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Applications · Neuroscience, Cognitive Science

Timothy Doyeon Kim, Thomas Luo, Tankut Can, Kamesh Krishnamurthy, Jonathan Pillow, Carlos Brody

Neural computations underlying processes such as decision-making, working memory, and motor control are thought to emerge from neural population dynamics. But estimating these dynamics remains a significant challenge. Here we introduce Flow-field Inference from Neural Data using deep Recurrent networks (FINDR), an unsupervised deep learning method for inferring low-dimensional, nonlinear, stochastic dynamics underlying neural population activity. Using spike train data from frontal brain regions of rats performing an auditory decision-making task, we demonstrate that FINDR performs competitively with existing methods in capturing the heterogeneous responses of individual neurons. When trained to disentangle task-relevant and irrelevant activity, FINDR uncovers interpretable low-dimensional dynamics. These dynamics can be visualized as flow fields and attractors, enabling direct tests of attractor-based theories of neural computation. We suggest FINDR as a powerful method for revealing the low-dimensional task-relevant dynamics of neural populations and their associated computations.

Applications · Neuroscience, Cognitive Science

Zachary Brown, David Carlson

The field of hypothesis generation promises to reduce costs in neuroscience by narrowing the range of interventional studies needed to study various phenomena. Existing machine learning methods can generate scientific hypotheses from complex datasets, but many approaches assume causal relationships are static over time, limiting their applicability to systems with dynamic, state-dependent behavior, such as the brain. While some techniques attempt dynamic causal discovery through factor models, they often restrict relationships to linear patterns or impose other simplifying assumptions. We propose a novel method that models dynamic graphs as a conditionally weighted superposition of static graphs, where each static graph can capture nonlinear relationships. This approach enables the detection of complex, time-varying interactions between variables beyond linear limitations. Our method improves f1-scores of predicted dynamic causal patterns by roughly 22-28% on average over baselines in some of our experiments, with some improvements reaching well over 60%. A case study on real brain data demonstrates our method's ability to uncover relationships linked to specific behavioral states, offering valuable insights into neural dynamics.

Applications · Neuroscience, Cognitive Science

Chen Wei, Chi Zhang, Jiachen Zou, Haotian Deng, Dietmar Heinke, Quanying Liu

Human decision-making in cognitive tasks and daily life exhibits considerable variability, shaped by factors such as task difficulty, individual preferences, and personal experiences. Understanding this variability across individuals is essential for uncovering the perceptual and decision-making mechanisms that humans rely on when faced with uncertainty and ambiguity. We propose a systematic Boundary Alignment Manipulation (BAM) framework for studying human perceptual variability through image generation. BAM combines perceptual boundary sampling in ANNs and human behavioral experiments to systematically investigate this phenomenon. Our perceptual boundary sampling algorithm generates stimuli along ANN perceptual boundaries that intrinsically induce significant perceptual variability. The efficacy of these stimuli is empirically validated through large-scale behavioral experiments involving 246 participants across 116,715 trials, culminating in the variMNIST dataset containing 19,943 systematically annotated images.Through personalized model alignment and adversarial generation, we establish a reliable method for simultaneously predicting and manipulating the divergent perceptual decisions of pairs of participants.This work bridges the gap between computational models and human individual difference research, providing new tools for personalized perception analysis. Code and data for this work are publicly available.

Applications · Neuroscience, Cognitive Science

Yuqin Dai, Zhouheng Yao, Chunfeng Song, Qihao Zheng, Weijian Mai, Kunyu Peng, Shuai Lu, Wanli Ouyang, Jian Yang, Jiamin Wu

Brain decoding aims to reconstruct visual perception of human subject from fMRI signals, which is crucial for understanding brain's perception mechanisms. Existing methods are confined to the single-subject paradigm due to substantial brain variability, which leads to weak generalization across individuals and incurs high training costs, exacerbated by limited availability of fMRI data. To address these challenges, we propose MindAligner, an explicit functional alignment framework for cross-subject brain decoding from limited fMRI data. The proposed MindAligner enjoys several merits. First, we learn a Brain Transfer Matrix (BTM) that projects the brain signals of an arbitrary new subject to one of the known subjects, enabling seamless use of pre-trained decoding models. Second, to facilitate reliable BTM learning, a Brain Functional Alignment module is proposed to perform soft cross-subject brain alignment under different visual stimuli with a multi-level brain alignment loss, uncovering fine-grained functional correspondences with high interpretability. Experiments indicate that MindAligner not only outperforms existing methods in visual decoding under data-limited conditions, but also provides valuable neuroscience insights in cross-subject functional analysis. The code will be made publicly available.

