GRAFT: Gain-Recalibrated Adapters for Transformer-Based Neural Population Activity Modeling

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.

Closed-loop brain-computer interfaces often require both a forecast of upcoming neural population activity and a readout of the animal's behavioral state. A single Mamba forecaster, trained only on next-step spike counts at Neuropixels scale, can deliver both in one forward pass. A lightweight per-session linear head reading the model's predicted rates decodes behavior better than the same linear classifier reading the raw spike counts, under matched temporal context. We test on the Steinmetz visual-discrimination benchmark, which spans 39 sessions, roughly 27,000 neurons, and 1,994 held-out trials. Across three training seeds, Mamba's predicted rates decode mouse choice at 75.7$\pm$0.2% trial vote, roughly 2.3 times chance level, and stimulus side at 66.1$\pm$0.6%, about twice chance. Compared to a matched 500 ms-context linear decoder on the raw spike counts, Mamba wins at trial vote by 4-6 pp on response and 4-6 pp on stimulus side. A session-start calibration block of about 100-150 trials brings the readout within 1-2 pp of asymptote, and the full pipeline fits inside the 50 ms bin budget on workstation-class GPUs typical of tethered chronic Neuropixels recordings.

Decoding continuous motor trajectories from neural activity is essential for developing practical brain-computer interfaces (BCIs). However, current neural decoders are constrained by the limited scale and heterogeneity of neural recordings. In contrast, behavioral data can be collected more readily and at substantially larger scale from humans, animals, simulations, and robotic systems. Here, we introduce NeuroPB, a framework that scales neural decoding by transferring knowledge from pretrained behavioral representations. NeuroPB first pretrains a motor encoder on large-scale motor behavior data and then aligns neural activity with the resulting behavioral representation space using a limited set of paired neural-behavioral recordings. A neural encoder and lightweight motor decoder are subsequently optimized to reconstruct continuous movement from the aligned neural representations. Across multiple macaque motor datasets, behavioral pretraining improves trajectory decoding, including an 11% $R^2$ increase on center-out and 8% on random-target compared with training the motor encoder from scratch. Notably, pretraining on robotic trajectories achieves performance comparable to pretraining on macaque trajectories, demonstrating that transferable kinematic structure is shared across biological and artificial models. Moreover, decoding performance improves as the scale and diversity of robotic pretraining data increase, when the amount of neural data is fixed. Pretraining also enhances generalization across recording sessions, subjects, and motor tasks, with only 10% calibration needed to match training from scratch. Overall, these results establish behavioral pretraining as a scalable source for neural decoding and provide a promising route toward high-performance and calibration-efficient BCIs under limited neural data.