Faculty Publications
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Item Ensemble deep neural models for automated abnormality detection and classification in precision care applications(Elsevier, 2023) Karthik, K.; Mayya, V.; Kamath S․, S.Radiological imaging is one of the most relied upon modalities in the clinical diagnosis and treatment planning process. Conventional diagnosis involves the manual analysis of radiology images by experienced radiologists, which is often a time-consuming and labor-intensive process. The scarcity of experienced radiologists and necessity of large-scale X-rays image analysis given the huge diagnosis workload at most hospitals stresses the need for automated clinical diagnosis systems capable of fast and accurate identification of abnormalities, disease characteristic identification, disease classification, and others. Such automated methods are thus a fundamental requirement in clinical workflow management applications. In this work, we present an approach for multitask clinical objectives such as disease classification and detection of abnormalities. The proposed model leverages the predictive power of deep neural models for enabling evidence-based diagnosis. During validation experiments, the model achieved an accuracy of 89.58% along with sensitivity and specificity of 85.83% and 90.83%, respectively, with an AUC (area under the ROC curve) of 95.84% for normal/no findings versus COVID-19 chest radiograph classification and an accuracy of 73.19% for upper extremity musculoskeletal images. The performance of the model for the classification and abnormality identification tasks, when benchmarked over multiple standard datasets, emphasizes its suitability and adaptability in real-world clinical settings, with significant improvements in radiology-based diagnosis workflow and patient care. © 2023 Elsevier Inc. All rights reserved.Item Autonomic computing in medical informatics: Accessing and retrieval of EMR(2009) Chandrashekharan, K.; Rao, A.; Sruthi, B.Medical informatics is an interdisciplinary field of research, where a great deal of collaboration is required to achieve efficient solutions. In this paper we bring in the concept of implementing autonomic computing in medical informatics. The work is in the aspect of maintaining and accessing patient's medical records and/or further retrieval of data in an efficient way with the role of autonomic computing in it. We exhibit a solution in the form of an automated system for EMR (electronic medical record), in this context. © 2009 IEEE.Item Medical Image Retrieval Using Manifold Ranking with Relevance Feedback(Institute of Electrical and Electronics Engineers Inc., 2018) Soundalgekar, P.; Kulkarni, M.; Nagaraju, D.; Kamath S․, S.Medical image retrieval (MedIR) is a challenging field in Visual information retrieval, due to the multi-dimensional and multi-modal context of the underlying content. Traditional models do not take the intrinsic characteristics of data into consideration and have achieved limited accuracy in application to medical images. Manifold Ranking (MR) is a technique that can be used in further optimizing precision and recall in MedIR applications as it ranks items by traversing a dynamically constructed content-specific information graph. In this paper, a MedIR approach based on Manifold Ranking is proposed. Medical images being multi-dimensional, exhibit underlying cluster and manifold information which enhances semantic relevance and allows for label uniformity. Hence, when adapted for MedIR, MR can help in achieving large-scale ranking across datasets as is the case in most medical imaging applications. In addition, a relevance feedback mechanism was also incorporated to support a learning based system. We show that MR achieved significant improvement in retrieval results with relevance feedback as compared to the Euclidean Distance (ED) rankings. This showcases the importance of analyzing the inherent latent structure in medical image data for better performance over traditional methods. © 2018 IEEE.Item Deep Neural Models for Early Diagnosis of Knee Osteoarthritis and Severity Grade Prediction(Springer Science and Business Media Deutschland GmbH, 2022) Shenoy, T.N.; Medayil, M.; Kamath S․, S.Osteoarthritis (OA) is a type of arthritis that results in malfunction and eventual loss of the cartilage of joints. It occurs when the cartilage that cushions the ends of the bones wear out. OA is the most common joint disease which frequently occurs after the age of 45 in case of males and 55 in the case of females. Manual detection of OA is a tedious and labour-intensive task and is performed by trained specialists. We propose a fully automated computer-aided diagnosis system to detect and grade osteoarthritis severity as per the Kellgren-Lawrence (KL) classification. In this paper, we experiment with various approaches for automated OA detection from X-ray images. Image-level information such as content descriptors and image transforms are identified and assigned weights using Fisher scores. KL-grade is then projected using weighted nearest neighbours, and different stages of OA severity are classified. Pre-processing, segmentation, and