Md. Mostafizer Rahman

Atsushi Shirafuji, Md. Mostafizer Rahman, Md Faizul Ibne Amin et al.

Programmers often struggle to identify and fix bugs in their programs. In recent years, many language models (LMs) have been proposed to fix erroneous programs and support error recovery. However, the LMs tend to generate solutions that differ from the original input programs. This leads to potential comprehension difficulties for users. In this paper, we propose an approach to suggest a correct program with minimal repair edits using CodeT5. We fine-tune a pre-trained CodeT5 on code pairs of wrong and correct programs and evaluate its performance with several baseline models. The experimental results show that the fine-tuned CodeT5 achieves a pass@100 of 91.95% and an average edit distance of the most similar correct program of 6.84, which indicates that at least one correct program can be suggested by generating 100 candidate programs. We demonstrate the effectiveness of LMs in suggesting program repair with minimal edits for solving introductory programming problems.

Md Faizul Ibne Amin, Yutaka Watanobe, Md. Mostafizer Rahman et al.

Programming is a core skill in computer science and software engineering (SE), yet identifying and resolving code errors remains challenging for both novice and experienced developers. While Large Language Models (LLMs) have shown remarkable capabilities in natural language understanding and generation tasks, their potential in domain-specific, complex scenarios, such as multi-label classification (MLC) of programming errors, remains underexplored. Recognizing this less-explored area, this study proposes a multi-label error classification (MLEC) framework for source code that leverages fine-tuned LLMs, including CodeT5-base, GraphCodeBERT, CodeT5+, UniXcoder, RoBERTa, PLBART, and CoTexT. These LLMs are integrated with deep learning (DL) architectures such as GRU, LSTM, BiLSTM, and BiLSTM with an additive attention mechanism (BiLSTM-A) to capture both syntactic and semantic features from a real-world student-written Python code error dataset. Extensive experiments across 32 model variants, optimized using Optuna-based hyperparameter tuning, have been evaluated using comprehensive multi-label metrics, including average accuracy, macro and weighted precision, recall, F1-score, exact match accuracy, One-error, Hamming loss, Jaccard similarity, and ROC-AUC (micro, macro, and weighted). Results show that the CodeT5+\_GRU model achieved the strongest performance, with a weighted F1-score of 0.8243, average accuracy of 91.84\%, exact match accuracy of 53.78\%, Hamming loss of 0.0816, and One error of 0.0708. These findings confirm the effectiveness of combining pretrained semantic encoders with efficient recurrent decoders. This work lays the foundation for developing intelligent, scalable tools for automated code feedback, with potential applications in programming education (PE) and broader SE domains.

Md Mostafizer Rahman, Ariful Islam Shiplu, Yutaka Watanobe et al.

Contextual embeddings generated by LLMs exhibit strong positional inductive biases, which can limit their ability to fully capture long-range, order-sensitive dependencies in highly structured source code. Consequently, how to further refine and enhance LLM embeddings for improved code understanding remains an open research question. To address this gap, we propose a hybrid LLM-RNN framework that reinforces LLM-generated contextual embeddings with a sequential RNN architecture. The embeddings reprocessing step aims to reinforce sequential semantics and strengthen order-aware dependencies inherent in source code. We evaluate the proposed hybrid models on both benchmark and real-world coding datasets. The experimental results show that the RoBERTa-BiGRU and CodeBERT-GRU models achieved accuracies of 66.40% and 66.03%, respectively, on the defect detection benchmark dataset, representing improvements of approximately 5.35% and 3.95% over the standalone RoBERTa and CodeBERT models. Furthermore, the CodeT5-GRU and CodeT5+-BiGRU models achieved accuracies of 67.90% and 67.79%, respectively, surpassing their base models and outperforming RoBERTa-BiGRU and CodeBERT-GRU by a notable margin. In addition, CodeT5-GRU model attains weighted and macro F1-scores of 67.18% and 67.00%, respectively, on the same dataset. Extensive experiments across three real-world datasets further demonstrate consistent and statistically significant improvements over standalone LLMs. Overall, our findings indicate that reprocessing contextual embeddings with RNN architectures enhances code understanding performance in LLM-based models.

Md. Imtyaz Ahmed, Md. Delwar Hossain, Md Mostafizer Rahman et al.

Cancer exhibits diverse and complex phenotypes driven by multifaceted molecular interactions. Recent biomedical research has emphasized the comprehensive study of such diseases by integrating multi-omics datasets (genome, proteome, transcriptome, epigenome). This approach provides an efficient method for identifying genetic variants associated with cancer and offers a deeper understanding of how the disease develops and spreads. However, it is challenging to comprehend complex interactions among the features of multi-omics datasets compared to single omics. In this paper, we analyze lung cancer multi-omics datasets from The Cancer Genome Atlas (TCGA). Using four statistical methods, LIMMA, the T test, Canonical Correlation Analysis (CCA), and the Wilcoxon test, we identified differentially expressed genes across gene expression, DNA methylation, and miRNA expression data. We then integrated these multi-omics data using the Kernel Machine Regression (KMR) approach. Our findings reveal significant interactions among the three omics: gene expression, miRNA expression, and DNA methylation in lung cancer. From our data analysis, we identified 38 genes significantly associated with lung cancer. From our data analysis, we identified 38 genes significantly associated with lung cancer. Among these, eight genes of highest ranking (PDGFRB, PDGFRA, SNAI1, ID1, FGF11, TNXB, ITGB1, ZIC1) were highlighted by rigorous statistical analysis. Furthermore, in silico studies identified three top-ranked potential candidate drugs (Selinexor, Orapred, and Capmatinib) that could play a crucial role in the treatment of lung cancer. These proposed drugs are also supported by the findings of other independent studies, which underscore their potential efficacy in the fight against lung cancer.

Md. Mostafizer Rahman, Ariful Islam Shiplu, Yutaka Watanobe et al.

Effectively analyzing the comments to uncover latent intentions holds immense value in making strategic decisions across various domains. However, several challenges hinder the process of sentiment analysis including the lexical diversity exhibited in comments, the presence of long dependencies within the text, encountering unknown symbols and words, and dealing with imbalanced datasets. Moreover, existing sentiment analysis tasks mostly leveraged sequential models to encode the long dependent texts and it requires longer execution time as it processes the text sequentially. In contrast, the Transformer requires less execution time due to its parallel processing nature. In this work, we introduce a novel hybrid deep learning model, RoBERTa-BiLSTM, which combines the Robustly Optimized BERT Pretraining Approach (RoBERTa) with Bidirectional Long Short-Term Memory (BiLSTM) networks. RoBERTa is utilized to generate meaningful word embedding vectors, while BiLSTM effectively captures the contextual semantics of long-dependent texts. The RoBERTa-BiLSTM hybrid model leverages the strengths of both sequential and Transformer models to enhance performance in sentiment analysis. We conducted experiments using datasets from IMDb, Twitter US Airline, and Sentiment140 to evaluate the proposed model against existing state-of-the-art methods. Our experimental findings demonstrate that the RoBERTa-BiLSTM model surpasses baseline models (e.g., BERT, RoBERTa-base, RoBERTa-GRU, and RoBERTa-LSTM), achieving accuracies of 80.74%, 92.36%, and 82.25% on the Twitter US Airline, IMDb, and Sentiment140 datasets, respectively. Additionally, the model achieves F1-scores of 80.73%, 92.35%, and 82.25% on the same datasets, respectively.