Daily Papers

In this paper, we introduce Recon3DMind, an innovative task aimed at reconstructing 3D visuals from Functional Magnetic Resonance Imaging (fMRI) signals, marking a significant advancement in the fields of cognitive neuroscience and computer vision. To support this pioneering task, we present the fMRI-Shape dataset, which includes data from 14 participants and features 360-degree videos of 3D objects to enable comprehensive fMRI signal capture across various settings, thereby laying a foundation for future research. Furthermore, we propose MinD-3D, a novel and effective three-stage framework specifically designed to decode the brain's 3D visual information from fMRI signals, demonstrating the feasibility of this challenging task. The framework begins by extracting and aggregating features from fMRI frames through a neuro-fusion encoder, subsequently employs a feature bridge diffusion model to generate visual features, and ultimately recovers the 3D object via a generative transformer decoder. We assess the performance of MinD-3D using a suite of semantic and structural metrics and analyze the correlation between the features extracted by our model and the visual regions of interest (ROIs) in fMRI signals. Our findings indicate that MinD-3D not only reconstructs 3D objects with high semantic relevance and spatial similarity but also significantly enhances our understanding of the human brain's capabilities in processing 3D visual information. Project page at: https://jianxgao.github.io/MinD-3D.

Reconstructing 3D visuals from functional Magnetic Resonance Imaging (fMRI) data, introduced as Recon3DMind in our conference work, is of significant interest to both cognitive neuroscience and computer vision. To advance this task, we present the fMRI-3D dataset, which includes data from 15 participants and showcases a total of 4768 3D objects. The dataset comprises two components: fMRI-Shape, previously introduced and accessible at https://huggingface.co/datasets/Fudan-fMRI/fMRI-Shape, and fMRI-Objaverse, proposed in this paper and available at https://huggingface.co/datasets/Fudan-fMRI/fMRI-Objaverse. fMRI-Objaverse includes data from 5 subjects, 4 of whom are also part of the Core set in fMRI-Shape, with each subject viewing 3142 3D objects across 117 categories, all accompanied by text captions. This significantly enhances the diversity and potential applications of the dataset. Additionally, we propose MinD-3D, a novel framework designed to decode 3D visual information from fMRI signals. The framework first extracts and aggregates features from fMRI data using a neuro-fusion encoder, then employs a feature-bridge diffusion model to generate visual features, and finally reconstructs the 3D object using a generative transformer decoder. We establish new benchmarks by designing metrics at both semantic and structural levels to evaluate model performance. Furthermore, we assess our model's effectiveness in an Out-of-Distribution setting and analyze the attribution of the extracted features and the visual ROIs in fMRI signals. Our experiments demonstrate that MinD-3D not only reconstructs 3D objects with high semantic and spatial accuracy but also deepens our understanding of how human brain processes 3D visual information. Project page at: https://jianxgao.github.io/MinD-3D.

This paper presents an annotated dataset of brain MRI images designed to advance the field of brain symmetry study. Magnetic resonance imaging (MRI) has gained interest in analyzing brain symmetry in neonatal infants, and challenges remain due to the vast size differences between fetal and adult brains. Classification methods for brain structural MRI use scales and visual cues to assess hemisphere symmetry, which can help diagnose neonatal patients by comparing hemispheres and anatomical regions of interest in the brain. Using the Developing Human Connectome Project dataset, this work presents a dataset comprising cerebral images extracted as slices across selected portions of interest for clinical evaluation . All the extracted images are annotated with the brain's midline. All the extracted images are annotated with the brain's midline. From the assumption that a decrease in symmetry is directly related to possible clinical pathologies, the dataset can contribute to a more precise diagnosis because it can be used to train deep learning model application in neonatal cerebral MRI anomaly detection from postnatal infant scans thanks to computer vision. Such models learn to identify and classify anomalies by identifying potential asymmetrical patterns in medical MRI images. Furthermore, this dataset can contribute to the research and development of methods using the relative symmetry of the two brain hemispheres for crucial diagnosis and treatment planning.

In the pursuit to understand the intricacies of human brain's visual processing, reconstructing dynamic visual experiences from brain activities emerges as a challenging yet fascinating endeavor. While recent advancements have achieved success in reconstructing static images from non-invasive brain recordings, the domain of translating continuous brain activities into video format remains underexplored. In this work, we introduce NeuroCine, a novel dual-phase framework to targeting the inherent challenges of decoding fMRI data, such as noises, spatial redundancy and temporal lags. This framework proposes spatial masking and temporal interpolation-based augmentation for contrastive learning fMRI representations and a diffusion model enhanced by dependent prior noise for video generation. Tested on a publicly available fMRI dataset, our method shows promising results, outperforming the previous state-of-the-art models by a notable margin of {20.97%}, {31.00%} and {12.30%} respectively on decoding the brain activities of three subjects in the fMRI dataset, as measured by SSIM. Additionally, our attention analysis suggests that the model aligns with existing brain structures and functions, indicating its biological plausibility and interpretability.

We present FOMO60K, a large-scale, heterogeneous dataset of 60,529 brain Magnetic Resonance Imaging (MRI) scans from 13,900 sessions and 11,187 subjects, aggregated from 16 publicly available sources. The dataset includes both clinical- and research-grade images, multiple MRI sequences, and a wide range of anatomical and pathological variability, including scans with large brain anomalies. Minimal preprocessing was applied to preserve the original image characteristics while reducing barriers to entry for new users. Accompanying code for self-supervised pretraining and finetuning is provided. FOMO60K is intended to support the development and benchmarking of self-supervised learning methods in medical imaging at scale.

This paper introduces a public dataset of 1.4 million procedurally-generated bicycle designs represented parametrically, as JSON files, and as rasterized images. The dataset is created through the use of a rendering engine which harnesses the BikeCAD software to generate vector graphics from parametric designs. This rendering engine is discussed in the paper and also released publicly alongside the dataset. Though this dataset has numerous applications, a principal motivation is the need to train cross-modal predictive models between parametric and image-based design representations. For example, we demonstrate that a predictive model can be trained to accurately estimate Contrastive Language-Image Pretraining (CLIP) embeddings from a parametric representation directly. This allows similarity relations to be established between parametric bicycle designs and text strings or reference images. Trained predictive models are also made public. The dataset joins the BIKED dataset family which includes thousands of mixed-representation human-designed bicycle models and several datasets quantifying design performance. The code and dataset can be found at: https://github.com/Lyleregenwetter/BIKED_multimodal/tree/main

We introduce 3DShape2VecSet, a novel shape representation for neural fields designed for generative diffusion models. Our shape representation can encode 3D shapes given as surface models or point clouds, and represents them as neural fields. The concept of neural fields has previously been combined with a global latent vector, a regular grid of latent vectors, or an irregular grid of latent vectors. Our new representation encodes neural fields on top of a set of vectors. We draw from multiple concepts, such as the radial basis function representation and the cross attention and self-attention function, to design a learnable representation that is especially suitable for processing with transformers. Our results show improved performance in 3D shape encoding and 3D shape generative modeling tasks. We demonstrate a wide variety of generative applications: unconditioned generation, category-conditioned generation, text-conditioned generation, point-cloud completion, and image-conditioned generation.

Every day, the human brain processes an immense volume of visual information, relying on intricate neural mechanisms to perceive and interpret these stimuli. Recent breakthroughs in functional magnetic resonance imaging (fMRI) have enabled scientists to extract visual information from human brain activity patterns. In this study, we present an innovative method for decoding brain activity into meaningful images and captions, with a specific focus on brain captioning due to its enhanced flexibility as compared to brain decoding into images. Our approach takes advantage of cutting-edge image captioning models and incorporates a unique image reconstruction pipeline that utilizes latent diffusion models and depth estimation. We utilized the Natural Scenes Dataset, a comprehensive fMRI dataset from eight subjects who viewed images from the COCO dataset. We employed the Generative Image-to-text Transformer (GIT) as our backbone for captioning and propose a new image reconstruction pipeline based on latent diffusion models. The method involves training regularized linear regression models between brain activity and extracted features. Additionally, we incorporated depth maps from the ControlNet model to further guide the reconstruction process. We evaluate our methods using quantitative metrics for both generated captions and images. Our brain captioning approach outperforms existing methods, while our image reconstruction pipeline generates plausible images with improved spatial relationships. In conclusion, we demonstrate significant progress in brain decoding, showcasing the enormous potential of integrating vision and language to better understand human cognition. Our approach provides a flexible platform for future research, with potential applications in various fields, including neural art, style transfer, and portable devices.

A central question for neuroscience is how to characterize brain representations of perceptual and cognitive content. An ideal characterization should distinguish different functional regions with robustness to noise and idiosyncrasies of individual brains that do not correspond to computational differences. Previous studies have characterized brain representations by their representational geometry, which is defined by the representational dissimilarity matrix (RDM), a summary statistic that abstracts from the roles of individual neurons (or responses channels) and characterizes the discriminability of stimuli. Here we explore a further step of abstraction: from the geometry to the topology of brain representations. We propose topological representational similarity analysis (tRSA), an extension of representational similarity analysis (RSA) that uses a family of geo-topological summary statistics that generalizes the RDM to characterize the topology while de-emphasizing the geometry. We evaluate this new family of statistics in terms of the sensitivity and specificity for model selection using both simulations and functional MRI (fMRI) data. In the simulations, the ground truth is a data-generating layer representation in a neural network model and the models are the same and other layers in different model instances (trained from different random seeds). In fMRI, the ground truth is a visual area and the models are the same and other areas measured in different subjects. Results show that topology-sensitive characterizations of population codes are robust to noise and interindividual variability and maintain excellent sensitivity to the unique representational signatures of different neural network layers and brain regions.

Deep neural networks have brought remarkable breakthroughs in medical image analysis. However, due to their data-hungry nature, the modest dataset sizes in medical imaging projects might be hindering their full potential. Generating synthetic data provides a promising alternative, allowing to complement training datasets and conducting medical image research at a larger scale. Diffusion models recently have caught the attention of the computer vision community by producing photorealistic synthetic images. In this study, we explore using Latent Diffusion Models to generate synthetic images from high-resolution 3D brain images. We used T1w MRI images from the UK Biobank dataset (N=31,740) to train our models to learn about the probabilistic distribution of brain images, conditioned on covariables, such as age, sex, and brain structure volumes. We found that our models created realistic data, and we could use the conditioning variables to control the data generation effectively. Besides that, we created a synthetic dataset with 100,000 brain images and made it openly available to the scientific community.

Prior to the deep learning era, shape was commonly used to describe the objects. Nowadays, state-of-the-art (SOTA) algorithms in medical imaging are predominantly diverging from computer vision, where voxel grids, meshes, point clouds, and implicit surface models are used. This is seen from numerous shape-related publications in premier vision conferences as well as the growing popularity of ShapeNet (about 51,300 models) and Princeton ModelNet (127,915 models). For the medical domain, we present a large collection of anatomical shapes (e.g., bones, organs, vessels) and 3D models of surgical instrument, called MedShapeNet, created to facilitate the translation of data-driven vision algorithms to medical applications and to adapt SOTA vision algorithms to medical problems. As a unique feature, we directly model the majority of shapes on the imaging data of real patients. As of today, MedShapeNet includes 23 dataset with more than 100,000 shapes that are paired with annotations (ground truth). Our data is freely accessible via a web interface and a Python application programming interface (API) and can be used for discriminative, reconstructive, and variational benchmarks as well as various applications in virtual, augmented, or mixed reality, and 3D printing. Exemplary, we present use cases in the fields of classification of brain tumors, facial and skull reconstructions, multi-class anatomy completion, education, and 3D printing. In future, we will extend the data and improve the interfaces. The project pages are: https://medshapenet.ikim.nrw/ and https://github.com/Jianningli/medshapenet-feedback

Deep implicit functions (DIFs) have emerged as a powerful paradigm for many computer vision tasks such as 3D shape reconstruction, generation, registration, completion, editing, and understanding. However, given a set of 3D shapes with associated covariates there is at present no shape representation method which allows to precisely represent the shapes while capturing the individual dependencies on each covariate. Such a method would be of high utility to researchers to discover knowledge hidden in a population of shapes. For scientific shape discovery, we propose a 3D Neural Additive Model for Interpretable Shape Representation (NAISR) which describes individual shapes by deforming a shape atlas in accordance to the effect of disentangled covariates. Our approach captures shape population trends and allows for patient-specific predictions through shape transfer. NAISR is the first approach to combine the benefits of deep implicit shape representations with an atlas deforming according to specified covariates. We evaluate NAISR with respect to shape reconstruction, shape disentanglement, shape evolution, and shape transfer on three datasets: 1) Starman, a simulated 2D shape dataset; 2) the ADNI hippocampus 3D shape dataset; and 3) a pediatric airway 3D shape dataset. Our experiments demonstrate that Starman achieves excellent shape reconstruction performance while retaining interpretability. Our code is available at https://github.com/uncbiag/NAISR{https://github.com/uncbiag/NAISR}.

Measuring geometric similarity between high-dimensional network representations is a topic of longstanding interest to neuroscience and deep learning. Although many methods have been proposed, only a few works have rigorously analyzed their statistical efficiency or quantified estimator uncertainty in data-limited regimes. Here, we derive upper and lower bounds on the worst-case convergence of standard estimators of shape distancex2014a measure of representational dissimilarity proposed by Williams et al. (2021).These bounds reveal the challenging nature of the problem in high-dimensional feature spaces. To overcome these challenges, we introduce a new method-of-moments estimator with a tunable bias-variance tradeoff. We show that this estimator achieves substantially lower bias than standard estimators in simulation and on neural data, particularly in high-dimensional settings. Thus, we lay the foundation for a rigorous statistical theory for high-dimensional shape analysis, and we contribute a new estimation method that is well-suited to practical scientific settings.

We introduce a benchmark to directly evaluate the alignment between human observers and vision models on a 3D shape inference task. We leverage an experimental design from the cognitive sciences which requires zero-shot visual inferences about object shape: given a set of images, participants identify which contain the same/different objects, despite considerable viewpoint variation. We draw from a diverse range of images that include common objects (e.g., chairs) as well as abstract shapes (i.e., procedurally generated `nonsense' objects). After constructing over 2000 unique image sets, we administer these tasks to human participants, collecting 35K trials of behavioral data from over 500 participants. This includes explicit choice behaviors as well as intermediate measures, such as reaction time and gaze data. We then evaluate the performance of common vision models (e.g., DINOv2, MAE, CLIP). We find that humans outperform all models by a wide margin. Using a multi-scale evaluation approach, we identify underlying similarities and differences between models and humans: while human-model performance is correlated, humans allocate more time/processing on challenging trials. All images, data, and code can be accessed via our project page.

Selecting appropriate datasets is critical in modern computer vision. However, no general-purpose tools exist to evaluate the extent to which two datasets differ. For this, we propose representing images - and by extension datasets - using Distributions of Neuron Activations (DNAs). DNAs fit distributions, such as histograms or Gaussians, to activations of neurons in a pre-trained feature extractor through which we pass the image(s) to represent. This extractor is frozen for all datasets, and we rely on its generally expressive power in feature space. By comparing two DNAs, we can evaluate the extent to which two datasets differ with granular control over the comparison attributes of interest, providing the ability to customise the way distances are measured to suit the requirements of the task at hand. Furthermore, DNAs are compact, representing datasets of any size with less than 15 megabytes. We demonstrate the value of DNAs by evaluating their applicability on several tasks, including conditional dataset comparison, synthetic image evaluation, and transfer learning, and across diverse datasets, ranging from synthetic cat images to celebrity faces and urban driving scenes.

