Tom Baden

Kevin Doran, Tom Baden

We demonstrate the effectiveness of using a simple neural network output, a categorical probability distribution, for the task of next spike prediction. This case study motivates an investigation into why this simple output structure is not commonly used with neural temporal point process models. We find evidence that many existing datasets for evaluating temporal point process models do not reveal much information about the underlying event generating processes, and many existing models perform well due to regularization effects of model size and constraints on output structure. We extend existing datasets and create new ones in order to explore outside of this information limited regime and find that outputting a simple categorical distribution is competitive across a wide range of datasets.

Lucas Theis, Philipp Berens, Emmanouil Froudarakis et al.

A fundamental challenge in calcium imaging has been to infer the timing of action potentials from the measured noisy calcium fluorescence traces. We systematically evaluate a range of spike inference algorithms on a large benchmark dataset recorded from varying neural tissue (V1 and retina) using different calcium indicators (OGB-1 and GCamp6). We show that a new algorithm based on supervised learning in flexible probabilistic models outperforms all previously published techniques, setting a new standard for spike inference from calcium signals. Importantly, it performs better than other algorithms even on datasets not seen during training. Future data acquired in new experimental conditions can easily be used to further improve its spike prediction accuracy and generalization performance. Finally, we show that comparing algorithms on artificial data is not informative about performance on real population imaging data, suggesting that a benchmark dataset may greatly facilitate future algorithmic developments.