classification of the X-ray images are achieved using data augmentation, deep neural network, and residual neural networks. We present experimental results and discussion with respect to the best-performing models in our experiments. © 2022, The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.Item A Comprehensive Review of Brain Tumor Detection and Segmentation Techniques(Springer Science and Business Media Deutschland GmbH, 2023) Azade, A.; Kumar, P.; Kamath S․, S.Brain tumors are particularly dangerous type of tumor, and if this is not treated in time it maybe prove to be deadly and may also spread across other body parts. Brain tumor is the swelling or growth of unwanted tissues in the brain that results from the unregulated and disordered division of cells. The presence of these tissues resulting abnormal behavior and lot of other complications. The detection of brain tumor is done by using different techniques out of which through magnetic resonance images (MRIs). The scanning process is a time-consuming manual task that needs the involvement of medical professionals. Automating the task of detection of the brain tumor while also grading the severity accurately can help in managing the patients’ disease effectively. As tumor tissue of different patients is different, automating such processes is often a challenging task. Researchers have incorporated image segmentation for extraction of suspicious regions from MRI, using image processing and AI-based techniques. Radiomic analysis also plays a big role in feature extraction processes. In this paper, we present a comprehensive review of existing approaches for brain tumour detection, covering deep neural models, radiomic analysis and segmentation-based methods for brain tumor classification and segmentation, along with a discussion on prevalent issues, challenges, and future directions of research. © 2023, The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.Item Transformer and Knowledge Based Siamese Models for Medical Document Retrieval(Institute of Electrical and Electronics Engineers Inc., 2023) Dash, A.; Merchant, A.M.; Chintawar, S.; Kamath S․, S.Vocabulary mismatch is a significant issue when it comes to query-based document retrieval in the medical field. Since the documents are typically authored by professionals, they may contain many specialized terms that are not widely understood or used. Traditional information retrieval (IR) models like vector space and best match-based models fail in this regard. Neural Learning to Rank (NLtR) and transformer models have attracted significant research attention in the field of IR. Recent works in the medical field utilize medical knowledge bases (KB) that map words to concepts and aid in connecting several words to the same concept. In this paper, we present various Siamese-structured transformer and knowledge-based retrieval models designed to address the retrieval issues in the medical domain. The experimental evaluation highlighted the superior performance of the proposed retrieval model, and the best one, based on the UMLSBert ENG transformer, achieved best-in-class performance with respect to all evaluation metrics. © 2023 IEEE.Item Multi-channel, convolutional attention based neural model for automated diagnostic coding of unstructured patient discharge summaries(Elsevier B.V., 2021) Mayya, V.; Kamath S?, S.S.; S. Krishnan, G.S.; Gangavarapu, T.Effective coding of patient records in hospitals is an essential requirement for epidemiology, billing, and managing insurance claims. The prevalent practice of manual coding, carried out by trained medical coders, is error-prone and time-consuming. Mitigating this labor-intensive process by developing diagnostic coding systems built on patients’ Electronic Medical Records (EMRs) is vital. However, developing nations with low digitization rates have limited availability of structured EMRs, thereby necessitating a need for systems that leverage unstructured data sources. Despite the rich clinical information available in such unstructured data, modeling them is complex, owing to the variety and sparseness of diagnostic codes, complex structural and temporal nature of summaries, and prolific use of medical jargon. This work proposes a context-attentive network to facilitate automatic diagnostic code assignment as a multi-label classification problem. The proposed model facilitates information aggregation across a patient's discharge summary via multi-channel, variable-sized convolutional filters to extract multi-granular snippets. The attention mechanism enables selecting vital segments in those snippets that map to the clinical codes. The model's superior performance underscores its effectiveness compared to the state-of-the-art on the MIMIC-III database. Additionally, experimental validation using the CodiEsp dataset exhibited the model's interpretability and explainability. © 2021 Elsevier B.V.Item An empirical study of preprocessing techniques with convolutional neural networks for accurate detection of chronic ocular diseases using fundus images(Springer, 2023) Mayya, V.; Kamath S․, S.K.; Kulkarni, U.; Surya, D.K.; Acharya, U.R.Chronic