Applications · Neuroscience, Cognitive Science

Muzhou Yu, Shuyun Lin, Lei Ma, Bo Lei, Kaisheng Ma

Advancements in generative models have promoted text- and image-based multi-context image generation. Brain signals, offering a direct representation of user intent, present new opportunities for image customization. However, it faces challenges in brain interpretation, cross-modal context fusion and retention. In this paper, we present MindCustomer to explore the blending of visual brain signals in multi-context image generation. We first design shared neural data augmentation for stable cross-subject brain embedding by introducing the Image-Brain Translator (IBT) to generate brain responses from visual images. Then, we propose an effective cross-modal information fusion pipeline that mask-freely adapts distinct semantics from image and brain contexts within a diffusion model. It resolves semantic conflicts for context preservation and enables harmonious context integration. During the fusion pipeline, we further utilize the IBT to transfer image context to the brain representation to mitigate the cross-modal disparity. MindCustomer enables cross-subject generation, delivering unified, high-quality, and natural image outputs. Moreover, it exhibits strong generalization for new subjects via few-shot learning, indicating the potential for practical application. As the first work for multi-context blending with brain signal, MindCustomer lays a foundational exploration and inspiration for future brain-controlled generative technologies.

Applications · Neuroscience, Cognitive Science

Yi Xie, Jaedong Hwang, Carlos Brody, David Tank, Ila R. Fiete

Brains excel at robust decision-making and data-efficient learning. Understanding the architectures and dynamics underlying these capabilities can inform inductive biases for deep learning. We present a multi-region brain model that explores the normative role of structured memory circuits in a spatially embedded binary decision-making task from neuroscience.We counterfactually compare the learning performance and neural representations of reinforcement learning (RL) agents with brain models of different interaction architectures between grid and place cells in the entorhinal cortex and hippocampus, coupled with an action-selection cortical recurrent neural network. We demonstrate that a specific architecture--where grid cells receive and jointly encode self-movement velocity signals and decision evidence increments--optimizes learning efficiency while best reproducing experimental observations relative to alternative architectures.Our findings thus suggest brain-inspired structured architectures for efficient RL. Importantly, the models make novel, testable predictions about organization and information flow within the entorhinal-hippocampal-neocortical circuit: we predict that grid cells must conjunctively encode position and evidence for effective spatial decision-making, directly motivating new neurophysiological experiments.

Applications · Neuroscience, Cognitive Science

Ryan Liu, Jiayi Geng, Addison J. Wu, Ilia Sucholutsky, Tania Lombrozo, Thomas Griffiths

Chain-of-thought (CoT) prompting has become a widely used strategy for improving large language and multimodal model performance. However, it is still an open question under which settings CoT systematically reduces performance. In this paper, we seek to identify the characteristics of tasks where CoT reduces performance by drawing inspiration from cognitive psychology, focusing on six representative tasks from the psychological literature where deliberation hurts performance in humans. In three of these tasks, state-of-the-art models exhibit significant performance drop-offs with CoT (up to 36.3\% absolute accuracy for OpenAI o1-preview compared to GPT-4o), while in others, CoT effects are mixed, with positive, neutral, and negative changes. While models and humans do not exhibit perfectly parallel cognitive processes, considering cases where thinking has negative consequences for humans helps identify settings where it negatively impacts models. By connecting the literature on human verbal thinking and deliberation with evaluations of CoT, we offer a perspective for understanding the impact of inference-time reasoning.

Applications · Neuroscience, Cognitive Science

Weihan Li, Yule Wang, Chengrui Li, Anqi Wu

Understanding and constructing brain communications that capture dynamic communications across multiple regions is fundamental to modern system neuroscience, yet current methods struggle to find time-varying region-level communications or scale to large neural datasets with long recording durations. We present a novel framework using Markovian Gaussian Processes to learn brain communications with time-varying temporal delays from multi-region neural recordings, named Adaptive Delay Model (ADM). Our method combines Gaussian Processes with State Space Models and employs parallel scan inference algorithms, enabling efficient scaling to large datasets while identifying concurrent communication patterns that evolve over time. This time-varying approach captures how brain region interactions shift dynamically during cognitive processes. Validated on synthetic and multi-region neural recordings datasets, our approach discovers both the directionality and temporal dynamics of neural communication. This work advances our understanding of distributed neural computation and provides a scalable tool for analyzing dynamic brain networks. Code is available at https://github.com/BRAINML-GT/Adaptive-Delay-Model.

