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Applications · Neuroscience, Cognitive Science

Anushri Arora, Jonathan Pillow

Low-rank recurrent neural networks (RNNs) provide a powerful framework for characterizing how neural systems solve complex cognitive tasks. However, fitting and interpreting these networks remains an important open problem. In this paper, we develop new methods for efficiently fitting low-rank RNNs in ''teacher-training'' settings. In particular, we build upon the neural engineering framework (NEF), in which RNNs are viewed as approximating an ordinary differential equation (ODE) of interest using a set of random nonlinear basis functions. This view provides geometric insight into how the choice of neural nonlinearity (e.g. tanh, ReLU) and the distribution of model parameters affects an RNN's representational capacity. We adapt this framework for online training and demonstrate better performance with significantly smaller networks compared to FORCE. Additionally, we outperform backpropagation-trained networks of similar size, while requiring substantially less training time. Next, we ask: how many neurons---and what distribution over their parameters---are needed to approximate a given dynamical system? To address this, we introduce methods for finding the smallest low-rank RNN to approximate a given dynamical system using an extension of orthogonal matching pursuit (OMP). We then consider infinite unit low-rank RNNs, which converge to a Gaussian Process (GP) over ODEs. In particular, we show that we can optimize the distribution over RNN parameters using the marginal likelihood under the equivalent GP covariance function---which can be computed in closed form for particular choices of nonlinearity. This results in substantially better training performance even for finite low-rank RNNs. Finally, we describe active learning methods for low-rank RNNs, which speed up training through the selection of maximally informative activity patterns.

Applications · Neuroscience, Cognitive Science

Emanuele Luconi, Dario Liscai, Carlo Baldassi, Alessandro Marin Vargas, Alessandro Sanzeni

Invariant object recognition-the ability to identify objects despite changes in appearance-is a hallmark of visual processing in the brain, yet its understanding remains a central challenge in systems neuroscience. Artificial neural networks trained to predict neural responses to visual stimuli (“digital twins”) could provide a powerful framework for studying such complex computations in silico. However, while current models accurately capture single-neuron responses within individual visual areas, their ability to reproduce how populations of neurons represent object identity, and how these representations transform across the cortical hierarchy, remains largely unexplored. Here we examine key functional signatures observed experimentally and find that current models account for hierarchical changes in basic single-neuron properties, such as receptive field size, but fail to capture more complex population-level phenomena, particularly invariant object representations. To address this gap, we introduce a biologically inspired hierarchical readout scheme that mirrors cortical anatomy, modeling each visual area as a projection from a distinct depth within a shared core network. This approach significantly improves the prediction of population-level representational transformations, outperforming standard models that use only the final layer, as well as alternatives with modified architecture, regularization, and loss function. Our results suggest that incorporating anatomical information provides a strong inductive bias in digital twin models, enabling them to better capture general principles of brain function.

Applications · Neuroscience, Cognitive Science

Adam J. Eisen, Mitchell Ostrow, Sarthak Chandra, Leo Kozachkov, Earl Miller, Ila Fiete

Biological function arises through the dynamical interactions of multiple subsystems, including those between brain areas, within gene regulatory networks, and more. A common approach to understanding these systems is to model the dynamics of each subsystem and characterize communication between them. An alternative approach is through the lens of control theory: how the subsystems control one another. This approach involves inferring the directionality, strength, and contextual modulation of control between subsystems. However, methods for understanding subsystem control are typically linear and cannot adequately describe the rich contextual effects enabled by nonlinear complex systems. To bridge this gap, we devise a data-driven nonlinear control-theoretic framework to characterize subsystem interactions via the Jacobian of the dynamics. We address the challenge of learning Jacobians from time-series data by proposing the JacobianODE, a deep learning method that leverages properties of the Jacobian to directly estimate it for arbitrary dynamical systems from data alone. We show that JacobianODE models outperform existing Jacobian estimation methods on challenging systems, including high-dimensional chaos. Applying our approach to a multi-area recurrent neural network (RNN) trained on a working memory selection task, we show that the “sensory” area gains greater control over the “cognitive” area over learning. Furthermore, we leverage the JacobianODE to directly control the trained RNN, enabling precise manipulation of its behavior. Our work lays the foundation for a theoretically grounded and data-driven understanding of interactions among biological subsystems.

