Emerging Artificial Intelligence Applications in Spatial Transcriptomics Analysis

Spatial transcriptomics (ST) has advanced significantly in the last few years. Such advancement comes with the urgent need for novel computational methods to handle the unique challenges of ST data analysis. Many artificial intelligence (AI) methods have been developed to utilize various machine learning and deep learning techniques for computational ST analysis. This review provides a comprehensive and up-to-date survey of current AI methods for ST analysis.

The Autodidactic Universe

We present an approach to cosmology in which the Universe learns its own physical laws. It does so by exploring a landscape of possible laws, which we express as a certain class of matrix models. We discover maps that put each of these matrix models in correspondence with both a gauge/gravity theory and a mathematical model of a learning machine, such as a deep recurrent, cyclic neural network. This establishes a correspondence between each solution of the physical theory and a run of a neural network. This correspondence is not an equivalence, partly because gauge theories emerge from $N \rightarrow \infty $ limits of the matrix models, whereas the same limits of the neural networks used here are not well-defined. We discuss in detail what it means to say that learning takes place in autodidactic systems, where there is no supervision. We propose that if the neural network model can be said to learn without supervision, the same can be said for the corresponding physical theory. We consider other protocols for autodidactic physical systems, such as optimization of graph variety, subset-replication using self-attention and look-ahead, geometrogenesis guided by reinforcement learning, structural learning using renormalization group techniques, and extensions. These protocols together provide a number of directions in which to explore the origin of physical laws based on putting machine learning architectures in correspondence with physical theories.