Latent factor analysis via dynamical systems (LFADS) is an RNN-based variational sequential autoencoder that achieves state-of-the-art performance in denoising high-dimensional neural activity for downstream applications in science and engineering. Recently introduced variants and extensions continue to demonstrate the applicability of the architecture to a wide variety of problems in neuroscience. Since the development of the original implementation of LFADS, new technologies have emerged that use dynamic computation graphs, minimize boilerplate code, compose model configuration files, and simplify large-scale training. Building on these modern Python libraries, we introduce lfads-torch -- a new open-source implementation of LFADS that unifies existing variants and is designed to be easier to understand, configure, and extend. Documentation, source code, and issue tracking are available at https://github.com/arsedler9/lfads-torch .

Artificial neural networks that can recover latent dynamics from recorded neural activity may provide a powerful avenue for identifying and interpreting the dynamical motifs underlying biological computation. Given that neural variance alone does not uniquely determine a latent dynamical system, interpretable architectures should prioritize accurate and low-dimensional latent dynamics. In this work, we evaluated the performance of sequential autoencoders (SAEs) in recovering latent chaotic attractors from simulated neural datasets. We found that SAEs with widely-used recurrent neural network (RNN)-based dynamics were unable to infer accurate firing rates at the true latent state dimensionality, and that larger RNNs relied upon dynamical features not present in the data. On the other hand, SAEs with neural ordinary differential equation (NODE)-based dynamics inferred accurate rates at the true latent state dimensionality, while also recovering latent trajectories and fixed point structure. Ablations reveal that this is mainly because NODEs (1) allow use of higher-capacity multi-layer perceptrons (MLPs) to model the vector field and (2) predict the derivative rather than the next state. Decoupling the capacity of the dynamics model from its latent dimensionality enables NODEs to learn the requisite low-D dynamics where RNN cells fail. Additionally, the fact that the NODE predicts derivatives imposes a useful autoregressive prior on the latent states. The suboptimal interpretability of widely-used RNN-based dynamics may motivate substitution for alternative architectures, such as NODE, that enable learning of accurate dynamics in low-dimensional latent spaces.

Neural population activity is theorized to reflect an underlying dynamical structure. This structure can be accurately captured using state space models with explicit dynamics, such as those based on recurrent neural networks (RNNs). However, using recurrence to explicitly model dynamics necessitates sequential processing of data, slowing real-time applications such as brain-computer interfaces. Here we introduce the Neural Data Transformer (NDT), a non-recurrent alternative. We test the NDT's ability to capture autonomous dynamical systems by applying it to synthetic datasets with known dynamics and data from monkey motor cortex during a reaching task well-modeled by RNNs. The NDT models these datasets as well as state-of-the-art recurrent models. Further, its non-recurrence enables 3.9ms inference, well within the loop time of real-time applications and more than 6 times faster than recurrent baselines on the monkey reaching dataset. These results suggest that an explicit dynamics model is not necessary to model autonomous neural population dynamics. Code: https://github.com/snel-repo/neural-data-transformers

Neuroscience is experiencing a data revolution in which many hundreds or thousands of neurons are recorded simultaneously. Currently, there is little consensus on how such data should be analyzed. Here we introduce LFADS (Latent Factor Analysis via Dynamical Systems), a method to infer latent dynamics from simultaneously recorded, single-trial, high-dimensional neural spiking data. LFADS is a sequential model based on a variational auto-encoder. By making a dynamical systems hypothesis regarding the generation of the observed data, LFADS reduces observed spiking to a set of low-dimensional temporal factors, per-trial initial conditions, and inferred inputs. We compare LFADS to existing methods on synthetic data and show that it significantly out-performs them in inferring neural firing rates and latent dynamics.