A Guideline for Open-Source Tools to Make Medical Imaging Data Ready for Artificial Intelligence Applications: A Society of Imaging Informatics in Medicine (SIIM) Survey.

In recent years, the role of Artificial Intelligence (AI) in medical imaging has become increasingly prominent, with the majority of AI applications approved by the FDA being in imaging and radiology in 2023. The surge in AI model development to tackle clinical challenges underscores the necessity for preparing high-quality medical imaging data. Proper data preparation is crucial as it fosters the creation of standardized and reproducible AI models while minimizing biases. Data curation transforms raw data into a valuable, organized, and dependable resource and is a fundamental process to the success of machine learning and analytical projects. Considering the plethora of available tools for data curation in different stages, it is crucial to stay informed about the most relevant tools within specific research areas. In the current work, we propose a descriptive outline for different steps of data curation while we furnish compilations of tools collected from a survey applied among members of the Society of Imaging Informatics (SIIM) for each of these stages. This collection has the potential to enhance the decision-making process for researchers as they select the most appropriate tool for their specific tasks.

Sumatriptan attenuates fear-learning despair induced by social isolation stress in mice: Mediating role of hypothalamic-pituitary-adrenal axis.

OBJECTIVES: Research has demonstrated that chronic stress experienced early in life can lead to impairments in memory and learning. These deficits are attributed to an imbalance in the interaction between glucocorticoids, the end product of the hypothalamic-pituitary-adrenal (HPA) axis, and glucocorticoid receptors in brain regions responsible for mediating memory, such as the hippocampus. This imbalance can result in detrimental conditions like neuroinflammation. The aim of this study was to assess the impact of sumatriptan, a selective agonist for 5-HT 1B/1D receptors, on fear learning capabilities in a chronic social isolation stress model in mice, with a particular focus on the role of the HPA axis. METHODS: Mice were assigned to two opposing conditions, including social condition (SC) and isolated condition (IC) for a duration of five weeks. All mice underwent passive avoidance test, with their subsequent freezing behavior serving as an indicator of fear retrieval. Mice in the IC group were administered either a vehicle, sumatriptan, GR-127935 (a selective antagonist for 5-HT 1B/1D receptors), or a combination of sumatriptan and GR-127935 during the testing sessions. At the end, all mice were sacrificed and samples of their serum and hippocampus were collected for further analysis. RESULTS: Isolation was found to significantly reduce freezing behavior (p<0.001). An increase in the freezing response among IC mice was observed following the administration of varying doses of sumatriptan, as indicated by a one-way ANOVA analysis (p<0.001). However, the mitigating effects of sumatriptan were reversed upon the administration of GR-127935. An ELISA assay conducted before and after the passive avoidance test revealed no significant change in serum corticosterone levels among SC mice. In contrast, a significant increase was observed among IC mice, suggesting hyper-responsiveness of the HPA axis in isolated animals. This hyper-responsiveness was ameliorated following the administration of sumatriptan. Furthermore, both the sumatriptan and SC groups exhibited a similar trend, showing a significant increase in the expression of hippocampal glucocorticoid receptors following the stress of the passive avoidance test. Lastly, the elevated production of inflammatory cytokines (TNF-α, IL-1ß) observed following social isolation was attenuated in the sumatriptan group. CONCLUSION: Sumatriptan improved fear learning probably through modulation of HPA axis and hippocampus neuroinflammation.

Checklist for Reproducibility of Deep Learning in Medical Imaging.

The application of deep learning (DL) in medicine introduces transformative tools with the potential to enhance prognosis, diagnosis, and treatment planning. However, ensuring transparent documentation is essential for researchers to enhance reproducibility and refine techniques. Our study addresses the unique challenges presented by DL in medical imaging by developing a comprehensive checklist using the Delphi method to enhance reproducibility and reliability in this dynamic field. We compiled a preliminary checklist based on a comprehensive review of existing checklists and relevant literature. A panel of 11 experts in medical imaging and DL assessed these items using Likert scales, with two survey rounds to refine responses and gauge consensus. We also employed the content validity ratio with a cutoff of 0.59 to determine item face and content validity. Round 1 included a 27-item questionnaire, with 12 items demonstrating high consensus for face and content validity that were then left out of round 2. Round 2 involved refining the checklist, resulting in an additional 17 items. In the last round, 3 items were deemed non-essential or infeasible, while 2 newly suggested items received unanimous agreement for inclusion, resulting in a final 26-item DL model reporting checklist derived from the Delphi process. The 26-item checklist facilitates the reproducible reporting of DL tools and enables scientists to replicate the study's results.

