A Benchmark Analysis of Graph and Non-Graph Methods for Caenorhabditis Elegans Neuron Classification

Understanding how a nervous system wires itself from birth to adulthood is a fundamental challenge in developmental neuroscience. We present DevoTG, a temporal graph framework that applies Temporal Graph Neural Networks (TGNs) to two complementary representations of C. elegans neural development: a Continuous-Time Dynamic Graph (CTDG) of cell division events derived from cell lineage data, and a Discrete-Time Dynamic Graph (DTDG) of the developing synaptic connectome spanning eight reconstructed electron-microscopy datasets. On the lineage prediction task, our TGN achieves a mean test AUC of 0.839 +/- 0.007 (5 seeds; validation AUC 0.937 +/- 0.001), outperforming a static GNN with the identical architecture by 26 AUC points (0.577 +/- 0.080), demonstrating that temporal memory is the decisive factor. Applied to the connectome DTDG, DevoTG identifies three connection stability classes (stable, developmental, and variable) across 225 neurons and 858 to 2,496 connections over development (L1 birth to adult), providing a temporal-graph-theoretic complement to the individual-variability classification of Witvliet et al. Analysis of hub command interneurons AVA, AVB, and AVE reveals their persistent centrality and how their integration roles are progressively reinforced across larval stages. Accompanying interactive visualizations (3D animated networks, centrality heatmaps, and a spatiotemporal lineage graph) make developmental dynamics accessible for biological hypothesis generation. DevoTG is open-source and designed for extension to other developing nervous systems. Code is publicly available at https://github.com/DevoLearn/DevoGraph/tree/main/DevoTG.

The aim of this work is to examine the connectomes of Caenorhabditis elegans through a computational lens using the reservoir computing framework. Connectomes are mappings of biological neural networks; C. elegans is the first organism for which physical connectomes covering the whole nervous system have been published. The connectomes of C. elegans used in this paper have been derived at different ages of the organism and are based on three different ways of measuring inter-cellular connections. They have, with minimal preprocessing, been implemented as reservoirs in the form of echo state networks, which are recurrent neural networks. In reservoir computing, the reservoir itself is not trained, rather the output of the reservoir is passed to a comparatively small read-out module in which training takes place. Training and testing is conducted in different neuro-inspired tasks, with the aim of using these tasks as a benchmark for the connectomes. This process has been repeated with different configurations of the reservoir and equally sized but randomized null models have been used for comparison. The results show that the biological wiring and a bio-informed configuration of input and output nodes of the reservoirs do not necessarily lead to better performance. Contrarily, the randomized null models are often outperforming the original connectomes on the chosen benchmarks. At the same time it becomes clear that the results depend a lot on the configuration of the reservoir and the way the connectome has been derived from the organism. Connectomes from different ages may produce varying outcome, without a clear trend becoming visible.

Graph attention networks (GATs) provide one of the best frameworks for learning node representations in relational data; but, existing variants such as Graph Attention Network (GAT) mainly operate on static graphs and rely on implicit temporal aggregation when applied to sequential data. In this paper, we introduce Electroencephalography-temporal Graph Attention Network (EEG-tGAT), a temporally augmented formulation of GATv2 that is tailored for affordance classification from interaction sequences. The proposed model incorporates temporal attention to modulate the contribution of different time segments and temporal dropout to regularize learning across temporally correlated observations. The design reflects the assumption that temporal dimensions in affordance data are not semantically uniform and that discriminative information may be unevenly distributed across time. Experimental results on affordance datasets show that EEG-tGAT achieves improved classification performance compared to GATv2. The observed gains helps to conclude that explicitly encoding temporal importance and enforcing temporal robustness introduce inductive biases that are much better aligned with the structure of affordance-driven interaction data. These findings show us that modest architectural changes to graph attention models can help one obtain consistent benefits when temporal relationships play a nontrivial role in the task.