A long-standing ambition for artificial intelligence (AI) in biomedicine is the development of AI systems that could eventually make major scientific discoveries, with the potential to be worthy of a Nobel Prize--fulfilling the Nobel Turing Challenge [1]. While the concept of an "AI scientist" is aspirational, advances in agent-based AI pave the way to the development of AI agents as conversable systems capable of skeptical learning and reasoning that coordinate large language models (LLMs), machine learning (ML) tools, experimental platforms, or even combinations of them [2-5] (Figure 1). The complexity of biological problems requires a multistage approach, where decomposing complex questions into simpler tasks is necessary. AI agents can break down a problem into manageable subtasks, which can then be addressed by agents with specialized functions for targeted problem-solving and integration of scientific knowledge, paving the way toward a future in which a major biomedical discovery is made solely by AI [2, 6].

Advances in artificial intelligence (AI) are fueling a new paradigm of discoveries in natural sciences. Today, AI has started to advance natural sciences by improving, accelerating, and enabling our understanding of natural phenomena at a wide range of spatial and temporal scales, giving rise to a new area of research known as AI for science (AI4Science). Being an emerging research paradigm, AI4Science is unique in that it is an enormous and highly interdisciplinary area. Thus, a unified and technical treatment of this field is needed yet challenging. This work aims to provide a technically thorough account of a subarea of AI4Science; namely, AI for quantum, atomistic, and continuum systems. These areas aim at understanding the physical world from the subatomic (wavefunctions and electron density), atomic (molecules, proteins, materials, and interactions), to macro (fluids, climate, and subsurface) scales and form an important subarea of AI4Science. A unique advantage of focusing on these areas is that they largely share a common set of challenges, thereby allowing a unified and foundational treatment. A key common challenge is how to capture physics first principles, especially symmetries, in natural systems by deep learning methods. We provide an in-depth yet intuitive account of techniques to achieve equivariance to symmetry transformations. We also discuss other common technical challenges, including explainability, out-of-distribution generalization, knowledge transfer with foundation and large language models, and uncertainty quantification. To facilitate learning and education, we provide categorized lists of resources that we found to be useful. We strive to be thorough and unified and hope this initial effort may trigger more community interests and efforts to further advance AI4Science.