Applications · Neuroscience, Cognitive Science

Belle Liu, Jacob I Sacks, Matthew Golub

Neural recording technologies now enable simultaneous recording of population activity across multiple brain regions, motivating the development of data-driven models of communication between recorded brain regions. Existing models can struggle to disentangle communication from the effects of unrecorded regions and local neural population dynamics. Here, we introduce Multi-Region Latent Factor Analysis via Dynamical Systems (MR-LFADS), a sequential variational autoencoder composed of region-specific recurrent networks. MR-LFADS features structured information bottlenecks, data-constrained communication, and unsupervised inference of unobserved inputs--features that specifically support disentangling of inter-regional communication, inputs from unobserved regions, and local population dynamics. MR-LFADS outperforms existing approaches at identifying communication across dozens of simulations of task-trained multi-region networks. Applied to large-scale electrophysiology, MR-LFADS predicts brain-wide effects of circuit perturbations that were not seen during model fitting. These validations on synthetic and real neural data suggest that MR-LFADS could serve as a powerful tool for uncovering the principles of brain-wide information processing.

Applications · Neuroscience, Cognitive Science

Zihan Huang, Wei Fang, Tong Bu, Peng Xue, Zecheng Hao, Wenxuan Liu, Yuanhong Tang, Zhaofei Yu, Tiejun Huang

Spiking Neural Networks (SNNs) exhibit significant potential due to their low energy consumption. Converting Artificial Neural Networks (ANNs) to SNNs is an efficient way to achieve high-performance SNNs. However, many conversion methods are based on rate coding, which requires numerous spikes and longer time-steps compared to directly trained SNNs, leading to increased energy consumption and latency. This article introduces differential coding for ANN-to-SNN conversion, a novel coding scheme that reduces spike counts and energy consumption by transmitting changes in rate information rather than rates directly, and explores its application across various layers. Additionally, the threshold iteration method is proposed to optimize thresholds based on activation distribution when converting Rectified Linear Units (ReLUs) to spiking neurons. Experimental results on various Convolutional Neural Networks (CNNs) and Transformers demonstrate that the proposed differential coding significantly improves accuracy while reducing energy consumption, particularly when combined with the threshold iteration method, achieving state-of-the-art performance. The source codes of the proposed method are available at https://github.com/h-z-h-cell/ANN-to-SNN-DCGS.

Applications · Neuroscience, Cognitive Science

Qi Xu, Jie Deng, Jiangrong Shen, Biwu Chen, Huajin Tang, Gang Pan

Event-based object detection has attracted increasing attention for its high temporal resolution, wide dynamic range, and asynchronous address-event representation. Leveraging these advantages, spiking neural networks (SNNs) have emerged as a promising approach, offering low energy consumption and rich spatiotemporal dynamics. To further enhance the performance of event-based object detection, this study proposes a novel hybrid spike vision Transformer (HsVT) model. The HsVT model integrates a spatial feature extraction module to capture local and global features, and a temporal feature extraction module to model time dependencies and long-term patterns in event sequences. This combination enables HsVT to capture spatiotemporal features, improving its capability in handling complex event-based object detection tasks. To support research in this area, we developed the Fall Detection dataset as a benchmark for event-based object detection tasks. The Fall DVS detection dataset protects facial privacy and reduces memory usage thanks to its event-based representation. Experimental results demonstrate that HsVT outperforms existing SNN methods and achieves competitive performance compared to ANN-based models, with fewer parameters and lower energy consumption.

Applications · Neuroscience, Cognitive Science

Abdulkadir Gokce, Martin Schrimpf

When trained on large-scale object classification datasets, certain artificial neural network models begin to approximate core object recognition behaviors and neural response patterns in the primate brain. While recent machine learning advances suggest that scaling compute, model size, and dataset size improves task performance, the impact of scaling on brain alignment remains unclear. In this study, we explore scaling laws for modeling the primate visual ventral stream by systematically evaluating over 600 models trained under controlled conditions on benchmarks spanning V1, V2, V4, IT and behavior. We find that while behavioral alignment continues to scale with larger models, neural alignment saturates. This observation remains true across model architectures and training datasets, even though models with stronger inductive biases and datasets with higher-quality images are more compute-efficient. Increased scaling is especially beneficial for higher-level visual areas, where small models trained on few samples exhibit only poor alignment. Our results suggest that while scaling current architectures and datasets might suffice for alignment with human core object recognition behavior, it will not yield improved models of the brain's visual ventral stream, highlighting the need for novel strategies in building brain models.

