Recent work indicates that low-dimensional dynamics of neural and behavioral data are often preserved across days and subjects. However, extracting these preserved dynamics remains challenging: high-dimensional neural population activity and the recorded neuron populations vary across recording sessions. While existing modeling tools can improve alignment between neural and behavioral data, they often operate on a per-subject basis or discretize behavior into categories, disrupting its natural continuity and failing to capture the underlying dynamics. We introduce Contrastive Aligned Neural DYnamics (CANDY), an end-to-end framework that aligns neural and behavioral data using rank-based contrastive learning, adapted for continuous behavioral variables, to project neural activity from different sessions onto a shared low-dimensional embedding space. CANDY fits a shared linear dynamical system to the aligned embeddings, enabling an interpretable model of the conserved temporal structure in the latent space.

The coordinated activity of neural populations underlies myriad brain functions. Manipulating this activity using brain stimulation techniques has great potential for scientific and clinical applications, as they causally influence the nervous system. To improve the accuracy by which one can manipulate neural activity, it is important to (1) take into account the pre-stimulation brain state, which can influence the brain's response to stimulation, and (2) adaptively update stimulation parameters over time to compensate for changes in the brain's response to stimulation. In this work, we propose Online MicroStimulation Optimization (OMiSO), a brain stimulation framework that leverages brain state information to find stimulation parameters that can drive neural population activity toward specified states. OMiSO includes two key advances: i) training a stimulation-response model that leverages the pre-stimulation brain state, and inverting this model to choose the stimulation parameters, and ii) updating this inverse model online using newly-observed responses to stimulation. We tested OMiSO using intracortical microstimulation with a "Utah" array and found that it outperformed competing methods that do not incorporate these advances. Taken together, OMiSO provides greater accuracy in achieving specified activity states, thereby advancing neuromodulation technologies for understanding the brain and for treating brain disorders.

Neurons process information in ways that depend on their cell type, connectivity, and the brain region in which they are embedded. However, inferring these factors from neural activity remains a significant challenge. To build general-purpose representations that allow for resolving information about a neuron's identity, we introduce NuCLR, a self-supervised framework that aims to learn representations of neural activity that allow for differentiating one neuron from the rest. NuCLRbrings together views of the same neuron observed at different times and across different stimuli and uses a contrastive objective to pull these representations together. To capture population context without assuming any fixed neuron ordering, we build a spatiotemporal transformer that integrates activity in a permutation-equivariant manner.

The primate visual system is typically divided into two streams -- the ventral stream, responsible for object recognition, and the dorsal stream, responsible for encoding spatial relations and motion. Recent studies have shown that convolutional neural networks (CNNs) pretrained on object recognition tasks are remarkably effective at predicting neuronal responses in the ventral stream, shedding light on the neural mechanisms underlying object recognition. However, similar models of the dorsal stream remain underdeveloped due to the lack of large scale datasets encompassing dorsal stream areas. To address this gap, we present STSBENCH, a dataset of large-scale, single neuron recordings from over 2,000 neurons in the superior temporal sulcus (STS), a nearly 50-fold increase over existing dorsal stream datasets, collected while Rhesus macaques viewed thousands of unique, natural videos. We show that our dataset can be used for benchmarking encoding models of dorsal stream neuronal responses and reconstructing visual input from neural activity.

Speech neuroprostheses aim to restore communication for people with severe paralysis by decoding speech directly from neural activity. To accelerate algorithmic progress, a recent benchmark released intracranial recordings from a paralyzed participant attempting to speak, along with a baseline decoding algorithm. Prior work on the benchmark showed impressive accuracy gains. However, these gains increased computational costs and were not demonstrated in a real-time decoding setting. Here, we make three contributions that pave the way towards accurate, efficient, and real-time neural speech decoding.

Brain-computer interfaces have shown great potential in motor and speech rehabilitation, but still suffer from low performance stability across days, mostly due to the instabilities in neural signals. These instabilities, partially caused by neuron deaths and electrode shifts, leading to channel-level variabilities among different recording days. Previous studies mostly focused on aligning multi-day neural signals onto a low-dimensional latent manifold to reduce the variabilities, while faced with difficulties when neural signals exhibit significant drift. Here, we propose to learn a channel-level invariant neural representation to address the variabilities in channels across days. It contains a channel-rearrangement module to learn stable representations against electrode shifts, and a channel reconstruction module to handle the missing neurons. The proposed method achieved the state-of-the-art performance with cross-day decoding tasks over two months, on multiple benchmark BCI datasets. The proposed approach showed good generalization ability that can be incorporated to different neural networks.

