Faculty Publications
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Item An enhanced protein secondary structure prediction using deep learning framework on hybrid profile based features(Elsevier Ltd, 2020) Kumar, P.; Bankapur, S.; Patil, N.Accurate protein secondary structure prediction (PSSP) is essential to identify structural classes, protein folds, and its tertiary structure. To identify the secondary structure, experimental methods exhibit higher precision with the trade-off of high cost and time. In this study, we propose an effective prediction model which consists of hybrid features of 42-dimensions with the combination of convolutional neural network (CNN) and bidirectional recurrent neural network (BRNN). The proposed model is accessed on four benchmark datasets such as CB6133, CB513, CASP10, and CAP11 using Q3, Q8, and segment overlap (Sov) metrics. The proposed model reported Q3 accuracy of 85.4%, 85.4%, 83.7%, 81.5%, and Q8 accuracy 75.8%, 73.5%, 72.2%, and 70% on CB6133, CB513, CASP10, and CAP11 datasets respectively. The results of the proposed model are improved by a minimum factor of 2.5% and 2.1% in Q3 and Q8 accuracy respectively, as compared to the popular existing models on CB513 dataset. Further, the quality of the Q3 results is validated by structural class prediction and compared with PSI-PRED. The experiment showed that the quality of the Q3 results of the proposed model is higher than that of PSI-PRED. © 2019 Elsevier B.V.Item An Enhanced Protein Fold Recognition for Low Similarity Datasets Using Convolutional and Skip-Gram Features with Deep Neural Network(Institute of Electrical and Electronics Engineers Inc., 2021) Bankapur, S.; Patil, N.The protein fold recognition is one of the important tasks of structural biology, which helps in addressing further challenges like predicting the protein tertiary structures and its functions. Many machine learning works are published to identify the protein folds effectively. However, very few works have reported the fold recognition accuracy above 80% on benchmark datasets. In this study, an effective set of global and local features are extracted from the proposed Convolutional (Conv) and SkipXGram bi-gram (SXGbg) techniques, and the fold recognition is performed using the proposed deep neural network. The performance of the proposed model reported 91.4% fold accuracy on one of the derived low similarity (< 25%) datasets of latest extended version of SCOPe_2.07. The proposed model is further evaluated on three popular and publicly available benchmark datasets such as DD, EDD, and TG and obtained 85.9%, 95.8%, and 88.8% fold accuracies, respectively. This work is first to report fold recognition accuracy above 85% on all the benchmark datasets. The performance of the proposed model has outperformed the best state-of-the-art models by 5% to 23% on DD, 2% to 19% on EDD, and 3% to 30% on TG dataset. © 2002-2011 IEEE.Item An effective feature extraction with deep neural network architecture for protein-secondary-structure prediction(Springer, 2021) Jayasimha, A.; Mudambi, R.; Pavan, P.; Lokaksha, B.M.; Bankapur, S.; Patil, N.With the increased importance of proteins in day-to-day life, it is imperative to know the protein functions. Deciphering protein structure elucidates protein functions. Experimental approaches for protein-structure analysis are expensive and time-consuming, and require high dexterity. Thus, finding a viable computational approach is vital. Due to the high complexity of predicting protein structure (tertiary structure) directly, research in this field aims at the protein-secondary-structure prediction which is directly related to its tertiary structure. This research aims at exploring a plethora of features, namely position-specific scoring matrices, hidden Markov model alignment matrices, and physicochemical properties, that carry rich information required to predict the secondary structure. Furthermore, it aims at exploring a suitable combination of the features which could capture diverse information about the protein secondary structure. Finally, a cascaded convolutional neural network and bidirectional long short-term memory architecture is fit on the models, and two evaluation metrics, namely, Q8 score and segment overlap score, are benchmarked on various datasets. Our proposed model trained on data of CB6133 dataset and tested on CB513 dataset beats the benchmark models by a minimum of 2.9%. © 2021, The Author(s), under exclusive licence to Springer-Verlag GmbH Austria, part of Springer Nature.Item Cardamom Plant Disease Detection Approach Using EfficientNetV2(Institute of Electrical and Electronics Engineers Inc., 2022) Sunil, C.K.; Jaidhar, C.D.; Patil, N.Cardamom is a queen of spices. It is indigenously grown in the evergreen forests of Karnataka, Kerala, Tamil Nadu, and the northeastern states of India. India is the third largest producer of cardamom. Plant diseases cause a catastrophic influence on food production safety; they reduce the eminence and quantum of agricultural products. Plant diseases may cause significantly high loss or no harvest in dreadful cases. Various diseases and pests affect the growth of cardamom plants at different stages and crop yields. This study concentrated on two diseases of cardamom plants, Colletotrichum Blight and Phyllosticta Leaf Spot of cardamom and three diseases of grape, Black Rot, ESCA, and Isariopsis Leaf Spot. Various methods have been proposed for plant disease detection, and deep learning has become the preferred method because of its spectacular accomplishment. In this study, U2-Net was used to remove the unwanted background of an input image by selecting multiscale features. This work proposes a cardamom plant disease detection approach using the EfficientNetV2 model. A comprehensive set of experiments was carried out to ascertain the performance of the proposed approach and compare it with other models such as EfficientNet and Convolutional Neural Network (CNN). The experimental results showed that the proposed approach achieved a detection accuracy of 98.26%. © 2013 IEEE.Item Segmentation and classification of white blood cancer cells from bone marrow microscopic images using duplet-convolutional neural network design(Springer, 2023) Devi, T.G.; Patil, N.; Rai, S.; Philipose, C.P.Cancer is a disease linked to the untamed and rapid division of cells in the body. Cancer detection through conventional methods like complete blood count is a tedious and time-consuming task