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Applications/Neuroscience, Cognitive Science

Paul Scotti, Atmadeep Banerjee, Jimmie Goode, Stepan Shabalin, Alex Nguyen, ethan cohen, Aidan Dempster, Nathalie Verlinde, Elad Yundler, David Weisberg 等

We present MindEye, a novel fMRI-to-image approach to retrieve and reconstruct viewed images from brain activity. Our model comprises two parallel submodules that are specialized for retrieval (using contrastive learning) and reconstruction (using a diffusion prior). MindEye can map fMRI brain activity to any high dimensional multimodal latent space, like CLIP image space, enabling image reconstruction using generative models that accept embeddings from this latent space. We comprehensively compare our approach with other existing methods, using both qualitative side-by-side comparisons and quantitative evaluations, and show that MindEye achieves state-of-the-art performance in both reconstruction and retrieval tasks. In particular, MindEye can retrieve the exact original image even among highly similar candidates indicating that its brain embeddings retain fine-grained image-specific information. This allows us to accurately retrieve images even from large-scale databases like LAION-5B. We demonstrate through ablations that MindEye's performance improvements over previous methods result from specialized submodules for retrieval and reconstruction, improved training techniques, and training models with orders of magnitude more parameters. Furthermore, we show that MindEye can better preserve low-level image features in the reconstructions by using img2img, with outputs from a separate autoencoder. All code is available on GitHub.

Applications/Neuroscience, Cognitive Science

Zijiao Chen, Jiaxin Qing, Juan Helen Zhou

Reconstructing human vision from brain activities has been an appealing task that helps to understand our cognitive process. Even though recent research has seen great success in reconstructing static images from non-invasive brain recordings, work on recovering continuous visual experiences in the form of videos is limited. In this work, we propose Mind-Video that learns spatiotemporal information from continuous fMRI data of the cerebral cortex progressively through masked brain modeling, multimodal contrastive learning with spatiotemporal attention, and co-training with an augmented Stable Diffusion model that incorporates network temporal inflation. We show that high-quality videos of arbitrary frame rates can be reconstructed with Mind-Video using adversarial guidance. The recovered videos were evaluated with various semantic and pixel-level metrics. We achieved an average accuracy of 85% in semantic classification tasks and 0.19 in structural similarity index (SSIM), outperforming the previous state-of-the-art by 45%. We also show that our model is biologically plausible and interpretable, reflecting established physiological processes.

Applications/Neuroscience, Cognitive Science

Jingyuan Sun, Mingxiao Li, Zijiao Chen, Yunhao Zhang, Shaonan Wang, Marie-Francine Moens

Decoding visual stimuli from neural responses recorded by functional Magnetic Resonance Imaging (fMRI) presents an intriguing intersection between cognitive neuroscience and machine learning, promising advancements in understanding human visual perception. However, the task is challenging due to the noisy nature of fMRI signals and the intricate pattern of brain visual representations. To mitigate these challenges, we introduce a two-phase fMRI representation learning framework. The first phase pre-trains an fMRI feature learner with a proposed Double-contrastive Mask Auto-encoder to learn denoised representations. The second phase tunes the feature learner to attend to neural activation patterns most informative for visual reconstruction with guidance from an image auto-encoder. The optimized fMRI feature learner then conditions a latent diffusion model to reconstruct image stimuli from brain activities. Experimental results demonstrate our model's superiority in generating high-resolution and semantically accurate images, substantially exceeding previous state-of-the-art methods by 39.34% in the 50-way-top-1 semantic classification accuracy. The code implementations is available at https://github.com/soinx0629/vis_dec_neurips/.