Empirically validating new 3D-printing related algorithms and implementations requires testing data representative of inputs encountered in the wild. An ideal benchmarking dataset should not only draw from the same distribution of shapes people print in terms of class (e.g., toys, mechanisms, jewelry), representation type (e.g., triangle soup meshes) and complexity (e.g., number of facets), but should also capture problems and artifacts endemic to 3D printing models (e.g., self-intersections, non-manifoldness). We observe that the contextual and geometric characteristics of 3D printing models differ significantly from those used for computer graphics applications, not to mention standard models (e.g., Stanford bunny, Armadillo, Fertility). We present a new dataset of 10,000 models collected from an online 3D printing model-sharing database. Via analysis of both geometric (e.g., triangle aspect ratios, manifoldness) and contextual (e.g., licenses, tags, classes) characteristics, we demonstrate that this dataset represents a more concise summary of real-world models used for 3D printing compared to existing datasets. To facilitate future research endeavors, we also present an online query interface to select subsets of the dataset according to project-specific characteristics. The complete dataset and per-model statistical data are freely available to the public.

We present MindEye, a novel fMRI-to-image approach to retrieve and reconstruct viewed images from brain activity. Our model comprises two parallel submodules that are specialized for retrieval (using contrastive learning) and reconstruction (using a diffusion prior). MindEye can map fMRI brain activity to any high dimensional multimodal latent space, like CLIP image space, enabling image reconstruction using generative models that accept embeddings from this latent space. We comprehensively compare our approach with other existing methods, using both qualitative side-by-side comparisons and quantitative evaluations, and show that MindEye achieves state-of-the-art performance in both reconstruction and retrieval tasks. In particular, MindEye can retrieve the exact original image even among highly similar candidates indicating that its brain embeddings retain fine-grained image-specific information. This allows us to accurately retrieve images even from large-scale databases like LAION-5B. We demonstrate through ablations that MindEye's performance improvements over previous methods result from specialized submodules for retrieval and reconstruction, improved training techniques, and training models with orders of magnitude more parameters. Furthermore, we show that MindEye can better preserve low-level image features in the reconstructions by using img2img, with outputs from a separate autoencoder. All code is available on GitHub.

We present a dataset of large-scale indoor spaces that provides a variety of mutually registered modalities from 2D, 2.5D and 3D domains, with instance-level semantic and geometric annotations. The dataset covers over 6,000m2 and contains over 70,000 RGB images, along with the corresponding depths, surface normals, semantic annotations, global XYZ images (all in forms of both regular and 360{\deg} equirectangular images) as well as camera information. It also includes registered raw and semantically annotated 3D meshes and point clouds. The dataset enables development of joint and cross-modal learning models and potentially unsupervised approaches utilizing the regularities present in large-scale indoor spaces. The dataset is available here: http://3Dsemantics.stanford.edu/

In this paper, we introduce fastHDMI, a Python package designed for efficient variable screening in high-dimensional datasets, particularly neuroimaging data. This work pioneers the application of three mutual information estimation methods for neuroimaging variable selection, a novel approach implemented via fastHDMI. These advancements enhance our ability to analyze the complex structures of neuroimaging datasets, providing improved tools for variable selection in high-dimensional spaces. Using the preprocessed ABIDE dataset, we evaluate the performance of these methods through extensive simulations. The tests cover a range of conditions, including linear and nonlinear associations, as well as continuous and binary outcomes. Our results highlight the superiority of the FFTKDE-based mutual information estimation for feature screening in continuous nonlinear outcomes, while binning-based methods outperform others for binary outcomes with nonlinear probability preimages. For linear simulations, both Pearson correlation and FFTKDE-based methods show comparable performance for continuous outcomes, while Pearson excels in binary outcomes with linear probability preimages. A comprehensive case study using the ABIDE dataset further demonstrates fastHDMI's practical utility, showcasing the predictive power of models built from variables selected using our screening techniques. This research affirms the computational efficiency and methodological strength of fastHDMI, significantly enriching the toolkit available for neuroimaging analysis.

Cycle consistency has long been exploited as a powerful prior for jointly optimizing maps within a collection of shapes. In this paper, we investigate its utility in the approaches of Deep Functional Maps, which are considered state-of-the-art in non-rigid shape matching. We first justify that under certain conditions, the learned maps, when represented in the spectral domain, are already cycle consistent. Furthermore, we identify the discrepancy that spectrally consistent maps are not necessarily spatially, or point-wise, consistent. In light of this, we present a novel design of unsupervised Deep Functional Maps, which effectively enforces the harmony of learned maps under the spectral and the point-wise representation. By taking advantage of cycle consistency, our framework produces state-of-the-art results in mapping shapes even under significant distortions. Beyond that, by independently estimating maps in both spectral and spatial domains, our method naturally alleviates over-fitting in network training, yielding superior generalization performance and accuracy within an array of challenging tests for both near-isometric and non-isometric datasets. Codes are available at https://github.com/rqhuang88/Spatiallyand-Spectrally-Consistent-Deep-Functional-Maps.

In this study, we aim to build up a model that can Segment Anything in radiology scans, driven by medical terminologies as Text prompts, termed as SAT. Our main contributions are three folds: (i) for dataset construction, we construct the first multi-modal knowledge tree on human anatomy, including 6502 anatomical terminologies; Then, we build up the largest and most comprehensive segmentation dataset for training, by collecting over 22K 3D medical image scans from72 segmentation datasets, across 497 classes, with careful standardization on both image scans and label space; (ii) for architecture design, we propose to inject medical knowledge into a text encoder via contrastive learning, and then formulate a universal segmentation model, that can be prompted by feeding in medical terminologies in text form; (iii) As a result, we have trained SAT-Nano (110M parameters) and SAT-Pro (447M parameters), demonstrating superior or comparable performance to 72 specialist models, i.e., nnU-Nets, U-Mamba or SwinUNETR, trained on each dataset/subsets. We validate SAT as a foundational segmentation model, with better generalization on external (cross-center) datasets, and can be further improved on specific tasks after fine-tuning adaptation. Comparing with state-of-the-art interactive segmentation model MedSAM, SAT demonstrate superior performance, scalability and robustness. We further compare SAT with BiomedParse, and observe SAT is significantly superior in both internal and external evaluation. Through extensive ablation study, we validate the benefit of domain knowledge on universal segmentation, especially on tail categories. As a use case, we demonstrate that SAT can act as a powerful out-of-the-box agent for large language models, enabling visual grounding in versatile application scenarios. All the data, codes, and models in this work have been released.

Current volumetric biomedical foundation models struggle to generalize as public 3D datasets are small and do not cover the broad diversity of medical procedures, conditions, anatomical regions, and imaging protocols. We address this by creating a representation learning method that instead anticipates strong domain shifts at training time itself. We first propose a data engine that synthesizes highly variable training samples that would enable generalization to new biomedical contexts. To then train a single 3D network for any voxel-level task, we develop a contrastive learning method that pretrains the network to be stable against nuisance imaging variation simulated by the data engine, a key inductive bias for generalization. This network's features can be used as robust representations of input images for downstream tasks and its weights provide a strong, dataset-agnostic initialization for finetuning on new datasets. As a result, we set new standards across both multimodality registration and few-shot segmentation, a first for any 3D biomedical vision model, all without (pre-)training on any existing dataset of real images.

Quantifying similarity between neural representations -- e.g. hidden layer activation vectors -- is a perennial problem in deep learning and neuroscience research. Existing methods compare deterministic responses (e.g. artificial networks that lack stochastic layers) or averaged responses (e.g., trial-averaged firing rates in biological data). However, these measures of _deterministic_ representational similarity ignore the scale and geometric structure of noise, both of which play important roles in neural computation. To rectify this, we generalize previously proposed shape metrics (Williams et al. 2021) to quantify differences in _stochastic_ representations. These new distances satisfy the triangle inequality, and thus can be used as a rigorous basis for many supervised and unsupervised analyses. Leveraging this novel framework, we find that the stochastic geometries of neurobiological representations of oriented visual gratings and naturalistic scenes respectively resemble untrained and trained deep network representations. Further, we are able to more accurately predict certain network attributes (e.g. training hyperparameters) from its position in stochastic (versus deterministic) shape space.

We propose a new representation for encoding 3D shapes as neural fields. The representation is designed to be compatible with the transformer architecture and to benefit both shape reconstruction and shape generation. Existing works on neural fields are grid-based representations with latents defined on a regular grid. In contrast, we define latents on irregular grids, enabling our representation to be sparse and adaptive. In the context of shape reconstruction from point clouds, our shape representation built on irregular grids improves upon grid-based methods in terms of reconstruction accuracy. For shape generation, our representation promotes high-quality shape generation using auto-regressive probabilistic models. We show different applications that improve over the current state of the art. First, we show results for probabilistic shape reconstruction from a single higher resolution image. Second, we train a probabilistic model conditioned on very low resolution images. Third, we apply our model to category-conditioned generation. All probabilistic experiments confirm that we are able to generate detailed and high quality shapes to yield the new state of the art in generative 3D shape modeling.

Human's perception of the visual world is shaped by the stereo processing of 3D information. Understanding how the brain perceives and processes 3D visual stimuli in the real world has been a longstanding endeavor in neuroscience. Towards this goal, we introduce a new neuroscience task: decoding 3D visual perception from EEG signals, a neuroimaging technique that enables real-time monitoring of neural dynamics enriched with complex visual cues. To provide the essential benchmark, we first present EEG-3D, a pioneering dataset featuring multimodal analysis data and extensive EEG recordings from 12 subjects viewing 72 categories of 3D objects rendered in both videos and images. Furthermore, we propose Neuro-3D, a 3D visual decoding framework based on EEG signals. This framework adaptively integrates EEG features derived from static and dynamic stimuli to learn complementary and robust neural representations, which are subsequently utilized to recover both the shape and color of 3D objects through the proposed diffusion-based colored point cloud decoder. To the best of our knowledge, we are the first to explore EEG-based 3D visual decoding. Experiments indicate that Neuro-3D not only reconstructs colored 3D objects with high fidelity, but also learns effective neural representations that enable insightful brain region analysis. The dataset and associated code will be made publicly available.

Image-to-fMRI encoding is important for both neuroscience research and practical applications. However, such "Brain-Encoders" have been typically trained per-subject and per fMRI-dataset, thus restricted to very limited training data. In this paper we propose a Universal Brain-Encoder, which can be trained jointly on data from many different subjects/datasets/machines. What makes this possible is our new voxel-centric Encoder architecture, which learns a unique "voxel-embedding" per brain-voxel. Our Encoder trains to predict the response of each brain-voxel on every image, by directly computing the cross-attention between the brain-voxel embedding and multi-level deep image features. This voxel-centric architecture allows the functional role of each brain-voxel to naturally emerge from the voxel-image cross-attention. We show the power of this approach to (i) combine data from multiple different subjects (a "Crowd of Brains") to improve each individual brain-encoding, (ii) quick & effective Transfer-Learning across subjects, datasets, and machines (e.g., 3-Tesla, 7-Tesla), with few training examples, and (iii) use the learned voxel-embeddings as a powerful tool to explore brain functionality (e.g., what is encoded where in the brain).

Objective: fMRI and derived measures such as functional connectivity (FC) have been used to predict brain age, general fluid intelligence, psychiatric disease status, and preclinical neurodegenerative disease. However, it is not always clear that all demographic confounds, such as age, sex, and race, have been removed from fMRI data. Additionally, many fMRI datasets are restricted to authorized researchers, making dissemination of these valuable data sources challenging. Methods: We create a variational autoencoder (VAE)-based model, DemoVAE, to decorrelate fMRI features from demographics and generate high-quality synthetic fMRI data based on user-supplied demographics. We train and validate our model using two large, widely used datasets, the Philadelphia Neurodevelopmental Cohort (PNC) and Bipolar and Schizophrenia Network for Intermediate Phenotypes (BSNIP). Results: We find that DemoVAE recapitulates group differences in fMRI data while capturing the full breadth of individual variations. Significantly, we also find that most clinical and computerized battery fields that are correlated with fMRI data are not correlated with DemoVAE latents. An exception are several fields related to schizophrenia medication and symptom severity. Conclusion: Our model generates fMRI data that captures the full distribution of FC better than traditional VAE or GAN models. We also find that most prediction using fMRI data is dependent on correlation with, and prediction of, demographics. Significance: Our DemoVAE model allows for generation of high quality synthetic data conditioned on subject demographics as well as the removal of the confounding effects of demographics. We identify that FC-based prediction tasks are highly influenced by demographic confounds.

In the image classification task, the most common approach is to resize all images in a dataset to a unique shape, while reducing their precision to a size which facilitates experimentation at scale. This practice has benefits from a computational perspective, but it entails negative side-effects on performance due to loss of information and image deformation. In this work we introduce the MAMe dataset, an image classification dataset with remarkable high resolution and variable shape properties. The goal of MAMe is to provide a tool for studying the impact of such properties in image classification, while motivating research in the field. The MAMe dataset contains thousands of artworks from three different museums, and proposes a classification task consisting on differentiating between 29 mediums (i.e. materials and techniques) supervised by art experts. After reviewing the singularity of MAMe in the context of current image classification tasks, a thorough description of the task is provided, together with dataset statistics. Experiments are conducted to evaluate the impact of using high resolution images, variable shape inputs and both properties at the same time. Results illustrate the positive impact in performance when using high resolution images, while highlighting the lack of solutions to exploit variable shapes. An additional experiment exposes the distinctiveness between the MAMe dataset and the prototypical ImageNet dataset. Finally, the baselines are inspected using explainability methods and expert knowledge, to gain insights on the challenges that remain ahead.

Recent learning-based approaches have made astonishing advances in calibrated medical imaging like computerized tomography (CT), yet they struggle to generalize in uncalibrated modalities -- notably magnetic resonance (MR) imaging, where performance is highly sensitive to the differences in MR contrast, resolution, and orientation. This prevents broad applicability to diverse real-world clinical protocols. We introduce Brain-ID, an anatomical representation learning model for brain imaging. With the proposed "mild-to-severe" intra-subject generation, Brain-ID is robust to the subject-specific brain anatomy regardless of the appearance of acquired images (e.g., contrast, deformation, resolution, artifacts). Trained entirely on synthetic data, Brain-ID readily adapts to various downstream tasks through only one layer. We present new metrics to validate the intra- and inter-subject robustness of Brain-ID features, and evaluate their performance on four downstream applications, covering contrast-independent (anatomy reconstruction/contrast synthesis, brain segmentation), and contrast-dependent (super-resolution, bias field estimation) tasks. Extensive experiments on six public datasets demonstrate that Brain-ID achieves state-of-the-art performance in all tasks on different MRI modalities and CT, and more importantly, preserves its performance on low-resolution and small datasets. Code is available at https://github.com/peirong26/Brain-ID.

We present ShapeNet: a richly-annotated, large-scale repository of shapes represented by 3D CAD models of objects. ShapeNet contains 3D models from a multitude of semantic categories and organizes them under the WordNet taxonomy. It is a collection of datasets providing many semantic annotations for each 3D model such as consistent rigid alignments, parts and bilateral symmetry planes, physical sizes, keywords, as well as other planned annotations. Annotations are made available through a public web-based interface to enable data visualization of object attributes, promote data-driven geometric analysis, and provide a large-scale quantitative benchmark for research in computer graphics and vision. At the time of this technical report, ShapeNet has indexed more than 3,000,000 models, 220,000 models out of which are classified into 3,135 categories (WordNet synsets). In this report we describe the ShapeNet effort as a whole, provide details for all currently available datasets, and summarize future plans.

