Many difficult scientific discovery tasks can only be solved in interactive ways, by combining intelligent computing techniques with intuitive and adaptive user interfaces. It is inevitable to use human intelligence in scientific discovery systems: human eyes can capture complex patterns and relationships, along with detecting the exceptional cases in a data set; the human brain can easily manipulate perceptions to make decisions. Ambient intelligence is about this kind of ubiquitous and autonomous human interaction with information. Scientific discovery is a process of creative perception and communication, dealing with questions like: how do we significantly reduce information while maintaining meaning, or how do we extract patterns from massive data and growing data resources. Originating from the SIGCHI Workshop on Ambient Intelligence for Scientific Discovery, this state-of-the-art survey is organized in three parts: new paradigms in scientific discovery, ambient cognition, and ambient intelligence systems. Many chapters share common features such as interaction, vision, language, and biomedicine.