Applications/Neuroscience, Cognitive Science

David Liu, Mate Lengyel

Neural spiking activity is generally variable, non-stationary, and exhibits complex dependencies on covariates, such as sensory input or behavior. These dependencies have been proposed to be signatures of specific computations, and so characterizing them with quantitative rigor is critical for understanding neural computations. Approaches based on point processes provide a principled statistical framework for modeling neural spiking activity. However, currently, they only allow the instantaneous mean, but not the instantaneous variability, of responses to depend on covariates. To resolve this limitation, we propose a scalable Bayesian approach generalizing modulated renewal processes using sparse variational Gaussian processes. We leverage pathwise conditioning for computing nonparametric priors over conditional interspike interval distributions and rely on automatic relevance determination to detect lagging interspike interval dependencies beyond renewal order. After systematically validating our method on synthetic data, we apply it to two foundational datasets of animal navigation: head direction cells in freely moving mice and hippocampal place cells in rats running along a linear track. Our model exhibits competitive or better predictive power compared to state-of-the-art baselines, and outperforms them in terms of capturing interspike interval statistics. These results confirm the importance of modeling covariate-dependent spiking variability, and further analyses of our fitted models reveal rich patterns of variability modulation beyond the temporal resolution of flexible count-based approaches.

Applications/Neuroscience, Cognitive Science

Théo Gnassounou, Rémi Flamary, Alexandre Gramfort

In many machine learning applications on signals and biomedical data, especially electroencephalogram (EEG), one major challenge is the variability of the data across subjects, sessions, and hardware devices. In this work, we propose a new method called Convolutional Monge Mapping Normalization ($\texttt{CMMN}$), which consists in filtering the signals in order to adapt their power spectrum density (PSD) to a Wasserstein barycenter estimated on training data. $\texttt{CMMN}$ relies on novel closed-form solutions for optimal transport mappings and barycenters and provides individual test time adaptation to new data without needing to retrain a prediction model. Numerical experiments on sleep EEG data show that $\texttt{CMMN}$ leads to significant and consistent performance gains independent from the neural network architecture when adapting between subjects, sessions, and even datasets collected with different hardware. Notably our performance gain is on par with much more numerically intensive Domain Adaptation (DA) methods and can be used in conjunction with those for even better performances.

Applications/Neuroscience, Cognitive Science

Dong Kyum Kim, Jea Kwon, Meeyoung Cha, C. Lee

The hippocampus plays a critical role in learning, memory, and spatial representation, processes that depend on the NMDA receptor (NMDAR). Inspired by recent findings that compare deep learning models to the hippocampus, we propose a new nonlinear activation function that mimics NMDAR dynamics. NMDAR-like nonlinearity shifts short-term working memory into long-term reference memory in transformers, thus enhancing a process that is similar to memory consolidation in the mammalian brain. We design a navigation task assessing these two memory functions and show that manipulating the activation function (i.e., mimicking the Mg$^{2+}$-gating of NMDAR) disrupts long-term memory processes. Our experiments suggest that place cell-like functions and reference memory reside in the feed-forward network layer of transformers and that nonlinearity drives these processes. We discuss the role of NMDAR-like nonlinearity in establishing this striking resemblance between transformer architecture and hippocampal spatial representation.

Applications/Neuroscience, Cognitive Science

Mufeng Tang, Helen Barron, Rafal Bogacz

Forming accurate memory of sequential stimuli is a fundamental function of biological agents. However, the computational mechanism underlying sequential memory in the brain remains unclear. Inspired by neuroscience theories and recent successes in applying predictive coding (PC) to \emph{static} memory tasks, in this work we propose a novel PC-based model for \emph{sequential} memory, called \emph{temporal predictive coding} (tPC). We show that our tPC models can memorize and retrieve sequential inputs accurately with a biologically plausible neural implementation. Importantly, our analytical study reveals that tPC can be viewed as a classical Asymmetric Hopfield Network (AHN) with an implicit statistical whitening process, which leads to more stable performance in sequential memory tasks of structured inputs. Moreover, we find that tPC exhibits properties consistent with behavioral observations and theories in neuroscience, thereby strengthening its biological relevance. Our work establishes a possible computational mechanism underlying sequential memory in the brain that can also be theoretically interpreted using existing memory model frameworks.

