Information Bottleneck Attribution for Visual Explanations of Diagnosis and Prognosis

Visual explanation methods have an important role in the prognosis of the patients where the annotated data is limited or unavailable. There have been several attempts to use gradient-based attribution methods to localize pathology from medical scans without using segmentation labels. This research direction has been impeded by the lack of robustness and reliability. These methods are highly sensitive to the network parameters. In this study, we introduce a robust visual explanation method to address this problem for medical applications. We provide an innovative visual explanation algorithm for general purpose and as an example application we demonstrate its effectiveness for quantifying lesions in the lungs caused by the Covid-19 with high accuracy and robustness without using dense segmentation labels. This approach overcomes the drawbacks of commonly used Grad-CAM and its extended versions. The premise behind our proposed strategy is that the information flow is minimized while ensuring the classifier prediction stays similar. Our findings indicate that the bottleneck condition provides a more stable severity estimation than the similar attribution methods. The source code will be publicly available upon publication.

Rapid artificial intelligence solutions in a pandemic-The COVID-19-20 Lung CT Lesion Segmentation Challenge.

Artificial intelligence (AI) methods for the automatic detection and quantification of COVID-19 lesions in chest computed tomography (CT) might play an important role in the monitoring and management of the disease. We organized an international challenge and competition for the development and comparison of AI algorithms for this task, which we supported with public data and state-of-the-art benchmark methods. Board Certified Radiologists annotated 295 public images from two sources (A and B) for algorithms training (n=199, source A), validation (n=50, source A) and testing (n=23, source A; n=23, source B). There were 1,096 registered teams of which 225 and 98 completed the validation and testing phases, respectively. The challenge showed that AI models could be rapidly designed by diverse teams with the potential to measure disease or facilitate timely and patient-specific interventions. This paper provides an overview and the major outcomes of the COVID-19 Lung CT Lesion Segmentation Challenge - 2020.

Information Bottleneck Attribution for Visual Explanations of Diagnosis and Prognosis.

Visual explanation methods have an important role in the prognosis of the patients where the annotated data is limited or unavailable. There have been several attempts to use gradient-based attribution methods to localize pathology from medical scans without using segmentation labels. This research direction has been impeded by the lack of robustness and reliability. These methods are highly sensitive to the network parameters. In this study, we introduce a robust visual explanation method to address this problem for medical applications. We provide an innovative visual explanation algorithm for general purpose and as an example application we demonstrate its effectiveness for quantifying lesions in the lungs caused by the Covid-19 with high accuracy and robustness without using dense segmentation labels. This approach overcomes the drawbacks of commonly used Grad-CAM and its extended versions. The premise behind our proposed strategy is that the information flow is minimized while ensuring the classifier prediction stays similar. Our findings indicate that the bottleneck condition provides a more stable severity estimation than the similar attribution methods. The source code will be publicly available upon publication.

AI-Assisted CT as a Clinical and Research Tool for COVID-19.

There is compelling support for widening the role of computed tomography (CT) for COVID-19 in clinical and research scenarios. Reverse transcription polymerase chain reaction (RT-PCR) testing, the gold standard for COVID-19 diagnosis, has two potential weaknesses: the delay in obtaining results and the possibility of RT-PCR test kits running out when demand spikes or being unavailable altogether. This perspective article discusses the potential use of CT in conjunction with RT-PCR in hospitals lacking sufficient access to RT-PCR test kits. The precedent for this approach is discussed based on the use of CT for COVID-19 diagnosis and screening in the United Kingdom and China. The hurdles and challenges are presented, which need addressing prior to realization of the potential roles for CT artificial intelligence (AI). The potential roles include a more accurate clinical classification, characterization for research roles and mechanisms, and informing clinical trial response criteria as a surrogate for clinical outcomes.

Rapid Artificial Intelligence Solutions in a Pandemic - The COVID-19-20 Lung CT Lesion Segmentation Challenge.

Artificial intelligence (AI) methods for the automatic detection and quantification of COVID-19 lesions in chest computed tomography (CT) might play an important role in the monitoring and management of the disease. We organized an international challenge and competition for the development and comparison of AI algorithms for this task, which we supported with public data and state-of-the-art benchmark methods. Board Certified Radiologists annotated 295 public images from two sources (A and B) for algorithms training (n=199, source A), validation (n=50, source A) and testing (n=23, source A; n=23, source B). There were 1,096 registered teams of which 225 and 98 completed the validation and testing phases, respectively. The challenge showed that AI models could be rapidly designed by diverse teams with the potential to measure disease or facilitate timely and patient-specific interventions. This paper provides an overview and the major outcomes of the COVID-19 Lung CT Lesion Segmentation Challenge - 2020.

