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Register a new userNeural Latents Benchmark 21: Evaluating latent variable models of neural population activity
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Advances in neural recording present increasing opportunities to study neural activity in unprecedented detail. Latent variable models (LVMs) are promising tools for analyzing this rich activity across diverse neural systems and behaviors, as LVMs do not depend on known relationships between the activity and external experimental variables. However, progress in latent variable modeling is currently impeded by a lack of standardization, resulting in methods being developed and compared in an ad hoc manner. To coordinate these modeling efforts, we introduce a benchmark suite for latent variable modeling of neural population activity. We curate four datasets of neural spiking activity from cognitive, sensory, and motor areas to promote models that apply to the wide variety of activity seen across these areas. We identify unsupervised evaluation as a common framework for evaluating models across datasets, and apply several baselines that demonstrate benchmark diversity. We release this benchmark through EvalAI. http://neurallatents.github.io
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An important problem in analysis of neural data is to characterize interactions across brain regions from high-dimensional multiple-electrode recordings during a behavioral experiment. Lead-lag effects indicate possible directional flows of neural information, but they are often transient, appearing during short intervals of time. Such non-stationary interactions can be difficult to identify, but they can be found by taking advantage of the replication structure inherent to many neurophysiological experiments. To describe non-stationary interactions between replicated pairs of high-dimensional time series, we developed a method of estimating latent, non-stationary cross-correlation. Our approach begins with an extension of probabilistic CCA to the time series setting, which provides a model-based interpretation of multiset CCA. Because the covariance matrix describing non-stationary dependence is high-dimensional, we assume sparsity of cross-correlations within a range of possible interesting lead-lag effects. We show that the method can perform well in realistic settings and we apply it to 192 simultaneous local field potential (LFP) recordings from prefrontal cortex (PFC) and visual cortex (area V4) during a visual memory task. We find lead-lag relationships that are highly plausible, being consistent with related results in the literature.
The recurrent neural networks (RNN) with richly distributed internal states and flexible non-linear transition functions, have overtaken the dynamic Bayesian networks such as the hidden Markov models (HMMs) in the task of modeling highly structured sequential data. These data, such as from speech and handwriting, often contain complex relationships between the underlaying variational factors and the observed data. The standard RNN model has very limited randomness or variability in its structure, coming from the output conditional probability model. This paper will present different ways of using high level latent random variables in RNN to model the variability in the sequential data, and the training method of such RNN model under the VAE (Variational Autoencoder) principle. We will explore possible ways of using adversarial method to train a variational RNN model. Contrary to competing approaches, our approach has theoretical optimum in the model training and provides better model training stability. Our approach also improves the posterior approximation in the variational inference network by a separated adversarial training step. Numerical results simulated from TIMIT speech data show that reconstruction loss and evidence lower bound converge to the same level and adversarial training loss converges to 0.
Latent dynamics discovery is challenging in extracting complex dynamics from high-dimensional noisy neural data. Many dimensionality reduction methods have been widely adopted to extract low-dimensional, smooth and time-evolving latent trajectories. However, simple state transition structures, linear embedding assumptions, or inflexible inference networks impede the accurate recovery of dynamic portraits. In this paper, we propose a novel latent dynamic model that is capable of capturing nonlinear, non-Markovian, long short-term time-dependent dynamics via recurrent neural networks and tackling complex nonlinear embedding via non-parametric Gaussian process. Due to the complexity and intractability of the model and its inference, we also provide a powerful inference network with bi-directional long short-term memory networks that encode both past and future information into posterior distributions. In the experiment, we show that our model outperforms other state-of-the-art methods in reconstructing insightful latent dynamics from both simulated and experimental neural datasets with either Gaussian or Poisson observations, especially in the low-sample scenario. Our codes and additional materials are available at https://github.com/sheqi/GP-RNN_UAI2019.
We study a network of spiking neurons with heterogeneous excitabilities connected via inhibitory delayed pulses. For globally coupled systems the increase of the inhibitory coupling reduces the number of firing neurons by following a Winner Takes All mechanism. For sufficiently large transmission delay we observe the emergence of collective oscillations in the system beyond a critical coupling value. Heterogeneity promotes neural inactivation and asynchronous dynamics and its effect can be counteracted by considering longer time delays. In sparse networks, inhibition has the counterintuitive effect of promoting neural reactivation of silent neurons for sufficiently large coupling. In this regime, current fluctuations are on one side responsible for neural firing of sub-threshold neurons and on the other side for their desynchronization. Therefore, collective oscillations are present only in a limited range of coupling values, which remains finite in the thermodynamic limit. Out of this range the dynamics is asynchronous and for very large inhibition neurons display a bursting behaviour alternating periods of silence with periods where they fire freely in absence of any inhibition.
Noninvasive medical neuroimaging has yielded many discoveries about the brain connectivity. Several substantial techniques mapping morphological, structural and functional brain connectivities were developed to create a comprehensive road map of neuronal activities in the human brain -namely brain graph. Relying on its non-Euclidean data type, graph neural network (GNN) provides a clever way of learning the deep graph structure and it is rapidly becoming the state-of-the-art leading to enhanced performance in various network neuroscience tasks. Here we review current GNN-based methods, highlighting the ways that they have been used in several applications related to brain graphs such as missing brain graph synthesis and disease classification. We conclude by charting a path toward a better application of GNN models in network neuroscience field for neurological disorder diagnosis and population graph integration. The list of papers cited in our work is available at https://github.com/basiralab/GNNs-in-Network-Neuroscience.
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