Applications/Neuroscience, Cognitive Science

Rylan Schaeffer, Mikail Khona, Tzuhsuan Ma, Cristobal Eyzaguirre, Sanmi Koyejo, Ila Fiete

To solve the spatial problems of mapping, localization and navigation, the mammalian lineage has developed striking spatial representations. One important spatial representation is the Nobel-prize winning grid cells: neurons that represent self-location, a local and aperiodic quantity, with seemingly bizarre non-local and spatially periodic activity patterns of a few discrete periods. Why has the mammalian lineage learnt this peculiar grid representation? Mathematical analysis suggests that this multi-periodic representation has excellent properties as an algebraic code with high capacity and intrinsic error-correction, but to date, synthesis of multi-modular grid cells in deep recurrent neural networks remains absent. In this work, we begin by identifying key insights from four families of approaches to answering the grid cell question: dynamical systems, coding theory, function optimization and supervised deep learning. We then leverage our insights to propose a new approach that elegantly combines the strengths of all four approaches. Our approach is a self-supervised learning (SSL) framework - including data, data augmentations, loss functions and a network architecture - motivated from a normative perspective, with no access to supervised position information. Without making assumptions about internal or readout representations, we show that multiple grid cell modules can emerge in networks trained on our SSL framework and that the networks generalize significantly beyond their training distribution. This work contains insights for neuroscientists interested in the origins of grid cells as well as machine learning researchers interested in novel SSL frameworks.

Applications/Neuroscience, Cognitive Science

Andrew Luo, Maggie Henderson, Leila Wehbe, Michael Tarr

A long standing goal in neuroscience has been to elucidate the functional organization of the brain. Within higher visual cortex, functional accounts have remained relatively coarse, focusing on regions of interest (ROIs) and taking the form of selectivity for broad categories such as faces, places, bodies, food, or words. Because the identification of such ROIs has typically relied on manually assembled stimulus sets consisting of isolated objects in non-ecological contexts, exploring functional organization without robust a priori hypotheses has been challenging. To overcome these limitations, we introduce a data-driven approach in which we synthesize images predicted to activate a given brain region using paired natural images and fMRI recordings, bypassing the need for category-specific stimuli. Our approach -- Brain Diffusion for Visual Exploration ("BrainDiVE") -- builds on recent generative methods by combining large-scale diffusion models with brain-guided image synthesis. Validating our method, we demonstrate the ability to synthesize preferred images with appropriate semantic specificity for well-characterized category-selective ROIs. We then show that BrainDiVE can characterize differences between ROIs selective for the same high-level category. Finally we identify novel functional subdivisions within these ROIs, validated with behavioral data. These results advance our understanding of the fine-grained functional organization of human visual cortex, and provide well-specified constraints for further examination of cortical organization using hypothesis-driven methods.

Applications/Neuroscience, Cognitive Science

Tahereh Toosi, Elias Issa

In natural vision, feedback connections support versatile visual inference capabilities such as making sense of the occluded or noisy bottom-up sensory information or mediating pure top-down processes such as imagination. However, the mechanisms by which the feedback pathway learns to give rise to these capabilities flexibly are not clear. We propose that top-down effects emerge through alignment between feedforward and feedback pathways, each optimizing its own objectives. To achieve this co-optimization, we introduce Feedback-Feedforward Alignment (FFA), a learning algorithm that leverages feedback and feedforward pathways as mutual credit assignment computational graphs, enabling alignment. In our study, we demonstrate the effectiveness of FFA in co-optimizing classification and reconstruction tasks on widely used MNIST and CIFAR10 datasets. Notably, the alignment mechanism in FFA endows feedback connections with emergent visual inference functions, including denoising, resolving occlusions, hallucination, and imagination. Moreover, FFA offers bio-plausibility compared to traditional backpropagation (BP) methods in implementation. By repurposing the computational graph of credit assignment into a goal-driven feedback pathway, FFA alleviates weight transport problems encountered in BP, enhancing the bio-plausibility of the learning algorithm. Our study presents FFA as a promising proof-of-concept for the mechanisms underlying how feedback connections in the visual cortex support flexible visual functions. This work also contributes to the broader field of visual inference underlying perceptual phenomena and has implications for developing more biologically inspired learning algorithms.