Deep-learning for automated detection of MSU deposits on DECT: evaluating impact on efficiency and reader confidence.

Introduction: Dual-energy CT (DECT) is a non-invasive way to determine the presence of monosodium urate (MSU) crystals in the workup of gout. Color-coding distinguishes MSU from calcium following material decomposition and post-processing. Manually identifying these foci (most commonly labeled green) is tedious, and an automated detection system could streamline the process. This study aims to evaluate the impact of a deep-learning (DL) algorithm developed for detecting green pixelations on DECT on reader time, accuracy, and confidence. Methods: We collected a sample of positive and negative DECTs, reviewed twice-once with and once without the DL tool-with a 2-week washout period. An attending musculoskeletal radiologist and a fellow separately reviewed the cases, simulating clinical workflow. Metrics such as time taken, confidence in diagnosis, and the tool's helpfulness were recorded and statistically analyzed. Results: We included thirty DECTs from different patients. The DL tool significantly reduced the reading time for the trainee radiologist (p = 0.02), but not for the attending radiologist (p = 0.15). Diagnostic confidence remained unchanged for both (p = 0.45). However, the DL model identified tiny MSU deposits that led to a change in diagnosis in two cases for the in-training radiologist and one case for the attending radiologist. In 3/3 of these cases, the diagnosis was correct when using DL. Conclusions: The implementation of the developed DL model slightly reduced reading time for our less experienced reader and led to improved diagnostic accuracy. There was no statistically significant difference in diagnostic confidence when studies were interpreted without and with the DL model.

Identifying Patients with CSF-Venous Fistula Using Brain MRI: A Deep Learning Approach.

BACKGROUND AND PURPOSE: Spontaneous intracranial hypotension is an increasingly recognized condition. Spontaneous intracranial hypotension is caused by a CSF leak, which is commonly related to a CSF-venous fistula. In patients with spontaneous intracranial hypotension, multiple intracranial abnormalities can be observed on brain MR imaging, including dural enhancement, "brain sag," and pituitary engorgement. This study seeks to create a deep learning model for the accurate diagnosis of CSF-venous fistulas via brain MR imaging. MATERIALS AND METHODS: A review of patients with clinically suspected spontaneous intracranial hypotension who underwent digital subtraction myelogram imaging preceded by brain MR imaging was performed. The patients were categorized as having a definite CSF-venous fistula, no fistula, or indeterminate findings on a digital subtraction myelogram. The data set was split into 5 folds at the patient level and stratified by label. A 5-fold cross-validation was then used to evaluate the reliability of the model. The predictive value of the model to identify patients with a CSF leak was assessed by using the area under the receiver operating characteristic curve for each validation fold. RESULTS: There were 129 patients were included in this study. The median age was 54 years, and 66 (51.2%) had a CSF-venous fistula. In discriminating between positive and negative cases for CSF-venous fistulas, the classifier demonstrated an average area under the receiver operating characteristic curve of 0.8668 with a standard deviation of 0.0254 across the folds. CONCLUSIONS: This study developed a deep learning model that can predict the presence of a spinal CSF-venous fistula based on brain MR imaging in patients with suspected spontaneous intracranial hypotension. However, further model refinement and external validation are necessary before clinical adoption. This research highlights the substantial potential of deep learning in diagnosing CSF-venous fistulas by using brain MR imaging.

Automated diagnosis of autism with artificial intelligence: State of the art.