Applications · Neuroscience, Cognitive Science

Pablo Samuel Castro, Nenad Tomasev, Ankit Anand, Navodita Sharma, Rishika Mohanta, Aparna Dev, Kuba Perlin, Siddhant Jain, Kyle Levin, Noemi Elteto 等

Symbolic models play a key role in cognitive science, expressing computationally precise hypotheses about how the brain implements a cognitive process. Identifying an appropriate model typically requires a great deal of effort and ingenuity on the part of a human scientist.Here, we adapt FunSearch (Romera-Paredes et al. 2024), a recently developed tool that uses Large Language Models (LLMs) in an evolutionary algorithm, to automatically discover symbolic cognitive models that accurately capture human and animal behavior.We consider datasets from three species performing a classic reward-learning task that has been the focus of substantial modeling effort, and find that the discovered programs outperform state-of-the-art cognitive models for each.The discovered programs can readily be interpreted as hypotheses about human and animal cognition, instantiating interpretable symbolic learning and decision-making algorithms. Broadly, these results demonstrate the viability of using LLM-powered program synthesis to propose novel scientific hypotheses regarding mechanisms of human and animal cognition.

Applications · Neuroscience, Cognitive Science

Kairong Yu, Tianqing Zhang, Qi Xu, Gang Pan, Hongwei Wang

Spiking Neural Networks (SNNs) are increasingly recognized for their biological plausibility and energy efficiency, positioning them as strong alternatives to Artificial Neural Networks (ANNs) in neuromorphic computing applications. SNNs inherently process temporal information by leveraging the precise timing of spikes, but balancing temporal feature utilization with low energy consumption remains a challenge. In this work, we introduce Temporal Shift module for Spiking Neural Networks (TS-SNN), which incorporates a novel Temporal Shift (TS) module to integrate past, present, and future spike features within a single timestep via a simple yet effective shift operation. A residual combination method prevents information loss by integrating shifted and original features. The TS module is lightweight, requiring only one additional learnable parameter, and can be seamlessly integrated into existing architectures with minimal additional computational cost. TS-SNN achieves state-of-the-art performance on benchmarks like CIFAR-10 (96.72\%), CIFAR-100 (80.28\%), and ImageNet (70.61\%) with fewer timesteps, while maintaining low energy consumption. This work marks a significant step forward in developing efficient and accurate SNN architectures.

Applications · Neuroscience, Cognitive Science

Ben Lonnqvist, Elsa Scialom, Abdulkadir Gokce, Zehra Merchant, Michael Herzog, Martin Schrimpf

Despite the tremendous success of deep learning in computer vision, models still fall behind humans in generalizing to new input distributions. Existing benchmarks do not investigate the specific failure points of models by analyzing performance under many controlled conditions. Our study systematically dissects where and why models struggle with contour integration - a hallmark of human vision -- by designing an experiment that tests object recognition under various levels of object fragmentation. Humans (n=50) perform at high accuracy, even with few object contours present. This is in contrast to models which exhibit substantially lower sensitivity to increasing object contours, with most of the over 1,000 models we tested barely performing above chance. Only at very large scales ($\sim5B$ training dataset size) do models begin to approach human performance. Importantly, humans exhibit an integration bias - a preference towards recognizing objects made up of directional fragments over directionless fragments. We find that not only do models that share this property perform better at our task, but that this bias also increases with model training dataset size, and training models to exhibit contour integration leads to high shape bias. Taken together, our results suggest that contour integration is a hallmark of object vision that underlies object recognition performance, and may be a mechanism learned from data at scale.

Applications · Neuroscience, Cognitive Science

Xinxu Wei, kanhao zhao, Yong Jiao, Hua Xie, Lifang He, Yu Zhang

Effectively utilizing extensive unlabeled high-density EEG data to improve performance in scenarios with limited labeled low-density EEG data presents a significant challenge. In this paper, we address this challenge by formulating it as a graph transfer learning and knowledge distillation problem. We propose a Unified Pre-trained Graph Contrastive Masked Autoencoder Distiller, named EEG-DisGCMAE, to bridge the gap between unlabeled and labeled as well as high- and low-density EEG data. Our approach introduces a novel unified graph self-supervised pre-training paradigm, which seamlessly integrates the graph contrastive pre-training with the graph masked autoencoder pre-training. Furthermore, we propose a graph topology distillation loss function, allowing a lightweight student model trained on low-density data to learn from a teacher model trained on high-density data during pre-training and fine-tuning. This method effectively handles missing electrodes through contrastive distillation. We validate the effectiveness of EEG-DisGCMAE across four classification tasks using two clinical EEG datasets with abundant data.