The impact and collateral damage of COVID-19 on prostate MRI and guided biopsy operations: Society of Abdominal Radiology Prostate Cancer Disease-Focused Panel survey analysis.

The Coronavirus disease 2019 (COVID-19) pandemic has significantly affected health care systems throughout the world. A Qualtrics survey was targeted for radiologists around the world to study its effect on the operations of prostate MRI studies and biopsies. Descriptive statistics were reported. A total of 60 complete responses from five continents were included in the analysis. 70% of the responses were from academic institutions. Among all participants, the median (range) number of prostate MRI was 20 (0, 135) per week before the COVID-19 pandemic versus 10 (0, 30) during the lockdown period; the median (range) number of prostate biopsies was 4.5 (0, 60) per week before the COVID-19 versus 0 (0, 12) during the lockdown period. Among the 30% who used bowel preparation for their patients prior to MRI routinely, 11% stopped the bowel preparation due to the pandemic. 47% reported that their radiology departments faced staff disruptions, while 68% reported changes in clinic schedules in other clinical departments, particularly urology, genitourinary medical oncology, and radiation oncology. Finally, COVID-19 pandemic was found to disrupt not only the clinical prostate MRI operations but also impacted prostate MRI/biopsy research in up to 50% of institutions. The impact of this collateral damage in delaying diagnosis and treatment of prostate cancer is yet to be explored.

Generalized chest CT and lab curves throughout the course of COVID-19.

A better understanding of temporal relationships between chest CT and labs may provide a reference for disease severity over the disease course. Generalized curves of lung opacity volume and density over time can be used as standardized references from well before symptoms develop to over a month after recovery, when residual lung opacities remain. 739 patients with COVID-19 underwent CT and RT-PCR in an outbreak setting between January 21st and April 12th, 2020. 29 of 739 patients had serial exams (121 CTs and 279 laboratory measurements) over 50 ± 16 days, with an average of 4.2 sequential CTs each. Sequential volumes of total lung, overall opacity and opacity subtypes (ground glass opacity [GGO] and consolidation) were extracted using deep learning and manual segmentation. Generalized temporal curves of CT and laboratory measurements were correlated. Lung opacities appeared 3.4 ± 2.2 days prior to symptom onset. Opacity peaked 1 day after symptom onset. GGO onset was earlier and resolved later than consolidation. Lactate dehydrogenase, and C-reactive protein peaked earlier than procalcitonin and leukopenia. The temporal relationships of quantitative CT features and clinical labs have distinctive patterns and peaks in relation to symptom onset, which may inform early clinical course in patients with mild COVID-19 pneumonia, or may shed light upon chronic lung effects or mechanisms of medical countermeasures in clinical trials.

Avelumab, a PD-L1 Inhibitor, in Combination with Hypofractionated Radiotherapy and the Abscopal Effect in Relapsed Refractory Multiple Myeloma.

LESSONS LEARNED: Despite the initial optimism for using immune checkpoint inhibition in the treatment of multiple myeloma, subsequent clinical studies have been disappointing. Preclinical studies have suggested that priming the immune system with various modalities in addition to checkpoint inhibition may overcome the relative T-cell exhaustion or senescence; however, in this small data set, radiotherapy with checkpoint inhibition did not appear to activate the antitumor immune response. BACKGROUND: Extramedullary disease (EMD) is recognized as an aggressive subentity of multiple myeloma (MM) with a need for novel therapeutic approaches. We therefore designed a proof-of-principle pilot study to evaluate the synergy between the combination of the anti-PD-L1, avelumab, and concomitant hypofractionated radiotherapy. METHODS: This was a single-arm phase II Simon two-stage single center study that was prematurely terminated because of the COVID-19 pandemic after enrolling four patients. Key eligibility included patients with relapsed/refractory multiple myeloma (RRMM) who had exhausted or were not candidates for standard therapy and had at least one lesion amenable to radiotherapy. Patients received avelumab until progression or intolerable toxicity and hypofractionated radiotherapy to a focal lesion in cycle 2. Radiotherapy was delayed until cycle 2 to allow the avelumab to reach a study state, given the important observation from previous studies that concomitant therapy is needed for the abscopal effect. RESULTS: At a median potential follow-up of 10.5 months, there were no objective responses, one minimal response, and two stable disease as best response. The median progression-free survival (PFS) was 5.3 months (95% confidence interval [CI]: 2.5-7.1 months), and no deaths occurred. There were no grade ≥3 and five grade 1-2 treatment-related adverse events. CONCLUSION: Avelumab in combination with radiotherapy for patients with RRMM and EMD was associated with very modest systemic clinical benefit; however, patients did benefit as usual from local radiotherapy. Furthermore, the combination was very well tolerated compared with historical RRMM treatment regimens.