Instance segmentation of neurons in volumetric light microscopy images of nervous systems enables groundbreaking research in neuroscience by facilitating joint functional and morphological analyses of neural circuits at cellular resolution. Yet said multi-neuron light microscopy data exhibits extremely challenging properties for the task of instance segmentation: Individual neurons have long-ranging, thin filamentous and widely branching morphologies, multiple neurons are tightly inter-weaved, and partial volume effects, uneven illumination and noise inherent to light microscopy severely impede local disentangling as well as long-range tracing of individual neurons. These properties reflect a current key challenge in machine learning research, namely to effectively capture long-range dependencies in the data. While respective methodological research is buzzing, to date methods are typically benchmarked on synthetic datasets. To address this gap, we release the FlyLight Instance Segmentation Benchmark (FISBe) dataset, the first publicly available multi-neuron light microscopy dataset with pixel-wise annotations. In addition, we define a set of instance segmentation metrics for benchmarking that we designed to be meaningful with regard to downstream analyses. Lastly, we provide three baselines to kick off a competition that we envision to both advance the field of machine learning regarding methodology for capturing long-range data dependencies, and facilitate scientific discovery in basic neuroscience.

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.

Image datasets are essential not only in validating existing methods in computer vision but also in developing new methods. Most existing image datasets focus on trichromatic intensity images to mimic human vision. However, polarization and spectrum, the wave properties of light that animals in harsh environments and with limited brain capacity often rely on, remain underrepresented in existing datasets. Although spectro-polarimetric datasets exist, these datasets have insufficient object diversity, limited illumination conditions, linear-only polarization data, and inadequate image count. Here, we introduce two spectro-polarimetric datasets: trichromatic Stokes images and hyperspectral Stokes images. These novel datasets encompass both linear and circular polarization; they introduce multiple spectral channels; and they feature a broad selection of real-world scenes. With our dataset in hand, we analyze the spectro-polarimetric image statistics, develop efficient representations of such high-dimensional data, and evaluate spectral dependency of shape-from-polarization methods. As such, the proposed dataset promises a foundation for data-driven spectro-polarimetric imaging and vision research. Dataset and code will be publicly available.

Small sample sizes are common in many disciplines, which necessitates pooling roughly similar datasets across multiple institutions to study weak but relevant associations between images and disease outcomes. Such data often manifest shift/imbalance in covariates (i.e., secondary non-imaging data). Controlling for such nuisance variables is common within standard statistical analysis, but the ideas do not directly apply to overparameterized models. Consequently, recent work has shown how strategies from invariant representation learning provides a meaningful starting point, but the current repertoire of methods is limited to accounting for shifts/imbalances in just a couple of covariates at a time. In this paper, we show how viewing this problem from the perspective of Category theory provides a simple and effective solution that completely avoids elaborate multi-stage training pipelines that would otherwise be needed. We show the effectiveness of this approach via extensive experiments on real datasets. Further, we discuss how this style of formulation offers a unified perspective on at least 5+ distinct problem settings, from self-supervised learning to matching problems in 3D reconstruction.

Stroke remains a leading cause of global morbidity and mortality, placing a heavy socioeconomic burden. Over the past decade, advances in endovascular reperfusion therapy and the use of CT and MRI imaging for treatment guidance have significantly improved patient outcomes and are now standard in clinical practice. To develop machine learning algorithms that can extract meaningful and reproducible models of brain function for both clinical and research purposes from stroke images - particularly for lesion identification, brain health quantification, and prognosis - large, diverse, and well-annotated public datasets are essential. While only a few datasets with (sub-)acute stroke data were previously available, several large, high-quality datasets have recently been made publicly accessible. However, these existing datasets include only MRI data. In contrast, our dataset is the first to offer comprehensive longitudinal stroke data, including acute CT imaging with angiography and perfusion, follow-up MRI at 2-9 days, as well as acute and longitudinal clinical data up to a three-month outcome. The dataset includes a training dataset of n = 150 and a test dataset of n = 100 scans. Training data is publicly available, while test data will be used exclusively for model validation. We are making this dataset available as part of the 2024 edition of the Ischemic Stroke Lesion Segmentation (ISLES) challenge (https://www.isles-challenge.org/), which continuously aims to establish benchmark methods for acute and sub-acute ischemic stroke lesion segmentation, aiding in creating open stroke imaging datasets and evaluating cutting-edge image processing algorithms.

Understanding functional representations within higher visual cortex is a fundamental question in computational neuroscience. While artificial neural networks pretrained on large-scale datasets exhibit striking representational alignment with human neural responses, learning image-computable models of visual cortex relies on individual-level, large-scale fMRI datasets. The necessity for expensive, time-intensive, and often impractical data acquisition limits the generalizability of encoders to new subjects and stimuli. BraInCoRL uses in-context learning to predict voxelwise neural responses from few-shot examples without any additional finetuning for novel subjects and stimuli. We leverage a transformer architecture that can flexibly condition on a variable number of in-context image stimuli, learning an inductive bias over multiple subjects. During training, we explicitly optimize the model for in-context learning. By jointly conditioning on image features and voxel activations, our model learns to directly generate better performing voxelwise models of higher visual cortex. We demonstrate that BraInCoRL consistently outperforms existing voxelwise encoder designs in a low-data regime when evaluated on entirely novel images, while also exhibiting strong test-time scaling behavior. The model also generalizes to an entirely new visual fMRI dataset, which uses different subjects and fMRI data acquisition parameters. Further, BraInCoRL facilitates better interpretability of neural signals in higher visual cortex by attending to semantically relevant stimuli. Finally, we show that our framework enables interpretable mappings from natural language queries to voxel selectivity.

The field of self-supervised learning (SSL) for 3D medical images lacks consistency and standardization. While many methods have been developed, it is impossible to identify the current state-of-the-art, due to i) varying and small pretraining datasets, ii) varying architectures, and iii) being evaluated on differing downstream datasets. In this paper, we bring clarity to this field and lay the foundation for further method advancements through three key contributions: We a) publish the largest publicly available pre-training dataset comprising 114k 3D brain MRI volumes, enabling all practitioners to pre-train on a large-scale dataset. We b) benchmark existing 3D self-supervised learning methods on this dataset for a state-of-the-art CNN and Transformer architecture, clarifying the state of 3D SSL pre-training. Among many findings, we show that pre-trained methods can exceed a strong from-scratch nnU-Net ResEnc-L baseline. Lastly, we c) publish the code of our pre-training and fine-tuning frameworks and provide the pre-trained models created during the benchmarking process to facilitate rapid adoption and reproduction.

We present a new dataset with the goal of advancing the state-of-the-art in object recognition by placing the question of object recognition in the context of the broader question of scene understanding. This is achieved by gathering images of complex everyday scenes containing common objects in their natural context. Objects are labeled using per-instance segmentations to aid in precise object localization. Our dataset contains photos of 91 objects types that would be easily recognizable by a 4 year old. With a total of 2.5 million labeled instances in 328k images, the creation of our dataset drew upon extensive crowd worker involvement via novel user interfaces for category detection, instance spotting and instance segmentation. We present a detailed statistical analysis of the dataset in comparison to PASCAL, ImageNet, and SUN. Finally, we provide baseline performance analysis for bounding box and segmentation detection results using a Deformable Parts Model.

In this paper, we present DendroMap, a novel approach to interactively exploring large-scale image datasets for machine learning (ML). ML practitioners often explore image datasets by generating a grid of images or projecting high-dimensional representations of images into 2-D using dimensionality reduction techniques (e.g., t-SNE). However, neither approach effectively scales to large datasets because images are ineffectively organized and interactions are insufficiently supported. To address these challenges, we develop DendroMap by adapting Treemaps, a well-known visualization technique. DendroMap effectively organizes images by extracting hierarchical cluster structures from high-dimensional representations of images. It enables users to make sense of the overall distributions of datasets and interactively zoom into specific areas of interests at multiple levels of abstraction. Our case studies with widely-used image datasets for deep learning demonstrate that users can discover insights about datasets and trained models by examining the diversity of images, identifying underperforming subgroups, and analyzing classification errors. We conducted a user study that evaluates the effectiveness of DendroMap in grouping and searching tasks by comparing it with a gridified version of t-SNE and found that participants preferred DendroMap. DendroMap is available at https://div-lab.github.io/dendromap/.

Despite the longstanding adage "an image is worth a thousand words," creating accurate and hyper-detailed image descriptions for training Vision-Language models remains challenging. Current datasets typically have web-scraped descriptions that are short, low-granularity, and often contain details unrelated to the visual content. As a result, models trained on such data generate descriptions replete with missing information, visual inconsistencies, and hallucinations. To address these issues, we introduce ImageInWords (IIW), a carefully designed human-in-the-loop annotation framework for curating hyper-detailed image descriptions and a new dataset resulting from this process. We validate the framework through evaluations focused on the quality of the dataset and its utility for fine-tuning with considerations for readability, comprehensiveness, specificity, hallucinations, and human-likeness. Our dataset significantly improves across these dimensions compared to recently released datasets (+66%) and GPT-4V outputs (+48%). Furthermore, models fine-tuned with IIW data excel by +31% against prior work along the same human evaluation dimensions. Given our fine-tuned models, we also evaluate text-to-image generation and vision-language reasoning. Our model's descriptions can generate images closest to the original, as judged by both automated and human metrics. We also find our model produces more compositionally rich descriptions, outperforming the best baseline by up to 6% on ARO, SVO-Probes, and Winoground datasets.

View-based methods have demonstrated promising performance in 3D shape understanding. However, they tend to make strong assumptions about the relations between views or learn the multi-view correlations indirectly, which limits the flexibility of exploring inter-view correlations and the effectiveness of target tasks. To overcome the above problems, this paper investigates flexible organization and explicit correlation learning for multiple views. In particular, we propose to incorporate different views of a 3D shape into a permutation-invariant set, referred to as View Set, which removes rigid relation assumptions and facilitates adequate information exchange and fusion among views. Based on that, we devise a nimble Transformer model, named VSFormer, to explicitly capture pairwise and higher-order correlations of all elements in the set. Meanwhile, we theoretically reveal a natural correspondence between the Cartesian product of a view set and the correlation matrix in the attention mechanism, which supports our model design. Comprehensive experiments suggest that VSFormer has better flexibility, efficient inference efficiency and superior performance. Notably, VSFormer reaches state-of-the-art results on various 3d recognition datasets, including ModelNet40, ScanObjectNN and RGBD. It also establishes new records on the SHREC'17 retrieval benchmark. The code and datasets are available at https://github.com/auniquesun/VSFormer.

Deep neural networks trained on Functional Connectivity (FC) networks extracted from functional Magnetic Resonance Imaging (fMRI) data have gained popularity due to the increasing availability of data and advances in model architectures, including Graph Neural Network (GNN). Recent research on the application of GNN to FC suggests that exploiting the time-varying properties of the FC could significantly improve the accuracy and interpretability of the model prediction. However, the high cost of acquiring high-quality fMRI data and corresponding phenotypic labels poses a hurdle to their application in real-world settings, such that a model na\"ively trained in a supervised fashion can suffer from insufficient performance or a lack of generalization on a small number of data. In addition, most Self-Supervised Learning (SSL) approaches for GNNs to date adopt a contrastive strategy, which tends to lose appropriate semantic information when the graph structure is perturbed or does not leverage both spatial and temporal information simultaneously. In light of these challenges, we propose a generative SSL approach that is tailored to effectively harness spatio-temporal information within dynamic FC. Our empirical results, experimented with large-scale (>50,000) fMRI datasets, demonstrate that our approach learns valuable representations and enables the construction of accurate and robust models when fine-tuned for downstream tasks.

A recent study has shown that large-scale visual datasets are very biased: they can be easily classified by modern neural networks. However, the concrete forms of bias among these datasets remain unclear. In this study, we propose a framework to identify the unique visual attributes distinguishing these datasets. Our approach applies various transformations to extract semantic, structural, boundary, color, and frequency information from datasets, and assess how much each type of information reflects their bias. We further decompose their semantic bias with object-level analysis, and leverage natural language methods to generate detailed, open-ended descriptions of each dataset's characteristics. Our work aims to help researchers understand the bias in existing large-scale pre-training datasets, and build more diverse and representative ones in the future. Our project page and code are available at http://boyazeng.github.io/understand_bias .

A long standing goal in neuroscience has been to elucidate the functional organization of the brain. Within higher visual cortex, functional accounts have remained relatively coarse, focusing on regions of interest (ROIs) and taking the form of selectivity for broad categories such as faces, places, bodies, food, or words. Because the identification of such ROIs has typically relied on manually assembled stimulus sets consisting of isolated objects in non-ecological contexts, exploring functional organization without robust a priori hypotheses has been challenging. To overcome these limitations, we introduce a data-driven approach in which we synthesize images predicted to activate a given brain region using paired natural images and fMRI recordings, bypassing the need for category-specific stimuli. Our approach -- Brain Diffusion for Visual Exploration ("BrainDiVE") -- builds on recent generative methods by combining large-scale diffusion models with brain-guided image synthesis. Validating our method, we demonstrate the ability to synthesize preferred images with appropriate semantic specificity for well-characterized category-selective ROIs. We then show that BrainDiVE can characterize differences between ROIs selective for the same high-level category. Finally we identify novel functional subdivisions within these ROIs, validated with behavioral data. These results advance our understanding of the fine-grained functional organization of human visual cortex, and provide well-specified constraints for further examination of cortical organization using hypothesis-driven methods.

We study the problem of recovering an underlying 3D shape from a set of images. Existing learning based approaches usually resort to recurrent neural nets, e.g., GRU, or intuitive pooling operations, e.g., max/mean poolings, to fuse multiple deep features encoded from input images. However, GRU based approaches are unable to consistently estimate 3D shapes given different permutations of the same set of input images as the recurrent unit is permutation variant. It is also unlikely to refine the 3D shape given more images due to the long-term memory loss of GRU. Commonly used pooling approaches are limited to capturing partial information, e.g., max/mean values, ignoring other valuable features. In this paper, we present a new feed-forward neural module, named AttSets, together with a dedicated training algorithm, named FASet, to attentively aggregate an arbitrarily sized deep feature set for multi-view 3D reconstruction. The AttSets module is permutation invariant, computationally efficient and flexible to implement, while the FASet algorithm enables the AttSets based network to be remarkably robust and generalize to an arbitrary number of input images. We thoroughly evaluate FASet and the properties of AttSets on multiple large public datasets. Extensive experiments show that AttSets together with FASet algorithm significantly outperforms existing aggregation approaches.

Despite progress in perceptual tasks such as image classification, computers still perform poorly on cognitive tasks such as image description and question answering. Cognition is core to tasks that involve not just recognizing, but reasoning about our visual world. However, models used to tackle the rich content in images for cognitive tasks are still being trained using the same datasets designed for perceptual tasks. To achieve success at cognitive tasks, models need to understand the interactions and relationships between objects in an image. When asked "What vehicle is the person riding?", computers will need to identify the objects in an image as well as the relationships riding(man, carriage) and pulling(horse, carriage) in order to answer correctly that "the person is riding a horse-drawn carriage". In this paper, we present the Visual Genome dataset to enable the modeling of such relationships. We collect dense annotations of objects, attributes, and relationships within each image to learn these models. Specifically, our dataset contains over 100K images where each image has an average of 21 objects, 18 attributes, and 18 pairwise relationships between objects. We canonicalize the objects, attributes, relationships, and noun phrases in region descriptions and questions answer pairs to WordNet synsets. Together, these annotations represent the densest and largest dataset of image descriptions, objects, attributes, relationships, and question answers.

