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Applications · Neuroscience, Cognitive Science

Yanchen Wang, Han Yu, Ari Blau, Yizi Zhang, International Brain Laboratory, Liam Paninski, Cole Hurwitz, Matthew R Whiteway

The brain can only be fully understood through the lens of the behavior it generates--a guiding principle in modern neuroscience research that nevertheless presents significant technical challenges. Many studies capture behavior with cameras, but video analysis approaches typically rely on specialized models requiring extensive labeled data. We address this limitation with BEAST (BEhavioral Analysis via Self-supervised pretraining of Transformers), a novel and scalable framework that pretrains experiment-specific vision transformers for diverse neuro-behavior analyses. BEAST combines masked autoencoding with temporal contrastive learning to effectively leverage unlabeled video data. Through comprehensive evaluation across multiple species, we demonstrate improved performance in three critical neuro-behavioral tasks: extracting behavioral features that correlate with neural activity, and pose estimation and action segmentation in both the single- and multi-animal settings. Our method establishes a powerful and versatile backbone model that accelerates behavioral analysis in scenarios where labeled data remains scarce.

Applications · Neuroscience, Cognitive Science

Rabia Gondur, Patricia Stan, Matthew A Smith, Benjamin Cowley

An ongoing quest in neuroscience is to find the preferred stimulus of a sensory neuron. This search lays the foundation for understanding how selectivity emerges in the primate visual stream---from simple edge-detecting neurons to highly-selective face neurons---as well as for the architectures and activation functions of deep neural networks. The prevailing notion is that a visual neuron primarily responds to a single preferred visual feature, like an oriented edge or the shape of an object, resulting in a 'one-tailed' distribution of responses to natural images. However, surprisingly, we instead find 'two-tailed' response distributions of primate visual cortical neurons, suggesting that these neurons have both preferred and anti-preferred stimuli. We experimentally validated anti-preferred stimuli by recording responses from macaque V4 to model-optimized stimuli. We find that these anti-preferred stimuli are important for describing a neuron's tuning, as both preferred and anti-preferred images are needed to predict a neuron's responses to natural images. Moreover, in a psychophysics task, humans rely on anti-preferred images to interpret and predict V4 stimulus tuning; this was not the case for internal units from a deep neural network. Interestingly, we find no discernible differences in image statistics between preferred and anti-preferred images. This suggests that by encoding anti-preferred features, a V4 population seemingly doubles its capacity for feature selectivity, allowing for a more flexible downstream readout. Overall, we establish anti-preferred stimuli as an important encoding property of V4 neurons. Our work embarks on a new quest in neuroscience to search for anti-preferred stimuli along the visual stream and offers a new perspective on how feature selectivity arises in the visual cortex and deep neural networks.

Applications · Neuroscience, Cognitive Science

Will Dorrell, Peter Latham, James Whittington

Why do neurons encode information the way they do? Normative answers to this question model neural activity as the solution to an optimisation problem; for example, the celebrated efficient coding hypothesis frames neural activity as the optimal encoding of information under efficiency constraints. Successful normative theories have varied dramatically in complexity, from simple linear models (Atick & Redlich, 1990), to complex deep neural networks (Lindsay, 2021). What complex models gain in flexibility, they lose in tractability and often understandability. Here, we split the difference by constructing a set of tractable but flexible normative representational theories. Instead of optimising the neural activities directly, following (Sengupta et al. 2018), we instead optimise the representational similarity, a matrix formed from the dot products of each pair of neural responses. Using this, we show that a large family of interesting optimisation problems are convex. This includes problems corresponding to linear and some non-linear neural networks, and problems from the literature not previously recognised as convex such as modified versions of semi-nonnegative matrix factorisation or nonnegative sparse coding. We put these findings to work in two ways. First, we extend previous results on modularity and mixed selectivity in neural activity; in so doing we provide the first necessary and sufficient identifiability result for a form of semi-nonnegative matrix factorisations. Second, we seek to understand the meaningfulness of single neural tuning curves as compared to neural representations. In particular we derive an identifiability result stating that, for an optimal representational similarity matrix, if neural tunings are `different enough' then they are uniquely linked to the optimal representational similarity, partially justifying the use of single neuron tuning analysis in neuroscience. In sum, we identify an interesting space of convex problems, and use that to derive neural coding results.

