Best rank-1 approximations without orthogonal invariance for the 1-norm

Data measured in the real-world is often composed of both a true signal, such as an image or experimental response, and a perturbation, such as noise or weak secondary effects. Low-rank matrix approximation is one commonly used technique to extract the true signal from the data. Given a matrix representation of the data, this method seeks the nearest low-rank matrix where the distance is measured using a matrix norm. The classic Eckart-Young-Mirsky theorem tells us how to use the Singular Value Decomposition (SVD) to compute a best low-rank approximation of a matrix for any orthogonally invariant norm. This leaves as an open question how to compute a best low-rank approximation for norms that are not orthogonally invariant, like the 1-norm. In this thesis, we present how to calculate the best rank-1 approximations for 2-by-n and n-by-2 matrices in the 1-norm. We consider both the operator induced 1-norm (maximum column 1-norm) and the Frobenius 1-norm (sum of absolute values over the matrix). We present some thoughts on how to extend the arguments to larger matrices

Assessment of COVID-19 data reporting in 100+ websites and apps in India

Introduction: India is among the top three countries in the world both in COVID-19 case and death counts. With the pandemic far from over, timely, transparent, and accessible reporting of COVID-19 data continues to be critical for India's pandemic efforts. Methods: We systematically analyze the quality of reporting of COVID-19 data in over one hundred government platforms (web and mobile) from India. Results: Our analyses reveal a lack of granular data in the reporting of COVID-19 surveillance, vaccination, and vacant bed availability. As of 5 June 2021, age and gender distribution are available for less than 22% of cases and deaths, and comorbidity distribution is available for less than 30% of deaths. Amid rising concerns of undercounting cases and deaths in India, our results highlight a patchy reporting of granular data even among the reported cases and deaths. Furthermore, total vaccination stratified by healthcare workers, frontline workers, and age brackets is reported by only 14 out of India's 36 subnationals (states and union territories). There is no reporting of adverse events following immunization by vaccine and event type. Discussion: By showing what, where, and how much data is missing, we highlight the need for a more responsible and transparent reporting of granular COVID-19 data in India

Assessment of COVID-19 data reporting in 100+ websites and apps in India.

India is among the top three countries in the world both in COVID-19 case and death counts. With the pandemic far from over, timely, transparent, and accessible reporting of COVID-19 data continues to be critical for India's pandemic efforts. We systematically analyze the quality of reporting of COVID-19 data in over one hundred government platforms (web and mobile) from India. Our analyses reveal a lack of granular data in the reporting of COVID-19 surveillance, vaccination, and vacant bed availability. As of 5 June 2021, age and gender distribution are available for less than 22% of cases and deaths, and comorbidity distribution is available for less than 30% of deaths. Amid rising concerns of undercounting cases and deaths in India, our results highlight a patchy reporting of granular data even among the reported cases and deaths. Furthermore, total vaccination stratified by healthcare workers, frontline workers, and age brackets is reported by only 14 out of India's 36 subnationals (states and union territories). There is no reporting of adverse events following immunization by vaccine and event type. By showing what, where, and how much data is missing, we highlight the need for a more responsible and transparent reporting of granular COVID-19 data in India

Learning image representations for content-based image retrieval of radiotherapy treatment plans

Objective. In this work, we propose a content-based image retrieval (CBIR) method for retrieving dose distributions of previously planned patients based on anatomical similarity. Retrieved dose distributions from this method can be incorporated into automated treatment planning workflows in order to streamline the iterative planning process. As CBIR has not yet been applied to treatment planning, our work seeks to understand which current machine learning models are most viable in this context. Approach. Our proposed CBIR method trains a representation model that produces latent space embeddings of a patient’s anatomical information. The latent space embeddings of new patients are then compared against those of previous patients in a database for image retrieval of dose distributions. All source code for this project is available on github. Main results. The retrieval performance of various CBIR methods is evaluated on a dataset consisting of both publicly available image sets and clinical image sets from our institution. This study compares various encoding methods, ranging from simple autoencoders to more recent Siamese networks like SimSiam, and the best performance was observed for the multitask Siamese network. Significance. Our current results demonstrate that excellent image retrieval performance can be obtained through slight changes to previously developed Siamese networks. We hope to integrate CBIR into automated planning workflow in future works.Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.RST/Medical Physics & Technolog

A molecularly integrated grade for meningioma.

BackgroundMeningiomas are the most common primary intracranial tumor in adults. Clinical care is currently guided by the World Health Organization (WHO) grade assigned to meningiomas, a 3-tiered grading system based on histopathology features, as well as extent of surgical resection. Clinical behavior, however, often fails to conform to the WHO grade. Additional prognostic information is needed to optimize patient management.MethodsWe evaluated whether chromosomal copy-number data improved prediction of time-to-recurrence for patients with meningioma who were treated with surgery, relative to the WHO schema. The models were developed using Cox proportional hazards, random survival forest, and gradient boosting in a discovery cohort of 527 meningioma patients and validated in 2 independent cohorts of 172 meningioma patients characterized by orthogonal genomic platforms.ResultsWe developed a 3-tiered grading scheme (Integrated Grades 1-3), which incorporated mitotic count and loss of chromosome 1p, 3p, 4, 6, 10, 14q, 18, 19, or CDKN2A. 32% of meningiomas reclassified to either a lower-risk or higher-risk Integrated Grade compared to their assigned WHO grade. The Integrated Grade more accurately identified meningioma patients at risk for recurrence, relative to the WHO grade, as determined by time-dependent area under the curve, average precision, and the Brier score.ConclusionWe propose a molecularly integrated grading scheme for meningiomas that significantly improves upon the current WHO grading system in prediction of progression-free survival. This framework can be broadly adopted by clinicians with relative ease using widely available genomic technologies and presents an advance in the care of meningioma patients

Targeted gene expression profiling predicts meningioma outcomes and radiotherapy responses

Surgery is the mainstay of treatment for meningioma, the most common primary intracranial tumor, but improvements in meningioma risk stratification are needed and indications for postoperative radiotherapy are controversial. Here we develop a targeted gene expression biomarker that predicts meningioma outcomes and radiotherapy responses. Using a discovery cohort of 173 meningiomas, we developed a 34-gene expression risk score and performed clinical and analytical validation of this biomarker on independent meningiomas from 12 institutions across 3 continents (N = 1,856), including 103 meningiomas from a prospective clinical trial. The gene expression biomarker improved discrimination of outcomes compared with all other systems tested (N = 9) in the clinical validation cohort for local recurrence (5-year area under the curve (AUC) 0.81) and overall survival (5-year AUC 0.80). The increase in AUC compared with the standard of care, World Health Organization 2021 grade, was 0.11 for local recurrence (95% confidence interval 0.07 to 0.17, P &lt; 0.001). The gene expression biomarker identified meningiomas benefiting from postoperative radiotherapy (hazard ratio 0.54, 95% confidence interval 0.37 to 0.78, P = 0.0001) and suggested postoperative management could be refined for 29.8% of patients. In sum, our results identify a targeted gene expression biomarker that improves discrimination of meningioma outcomes, including prediction of postoperative radiotherapy responses.</p