This paper presents the novel Dual Stream Graph-Transformer Fusion (DS-GTF) architecture designed specifically for classifying task-based Magnetoencephalography (MEG) data. In the spatial stream, inputs are initially represented as graphs, which are then passed through graph attention networks (GAT) to extract spatial patterns. Two methods, TopK and Thresholded Adjacency are introduced for initializing the adjacency matrix used in the GAT. In the temporal stream, the Transformer Encoder receives concatenated windowed input MEG data and learns new temporal representations. The learned temporal and spatial representations from both streams are fused before reaching the output layer. Experimental results demonstrate an enhancement in classification performance and a reduction in standard deviation across multiple test subjects compared to other examined models.
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.
The remarkable success of large language models (LLMs) across various multi-modality applications is well established. However, integrating large language models with humans, or brain dynamics, remains relatively unexplored. In this paper, we introduce BELT-2, a pioneering multi-task model designed to enhance both encoding and decoding performance from EEG signals. To bolster the quality of the EEG encoder, BELT-2 is the first work to innovatively 1) adopt byte-pair encoding (BPE)-level EEG-language alignment and 2) integrate multi-task training and decoding in the EEG domain. Inspired by the idea of \textbf{\textit{Bridging the Brain with GPT}}, we further connect the multi-task EEG encoder with LLMs by utilizing prefix-tuning on intermediary output from the EEG encoder. These innovative efforts make BELT-2 a pioneering breakthrough, making it the first work in the field capable of decoding coherent and readable sentences from non-invasive brain signals. Our experiments highlight significant advancements over prior techniques in both quantitative and qualitative measures, achieving a decoding performance with a BLEU-1 score of 52.2\% on the ZuCo dataset. Furthermore, BELT-2 shows a remarkable improvement ranging from 31\% to 162\% on other translation benchmarks. Codes can be accessed via the provided anonymous link~\footnote{https://anonymous.4open.science/r/BELT-2-0048}.
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.
Modern Machine Learning (ML) has significantly advanced various research fields, but the opaque nature of ML models hinders their adoption in several domains. Explainable AI (XAI) addresses this challenge by providing additional information to help users understand the internal decision-making process of ML models. In the field of neuroscience, enriching a ML model for brain decoding with attribution-based XAI techniques means being able to highlight which brain areas correlate with the task at hand, thus offering valuable insights to domain experts. In this paper, we analyze human and Computer Vision (CV) systems in parallel, training and explaining two ML models based respectively on functional Magnetic Resonance Imaging (fMRI) and movie frames. We do so by leveraging the "StudyForrest" dataset, which includes functional Magnetic Resonance Imaging (fMRI) scans of subjects watching the "Forrest Gump" movie, emotion annotations, and eye-tracking data. For human vision the ML task is to link fMRI data with emotional annotations, and the explanations highlight the brain regions strongly correlated with the label. On the other hand, for computer vision, the input data is movie frames, and the explanations are pixel-level heatmaps. We cross-analyzed our results, linking human attention (obtained through eye-tracking) with XAI saliency on CV models and brain region activations. We show how a parallel analysis of human and computer vision can provide useful information for both the neuroscience community (allocation theory) and the ML community (biological plausibility of convolutional models).
Language, as an information medium created by advanced organisms, has always been a concern of neuroscience regarding how it is represented in the brain. Decoding linguistic representations in the evoked brain has shown groundbreaking achievements, thanks to the rapid improvement of neuroimaging, medical technology, life sciences and artificial intelligence. In this work, we present a taxonomy of brain-to-language decoding of both textual and speech formats. This work integrates two types of research: neuroscience focusing on language understanding and deep learning-based brain decoding. Generating discernible language information from brain activity could not only help those with limited articulation, especially amyotrophic lateral sclerosis (ALS) patients but also open up a new way for the next generation's brain-computer interface (BCI). This article will help brain scientists and deep-learning researchers to gain a bird's eye view of fine-grained language perception, and thus facilitate their further investigation and research of neural process and language decoding.
Brain decoding techniques are essential for understanding the neurocognitive system. Although numerous methods have been introduced in this field, accurately aligning complex external stimuli with brain activities remains a formidable challenge. To alleviate alignment difficulties, many studies have simplified their models by employing single-task paradigms and establishing direct links between brain/world through classification strategies. Despite improvements in decoding accuracy, this strategy frequently encounters issues with generality when adapting these models to various task paradigms. To address this issue, this study introduces a user-friendly decoding model that enables dynamic communication with the brain, as opposed to the static decoding approaches utilized by traditional studies. The model functions as a brain simulator, allowing for interactive engagement with the brain and enabling the decoding of a subject's experiences through dialogue-like queries. Uniquely, our model is trained in a completely unsupervised and task-free manner. Our experiments demonstrate the feasibility and versatility of our proposed method. Notably, our model demonstrates exceptional capabilities in signal compression, successfully representing the entire brain signal of approximately 185,751 voxels with just 32 signals. Furthermore, we show how our model can integrate seamlessly with multimodal models, thus enhancing the potential for controlling brain decoding through textual or image inputs.
