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Acute Lymphoblastic Leukemia (ALL) is a life-threatening type of cancer wherein mortality rate is unquestionably high. Early detection of ALL can reduce both the rate of fatality as well as improve the diagnosis plan for patients. In this study, we developed the ALL Detector (ALLD), which is a deep learning-based network to distinguish ALL patients from healthy individuals based on blast cell microscopic images. We evaluated multiple DL-based models and the ResNet-based model performed the best with 98% accuracy in the classification task. We also compared the performance of ALLD against state-of-the-art tools utilized for the same purpose, and ALLD outperformed them all. We believe that ALLD will support pathologists to explicitly diagnose ALL in the early stages and reduce the burden on clinical practice overall. © 2022 The authors and IOS Press.
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Promoter regions of long non-coding RNA (lncRNA) genes are crucial to understand their transcriptional regulatory pattern. LncRNA genes, being more cryptic than protein-coding genes in terms of their functionality and biogenesis divergence, are lacking in number of existing studies to elucidate the roles of their promoters compared to their counterparts. Based on the overlap between epigenetic marks and transcription start sites, human lncRNAs were categorized into two broad categories: enhancer-originated lncRNAs (e-lncRNAs) and promoter-originated lncRNAs (p-lncRNAs) and hence these two groups are subject to distinct transcriptional regulatory programs. To understand the difference in the transcriptional regulatory mechanisms that governs p- and e-lncRNAs, we studied the promoter sequences of these two groups of lncRNAs including distinct transcription factor (TF) proteins that favor p-over e-lncRNA (and vice versa). In addition, we developed a convolution neural network (CNN) based deep learning (DL) framework DeePEL (deep p-, e-lncRNA promoter recognizer), to classify the promoter of p- and e-lncRNAs. To the best of our knowledge, this is the first attempt to classify these two groups of lncRNA promoters, using sequence and TF information, based on DL framework. We report several sequence specific signatures in the promoter regions as well as several distinct TFs specific to groups of lncRNAs that will help in understanding the promoter-proximal transcriptional regulation of p-lncRNAs and e-lncRNAs. © 2019 IEEE.
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Dual-energy X-ray absorptiometry (DXA) has been traditionally used to assess body composition covering bone, fat and muscle content. Cardiovascular disease (CVD) has deleterious effects on bone health and fat composition. Therefore, early detection of bone health, fat and muscle composition would help to anticipate a proper diagnosis and treatment plan for CVD patients. In this study, we leveraged machine learning (ML)-based models to predict CVD using DXA, demonstrating that it can be considered an innovative approach for early detection of CVD. We leveraged state-of-the-art ML models to classify the CVD group from non-CVD group. The proposed logistic regression-based model achieved nearly 80% accuracy. Overall, the bone mineral density, fat content, muscle mass and bone surface area measurements were elevated in the CVD group compared to non-CVD group. Ablation study revealed a more successful discriminatory power of fat content and bone mineral density than muscle mass and bone areas. To the best of our knowledge, this work is the first ML model to reveal the association between DXA measurements and CVD in the Qatari population. We believe this study will open new avenues of introducing DXA in creating the diagnosis and treatment plan of cardiovascular diseases. © 2022 The authors and IOS Press.
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Alzheimer's Disease (AD) is a neurodegenerative disease that causes complications with thinking capability, memory and behavior. AD is a major public health problem among the elderly in developed and developing countries. With the growth of AD around the world, there is a need to further expand our understanding of the roles different clinical measurements can have in the diagnosis of AD. In this work, we propose a machine learning-based technique to distinguish control subjects with no cognitive impairments, AD subjects, and subjects with mild cognitive impairment (MCI), often seen as precursors of AD. We utilized several machine learning (ML) techniques and found that Gradient Boosting Decision Trees achieved the highest performance above 84% classification accuracy. Also, we determined the importance of the features (clinical biomarkers) contributing to the proposed multi-class classification system. Further investigation on the biomarkers will pave the way to introduce better treatment plan for AD patients. © 2020 The authors and IOS Press.
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