Applications · Neuroscience, Cognitive Science

Wei Gu, Tianming Luo, Qiran Zhang, Mohan Ye, Xiao Shen, Wenxin Chen, Yunhuan Li, Yichen Zhang, Jing Hong, Bao-liang Lu 等

Interpreting clinical electroencephalography (EEG) is a laborious, subjective process, and existing computational models are limited to narrow classification tasks rather than holistic interpretation. A key bottleneck for applying powerful Large Vision-Language Models (LVLMs) to this domain is the scarcity of datasets pairing EEG visualizations with fine-grained, expert-level annotations. We address this by introducing CerebraGloss, an instruction-tuned LVLM for nuanced EEG interpretation. We first introduce a novel, automated data generation pipeline, featuring a bespoke YOLO-based waveform detector, to programmatically create a large-scale corpus of EEG-text instruction data. Using this data, we develop CerebraGloss, the first model of its kind capable of unified, generative analysis—performing tasks from detailed waveform description to multi-turn, context-aware dialogue. To evaluate this new capability, we construct and release CerebraGloss-Bench, a comprehensive benchmark for open-ended EEG interpretation. CerebraGloss demonstrates strong performance, surpassing leading LVLMs, including proprietary models like GPT-5, on this benchmark and achieving a new state-of-the-art on the TUSZ seizure detection task. Models, benchmark and tools are available at https://github.com/iewug/CerebraGloss.

Applications · Neuroscience, Cognitive Science

Pinyuan Feng, Hossein Adeli, Wenxuan Guo, Fan Cheng, Ethan Hwang, Nikolaus Kriegeskorte

Recent work has demonstrated that complex visual stimuli can be decoded from human brain activity using deep generative models, offering new ways to probe how the brain represents real-world scenes. However, many existing approaches first map brain signals into intermediate image or text feature spaces before guiding the generative process, which obscures the contributions of different brain areas to the final reconstruction output. In this work, we propose NeuroAdapter, a visual decoding framework that directly conditions a latent diffusion model on brain representations, bypassing the need for intermediate feature spaces. Our method demonstrates competitive visual reconstruction quality on public fMRI datasets compared to prior work, while providing greater transparency into how brain signals drive visual reconstruction. To this end, we introduce an Image–Brain BI-directional interpretability framework (IBBI) that analyzes cross-attention patterns across diffusion denoising steps to reveal how different cortical areas influence the unfolding generative trajectory. Our work highlights the potential of end-to-end brain-to-image reconstruction and establishes a path for interpretable neural decoding.

Deep Learning · Generative Models and Autoencoders

Boshi Wang, Huan Sun

Despite their impressive capabilities, LLMs exhibit a basic generalization failure known as the *Reversal Curse*, where they struggle to learn reversible factual associations. Understanding why this occurs could help identify weaknesses in current models and advance their generalization and robustness. In this paper, we conjecture that the Reversal Curse in LLMs is a manifestation of the long-standing *binding problem* in cognitive science, neuroscience and AI. Specifically, we hypothesize two primary causes of the Reversal Curse stemming from transformers' limitations in conceptual binding: the *inconsistency* and *entanglements* of concept representations. We perform a series of experiments that support these conjectures. Our exploration leads to a model design based on JEPA (Joint-Embedding Predictive Architecture) that for the first time breaks the Reversal Curse without side-stepping it with specialized data augmentation or non-causal masking, and moreover, generalization could be further improved by incorporating special memory layers that support disentangled concept representations. Our research opens up the broader fundamental challenge of designing models capable of learning systematic conceptual binding with less human scaffolding.

Applications · Neuroscience, Cognitive Science

Yuqi Yang, Tengjun Liu, Haiyan Zhang, Wang Ruixue, Xuchao Chen, Mingkang Li, Yansong Chua, Nenggan Zheng, Shaomin Zhang

The emergence of large-scale neural activity datasets provides new opportunities to enhance the generalization of neural decoding models. However, it remains a practical challenge to design neural decoders for fully implantable brain-machine interfaces (iBMIs) that achieve high accuracy, strong generalization, and low computational cost, which are essential for reliable, long-term deployment under strict power and hardware constraints. To address this, we propose the Re-parametrized self-Attention Spiking Neural Network (RAT SNN) with a cross-condition pretraining framework to integrate neural variability and adapt to stringent computational constraints. Specifically, our approach introduces multi-timescale dynamic spiking neurons to capture the complex temporal variability of neural activity. We refine spike-driven attention within a lightweight, re-parameterized architecture that enables accumulate-only operations between spiking neurons without sacrificing decoding accuracy. Furthermore, we develop a stepwise training pipeline to systematically integrate neural variability across conditions, including neural temporal drift, subjects and tasks. Building on these advances, we construct a pretrained model capable of rapid generalization to unseen conditions with high performance. We demonstrate that RAT SNN consistently outperforms leading SNN baselines and matches the accuracy of state-of-the-art artificial neural network (ANN) models with much lower computational cost under both seen and unseen conditions across various datasets. Collectively, pretrained-RAT SNN represents a high-performance, highly generalizable, and energy-efficient prototype of an SNN foundation model for fully iBMI. Code is available at [RAT SNN GitHub](https://github.com/YangYangYangYuqi/RAT-SNN).

