MindEye2: Shared-Subject Models Enable fMRI-To-Image With 1 Hour of Data

Reconstructions of visual perception from brain activity have improved tremendously, but the practical utility of such methods has been limited. This is because such models are trained independently per subject where each subject requires dozens of hours of expensive fMRI training data to attain high-quality results. The present work showcases high-quality reconstructions using only 1 hour of fMRI training data. We pretrain our model across 7 subjects and then fine-tune on minimal data from a new subject. Our novel functional alignment procedure linearly maps all brain data to a shared-subject latent space, followed by a shared non-linear mapping to CLIP image space. We then map from CLIP space to pixel space by fine-tuning Stable Diffusion XL to accept CLIP latents as inputs instead of text. This approach improves out-of-subject generalization with limited training data and also attains state-of-the-art image retrieval and reconstruction metrics compared to single-subject approaches. MindEye2 demonstrates how accurate reconstructions of perception are possible from a single visit to the MRI facility. All code is available on GitHub.

How does the primate brain combine generative and discriminative computations in vision?

Vision is widely understood as an inference problem. However, two contrasting conceptions of the inference process have each been influential in research on biological vision as well as the engineering of machine vision. The first emphasizes bottom-up signal flow, describing vision as a largely feedforward, discriminative inference process that filters and transforms the visual information to remove irrelevant variation and represent behaviorally relevant information in a format suitable for downstream functions of cognition and behavioral control. In this conception, vision is driven by the sensory data, and perception is direct because the processing proceeds from the data to the latent variables of interest. The notion of "inference" in this conception is that of the engineering literature on neural networks, where feedforward convolutional neural networks processing images are said to perform inference. The alternative conception is that of vision as an inference process in Helmholtz's sense, where the sensory evidence is evaluated in the context of a generative model of the causal processes giving rise to it. In this conception, vision inverts a generative model through an interrogation of the evidence in a process often thought to involve top-down predictions of sensory data to evaluate the likelihood of alternative hypotheses. The authors include scientists rooted in roughly equal numbers in each of the conceptions and motivated to overcome what might be a false dichotomy between them and engage the other perspective in the realm of theory and experiment. The primate brain employs an unknown algorithm that may combine the advantages of both conceptions. We explain and clarify the terminology, review the key empirical evidence, and propose an empirical research program that transcends the dichotomy and sets the stage for revealing the mysterious hybrid algorithm of primate vision.

Brain-optimized inference improves reconstructions of fMRI brain activity

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.

Second Sight: Using brain-optimized encoding models to align image distributions with human brain activity

Two recent developments have accelerated progress in image reconstruction from human brain activity: large datasets that offer samples of brain activity in response to many thousands of natural scenes, and the open-sourcing of powerful stochastic image-generators that accept both low- and high-level guidance. Most work in this space has focused on obtaining point estimates of the target image, with the ultimate goal of approximating literal pixel-wise reconstructions of target images from the brain activity patterns they evoke. This emphasis belies the fact that there is always a family of images that are equally compatible with any evoked brain activity pattern, and the fact that many image-generators are inherently stochastic and do not by themselves offer a method for selecting the single best reconstruction from among the samples they generate. We introduce a novel reconstruction procedure (Second Sight) that iteratively refines an image distribution to explicitly maximize the alignment between the predictions of a voxel-wise encoding model and the brain activity patterns evoked by any target image. We show that our process converges on a distribution of high-quality reconstructions by refining both semantic content and low-level image details across iterations. Images sampled from these converged image distributions are competitive with state-of-the-art reconstruction algorithms. Interestingly, the time-to-convergence varies systematically across visual cortex, with earlier visual areas generally taking longer and converging on narrower image distributions, relative to higher-level brain areas. Second Sight thus offers a succinct and novel method for exploring the diversity of representations across visual brain areas.

Reconstructing seen images from human brain activity via guided stochastic search

Visual reconstruction algorithms are an interpretive tool that map brain activity to pixels. Past reconstruction algorithms employed brute-force search through a massive library to select candidate images that, when passed through an encoding model, accurately predict brain activity. Here, we use conditional generative diffusion models to extend and improve this search-based strategy. We decode a semantic descriptor from human brain activity (7T fMRI) in voxels across most of visual cortex, then use a diffusion model to sample a small library of images conditioned on this descriptor. We pass each sample through an encoding model, select the images that best predict brain activity, and then use these images to seed another library. We show that this process converges on high-quality reconstructions by refining low-level image details while preserving semantic content across iterations. Interestingly, the time-to-convergence differs systematically across visual cortex, suggesting a succinct new way to measure the diversity of representations across visual brain areas.

Semantic scene descriptions as an objective of human vision

Interpreting the meaning of a visual scene requires not only identification of its constituent objects, but also a rich semantic characterization of object interrelations. Here, we study the neural mechanisms underlying visuo-semantic transformations by applying modern computational techniques to a large-scale 7T fMRI dataset of human brain responses elicited by complex natural scenes. Using semantic embeddings obtained by applying linguistic deep learning models to human-generated scene descriptions, we identify a widely distributed network of brain regions that encode semantic scene descriptions. Importantly, these semantic embeddings better explain activity in these regions than traditional object category labels. In addition, they are effective predictors of activity despite the fact that the participants did not actively engage in a semantic task, suggesting that visuo-semantic transformations are a default mode of vision. In support of this view, we then show that highly accurate reconstructions of scene captions can be directly linearly decoded from patterns of brain activity. Finally, a recurrent convolutional neural network trained on semantic embeddings further outperforms semantic embeddings in predicting brain activity, providing a mechanistic model of the brain's visuo-semantic transformations. Together, these experimental and computational results suggest that transforming visual input into rich semantic scene descriptions may be a central objective of the visual system, and that focusing efforts on this new objective may lead to improved models of visual information processing in the human brain.

NeuroGen: activation optimized image synthesis for discovery neuroscience

Functional MRI (fMRI) is a powerful technique that has allowed us to characterize visual cortex responses to stimuli, yet such experiments are by nature constructed based on a priori hypotheses, limited to the set of images presented to the individual while they are in the scanner, are subject to noise in the observed brain responses, and may vary widely across individuals. In this work, we propose a novel computational strategy, which we call NeuroGen, to overcome these limitations and develop a powerful tool for human vision neuroscience discovery. NeuroGen combines an fMRI-trained neural encoding model of human vision with a deep generative network to synthesize images predicted to achieve a target pattern of macro-scale brain activation. We demonstrate that the reduction of noise that the encoding model provides, coupled with the generative network's ability to produce images of high fidelity, results in a robust discovery architecture for visual neuroscience. By using only a small number of synthetic images created by NeuroGen, we demonstrate that we can detect and amplify differences in regional and individual human brain response patterns to visual stimuli. We then verify that these discoveries are reflected in the several thousand observed image responses measured with fMRI. We further demonstrate that NeuroGen can create synthetic images predicted to achieve regional response patterns not achievable by the best-matching natural images. The NeuroGen framework extends the utility of brain encoding models and opens up a new avenue for exploring, and possibly precisely controlling, the human visual system.