Deciphering the human visual experience through brain activities captured by fMRI represents a compelling and cutting-edge challenge in the field of neuroscience research. Compared to merely predicting the viewed image itself, decoding brain activity into meaningful captions provides a higher-level interpretation and summarization of visual information, which naturally enhances the application flexibility in real-world situations. In this work, we introduce MindSemantix, a novel multi-modal framework that enables LLMs to comprehend visually-evoked semantic content in brain activity. Our MindSemantix explores a more ideal brain captioning paradigm by weaving LLMs into brain activity analysis, crafting a seamless, end-to-end Brain-Language Model. To effectively capture semantic information from brain responses, we propose Brain-Text Transformer, utilizing a Brain Q-Former as its core architecture. It integrates a pre-trained brain encoder with a frozen LLM to achieve multi-modal alignment of brain-vision-language and establish a robust brain-language correspondence. To enhance the generalizability of neural representations, we pre-train our brain encoder on a large-scale, cross-subject fMRI dataset using self-supervised learning techniques. MindSemantix provides more feasibility to downstream brain decoding tasks such as stimulus reconstruction. Conditioned by MindSemantix captioning, our framework facilitates this process by integrating with advanced generative models like Stable Diffusion and excels in understanding brain visual perception. MindSemantix generates high-quality captions that are deeply rooted in the visual and semantic information derived from brain activity. This approach has demonstrated substantial quantitative improvements over prior art. Our code will be released.
Research efforts for visual decoding from fMRI signals have attracted considerable attention in research community. Still multi-subject fMRI decoding with one model has been considered intractable due to the drastic variations in fMRI signals between subjects and even within the same subject across different trials. To address current limitations in multi-subject brain decoding, here we introduce a novel semantic alignment method of multi-subject fMRI signals using so-called MindFormer. This model is specifically designed to generate fMRI-conditioned feature vectors that can be used for conditioning Stable Diffusion model for fMRI- to-image generation or large language model (LLM) for fMRI-to-text generation. More specifically, MindFormer incorporates two key innovations: 1) a subject specific token that effectively capture individual differences in fMRI signals while synergistically combines multi subject fMRI data for training, and 2) a novel feature embedding and training scheme based on the IP-Adapter to extract semantically meaningful features from fMRI signals. Our experimental results demonstrate that MindFormer generates semantically consistent images and text across different subjects. Since our MindFormer maintains semantic fidelity by fully utilizing the training data across different subjects by significantly surpassing existing models in multi-subject brain decoding, this may help deepening our understanding of neural processing variations among individuals.
Brain decoding, which aims at reconstructing visual stimuli from brain signals, primarily utilizing functional magnetic resonance imaging (fMRI), has recently made positive progress. However, it is impeded by significant challenges such as the difficulty of acquiring fMRI-image pairs and the variability of individuals, etc. Most methods have to adopt the per-subject-per-model paradigm, greatly limiting their applications. To alleviate this problem, we introduce a new and meaningful task, few-shot brain decoding, while it will face two inherent difficulties: 1) the scarcity of fMRI-image pairs and the noisy signals can easily lead to overfitting; 2) the inadequate guidance complicates the training of a robust encoder. Therefore, a novel framework named MindShot, is proposed to achieve effective few-shot brain decoding by leveraging cross-subject prior knowledge. Firstly, inspired by the hemodynamic response function (HRF), the HRF adapter is applied to eliminate unexplainable cognitive differences between subjects with small trainable parameters. Secondly, a Fourier-based cross-subject supervision method is presented to extract additional high-level and low-level biological guidance information from signals of other subjects. Under the MindShot, new subjects and pretrained individuals only need to view images of the same semantic class, significantly expanding the model's applicability. Experimental results demonstrate MindShot's ability of reconstructing semantically faithful images in few-shot scenarios and outperforms methods based on the per-subject-per-model paradigm. The promising results of the proposed method not only validate the feasibility of few-shot brain decoding but also provide the possibility for the learning of large models under the condition of reducing data dependence.
Brain-computer interfaces have promising medical and scientific applications for aiding speech and studying the brain. In this work, we propose an information-based evaluation metric for brain-to-text decoders. Using this metric, we examine two methods to augment existing state-of-the-art continuous text decoders. We show that these methods, in concert, can improve brain decoding performance by upwards of 40% when compared to a baseline model. We further examine the informatic properties of brain-to-text decoders and show empirically that they have Zipfian power law dynamics. Finally, we provide an estimate for the idealized performance of an fMRI-based text decoder. We compare this idealized model to our current model, and use our information-based metric to quantify the main sources of decoding error. We conclude that a practical brain-to-text decoder is likely possible given further algorithmic improvements.
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.
