Today the human lives in the age of information and technology. Information is the key, the power, and the engine that moves the world's economy. The world is moving with market data, medical epidemiologic sets, Internet browsing records, geological survey data, complex engineering models, and so on. Health Sciences are fully embedded in information technology. Health science and Biology are very complex fields and have made a long walk from ancient times. In the early 80's, AI in medicine was the primary concern while developing medical expert systems in specialized medical domains to support diagnostic decision-making. The main problems addressed at this early stage of expert system research concerned knowledge acquisition, knowledge representation, reasoning, and explanation. Now there are many modern hospitals and health care institutions, which are well equipped with monitoring and other advanced data collection devices. The need for knowledge on the domain or the data analysis process becomes essential in biomedical applications, as medical decision making needs to be supported by arguments based on basic medical and pharmacological knowledge. The new tool for analyses of biomedical applications is "Intelligent Data Analysis (IDA)." Intelligent Data Analysis can be defined as specialized statistical, pattern recognition, machine learning, data abstraction, and visualization tools for analysis of data and discovery of mechanisms that created the data. The main idea underlying the concept of Intelligent Data Analysis is extracting knowledge from a vast amount of data with many variables, that represents very complex, non-linear, real-life problems. Moreover, Intelligent Data Analysis can help to start from the raw data, coping with prediction tasks without knowing the theoretical description of the underlying process, classification tasks of new events based on past ones, or modelling the aforementioned unknown process. Deep learning is one of the fast-growing technologies, which could learn, reason, and understand the data around. Recently, we have observed several significant breakthroughs in research on artificial intelligence, including self-driving cars, computer Go, image recognition, speech recognition, and machine translation. Deep learning has been tremendously successful at object recognition and detection, localization, scene classification, action recognition, and caption generation. For example, convolutional neural networks (CNNs) have become powerful machine-learning models for various vision-based applications to represent mid-level and high-level abstractions obtained from raw data (e.g., medical images). Deep neural networks have also gained considerable commercial interest due to the development of new variants using high-performance GPUs. This special issue focuses on recent advances, challenges, and future perspectives about intelligent data analysis methods applied in biomedical studies in different domains of knowledge. From around 50 submitted articles to this particular section, 12 pa...