Understanding how the brain's complex nonlinear dynamics give rise to cognitive function remains a central challenge in neuroscience. While brain functional dynamics exhibits scale-free and multifractal properties across temporal scales, conventional neuroimaging analytics assume linearity and stationarity, failing to capture frequency-specific neural computations. Here, we introduce Multi-Band Brain Net (MBBN), the first transformer-based framework to explicitly model frequency-specific spatiotemporal brain dynamics from fMRI. MBBN integrates biologically-grounded frequency decomposition with multi-band self-attention mechanisms, enabling discovery of previously undetectable frequency-dependent network interactions. Trained on 49,673 individuals across three large-scale cohorts (UK Biobank, ABCD, ABIDE), MBBN sets a new state-of-the-art in predicting psychiatric and cognitive outcomes (depression, ADHD, ASD), showing particular strength in classification tasks with up to 52.5\% higher AUROC and provides a novel framework for predicting cognitive intelligence scores. Frequency-resolved analyses uncover disorder-specific signatures: in ADHD, high-frequency fronto-sensorimotor connectivity is attenuated and opercular somatosensory nodes emerge as dynamic hubs; in ASD, orbitofrontal-somatosensory circuits show focal high-frequency disruption together with enhanced ultra-low-frequency coupling between the temporo-parietal junction and prefrontal cortex. By integrating scale-aware neural dynamics with deep learning, MBBN delivers more accurate and interpretable biomarkers, opening avenues for precision psychiatry and developmental neuroscience.
Computational neuroimaging involves analyzing brain images or signals to provide mechanistic insights and predictive tools for human cognition and behavior. While diffusion models have shown stability and high-quality generation in natural images, there is increasing interest in adapting them to analyze brain data for various neurological tasks such as data enhancement, disease diagnosis and brain decoding. This survey provides an overview of recent efforts to integrate diffusion models into computational neuroimaging. We begin by introducing the common neuroimaging data modalities, follow with the diffusion formulations and conditioning mechanisms. Then we discuss how the variations of the denoising starting point, condition input and generation target of diffusion models are developed and enhance specific neuroimaging tasks. For a comprehensive overview of the ongoing research, we provide a publicly available repository at https://github.com/JoeZhao527/dm4neuro.
Current AI frameworks for brain decoding and encoding, typically train and test models within the same datasets. This limits their utility for brain computer interfaces (BCI) or neurofeedback, for which it would be useful to pool experiences across individuals to better simulate stimuli not sampled during training. A key obstacle to model generalisation is the degree of variability of inter-subject cortical organisation, which makes it difficult to align or compare cortical signals across participants. In this paper we address this through the use of surface vision transformers, which build a generalisable model of cortical functional dynamics, through encoding the topography of cortical networks and their interactions as a moving image across a surface. This is then combined with tri-modal self-supervised contrastive (CLIP) alignment of audio, video, and fMRI modalities to enable the retrieval of visual and auditory stimuli from patterns of cortical activity (and vice-versa). We validate our approach on 7T task-fMRI data from 174 healthy participants engaged in the movie-watching experiment from the Human Connectome Project (HCP). Results show that it is possible to detect which movie clips an individual is watching purely from their brain activity, even for individuals and movies not seen during training. Further analysis of attention maps reveals that our model captures individual patterns of brain activity that reflect semantic and visual systems. This opens the door to future personalised simulations of brain function. Code & pre-trained models will be made available at https://github.com/metrics-lab/sim, processed data for training will be available upon request at https://gin.g-node.org/Sdahan30/sim.