Applications · Neuroscience, Cognitive Science

Yinsong Yan, Yujie Wu, Jibin Wu

Spiking Neural Networks (SNNs) are regarded as energy-efficient neural architectures due to their event-driven, spike-based computation paradigm. However, existing SNNs suffer from two fundamental limitations: (1) the constrained representational space imposed by binary spike firing mechanisms, which restricts the network's capacity to encode complex spatiotemporal patterns, and (2) the ineffective design of surrogate gradient functions that leads to gradient mismatch issues and suboptimal learning dynamics. To address these challenges, we propose the Parametric Invertible Transformation (PIT), which operates in a conjugate manner with neuronal dynamics to achieve adaptive modulation and augmented spike representations simultaneously. Second, we design an auxiliary gradient correction term to mitigate the gradient mismatch issue and oscillation phenomena during training. Moreover, we introduce a theoretical framework for analyzing the spatiotemporal representation space of SNNs. Extensive experiments on both static and neuromorphic datasets demonstrate state-of-the-art performance with our proposed method. This approach lays the theoretical foundation for expanding the spatiotemporal representations of SNNs, offering a viable pathway for developing low-latency and high-performance neuromorphic processing systems in resource-constrained environments. The code is available at https://github.com/YinsongYan/ICLR26.

Applications · Neuroscience, Cognitive Science

Max Wolff, Thomas Klein, Evgenia Rusak, Felix Wichmann, Wieland Brendel

Despite their impressive performance on computer vision benchmarks, Deep Neural Networks (DNNs) still fall short of adequately modeling human visual behavior, as measured by error consistency and shape bias. Recent work hypothesized that behavioral alignment can be drastically improved through generative - rather than discriminative - classifiers, with far-reaching implications for models of human vision. Here, we instead show that the increased alignment of generative models can be largely explained by a seemingly innocuous resizing operation in the generative model which effectively acts as a low-pass filter. In a series of controlled experiments, we show that removing high-frequency spatial information from discriminative models like CLIP drastically increases their behavioral alignment. Simply blurring images at test-time - rather than training on blurred images - achieves a new state-of-the-art score on the model-vs-human benchmark, halving the current alignment gap between DNNs and human observers. Furthermore, low-pass filters are likely optimal, which we demonstrate by directly optimizing filters for alignment. To contextualize the performance of optimal filters, we compute the frontier of all possible pareto-optimal solutions to the benchmark, which was formerly unknown. We explain our findings by observing that the frequency spectrum of optimal Gaussian filters roughly matches the spectrum of band-pass filters implemented by the human visual system. We show that the contrast sensitivity function, describing the inverse of the contrast threshold required for humans to detect a sinusoidal grating as a function of spatiotemporal frequency, is approximated well by Gaussian filters of a specific width.

Applications · Neuroscience, Cognitive Science

Jingying Ma, Feng Wu, QIKA LIN, Yucheng Xing, Chenyu Liu, Ziyu Jia, Mengling Feng

Electroencephalography (EEG) provides real-time insights into brain activity and supports diverse applications in neuroscience. While EEG foundation models (EFMs) have emerged to address the scalability issues of task-specific models, current approaches still yield clinically uninterpretable and weakly discriminative representations, inefficiently capturing global dependencies and neglecting important local neural events. We present CodeBrain, a two-stage EFM designed to fill this gap. In the first stage, we introduce the TFDual-Tokenizer, which decouples heterogeneous temporal and frequency EEG signals into discrete tokens, quadratically expanding the representation space to enhance discriminative power and offering domain-specific representation-level interpretability by suggesting potential links to neural events and spectral rhythms. In the second stage, we propose the multi-scale EEGSSM architecture, which combines structured global convolution with sliding window attention to efficiently capture both sparse long-range and local dependencies, reflecting the brain’s small-world topology. Pretrained on the largest public EEG corpus, CodeBrain achieves strong generalization across eight downstream tasks and ten datasets under distribution shifts, supported by comprehensive ablations, scaling-law analyzes, and interpretability evaluations. The code and the pretrained weights are available at https://github.com/jingyingma01/CodeBrain.

