Negative Binomial Variational Autoencoders for Overdispersed Latent Modeling

Abstract: Biological neurons communicate through spike trains, discrete, irregular bursts of activity that exhibit variability far beyond the modeling capacity of conventional variational autoencoders (VAEs). Recent work, such as the Poisson-VAE, makes a biologically inspired move by modeling spike counts using the Poisson distribution. However, they impose a rigid constraint: equal mean and variance, which fails to reflect the true stochastic nature of neural activity. In this work, we challenge this constraint and introduce NegBio-VAE, a principled extension of the VAE framework that models spike counts using the negative binomial distribution. This shift grants explicit control over dispersion, unlocking a broader and more accurate family of neural representations. We further develop two ELBO optimization schemes and two differentiable reparameterization strategies tailored to the negative binomial setting. By introducing one additional dispersion parameter, NegBio-VAE generalizes the Poisson latent model to a negative binomial formulation. Empirical results demonstrate this minor yet impactful change leads to significant gains in reconstruction fidelity, highlighting the importance of explicitly modeling overdispersion in spike-like activations.