Magnetic resonance imaging (MRI) is a central modality for stroke imaging. It is used upon patient admission to make treatment decisions such as selecting patients for intravenous thrombolysis or endovascular therapy. MRI is later used in the duration of hospital stay to predict outcome by visualizing infarct core size and location. Furthermore, it may be used to characterize stroke etiology, e.g. differentiation between (cardio)-embolic and non-embolic stroke. Computer based automated medical image processing is increasingly finding its way into clinical routine. Previous iterations of the Ischemic Stroke Lesion Segmentation (ISLES) challenge have aided in the generation of identifying benchmark methods for acute and sub-acute ischemic stroke lesion segmentation. Here we introduce an expert-annotated, multicenter MRI dataset for segmentation of acute to subacute stroke lesions. This dataset comprises 400 multi-vendor MRI cases with high variability in stroke lesion size, quantity and location. It is split into a training dataset of n=250 and a test dataset of n=150. All training data will be made publicly available. The test dataset will be used for model validation only and will not be released to the public. This dataset serves as the foundation of the ISLES 2022 challenge with the goal of finding algorithmic methods to enable the development and benchmarking of robust and accurate segmentation algorithms for ischemic stroke.

Representational analysis explores how input data of a neural system are encoded in high dimensional spaces of its distributed neural activations, and how we can compare different systems, for instance, artificial neural networks and brains, on those grounds. While existing methods offer important insights, they typically do not account for local intrinsic geometrical properties within the high-dimensional representation spaces. To go beyond these limitations, we explore Ollivier-Ricci curvature and Ricci flow as tools to study the alignment of representations between humans and artificial neural systems on a geometric level. As a proof-of-principle study, we compared the representations of face stimuli between VGG-Face, a human-aligned version of VGG-Face, and corresponding human similarity judgments from a large online study. Using this discrete geometric framework, we were able to identify local structural similarities and differences by examining the distributions of node and edge curvature and higher-level properties by detecting and comparing community structure in the representational graphs.

We study the intriguing connection between visual data, deep networks, and the brain. Our method creates a universal channel alignment by using brain voxel fMRI response prediction as the training objective. We discover that deep networks, trained with different objectives, share common feature channels across various models. These channels can be clustered into recurring sets, corresponding to distinct brain regions, indicating the formation of visual concepts. Tracing the clusters of channel responses onto the images, we see semantically meaningful object segments emerge, even without any supervised decoder. Furthermore, the universal feature alignment and the clustering of channels produce a picture and quantification of how visual information is processed through the different network layers, which produces precise comparisons between the networks.

State-of-the-art systems neuroscience experiments yield large-scale multimodal data, and these data sets require new tools for analysis. Inspired by the success of large pretrained models in vision and language domains, we reframe the analysis of large-scale, cellular-resolution neuronal spiking data into an autoregressive spatiotemporal generation problem. Neuroformer is a multimodal, multitask generative pretrained transformer (GPT) model that is specifically designed to handle the intricacies of data in systems neuroscience. It scales linearly with feature size, can process an arbitrary number of modalities, and is adaptable to downstream tasks, such as predicting behavior. We first trained Neuroformer on simulated datasets, and found that it both accurately predicted simulated neuronal circuit activity, and also intrinsically inferred the underlying neural circuit connectivity, including direction. When pretrained to decode neural responses, the model predicted the behavior of a mouse with only few-shot fine-tuning, suggesting that the model begins learning how to do so directly from the neural representations themselves, without any explicit supervision. We used an ablation study to show that joint training on neuronal responses and behavior boosted performance, highlighting the model's ability to associate behavioral and neural representations in an unsupervised manner. These findings show that Neuroformer can analyze neural datasets and their emergent properties, informing the development of models and hypotheses associated with the brain.

Massive data corpora like WebText, Wikipedia, Conceptual Captions, WebImageText, and LAION have propelled recent dramatic progress in AI. Large neural models trained on such datasets produce impressive results and top many of today's benchmarks. A notable omission within this family of large-scale datasets is 3D data. Despite considerable interest and potential applications in 3D vision, datasets of high-fidelity 3D models continue to be mid-sized with limited diversity of object categories. Addressing this gap, we present Objaverse 1.0, a large dataset of objects with 800K+ (and growing) 3D models with descriptive captions, tags, and animations. Objaverse improves upon present day 3D repositories in terms of scale, number of categories, and in the visual diversity of instances within a category. We demonstrate the large potential of Objaverse via four diverse applications: training generative 3D models, improving tail category segmentation on the LVIS benchmark, training open-vocabulary object-navigation models for Embodied AI, and creating a new benchmark for robustness analysis of vision models. Objaverse can open new directions for research and enable new applications across the field of AI.

This paper presents a large publicly available multi-center lumbar spine magnetic resonance imaging (MRI) dataset with reference segmentations of vertebrae, intervertebral discs (IVDs), and spinal canal. The dataset includes 447 sagittal T1 and T2 MRI series from 218 patients with a history of low back pain. It was collected from four different hospitals and was divided into a training (179 patients) and validation (39 patients) set. An iterative data annotation approach was used by training a segmentation algorithm on a small part of the dataset, enabling semi-automatic segmentation of the remaining images. The algorithm provided an initial segmentation, which was subsequently reviewed, manually corrected, and added to the training data. We provide reference performance values for this baseline algorithm and nnU-Net, which performed comparably. We set up a continuous segmentation challenge to allow for a fair comparison of different segmentation algorithms. This study may encourage wider collaboration in the field of spine segmentation, and improve the diagnostic value of lumbar spine MRI.

We introduce MedMNIST v2, a large-scale MNIST-like dataset collection of standardized biomedical images, including 12 datasets for 2D and 6 datasets for 3D. All images are pre-processed into a small size of 28x28 (2D) or 28x28x28 (3D) with the corresponding classification labels so that no background knowledge is required for users. Covering primary data modalities in biomedical images, MedMNIST v2 is designed to perform classification on lightweight 2D and 3D images with various dataset scales (from 100 to 100,000) and diverse tasks (binary/multi-class, ordinal regression, and multi-label). The resulting dataset, consisting of 708,069 2D images and 10,214 3D images in total, could support numerous research / educational purposes in biomedical image analysis, computer vision, and machine learning. We benchmark several baseline methods on MedMNIST v2, including 2D / 3D neural networks and open-source / commercial AutoML tools. The data and code are publicly available at https://medmnist.com/.

Availability of large and diverse medical datasets is often challenged by privacy and data sharing restrictions. For successful application of machine learning techniques for disease diagnosis, prognosis, and precision medicine, large amounts of data are necessary for model building and optimization. To help overcome such limitations in the context of brain MRI, we present NeuroSynth: a collection of generative models of normative regional volumetric features derived from structural brain imaging. NeuroSynth models are trained on real brain imaging regional volumetric measures from the iSTAGING consortium, which encompasses over 40,000 MRI scans across 13 studies, incorporating covariates such as age, sex, and race. Leveraging NeuroSynth, we produce and offer 18,000 synthetic samples spanning the adult lifespan (ages 22-90 years), alongside the model's capability to generate unlimited data. Experimental results indicate that samples generated from NeuroSynth agree with the distributions obtained from real data. Most importantly, the generated normative data significantly enhance the accuracy of downstream machine learning models on tasks such as disease classification. Data and models are available at: https://huggingface.co/spaces/rongguangw/neuro-synth.

Data is a crucial component of machine learning. The field is reliant on data to train, validate, and test models. With increased technical capabilities, machine learning research has boomed in both academic and industry settings, and one major focus has been on computer vision. Computer vision is a popular domain of machine learning increasingly pertinent to real-world applications, from facial recognition in policing to object detection for autonomous vehicles. Given computer vision's propensity to shape machine learning research and impact human life, we seek to understand disciplinary practices around dataset documentation - how data is collected, curated, annotated, and packaged into datasets for computer vision researchers and practitioners to use for model tuning and development. Specifically, we examine what dataset documentation communicates about the underlying values of vision data and the larger practices and goals of computer vision as a field. To conduct this study, we collected a corpus of about 500 computer vision datasets, from which we sampled 114 dataset publications across different vision tasks. Through both a structured and thematic content analysis, we document a number of values around accepted data practices, what makes desirable data, and the treatment of humans in the dataset construction process. We discuss how computer vision datasets authors value efficiency at the expense of care; universality at the expense of contextuality; impartiality at the expense of positionality; and model work at the expense of data work. Many of the silenced values we identify sit in opposition with social computing practices. We conclude with suggestions on how to better incorporate silenced values into the dataset creation and curation process.

Sparse autoencoders have recently produced dictionaries of high-dimensional vectors corresponding to the universe of concepts represented by large language models. We find that this concept universe has interesting structure at three levels: 1) The "atomic" small-scale structure contains "crystals" whose faces are parallelograms or trapezoids, generalizing well-known examples such as (man-woman-king-queen). We find that the quality of such parallelograms and associated function vectors improves greatly when projecting out global distractor directions such as word length, which is efficiently done with linear discriminant analysis. 2) The "brain" intermediate-scale structure has significant spatial modularity; for example, math and code features form a "lobe" akin to functional lobes seen in neural fMRI images. We quantify the spatial locality of these lobes with multiple metrics and find that clusters of co-occurring features, at coarse enough scale, also cluster together spatially far more than one would expect if feature geometry were random. 3) The "galaxy" scale large-scale structure of the feature point cloud is not isotropic, but instead has a power law of eigenvalues with steepest slope in middle layers. We also quantify how the clustering entropy depends on the layer.

Spine-related diseases have high morbidity and cause a huge burden of social cost. Spine imaging is an essential tool for noninvasively visualizing and assessing spinal pathology. Segmenting vertebrae in computed tomography (CT) images is the basis of quantitative medical image analysis for clinical diagnosis and surgery planning of spine diseases. Current publicly available annotated datasets on spinal vertebrae are small in size. Due to the lack of a large-scale annotated spine image dataset, the mainstream deep learning-based segmentation methods, which are data-driven, are heavily restricted. In this paper, we introduce a large-scale spine CT dataset, called CTSpine1K, curated from multiple sources for vertebra segmentation, which contains 1,005 CT volumes with over 11,100 labeled vertebrae belonging to different spinal conditions. Based on this dataset, we conduct several spinal vertebrae segmentation experiments to set the first benchmark. We believe that this large-scale dataset will facilitate further research in many spine-related image analysis tasks, including but not limited to vertebrae segmentation, labeling, 3D spine reconstruction from biplanar radiographs, image super-resolution, and enhancement.

Curvilinear object segmentation plays a crucial role across various applications, yet datasets in this domain often suffer from small scale due to the high costs associated with data acquisition and annotation. To address these challenges, this paper introduces a novel approach for expanding curvilinear object segmentation datasets, focusing on enhancing the informativeness of generated data and the consistency between semantic maps and generated images. Our method enriches synthetic data informativeness by generating curvilinear objects through their multiple textual features. By combining textual features from each sample in original dataset, we obtain synthetic images that beyond the original dataset's distribution. This initiative necessitated the creation of the Curvilinear Object Segmentation based on Text Generation (COSTG) dataset. Designed to surpass the limitations of conventional datasets, COSTG incorporates not only standard semantic maps but also some textual descriptions of curvilinear object features. To ensure consistency between synthetic semantic maps and images, we introduce the Semantic Consistency Preserving ControlNet (SCP ControlNet). This involves an adaptation of ControlNet with Spatially-Adaptive Normalization (SPADE), allowing it to preserve semantic information that would typically be washed away in normalization layers. This modification facilitates more accurate semantic image synthesis. Experimental results demonstrate the efficacy of our approach across three types of curvilinear objects (angiography, crack and retina) and six public datasets (CHUAC, XCAD, DCA1, DRIVE, CHASEDB1 and Crack500). The synthetic data generated by our method not only expand the dataset, but also effectively improves the performance of other curvilinear object segmentation models. Source code and dataset are available at https://github.com/tanlei0/COSTG.

Attention Deficit Hyperactive Disorder (ADHD) is a common behavioral problem affecting children. In this work, we investigate the automatic classification of ADHD subjects using the resting state Functional Magnetic Resonance Imaging (fMRI) sequences of the brain. We show that the brain can be modeled as a functional network, and certain properties of the networks differ in ADHD subjects from control subjects. We compute the pairwise correlation of brain voxels' activity over the time frame of the experimental protocol which helps to model the function of a brain as a network. Different network features are computed for each of the voxels constructing the network. The concatenation of the network features of all the voxels in a brain serves as the feature vector. Feature vectors from a set of subjects are then used to train a PCA-LDA (principal component analysis-linear discriminant analysis) based classifier. We hypothesized that ADHD-related differences lie in some specific regions of the brain and using features only from those regions is sufficient to discriminate ADHD and control subjects. We propose a method to create a brain mask that includes the useful regions only and demonstrate that using the feature from the masked regions improves classification accuracy on the test data set. We train our classifier with 776 subjects and test on 171 subjects provided by The Neuro Bureau for the ADHD-200 challenge. We demonstrate the utility of graph-motif features, specifically the maps that represent the frequency of participation of voxels in network cycles of length 3. The best classification performance (69.59%) is achieved using 3-cycle map features with masking. Our proposed approach holds promise in being able to diagnose and understand the disorder.

In this paper we introduce a novel family of attributed graphs for the purpose of shape discrimination. Our graphs typically arise from variations on the Mapper graph construction, which is an approximation of the Reeb graph for point cloud data. Our attributions enrich these constructions with (persistent) homology in ways that are provably stable, thereby recording extra topological information that is typically lost in these graph constructions. We provide experiments which illustrate the use of these invariants for shape representation and classification. In particular, we obtain competitive shape classification results when using our topologically attributed graphs as inputs to a simple graph neural network classifier.

Nucleus segmentation is a challenging task due to the crowded distribution and blurry boundaries of nuclei. Recent approaches represent nuclei by means of polygons to differentiate between touching and overlapping nuclei and have accordingly achieved promising performance. Each polygon is represented by a set of centroid-to-boundary distances, which are in turn predicted by features of the centroid pixel for a single nucleus. However, using the centroid pixel alone does not provide sufficient contextual information for robust prediction and thus degrades the segmentation accuracy. To handle this problem, we propose a Context-aware Polygon Proposal Network (CPP-Net) for nucleus segmentation. First, we sample a point set rather than one single pixel within each cell for distance prediction. This strategy substantially enhances contextual information and thereby improves the robustness of the prediction. Second, we propose a Confidence-based Weighting Module, which adaptively fuses the predictions from the sampled point set. Third, we introduce a novel Shape-Aware Perceptual (SAP) loss that constrains the shape of the predicted polygons. Here, the SAP loss is based on an additional network that is pre-trained by means of mapping the centroid probability map and the pixel-to-boundary distance maps to a different nucleus representation. Extensive experiments justify the effectiveness of each component in the proposed CPP-Net. Finally, CPP-Net is found to achieve state-of-the-art performance on three publicly available databases, namely DSB2018, BBBC06, and PanNuke. Code of this paper is available at \url{https://github.com/csccsccsccsc/cpp-net

Understanding the property of neural populations (or voxels) in the human brain can advance our comprehension of human perceptual and cognitive processing capabilities and contribute to developing brain-inspired computer models. Recent encoding models using deep neural networks (DNNs) have successfully predicted voxel-wise activity. However, interpreting the properties that explain voxel responses remains challenging because of the black-box nature of DNNs. As a solution, we propose LLM-assisted Visual Cortex Captioning (LaVCa), a data-driven approach that uses large language models (LLMs) to generate natural-language captions for images to which voxels are selective. By applying LaVCa for image-evoked brain activity, we demonstrate that LaVCa generates captions that describe voxel selectivity more accurately than the previously proposed method. Furthermore, the captions generated by LaVCa quantitatively capture more detailed properties than the existing method at both the inter-voxel and intra-voxel levels. Furthermore, a more detailed analysis of the voxel-specific properties generated by LaVCa reveals fine-grained functional differentiation within regions of interest (ROIs) in the visual cortex and voxels that simultaneously represent multiple distinct concepts. These findings offer profound insights into human visual representations by assigning detailed captions throughout the visual cortex while highlighting the potential of LLM-based methods in understanding brain representations. Please check out our webpage at https://sites.google.com/view/lavca-llm/

CNNs achieve remarkable performance by leveraging deep, over-parametrized architectures, trained on large datasets. However, they have limited generalization ability to data outside the training domain, and a lack of robustness to noise and adversarial attacks. By building better inductive biases, we can improve robustness and also obtain smaller networks that are more memory and computationally efficient. While standard CNNs use matrix computations, we study tensor layers that involve higher-order computations and provide better inductive bias. Specifically, we impose low-rank tensor structures on the weights of tensor regression layers to obtain compact networks, and propose tensor dropout, a randomization in the tensor rank for robustness. We show that our approach outperforms other methods for large-scale image classification on ImageNet and CIFAR-100. We establish a new state-of-the-art accuracy for phenotypic trait prediction on the largest dataset of brain MRI, the UK Biobank brain MRI dataset, where multi-linear structure is paramount. In all cases, we demonstrate superior performance and significantly improved robustness, both to noisy inputs and to adversarial attacks. We rigorously validate the theoretical validity of our approach by establishing the link between our randomized decomposition and non-linear dropout.