Applications · Neuroscience, Cognitive Science

Ian Christopher Tanoh, Michael Deistler, Jakob H Macke, Scott Linderman

Multi-compartment Hodgkin-Huxley models are biophysical models of how electrical signals propagate throughout a neuron, and they form the basis of our knowledge of neural computation at the cellular level. However, these models have many free parameters that must be estimated for each cell, and existing fitting methods rely on intracellular voltage measurements that are highly challenging to obtain in-vivo. Recent advances in neural recording technology with high-density probes and arrays enable dense sampling of extracellular voltage from many sites surrounding a neuron, allowing indirect measurement of many compartments of a cell simultaneously. Here, we propose a method for inferring the underlying membrane voltage, biophysical parameters, and the neuron's position relative to the probe, using extracellular measurements alone. We use an Extended Kalman Filter to infer membrane voltage and channel states using efficient, differentiable simulators. Then, we learn the model parameters by maximizing the marginal likelihood using gradient-based methods. We demonstrate the performance of this approach using simulated data and real neuron morphologies.

Applications · Neuroscience, Cognitive Science

Christian Internò, Robert Geirhos, Markus Olhofer, Sunny Liu, Barbara Hammer, David Klindt

The rapid advancement of generative AI enables highly realistic synthetic video, posing significant challenges for content authentication and raising urgent concerns about misuse. Existing detection methods often struggle with generalization and capturing subtle temporal inconsistencies. We propose $ReStraV$ ($Re$presentation $Stra$ightening for $V$ideo), a novel approach to distinguish natural from AI-generated videos. Inspired by the ``perceptual straightening'' hypothesis—which suggests real-world video trajectories become more straight in neural representation domain—we analyze deviations from this expected geometric property. Using a pre-trained self-supervised vision transformer (DINOv2), we quantify the temporal curvature and stepwise distance in the model's representation domain. We aggregate statistical and signals descriptors of these measures for each video and train a classifier. Our analysis shows that AI-generated videos exhibit significantly different curvature and distance patterns compared to real videos. A lightweight classifier achieves state-of-the-art detection performance (e.g., $97.17$ % accuracy and $98.63$ % AUROC on the VidProM benchmark, substantially outperforming existing image- and video-based methods. ReStraV is computationally efficient, it is offering a low-cost and effective detection solution. This work provides new insights into using neural representation geometry for AI-generated video detection.

Applications · Neuroscience, Cognitive Science

Wen Xiong, Junzhong Ji, Jinduo Liu

Pre-trained Large language models (LLMs) have shown impressive advancements in functional magnetic resonance imaging (fMRI) analysis and causal discovery. Considering the unique nature of the causal discovery field, which focuses on extracting causal graphs from observed data, research on LLMs in this field is still at an early exploratory stage. As a subfield of causal discovery, effective connectivity (EC) has received even less attention, and LLM-based approaches in EC remain unexplored. Existing LLM-based approaches for causal discovery typically rely on iterative querying to assess the causal influence between variable pairs, without any model adaptation or fine-tuning, making them ill-suited for handling the cross-modal gap and complex causal structures. To this end, we propose BrainEC-LLM, the first method to fine-tune LLMs for estimating brain EC from fMRI data. Specifically, multiscale decomposition mixing module decomposes fMRI time series data into short-term and long-term multiscale trends, then mixing them in bottom-up (fine to coarse) and top-down (coarse to fine) manner to extract multiscale temporal variations. And cross attention is applied with pre-trained word embeddings to ensure consistency between the fMRI input and pre-trained natural language. The experimental results on simulated and real resting-state fMRI datasets demonstrate that BrainEC-LLM can achieve superior performance when compared to state-of-the-art baselines.