Autism spectrum disorder (ASD) represents a panel of conditions that begin during the developmental period and result in impairments of personal, social, academic, or occupational functioning. Early diagnosis is directly related to a better prognosis. Unfortunately, the diagnosis of ASD requires a long and exhausting subjective process. We aimed to review the state of the art for automated autism diagnosis and recognition in this research. In February 2022, we searched multiple databases and sources of gray literature for eligible studies. We used an adapted version of the QUADAS-2 tool to assess the risk of bias in the studies. A brief report of the methods and results of each study is presented. Data were synthesized for each modality separately using the Split Component Synthesis (SCS) method. We assessed heterogeneity using the I 2 statistics and evaluated publication bias using trim and fill tests combined with ln DOR. Confidence in cumulative evidence was assessed using the GRADE approach for diagnostic studies. We included 344 studies from 186,020 participants (51,129 are estimated to be unique) for nine different modalities in this review, from which 232 reported sufficient data for meta-analysis. The area under the curve was in the range of 0.71-0.90 for all the modalities. The studies on EEG data provided the best accuracy, with the area under the curve ranging between 0.85 and 0.93. We found that the literature is rife with bias and methodological/reporting flaws. Recommendations are provided for future research to provide better studies and fill in the current knowledge gaps.

THA-AID: Deep Learning Tool for Total Hip Arthroplasty Automatic Implant Detection With Uncertainty and Outlier Quantification.

BACKGROUND: Revision total hip arthroplasty (THA) requires preoperatively identifying in situ implants, a time-consuming and sometimes unachievable task. Although deep learning (DL) tools have been attempted to automate this process, existing approaches are limited by classifying few femoral and zero acetabular components, only classify on anterior-posterior (AP) radiographs, and do not report prediction uncertainty or flag outlier data. METHODS: This study introduces Total Hip Arhtroplasty Automated Implant Detector (THA-AID), a DL tool trained on 241,419 radiographs that identifies common designs of 20 femoral and 8 acetabular components from AP, lateral, or oblique views and reports prediction uncertainty using conformal prediction and outlier detection using a custom framework. We evaluated THA-AID using internal, external, and out-of-domain test sets and compared its performance with human experts. RESULTS: THA-AID achieved internal test set accuracies of 98.9% for both femoral and acetabular components with no significant differences based on radiographic view. The femoral classifier also achieved 97.0% accuracy on the external test set. Adding conformal prediction increased true label prediction by 0.1% for acetabular and 0.7 to 0.9% for femoral components. More than 99% of out-of-domain and >89% of in-domain outlier data were correctly identified by THA-AID. CONCLUSIONS: The THA-AID is an automated tool for implant identification from radiographs with exceptional performance on internal and external test sets and no decrement in performance based on radiographic view. Importantly, this is the first study in orthopedics to our knowledge including uncertainty quantification and outlier detection of a DL model.

Quantifying Uncertainty in Deep Learning of Radiologic Images.

In recent years, deep learning (DL) has shown impressive performance in radiologic image analysis. However, for a DL model to be useful in a real-world setting, its confidence in a prediction must also be known. Each DL model's output has an estimated probability, and these estimated probabilities are not always reliable. Uncertainty represents the trustworthiness (validity) of estimated probabilities. The higher the uncertainty, the lower the validity. Uncertainty quantification (UQ) methods determine the uncertainty level of each prediction. Predictions made without UQ methods are generally not trustworthy. By implementing UQ in medical DL models, users can be alerted when a model does not have enough information to make a confident decision. Consequently, a medical expert could reevaluate the uncertain cases, which would eventually lead to gaining more trust when using a model. This review focuses on recent trends using UQ methods in DL radiologic image analysis within a conceptual framework. Also discussed in this review are potential applications, challenges, and future directions of UQ in DL radiologic image analysis.

Reproducibility of Deep Learning Algorithms Developed for Medical Imaging Analysis: A Systematic Review.

Since 2000, there have been more than 8000 publications on radiology artificial intelligence (AI). AI breakthroughs allow complex tasks to be automated and even performed beyond human capabilities. However, the lack of details on the methods and algorithm code undercuts its scientific value. Many science subfields have recently faced a reproducibility crisis, eroding trust in processes and results, and influencing the rise in retractions of scientific papers. For the same reasons, conducting research in deep learning (DL) also requires reproducibility. Although several valuable manuscript checklists for AI in medical imaging exist, they are not focused specifically on reproducibility. In this study, we conducted a systematic review of recently published papers in the field of DL to evaluate if the description of their methodology could allow the reproducibility of their findings. We focused on the Journal of Digital Imaging (JDI), a specialized journal that publishes papers on AI and medical imaging. We used the keyword "Deep Learning" and collected the articles published between January 2020 and January 2022. We screened all the articles and included the ones which reported the development of a DL tool in medical imaging. We extracted the reported details about the dataset, data handling steps, data splitting, model details, and performance metrics of each included article. We found 148 articles. Eighty were included after screening for articles that reported developing a DL model for medical image analysis. Five studies have made their code publicly available, and 35 studies have utilized publicly available datasets. We provided figures to show the ratio and absolute count of reported items from included studies. According to our cross-sectional study, in JDI publications on DL in medical imaging, authors infrequently report the key elements of their study to make it reproducible.