Applications · Neuroscience, Cognitive Science

Zheng Huang, Enpei Zhang, Weikang Qiu, Yinghao Cai, Carl Yang, Elynn Chen, Xiang Zhang, Rex Ying, Dawei Zhou, Yujun Yan

Understanding how the brain encodes visual information is a central challenge in neuroscience and machine learning. A promising approach is to reconstruct visual stimuli—essentially images—from functional Magnetic Resonance Imaging (fMRI) signals. This involves two stages: transforming fMRI signals into a latent space and then using a pre-trained generative model to reconstruct images. The reconstruction quality depends on how similar the latent space is to the structure of neural activity and how well the generative model produces images from that space. Yet, it remains unclear which type of latent space best supports this transformation and how it should be organized to represent visual stimuli effectively. We present two key findings. First, fMRI signals are more similar to the text space of a language model than to either a vision-based space or a joint text–image space. Second, text representations and the generative model should be adapted to capture the compositional nature of visual stimuli, including objects, their detailed attributes, and relationships. Building on these insights, we propose PRISM, a model that Projects fMRI sIgnals into a Structured text space as an interMediate representation for visual stimuli reconstruction. It includes an object-centric diffusion module that generates images by composing individual objects to reduce object detection errors, and an attribute/relationship search module that automatically identifies key attributes and relationships that best align with the neural activity. Extensive experiments on real-world datasets demonstrate that our framework outperforms existing methods, achieving up to an 6% reduction in perceptual loss. These results highlight the importance of using structured text as an intermediate space to bridge fMRI signals and image reconstruction. Codes are available at https://github.com/GraphmindDartmouth/PRISM.

Applications · Neuroscience, Cognitive Science

Yiting Dong, Jianhao Ding, Zijie Xu, Tong Bu, Zhaofei Yu, Tiejun Huang

Spiking Neural Networks (SNNs), with their temporal processing capabilities and biologically plausible dynamics, offer a natural platform for unsupervised representation learning. However, current unsupervised SNNs predominantly employ shallow architectures or localized plasticity rules, limiting their ability to model long-range temporal dependencies and maintain temporal feature consistency. This results in semantically unstable representations, thereby impeding the development of deep unsupervised SNNs for large-scale temporal video data. We propose PredNext, which explicitly models temporal relationships through cross-view future Step Prediction and Clip Prediction. This plug-and-play module seamlessly integrates with diverse self-supervised objectives. We firstly establish standard benchmarks for SNN self-supervised learning on UCF101, HMDB51, and MiniKinetics, which are substantially larger than conventional DVS datasets. PredNext delivers significant performance improvements across different tasks and self-supervised methods. PredNext achieves performance comparable to ImageNet-pretrained supervised weights, through unsupervised training solely on UCF101. Additional experiments demonstrate that PredNext, distinct from forced consistency constraints, substantially improves temporal feature consistency while enhancing network generalization capabilities. This work provides a effective foundation for unsupervised deep SNNs on large-scale temporal video data.

Applications · Neuroscience, Cognitive Science

Shaolong Wei, Qiyu Sun, Mingliang Wang, Liang Sun, Weiping Ding, Jiashuang Huang

Modeling the temporal dynamics of the human brain remains a core challenge in computational neuroscience and artificial intelligence. Traditional methods often ignore the biological spike characteristics of brain activity and find it difficult to reveal the dynamic dependencies and causal interactions between brain regions, limiting their effectiveness in brain function research and clinical applications. To address this issue, we propose a Spike-based Digital Brain (Spike-DB), a novel fundamental model that introduces the spike computing paradigm into brain time series modeling. Spike-DB encodes fMRI signals as spike trains and learns the temporal driving relationships between anchor and target regions to achieve high-precision prediction of brain activity and reveal underlying causal dependencies and dynamic relationship characteristics. Based on Spike-DB, we further conducted downstream tasks including brain disease classification, abnormal brain region identification, and effective connectivity inference. Experimental results on real-world epilepsy datasets and the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset show that Spike-DB outperforms existing mainstream methods in both prediction accuracy and downstream tasks, demonstrating its broad potential in clinical applications and brain science research. Our code is available at https://github.com/UAIBC-Brain/Spike-DB.