Applications · Neuroscience, Cognitive Science

Zhi Zhou, Tan Yuhao, Zenan Li, Yuan Yao, Lan-Zhe Guo, Yu-Feng Li, Xiaoxing Ma

Test-time scaling seeks to improve the reasoning performance of large language models (LLMs) by adding computational resources. A prevalent approach within the field is *sampling-based test-time scaling methods*, which enhance reasoning by generating multiple reasoning paths for a given input during inference. However, despite its practical success, the theoretical foundations remain underexplored. In this paper, we provide the first theoretical framework for analyzing sampling-based test-time scaling methods, grounded in the perspective of confidence estimation. Based on the framework, we analyze two dominant paradigms: self-consistency and perplexity, and reveal key limitations: self-consistency suffers from high estimation error while perplexity exhibits substantial modeling error and possible degradation of the estimation error convergence. To address these limitations, we introduce RPC, a hybrid method that leverages our theoretical insights through two key components: *Perplexity Consistency* and *Reasoning Pruning*. *Perplexity Consistency* combines the strengths of self-consistency and perplexity, boosting the convergence rate of estimation error from linear to exponential while preserving model error. *Reasoning Pruning* prevents degradation by eliminating low-probability reasoning paths. Both theoretical analysis and empirical results across seven benchmark datasets demonstrate that RPC has a strong potential for reducing reasoning error. Notably, RPC achieves reasoning performance comparable to self-consistency while not only enhancing confidence reliability but also reducing sampling costs by 50%. The code and resources are available at https://wnjxyk.github.io/RPC.

Applications · Neuroscience, Cognitive Science

Miran Özdogan, Gilad Landau, Gereon Elvers, Dulhan Jayalath, Pratik Somaiya, Francesco Mantegna, Mark Woolrich, Oiwi Parker Jones

LibriBrain represents the largest single-subject MEG dataset to date for speech decoding, with over 50 hours of recordings---5$\times$ larger than the next comparable dataset and 50$\times$ larger than most. This unprecedented `depth' of within-subject data enables exploration of neural representations at a scale previously unavailable with non-invasive methods. LibriBrain comprises high-quality MEG recordings together with detailed annotations from a single participant listening to naturalistic spoken English, covering nearly the full Sherlock Holmes canon. Designed to support advances in neural decoding, LibriBrain comes with a Python library for streamlined integration with deep learning frameworks, standard data splits for reproducibility, and baseline results for three foundational decoding tasks: speech detection, phoneme classification, and word classification. Baseline experiments demonstrate that increasing training data yields substantial improvements in decoding performance, highlighting the value of scaling up deep, within-subject datasets. By releasing this dataset, we aim to empower the research community to advance speech decoding methodologies and accelerate the development of safe, effective clinical brain-computer interfaces.

Applications · Neuroscience, Cognitive Science

Kijung Yoon

Inferring synaptic connectivity from neural population activity is a fundamental challenge in computational neuroscience, complicated by partial observability and mismatches between inference models and true circuit dynamics. In this study, we propose a graph-based neural inference model that simultaneously predicts neural activity and infers latent connectivity by modeling neurons as interacting nodes in a graph. The architecture features two distinct modules: one for learning structural connectivity and another for predicting future spiking activity via a graph neural network (GNN). Our model accommodates unobserved neurons through auxiliary nodes, allowing for inference in partially observed circuits. We evaluate this approach using synthetic data generated from ring attractor network models and real spike recordings from head direction cells in mice. Across a wide range of conditions, including varying recurrent connectivity, external inputs, and incomplete observations, our model reliably resolves spurious correlations and recovers accurate weight profiles. When applied to real data, the inferred connectivity aligns with theoretical predictions of continuous attractor models. These results highlight the potential of GNN-based models to infer latent neural circuitry through self-supervised structure learning, while leveraging the spike prediction task to flexibly link connectivity and dynamics across both simulated and biological neural systems.

Applications · Neuroscience, Cognitive Science

Xiangyuan Peng, Xingsi Dong, Si Wu

We propose Grid-like Code Quantization (GCQ), a brain-inspired method for compressing observation-action sequences into discrete representations using grid-like patterns in attractor dynamics. Unlike conventional vector quantization approaches that operate on static inputs, GCQ performs spatiotemporal compression through an action-conditioned codebook, where codewords are derived from continuous attractor neural networks and dynamically selected based on actions. This enables GCQ to jointly compress space and time, serving as a unified world model. The resulting representation supports long-horizon prediction, goal-directed planning, and inverse modeling. Experiments across diverse tasks demonstrate GCQ's effectiveness in compact encoding and downstream performance. Our work offers both a computational tool for efficient sequence modeling and a theoretical perspective on the formation of grid-like codes in neural systems.