Ocular Diseases (COD) such as myopia, diabetic retinopathy, age-related macular degeneration, glaucoma, and cataract can affect the eye and may even lead to severe vision impairment or blindness. According to a recent World Health Organization (WHO) report on vision, at least 2.2 billion individuals worldwide suffer from vision impairment. Often, overt signs indicative of COD do not manifest until the disease has progressed to an advanced stage. However, if COD is detected early, vision impairment can be avoided by early intervention and cost-effective treatment. Ophthalmologists are trained to detect COD by examining certain minute changes in the retina, such as microaneurysms, macular edema, hemorrhages, and alterations in the blood vessels. The range of eye conditions is diverse, and each of these conditions requires a unique patient-specific treatment. Convolutional neural networks (CNNs) have demonstrated significant potential in multi-disciplinary fields, including the detection of a variety of eye diseases. In this study, we combined several preprocessing approaches with convolutional neural networks to accurately detect COD in eye fundus images. To the best of our knowledge, this is the first work that provides a qualitative analysis of preprocessing approaches for COD classification using CNN models. Experimental results demonstrate that CNNs trained on the region of interest segmented images outperform the models trained on the original input images by a substantial margin. Additionally, an ensemble of three preprocessing techniques outperformed other state-of-the-art approaches by 30% and 3%, in terms of Kappa and F1 scores, respectively. The developed prototype has been extensively tested and can be evaluated on more comprehensive COD datasets for deployment in the clinical setup. © 2022, The Author(s).Item Automated hard exudate segmentation using neural encoders and attention mechanisms for diabetic retinopathy diagnosis(Inderscience Publishers, 2023) Gawas, P.; Sowmya Kamath, S.Diabetic retinopathy (DR) is a complication caused by increased blood glucose levels, which causes retinal damage in diabetic patients’ eyes. If not discovered and treated early, it can lead to vision loss. Hard exudates (HE) are one of its characteristic signs. Identification of HE is a paramount step in early diagnosis of DR. In this work, the suitability of U-Net-based deep CNN with different encoder configurations and attention gates (AG) is experimented, for HE segmentation. The proposed models were benchmarked on the standard IDRiD dataset. To overcome the challenges related to the limited dataset, data augmentation techniques were also applied to generate image patches and used for model training. Extensive experiments on the dataset revealed that U-Net with AG achieved an accuracy of 98.8%. The U-Net with ResNet50 as the encoder backbone achieved an accuracy of 98.64%. The findings show that the presented models are effective and suitable for early-stage clinical diagnosis. © © 2023 Inderscience Enterprises Ltd.Item MSDNet: a deep neural ensemble model for abnormality detection and classification of plain radiographs(Springer Science and Business Media Deutschland GmbH, 2023) Karthik, K.; Kamath S․, S.S.Modern medical diagnostic techniques facilitate accurate diagnosis and treatment recommendations in healthcare. Such diagnostics procedures are performed daily in large numbers, thus, the clinical interpretation workload of radiologists is very high. Identification of abnormalities is a predominantly manual task that is performed by radiologists before the medical scans are available to the patient’s referring doctor for further recommendations. On the other hand, for a radiologist to delineate the imaging study’s findings/observations as a textual report is also a tedious task. Automated methods for radiographic image examination for identifying abnormalities and generating reliable radiology report are thus a fundamental requirement in clinical workflow management applications. In this work, we present an automated approach for abnormality classification, localization and diagnostic report retrieval for identified abnormalities. We propose MSDNet, an ensemble of Convolutional Neural models for abnormality classification, which combines the features of multiple CNN models to enhance abnormality classification performance. The proposed model also is designed to localize and visualize the detected abnormality on the radiograph image, based on an abnormal region detection algorithm to further optimize the diagnosis quality. Furthermore, the extracted features generated by MSDNet are used to automatically generate the diagnosis text report using an automatic content-based report retrieval algorithm. The upper extremity musculo-skeletal images from the MURA dataset and chest X-ray images from Indiana dataset were used for the experimental evaluation of the proposed approach. The proposed model achieved promising results, with an accuracy of 82.69%, showing its significant impact on alleviating radiologists’ cognitive load, thus improving the overall efficiency. © 2022, The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.