High Dimensional Neural Data
High Dimensional Neural Data
Rastermap: Extracting structure from high dimensional neural data
Large-scale neural recordings contain high-dimensional structure that cannot be easily captured by existing data visualization methods. We therefore developed an embedding algorithm called Rastermap, which captures highly nonlinear relationships between neurons, and provides useful visualizations by assigning each neuron to a location in the embedding space. Compared to standard algorithms such as t-SNE and UMAP, Rastermap finds finer and higher dimensional patterns of neural variability, as measured by quantitative benchmarks. We applied Rastermap to a variety of datasets, including spontaneous neural activity, neural activity during a virtual reality task, widefield neural imaging data during a 2AFC task, artificial neural activity from an agent playing atari games, and neural responses to visual textures. We found within these datasets unique subpopulations of neurons encoding abstract properties of the environment.
Understanding neural dynamics in high dimensions across multiple timescales: from perception to motor control and learning
Remarkable advances in experimental neuroscience now enable us to simultaneously observe the activity of many neurons, thereby providing an opportunity to understand how the moment by moment collective dynamics of the brain instantiates learning and cognition. However, efficiently extracting such a conceptual understanding from large, high dimensional neural datasets requires concomitant advances in theoretically driven experimental design, data analysis, and neural circuit modeling. We will discuss how the modern frameworks of high dimensional statistics and deep learning can aid us in this process. In particular we will discuss: (1) how unsupervised tensor component analysis and time warping can extract unbiased and interpretable descriptions of how rapid single trial circuit dynamics change slowly over many trials to mediate learning; (2) how to tradeoff very different experimental resources, like numbers of recorded neurons and trials to accurately discover the structure of collective dynamics and information in the brain, even without spike sorting; (3) deep learning models that accurately capture the retina’s response to natural scenes as well as its internal structure and function; (4) algorithmic approaches for simplifying deep network models of perception; (5) optimality approaches to explain cell-type diversity in the first steps of vision in the retina.
Theoretical and computational approaches to neuroscience with complex models in high dimensions across multiple timescales: from perception to motor control and learning
Remarkable advances in experimental neuroscience now enable us to simultaneously observe the activity of many neurons, thereby providing an opportunity to understand how the moment by moment collective dynamics of the brain instantiates learning and cognition. However, efficiently extracting such a conceptual understanding from large, high dimensional neural datasets requires concomitant advances in theoretically driven experimental design, data analysis, and neural circuit modeling. We will discuss how the modern frameworks of high dimensional statistics and deep learning can aid us in this process. In particular we will discuss: how unsupervised tensor component analysis and time warping can extract unbiased and interpretable descriptions of how rapid single trial circuit dynamics change slowly over many trials to mediate learning; how to tradeoff very different experimental resources, like numbers of recorded neurons and trials to accurately discover the structure of collective dynamics and information in the brain, even without spike sorting; deep learning models that accurately capture the retina’s response to natural scenes as well as its internal structure and function; algorithmic approaches for simplifying deep network models of perception; optimality approaches to explain cell-type diversity in the first steps of vision in the retina.