Faculty Publications
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Item Stroke classification from computed tomography scans using 3D convolutional neural network(Elsevier Ltd, 2022) Neethi, A.S.; Niyas, S.; Kannath, S.K.; Mathew, J.; Anzar, A.M.; Rajan, J.Stroke is a cerebrovascular condition with a significant morbidity and mortality rate and causes physical disabilities for survivors. Once the symptoms are identified, it requires a time-critical diagnosis with the help of the most commonly available imaging techniques. Computed tomography (CT) scans are used worldwide for preliminary stroke diagnosis. It demands the expertise and experience of a radiologist to identify the stroke type, which is critical for initiating the treatment. This work attempts to gather those domain skills and build a model from CT scans to diagnose stroke. The non-contrast computed tomography (NCCT) scan of the brain comprises volumetric images or a 3D stack of image slices. So, a model that aims to solve the problem by targeting a 2D slice may fail to address the volumetric nature. We propose a 3D-based fully convolutional classification model to identify stroke cases from CT images that take into account the contextual longitudinal composition of volumetric data. We formulate a custom pre-processing module to enhance the scans and aid in improving the classification performance. Some of the significant challenges faced by 3D CNN are the less number of training samples, and the number of scans is mostly biased in favor of normal patients. In this work, the limitation of insufficient training volume and class imbalanced data have been rectified with the help of a strided slicing approach. A block-wise design was used to formulate the proposed network, with the initial part focusing on adjusting the dimensionality, at the same time retaining the features. Later on, the accumulated feature maps were effectively learned utilizing bundled convolutions and skip connections. The results of the proposed method were compared against 3D CNN stroke classification models on NCCT, various 3D CNN architectures on other brain imaging modalities, and 3D extensions of some of the classical CNN architectures. The proposed method achieved an improvement of 14.28% in the F1-score over the state-of-the-art 3D CNN stroke classification model. © 2022 Elsevier LtdItem A novel deep classifier framework for automated molecular subtyping of breast carcinoma using immunohistochemistry image analysis(Elsevier Ltd, 2022) Mathew, T.; Niyas, S.; Johnpaul, C.I.; Kini, J.; Rajan, J.Breast carcinoma has various subtypes based on the genetic factors involved in the pathogenesis of the malignancy. Identifying the exact subtype and providing targeted treatment to the patient can improve the survival chances. Molecular subtyping through immunohistochemistry analysis is a pathology procedure to determine the subtype of breast cancer. The existing manual procedure is tedious and involves assessing the status of the four vital molecular biomarkers present in the tumor tissues. In this paper, a deep learning-based framework for automated molecular subtyping of breast cancer is proposed. Digital slide images of the four biomarkers are separately processed by the proposed framework. In the preprocessing stage, the non-informative background regions from the images are separated. The patches extracted from the foreground regions are classified into target classes using convolutional neural network models trained for this purpose. Classification results are post-processed to predict the status of all the four biomarkers. The predictions for the individual biomarkers are finally consolidated as per clinical guidelines to determine the subtype of the cancer. The proposed system is evaluated for the performance of individual biomarker status prediction and patient-level subtype classification.For patient-level evaluation of biomarkers ER, PR, K67, and HER2, the proposed method gives F1 Scores 1.00, 1.00, 0.90, and 0.94 respectively, whereas for molecular subtyping an F1 score of 0.89 is obtained. In both these aspects, the proposed framework has given significant results that show the effectiveness of our approach. © 2022 Elsevier LtdItem Semi-supervised structure attentive temporal mixup coherence for medical image segmentation(Elsevier B.V., 2022) Pawan, S.J.; Jeevan, G.; Rajan, J.Deep convolutional neural networks have shown eminent performance in medical image segmentation in supervised learning. However, this success is predicated on the availability of large volumes of pixel-level labeled data, making these approaches impractical when labeled data is scarce. On the other hand, semi-supervised learning utilizes pertinent information from unlabeled data along with minimal labeled data, alleviating the demand for labeled data. In this paper, we leverage the mixup-based risk minimization operator in a student–teacher-based semi-supervised paradigm along with structure-aware constraints to enforce consistency coherence among the student predictions for unlabeled samples and the teacher predictions for the corresponding mixup sample by significantly diminishing the need