Machine Learning-Based Genomic Linguistic Analysis (Gene Sequence Feature Learning): A Case Study on Predicting Heavy Metal Response Genes in Rice

This study explores the application of machine learning-based genetic linguistics for identifying heavy metal response genes in rice (Oryza sativa). By integrating convolutional neural networks and random forest algorithms, we developed a hybrid model capable of extracting and learning meaningful features from gene sequences, such as k-mer frequencies and physicochemical properties. The model was trained and tested on datasets of genes, achieving high predictive performance (precision: 0.89, F1-score: 0.82). RNA-seq and qRT-PCR experiments conducted on rice leaves which exposed to Hg0, revealed differential expression of genes associated with heavy metal responses, which validated the model's predictions. Co-expression network analysis identified 103 related genes, and a literature review indicated that these genes are highly likely to be involved in heavy metal-related biological processes. By integrating and comparing the analysis results with those of differentially expressed genes (DEGs), the validity of the new machine learning method was further demonstrated. This study highlights the efficacy of combining machine learning with genetic linguistics for large-scale gene prediction. It demonstrates a cost-effective and efficient approach for uncovering molecular mechanisms underlying heavy metal responses, with potential applications in developing stress-tolerant crop varieties.

ViT2EEG: Leveraging Hybrid Pretrained Vision Transformers for EEG Data

In this study, we demonstrate the application of a hybrid Vision Transformer (ViT) model, pretrained on ImageNet, on an electroencephalogram (EEG) regression task. Despite being originally trained for image classification tasks, when fine-tuned on EEG data, this model shows a notable increase in performance compared to other models, including an identical architecture ViT trained without the ImageNet weights. This discovery challenges the traditional understanding of model generalization, suggesting that Transformer models pretrained on seemingly unrelated image data can provide valuable priors for EEG regression tasks with an appropriate fine-tuning pipeline. The success of this approach suggests that the features extracted by ViT models in the context of visual tasks can be readily transformed for the purpose of EEG predictive modeling. We recommend utilizing this methodology not only in neuroscience and related fields, but generally for any task where data collection is limited by practical, financial, or ethical constraints. Our results illuminate the potential of pretrained models on tasks that are clearly distinct from their original purpose.

Two Heads are Better than One: A Bio-inspired Method for Improving Classification on EEG-ET Data

Classifying EEG data is integral to the performance of Brain Computer Interfaces (BCI) and their applications. However, external noise often obstructs EEG data due to its biological nature and complex data collection process. Especially when dealing with classification tasks, standard EEG preprocessing approaches extract relevant events and features from the entire dataset. However, these approaches treat all relevant cognitive events equally and overlook the dynamic nature of the brain over time. In contrast, we are inspired by neuroscience studies to use a novel approach that integrates feature selection and time segmentation of EEG data. When tested on the EEGEyeNet dataset, our proposed method significantly increases the performance of Machine Learning classifiers while reducing their respective computational complexity.