Recent research in medical image analysis with deep learning almost exclusively focuses on grid- or voxel-based data representations. We challenge this common choice by introducing MedFuncta, a modality-agnostic continuous data representation based on neural fields. We demonstrate how to scale neural fields from single instances to large datasets by exploiting redundancy in medical signals and by applying an efficient meta-learning approach with a context reduction scheme. We further address the spectral bias in commonly used SIREN activations, by introducing an omega_0-schedule, improving reconstruction quality and convergence speed. We validate our proposed approach on a large variety of medical signals of different dimensions and modalities (1D: ECG; 2D: Chest X-ray, Retinal OCT, Fundus Camera, Dermatoscope, Colon Histopathology, Cell Microscopy; 3D: Brain MRI, Lung CT) and successfully demonstrate that we can solve relevant downstream tasks on these representations. We additionally release a large-scale dataset of > 550k annotated neural fields to promote research in this direction.

We propose a novel method for discovering shape regions that strongly correlate with user-prescribed tags. For example, given a collection of chairs tagged as either "has armrest" or "lacks armrest", our system correctly highlights the armrest regions as the main distinctive parts between the two chair types. To obtain point-wise predictions from shape-wise tags we develop a novel neural network architecture that is trained with tag classification loss, but is designed to rely on segmentation to predict the tag. Our network is inspired by U-Net, but we replicate shallow U structures several times with new skip connections and pooling layers, and call the resulting architecture "WU-Net". We test our method on segmentation benchmarks and show that even with weak supervision of whole shape tags, our method can infer meaningful semantic regions, without ever observing shape segmentations. Further, once trained, the model can process shapes for which the tag is entirely unknown. As a bonus, our architecture is directly operational under full supervision and performs strongly on standard benchmarks. We validate our method through experiments with many variant architectures and prior baselines, and demonstrate several applications.

Invasive brain-computer interfaces have garnered significant attention due to their high performance. The current intracranial stereoElectroEncephaloGraphy (sEEG) foundation models typically build univariate representations based on a single channel. Some of them further use Transformer to model the relationship among channels. However, due to the locality and specificity of brain computation, their performance on more difficult tasks, e.g., speech decoding, which demands intricate processing in specific brain regions, is yet to be fully investigated. We hypothesize that building multi-variate representations within certain brain regions can better capture the specific neural processing. To explore this hypothesis, we collect a well-annotated Chinese word-reading sEEG dataset, targeting language-related brain networks, over 12 subjects. Leveraging this benchmark dataset, we developed the Du-IN model that can extract contextual embeddings from specific brain regions through discrete codebook-guided mask modeling. Our model achieves SOTA performance on the downstream 61-word classification task, surpassing all baseline models. Model comparison and ablation analysis reveal that our design choices, including (i) multi-variate representation by fusing channels in vSMC and STG regions and (ii) self-supervision by discrete codebook-guided mask modeling, significantly contribute to these performances. Collectively, our approach, inspired by neuroscience findings, capitalizing on multi-variate neural representation from specific brain regions, is suitable for invasive brain modeling. It marks a promising neuro-inspired AI approach in BCI.

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.

Convolutional Neural Networks (CNNs) are commonly thought to recognise objects by learning increasingly complex representations of object shapes. Some recent studies suggest a more important role of image textures. We here put these conflicting hypotheses to a quantitative test by evaluating CNNs and human observers on images with a texture-shape cue conflict. We show that ImageNet-trained CNNs are strongly biased towards recognising textures rather than shapes, which is in stark contrast to human behavioural evidence and reveals fundamentally different classification strategies. We then demonstrate that the same standard architecture (ResNet-50) that learns a texture-based representation on ImageNet is able to learn a shape-based representation instead when trained on "Stylized-ImageNet", a stylized version of ImageNet. This provides a much better fit for human behavioural performance in our well-controlled psychophysical lab setting (nine experiments totalling 48,560 psychophysical trials across 97 observers) and comes with a number of unexpected emergent benefits such as improved object detection performance and previously unseen robustness towards a wide range of image distortions, highlighting advantages of a shape-based representation.

3D shape is a crucial but heavily underutilized cue in today's computer vision systems, mostly due to the lack of a good generic shape representation. With the recent availability of inexpensive 2.5D depth sensors (e.g. Microsoft Kinect), it is becoming increasingly important to have a powerful 3D shape representation in the loop. Apart from category recognition, recovering full 3D shapes from view-based 2.5D depth maps is also a critical part of visual understanding. To this end, we propose to represent a geometric 3D shape as a probability distribution of binary variables on a 3D voxel grid, using a Convolutional Deep Belief Network. Our model, 3D ShapeNets, learns the distribution of complex 3D shapes across different object categories and arbitrary poses from raw CAD data, and discovers hierarchical compositional part representations automatically. It naturally supports joint object recognition and shape completion from 2.5D depth maps, and it enables active object recognition through view planning. To train our 3D deep learning model, we construct ModelNet -- a large-scale 3D CAD model dataset. Extensive experiments show that our 3D deep representation enables significant performance improvement over the-state-of-the-arts in a variety of tasks.

Neuroimage processing tasks like segmentation, reconstruction, and registration are central to the study of neuroscience. Robust deep learning strategies and architectures used to solve these tasks are often similar. Yet, when presented with a new task or a dataset with different visual characteristics, practitioners most often need to train a new model, or fine-tune an existing one. This is a time-consuming process that poses a substantial barrier for the thousands of neuroscientists and clinical researchers who often lack the resources or machine-learning expertise to train deep learning models. In practice, this leads to a lack of adoption of deep learning, and neuroscience tools being dominated by classical frameworks. We introduce Neuralizer, a single model that generalizes to previously unseen neuroimaging tasks and modalities without the need for re-training or fine-tuning. Tasks do not have to be known a priori, and generalization happens in a single forward pass during inference. The model can solve processing tasks across multiple image modalities, acquisition methods, and datasets, and generalize to tasks and modalities it has not been trained on. Our experiments on coronal slices show that when few annotated subjects are available, our multi-task network outperforms task-specific baselines without training on the task.

In this study, we present a technique that spans multi-scale views (global scale -- meaning brain network-level and local scale -- examining each individual ROI that constitutes the network) applied to resting-state fMRI volumes. Deep learning based classification is utilized in understanding neurodegeneration. The novelty of the proposed approach lies in utilizing two extreme scales of analysis. One branch considers the entire network within graph-analysis framework. Concurrently, the second branch scrutinizes each ROI within a network independently, focusing on evolution of dynamics. For each subject, graph-based approach employs partial correlation to profile the subject in a single graph where each ROI is a node, providing insights into differences in levels of participation. In contrast, non-linear analysis employs recurrence plots to profile a subject as a multichannel 2D image, revealing distinctions in underlying dynamics. The proposed approach is employed for classification of a cohort of 50 healthy control (HC) and 50 Mild Cognitive Impairment (MCI), sourced from ADNI dataset. Results point to: (1) reduced activity in ROIs such as PCC in MCI (2) greater activity in occipital in MCI, which is not seen in HC (3) when analysed for dynamics, all ROIs in MCI show greater predictability in time-series.

Food computing is both important and challenging in computer vision (CV). It significantly contributes to the development of CV algorithms due to its frequent presence in datasets across various applications, ranging from classification and instance segmentation to 3D reconstruction. The polymorphic shapes and textures of food, coupled with high variation in forms and vast multimodal information, including language descriptions and nutritional data, make food computing a complex and demanding task for modern CV algorithms. 3D food modeling is a new frontier for addressing food-related problems, due to its inherent capability to deal with random camera views and its straightforward representation for calculating food portion size. However, the primary hurdle in the development of algorithms for food object analysis is the lack of nutrition values in existing 3D datasets. Moreover, in the broader field of 3D research, there is a critical need for domain-specific test datasets. To bridge the gap between general 3D vision and food computing research, we propose MetaFood3D. This dataset consists of 637 meticulously labeled 3D food objects across 108 categories, featuring detailed nutrition information, weight, and food codes linked to a comprehensive nutrition database. The dataset emphasizes intra-class diversity and includes rich modalities such as textured mesh files, RGB-D videos, and segmentation masks. Experimental results demonstrate our dataset's significant potential for improving algorithm performance, highlight the challenging gap between video captures and 3D scanned data, and show the strength of the MetaFood3D dataset in high-quality data generation, simulation, and augmentation.

Resection and whole brain radiotherapy (WBRT) are the standards of care for the treatment of patients with brain metastases (BM) but are often associated with cognitive side effects. Stereotactic radiosurgery (SRS) involves a more targeted treatment approach and has been shown to avoid the side effects associated with WBRT. However, SRS requires precise identification and delineation of BM. While many AI algorithms have been developed for this purpose, their clinical adoption has been limited due to poor model performance in the clinical setting. Major reasons for non-generalizable algorithms are the limitations in the datasets used for training the AI network. The purpose of this study was to create a large, heterogenous, annotated BM dataset for training and validation of AI models to improve generalizability. We present a BM dataset of 200 patients with pretreatment T1, T1 post-contrast, T2, and FLAIR MR images. The dataset includes contrast-enhancing and necrotic 3D segmentations on T1 post-contrast and whole tumor (including peritumoral edema) 3D segmentations on FLAIR. Our dataset contains 975 contrast-enhancing lesions, many of which are sub centimeter, along with clinical and imaging feature information. We used a streamlined approach to database-building leveraging a PACS-integrated segmentation workflow.

Learning image representations using synthetic data allows training neural networks without some of the concerns associated with real images, such as privacy and bias. Existing work focuses on a handful of curated generative processes which require expert knowledge to design, making it hard to scale up. To overcome this, we propose training with a large dataset of twenty-one thousand programs, each one generating a diverse set of synthetic images. These programs are short code snippets, which are easy to modify and fast to execute using OpenGL. The proposed dataset can be used for both supervised and unsupervised representation learning, and reduces the gap between pre-training with real and procedurally generated images by 38%.

Existing volumetric medical image segmentation models are typically task-specific, excelling at specific target but struggling to generalize across anatomical structures or modalities. This limitation restricts their broader clinical use. In this paper, we introduce SAM-Med3D for general-purpose segmentation on volumetric medical images. Given only a few 3D prompt points, SAM-Med3D can accurately segment diverse anatomical structures and lesions across various modalities. To achieve this, we gather and process a large-scale 3D medical image dataset, SA-Med3D-140K, from a blend of public sources and licensed private datasets. This dataset includes 22K 3D images and 143K corresponding 3D masks. Then SAM-Med3D, a promptable segmentation model characterized by the fully learnable 3D structure, is trained on this dataset using a two-stage procedure and exhibits impressive performance on both seen and unseen segmentation targets. We comprehensively evaluate SAM-Med3D on 16 datasets covering diverse medical scenarios, including different anatomical structures, modalities, targets, and zero-shot transferability to new/unseen tasks. The evaluation shows the efficiency and efficacy of SAM-Med3D, as well as its promising application to diverse downstream tasks as a pre-trained model. Our approach demonstrates that substantial medical resources can be utilized to develop a general-purpose medical AI for various potential applications. Our dataset, code, and models are available at https://github.com/uni-medical/SAM-Med3D.

Reconstructing 3D shapes from planar cross-sections is a challenge inspired by downstream applications like medical imaging and geographic informatics. The input is an in/out indicator function fully defined on a sparse collection of planes in space, and the output is an interpolation of the indicator function to the entire volume. Previous works addressing this sparse and ill-posed problem either produce low quality results, or rely on additional priors such as target topology, appearance information, or input normal directions. In this paper, we present OReX, a method for 3D shape reconstruction from slices alone, featuring a Neural Field as the interpolation prior. A modest neural network is trained on the input planes to return an inside/outside estimate for a given 3D coordinate, yielding a powerful prior that induces smoothness and self-similarities. The main challenge for this approach is high-frequency details, as the neural prior is overly smoothing. To alleviate this, we offer an iterative estimation architecture and a hierarchical input sampling scheme that encourage coarse-to-fine training, allowing the training process to focus on high frequencies at later stages. In addition, we identify and analyze a ripple-like effect stemming from the mesh extraction step. We mitigate it by regularizing the spatial gradients of the indicator function around input in/out boundaries during network training, tackling the problem at the root. Through extensive qualitative and quantitative experimentation, we demonstrate our method is robust, accurate, and scales well with the size of the input. We report state-of-the-art results compared to previous approaches and recent potential solutions, and demonstrate the benefit of our individual contributions through analysis and ablation studies.

Autoregressive next-token prediction is a standard pretraining method for large-scale language models, but its application to vision tasks is hindered by the non-sequential nature of image data, leading to cumulative errors. Most vision models employ masked autoencoder (MAE) based pretraining, which faces scalability issues. To address these challenges, we introduce TokenUnify, a novel pretraining method that integrates random token prediction, next-token prediction, and next-all token prediction. We provide theoretical evidence demonstrating that TokenUnify mitigates cumulative errors in visual autoregression. Cooperated with TokenUnify, we have assembled a large-scale electron microscopy (EM) image dataset with ultra-high resolution, ideal for creating spatially correlated long sequences. This dataset includes over 120 million annotated voxels, making it the largest neuron segmentation dataset to date and providing a unified benchmark for experimental validation. Leveraging the Mamba network inherently suited for long-sequence modeling on this dataset, TokenUnify not only reduces the computational complexity but also leads to a significant 45\% improvement in segmentation performance on downstream EM neuron segmentation tasks compared to existing methods. Furthermore, TokenUnify demonstrates superior scalability over MAE and traditional autoregressive methods, effectively bridging the gap between pretraining strategies for language and vision models. Code is available at https://github.com/ydchen0806/TokenUnify.

Multi-subject fMRI studies are challenging due to the high variability of both brain anatomy and functional brain topographies across participants. An effective way of aggregating multi-subject fMRI data is to extract a shared representation that filters out unwanted variability among subjects. Some recent work has implemented probabilistic models to extract a shared representation in task fMRI. In the present work, we improve upon these models by incorporating temporal information in the common latent structures. We introduce a new model, Shared Gaussian Process Factor Analysis (S-GPFA), that discovers shared latent trajectories and subject-specific functional topographies, while modelling temporal correlation in fMRI data. We demonstrate the efficacy of our model in revealing ground truth latent structures using simulated data, and replicate experimental performance of time-segment matching and inter-subject similarity on the publicly available Raider and Sherlock datasets. We further test the utility of our model by analyzing its learned model parameters in the large multi-site SPINS dataset, on a social cognition task from participants with and without schizophrenia.