Reconstructing perceived images from human brain activity forms a crucial link between human and machine learning through Brain-Computer Interfaces. Early methods primarily focused on training separate models for each individual to account for individual variability in brain activity, overlooking valuable cross-subject commonalities. Recent advancements have explored multisubject methods, but these approaches face significant challenges, particularly in data privacy and effectively managing individual variability. To overcome these challenges, we introduce BrainGuard, a privacy-preserving collaborative training framework designed to enhance image reconstruction from multisubject fMRI data while safeguarding individual privacy. BrainGuard employs a collaborative global-local architecture where individual models are trained on each subject's local data and operate in conjunction with a shared global model that captures and leverages cross-subject patterns. This architecture eliminates the need to aggregate fMRI data across subjects, thereby ensuring privacy preservation. To tackle the complexity of fMRI data, BrainGuard integrates a hybrid synchronization strategy, enabling individual models to dynamically incorporate parameters from the global model. By establishing a secure and collaborative training environment, BrainGuard not only protects sensitive brain data but also improves the image reconstructions accuracy. Extensive experiments demonstrate that BrainGuard sets a new benchmark in both high-level and low-level metrics, advancing the state-of-the-art in brain decoding through its innovative design.
The decoding of continuously spoken speech from neuronal activity has the potential to become an important clinical solution for paralyzed patients. Deep Learning Brain Computer Interfaces (BCIs) have recently successfully mapped neuronal activity to text contents in subjects who attempted to formulate speech. However, only small BCI datasets are available. In contrast, labeled data and pre-trained models for the closely related task of speech recognition from audio are widely available. One such model is Wav2Vec2 which has been trained in a self-supervised fashion to create meaningful representations of speech audio data. In this study, we show that patterns learned by Wav2Vec2 are transferable to brain data. Specifically, we replace its audio feature extractor with an untrained Brain Feature Extractor (BFE) model. We then execute full fine-tuning with pre-trained weights for Wav2Vec2, training ''from scratch'' without pre-trained weights as well as freezing a pre-trained Wav2Vec2 and training only the BFE each for 45 different BFE architectures. Across these experiments, the best run is from full fine-tuning with pre-trained weights, achieving a Character Error Rate (CER) of 18.54\%, outperforming the best training from scratch run by 20.46\% and that of frozen Wav2Vec2 training by 15.92\% percentage points. These results indicate that knowledge transfer from audio speech recognition to brain decoding is possible and significantly improves brain decoding performance for the same architectures. Related source code is available at https://github.com/tfiedlerdev/Wav2Vec2ForBrain.
With the advancements in Large Language and Latent Diffusion models, brain decoding has achieved remarkable results in recent years. The works on the NSD dataset, with stimuli images from the COCO dataset, leverage the embeddings from the CLIP model for image reconstruction and GIT for captioning. However, the current captioning approach introduces the challenge of potential data contamination given that the GIT model was trained on the COCO dataset. In this work, we present an alternative method for decoding brain signals into image captions by predicting a DINOv2 model's embedding of an image from the corresponding fMRI signal and then providing its [CLS] token as the prefix to the GPT-2 language model which decreases computational requirements considerably. Additionally, instead of commonly used Linear Regression, we explore 3D Convolutional Neural Network mapping of fMRI signals to image embedding space for better accounting positional information of voxels.
Brain decoding aims to reconstruct original stimuli from fMRI signals, providing insights into interpreting mental content. Current approaches rely heavily on subject-specific models due to the complex brain processing mechanisms and the variations in fMRI signals across individuals. Therefore, these methods greatly limit the generalization of models and fail to capture cross-subject commonalities. To address this, we present UniBrain, a unified brain decoding model that requires no subject-specific parameters. Our approach includes a group-based extractor to handle variable fMRI signal lengths, a mutual assistance embedder to capture cross-subject commonalities, and a bilevel feature alignment scheme for extracting subject-invariant features. We validate our UniBrain on the brain decoding benchmark, achieving comparable performance to current state-of-the-art subject-specific models with extremely fewer parameters. We also propose a generalization benchmark to encourage the community to emphasize cross-subject commonalities for more general brain decoding. Our code is available at https://github.com/xiaoyao3302/UniBrain.