Applications · Neuroscience, Cognitive Science

Shuai Huang, Huan Luo, Haodong Jing, Qixian Zhang, Litao Chang, Yating Feng, Xiao Lin, Chendong Qin, Han Chen, Shuwen Jia 等

Translating brain activity into meaningful visual content has long been recognized as a fundamental challenge in neuroscience and brain-computer interface research. Recent advances in EEG-based neural decoding have shown promise, yet two critical limitations remain in this area: poor generalization across subjects and constraints to specific visual tasks. We introduce NEED, the first unified framework achieving zero-shot cross-subject and cross-task generalization for EEG-based visual reconstruction. Our approach addresses three fundamental challenges: (1) cross-subject variability through an Individual Adaptation Module pretrained on multiple EEG datasets to normalize subject-specific patterns, (2) limited spatial resolution and complex temporal dynamics via a dual-pathway architecture capturing both low-level visual dynamics and high-level semantics, and (3) task specificity constraints through a unified inference mechanism adaptable to different visual domains. For video reconstruction, NEED achieves better performance than existing methods. Importantly, Our model maintains 93.7% of within-subject classification performance and 92.4% of visual reconstruction quality when generalizing to unseen subjects, while achieving an SSIM of 0.352 when transferring directly to static image reconstruction without fine-tuning, demonstrating how neural decoding can move beyond subject and task boundaries toward truly generalizable brain-computer interfaces.

Applications · Neuroscience, Cognitive Science

Yuki Minai, Joana Soldado-Magraner, Byron M Yu, Matthew Smith

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 it provides a tool to causally influence brain function. 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.

Applications · Neuroscience, Cognitive Science

Wentao Lu, Dong Nie, Pengcheng Xue, Zheng Cui, Piji Li, Daoqiang Zhang, Xuyun Wen

Decoding natural language text from non-invasive brain signals, such as functional magnetic resonance imaging (fMRI), remains a central challenge in brain-computer interface research. While recent advances in large language models (LLMs) have enabled open-vocabulary fMRI-to-text decoding, existing frameworks typically process the entire fMRI sequence in a single step, leading to performance degradation when handling long input sequences due to memory overload and semantic drift. To address this limitation, we propose a brain-inspired sequential fMRI-to-text decoding framework that mimics the human cognitive strategy of segmented and inductive language processing. Specifically, we divide long fMRI time series into consecutive segments aligned with optimal language comprehension length. Each segment is decoded incrementally, followed by a wrap-up mechanism that summarizes the semantic content and incorporates it as prior knowledge into subsequent decoding steps. This sequence-wise approach alleviates memory burden and ensures semantic continuity across segments. In addition, we introduce a text-guided masking strategy integrated with a masked autoencoder (MAE) framework for fMRI representation learning. This method leverages attention distributions over key semantic tokens to selectively mask the corresponding fMRI time points, and employs MAE to guide the model toward focusing on neural activity at semantically salient moments, thereby enhancing the capability of fMRI embeddings to represent textual information. Experimental results on the two datasets demonstrate that our method significantly outperforms state-of-the-art approaches, with performance gains increasing as decoding length grows.

Applications · Neuroscience, Cognitive Science

Tianhao Chu, Yuling Wu, Neil Burgess, Zilong Ji, Si Wu

Path integration is essential for spatial navigation. Experimental studies have identified neural correlates for path integration, but exactly how the neural system accomplishes this computation remains unresolved. Here, we adopt recurrent neural networks (RNNs) trained to perform a path integration task to explore this issue. After training, we borrow neuroscience prior knowledge and methods to unfold the black box of the trained model, including: clarifying neuron types based on their receptive fields, dissecting information flows between neuron groups by pruning their connections, and analyzing internal dynamics of neuron groups using the attractor framework. Intriguingly, we uncover a hierarchical information processing pathway embedded in the RNN model, along which velocity information of an agent is first forwarded to band cells, band and grid cells then coordinate to carry out path integration, and finally grid cells output the agent location. Inspired by the RNN-based study, we construct a neural circuit model, in which band cells form one-dimensional (1D) continuous attractor neural networks (CANNs) and serve as upstream neurons to support downstream grid cells to carry out path integration in the 2D space. Our study challenges the conventional view of considering grid cells as the principal velocity integrator, and supports a neural circuit model with the hierarchy of band and grid cells.

