Electroencephalography (EEG) is crucial for recording brain activity, with applications in medicine, neuroscience, and brain-computer interfaces (BCI). However, challenges such as low signal-to-noise ratio (SNR), high inter-subject variability, and channel mismatch complicate the extraction of robust, universal EEG representations. We propose EEGPT, a novel 10-million-parameter pretrained transformer model designed for universal EEG feature extraction. In EEGPT, a mask-based dual self-supervised learning method for efficient feature extraction is designed. Compared to other mask-based self-supervised learning methods, EEGPT introduces spatio-temporal representation alignment. This involves constructing a self-supervised task based on EEG representations that possess high SNR and rich semantic information, rather than on raw signals. Consequently, this approach mitigates the issue of poor feature quality typically extracted from low SNR signals. Additionally, EEGPT's hierarchical structure processes spatial and temporal information separately, reducing computational complexity while increasing flexibility and adaptability for BCI applications. By training on a large mixed multi-task EEG dataset, we fully exploit EEGPT's capabilities.

The class distribution of smaller datasets match the class distribution of the complete dataset. Weperformed apreliminary ablation analysis with oneofthedataset, NIH-Chest Xray dataset, to understand towhich blocks ofResNet-50 should we apply the intermediate loss. Theclassdistribution of smaller datasets match the class distribution of the complete dataset. Theclassdistribution of smaller datasets match the class distribution of the complete dataset. The preliminary ablation study gave the evidence that applying intermediate loss to all blocks yielded superior results.

Our code is available at: https://github.com/LINs-lab/ReLA .

Self-supervised representation learning approaches haverecently surpassed their supervised learning counterparts on downstream tasks like object detection andimage classification.

Unsupervised semantic segmentation is a challenging task that segments images into semantic groups without manual annotation. Prior works have primarily focused on leveraging prior knowledge of semantic consistency or priori concepts from self-supervised learning methods, which often overlook the coherence property of image segments. In this paper, we demonstrate that the smoothness prior, asserting that close features in a metric space share the same semantics, can significantly simplify segmentation by casting unsupervised semantic segmentation as an energy minimization problem. Under this paradigm, we propose a novel approach called SmooSeg that harnesses self-supervised learning methods to model the closeness relationships among observations as smoothness signals. To effectively discover coherent semantic segments, we introduce a novel smoothness loss that promotes piecewise smoothness within segments while preserving discontinuities across different segments. Additionally, to further enhance segmentation quality, we design an asymmetric teacher-student style predictor that generates smoothly updated pseudo labels, facilitating an optimal fit between observations and labeling outputs. Thanks to the rich supervision cues of the smoothness prior, our SmooSeg significantly outperforms STEGO in terms of pixel accuracy on three datasets: COCOStuff (+14.9\%),

Predicting phenotypes from gene expression data is a crucial task in biomedical research, enabling insights into disease mechanisms, drug responses, and personalized medicine. Traditional machine learning and deep learning rely on supervised learning, which requires large quantities of labeled data that are costly and time-consuming to obtain in the case of gene expression data. Self-supervised learning has recently emerged as a promising approach to overcome these limitations by extracting information directly from the structure of unlabeled data. In this study, we investigate the application of state-of-the-art self-supervised learning methods to bulk gene expression data for phenotype prediction. We selected three self-supervised methods, based on different approaches, to assess their ability to exploit the inherent structure of the data and to generate qualitative representations which can be used for downstream predictive tasks. By using several publicly available gene expression datasets, we demonstrate how the selected methods can effectively capture complex information and improve phenotype prediction accuracy. The results obtained show that self-supervised learning methods can outperform traditional supervised models besides offering significant advantage by reducing the dependency on annotated data. We provide a comprehensive analysis of the performance of each method by highlighting their strengths and limitations. We also provide recommendations for using these methods depending on the case under study. Finally, we outline future research directions to enhance the application of self-supervised learning in the field of gene expression data analysis. This study is the first work that deals with bulk RNA-Seq data and self-supervised learning.