Federated semi-supervised learning for COVID region segmentation in chest CT using multi-national data from China, Italy, Japan.

The recent outbreak of Coronavirus Disease 2019 (COVID-19) has led to urgent needs for reliable diagnosis and management of SARS-CoV-2 infection. The current guideline is using RT-PCR for testing. As a complimentary tool with diagnostic imaging, chest Computed Tomography (CT) has been shown to be able to reveal visual patterns characteristic for COVID-19, which has definite value at several stages during the disease course. To facilitate CT analysis, recent efforts have focused on computer-aided characterization and diagnosis with chest CT scan, which has shown promising results. However, domain shift of data across clinical data centers poses a serious challenge when deploying learning-based models. A common way to alleviate this issue is to fine-tune the model locally with the target domains local data and annotations. Unfortunately, the availability and quality of local annotations usually varies due to heterogeneity in equipment and distribution of medical resources across the globe. This impact may be pronounced in the detection of COVID-19, since the relevant patterns vary in size, shape, and texture. In this work, we attempt to find a solution for this challenge via federated and semi-supervised learning. A multi-national database consisting of 1704 scans from three countries is adopted to study the performance gap, when training a model with one dataset and applying it to another. Expert radiologists manually delineated 945 scans for COVID-19 findings. In handling the variability in both the data and annotations, a novel federated semi-supervised learning technique is proposed to fully utilize all available data (with or without annotations). Federated learning avoids the need for sensitive data-sharing, which makes it favorable for institutions and nations with strict regulatory policy on data privacy. Moreover, semi-supervision potentially reduces the annotation burden under a distributed setting. The proposed framework is shown to be effective compared to fully supervised scenarios with conventional data sharing instead of model weight sharing.

CT and clinical assessment in asymptomatic and pre-symptomatic patients with early SARS-CoV-2 in outbreak settings.

OBJECTIVES: The early infection dynamics of patients with SARS-CoV-2 are not well understood. We aimed to investigate and characterize associations between clinical, laboratory, and imaging features of asymptomatic and pre-symptomatic patients with SARS-CoV-2. METHODS: Seventy-four patients with RT-PCR-proven SARS-CoV-2 infection were asymptomatic at presentation. All were retrospectively identified from 825 patients with chest CT scans and positive RT-PCR following exposure or travel risks in outbreak settings in Japan and China. CTs were obtained for every patient within a day of admission and were reviewed for infiltrate subtypes and percent with assistance from a deep learning tool. Correlations of clinical, laboratory, and imaging features were analyzed and comparisons were performed using univariate and multivariate logistic regression. RESULTS: Forty-eight of 74 (65%) initially asymptomatic patients had CT infiltrates that pre-dated symptom onset by 3.8 days. The most common CT infiltrates were ground glass opacities (45/48; 94%) and consolidation (22/48; 46%). Patient body temperature (p < 0.01), CRP (p < 0.01), and KL-6 (p = 0.02) were associated with the presence of CT infiltrates. Infiltrate volume (p = 0.01), percent lung involvement (p = 0.01), and consolidation (p = 0.043) were associated with subsequent development of symptoms. CONCLUSIONS: COVID-19 CT infiltrates pre-dated symptoms in two-thirds of patients. Body temperature elevation and laboratory evaluations may identify asymptomatic patients with SARS-CoV-2 CT infiltrates at presentation, and the characteristics of CT infiltrates could help identify asymptomatic SARS-CoV-2 patients who subsequently develop symptoms. The role of chest CT in COVID-19 may be illuminated by a better understanding of CT infiltrates in patients with early disease or SARS-CoV-2 exposure. KEY POINTS: • Forty-eight of 74 (65%) pre-selected asymptomatic patients with SARS-CoV-2 had abnormal chest CT findings. • CT infiltrates pre-dated symptom onset by 3.8 days (range 1-5). • KL-6, CRP, and elevated body temperature identified patients with CT infiltrates. Higher infiltrate volume, percent lung involvement, and pulmonary consolidation identified patients who developed symptoms.

Determination of disease severity in COVID-19 patients using deep learning in chest X-ray images.