for labeled data. Besides, due to the intrinsic simplicity of the linear combination operation used for generating mixup samples, the proposed method stands at a computational advantage over existing consistency regularization-based SSL methods. We experimentally validate the performance of the proposed model on two public benchmark datasets, namely the Left Atrial (LA) and Automatic Cardiac Diagnosis Challenge (ACDC) datasets. Notably, on the LA dataset's lowest labeled data set-up (5%), the proposed method significantly improved the Dice Similarity Coefficient and the Jaccard Similarity Coefficient by 1.08% and 1.46%, respectively. Furthermore, we demonstrate the efficacy of the proposed method with a consistent improvement across various labeled data proportions on the aforementioned datasets. © 2022 Nalecz Institute of Biocybernetics and Biomedical Engineering of the Polish Academy of SciencesItem Automated Molecular Subtyping of Breast Carcinoma Using Deep Learning Techniques(Institute of Electrical and Electronics Engineers Inc., 2023) Niyas, S.; Bygari, R.; Naik, R.; Viswanath, B.; Ugwekar, D.; Mathew, T.; Kavya, J.; Kini, J.R.; Rajan, J.Objective: Molecular subtyping is an important procedure for prognosis and targeted therapy of breast carcinoma, the most common type of malignancy affecting women. Immunohistochemistry (IHC) analysis is the widely accepted method for molecular subtyping. It involves the assessment of the four molecular biomarkers namely estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2), and antigen Ki67 using appropriate antibody reagents. Conventionally, these biomarkers are assessed manually by a pathologist, who finally combines individual results to identify the molecular subtype. Molecular subtyping necessitates the status of all the four biomarkers together, and to the best of our knowledge, no such automated method exists. This paper proposes a novel deep learning framework for automatic molecular subtyping of breast cancer from IHC images. Methods and procedures: A modified LadderNet architecture is proposed to segment the immunopositive elements from ER, PR, HER2, and Ki67 biomarker slides. This architecture uses long skip connections to pass encoder feature space from different semantic levels to the decoder layers, allowing concurrent learning with multi-scale features. The entire architecture is an ensemble of multiple fully convolutional neural networks, and learning pathways are chosen adaptively based on input data. The segmentation stage is followed by a post-processing stage to quantify the extent of immunopositive elements to predict the final status for each biomarker. Results: The performance of segmentation models for each IHC biomarker is evaluated qualitatively and quantitatively. Furthermore, the biomarker prediction results are also evaluated. The results obtained by our method are highly in concordance with manual assessment by pathologists. Clinical impact: Accurate automated molecular subtyping can speed up this pathology procedure, reduce pathologists' workload and associated costs, and facilitate targeted treatment to obtain better outcomes. © 2013 IEEE.Item An automated deep learning pipeline for detecting user errors in spirometry test(Elsevier Ltd, 2024) Bonthada, S.; Pariserum Perumal, S.P.; Naik, P.P.; Mahesh, M.A.; Rajan, J.Spirometer is used as a major diagnostic tool for obstructive airway diseases and a monitoring tool for therapy response and disease staging over time. It is a sophisticated medical device employed to quantify flow and volume of air exhaled by a subject during a specific testing period. The essential metrics obtained from the spirometry test, play a crucial role in enabling healthcare professionals to thoroughly evaluate the respiratory health and condition of the individual under examination. Several spirometer measurements including Forced Vital Capacity (FVC) and Forced Expiratory Volume (FEV) serve as guidelines for diagnosis and prognosis of Chronic Obstructive Pulmonary Diseases (COPD) and asthma. However, user errors caused by different reasons, including improper handling of the equipment and poor performance during the maneuvers of the expiratory airflow, end up in incorrect treatment directions. To ensure accurate results, spirometry tests traditionally require the presence of a skilled professional to identify and address these errors promptly. A novel machine learning approach is proposed in this paper to automatically identify four such user errors based on Volume-Time and Flow-Volume graphs. By detecting specific errors and providing immediate feedback to patients, reliability and accuracy of spirometry results will be improved and the need for trained professionals will be reduced. The implementation facilitates the widespread adoption of spirometry, particularly in low-resource telemedicine settings. This work implements a binary classification model distinguishing between normal and error test samples, achieving a prediction accuracy of 93%. Additionally, a 4-way classification model is presented for identifying individual error sub-types, demonstrating a prediction accuracy of 94%. © 2023 Elsevier Ltd