A Comparison of Three Different Deep Learning-Based Models to Predict the MGMT Promoter Methylation Status in Glioblastoma Using Brain MRI.

Glioblastoma (GBM) is the most common primary malignant brain tumor in adults. The standard treatment for GBM consists of surgical resection followed by concurrent chemoradiotherapy and adjuvant temozolomide. O-6-methylguanine-DNA methyltransferase (MGMT) promoter methylation status is an important prognostic biomarker that predicts the response to temozolomide and guides treatment decisions. At present, the only reliable way to determine MGMT promoter methylation status is through the analysis of tumor tissues. Considering the complications of the tissue-based methods, an imaging-based approach is preferred. This study aimed to compare three different deep learning-based approaches for predicting MGMT promoter methylation status. We obtained 576 T2WI with their corresponding tumor masks, and MGMT promoter methylation status from, The Brain Tumor Segmentation (BraTS) 2021 datasets. We developed three different models: voxel-wise, slice-wise, and whole-brain. For voxel-wise classification, methylated and unmethylated MGMT tumor masks were made into 1 and 2 with 0 background, respectively. We converted each T2WI into 32 × 32 × 32 patches. We trained a 3D-Vnet model for tumor segmentation. After inference, we constructed the whole brain volume based on the patch's coordinates. The final prediction of MGMT methylation status was made by majority voting between the predicted voxel values of the biggest connected component. For slice-wise classification, we trained an object detection model for tumor detection and MGMT methylation status prediction, then for final prediction, we used majority voting. For the whole-brain approach, we trained a 3D Densenet121 for prediction. Whole-brain, slice-wise, and voxel-wise, accuracy was 65.42% (SD 3.97%), 61.37% (SD 1.48%), and 56.84% (SD 4.38%), respectively.

Machine Learning in Cardiovascular Imaging: A Scoping Review of Published Literature.

Purpose of Review: In this study, we planned and carried out a scoping review of the literature to learn how machine learning (ML) has been investigated in cardiovascular imaging (CVI). Recent Findings: During our search, we found numerous studies that developed or utilized existing ML models for segmentation, classification, object detection, generation, and regression applications involving cardiovascular imaging data. We first quantitatively investigated the different aspects of study characteristics, data handling, model development, and performance evaluation in all studies that were included in our review. We then supplemented these findings with a qualitative synthesis to highlight the common themes in the studied literature and provided recommendations to pave the way for upcoming research. Summary: ML is a subfield of artificial intelligence (AI) that enables computers to learn human-like decision-making from data. Due to its novel applications, ML is gaining more and more attention from researchers in the healthcare industry. Cardiovascular imaging is an active area of research in medical imaging with lots of room for incorporating new technologies, like ML. Supplementary Information: The online version contains supplementary material available at 10.1007/s40134-022-00407-8.

A deep learning algorithm for detecting lytic bone lesions of multiple myeloma on CT.

BACKGROUND: Whole-body low-dose CT is the recommended initial imaging modality to evaluate bone destruction as a result of multiple myeloma. Accurate interpretation of these scans to detect small lytic bone lesions is time intensive. A functional deep learning) algorithm to detect lytic lesions on CTs could improve the value of these CTs for myeloma imaging. Our objectives were to develop a DL algorithm and determine its performance at detecting lytic lesions of multiple myeloma. METHODS: Axial slices (2-mm section thickness) from whole-body low-dose CT scans of subjects with biochemically confirmed plasma cell dyscrasias were included in the study. Data were split into train and test sets at the patient level targeting a 90%/10% split. Two musculoskeletal radiologists annotated lytic lesions on the images with bounding boxes. Subsequently, we developed a two-step deep learning model comprising bone segmentation followed by lesion detection. Unet and "You Look Only Once" (YOLO) models were used as bone segmentation and lesion detection algorithms, respectively. Diagnostic performance was determined using the area under the receiver operating characteristic curve (AUROC). RESULTS: Forty whole-body low-dose CTs from 40 subjects yielded 2193 image slices. A total of 5640 lytic lesions were annotated. The two-step model achieved a sensitivity of 91.6% and a specificity of 84.6%. Lesion detection AUROC was 90.4%. CONCLUSION: We developed a deep learning model that detects lytic bone lesions of multiple myeloma on whole-body low-dose CTs with high performance. External validation is required prior to widespread adoption in clinical practice.