When trained on large-scale object classification datasets, certain artificial neural network models begin to approximate core object recognition (COR) behaviors and neural response patterns in the primate visual ventral stream (VVS). While recent machine learning advances suggest that scaling model size, dataset size, and compute resources improve task performance, the impact of scaling on brain alignment remains unclear. In this study, we explore scaling laws for modeling the primate VVS by systematically evaluating over 600 models trained under controlled conditions on benchmarks spanning V1, V2, V4, IT and COR behaviors. We observe 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 bias 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. Finally, we develop a scaling recipe, indicating that a greater proportion of compute should be allocated to data samples over model size. Our results suggest that while scaling alone might suffice for alignment with human core object recognition behavior, it will not yield improved models of the brain's visual ventral stream with current architectures and datasets, highlighting the need for novel strategies in building brain-like models.
Visual brain decoding aims to decode visual information from human brain activities. Despite the great progress, one critical limitation of current brain decoding research lies in the lack of generalization capability to unseen subjects. Prior works typically focus on decoding brain activity of individuals based on the observation that different subjects exhibit different brain activities, while it remains unclear whether brain decoding can be generalized to unseen subjects. This study aims to answer this question. We first consolidate an image-fMRI dataset consisting of stimulus-image and fMRI-response pairs, involving 177 subjects in the movie-viewing task of the Human Connectome Project (HCP). This dataset allows us to investigate the brain decoding performance with the increase of participants. We then present a learning paradigm that applies uniform processing across all subjects, instead of employing different network heads or tokenizers for individuals as in previous methods, which can accommodate a large number of subjects to explore the generalization capability across different subjects. A series of experiments are conducted and we have the following findings. First, the network exhibits clear generalization capabilities with the increase of training subjects. Second, the generalization capability is common to popular network architectures (MLP, CNN and Transformer). Third, the generalization performance is affected by the similarity between subjects. Our findings reveal the inherent similarities in brain activities across individuals. With the emerging of larger and more comprehensive datasets, it is possible to train a brain decoding foundation model in the future. Codes and models can be found at https://github.com/Xiangtaokong/TGBD.
Functional magnetic resonance imaging (fMRI) is an indispensable tool in modern neuroscience, providing a non-invasive window into whole-brain dynamics at millimeter-scale spatial resolution. However, fMRI is constrained by issues such as high operation costs and immobility. With the rapid advancements in cross-modality synthesis and brain decoding, the use of deep neural networks has emerged as a promising solution for inferring whole-brain, high-resolution fMRI features directly from electroencephalography (EEG), a more widely accessible and portable neuroimaging modality. Nonetheless, the complex projection from neural activity to fMRI hemodynamic responses and the spatial ambiguity of EEG pose substantial challenges both in modeling and interpretability. Relatively few studies to date have developed approaches for EEG-fMRI translation, and although they have made significant strides, the inference of fMRI signals in a given study has been limited to a small set of brain areas and to a single condition (i.e., either resting-state or a specific task). The capability to predict fMRI signals in other brain areas, as well as to generalize across conditions, remain critical gaps in the field. To tackle these challenges, we introduce a novel and generalizable framework: NeuroBOLT, i.e., Neuro-to-BOLD Transformer, which leverages multi-dimensional representation learning from temporal, spatial, and spectral domains to translate raw EEG data to the corresponding fMRI activity signals across the brain. Our experiments demonstrate that NeuroBOLT effectively reconstructs unseen resting-state fMRI signals from primary sensory, high-level cognitive areas, and deep subcortical brain regions, achieving state-of-the-art accuracy with the potential to generalize across varying conditions and sites, which significantly advances the integration of these two modalities.
