which is illustrated using demonstrative examples. Then, it reviews a number of published studies and progresses made to date in the investigation and improvement of feature reproducibility and model performance. Lastly, it discusses potential strategies and practical considerations to reduce feature variability and improve the quality of radiomics study. This review focuses on CT image acquisition, tumor segmentation, quantitative feature extraction, and the disease of lung cancer.

Identifying Robust Radiomics Features for Lung Cancer by Using In-Vivo and Phantom Lung Lesions

We propose a novel framework for determining radiomics feature robustness by considering the effects of both biological and noise signals. This framework is preliminarily tested in a study predicting the epidermal growth factor receptor (EGFR) mutation status in non-small cell lung cancer (NSCLC) patients. Pairs of CT images (baseline, 3-week post therapy) of 46 NSCLC patients with known EGFR mutation status were collected and a FDA-customized anthropomorphic thoracic phantom was scanned on two vendors' scanners at four different tube currents. Delta radiomics features were extracted from the NSCLC patient CTs and reproducible, non-redundant, and informative features were identified. The feature value differences between EGFR mutant and EGFR wildtype patients were quantitatively measured as the biological signal. Similarly, radiomics features were extracted from the phantom CTs. A pairwise comparison between settings resulted in a feature value difference that was quantitatively measured as the noise signal. Biological signals were compared to noise signals at each setting to determine if the distributions were significantly different by two-sample t-test, and thus robust. Four optimal features were selected to predict EGFR mutation status, Tumor-Mass, Sigmoid-Offset-Mean, Gabor-Energy and DWT-Energy, which quantified tumor mass, tumor-parenchyma density transition at boundary, line-like pattern inside tumor and intratumoral heterogeneity, respectively. The first three variables showed robustness across the majority of studied CT acquisition parameters. The textual feature DWT-Energy was less robust. The proposed framework was able to determine robustness of radiomics features at specific settings by comparing biological signal to noise signal. Identification of robust radiomics features may improve the generalizability of radiomics models in future studies.

Radiomics Texture Analysis for the Identification of Colorectal Liver Metastases Sensitive to First-Line Oxaliplatin-Based Chemotherapy

OBJECTIVE

The aim of this study was to develop a radiomics-based prediction model for the response of colorectal liver metastases to oxaliplatin-based chemotherapy.

METHODS

Forty-two consecutive patients treated with oxaliplatin-based first-line chemotherapy for colorectal liver metastasis at our institution from August 2013 to October 2019 were enrolled in this retrospective study. Overall, 126 liver metastases were chronologically divided into the training (n = 94) and validation (n = 32) cohorts. Regions of interest were manually segmented, and the best response to chemotherapy was decided based on Response Evaluation Criteria in Solid Tumors (RECIST). Patients who achieved clinical complete and partial response according to RECIST were defined as good responders. Radiomics features were extracted from the pretreatment enhanced computed tomography scans, and a radiomics score was calculated using the least absolute shrinkage and selection operator regression model in a trial cohort.

RESULTS

The radiomics score significantly discriminated good responders in both the trial (area under the curve [AUC] 0.8512, 95% confidence interval [CI] 0.7719-0.9305; p < 0.0001) and validation (AUC 0.7792, 95% CI 0.6176-0.9407; p < 0.0001) cohorts. Multivariate analysis revealed that high radiomics scores greater than - 0.06 (odds ratio [OR] 23.803, 95% CI 8.432-80.432; p < 0.0001), clinical non-T4 (OR 6.054, 95% CI 2.164-18.394; p = 0.0005), and metachronous disease (OR 11.787, 95% CI 2.333-70.833; p = 0.0025) were independently associated with good response.

CONCLUSIONS

Radiomics signatures may be a potential biomarker for the early prediction of chemosensitivity in colorectal liver metastases. This approach may support the treatment strategy for colorectal liver metastasis.

Reinventing radiation therapy with machine learning and imaging bio-markers (radiomics): State-of-the-art, challenges and perspectives

Radiation therapy is a pivotal cancer treatment that has significantly progressed over the last decade due to numerous technological breakthroughs. Imaging is now playing a critical role on deployment of the clinical workflow, both for treatment planning and treatment delivery. Machine-learning analysis of predefined features extracted from medical images, i.e. radiomics, has emerged as a promising clinical tool for a wide range of clinical problems addressing drug development, clinical diagnosis, treatment selection and implementation as well as prognosis. Radiomics denotes a paradigm shift redefining medical images as a quantitative asset for data-driven precision medicine. The adoption of machine-learning in a clinical setting and in particular of radiomics features requires the selection of robust, representative and clinically interpretable biomarkers that are properly evaluated on a representative clinical data set. To be clinically relevant, radiomics must not only improve patients' management with great accuracy but also be reproducible and generalizable. Hence, this review explores the existing literature and exposes its potential technical caveats, such as the lack of quality control, standardization, sufficient sample size, type of data collection, and external validation. Based upon the analysis of 165 original research studies based on PET, CT-scan, and MRI, this review provides an overview of new concepts, and hypotheses generating findings that should be validated. In particular, it describes evolving research trends to enhance several clinical tasks such as prognostication, treatment planning, response assessment, prediction of recurrence/relapse, and prediction of toxicity. Perspectives regarding the implementation of an AI-based radiotherapy workflow are presented.