Matias Cosarinsky

Roman Beliy, Matias Cosarinsky, Oliver Heinimann et al.

Decoding visual content from fMRI signals recorded while a person views images, and specifically answering questions about the seen images, is a long-standing challenge. While significant progress has been made in recent years in visual question answering (VQA) from fMRI, performance remains limited. Moreover, although recent models can make increasingly accurate predictions, they have rarely been used as tools for understanding the structure of visual representations in the brain. We present Brain-IT-VQA, a framework for visual question answering from fMRI. Building on the Brain Interaction Transformer (Brain-IT), our method decodes language tokens from brain activity and integrates them with a language model to answer visual questions. Our model substantially outperforms previous fMRI-based captioning and VQA approaches. We further introduce NSD-VQA, a new dataset and benchmark for visual question answering from fMRI. Unlike existing image-fMRI VQA datasets, which typically provide only a few broad and weakly controlled questions per image, NSD-VQA provides on average 20 question-answer pairs per image across 20 controlled question categories that disentangle multiple levels of visual understanding. This enables more reliable and interpretable evaluation despite limited fMRI test data. Together, Brain-IT-VQA and NSD-VQA provide both a strong predictive framework and a tool for studying brain representations. Using this benchmark, we quantify which forms of visual and semantic information can be reliably decoded from fMRI responses to natural images. We further analyze the contributions of different brain regions across question types.

Navve Wasserman, Matias Cosarinsky, Yuval Golbari et al.

Understanding how the human brain represents visual concepts, and in which brain regions these representations are encoded, remains a long-standing challenge. Decades of work have advanced our understanding of visual representations, yet brain signals remain large and complex, and the space of possible visual concepts is vast. As a result, most studies remain small-scale, rely on manual inspection, focus on specific regions and properties, and rarely include systematic validation. We present a large-scale, automated framework for discovering and explaining visual representations across the human cortex. Our method comprises two main stages. First, we discover candidate interpretable patterns in fMRI activity through unsupervised, data-driven decomposition methods. Next, we explain each pattern by identifying the set of natural images that most strongly elicit it and generating a natural-language description of their shared visual meaning. To scale this process, we introduce an automated pipeline that tests multiple candidate explanations, assigns quantitative reliability scores, and selects the most consistent description for each voxel pattern. Our framework reveals thousands of interpretable patterns spanning many distinct visual concepts, including fine-grained representations previously unreported.

Yuval Golbari, Navve Wasserman, Matias Cosarinsky et al.

Identifying which brain regions represent a visual concept in the human brain is a central challenge in neuroscience. Existing approaches have localized coarse functional regions (e.g., faces, places) through activation maximization, identifying regions that activate strongly for a target concept relative to other concepts. Yet strong activation alone does not establish that a region represents the concept itself, as responses may instead be driven by correlated visual or semantic cues. We introduce BrainCause, an automated framework that combines generative and brain models to synthesize controlled stimuli and validate neural representations through targeted causal testing. Given a query specifying a concept of interest, our framework constructs targeted stimulus sets comprising concept images, counterfactual edits that remove the target concept while preserving other image content, and images with candidate correlated distractors. It then uses an image-to-fMRI encoding model to predict brain responses and searches for representations that respond specifically to the target concept over correlated alternatives. BrainCause returns validated candidate representations and proposes follow-up fMRI experiments to further test or extend its discoveries. Our approach successfully recovers known functional localizations and identifies new candidate representations across dozens of concepts, validated on both predicted and measured fMRI data. Critically, we show that without causal validation, a large fraction of localizations would be false positives, confirming that activation alone is insufficient evidence of representation.

Matias Cosarinsky, Ramiro Billot, Lucas Mansilla et al.

Assessing the quality of automatic image segmentation is crucial in clinical practice, but often very challenging due to the limited availability of ground truth annotations. Reverse Classification Accuracy (RCA) is an approach that estimates the quality of new predictions on unseen samples by training a segmenter on those predictions, and then evaluating it against existing annotated images. In this work, we introduce Conformal In-Context RCA, a novel method for automatically estimating segmentation quality with statistical guarantees in the absence of ground-truth annotations, which consists of two main innovations. First, In-Context RCA, which leverages recent in-context learning models for image segmentation and incorporates retrieval-augmentation techniques to select the most relevant reference images. This approach enables efficient quality estimation with minimal reference data while avoiding the need of training additional models. Second, we introduce Conformal RCA, which extends both the original RCA framework and In-Context RCA to go beyond point estimation. Using tools from split conformal prediction, Conformal RCA produces prediction intervals for segmentation quality providing statistical guarantees that the true score lies within the estimated interval with a user-specified probability. Validated across 10 different medical imaging tasks in various organs and modalities, our methods demonstrate robust performance and computational efficiency, offering a promising solution for automated quality control in clinical workflows, where fast and reliable segmentation assessment is essential. The code is available at https://github.com/mcosarinsky/Conformal-In-Context-RCA.

Matias Cosarinsky, Nicolas Gaggion, Rodrigo Echeveste et al.

In this work, we study uncertainty estimation for anatomical landmark-based segmentation on chest X-rays. Inspired by hybrid neural network architectures that combine standard image convolutional encoders with graph-based generative decoders, and leveraging their variational latent space, we derive two complementary measures: (i) latent uncertainty, captured directly from the learned distribution parameters, and (ii) predictive uncertainty, obtained by generating multiple stochastic output predictions from latent samples. Through controlled corruption experiments we show that both uncertainty measures increase with perturbation severity, reflecting both global and local degradation. We demonstrate that these uncertainty signals can identify unreliable predictions by comparing with manual ground-truth, and support out-of-distribution detection on the CheXmask dataset. More importantly, we release CheXmask-U (huggingface.co/datasets/mcosarinsky/CheXmask-U), a large scale dataset of 657,566 chest X-ray landmark segmentations with per-node uncertainty estimates, enabling researchers to account for spatial variations in segmentation quality when using these anatomical masks. Our findings establish uncertainty estimation as a promising direction to enhance robustness and safe deployment of landmark-based anatomical segmentation methods in chest X-ray. A fully working interactive demo of the method is available at huggingface.co/spaces/matiasky/CheXmask-U and the source code at github.com/mcosarinsky/CheXmask-U.

Jingchen Zou, Jianqiang Li, Gabriel Jimenez et al.

The performance of medical image segmentation models is usually evaluated using metrics like the Dice score and Hausdorff distance, which compare predicted masks to ground truth annotations. However, when applying the model to unseen data, such as in clinical settings, it is often impractical to annotate all the data, making the model's performance uncertain. To address this challenge, we propose the Segmentation Performance Evaluator (SPE), a framework for estimating segmentation models' performance on unlabeled data. This framework is adaptable to various evaluation metrics and model architectures. Experiments on six publicly available datasets across six evaluation metrics including pixel-based metrics such as Dice score and distance-based metrics like HD95, demonstrated the versatility and effectiveness of our approach, achieving a high correlation (0.956$\pm$0.046) and low MAE (0.025$\pm$0.019) compare with real Dice score on the independent test set. These results highlight its ability to reliably estimate model performance without requiring annotations. The SPE framework integrates seamlessly into any model training process without adding training overhead, enabling performance estimation and facilitating the real-world application of medical image segmentation algorithms. The source code is publicly available