In cognitive neuroscience and brain-computer interface research, accurately predicting imagined stimuli is crucial. This study investigates the effectiveness of Domain Adaptation (DA) in enhancing imagery prediction using primarily visual data from fMRI scans of 18 subjects. Initially, we train a baseline model on visual stimuli to predict imagined stimuli, utilizing data from 14 brain regions. We then develop several models to improve imagery prediction, comparing different DA methods. Our results demonstrate that DA significantly enhances imagery prediction in binary classification on our dataset, as well as in multiclass classification on a publicly available dataset. We then conduct a DA-enhanced searchlight analysis, followed by permutation-based statistical tests to identify brain regions where imagery decoding is consistently above chance across subjects. Our DA-enhanced searchlight predicts imagery contents in a highly distributed set of brain regions, including the visual cortex and the frontoparietal cortex, thereby outperforming standard cross-domain classification methods. The complete code and data for this paper have been made openly available for the use of the scientific community.
Advances in brain decoding, particularly visual image reconstruction, have sparked discussions about the societal implications and ethical considerations of neurotechnology. As these methods aim to recover visual experiences from brain activity and achieve prediction beyond training samples (zero-shot prediction), it is crucial to assess their capabilities and limitations to inform public expectations and regulations. Our case study of recent text-guided reconstruction methods, which leverage a large-scale dataset (Natural Scene Dataset, NSD) and text-to-image diffusion models, reveals limitations in their generalizability. We found poor performance when applying these methods to a different dataset designed to prevent category overlaps between training and test sets. UMAP visualization of the text features with NSD images showed a limited diversity of semantic and visual clusters, with overlap between training and test sets. Formal analysis and simulations demonstrated that clustered training samples can lead to "output dimension collapse," restricting predictable output feature dimensions. Simulations further showed that diversifying the training set improved generalizability. However, text features alone are insufficient for mapping to the visual space. We argue that recent realistic reconstructions may primarily be a blend of classification into trained categories and generation of inauthentic images through text-to-image diffusion (hallucination). Diverse datasets and compositional representations spanning the image space are essential for genuine zero-shot prediction. Interdisciplinary discussions grounded in understanding the current capabilities and limitations, as well as ethical considerations, of the technology are crucial for its responsible development.
Brain decoding, a pivotal field in neuroscience, aims to reconstruct stimuli from acquired brain signals, primarily utilizing functional magnetic resonance imaging (fMRI). Currently, brain decoding is confined to a per-subject-per-model paradigm, limiting its applicability to the same individual for whom the decoding model is trained. This constraint stems from three key challenges: 1) the inherent variability in input dimensions across subjects due to differences in brain size; 2) the unique intrinsic neural patterns, influencing how different individuals perceive and process sensory information; 3) limited data availability for new subjects in real-world scenarios hampers the performance of decoding models. In this paper, we present a novel approach, MindBridge, that achieves cross-subject brain decoding by employing only one model. Our proposed framework establishes a generic paradigm capable of addressing these challenges by introducing biological-inspired aggregation function and novel cyclic fMRI reconstruction mechanism for subject-invariant representation learning. Notably, by cycle reconstruction of fMRI, MindBridge can enable novel fMRI synthesis, which also can serve as pseudo data augmentation. Within the framework, we also devise a novel reset-tuning method for adapting a pretrained model to a new subject. Experimental results demonstrate MindBridge's ability to reconstruct images for multiple subjects, which is competitive with dedicated subject-specific models. Furthermore, with limited data for a new subject, we achieve a high level of decoding accuracy, surpassing that of subject-specific models. This advancement in cross-subject brain decoding suggests promising directions for wider applications in neuroscience and indicates potential for more efficient utilization of limited fMRI data in real-world scenarios. Project page: https://littlepure2333.github.io/MindBridge
We address prevailing challenges of the brain-powered research, departing from the observation that the literature hardly recover accurate spatial information and require subject-specific models. To address these challenges, we propose UMBRAE, a unified multimodal decoding of brain signals. First, to extract instance-level conceptual and spatial details from neural signals, we introduce an efficient universal brain encoder for multimodal-brain alignment and recover object descriptions at multiple levels of granularity from subsequent multimodal large language model (MLLM). Second, we introduce a cross-subject training strategy mapping subject-specific features to a common feature space. This allows a model to be trained on multiple subjects without extra resources, even yielding superior results compared to subject-specific models. Further, we demonstrate this supports weakly-supervised adaptation to new subjects, with only a fraction of the total training data. Experiments demonstrate that UMBRAE not only achieves superior results in the newly introduced tasks but also outperforms methods in well established tasks. To assess our method, we construct and share with the community a comprehensive brain understanding benchmark BrainHub. Our code and benchmark are available at https://weihaox.github.io/UMBRAE.