Applications · Neuroscience, Cognitive Science

Haozhe Shan, Sun Minni, Lea Duncker

The ability to continually learn new skills, retain, and flexibly deploy them to accomplish goals is a key feature of intelligent and efficient behavior. However, the neural mechanisms facilitating the continual learning and flexible (re-)composition of skills remain elusive. Here, we study continual learning and the compositional reuse of learned computations in recurrent neural network (RNN) models using a novel two-system approach: one system that infers 'what' computation to perform, and one that implements 'how' to perform it. We focus on a set of compositional cognitive tasks commonly studied in neuroscience. To construct the 'what' system, we first show that a large family of tasks can be systematically described by a probabilistic generative model, where compositionality stems from a shared underlying vocabulary of discrete task-epochs. The shared epoch structure makes these tasks inherently compositional. We first show that this compositionality can be systematically described by a probabilistic generative model. Furthermore, we develop an unsupervised online learning approach that can learn this model on a single-trial basis, building its vocabulary incrementally as it is exposed to new tasks, and inferring the latent epoch structure as a time-varying computational context within a trial. We implement the 'how' system as an RNN whose low-rank components are composed according to the context inferred by the 'what' system. The contextual inference facilitates the creation, learning, and reuse of the low-rank RNN components as new tasks are introduced sequentially, enabling continual learning without catastrophic forgetting. Using an example task set, we demonstrate the efficacy and competitive performance of this two-system learning framework, its potential for forward and backward transfer, as well as few-shot learning via re-composition.

Applications · Neuroscience, Cognitive Science

Yuhan Helena Liu, Victor Geadah, Jonathan Pillow

Understanding how animals learn is a central challenge in neuroscience, with growing relevance to the development of animal- or human-aligned artificial intelligence. However, existing approaches tend to assume fixed parametric forms for the learning rule (e.g., Q-learning, policy gradient), which may not accurately describe the complex forms of learning employed by animals in realistic settings. Here we address this gap by developing a framework to infer learning rules directly from behavioral data collected during *de novo* task learning. We assume that animals follow a decision policy parameterized by a generalized linear model (GLM), and we model their learning rule—the mapping from task covariates to per-trial weight updates—using a deep neural network (DNN). This formulation allows flexible, data-driven inference of learning rules while maintaining an interpretable form of the decision policy itself. To capture more complex learning dynamics, we introduce a recurrent neural network (RNN) variant that relaxes the Markovian assumption that learning depends solely on covariates of the current trial, allowing for learning rules that integrate information over multiple trials. Simulations demonstrate that the framework can recover ground-truth learning rules. We applied our DNN and RNN-based methods to a large behavioral dataset from mice learning to perform a sensory decision-making task and found that they outperformed traditional RL learning rules at predicting the learning trajectories of held-out mice. The inferred learning rules exhibited reward-history–dependent learning dynamics, with larger updates following sequences of rewarded trials. Overall, these methods provide a flexible framework for inferring learning rules from behavioral data in *de novo* learning tasks, setting the stage for improved animal training protocols and the development of behavioral digital twins.

Applications · Neuroscience, Cognitive Science

Pranav Mamidanna, Thomas Klotz, Dimitrios Chalatsis, Agnese Grison, Irene Mendez Guerra, Shihan Ma, Arnault Caillet, Simon Avrillon, Robin Rohlén, Dario Farina

Neural source separation enables the extraction of individual spike trains from complex electrophysiological recordings. When applied to electromyographic (EMG) signals, it provides a unique window into the motor output of the nervous system by isolating the spiking activity of motor units (MUs). MU decomposition from EMG signals is currently the only scalable neural interfacing approach available in behaving humans and has become foundational in motor neuroscience and neuroprosthetics. However, unlike related domains such as spike sorting or electroencephalography (EEG) analysis, decomposition of EMG signals lacks open benchmarks that reflect the diversity of muscles, movement contexts, and noise sources encountered in practice.To address this gap, we introduce MUniverse, a modular simulation and benchmarking suite for decomposing EMG signals into individual MU spiking activity. MUniverse provides: (1) a simulation stack with a user-friendly interface to a state-of-the-art EMG generator; (2) a curated library of datasets across synthetic, hybrid synthetic-real data with ground truth spikes, and experimental EMG; (3) a set of internal and external decomposition pipelines; and (4) a unified benchmark with well-defined tasks, standard evaluation metrics, and baseline results from established decomposition pipelines.MUniverse is designed for extensibility, reproducibility, and community use, and all datasets are distributed with standardised metadata (Croissant, BIDS). By standardising evaluation and enabling dataset simulation at scale, MUniverse aims to catalyze progress on this long-standing neural signal processing problem.