Decoding non-invasive brain recordings is pivotal for advancing our understanding of human cognition but faces challenges due to individual differences and complex neural signal representations. Traditional methods often require customized models and extensive trials, lacking interpretability in visual reconstruction tasks. Our framework integrates 3D brain structures with visual semantics using a Vision Transformer 3D. This unified feature extractor efficiently aligns fMRI features with multiple levels of visual embeddings, eliminating the need for subject-specific models and allowing extraction from single-trial data. The extractor consolidates multi-level visual features into one network, simplifying integration with Large Language Models (LLMs). Additionally, we have enhanced the fMRI dataset with diverse fMRI-image-related textual data to support multimodal large model development. Integrating with LLMs enhances decoding capabilities, enabling tasks such as brain captioning, complex reasoning, concept localization, and visual reconstruction. Our approach demonstrates superior performance across these tasks, precisely identifying language-based concepts within brain signals, enhancing interpretability, and providing deeper insights into neural processes. These advances significantly broaden the applicability of non-invasive brain decoding in neuroscience and human-computer interaction, setting the stage for advanced brain-computer interfaces and cognitive models.
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.
In the context of Brain-Computer Interfaces, we propose an adaptive method that reaches offline performance level while being usable online without requiring supervision. Interestingly, our method does not require retraining the model, as it consists in using a frozen efficient deep learning backbone while continuously realigning data, both at input and latent spaces, based on streaming observations. We demonstrate its efficiency for Motor Imagery brain decoding from electroencephalography data, considering challenging cross-subject scenarios. For reproducibility, we share the code of our experiments.
The development of algorithms to accurately decode of neural information is a long-standing effort in the field of neuroscience. Brain decoding is typically employed by training machine learning models to map neural data onto a preestablished vector representation of stimulus features. These vectors are usually derived from image- and/or text-based feature spaces. Nonetheless, the intrinsic characteristics of these vectors might be fundamentally different than those encoded by the brain, limiting the ability of algorithms to accurately learn this mapping. To address this issue, here, we propose a representation learning framework, called brain-aligning of semantic vectors, that fine-tunes pretrained feature vectors to better align with the structure of neural representations of visual stimuli in the human brain. We trained this model with functional magnetic resonance imaging (fMRI) data representing 150 visual stimulus categories; then, we performed zero-shot brain decoding on 1) fMRI, 2) magnetoencephalography (MEG), and 3) electrocorticography (ECoG) data reflecting neural representations of visual stimuli. By using fMRI-based brain-aligned vectors, the zero-shot decoding accuracy all three neuroimaging datasets increased. This finding underscores the potential of leveraging a richer array of brainderived features to increase the performance of brain decoding algorithms.
Objective: Most current wearable tonic-clonic seizure (TCS) detection systems are based on extra-cerebral signals, such as electromyography (EMG) or accelerometry (ACC). Although many of these devices show good sensitivity in seizure detection, their false positive rates (FPR) are still relatively high. Wearable EEG may improve performance; however, studies investigating this remain scarce. This paper aims 1) to investigate the possibility of detecting TCSs with a behind-the-ear, two-channel wearable EEG, and 2) to evaluate the added value of wearable EEG to other non-EEG modalities in multimodal TCS detection. Method: We included 27 participants with a total of 44 TCSs from the European multicenter study SeizeIT2. The multimodal wearable detection system Sensor Dot (Byteflies) was used to measure two-channel, behind-the-ear EEG, EMG, electrocardiography (ECG), ACC and gyroscope (GYR). First, we evaluated automatic unimodal detection of TCSs, using performance metrics such as sensitivity, precision, FPR and F1-score. Secondly, we fused the different modalities and again assessed performance. Algorithm-labeled segments were then provided to a neurologist and a wearable data expert, who reviewed and annotated the true positive TCSs, and discarded false positives (FPs). Results: Wearable EEG outperformed the other modalities in unimodal TCS detection by achieving a sensitivity of 100.0% and a FPR of 10.3/24h (compared to 97.7% sensitivity and 30.9/24h FPR for EMG; 95.5% sensitivity and 13.9 FPR for ACC). The combination of wearable EEG and EMG achieved overall the most clinically useful performance in offline TCS detection with a sensitivity of 97.7%, a FPR of 0.4/24 h, a precision of 43.0%, and a F1-score of 59.7%. Subsequent visual review of the automated detections resulted in maximal sensitivity and zero FPs.
Motivated by the challenge of seamless cross-dataset transfer in EEG signal processing, this article presents an exploratory study on the use of Joint Embedding Predictive Architectures (JEPAs). In recent years, self-supervised learning has emerged as a promising approach for transfer learning in various domains. However, its application to EEG signals remains largely unexplored. In this article, we introduce Signal-JEPA for representing EEG recordings which includes a novel domain-specific spatial block masking strategy and three novel architectures for downstream classification. The study is conducted on a 54 subjects dataset and the downstream performance of the models is evaluated on three different BCI paradigms: motor imagery, ERP and SSVEP. Our study provides preliminary evidence for the potential of JEPAs in EEG signal encoding. Notably, our results highlight the importance of spatial filtering for accurate downstream classification and reveal an influence of the length of the pre-training examples but not of the mask size on the downstream performance.
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.