prone to human errors. The introduction of image processing techniques and computer-aided diagnostics is beneficial to this field as the results obtained by utilizing these methods are quick and accurate. The proposed method in this paper uses a design Convolutional Leaky RELU with CatBoost and XGBoost (CLR-CXG) to segment the images and extract the important features that help in classification. The binary classification algorithm and gradient boosting algorithm CatBoost (Categorical Boost) and XGBoost (Extreme Gradient Boost) are implemented individually. Moreover, Convolutional Leaky RELU with CatBoost (CLRC) is designed to decrease bias and provide high accuracy, while Convolutional Leaky RELU with XGBoost (CLRXG) is designed for classification or regression prediction problems which will increase the speed of executing the algorithm and improve its performance. Thus the CLR-CXG classifies the test images into Acute Lymphoblastic Leukemia (ALL) or Multiple Myeloma (MM). Finally, the CLRC algorithm achieved 100% accuracy in classifying cancer cells, and the recorded run time is 10s. Moreover, the CLRXG algorithm has gained an accuracy of 97.12% for classifying cancer cells and 12 s for executing the process. © 2023, The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.Item Real-time microscopy image-based segmentation and classification models for cancer cell detection(Springer, 2023) Devi, T.G.; Patil, N.; Rai, S.; Philipose, C.P.Image processing techniques and algorithms are extensively used for biomedical applications. Convolution Neural Network (CNN) is gaining popularity in fields such as the analysis of complex documents and images, which qualifies the approach to be used in biomedical applications. The key drawback of the CNN application is that it can’t call the previous layer output following the layer’s input. To address this issue, the present research has proposed the novel Modified U-Net architecture with ELU Activation Framework (MU-EAF) to detect and classify cancerous cells in the blood smear images. The system is trained with 880 samples, of which 220 samples were utilized in the validation model, and 31 images were utilized to verify the proposed model. The identified mask output of the segmentation model in the predicted mask fits the classification model to identify the cancer cell occurrence in the collected images. In addition, the segmentation evaluation is done by matching each pixel of the ground truth mask (labels) to the predicted labels from the model. The performance metrics for evaluating the segmentation of images are pixel accuracy, dice coefficient (F1-score), and Jaccard coefficient. Moreover, the model is compared with VGG-16 and simple modified CNN models, which have four blocks, each consisting of a convolutional layer, batch normalization, and activation layer with RELU activation function that are implemented and for assessing the same images used for the proposed model. The proposed model shows higher accuracy in comparison. © 2023, The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.Item Optimization-based convolutional neural model for the classification of white blood cells(Springer Nature, 2024) Devi, T.G.; Patil, N.White blood cells (WBCs) are one of the most significant parts of the human immune system, and they play a crucial role in diagnosing the characteristics of pathologists and blood-related diseases. The characteristics of WBCs are well-defined based on the morphological behavior of their nuclei, and the number and types of WBCs can often determine the presence of diseases or illnesses. Generally, there are different types of WBCs, and the accurate classification of WBCs helps in proper diagnosis and treatment. Although various classification models were developed in the past, they face issues like less classification accuracy, high error rate, and large execution. Hence, a novel classification strategy named the African Buffalo-based Convolutional Neural Model (ABCNM) is proposed to classify the types of WBCs accurately. The proposed strategy commences with collecting WBC sample databases, which are preprocessed and trained into the system for classification. The preprocessing phase removes the noises and training flaws, which helps improve the dataset's quality and consistency. Further, feature extraction is performed to segment the WBCs, and African Buffalo fitness is updated in the classification layer for the correct classification of WBCs. The proposed framework is modeled in Python, and the experimental analysis depicts that it achieved 99.12% accuracy, 98.16% precision, 99% sensitivity, 99.04% specificity, and 99.02% f-measure. Furthermore, a comparative assessment with the existing techniques validated that the proposed strategy obtained better performances than the conventional models. © The Author(s) 2024.Item Integrating Evolutionary and Structural Properties for Protein Interaction Site Prediction Using Graph and Temporal Convolutions(Institute of Electrical and Electronics Engineers Inc., 2025) Bhat, P.; Patil, N.Predicting protein interaction sites is crucial for tasks such as constructing protein interaction networks, analyzing protein functions, studying molecular-level pathology, and designing novel drugs. However, the restricted predictive performance of sequence-based computational approaches has led to the rise of structure-oriented approaches. Existing cutting-edge methods mostly focus on the secondary structural features, leaving significant scope for further performance improvement. This study incorporates additional structural features from a tertiary-level perspective to derive composite features using graph and temporal convolutions. A hybrid weighted loss function efficiently handles the class imbalance. A fully connected neural network generates the final predictions. The outlined model is tested on various publicly accessible datasets, showing a substantial improvement in performance over leading models. Comparative analysis with the best models from the literature reports enhancement in the Matthews Correlation Coefficient(MCC) and Area under the precision-recall curve (AUPRC) by 4.8% and 4.1% on the Test_60 dataset, 9.8% and 11.2% on the Test_315 dataset, 10.4% and 11.5% on the Dtestset72 dataset, 12.6% and 13.9% on the PDBtestset164 dataset and 10% and 13.1% on the Test_84 dataset. Finally, the statistical t-test showcases the significance of the proposed model in the protein interaction site prediction task. © 2025 IEEE.