Applications · Neuroscience, Cognitive Science

Reece Keller, Alyn Kirsch, Felix Pei, Xaq Pitkow, Leo Kozachkov, Aran Nayebi

Autonomy is a hallmark of animal intelligence, enabling adaptive and intelligent behavior in complex environments without relying on external reward or task structure. Existing reinforcement learning approaches to exploration in reward-free environments, including a class of methods known as *model-based intrinsic motivation*, exhibit inconsistent exploration patterns and do not converge to an exploratory policy, thus failing to capture robust autonomous behaviors observed in animals. Moreover, systems neuroscience has largely overlooked the neural basis of autonomy, focusing instead on experimental paradigms where animals are motivated by external reward rather than engaging in ethological, naturalistic and task-independent behavior. To bridge these gaps, we introduce a novel model-based intrinsic drive explicitly designed after the principles of autonomous exploration in animals. Our method (3M-Progress) achieves animal-like exploration by tracking divergence between an online world model and a fixed prior learned from an ecological niche. To the best of our knowledge, we introduce the first autonomous embodied agent that predicts brain data entirely from self-supervised optimization of an intrinsic goal—without any behavioral or neural training data—demonstrating that 3M-Progress agents capture the explainable variance in behavioral patterns and whole-brain neural-glial dynamics recorded from autonomously behaving larval zebrafish, thereby providing the first goal-driven, population-level model of neural-glial computation. Our findings establish a computational framework connecting model-based intrinsic motivation to naturalistic behavior, providing a foundation for building artificial agents with animal-like autonomy.

Applications · Neuroscience, Cognitive Science

Alexander Ratzan, Sidharth Goel, Junhao Wen, Christos Davatzikos, Erdem Varol

Spatial location and molecular interactions have long been linked to the connectivity patterns of neural circuits. Yet, at the macroscale of human brain networks, the interplay between spatial position, gene expression, and connectivity remains incompletely understood. Recent efforts to map the human transcriptome and connectome have yielded spatially resolved brain atlases, however modeling the relationship between high-dimensional transcriptomic data and connectivity while accounting for inherent spatial confounds presents a significant challenge. In this paper, we present the first deep learning approaches for predicting whole-brain functional connectivity from gene expression and regional spatial coordinates, including our proposed Spatiomolecular Transformer (SMT). SMT explicitly models biological context by tokenizing genes based on their transcription start site (TSS) order to capture multi-scale genomic organization, and incorporating regional 3D spatial location via a dedicated context [CLS] token within its multi-head self-attention mechanism. We rigorously benchmark context-aware neural networks, including SMT and a single-gene resolution Multilayer-Perceptron (MLP), to established rules-based and bilinear methods. Crucially, to ensure that learned relationships in any model are not mere artifacts of spatial proximity, we introduce novel spatiomolecular null maps, preserving both spatial and transcriptomic autocorrelation. Context-aware neural networks outperform linear methods, significantly exceed our stringent null shuffle models, and generalize across diverse connectomic datasets and parcellation resolutions. Together, these findings demonstrate a strong, predictable link between the spatial distributions of gene expression and functional brain network architecture, and establish a rigorously validated deep learning framework for decoding this relationship. Code to reproduce our results is available at: github.com/neuroinfolab/GeneEx2Conn.

Applications · Neuroscience, Cognitive Science

Eray Erturk, Maryam Shanechi

Real-time decoding of target variables from multiple simultaneously recorded neural time-series modalities, such as discrete spiking activity and continuous field potentials, is important across various neuroscience applications. However, a major challenge for doing so is that different neural modalities can have different timescales (i.e., sampling rates) and different probabilistic distributions, or can even be missing at some time-steps. Existing nonlinear models of multimodal neural activity do not address different timescales or missing samples across modalities. Further, some of these models do not allow for real-time decoding. Here, we develop a learning framework that can enable real-time recursive decoding while nonlinearly aggregating information across multiple modalities with different timescales and distributions and with missing samples. This framework consists of 1) a multiscale encoder that nonlinearly aggregates information after learning within-modality dynamics to handle different timescales and missing samples in real time, 2) a multiscale dynamical backbone that extracts multimodal temporal dynamics and enables real-time recursive decoding, and 3) modality-specific decoders to account for different probabilistic distributions across modalities. In both simulations and three distinct multiscale brain datasets, we show that our model can aggregate information across modalities with different timescales and distributions and missing samples to improve real-time target decoding. Further, our method outperforms various linear and nonlinear multimodal benchmarks in doing so.