Characterizing interactions between brain areas is a fundamental goal of systems neuroscience. While such analyses are possible when areas are recorded simultaneously, it is rare to observe all combinations of areas of interest within a single animal or recording session. How can we leverage multi-animal datasets to better understand multi-area interactions? Building on recent progress in large-scale, multi-animal models, we introduce NeuroPaint, a masked autoencoding approach for inferring the dynamics of unrecorded brain areas. By training across animals with overlapping subsets of recorded areas, NeuroPaint learns to reconstruct activity in missing areas based on shared structure across individuals. We train and evaluate our approach on synthetic data and two multi-animal, multi-area Neuropixels datasets. Our results demonstrate that models trained across animals with partial observations can successfully in-paint the dynamics of unrecorded areas, enabling 39th Conference on Neural Information Processing Systems (NeurIPS 2025).

The brain's diverse spatiotemporal activity patterns are fundamental to cognition and consciousness, yet how these macroscopic dynamics emerge from microscopic neural circuitry remains a critical challenge. We take a step in this direction by developing a spatially extended neural network model integrated with a spectral theory of its connectivity matrix. Our theory quantitatively demonstrates how local structural parameters, such as E/I neuron projection ranges, connection strengths, and density determine distinct features of the eigenvalue spectrum, specifically outlier eigenvalues and a bulk disk. These spectral signatures, in turn, precisely predict the network's emergent global dynamical regime, encompassing asynchronous states, synchronous states, oscillations, localized activity bumps, traveling waves, and chaos. Motivated by observations of shifting cortical dynamics in mice across arousal states, our framework not only provides a possible explanation for repertoire of behaviors but also offers a principled starting point for inferring underlying effective connectivity changes from macroscopic brain activity. By mechanistically linking neural structure to dynamics, this work advances a principled framework for dissecting how large-scale activity patterns--central to cognition and open questions in consciousness research--arise from, and constrain, local circuitry.

Neural networks are often described as black boxes, reflecting the significant challenge of understanding their internal workings and interactions. We propose a different perspective that challenges the prevailing view: rather than being inscrutable, neural networks exhibit patterns in their raw population activity that mirror regularities in the training data. We refer to this as the Reflection Hypothesis and provide evidence for this phenomenon in both simple recurrent neural networks (RNNs) and complex large language models (LLMs). Building on this insight, we propose to leverage our cognitive tendency of chunking to segment high-dimensional neural population dynamics into interpretable units that reflect underlying concepts. We propose three methods to extract recurring chunks on a neural population level, complementing each other based on label availability and neural data dimensionality.

Real-time decoding of neural activity is central to neuroscience and neurotechnology applications, from closed-loop experiments to brain-computer interfaces, where models are subject to strict latency constraints. Traditional methods, including simple recurrent neural networks, are fast and lightweight but often struggle to generalize to unseen data. In contrast, recent Transformer-based approaches leverage large-scale pretraining for strong generalization performance, but typically have much larger computational requirements and are not always suitable for lowresource or real-time settings. To address these shortcomings, we present POSSM, a novel hybrid architecture that combines individual spike tokenization via a crossattention module with a recurrent state-space model (SSM) backbone to enable (1) fast and causal online prediction on neural activity and (2) efficient generalization to new sessions, individuals, and tasks through multi-dataset pretraining. We evaluate POSSM's decoding performance and inference speed on intracortical decoding of monkey motor tasks, and show that it extends to clinical applications, namely handwriting and speech decoding in human subjects. Notably, we demonstrate that pretraining on monkey motor-cortical recordings improves decoding performance on the human handwriting task, highlighting the exciting potential for cross-species transfer. In all of these tasks, we find that POSSM achieves decoding accuracy comparable to state-of-the-art Transformers, at a fraction of the inference cost (up to 9 faster on GPU). These results suggest that hybrid SSMs are a promising approach to bridging the gap between accuracy, inference speed, and generalization when training neural decoders for real-time, closed-loop applications.