Applications/Neuroscience, Cognitive Science

Marco Celotto, Jan Bím, Alejandro Tlaie, Vito De Feo, Alessandro Toso, Stefan Lemke, Daniel Chicharro, Hamed Nili, Malte Bieler, Ileana Hanganu-Opatz 等

Quantifying the amount, content and direction of communication between brain regions is key to understanding brain function. Traditional methods to analyze brain activity based on the Wiener-Granger causality principle quantify the overall information propagated by neural activity between simultaneously recorded brain regions, but do not reveal the information flow about specific features of interest (such as sensory stimuli). Here, we develop a new information theoretic measure termed Feature-specific Information Transfer (FIT), quantifying how much information about a specific feature flows between two regions. FIT merges the Wiener-Granger causality principle with information-content specificity. We first derive FIT and prove analytically its key properties. We then illustrate and test them with simulations of neural activity, demonstrating that FIT identifies, within the total information propagated between regions, the information that is transmitted about specific features. We then analyze three neural datasets obtained with different recording methods, magneto- and electro-encephalography, and spiking activity, to demonstrate the ability of FIT to uncover the content and direction of information flow between brain regions beyond what can be discerned with traditional analytical methods. FIT can improve our understanding of how brain regions communicate by uncovering previously unaddressed feature-specific information flow.

Applications/Neuroscience, Cognitive Science

Wayne Soo, Vishwa Goudar, Xiao-Jing Wang

Training recurrent neural networks (RNNs) has become a go-to approach for generating and evaluating mechanistic neural hypotheses for cognition. The ease and efficiency of training RNNs with backpropagation through time and the availability of robustly supported deep learning libraries has made RNN modeling more approachable and accessible to neuroscience. Yet, a major technical hindrance remains. Cognitive processes such as working memory and decision making involve neural population dynamics over a long period of time within a behavioral trial and across trials. It is difficult to train RNNs to accomplish tasks where neural representations and dynamics have long temporal dependencies without gating mechanisms such as LSTMs or GRUs which currently lack experimental support and prohibit direct comparison between RNNs and biological neural circuits. We tackled this problem based on the idea of specialized skip-connections through time to support the emergence of task-relevant dynamics, and subsequently reinstitute biological plausibility by reverting to the original architecture. We show that this approach enables RNNs to successfully learn cognitive tasks that prove impractical if not impossible to learn using conventional methods. Over numerous tasks considered here, we achieve less training steps and shorter wall-clock times, particularly in tasks that require learning long-term dependencies via temporal integration over long timescales or maintaining a memory of past events in hidden-states. Our methods expand the range of experimental tasks that biologically plausible RNN models can learn, thereby supporting the development of theory for the emergent neural mechanisms of computations involving long-term dependencies.

Applications/Neuroscience, Cognitive Science

Qiang Gao, Xiaojun Shan, Yuchen Zhang, Fan Zhou

As there exist competitive subnetworks within a dense network in concert with Lottery Ticket Hypothesis, we introduce a novel neuron-wise task incremental learning method, namely Data-free Subnetworks (DSN), which attempts to enhance the elastic knowledge transfer across the tasks that sequentially arrive. Specifically, DSN primarily seeks to transfer knowledge to the new coming task from the learned tasks by selecting the affiliated weights of a small set of neurons to be activated, including the reused neurons from prior tasks via neuron-wise masks. And it also transfers possibly valuable knowledge to the earlier tasks via data-free replay. Especially, DSN inherently relieves the catastrophic forgetting and the unavailability of past data or possible privacy concerns. The comprehensive experiments conducted on four benchmark datasets demonstrate the effectiveness of the proposed DSN in the context of task-incremental learning by comparing it to several state-of-the-art baselines. In particular, DSN enables the knowledge transfer to the earlier tasks, which is often overlooked by prior efforts.