Analyzing electroencephalographic (EEG) time series can be challenging, especially with deep neural networks, due to the large variability among human subjects and often small datasets. To address these challenges, various strategies, such as self-supervised learning, have been suggested, but they typically rely on extensive empirical datasets. Inspired by recent advances in computer vision, we propose a pretraining task termed "frequency pretraining" to pretrain a neural network for sleep staging by predicting the frequency content of randomly generated synthetic time series. Our experiments demonstrate that our method surpasses fully supervised learning in scenarios with limited data and few subjects, and matches its performance in regimes with many subjects. Furthermore, our results underline the relevance of frequency information for sleep stage scoring, while also demonstrating that deep neural networks utilize information beyond frequencies to enhance sleep staging performance, which is consistent with previous research. We anticipate that our approach will be advantageous across a broad spectrum of applications where EEG data is limited or derived from a small number of subjects, including the domain of brain-computer interfaces.
Deciphering visual content from functional Magnetic Resonance Imaging (fMRI) helps illuminate the human vision system. However, the scarcity of fMRI data and noise hamper brain decoding model performance. Previous approaches primarily employ subject-specific models, sensitive to training sample size. In this paper, we explore a straightforward but overlooked solution to address data scarcity. We propose shallow subject-specific adapters to map cross-subject fMRI data into unified representations. Subsequently, a shared deeper decoding model decodes cross-subject features into the target feature space. During training, we leverage both visual and textual supervision for multi-modal brain decoding. Our model integrates a high-level perception decoding pipeline and a pixel-wise reconstruction pipeline guided by high-level perceptions, simulating bottom-up and top-down processes in neuroscience. Empirical experiments demonstrate robust neural representation learning across subjects for both pipelines. Moreover, merging high-level and low-level information improves both low-level and high-level reconstruction metrics. Additionally, we successfully transfer learned general knowledge to new subjects by training new adapters with limited training data. Compared to previous state-of-the-art methods, notably pre-training-based methods (Mind-Vis and fMRI-PTE), our approach achieves comparable or superior results across diverse tasks, showing promise as an alternative method for cross-subject fMRI data pre-training. Our code and pre-trained weights will be publicly released at https://github.com/YulongBonjour/See_Through_Their_Minds.
We introduce Brain-Artificial Intelligence Interfaces (BAIs) as a new class of Brain-Computer Interfaces (BCIs). Unlike conventional BCIs, which rely on intact cognitive capabilities, BAIs leverage the power of artificial intelligence to replace parts of the neuro-cognitive processing pipeline. BAIs allow users to accomplish complex tasks by providing high-level intentions, while a pre-trained AI agent determines low-level details. This approach enlarges the target audience of BCIs to individuals with cognitive impairments, a population often excluded from the benefits of conventional BCIs. We present the general concept of BAIs and illustrate the potential of this new approach with a Conversational BAI based on EEG. In particular, we show in an experiment with simulated phone conversations that the Conversational BAI enables complex communication without the need to generate language. Our work thus demonstrates, for the first time, the ability of a speech neuroprosthesis to enable fluent communication in realistic scenarios with non-invasive technologies.