Applications · Neuroscience, Cognitive Science

Chi-Ning Chou, Hang Le, Yichen Wang, SueYeon Chung

Integrating task-relevant information into neural representations is a fundamental ability of both biological and artificial intelligence systems. Recent theories have categorized learning into two regimes: the rich regime, where neural networks actively learn task-relevant features, and the lazy regime, where networks behave like random feature models. Yet this simple lazy–rich dichotomy overlooks a diverse underlying taxonomy of feature learning, shaped by differences in learning algorithms, network architectures, and data properties. To address this gap, we introduce an analysis framework to study feature learning via the geometry of neural representations. Rather than inspecting individual learned features, we characterize how task-relevant representational manifolds evolve throughout the learning process. We show, in both theoretical and empirical settings, that as networks learn features, task-relevant manifolds untangle, with changes in manifold geometry revealing distinct learning stages and strategies beyond the lazy–rich dichotomy. This framework provides novel insights into feature learning across neuroscience and machine learning, shedding light on structural inductive biases in neural circuits and the mechanisms underlying out-of-distribution generalization.

Applications · Neuroscience, Cognitive Science

Luca M. Schulze Buschoff, Konstantinos Voudouris, Elif Akata, Matthias Bethge, Josh Tenenbaum, Eric Schulz

Pre-trained vision language models still fall short of human visual cognition. In an effort to improve visual cognition and align models with human behavior, we introduce visual stimuli and human judgments on visual cognition tasks, allowing us to systematically evaluate performance across cognitive domains under a consistent environment. We fine-tune models on ground truth data for intuitive physics and causal reasoning and find that this improves model performance in the respective fine-tuning domain. Furthermore, it can improve model alignment with human behavior. However, we find that task-specific fine-tuning does not contribute to robust human-like generalization to data with other visual characteristics or to tasks in other cognitive domains.

Applications · Neuroscience, Cognitive Science

Lusen Zhao, Zihan Huang, Ding Jianhao, Zhaofei Yu

ANN-to-SNN conversion has emerged as a key approach to train Spiking Neural Networks (SNNs), particularly for Transformer architectures, as it maps pre-trained ANN parameters to SNN equivalents without requiring retraining, thereby preserving ANN accuracy while eliminating training costs. Among various coding methods used in ANN-to-SNN conversion, time-to-first-spike (TTFS) coding, which allows each neuron to at most one spike, offers significantly lower energy consumption. However, while previous TTFS-based SNNs have achieved comparable performance with convolutional ANNs, the attention mechanism and nonlinear layers in Transformer architectures remains a challenge by existing SNNs with TTFS coding. This paper proposes a new neuron structure for TTFS coding that expands its representational range and enhances the capability to process nonlinear functions, along with detailed designs of nonlinear neurons for different layers in Transformer. Experimental results on different models demonstrate that our proposed method can achieve high accuracy with significantly lower energy consumption. To the best of our knowledge, this is the first work to focus on converting Transformer to SNN with TTFS coding.

Applications · Neuroscience, Cognitive Science

Amin Nejatbakhsh, Yixin Wang

Neural circuits produce signals that are complex and nonlinear. To facilitate the understanding of neural dynamics, a popular approach is to fit state space models (SSM) to the data and analyze the dynamics of the low-dimensional latent variables. Despite the power of SSM to explain the dynamics of neural circuits, these models have been shown to merely capture statistical associations in the data and cannot be causally interpreted. Therefore, an important research problem is to build models that can predict neural dynamics under causal manipulations. Here, we propose interventional state-space models (iSSM), a class of causal models that can predict neural responses to novel perturbations. We draw on recent advances in causal dynamical systems and present theoretical results for the identifiability of iSSM. In simulations of the motor cortex, we show that iSSM can recover the true latents and the underlying dynamics. In addition, we illustrate two applications of iSSM in biological datasets. First, we applied iSSM to a dataset of calcium recordings from ALM neurons in mice during photostimulation. Second, we applied iSSM to a dataset of electrophysiological recordings from macaque dlPFC during micro-stimulation. In both cases, we show that iSSM outperforms SSM and results in identifiable parameters. The code is available at https://github.com/amin-nejat/issm.