In daily life, humans utilize hands to manipulate objects. Modeling the shape of objects that are manipulated by the hand is essential for AI to comprehend daily tasks and to learn manipulation skills. However, previous approaches have encountered difficulties in reconstructing the precise shapes of hand-held objects, primarily owing to a deficiency in prior shape knowledge and inadequate data for training. As illustrated, given a particular type of tool, such as a mug, despite its infinite variations in shape and appearance, humans have a limited number of 'effective' modes and poses for its manipulation. This can be attributed to the fact that humans have mastered the shape prior of the 'mug' category, and can quickly establish the corresponding relations between different mug instances and the prior, such as where the rim and handle are located. In light of this, we propose a new method, CHORD, for Category-level Hand-held Object Reconstruction via shape Deformation. CHORD deforms a categorical shape prior for reconstructing the intra-class objects. To ensure accurate reconstruction, we empower CHORD with three types of awareness: appearance, shape, and interacting pose. In addition, we have constructed a new dataset, COMIC, of category-level hand-object interaction. COMIC contains a rich array of object instances, materials, hand interactions, and viewing directions. Extensive evaluation shows that CHORD outperforms state-of-the-art approaches in both quantitative and qualitative measures. Code, model, and datasets are available at https://kailinli.github.io/CHORD.

Curating a large scale medical imaging dataset for machine learning applications is both time consuming and expensive. Balancing the workload between model development, data collection and annotations is difficult for machine learning practitioners, especially under time constraints. Causal analysis is often used in medicine and economics to gain insights about the effects of actions and policies. In this paper we explore the effect of dataset interventions on the output of image classification models. Through a causal approach we investigate the effects of the quantity and type of data we need to incorporate in a dataset to achieve better performance for specific subtasks. The main goal of this paper is to highlight the potential of causal analysis as a tool for resource optimization for developing medical imaging ML applications. We explore this concept with a synthetic dataset and an exemplary use-case for Diabetic Retinopathy image analysis.

Deep generative models of 3D shapes have received a great deal of research interest. Yet, almost all of them generate discrete shape representations, such as voxels, point clouds, and polygon meshes. We present the first 3D generative model for a drastically different shape representation --- describing a shape as a sequence of computer-aided design (CAD) operations. Unlike meshes and point clouds, CAD models encode the user creation process of 3D shapes, widely used in numerous industrial and engineering design tasks. However, the sequential and irregular structure of CAD operations poses significant challenges for existing 3D generative models. Drawing an analogy between CAD operations and natural language, we propose a CAD generative network based on the Transformer. We demonstrate the performance of our model for both shape autoencoding and random shape generation. To train our network, we create a new CAD dataset consisting of 178,238 models and their CAD construction sequences. We have made this dataset publicly available to promote future research on this topic.

We introduce an unsupervised feature learning approach that embeds 3D shape information into a single-view image representation. The main idea is a self-supervised training objective that, given only a single 2D image, requires all unseen views of the object to be predictable from learned features. We implement this idea as an encoder-decoder convolutional neural network. The network maps an input image of an unknown category and unknown viewpoint to a latent space, from which a deconvolutional decoder can best "lift" the image to its complete viewgrid showing the object from all viewing angles. Our class-agnostic training procedure encourages the representation to capture fundamental shape primitives and semantic regularities in a data-driven manner---without manual semantic labels. Our results on two widely-used shape datasets show 1) our approach successfully learns to perform "mental rotation" even for objects unseen during training, and 2) the learned latent space is a powerful representation for object recognition, outperforming several existing unsupervised feature learning methods.

Neural decoding, the process of understanding how brain activity corresponds to different stimuli, has been a primary objective in cognitive sciences. Over the past three decades, advancements in functional Magnetic Resonance Imaging and machine learning have greatly improved our ability to map visual stimuli to brain activity, especially in the visual cortex. Concurrently, research has expanded into decoding more complex processes like language and memory across the whole brain, utilizing techniques to handle greater variability and improve signal accuracy. We argue that "seeing" involves more than just mapping visual stimuli onto the visual cortex; it engages the entire brain, as various emotions and cognitive states can emerge from observing different scenes. In this paper, we develop algorithms to enhance our understanding of visual processes by incorporating whole-brain activation maps while individuals are exposed to visual stimuli. We utilize large-scale fMRI encoders and Image generative models pre-trained on large public datasets, which are then fine-tuned through Image-fMRI contrastive learning. Our models hence can decode visual experience across the entire cerebral cortex, surpassing the traditional confines of the visual cortex. We first compare our method with state-of-the-art approaches to decoding visual processing and show improved predictive semantic accuracy by 43%. A network ablation analysis suggests that beyond the visual cortex, the default mode network contributes most to decoding stimuli, in line with the proposed role of this network in sense-making and semantic processing. Additionally, we implemented zero-shot imagination decoding on an extra validation dataset, achieving a p-value of 0.0206 for mapping the reconstructed images and ground-truth text stimuli, which substantiates the model's capability to capture semantic meanings across various scenarios.

We present a new challenging dataset, CPPE - 5 (Medical Personal Protective Equipment), with the goal to allow the study of subordinate categorization of medical personal protective equipments, which is not possible with other popular data sets that focus on broad-level categories (such as PASCAL VOC, ImageNet, Microsoft COCO, OpenImages, etc). To make it easy for models trained on this dataset to be used in practical scenarios in complex scenes, our dataset mainly contains images that show complex scenes with several objects in each scene in their natural context. The image collection for this dataset focuses on: obtaining as many non-iconic images as possible and making sure all the images are real-life images, unlike other existing datasets in this area. Our dataset includes 5 object categories (coveralls, face shields, gloves, masks, and goggles), and each image is annotated with a set of bounding boxes and positive labels. We present a detailed analysis of the dataset in comparison to other popular broad category datasets as well as datasets focusing on personal protective equipments, we also find that at present there exist no such publicly available datasets. Finally, we also analyze performance and compare model complexities on baseline and state-of-the-art models for bounding box results. Our code, data, and trained models are available at https://git.io/cppe5-dataset.

3D Gaussian Splatting (3DGS) has become the de facto method of 3D representation in many vision tasks. This calls for the 3D understanding directly in this representation space. To facilitate the research in this direction, we first build a large-scale dataset of 3DGS using the commonly used ShapeNet and ModelNet datasets. Our dataset ShapeSplat consists of 65K objects from 87 unique categories, whose labels are in accordance with the respective datasets. The creation of this dataset utilized the compute equivalent of 2 GPU years on a TITAN XP GPU. We utilize our dataset for unsupervised pretraining and supervised finetuning for classification and segmentation tasks. To this end, we introduce \textit{Gaussian-MAE}, which highlights the unique benefits of representation learning from Gaussian parameters. Through exhaustive experiments, we provide several valuable insights. In particular, we show that (1) the distribution of the optimized GS centroids significantly differs from the uniformly sampled point cloud (used for initialization) counterpart; (2) this change in distribution results in degradation in classification but improvement in segmentation tasks when using only the centroids; (3) to leverage additional Gaussian parameters, we propose Gaussian feature grouping in a normalized feature space, along with splats pooling layer, offering a tailored solution to effectively group and embed similar Gaussians, which leads to notable improvement in finetuning tasks.

The human brain is a complex, dynamic network, which is commonly studied using functional magnetic resonance imaging (fMRI) and modeled as network of Regions of interest (ROIs) for understanding various brain functions. Recent studies utilize deep learning approaches to learn the brain network representation based on functional connectivity (FC) profile, broadly falling into two main categories. The Fixed-FC approaches, utilizing the FC profile which represents the linear temporal relation within the brain network, are limited by failing to capture informative brain temporal dynamics. On the other hand, the Dynamic-FC approaches, modeling the evolving FC profile over time, often exhibit less satisfactory performance due to challenges in handling the inherent noisy nature of fMRI data. To address these challenges, we propose Brain Masked Auto-Encoder (BrainMAE) for learning representations directly from fMRI time-series data. Our approach incorporates two essential components: a region-aware graph attention mechanism designed to capture the relationships between different brain ROIs, and a novel self-supervised masked autoencoding framework for effective model pre-training. These components enable the model to capture rich temporal dynamics of brain activity while maintaining resilience to inherent noise in fMRI data. Our experiments demonstrate that BrainMAE consistently outperforms established baseline methods by significant margins in four distinct downstream tasks. Finally, leveraging the model's inherent interpretability, our analysis of model-generated representations reveals findings that resonate with ongoing research in the field of neuroscience.

The integration of neural-network-based systems into clinical practice is limited by challenges related to domain generalization and robustness. The computer vision community established benchmarks such as ImageNet-C as a fundamental prerequisite to measure progress towards those challenges. Similar datasets are largely absent in the medical imaging community which lacks a comprehensive benchmark that spans across imaging modalities and applications. To address this gap, we create and open-source MedMNIST-C, a benchmark dataset based on the MedMNIST+ collection covering 12 datasets and 9 imaging modalities. We simulate task and modality-specific image corruptions of varying severity to comprehensively evaluate the robustness of established algorithms against real-world artifacts and distribution shifts. We further provide quantitative evidence that our simple-to-use artificial corruptions allow for highly performant, lightweight data augmentation to enhance model robustness. Unlike traditional, generic augmentation strategies, our approach leverages domain knowledge, exhibiting significantly higher robustness when compared to widely adopted methods. By introducing MedMNIST-C and open-sourcing the corresponding library allowing for targeted data augmentations, we contribute to the development of increasingly robust methods tailored to the challenges of medical imaging. The code is available at https://github.com/francescodisalvo05/medmnistc-api .

Significant progress has been made in training large generative models for natural language and images. Yet, the advancement of 3D generative models is hindered by their substantial resource demands for training, along with inefficient, non-compact, and less expressive representations. This paper introduces Make-A-Shape, a new 3D generative model designed for efficient training on a vast scale, capable of utilizing 10 millions publicly-available shapes. Technical-wise, we first innovate a wavelet-tree representation to compactly encode shapes by formulating the subband coefficient filtering scheme to efficiently exploit coefficient relations. We then make the representation generatable by a diffusion model by devising the subband coefficients packing scheme to layout the representation in a low-resolution grid. Further, we derive the subband adaptive training strategy to train our model to effectively learn to generate coarse and detail wavelet coefficients. Last, we extend our framework to be controlled by additional input conditions to enable it to generate shapes from assorted modalities, e.g., single/multi-view images, point clouds, and low-resolution voxels. In our extensive set of experiments, we demonstrate various applications, such as unconditional generation, shape completion, and conditional generation on a wide range of modalities. Our approach not only surpasses the state of the art in delivering high-quality results but also efficiently generates shapes within a few seconds, often achieving this in just 2 seconds for most conditions.

While recent advancements in vision-language models have revolutionized multi-modal understanding, it remains unclear whether they possess the capabilities of comprehending the generated images. Compared to real data, synthetic images exhibit a higher degree of diversity in both content and style, for which there are significant difficulties for the models to fully apprehend. To this end, we present a large-scale dataset, JourneyDB, for multi-modal visual understanding in generative images. Our curated dataset covers 4 million diverse and high-quality generated images paired with the text prompts used to produce them. We further design 4 benchmarks to quantify the performance of generated image understanding in terms of both content and style interpretation. These benchmarks include prompt inversion, style retrieval, image captioning and visual question answering. Lastly, we assess the performance of current state-of-the-art multi-modal models when applied to JourneyDB, and provide an in-depth analysis of their strengths and limitations in generated content understanding. We hope the proposed dataset and benchmarks will facilitate the research in the field of generative content understanding. The dataset will be available on https://journeydb.github.io.

Deep-learning-based brain magnetic resonance imaging (MRI) reconstruction methods have the potential to accelerate the MRI acquisition process. Nevertheless, the scientific community lacks appropriate benchmarks to assess MRI reconstruction quality of high-resolution brain images, and evaluate how these proposed algorithms will behave in the presence of small, but expected data distribution shifts. The Multi-Coil Magnetic Resonance Image (MC-MRI) Reconstruction Challenge provides a benchmark that aims at addressing these issues, using a large dataset of high-resolution, three-dimensional, T1-weighted MRI scans. The challenge has two primary goals: 1) to compare different MRI reconstruction models on this dataset and 2) to assess the generalizability of these models to data acquired with a different number of receiver coils. In this paper, we describe the challenge experimental design, and summarize the results of a set of baseline and state of the art brain MRI reconstruction models. We provide relevant comparative information on the current MRI reconstruction state-of-the-art and highlight the challenges of obtaining generalizable models that are required prior to broader clinical adoption. The MC-MRI benchmark data, evaluation code and current challenge leaderboard are publicly available. They provide an objective performance assessment for future developments in the field of brain MRI reconstruction.

Deep learning has demonstrated remarkable success in medical image segmentation and computer-aided diagnosis. In particular, numerous advanced methods have achieved state-of-the-art performance in brain tumor segmentation from MRI scans. While recent studies in other medical imaging domains have revealed that integrating textual reports with visual data can enhance segmentation accuracy, the field of brain tumor analysis lacks a comprehensive dataset that combines radiological images with corresponding textual annotations. This limitation has hindered the exploration of multimodal approaches that leverage both imaging and textual data. To bridge this critical gap, we introduce the TextBraTS dataset, the first publicly available volume-level multimodal dataset that contains paired MRI volumes and rich textual annotations, derived from the widely adopted BraTS2020 benchmark. Building upon this novel dataset, we propose a novel baseline framework and sequential cross-attention method for text-guided volumetric medical image segmentation. Through extensive experiments with various text-image fusion strategies and templated text formulations, our approach demonstrates significant improvements in brain tumor segmentation accuracy, offering valuable insights into effective multimodal integration techniques. Our dataset, implementation code, and pre-trained models are publicly available at https://github.com/Jupitern52/TextBraTS.

This paper investigates discrepancies in how neural networks learn from different imaging domains, which are commonly overlooked when adopting computer vision techniques from the domain of natural images to other specialized domains such as medical images. Recent works have found that the generalization error of a trained network typically increases with the intrinsic dimension (d_{data}) of its training set. Yet, the steepness of this relationship varies significantly between medical (radiological) and natural imaging domains, with no existing theoretical explanation. We address this gap in knowledge by establishing and empirically validating a generalization scaling law with respect to d_{data}, and propose that the substantial scaling discrepancy between the two considered domains may be at least partially attributed to the higher intrinsic ``label sharpness'' (K_F) of medical imaging datasets, a metric which we propose. Next, we demonstrate an additional benefit of measuring the label sharpness of a training set: it is negatively correlated with the trained model's adversarial robustness, which notably leads to models for medical images having a substantially higher vulnerability to adversarial attack. Finally, we extend our d_{data} formalism to the related metric of learned representation intrinsic dimension (d_{repr}), derive a generalization scaling law with respect to d_{repr}, and show that d_{data} serves as an upper bound for d_{repr}. Our theoretical results are supported by thorough experiments with six models and eleven natural and medical imaging datasets over a range of training set sizes. Our findings offer insights into the influence of intrinsic dataset properties on generalization, representation learning, and robustness in deep neural networks. Code link: https://github.com/mazurowski-lab/intrinsic-properties

Quantitative susceptibility maps from magnetic resonance images can provide both prognostic and diagnostic information in multiple sclerosis, a neurodegenerative disease characterized by the formation of lesions in white matter brain tissue. In particular, susceptibility maps provide adequate contrast to distinguish between "rim" lesions, surrounded by deposited paramagnetic iron, and "non-rim" lesion types. These paramagnetic rim lesions (PRLs) are an emerging biomarker in multiple sclerosis. Much effort has been devoted to both detection and segmentation of such lesions to monitor longitudinal change. As paramagnetic rim lesions are rare, addressing this problem requires confronting the class imbalance between rim and non-rim lesions. We produce synthetic quantitative susceptibility maps of paramagnetic rim lesions and show that inclusion of such synthetic data improves classifier performance and provide a multi-channel extension to generate accompanying contrasts and probabilistic segmentation maps. We exploit the projection capability of our trained generative network to demonstrate a novel denoising approach that allows us to train on ambiguous rim cases and substantially increase the minority class. We show that both synthetic lesion synthesis and our proposed rim lesion label denoising method best approximate the unseen rim lesion distribution and improve detection in a clinically interpretable manner. We release our code and generated data at https://github.com/agr78/PRLx-GAN upon publication.

