Hybrid Deep Neural Network for Handling Data Imbalance in Precursor MicroRNA

Deep Learning for Genomics: From Early Neural Nets to Modern Large Language Models

The data explosion driven by advancements in genomic research, such as high-throughput sequencing techniques, is constantly challenging conventional methods used in genomics. In parallel with the urgent demand for robust algorithms, deep learning has succeeded in various fields such as vision, speech, and text processing. Yet genomics entails unique challenges to deep learning, since we expect a superhuman intelligence that explores beyond our knowledge to interpret the genome from deep learning. A powerful deep learning model should rely on the insightful utilization of task-specific knowledge. In this paper, we briefly discuss the strengths of different deep learning models from a genomic perspective so as to fit each particular task with proper deep learning-based architecture, and we remark on practical considerations of developing deep learning architectures for genomics. We also provide a concise review of deep learning applications in various aspects of genomic research and point out current challenges and potential research directions for future genomics applications. We believe the collaborative use of ever-growing diverse data and the fast iteration of deep learning models will continue to contribute to the future of genomics.

A Novel Classification Method Based on a Two-Phase Technique for Learning Imbalanced Text Data

The problem of imbalanced data has a heavy impact on the performance of learning models. In the case of an imbalanced text dataset, minority class data are often classified to the majority class, resulting in a loss of minority information and low accuracy. Thus, it is a serious challenge to determine how to tackle the high imbalance ratio distribution of datasets. Here, we propose a novel classification method for learning tasks with imbalanced test data. It aims to construct a method for data preprocessing that researchers can apply to their learning tasks with imbalanced text data and save the efforts to search for more dedicated learning tools. In our proposed method, there are two core stages. In stage one, balanced datasets are generated using an asymmetric cost-sensitive support vector machine; in stage two, the balanced dataset is classified using the symmetric cost-sensitive support vector machine. In addition, the learning parameters in both stages are adjusted with a genetic algorithm to create an optimal model. A Yelp review dataset was used to validate the effectiveness of the proposed method. The experimental results showed that the proposed method led to a better performance subject to the targeted dataset, with at least 75% accuracy, and revealed that this new method significantly improved the learning approach.