SpikeSSL: A Universal Spike Inference Framework with Dynamics-Informed State-Space Layers

Large-scale calcium imaging has created an opportunity to build foundation-style models for neural population dynamics, but a central question remains unresolved: \textbf{whether a model pretrained on one collection of recordings can generalize to new datasets, experimental paradigms, and even species.} Existing approaches are often designed for specific tasks and evaluated on a single dataset, making it unclear whether their learned representations are reusable for new calcium trace datasets. To tackle this gap, we present \textbf{CAPT}, a \textbf{C}ontinuous \textbf{A}utoregressive \textbf{P}opulation \textbf{T}ransformer for calcium population dynamics. CAPT models continuous calcium traces directly through a continuous patch tokenization strategy and is trained autoregressively, enabling end-to-end pretraining and adaptation to diverse downstream tasks. We first pretrain CAPT on a large-scale mouse calcium imaging dataset and evaluate its transferability across independent mouse, larval zebrafish, and \textit{C. elegans} datasets collected by different laboratories. In these transfer settings, the pretrained backbone is frozen and only adaptation modules are updated. Across neural population forecasting and behavior decoding tasks, CAPT consistently outperforms specialized and general-purpose baselines. Alongside predictive performance, multimodal analyses using NeuroPAL annotations in \textit{C. elegans} datasets show that CAPT embeddings form a shared functional space across datasets and capture anatomical cell-identity-related structure. These results suggest that the continuous autoregressive modeling opens up possibilities for a simple route towards general-purpose neural foundation models for calcium imaging, which can generalize across datasets, experimental paradigms, and species. Code is available at https://github.com/TSuXinH/CAPT.

Large language models (LLMs) achieve strong performance across many tasks but rely on dense multiply-accumulate (MAC) operations during inference, resulting in high energy cost. Spiking neural networks (SNNs) offer an event-driven alternative in which synaptic integration uses lightweight accumulation. However, spike-driven LLM inference remains difficult because outlier-heavy activations typically require long firing windows or auxiliary non-spiking paths. We propose QuantaSpike, a short-window spike-driven quantization framework for LLMs built around Logarithmic Ternary Integrate-and-Fire (LTIF) neurons. LTIF uses ternary events with power-of-two membrane-response quanta, improving the information represented by each firing step while retaining shift-ACC-compatible computation. QuantaSpike combines this neuron with group-adaptive gain and selective outlier admission: normal values use residual LTIF steps, whereas admitted outliers receive one additional onset spike before entering the same residual dynamics. Across OPT and Llama-2, QuantaSpike achieves state-of-the-art or competitive perplexity and zero-shot accuracy among spike-driven LLM quantization methods. It also transfers to newer dense LLMs, remaining close to the FP16 reference on Llama-3-8B and Qwen3-8B under the same four-step firing window. Analytical linear-energy projections show that QuantaSpike reduces the energy of one linear transformation by about $80.0\%$ on OPT models and $67.1\%$ on Llama-2 models relative to SpikeQuant, providing an accurate and energy-efficient spike-driven path for LLM inference.

Robust and accurate neural decoders are integral to neurotechnologies such as brain-computer interfaces and closed-loop experiments. Recent work has shown that tokenizing neural data at the spike level facilitates multi-session pretraining and delivers state-of-the-art decoding performance. However, current spike-based models are restricted to supervised learning (SL), limiting training to datasets with paired behavioural labels. To address this limitation, we introduce MOJO (Masked autOencoder-based JOint training), a training framework for spike-tokenizing models that jointly leverages self-supervised learning (SSL) via masked autoencoding and SL objectives. We evaluate MOJO on three spiking datasets spanning monkey motor cortex during reaching tasks and multi-regional mouse recordings during vision and decision making tasks, demonstrating superior performance over purely SL-trained models. This improvement is especially pronounced when training with limited labelled data, particularly in few-shot finetuning, where only a small amount of labelled data from a new session is available. Incorporating SSL also yields more interpretable neuronal representations, improving performance on brain region classification and spike-statistics prediction without explicit optimization for these tasks. We further show that MOJO generalizes beyond spiking data to human electrocorticography during speech, where it continues to outperform purely SL-trained models and achieves performance comparable to neuro-foundation models (NFMs) designed specifically for continuous signals. Overall, augmenting spike-tokenizing models with SSL improves performance in label-impoverished settings and enables the use of unlabelled data across various tasks and species, while generalizing to other neural modalities. These results suggest a path towards more flexible and scalable data usage when training NFMs.