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.

Deep-learning models can extract a rich assortment of features from data. Which features a model uses depends not only on predictivity-how reliably a feature indicates train-set labels-but also on availability-how easily the feature can be extracted, or leveraged, from inputs. The literature on shortcut learning has noted examples in which models privilege one feature over another, for example texture over shape and image backgrounds over foreground objects. Here, we test hypotheses about which input properties are more available to a model, and systematically study how predictivity and availability interact to shape models' feature use. We construct a minimal, explicit generative framework for synthesizing classification datasets with two latent features that vary in predictivity and in factors we hypothesize to relate to availability, and quantify a model's shortcut bias-its over-reliance on the shortcut (more available, less predictive) feature at the expense of the core (less available, more predictive) feature. We find that linear models are relatively unbiased, but introducing a single hidden layer with ReLU or Tanh units yields a bias. Our empirical findings are consistent with a theoretical account based on Neural Tangent Kernels. Finally, we study how models used in practice trade off predictivity and availability in naturalistic datasets, discovering availability manipulations which increase models' degree of shortcut bias. Taken together, these findings suggest that the propensity to learn shortcut features is a fundamental characteristic of deep nonlinear architectures warranting systematic study given its role in shaping how models solve tasks.

Image registration is the process of bringing different images into a common coordinate system - a technique widely used in various applications of computer vision, such as remote sensing, image retrieval, and, most commonly, medical imaging. Deep learning based techniques have been applied successfully to tackle various complex medical image processing problems, including medical image registration. Over the years, several image registration techniques have been proposed using deep learning. Deformable image registration techniques such as Voxelmorph have been successful in capturing finer changes and providing smoother deformations. However, Voxelmorph, as well as ICNet and FIRE, do not explicitly encode global dependencies (i.e. the overall anatomical view of the supplied image) and, therefore, cannot track large deformations. In order to tackle the aforementioned problems, this paper extends the Voxelmorph approach in three different ways. To improve the performance in case of small as well as large deformations, supervision of the model at different resolutions has been integrated using a multi-scale UNet. To support the network to learn and encode the minute structural co-relations of the given image-pairs, a self-constructing graph network (SCGNet) has been used as the latent of the multi-scale UNet - which can improve the learning process of the model and help the model to generalise better. And finally, to make the deformations inverse-consistent, cycle consistency loss has been employed. On the task of registration of brain MRIs, the proposed method achieved significant improvements over ANTs and VoxelMorph, obtaining a Dice score of 0.8013 \pm 0.0243 for intramodal and 0.6211 \pm 0.0309 for intermodal, while VoxelMorph achieved 0.7747 \pm 0.0260 and 0.6071 \pm 0.0510, respectively

There is renewed interest in modeling and understanding the nervous system of the nematode Caenorhabditis elegans (C. elegans), as this small model system provides a path to bridge the gap between nervous system structure (connectivity) and function (physiology). However, existing physiology datasets, whether involving passive recording or stimulation, are in distinct formats, and connectome datasets require preprocessing before analysis can commence. Here we compile and homogenize datasets of neural activity and connectivity. Our neural activity dataset is derived from 11 C. elegans neuroimaging experiments, while our connectivity dataset is compiled from 9 connectome annotations based on 3 primary electron microscopy studies and 1 signal propagation study. Physiology datasets, collected under varying protocols, measure calcium fluorescence in labeled subsets of the worm's 300 neurons. Our preprocessing pipeline standardizes these datasets by consistently ordering labeled neurons and resampling traces to a common sampling rate, yielding recordings from approximately 900 worms and 250 uniquely labeled neurons. The connectome datasets, collected from electron microscopy reconstructions, represent the entire nervous system as a graph of connections. Our collection is accessible on HuggingFace, facilitating analysis of the structure-function relationship in biology using modern neural network architectures and enabling cross-lab and cross-animal comparisons.

Vision-Language Models (VLMs) have shown impressive performance in vision tasks, but adapting them to new domains often requires expensive fine-tuning. Prompt tuning techniques, including textual, visual, and multimodal prompting, offer efficient alternatives by leveraging learnable prompts. However, their application to Vision-Language Segmentation Models (VLSMs) and evaluation under significant domain shifts remain unexplored. This work presents an open-source benchmarking framework, TuneVLSeg, to integrate various unimodal and multimodal prompt tuning techniques into VLSMs, making prompt tuning usable for downstream segmentation datasets with any number of classes. TuneVLSeg includes 6 prompt tuning strategies on various prompt depths used in 2 VLSMs totaling of 8 different combinations. We test various prompt tuning on 8 diverse medical datasets, including 3 radiology datasets (breast tumor, echocardiograph, chest X-ray pathologies) and 5 non-radiology datasets (polyp, ulcer, skin cancer), and two natural domain segmentation datasets. Our study found that textual prompt tuning struggles under significant domain shifts, from natural-domain images to medical data. Furthermore, visual prompt tuning, with fewer hyperparameters than multimodal prompt tuning, often achieves performance competitive to multimodal approaches, making it a valuable first attempt. Our work advances the understanding and applicability of different prompt-tuning techniques for robust domain-specific segmentation. The source code is available at https://github.com/naamiinepal/tunevlseg.

Understanding the functional organization of higher visual cortex is a central focus in neuroscience. Past studies have primarily mapped the visual and semantic selectivity of neural populations using hand-selected stimuli, which may potentially bias results towards pre-existing hypotheses of visual cortex functionality. Moving beyond conventional approaches, we introduce a data-driven method that generates natural language descriptions for images predicted to maximally activate individual voxels of interest. Our method -- Semantic Captioning Using Brain Alignments ("BrainSCUBA") -- builds upon the rich embedding space learned by a contrastive vision-language model and utilizes a pre-trained large language model to generate interpretable captions. We validate our method through fine-grained voxel-level captioning across higher-order visual regions. We further perform text-conditioned image synthesis with the captions, and show that our images are semantically coherent and yield high predicted activations. Finally, to demonstrate how our method enables scientific discovery, we perform exploratory investigations on the distribution of "person" representations in the brain, and discover fine-grained semantic selectivity in body-selective areas. Unlike earlier studies that decode text, our method derives voxel-wise captions of semantic selectivity. Our results show that BrainSCUBA is a promising means for understanding functional preferences in the brain, and provides motivation for further hypothesis-driven investigation of visual cortex.

Insufficient data is a long-standing challenge for Brain-Computer Interface (BCI) to build a high-performance deep learning model. Though numerous research groups and institutes collect a multitude of EEG datasets for the same BCI task, sharing EEG data from multiple sites is still challenging due to the heterogeneity of devices. The significance of this challenge cannot be overstated, given the critical role of data diversity in fostering model robustness. However, existing works rarely discuss this issue, predominantly centering their attention on model training within a single dataset, often in the context of inter-subject or inter-session settings. In this work, we propose a hierarchical personalized Federated Learning EEG decoding (FLEEG) framework to surmount this challenge. This innovative framework heralds a new learning paradigm for BCI, enabling datasets with disparate data formats to collaborate in the model training process. Each client is assigned a specific dataset and trains a hierarchical personalized model to manage diverse data formats and facilitate information exchange. Meanwhile, the server coordinates the training procedure to harness knowledge gleaned from all datasets, thus elevating overall performance. The framework has been evaluated in Motor Imagery (MI) classification with nine EEG datasets collected by different devices but implementing the same MI task. Results demonstrate that the proposed frame can boost classification performance up to 16.7% by enabling knowledge sharing between multiple datasets, especially for smaller datasets. Visualization results also indicate that the proposed framework can empower the local models to put a stable focus on task-related areas, yielding better performance. To the best of our knowledge, this is the first end-to-end solution to address this important challenge.

This paper introduces a network for volumetric segmentation that learns from sparsely annotated volumetric images. We outline two attractive use cases of this method: (1) In a semi-automated setup, the user annotates some slices in the volume to be segmented. The network learns from these sparse annotations and provides a dense 3D segmentation. (2) In a fully-automated setup, we assume that a representative, sparsely annotated training set exists. Trained on this data set, the network densely segments new volumetric images. The proposed network extends the previous u-net architecture from Ronneberger et al. by replacing all 2D operations with their 3D counterparts. The implementation performs on-the-fly elastic deformations for efficient data augmentation during training. It is trained end-to-end from scratch, i.e., no pre-trained network is required. We test the performance of the proposed method on a complex, highly variable 3D structure, the Xenopus kidney, and achieve good results for both use cases.

The power of DNNs relies heavily on the quantity and quality of training data. However, collecting and annotating data on a large scale is often expensive and time-consuming. To address this issue, we explore a new task, termed dataset expansion, aimed at expanding a ready-to-use small dataset by automatically creating new labeled samples. To this end, we present a Guided Imagination Framework (GIF) that leverages cutting-edge generative models like DALL-E2 and Stable Diffusion (SD) to "imagine" and create informative new data from the input seed data. Specifically, GIF conducts data imagination by optimizing the latent features of the seed data in the semantically meaningful space of the prior model, resulting in the creation of photo-realistic images with new content. To guide the imagination towards creating informative samples for model training, we introduce two key criteria, i.e., class-maintained information boosting and sample diversity promotion. These criteria are verified to be essential for effective dataset expansion: GIF-SD obtains 13.5% higher model accuracy on natural image datasets than unguided expansion with SD. With these essential criteria, GIF successfully expands small datasets in various scenarios, boosting model accuracy by 36.9% on average over six natural image datasets and by 13.5% on average over three medical datasets. The source code is available at https://github.com/Vanint/DatasetExpansion.

Although the preservation of shape continuity and physiological anatomy is a natural assumption in the segmentation of medical images, it is often neglected by deep learning methods that mostly aim for the statistical modeling of input data as pixels rather than interconnected structures. In biological structures, however, organs are not separate entities; for example, in reality, a severed vessel is an indication of an underlying problem, but traditional segmentation models are not designed to strictly enforce the continuity of anatomy, potentially leading to inaccurate medical diagnoses. To address this issue, we propose a graph-based approach that enforces the continuity and connectivity of anatomical topology in medical images. Our method encodes the continuity of shapes as a graph constraint, ensuring that the network's predictions maintain this continuity. We evaluate our method on two public benchmarks on retinal vessel segmentation, showing significant improvements in connectivity metrics compared to traditional methods while getting better or on-par performance on segmentation metrics.

Over the past decade, predictive modeling of neural responses in the primate visual system has advanced significantly, largely driven by various DNN approaches. These include models optimized directly for visual recognition, cross-modal alignment through contrastive objectives, neural response prediction from scratch, and large language model embeddings.Likewise, different readout mechanisms, ranging from fully linear to spatial-feature factorized methods have been explored for mapping network activations to neural responses. Despite the diversity of these approaches, it remains unclear which method performs best across different visual regions. In this study, we systematically compare these approaches for modeling the human visual system and investigate alternative strategies to improve response predictions. Our findings reveal that for early to mid-level visual areas, response-optimized models with visual inputs offer superior prediction accuracy, while for higher visual regions, embeddings from LLMs based on detailed contextual descriptions of images and task-optimized models pretrained on large vision datasets provide the best fit. Through comparative analysis of these modeling approaches, we identified three distinct regions in the visual cortex: one sensitive primarily to perceptual features of the input that are not captured by linguistic descriptions, another attuned to fine-grained visual details representing semantic information, and a third responsive to abstract, global meanings aligned with linguistic content. We also highlight the critical role of readout mechanisms, proposing a novel scheme that modulates receptive fields and feature maps based on semantic content, resulting in an accuracy boost of 3-23% over existing SOTAs for all models and brain regions. Together, these findings offer key insights into building more precise models of the visual system.

Graph Transformers have recently been successful in various graph representation learning tasks, providing a number of advantages over message-passing Graph Neural Networks. Utilizing Graph Transformers for learning the representation of the brain functional connectivity network is also gaining interest. However, studies to date have underlooked the temporal dynamics of functional connectivity, which fluctuates over time. Here, we propose a method for learning the representation of dynamic functional connectivity with Graph Transformers. Specifically, we define the connectome embedding, which holds the position, structure, and time information of the functional connectivity graph, and use Transformers to learn its representation across time. We perform experiments with over 50,000 resting-state fMRI samples obtained from three datasets, which is the largest number of fMRI data used in studies by far. The experimental results show that our proposed method outperforms other competitive baselines in gender classification and age regression tasks based on the functional connectivity extracted from the fMRI data.

Semantic segmentation of medical images aims to associate a pixel with a label in a medical image without human initialization. The success of semantic segmentation algorithms is contingent on the availability of high-quality imaging data with corresponding labels provided by experts. We sought to create a large collection of annotated medical image datasets of various clinically relevant anatomies available under open source license to facilitate the development of semantic segmentation algorithms. Such a resource would allow: 1) objective assessment of general-purpose segmentation methods through comprehensive benchmarking and 2) open and free access to medical image data for any researcher interested in the problem domain. Through a multi-institutional effort, we generated a large, curated dataset representative of several highly variable segmentation tasks that was used in a crowd-sourced challenge - the Medical Segmentation Decathlon held during the 2018 Medical Image Computing and Computer Aided Interventions Conference in Granada, Spain. Here, we describe these ten labeled image datasets so that these data may be effectively reused by the research community.

We present DAD-3DHeads, a dense and diverse large-scale dataset, and a robust model for 3D Dense Head Alignment in the wild. It contains annotations of over 3.5K landmarks that accurately represent 3D head shape compared to the ground-truth scans. The data-driven model, DAD-3DNet, trained on our dataset, learns shape, expression, and pose parameters, and performs 3D reconstruction of a FLAME mesh. The model also incorporates a landmark prediction branch to take advantage of rich supervision and co-training of multiple related tasks. Experimentally, DAD-3DNet outperforms or is comparable to the state-of-the-art models in (i) 3D Head Pose Estimation on AFLW2000-3D and BIWI, (ii) 3D Face Shape Reconstruction on NoW and Feng, and (iii) 3D Dense Head Alignment and 3D Landmarks Estimation on DAD-3DHeads dataset. Finally, the diversity of DAD-3DHeads in camera angles, facial expressions, and occlusions enables a benchmark to study in-the-wild generalization and robustness to distribution shifts. The dataset webpage is https://p.farm/research/dad-3dheads.

This paper demonstrates how to use generative models trained for image synthesis as tools for visual data mining. Our insight is that since contemporary generative models learn an accurate representation of their training data, we can use them to summarize the data by mining for visual patterns. Concretely, we show that after finetuning conditional diffusion models to synthesize images from a specific dataset, we can use these models to define a typicality measure on that dataset. This measure assesses how typical visual elements are for different data labels, such as geographic location, time stamps, semantic labels, or even the presence of a disease. This analysis-by-synthesis approach to data mining has two key advantages. First, it scales much better than traditional correspondence-based approaches since it does not require explicitly comparing all pairs of visual elements. Second, while most previous works on visual data mining focus on a single dataset, our approach works on diverse datasets in terms of content and scale, including a historical car dataset, a historical face dataset, a large worldwide street-view dataset, and an even larger scene dataset. Furthermore, our approach allows for translating visual elements across class labels and analyzing consistent changes.

