Recovering Sparse Neural Connectivity from Partial Measurements: A Covariance-Based Approach with Granger-Causality Refinement

Connectivity structure shapes neural computation, but inferring this structure from population recordings is degenerate: multiple connectivity structures can generate identical dynamics. Recent work uses low-rank recurrent neural networks (lrRNNs) to infer low-dimensional latent dynamics and connectivity from observed activity, enabling a mechanistic interpretation of the dynamics. However, standard approaches for training lrRNNs can recover spurious structures irrelevant to the underlying dynamics. We first characterize the identifiability of connectivity structures in lrRNNs and determine conditions under which a unique solution exists. To find such solutions, we develop an inference framework based on maximum entropy and continuous normalizing flows (CNFs), trained via flow matching. Instead of estimating a single connectivity matrix, our method learns a distribution over connection weights that is maximally unbiased over unidentifiable components while matching the observed dynamics. This approach captures complex yet necessary distributions such as heavy-tailed connectivity found in empirical data. We validate our method on synthetic datasets with connectivity structures that generate multistable attractors, limit cycles, and ring attractors, and demonstrate its applicability in recordings from rat frontal cortex during decision-making. Our framework shifts circuit inference from recovering connectivity to identifying which connectivity structures are computationally required, and which are artifacts of underconstrained inference.

Real-time recurrent learning (RTRL) computes exact online gradients by propagating a Jacobian tensor forward through recurrent dynamics, but at O(n^4) cost per step. Prior work has sought structured approximations (rank-1 compression, graph-based sparsity, Kronecker factorization). We show that, in the continuous error signal regime, the recurrent Jacobian is massively redundant:propagating through a random 6% of paths (k=4 of n=64) recovers 84 +/- 6% of full RTRL's adaptation ability across five seeds, and the absolute count k=4 remains effective from n=64 to n=256 (6% to 1.6%, recovery 84 to 78%), meaning sparse RTRL becomes relatively cheaper as networks grow. In RNNs, the recovery is selection-invariant (even adversarial path selection works) and exhibits a step-function transition from zero to any nonzero propagation. Spectral analysis reveals the mechanism: the Jacobian is full-rank but near-isotropic (condition numbers 2.6-6.5), so any random subset provides a directionally representative gradient estimate. On chaotic dynamics (Lorenz attractor), sparse propagation is more numerically stable than full RTRL (CV 13% vs. 88%), as subsampling avoids amplifying pathological spectral modes. The redundancy extends to LSTMs (k=4 matches full RTRL) and to transformers via sparse gradient transport (50% head sparsity outperforms the dense reference; 33% is borderline), with higher thresholds reflecting head specialization rather than isotropy. On real primate neural data, sparse RTRL (k=4) adapts online to cross-session electrode drift (80 +/- 11% recovery, 5 seeds), where sparse propagation is again more stable than full RTRL. Without continuous error signal, Jacobian propagation accumulates numerical drift and degrades all RTRL variants, a scope condition for all forward-mode methods. Results hold with SGD (92 +/- 1% recovery), suggesting independence from optimizer choice.

Training recurrent neuronal networks consisting of excitatory (E) and inhibitory (I) units with additive noise for working memory computation slows and diversifies inhibitory timescales, leading to improved task performance that is attributed to emergent marginally stable equilibria [PNAS 122 (2025) e2316745122]. Yet the link between trained network characteristics and their roles in shaping desirable dynamical landscapes remains unexplored. Here, we investigate the Jacobian matrices describing the dynamics near these equilibria and show that they are sparse, non-Hermitian rectangular-block matrices modified by heterogeneous synaptic decay timescales and activation-function gains. We specify a random matrix ensemble that faithfully captures the spectra of trained Jacobian matrices, arising from the inhibitory core - excitatory periphery network motif (pruned E weights, broadly distributed I weights) observed post-training. An analytic theory of this ensemble is developed using statistical field theory methods: a Hermitized resolvent representation of the spectral density is processed with a supersymmetry-based treatment in the style of Fyodorov and Mirlin. In this manner, an analytic description of the spectral edge is obtained, relating statistical parameters of the Jacobians (sparsity, weight variances, E/I ratio, and the distributions of timescales and gains) to near-critical features of the equilibria essential for robust working memory computation.