PURPOSE: Chest X-ray plays a key role in diagnosis and management of COVID-19 patients and imaging features associated with clinical elements may assist with the development or validation of automated image analysis tools. We aimed to identify associations between clinical and radiographic features as well as to assess the feasibility of deep learning applied to chest X-rays in the setting of an acute COVID-19 outbreak. METHODS: A retrospective study of X-rays, clinical, and laboratory data was performed from 48 SARS-CoV-2 RT-PCR positive patients (age 60±17 years, 15 women) between February 22 and March 6, 2020 from a tertiary care hospital in Milan, Italy. Sixty-five chest X-rays were reviewed by two radiologists for alveolar and interstitial opacities and classified by severity on a scale from 0 to 3. Clinical factors (age, symptoms, comorbidities) were investigated for association with opacity severity and also with placement of central line or endotracheal tube. Deep learning models were then trained for two tasks: lung segmentation and opacity detection. Imaging characteristics were compared to clinical datapoints using the unpaired student's t-test or Mann-Whitney U test. Cohen's kappa analysis was used to evaluate the concordance of deep learning to conventional radiologist interpretation. RESULTS: Fifty-six percent of patients presented with alveolar opacities, 73% had interstitial opacities, and 23% had normal X-rays. The presence of alveolar or interstitial opacities was statistically correlated with age (P = 0.008) and comorbidities (P = 0.005). The extent of alveolar or interstitial opacities on baseline X-ray was significantly associated with the presence of endotracheal tube (P = 0.0008 and P = 0.049) or central line (P = 0.003 and P = 0.007). In comparison to human interpretation, the deep learning model achieved a kappa concordance of 0.51 for alveolar opacities and 0.71 for interstitial opacities. CONCLUSION: Chest X-ray analysis in an acute COVID-19 outbreak showed that the severity of opacities was associated with advanced age, comorbidities, as well as acuity of care. Artificial intelligence tools based upon deep learning of COVID-19 chest X-rays are feasible in the acute outbreak setting.

Artificial intelligence for the detection of COVID-19 pneumonia on chest CT using multinational datasets.

Chest CT is emerging as a valuable diagnostic tool for clinical management of COVID-19 associated lung disease. Artificial intelligence (AI) has the potential to aid in rapid evaluation of CT scans for differentiation of COVID-19 findings from other clinical entities. Here we show that a series of deep learning algorithms, trained in a diverse multinational cohort of 1280 patients to localize parietal pleura/lung parenchyma followed by classification of COVID-19 pneumonia, can achieve up to 90.8% accuracy, with 84% sensitivity and 93% specificity, as evaluated in an independent test set (not included in training and validation) of 1337 patients. Normal controls included chest CTs from oncology, emergency, and pneumonia-related indications. The false positive rate in 140 patients with laboratory confirmed other (non COVID-19) pneumonias was 10%. AI-based algorithms can readily identify CT scans with COVID-19 associated pneumonia, as well as distinguish non-COVID related pneumonias with high specificity in diverse patient populations.

Preparation of a radiology department in an Italian hospital dedicated to COVID-19 patients.

Preparedness for the ongoing coronavirus disease 2019 (COVID-19) and its spread in Italy called for setting up of adequately equipped and dedicated health facilities to manage sick patients while protecting healthcare workers, uninfected patients, and the community. In our country, in a short time span, the demand for critical care beds exceeded supply. A new sequestered hospital completely dedicated to intensive care (IC) for isolated COVID-19 patients needed to be designed, constructed, and deployed. Along with this new initiative, the new concept of "Pandemic Radiology Unit" was implemented as a practical solution to the emerging crisis, born out of a critical and urgent acute need. The present article describes logistics, planning, and practical design issues for such a pandemic radiology and critical care unit (e.g., space, infection control, safety of healthcare workers, etc.) adopted in the IC Hospital Unit for the care and management of COVID-19 patients.

Disposable Isolation Device to Reduce COVID-19 Contamination During CT Scanning.

RATIONALE AND OBJECTIVES: The use of chest computed tomography (CT) in the era of the COVID-19 pandemic raises concern regarding the transmission risks to patients and staff caused by CT room contamination. Meanwhile the Center for Disease Control guidance for air exchange in between patients may heavily impact workflows. To design a portable custom isolation device to reduce imaging equipment contamination during a pandemic. MATERIALS AND METHODS: Center for Disease Control air exchange guidelines and requirements were reviewed. Device functional requirements were outlined and designed. Engineering requirements were reviewed. Methods of practice and risk mitigation plans were outlined including donning and doffing procedures and failure modes. Cost impact was assessed in terms of CT patient throughput. RESULTS: CT air exchange solutions and alternatives were reviewed. Multiple isolation bag device designs were considered. Several designs were custom fabricated, prototyped and reduced to practice. A final design was tested on volunteers for comfort, test-fit, air seal, and breathability. Less than 14 times enhanced patient throughput was estimated, in an ideal setting, which could more than counterbalance the cost of the device itself. CONCLUSION: A novel isolation bag device is feasible for use in CT and might facilitate containment and reduce contamination in radiology departments during the COVID Pandemic.