Mitigating Bias in Radiology Machine Learning: 2. Model Development.

There are increasing concerns about the bias and fairness of artificial intelligence (AI) models as they are put into clinical practice. Among the steps for implementing machine learning tools into clinical workflow, model development is an important stage where different types of biases can occur. This report focuses on four aspects of model development where such bias may arise: data augmentation, model and loss function, optimizers, and transfer learning. This report emphasizes appropriate considerations and practices that can mitigate biases in radiology AI studies. Keywords: Model, Bias, Machine Learning, Deep Learning, Radiology © RSNA, 2022.

Mitigating Bias in Radiology Machine Learning: 3. Performance Metrics.

The increasing use of machine learning (ML) algorithms in clinical settings raises concerns about bias in ML models. Bias can arise at any step of ML creation, including data handling, model development, and performance evaluation. Potential biases in the ML model can be minimized by implementing these steps correctly. This report focuses on performance evaluation and discusses model fitness, as well as a set of performance evaluation toolboxes: namely, performance metrics, performance interpretation maps, and uncertainty quantification. By discussing the strengths and limitations of each toolbox, our report highlights strategies and considerations to mitigate and detect biases during performance evaluations of radiology artificial intelligence models. Keywords: Segmentation, Diagnosis, Convolutional Neural Network (CNN) © RSNA, 2022.

Mitigating Bias in Radiology Machine Learning: 1. Data Handling.

Minimizing bias is critical to adoption and implementation of machine learning (ML) in clinical practice. Systematic mathematical biases produce consistent and reproducible differences between the observed and expected performance of ML systems, resulting in suboptimal performance. Such biases can be traced back to various phases of ML development: data handling, model development, and performance evaluation. This report presents 12 suboptimal practices during data handling of an ML study, explains how those practices can lead to biases, and describes what may be done to mitigate them. Authors employ an arbitrary and simplified framework that splits ML data handling into four steps: data collection, data investigation, data splitting, and feature engineering. Examples from the available research literature are provided. A Google Colaboratory Jupyter notebook includes code examples to demonstrate the suboptimal practices and steps to prevent them. Keywords: Data Handling, Bias, Machine Learning, Deep Learning, Convolutional Neural Network (CNN), Computer-aided Diagnosis (CAD) © RSNA, 2022.

The mirror mechanism in schizophrenia: A systematic review and qualitative meta-analysis.

Background: Mirror neuron system (MNS) consists of visuomotor neurons that are responsible for the mirror neuron activity (MNA), meaning that each time an individual observes another individual performing an action, these neurons encode that action, and are activated in the observer's cortical motor system. Previous studies report its malfunction in autism, opening doors to investigate the underlying pathophysiology of the disorder in a more elaborate way and coming up with new rehabilitation methods. The study of MNA function in schizophrenia patients has not been as frequent and conclusive as in autism. In this research, we aimed to evaluate the functional integrity of MNA and the microstructural integrity of MNS in schizophrenia patients. Methods: We included case-control studies that have evaluated MNA in schizophrenia patients compared to healthy controls using a variety of objective assessment tools. In August 2022, we searched Embase, PubMed, and Web of Science for eligible studies. We used an adapted version of the NIH Quality Assessment of Case-Control Studies tool to assess the quality of the included studies. Evidence was analyzed using vote counting methods of the direction of the effect and was tested statistically using the Sign test. Certainty of evidence was assessed using CERQual. Results: We included 32 studies for the analysis. Statistical tests revealed decreased MNA (p = 0.002) in schizophrenia patients. The certainty of the evidence was judged to be moderate. Investigations of heterogeneity revealed a possible relationship between the age and the positive symptoms of participants in the included studies and the direction of the observed effect. Discussion: This finding contributes to gaining a better understanding of the underlying pathophysiology of the disorder by revealing its possible relation to some of the symptoms in schizophrenia patients, while also highlighting a new commonality with autism. Systematic review registration: PROSPERO identifier: CRD42021236453.

