MOTIVATION: 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. RESULTS: 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. AVAILABILITY AND IMPLEMENTATION: The code and results are available at https://github.com/kdradjat/ssrl-rnaseq.

In a large domain of classification problems for real applications, like human activity recognition, separable spaces between groups of concepts are easier to learn than each concept alone. This is because the search space biases required to separate groups of classes (or concepts) are more relevant than the ones needed to separate classes individually. For example, it is easier to learn the activities related to the body movements group (running, walking) versus "on-wheels" activities group (bicycling, driving a car), before learning more specific classes inside each of these groups. Despite the obvious interest of this approach, our theoretical analysis shows a high complexity for finding an exact solution. We propose in this paper an original approach based on the association of clustering and classification approaches to overcome this limitation. We propose a better approach to learn the concepts by grouping classes recursively rather than learning them class by class. We introduce an effective greedy algorithm and two theoretical measures, namely cohesion and dispersion, to evaluate the connection between the clusters and the classes. Extensive experiments on the SHL dataset show that our approach improves classification performances while reducing the number of instances used to learn each concept.

Monitoring industrial infrastructures are undergoing a critical transformation with industry 4.0. Monitoring solutions must follow the system behavior in real time and must adapt to its continuous change. We propose in this paper an autoencoder model-based approach for tracking abnormalities in industrial application. A set of sensors collects data from turbo-compressors and an original two-level machine learning LSTM autoencoder architecture defines a continuous nominal vibration model. Normalized thresholds (ISO 20816) between the model and the system generates a possible abnormal situation to diagnose. Experimental results, including hyper-parameter optimization on large real data and domain expert analysis, show that our proposed solution gives promising results.

Infant's cry is an innate response to express several situations including pain, disturbance and discomfort. Therefore the automatic recognition of infant cries patterns is the key factor to develop successful ambient intelligence applications to enhance the quality of life of both infants and parents. This paper proposes a complete machine learning process including consistent dataset generation from infant cries and selecting appropriate sound features, with promising experimental results for enhancing the monitoring of infants in real world settings. The originality of the proposed approach lies in its ability to detect and analyze automatically discomfort signals, which recurrently affects 20 to 25% of newborns. The machine learning process includes low-level audio features selection methods from labeled infant pre-cry recordings as well as high-level features characterizing the envelop of the crying. The classification is performed using ensemble learning methods after a stage of features selection. The exploitation of pre-crying signals to improve the quality of the recognition is another important aspect of the proposed approach, which optimizes the accuracy of the learning step as it is shown by the obtained results on a real dataset. This result gives the opportunity to develop new baby monitors able to anticipate the infants needs.