Applications · Neuroscience, Cognitive Science

Huan LUO, Na Lu, Xiaopeng Wang, Xu Niu

Generalization in EEG-based motor imagery (MI) brain-computer interfaces (BCIs) is hampered by cross-subject and cross-session variability. Although large-scale EEG pretraining has advanced representation learning, their practical deployment is hindered by the need for costly fine-tuning to overcome significant domain shifts. Test-time adaptation (TTA) methods that adapt models during inference offer a promising solution. However, existing EEG-TTA methods either rely on gradient-based fine-tuning (suffering from high computational cost and catastrophic forgetting) or data alignment strategies (failing to capture shifts in temporal predictive embeddings). To address these limitations, we propose BTTA-DG, a novel Bayesian Test-Time Adaptation framework that performs efficient, gradient-free adaptation by modeling the distribution of temporal predictive embeddings. Our approach first employs a lightweight SincAdaptNet with learnable filters to extract task-specific frequency bands. We then introduce a novel Dirichlet feature projection that maps temporal embeddings onto a compact and interpretable parameter space, effectively capturing the concentration of time-varying predictive evidence. Adaptation is achieved via a GMM-driven Bayesian inference mechanism, which models the historical distribution of these Dirichlet parameters and fuses this evidence with the model's prior predictions to calibrate outputs for the target domain. Extensive experiments show that BTTA‑DG significantly outperforms previous EEG‑TTA methods, achieving state‑of‑the‑art accuracy while running at real‑time speed. Furthermore, visualizations confirm the physiological interpretability of our learned filters and the robust class separability of our Dirichlet feature space.

Applications · Neuroscience, Cognitive Science

Shunsuke Onoo, Yoshihiro Nagano, Yukiyasu Kamitani

Sensory representation is typically understood through a hierarchical-causal framework where progressively abstract features are extracted sequentially. However, this causal view fails to explain misrepresentation, a phenomenon better handled by an informational and teleological view based on decodable content and downstream functions. This creates a tension: how does a system that abstracts away details preserve the fine-grained information needed for downstream functions? We propose readout representation to resolve this, defining representation by the information recoverable from features, rather than their causal origin. Empirically, we show that inputs can be accurately reconstructed even from heavily perturbed mid-level features, demonstrating that a single input corresponds to a broad, redundant region of feature space, challenging the causal mapping perspective. To quantify this property, we introduce representation size, a metric linked to model robustness and representational redundancy. Our framework offers a new lens for analyzing how both biological and artificial neural systems learn complex features while maintaining robust, information-rich representations of the world.

Applications · Neuroscience, Cognitive Science

RUI LIU, Zhige Chen, Pengshu, Wenlong You, Zhi-An Huang, Jibin Wu, KC Tan

Decoding complex auditory experiences from non-invasive EEG is a rapidly emerging field that holds significant promise for advancing both fundamental neuroscience and human-machine interaction technologies. Recent developments in EEG foundation models have yielded powerful neural representations that are promising for auditory decoding. However, the effectiveness of these models remains fundamentally constrained by their limited integration with acoustic stimulus information. Specifically, the lack of deep coupling between neural signals and auditory inputs hampers the models’ ability to generalize effectively across diverse auditory tasks. To bridge this gap, we introduce MindMix, a multimodal foundation model designed to bridge the gap between unimodal EEG foundations and task-specific auditory decoders. MindMix employs a two-stage training strategy: first, a high-capacity EEG encoder is pre-trained on over 3,000 hours of EEG data to learn generalized EEG features that can transfer across tasks and subjects. Second, the model learns the neural-acoustic mapping using over 100 hours of paired data, facilitated by our novel Cross-Attention Low-Rank Alignment module, which facilitates fine-grained, cross-modal information integration. Experimental results demonstrate that MindMix substantially surpassing existing baselines across a range of auditory decoding tasks, including auditory attention decoding, auditory emotion recognition, and cross-modal retrieval. This work thus establishes a foundation for future research in multimodal brain decoding and auditory brain-computer interfaces. Our code is available at https://github.com/CookieMikeLiu/MindMix.