In the era of Artificial Intelligence Generated Content (AIGC), conditional multimodal synthesis technologies (e.g., text-to-image, text-to-video, text-to-audio, etc) are gradually reshaping the natural content in the real world. The key to multimodal synthesis technology is to establish the mapping relationship between different modalities. Brain signals, serving as potential reflections of how the brain interprets external information, exhibit a distinctive One-to-Many correspondence with various external modalities. This correspondence makes brain signals emerge as a promising guiding condition for multimodal content synthesis. Brian-conditional multimodal synthesis refers to decoding brain signals back to perceptual experience, which is crucial for developing practical brain-computer interface systems and unraveling complex mechanisms underlying how the brain perceives and comprehends external stimuli. This survey comprehensively examines the emerging field of AIGC-based Brain-conditional Multimodal Synthesis, termed AIGC-Brain, to delineate the current landscape and future directions. To begin, related brain neuroimaging datasets, functional brain regions, and mainstream generative models are introduced as the foundation of AIGC-Brain decoding and analysis. Next, we provide a comprehensive taxonomy for AIGC-Brain decoding models and present task-specific representative work and detailed implementation strategies to facilitate comparison and in-depth analysis. Quality assessments are then introduced for both qualitative and quantitative evaluation. Finally, this survey explores insights gained, providing current challenges and outlining prospects of AIGC-Brain. Being the inaugural survey in this domain, this paper paves the way for the progress of AIGC-Brain research, offering a foundational overview to guide future work.
The release of large datasets and developments in AI have led to dramatic improvements in decoding methods that reconstruct seen images from human brain activity. We evaluate the prospect of further improving recent decoding methods by optimizing for consistency between reconstructions and brain activity during inference. We sample seed reconstructions from a base decoding method, then iteratively refine these reconstructions using a brain-optimized encoding model that maps images to brain activity. At each iteration, we sample a small library of images from an image distribution (a diffusion model) conditioned on a seed reconstruction from the previous iteration. We select those that best approximate the measured brain activity when passed through our encoding model, and use these images for structural guidance during the generation of the small library in the next iteration. We reduce the stochasticity of the image distribution at each iteration, and stop when a criterion on the "width" of the image distribution is met. We show that when this process is applied to recent decoding methods, it outperforms the base decoding method as measured by human raters, a variety of image feature metrics, and alignment to brain activity. These results demonstrate that reconstruction quality can be significantly improved by explicitly aligning decoding distributions to brain activity distributions, even when the seed reconstruction is output from a state-of-the-art decoding algorithm. Interestingly, the rate of refinement varies systematically across visual cortex, with earlier visual areas generally converging more slowly and preferring narrower image distributions, relative to higher-level brain areas. Brain-optimized inference thus offers a succinct and novel method for improving reconstructions and exploring the diversity of representations across visual brain areas.
The limited data availability and the low signal-to-noise ratio of fMRI signals lead to the challenging task of fMRI-to-image retrieval. State-of-the-art MindEye remarkably improves fMRI-to-image retrieval performance by leveraging a large model, i.e., a 996M MLP Backbone per subject, to align fMRI embeddings to the final hidden layer of CLIP's Vision Transformer (ViT). However, significant individual variations exist among subjects, even under identical experimental setups, mandating the training of large subject-specific models. The substantial parameters pose significant challenges in deploying fMRI decoding on practical devices. To this end, we propose Lite-Mind, a lightweight, efficient, and robust brain representation learning paradigm based on Discrete Fourier Transform (DFT), which efficiently aligns fMRI voxels to fine-grained information of CLIP. We elaborately design a DFT backbone with Spectrum Compression and Frequency Projector modules to learn informative and robust voxel embeddings. Our experiments demonstrate that Lite-Mind achieves an impressive 94.6% fMRI-to-image retrieval accuracy on the NSD dataset for Subject 1, with 98.7% fewer parameters than MindEye. Lite-Mind is also proven to be able to be migrated to smaller fMRI datasets and establishes a new state-of-the-art for zero-shot classification on the GOD dataset.