Applications/Neuroscience, Cognitive Science

Chaofei Fan, Nick Hahn, Foram Kamdar, Donald Avansino, Guy Wilson, Leigh Hochberg, Krishna V Shenoy, Jaimie Henderson, Francis Willett

Intracortical brain-computer interfaces (iBCIs) have shown promise for restoring rapid communication to people with neurological disorders such as amyotrophic lateral sclerosis (ALS). However, to maintain high performance over time, iBCIs typically need frequent recalibration to combat changes in the neural recordings that accrue over days. This requires iBCI users to stop using the iBCI and engage in supervised data collection, making the iBCI system hard to use. In this paper, we propose a method that enables self-recalibration of communication iBCIs without interrupting the user. Our method leverages large language models (LMs) to automatically correct errors in iBCI outputs. The self-recalibration process uses these corrected outputs ("pseudo-labels") to continually update the iBCI decoder online. Over a period of more than one year (403 days), we evaluated our Continual Online Recalibration with Pseudo-labels (CORP) framework with one clinical trial participant. CORP achieved a stable decoding accuracy of 93.84% in an online handwriting iBCI task, significantly outperforming other baseline methods. Notably, this is the longest-running iBCI stability demonstration involving a human participant. Our results provide the first evidence for long-term stabilization of a plug-and-play, high-performance communication iBCI, addressing a major barrier for the clinical translation of iBCIs.

Applications/Neuroscience, Cognitive Science

Saber Sheybani, Himanshu Hansaria, Justin Wood, Linda Smith, Zoran Tiganj

Infants possess a remarkable ability to rapidly learn and process visual inputs. As an infant's mobility increases, so does the variety and dynamics of their visual inputs. Is this change in the properties of the visual inputs beneficial or even critical for the proper development of the visual system? To address this question, we used video recordings from infants wearing head-mounted cameras to train a variety of self-supervised learning models. Critically, we separated the infant data by age group and evaluated the importance of training with a curriculum aligned with developmental order. We found that initiating learning with the data from the youngest age group provided the strongest learning signal and led to the best learning outcomes in terms of downstream task performance. We then showed that the benefits of the data from the youngest age group are due to the slowness and simplicity of the visual experience. The results provide strong empirical evidence for the importance of the properties of the early infant experience and developmental progression in training. More broadly, our approach and findings take a noteworthy step towards reverse engineering the learning mechanisms in newborn brains using image-computable models from artificial intelligence.

Applications/Neuroscience, Cognitive Science

Ke Yi, Yansen Wang, Kan Ren, Dongsheng Li

Large-scale pre-training has shown great potential to enhance models on downstream tasks in vision and language. Developing similar techniques for scalp electroencephalogram (EEG) is suitable since unlabelled data is plentiful. Meanwhile, various sampling channel selections and inherent structural and spatial information bring challenges and avenues to improve existing pre-training strategies further. In order to break boundaries between different EEG resources and facilitate cross-dataset EEG pre-training, we propose to map all kinds of channel selections to a unified topology. We further introduce MMM, a pre-training framework with Multi-dimensional position encoding, Multi-level channel hierarchy, and Multi-stage pre-training strategy built on the unified topology to obtain topology-agnostic representations. Experiments demonstrate that our approach yields impressive improvements over previous state-of-the-art techniques on emotional recognition benchmark datasets.