Applications · Neuroscience, Cognitive Science

Yanchen Wang, Joy Hsu, Ehsan Adeli, Jiajun Wu

We propose NEURONA, a neuro-symbolic framework for fMRI decoding and concept grounding in neural activity. Leveraging image- and video-based fMRI question-answering datasets, NEURONA learns to decode interacting concepts from visual stimuli based on patterns of fMRI responses, integrating symbolic reasoning and compositional execution with fMRI grounding across brain regions. We demonstrate that incorporating structural priors (e.g., compositional predicate-argument dependencies between concepts) into the decoding process significantly improves both decoding accuracy over precise queries, and notably, generalization to unseen queries at test time. With NEURONA, we highlight neuro-symbolic frameworks as promising tools for understanding neural activity.

Applications · Neuroscience, Cognitive Science

Jian-Qiao Zhu, Hanbo Xie, Dilip Arumugam, Robert Wilson, Thomas L. Griffiths

A central goal of cognitive modeling is to develop models that not only predict human behavior but also provide insight into the underlying cognitive mechanisms. While neural network models trained on large-scale behavioral data often achieve strong predictive performance, they typically fall short in offering interpretable explanations of the cognitive processes they capture. In this work, we explore the potential of pretrained large language models (LLMs) to serve as dual-purpose cognitive models--capable of both accurate prediction and interpretable explanation in natural language. Specifically, we employ reinforcement learning with outcome-based rewards to guide LLMs toward generating explicit reasoning traces for explaining human risky choices. Our findings demonstrate that this approach produces high-quality explanations alongside strong quantitative predictions of human decisions.

Applications · Neuroscience, Cognitive Science

Dehao Zhang, Fukai Guo, Shuai Wang, Jingya Wang, Jieyuan Zhang, Yimeng Shan, Malu Zhang, Yang Yang, Haizhou Li

Integrating Spiking Neural Networks (SNNs) with Transformer architectures offers a promising pathway to balance energy efficiency and performance, particularly for edge vision applications. However, existing Spiking Transformers face two critical challenges: (i) a substantial performance gap compared to their Artificial Neural Networks (ANNs) counterparts and (ii) high memory overhead during inference. Through theoretical analysis, we attribute both limitations to the Spiking Self-Attention (SSA) mechanism: the lack of locality bias and the need to store large attention matrices. Inspired by the localized receptive fields (LRF) and membrane-potential dynamics of biological visual neurons, we propose LRF-Dyn, which uses spiking neurons with localized receptive fields to compute attention while reducing memory requirements. Specifically, we introduce a LRF method into SSA to assign higher weights to neighboring regions, strengthening local modeling and improving performance. Building on this, we approximate the resulting attention computation via charge–fire–reset dynamics, eliminating explicit attention-matrix storage and reducing inference-time memory. Extensive experiments on visual tasks confirm that our method reduces memory overhead while delivering significant performance improvements. These results establish it as a key unit for achieving energy-efficient Spiking Transformers.

Applications · Neuroscience, Cognitive Science

Ling Zhan, Zhen Li, Junjie Huang, Tao Jia

Benchmarking the hundreds of functional connectivity (FC) modeling methods on large-scale fMRI datasets is critical for reproducible neuroscience. However, the combinatorial explosion of model–data pairings makes exhaustive evaluation computationally prohibitive, preventing such assessments from becoming a routine pre-analysis step. To break this bottleneck, we reframe the challenge of FC benchmarking by selecting a small, representative *core-set* whose sole purpose is to preserve the relative performance ranking of FC operators. We formalize this as a ranking-preserving subset selection problem and propose **S**tructure-aware **C**ontrastive **L**earning for **C**ore-set **S**election (**SCLCS**), a self-supervised framework to select these core-sets. **SCLCS** first uses an adaptive Transformer to learn each sample's unique FC structure. It then introduces a novel **S**tructural **P**erturbation **S**core (**SPS**) to quantify the stability of these learned structures during training, identifying samples that represent foundational connectivity archetypes. Finally, while **SCLCS** identifies stable samples via a top-$k$ ranking, we further introduce a **density-balanced sampling strategy** as a necessary correction to promote diversity, ensuring the final core-set is both structurally robust and distributionally representative. On the large-scale REST-meta-MDD dataset, **SCLCS** preserves the ground-truth model ranking with just 10% of the data, outperforming state-of-the-art (SOTA) core-set selection methods by up to 23.2% in ranking consistency (nDCG@k). To our knowledge, this is the first work to formalize core-set selection for FC operator benchmarking, thereby making large-scale operators comparisons a feasible and integral part of computational neuroscience. Code is publicly available on: [https://github.com/lzhan94swu/SCLCS](https://github.com/lzhan94swu/SCLCS)