Machine Learning and Deep Learning in Cardiothoracic Imaging: A Scoping Review.

Machine-learning (ML) and deep-learning (DL) algorithms are part of a group of modeling algorithms that grasp the hidden patterns in data based on a training process, enabling them to extract complex information from the input data. In the past decade, these algorithms have been increasingly used for image processing, specifically in the medical domain. Cardiothoracic imaging is one of the early adopters of ML/DL research, and the COVID-19 pandemic resulted in more research focus on the feasibility and applications of ML/DL in cardiothoracic imaging. In this scoping review, we systematically searched available peer-reviewed medical literature on cardiothoracic imaging and quantitatively extracted key data elements in order to get a big picture of how ML/DL have been used in the rapidly evolving cardiothoracic imaging field. During this report, we provide insights on different applications of ML/DL and some nuances pertaining to this specific field of research. Finally, we provide general suggestions on how researchers can make their research more than just a proof-of-concept and move toward clinical adoption.

A deep learning model for discriminating true progression from pseudoprogression in glioblastoma patients.

INTRODUCTION: Glioblastomas (GBMs) are highly aggressive tumors. A common clinical challenge after standard of care treatment is differentiating tumor progression from treatment-related changes, also known as pseudoprogression (PsP). Usually, PsP resolves or stabilizes without further treatment or a course of steroids, whereas true progression (TP) requires more aggressive management. Differentiating PsP from TP will affect the patient's outcome. This study investigated using deep learning to distinguish PsP MRI features from progressive disease. METHOD: We included GBM patients with a new or increasingly enhancing lesion within the original radiation field. We labeled those who subsequently were stable or improved on imaging and clinically as PsP and those with clinical and imaging deterioration as TP. A subset of subjects underwent a second resection. We labeled these subjects as PsP, or TP based on the histological diagnosis. We coregistered contrast-enhanced T1 MRIs with T2-weighted images for each patient and used them as input to a 3-D Densenet121 model and using five-fold cross-validation to predict TP vs PsP. RESULT: We included 124 patients who met the criteria, and of those, 63 were PsP and 61 were TP. We trained a deep learning model that achieved 76.4% (range 70-84%, SD 5.122) mean accuracy over the 5 folds, 0.7560 (range 0.6553-0.8535, SD 0.069) mean AUROCC, 88.72% (SD 6.86) mean sensitivity, and 62.05% (SD 9.11) mean specificity. CONCLUSION: We report the development of a deep learning model that distinguishes PsP from TP in GBM patients treated per the Stupp protocol. Further refinement and external validation are required prior to widespread adoption in clinical practice.

Abstract screening using the automated tool Rayyan: results of effectiveness in three diagnostic test accuracy systematic reviews.

OBJECTIVE: To evaluate the performance of the automated abstract screening tool Rayyan. METHODS: The records obtained from the search for three systematic reviews were manually screened in four stages. At the end of each stage, Rayyan was used to predict the eligibility score for the remaining records. At two different thresholds (≤2.5 and < 2.5 for exclusion of a record) Rayyan-generated ratings were compared with the decisions made by human reviewers in the manual screening process and the tool's accuracy metrics were calculated. RESULTS: Two thousand fifty-four records were screened manually, of which 379 were judged to be eligible for full-text assessment, and 112 were eventually included in the final review. For finding records eligible for full-text assessment, at the threshold of < 2.5 for exclusion, Rayyan managed to achieve sensitivity values of 97-99% with specificity values of 19-58%, while at the threshold of ≤2.5 for exclusion it had a specificity of 100% with sensitivity values of 1-29%. For the task of finding eligible reports for inclusion in the final review, almost similar results were obtained. DISCUSSION: At the threshold of < 2.5 for exclusion, Rayyan managed to be a reliable tool for excluding ineligible records, but it was not much reliable for finding eligible records. We emphasize that this study was conducted on diagnostic test accuracy reviews, which are more difficult to screen due to inconsistent terminology.