Applications/Neuroscience, Cognitive Science

xiaolong zou, Zhikun Chu, Qinghai Guo, Jie Cheng, Bo Ho, Si Wu, Yuanyuan Mi

Temporal sequence processing is fundamental in brain cognitive functions. Experimental data has indicated that the representations of ordinal information and contents of temporal sequences are disentangled in the brain, but the neural mechanism underlying this disentanglement remains largely unclear. Here, we investigate how recurrent neural circuits learn to represent the abstract order structure of temporal sequences, and how this disentangled representation of order structure from that of contents facilitates the processing of temporal sequences. We show that with an appropriate learn protocol, a recurrent neural circuit can learn a set of tree-structured attractor states to encode the corresponding tree-structured orders of given temporal sequences. This abstract temporal order template can then be bound with different contents, allowing for flexible and robust temporal sequence processing. Using a transfer learning task, we demonstrate that the reuse of a temporal order template facilitates the acquisition of new temporal sequences of the same or similar ordinal structure. Using a key-word spotting task, we demonstrate that the attractor representation of order structure improves the robustness of temporal sequence discrimination, if the ordinal information is the key to differentiate different sequences. We hope this study gives us insights into the neural mechanism of representing the ordinal information of temporal sequences in the brain, and helps us to develop brain-inspired temporal sequence processing algorithms.

Applications/Neuroscience, Cognitive Science

Ankit Vishnubhotla, Charlotte Loh, Akash Srivastava, Liam Paninski, Cole Hurwitz

Contrastive learning is quickly becoming an essential tool in neuroscience for extracting robust and meaningful representations of neural activity. Despite numerous applications to neuronal population data, there has been little exploration of how these methods can be adapted to key primary data analysis tasks such as spike sorting or cell-type classification. In this work, we propose a novel contrastive learning framework, CEED (Contrastive Embeddings for Extracellular Data), for high-density extracellular recordings. We demonstrate that through careful design of the network architecture and data augmentations, it is possible to generically extract representations that far outperform current specialized approaches. We validate our method across multiple high-density extracellular recordings. All code used to run CEED can be found at https://github.com/ankitvishnu23/CEED.

Applications/Neuroscience, Cognitive Science

Mehdi Azabou, Vinam Arora, Venkataramana Ganesh, Ximeng Mao, Santosh Nachimuthu, Michael Mendelson, Blake Richards, Matthew Perich, Guillaume Lajoie, Eva Dyer

Our ability to use deep learning approaches to decipher neural activity would likely benefit from greater scale, in terms of both the model size and the datasets. However, the integration of many neural recordings into one unified model is challenging, as each recording contains the activity of different neurons from different individual animals. In this paper, we introduce a training framework and architecture designed to model the population dynamics of neural activity across diverse, large-scale neural recordings. Our method first tokenizes individual spikes within the dataset to build an efficient representation of neural events that captures the fine temporal structure of neural activity. We then employ cross-attention and a PerceiverIO backbone to further construct a latent tokenization of neural population activities. Utilizing this architecture and training framework, we construct a large-scale multi-session model trained on large datasets from seven nonhuman primates, spanning over 158 different sessions of recording from over 27,373 neural units and over 100 hours of recordings. In a number of different tasks, we demonstrate that our pretrained model can be rapidly adapted to new, unseen sessions with unspecified neuron correspondence, enabling few-shot performance with minimal labels. This work presents a powerful new approach for building deep learning tools to analyze neural data and stakes out a clear path to training at scale for neural decoding models.

Applications/Neuroscience, Cognitive Science

Evren Gokcen, Anna Jasper, Alison Xu, Adam Kohn, Christian Machens, Byron M Yu

Modern recording techniques now allow us to record from distinct neuronal populations in different brain networks. However, especially as we consider multiple (more than two) populations, new conceptual and statistical frameworks are needed to characterize the multi-dimensional, concurrent flow of signals among these populations. Here, we develop a dimensionality reduction framework that determines (1) the subset of populations described by each latent dimension, (2) the direction of signal flow among those populations, and (3) how those signals evolve over time within and across experimental trials. We illustrate these features in simulation, and further validate the method by applying it to previously studied recordings from neuronal populations in macaque visual areas V1 and V2. Then we study interactions across select laminar compartments of areas V1, V2, and V3d, recorded simultaneously with multiple Neuropixels probes. Our approach uncovered signatures of selective communication across these three areas that related to their retinotopic alignment. This work advances the study of concurrent signaling across multiple neuronal populations.