neural engineers

Abstract: Large language models (LLMs) are increasingly used as computational models of human language processing, yet it remains unclear which components of their representations drive alignment with neural activity. Here, we use ridge reduced-rank regression to identify the brain-predictive subspace of LLM representations: the representational directions that support linear prediction of neural responses. Across three naturalistic language-listening datasets spanning intracranial electrophysiology and fMRI, and six model conditions spanning autoregressive, bidirectional masked, and randomly initialized language models, we find that full linear encoding performance can be recovered using only 1-3% of the original embedding dimensionality. These low-dimensional subspaces generalize across held-out participants and, to a lesser extent, across datasets, suggesting that neural predictivity is concentrated in a compact and partially shared representational space. We next compare these brain-predictive directions with the principal axes of variation in the embeddings. Principal component analysis requires substantially more dimensions to recover neural prediction, demonstrating that the directions most useful for predicting neural activity are distinct from those capturing the most overall variance within LLM representations themselves. Finally, characterizing the learned subspaces allows us to surface interpretable features that are overrepresented in neural activity above and beyond the LLM representations. Together, these results show that LLM-brain alignment is supported by a small, structured subset of model representations and provides a framework for better understanding exactly why these representations align. Code can be found at: https://github.com/thefinnlab/low-rank-alignment

Abstract: High-dimensional count data are common in scientific applications, but most diffusion and flow models are designed for continuous or categorical data, and generation often requires many sequential model evaluations. We propose Count Flow Map, a generative model that learns finite-time transitions directly in count space for one- or few-step generation. Our model directly learns stochastic transitions over finite time intervals, using Poisson births and Binomial deaths to preserve nonnegative integer counts without a predefined maximum. These transition models are trained to match the underlying local birth--death dynamics and to maintain consistency across step sizes. We characterize the connection between local dynamics and finite-time transition consistency and derive a bound on the generation error. After validating Count Flow Map in several simulations, including a high-dimensional, high-count setting, we apply it to single-cell drug perturbation prediction and neural population forecasting, where it captures perturbation responses and supports forecasts of high-activity events with only one or a few model evaluations. Together, these experiments demonstrate that Count Flow Map enables high-quality generation directly in count space across inference budgets, from one-step to few-step generation, using a single trained model.

Abstract: The brain needs an accurate internal model of the world to generate predictions and guide behavior. However, it must estimate the statistical structure of the environment from limited experience. This is particularly difficult for rare events, whose observed frequencies in a limited sample may substantially under- or overestimate their true frequencies. How the brain constructs an accurate internal model despite this sampling problem remains unclear. We address this problem using a Bayesian Confidence Propagation Neural Network (BCPNN) trained on event sequences from a Markov-chain random walk with controlled event frequencies. Treating the underlying Markov structure as the ground truth, we train the network on limited sample of event sequences and then allow it to generate autonomous replay based on the learned structure. We evaluate replay fidelity at the levels of both marginal event frequencies and conditional transition structure. We find that moderate neural noise, modeled as temporally correlated random fluctuations in unit activity during replay, is critical for faithful internal simulation. Without this variability, deterministic replay systematically under- or overrepresents rare events, whereas moderate noise restores both their marginal and conditional occurrence. Moderate noise also broadens the range of parameter values that produce accurate replay, making the model more robust to parameter variation. Together, these results support noise-assisted internal simulation as a potential mechanism for compensating for sampling errors arising from limited experience. Our model also provides a testable framework for investigating how altered neural variability may impair internal-model fidelity in disorders such as Parkinson's disease.

Abstract: Invasive neural recordings provide high-fidelity measurements of brain activity, with signals such as intracranial EEG (iEEG) and intracortical spiking activity capturing neural dynamics at different spatial and temporal scales. Yet existing neural foundation models have largely been developed independently for different invasive recording paradigms, leaving joint pretraining across heterogeneous invasive signals underexplored. In this work, we introduce iBrain, a unified foundation model that jointly learns from iEEG and spiking activity. iBrain employs signal-specific encoders to accommodate their distinct signal characteristics and a shared spatiotemporal Transformer backbone to model dependencies across recording channels and time. We pretrain iBrain on over 7,000 hours of heterogeneous neural recordings using masked signal reconstruction and channel-view alignment, promoting contextual modeling of neural dynamics and robustness across different channels. iBrain consistently outperforms single-signal pretraining baselines and achieves state-of-the-art performance on multiple benchmarks. Further experiments demonstrate that iBrain exhibits transferability and data efficiency across diverse recording settings. These results highlight the potential of joint pretraining on heterogeneous invasive neural recordings to support scalable neural modeling and transferable representations across recording settings and downstream tasks.