Browsing by Author "Nandi, Dip"

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A Novel Hybrid Approach for Classifying Osteosarcoma Using Deep Feature Extraction and Multilayer Perceptron
(MDPI, 2023-06-18) Aziz, Md. Tarek; Mahmud, S. M. Hasan; Elahe, Md. Fazla; Jahan, Hosney; Rahman, Md Habibur; Nandi, Dip; Smirani, Lassaad K.; Ahmed, Kawsar; Bui, Francis M.; Moni, Mohammad Ali
Osteosarcoma is the most common type of bone cancer that tends to occur in teenagers and young adults. Due to crowded context, inter-class similarity, inter-class variation, and noise in H&E-stained (hematoxylin and eosin stain) histology tissue, pathologists frequently face difficulty in osteosarcoma tumor classification. In this paper, we introduced a hybrid framework for improving the efficiency of three types of osteosarcoma tumor (nontumor, necrosis, and viable tumor) classification by merging different types of CNN-based architectures with a multilayer perceptron (MLP) algorithm on the WSI (whole slide images) dataset. We performed various kinds of preprocessing on the WSI images. Then, five pre-trained CNN models were trained with multiple parameter settings to extract insightful features via transfer learning, where convolution combined with pooling was utilized as a feature extractor. For feature selection, a decision tree-based RFE was designed to recursively eliminate less significant features to improve the model generalization performance for accurate prediction. Here, a decision tree was used as an estimator to select the different features. Finally, a modified MLP classifier was employed to classify binary and multiclass types of osteosarcoma under the five-fold CV to assess the robustness of our proposed hybrid model. Moreover, the feature selection criteria were analyzed to select the optimal one based on their execution time and accuracy. The proposed model achieved an accuracy of 95.2% for multiclass classification and 99.4% for binary classification. Experimental findings indicate that our proposed model significantly outperforms existing methods; therefore, this model could be applicable to support doctors in osteosarcoma diagnosis in clinics. In addition, our proposed model is integrated into a web application using the FastAPI web framework to provide a real-time prediction.
An LSTM network-based model with attention techniques for predicting linear T-cell epitopes of the hepatitis C virus
(Scopus, 2024) Hosen, Md. Faruk; Mahmud, S. M. Hasan; Goh, Kah Ong Michael; Uddin, Muhammad Shahin; Nandi, Dip; Shatabda, Swakkhar; Shoombuatong, Watshara
: Hepatitis C virus (HCV) infection remains a significant global health challenge, often resulting in severe longterm physical complexity and even death. Since its discovery, HCV has exhibited substantial genetic variability, complicating vaccine development. Although some therapeutic approach have shown efficacy against certain HCV genotypes, a universally effective vaccine is still lacking. Recent research suggests that the body’s cellular immune response, particularly T cell epitopes of HCV (TCE-HCVs), plays a vital role in fighting the virus. Therefore, the precise and rapid identification of TCE-HCVs is essential for chronic HCV infection. In this work, we proposed a novel TCE-HCVs prediction model AttLSTM, which combines attention mechanism and long shortterm memory (LSTM). Specifically, we employed four robust feature encoding techniques: One-Hot Encoding, Global Vectors (GloVe), fastText, and Word2Vec to encode protein sequences. Additionally, k-mer embedding was utilized to help the model identify significant subsequence fragments within the protein sequences. To optimize the model’s performance, irrelevant features are eliminated using the SHapley Additive exPlanations (SHAP) approach. The resulting optimal feature subset was then fed into the AttLSTM model to identify TCEHCVs. The attention mechanism in this model dynamically captures the pairwise correlations of each neighboring target pair within a sliding window, thereby enhancing the understanding of the local environment of target residues. Extensive experiments showed that AttLSTM outperformed conventional machine learning (ML) classifiers in predictive performance. Notably, in k-fold cross validation, AttLSTM achieved superior performance compared to existing methods with accuracy of 80.77 %, MCC of 0.632, and AUC of 0.891. This exceptional performance indicates that AttLSTM has a strong predictive capability for identifying TCE-HCVs. We anticipate that AttLSTM will expedite the rapid identification of promising TCE-HCVs, aiding in the development of diagnostic and immunotherapeutic treatments for HCV in the future.
Detection of Different Stages of Alzheimer’s Disease Using CNN Classifier
(Tech Science Press, 2023-10-08) Mahmud, S M Hasan; Ali, Md Mamun; Shahriar, Mohammad Fahim; Al-Zahrani, Fahad Ahmed; Ahmed, Kawsar; Nandi, Dip; Bui, Francis M.
Alzheimer’s disease (AD) is a neurodevelopmental impairment that results in a person’s behavior, thinking, and memory loss. The most common symptoms of AD are losing memory and early aging. In addition to these, there are several serious impacts of AD. However, the impact of AD can be mitigated by early-stage detection though it cannot be cured permanently. Early-stage detection is the most challenging task for controlling and mitigating the impact of AD. The study proposes a predictive model to detect AD in the initial phase based on machine learning and a deep learning approach to address the issue. To build a predictive model, open-source data was collected where five stages of images of AD were available as Cognitive Normal (CN), Early Mild Cognitive Impairment (EMCI), Mild Cognitive Impairment (MCI), Late Mild Cognitive Impairment (LMCI), and AD. Every stage of AD is considered as a class, and then the dataset was divided into three parts binary class, three class, and five class. In this research, we applied different preprocessing steps with augmentation techniques to efficiently identify AD. It integrates a random oversampling technique to handle the imbalance problem from target classes, mitigating the model overfitting and biases. Then three machine learning classifiers, such as random forest (RF), K-Nearest neighbor (KNN), and support vector machine (SVM), and two deep learning methods, such as convolutional neuronal network (CNN) and artificial neural network (ANN) were applied on these datasets. After analyzing the performance of the used models and the datasets, it is found that CNN with binary class outperformed 88.20% accuracy. The result of the study indicates that the model is highly potential to detect AD in the initial phase.