Before deployment in the real-world deep neural networks require thorough evaluation of how they handle both knowns, inputs represented in the training data, and unknowns (anomalies). This is especially important for scene understanding tasks with safety critical applications, such as in autonomous driving. Existing datasets allow evaluation of only knowns or unknowns - but not both, which is required to establish "in the wild" suitability of deep neural network models. To bridge this gap, we propose a novel anomaly segmentation dataset, ISSU, that features a diverse set of anomaly inputs from cluttered real-world environments. The dataset is twice larger than existing anomaly segmentation datasets, and provides a training, validation and test set for controlled in-domain evaluation. The test set consists of a static and temporal part, with the latter comprised of videos. The dataset provides annotations for both closed-set (knowns) and anomalies, enabling closed-set and open-set evaluation. The dataset covers diverse conditions, such as domain and cross-sensor shift, illumination variation and allows ablation of anomaly detection methods with respect to these variations. Evaluation results of current state-of-the-art methods confirm the need for improvements especially in domain-generalization, small and large object segmentation.

Large datasets that were made publicly available to the research community over the last 20 years have been a key enabling factor for the advances in deep learning algorithms for NLP or computer vision. These datasets are generally pairs of aligned image / manually annotated metadata, where images are photographs of everyday life. Scholarly and historical content, on the other hand, treat subjects that are not necessarily popular to a general audience, they may not always contain a large number of data points, and new data may be difficult or impossible to collect. Some exceptions do exist, for instance, scientific or health data, but this is not the case for cultural heritage (CH). The poor performance of the best models in computer vision - when tested over artworks - coupled with the lack of extensively annotated datasets for CH, and the fact that artwork images depict objects and actions not captured by photographs, indicate that a CH-specific dataset would be highly valuable for this community. We propose DEArt, at this point primarily an object detection and pose classification dataset meant to be a reference for paintings between the XIIth and the XVIIIth centuries. It contains more than 15000 images, about 80% non-iconic, aligned with manual annotations for the bounding boxes identifying all instances of 69 classes as well as 12 possible poses for boxes identifying human-like objects. Of these, more than 50 classes are CH-specific and thus do not appear in other datasets; these reflect imaginary beings, symbolic entities and other categories related to art. Additionally, existing datasets do not include pose annotations. Our results show that object detectors for the cultural heritage domain can achieve a level of precision comparable to state-of-art models for generic images via transfer learning.

Driven by advances in recording technology, large-scale high-dimensional datasets have emerged across many scientific disciplines. Especially in biology, clustering is often used to gain insights into the structure of such datasets, for instance to understand the organization of different cell types. However, clustering is known to scale poorly to high dimensions, even though the exact impact of dimensionality is unclear as current benchmark datasets are mostly two-dimensional. Here we propose MNIST-Nd, a set of synthetic datasets that share a key property of real-world datasets, namely that individual samples are noisy and clusters do not perfectly separate. MNIST-Nd is obtained by training mixture variational autoencoders with 2 to 64 latent dimensions on MNIST, resulting in six datasets with comparable structure but varying dimensionality. It thus offers the chance to disentangle the impact of dimensionality on clustering. Preliminary common clustering algorithm benchmarks on MNIST-Nd suggest that Leiden is the most robust for growing dimensions.

The process of reconstructing experiences from human brain activity offers a unique lens into how the brain interprets and represents the world. In this paper, we introduce a method for reconstructing music from brain activity, captured using functional magnetic resonance imaging (fMRI). Our approach uses either music retrieval or the MusicLM music generation model conditioned on embeddings derived from fMRI data. The generated music resembles the musical stimuli that human subjects experienced, with respect to semantic properties like genre, instrumentation, and mood. We investigate the relationship between different components of MusicLM and brain activity through a voxel-wise encoding modeling analysis. Furthermore, we discuss which brain regions represent information derived from purely textual descriptions of music stimuli. We provide supplementary material including examples of the reconstructed music at https://google-research.github.io/seanet/brain2music

In visual decision making, high-level features, such as object categories, have a strong influence on choice. However, the impact of low-level features on behavior is less understood partly due to the high correlation between high- and low-level features in the stimuli presented (e.g., objects of the same category are more likely to share low-level features). To disentangle these effects, we propose a method that de-correlates low- and high-level visual properties in a novel set of stimuli. Our method uses two Convolutional Neural Networks (CNNs) as candidate models of the ventral visual stream: the CORnet-S that has high neural predictivity in high-level, IT-like responses and the VGG-16 that has high neural predictivity in low-level responses. Triplets (root, image1, image2) of stimuli are parametrized by the level of low- and high-level similarity of images extracted from the different layers. These stimuli are then used in a decision-making task where participants are tasked to choose the most similar-to-the-root image. We found that different networks show differing abilities to predict the effects of low-versus-high-level similarity: while CORnet-S outperforms VGG-16 in explaining human choices based on high-level similarity, VGG-16 outperforms CORnet-S in explaining human choices based on low-level similarity. Using Brain-Score, we observed that the behavioral prediction abilities of different layers of these networks qualitatively corresponded to their ability to explain neural activity at different levels of the visual hierarchy. In summary, our algorithm for stimulus set generation enables the study of how different representations in the visual stream affect high-level cognitive behaviors.

Human affect recognition has been a significant topic in psychophysics and computer vision. However, the currently published datasets have many limitations. For example, most datasets contain frames that contain only information about facial expressions. Due to the limitations of previous datasets, it is very hard to either understand the mechanisms for affect recognition of humans or generalize well on common cases for computer vision models trained on those datasets. In this work, we introduce a brand new large dataset, the Video-based Emotion and Affect Tracking in Context Dataset (VEATIC), that can conquer the limitations of the previous datasets. VEATIC has 124 video clips from Hollywood movies, documentaries, and home videos with continuous valence and arousal ratings of each frame via real-time annotation. Along with the dataset, we propose a new computer vision task to infer the affect of the selected character via both context and character information in each video frame. Additionally, we propose a simple model to benchmark this new computer vision task. We also compare the performance of the pretrained model using our dataset with other similar datasets. Experiments show the competing results of our pretrained model via VEATIC, indicating the generalizability of VEATIC. Our dataset is available at https://veatic.github.io.

Despite the growing scale of medical Vision-Language datasets, the impact of dataset quality on model performance remains under-explored. We introduce Open-PMC, a high-quality medical dataset from PubMed Central, containing 2.2 million image-text pairs, enriched with image modality annotations, subfigures, and summarized in-text references. Notably, the in-text references provide richer medical context, extending beyond the abstract information typically found in captions. Through extensive experiments, we benchmark Open-PMC against larger datasets across retrieval and zero-shot classification tasks. Our results show that dataset quality-not just size-drives significant performance gains. We complement our benchmark with an in-depth analysis of feature representation. Our findings highlight the crucial role of data curation quality in advancing multimodal medical AI. We release Open-PMC, along with the trained models and our codebase.

3D scene understanding is a long-standing challenge in computer vision and a key component in enabling mixed reality, wearable computing, and embodied AI. Providing a solution to these applications requires a multifaceted approach that covers scene-centric, object-centric, as well as interaction-centric capabilities. While there exist numerous datasets approaching the former two problems, the task of understanding interactable and articulated objects is underrepresented and only partly covered by current works. In this work, we address this shortcoming and introduce (1) an expertly curated dataset in the Universal Scene Description (USD) format, featuring high-quality manual annotations, for instance, segmentation and articulation on 280 indoor scenes; (2) a learning-based model together with a novel baseline capable of predicting part segmentation along with a full specification of motion attributes, including motion type, articulated and interactable parts, and motion parameters; (3) a benchmark serving to compare upcoming methods for the task at hand. Overall, our dataset provides 8 types of annotations - object and part segmentations, motion types, movable and interactable parts, motion parameters, connectivity, and object mass annotations. With its broad and high-quality annotations, the data provides the basis for holistic 3D scene understanding models. All data is provided in the USD format, allowing interoperability and easy integration with downstream tasks. We provide open access to our dataset, benchmark, and method's source code.

We present the 2017 Visual Domain Adaptation (VisDA) dataset and challenge, a large-scale testbed for unsupervised domain adaptation across visual domains. Unsupervised domain adaptation aims to solve the real-world problem of domain shift, where machine learning models trained on one domain must be transferred and adapted to a novel visual domain without additional supervision. The VisDA2017 challenge is focused on the simulation-to-reality shift and has two associated tasks: image classification and image segmentation. The goal in both tracks is to first train a model on simulated, synthetic data in the source domain and then adapt it to perform well on real image data in the unlabeled test domain. Our dataset is the largest one to date for cross-domain object classification, with over 280K images across 12 categories in the combined training, validation and testing domains. The image segmentation dataset is also large-scale with over 30K images across 18 categories in the three domains. We compare VisDA to existing cross-domain adaptation datasets and provide a baseline performance analysis using various domain adaptation models that are currently popular in the field.

We investigate the problem of training generative models on a very sparse collection of 3D models. We use geometrically motivated energies to augment and thus boost a sparse collection of example (training) models. We analyze the Hessian of the as-rigid-as-possible (ARAP) energy to sample from and project to the underlying (local) shape space, and use the augmented dataset to train a variational autoencoder (VAE). We iterate the process of building latent spaces of VAE and augmenting the associated dataset, to progressively reveal a richer and more expressive generative space for creating geometrically and semantically valid samples. Our framework allows us to train generative 3D models even with a small set of good quality 3D models, which are typically hard to curate. We extensively evaluate our method against a set of strong baselines, provide ablation studies and demonstrate application towards establishing shape correspondences. We present multiple examples of interesting and meaningful shape variations even when starting from as few as 3-10 training shapes.

Recent fMRI-to-image approaches mainly focused on associating fMRI signals with specific conditions of pre-trained diffusion models. These approaches, while producing high-quality images, capture only a limited aspect of the complex information in fMRI signals and offer little detailed control over image creation. In contrast, this paper proposes to directly modulate the generation process of diffusion models using fMRI signals. Our approach, NeuroPictor, divides the fMRI-to-image process into three steps: i) fMRI calibrated-encoding, to tackle multi-individual pre-training for a shared latent space to minimize individual difference and enable the subsequent cross-subject training; ii) fMRI-to-image cross-subject pre-training, perceptually learning to guide diffusion model with high- and low-level conditions across different individuals; iii) fMRI-to-image single-subject refining, similar with step ii but focus on adapting to particular individual. NeuroPictor extracts high-level semantic features from fMRI signals that characterizing the visual stimulus and incrementally fine-tunes the diffusion model with a low-level manipulation network to provide precise structural instructions. By training with over 60,000 fMRI-image pairs from various individuals, our model enjoys superior fMRI-to-image decoding capacity, particularly in the within-subject setting, as evidenced in benchmark datasets. Project page: https://jingyanghuo.github.io/neuropictor/.

It is natural to represent objects in terms of their parts. This has the potential to improve the performance of algorithms for object recognition and segmentation but can also help for downstream tasks like activity recognition. Research on part-based models, however, is hindered by the lack of datasets with per-pixel part annotations. This is partly due to the difficulty and high cost of annotating object parts so it has rarely been done except for humans (where there exists a big literature on part-based models). To help address this problem, we propose PartImageNet, a large, high-quality dataset with part segmentation annotations. It consists of 158 classes from ImageNet with approximately 24,000 images. PartImageNet is unique because it offers part-level annotations on a general set of classes including non-rigid, articulated objects, while having an order of magnitude larger size compared to existing part datasets (excluding datasets of humans). It can be utilized for many vision tasks including Object Segmentation, Semantic Part Segmentation, Few-shot Learning and Part Discovery. We conduct comprehensive experiments which study these tasks and set up a set of baselines. The dataset and scripts are released at https://github.com/TACJu/PartImageNet.

We use tools from geometric statistics to analyze the usual estimation procedure of a template shape. This applies to shapes from landmarks, curves, surfaces, images etc. We demonstrate the asymptotic bias of the template shape estimation using the stratified geometry of the shape space. We give a Taylor expansion of the bias with respect to a parameter sigma describing the measurement error on the data. We propose two bootstrap procedures that quantify the bias and correct it, if needed. They are applicable for any type of shape data. We give a rule of thumb to provide intuition on whether the bias has to be corrected. This exhibits the parameters that control the bias' magnitude. We illustrate our results on simulated and real shape data.

Machine learning models will often fail when deployed in an environment with a data distribution that is different than the training distribution. When multiple environments are available during training, many methods exist that learn representations which are invariant across the different distributions, with the hope that these representations will be transportable to unseen domains. In this work, we present a nonparametric strategy for learning invariant representations based on the recently-proposed Nadaraya-Watson (NW) head. The NW head makes a prediction by comparing the learned representations of the query to the elements of a support set that consists of labeled data. We demonstrate that by manipulating the support set, one can encode different causal assumptions. In particular, restricting the support set to a single environment encourages the model to learn invariant features that do not depend on the environment. We present a causally-motivated setup for our modeling and training strategy and validate on three challenging real-world domain generalization tasks in computer vision.

Magnetic resonance imaging (MRI) is the standard modality to understand human brain structure and function in vivo (antemortem). Decades of research in human neuroimaging has led to the widespread development of methods and tools to provide automated volume-based segmentations and surface-based parcellations which help localize brain functions to specialized anatomical regions. Recently ex vivo (postmortem) imaging of the brain has opened-up avenues to study brain structure at sub-millimeter ultra high-resolution revealing details not possible to observe with in vivo MRI. Unfortunately, there has been limited methodological development in ex vivo MRI primarily due to lack of datasets and limited centers with such imaging resources. Therefore, in this work, we present one-of-its-kind dataset of 82 ex vivo T2w whole brain hemispheres MRI at 0.3 mm isotropic resolution spanning Alzheimer's disease and related dementias. We adapted and developed a fast and easy-to-use automated surface-based pipeline to parcellate, for the first time, ultra high-resolution ex vivo brain tissue at the native subject space resolution using the Desikan-Killiany-Tourville (DKT) brain atlas. This allows us to perform vertex-wise analysis in the template space and thereby link morphometry measures with pathology measurements derived from histology. We will open-source our dataset docker container, Jupyter notebooks for ready-to-use out-of-the-box set of tools and command line options to advance ex vivo MRI clinical brain imaging research on the project webpage.

Accurately estimating the 3D pose and shape is an essential step towards understanding animal behavior, and can potentially benefit many downstream applications, such as wildlife conservation. However, research in this area is held back by the lack of a comprehensive and diverse dataset with high-quality 3D pose and shape annotations. In this paper, we propose Animal3D, the first comprehensive dataset for mammal animal 3D pose and shape estimation. Animal3D consists of 3379 images collected from 40 mammal species, high-quality annotations of 26 keypoints, and importantly the pose and shape parameters of the SMAL model. All annotations were labeled and checked manually in a multi-stage process to ensure highest quality results. Based on the Animal3D dataset, we benchmark representative shape and pose estimation models at: (1) supervised learning from only the Animal3D data, (2) synthetic to real transfer from synthetically generated images, and (3) fine-tuning human pose and shape estimation models. Our experimental results demonstrate that predicting the 3D shape and pose of animals across species remains a very challenging task, despite significant advances in human pose estimation. Our results further demonstrate that synthetic pre-training is a viable strategy to boost the model performance. Overall, Animal3D opens new directions for facilitating future research in animal 3D pose and shape estimation, and is publicly available.

ImageNet has become a reputable resource for transfer learning, allowing the development of efficient ML models with reduced training time and data requirements. However, vibration analysis in predictive maintenance, structural health monitoring, and fault diagnosis, lacks a comparable large-scale, annotated dataset to facilitate similar advancements. To address this, a dataset framework is proposed that begins with bearing vibration data as an initial step towards creating a universal dataset for vibration-based spectrogram analysis for all machinery. The initial framework includes a collection of bearing vibration signals from various publicly available datasets. To demonstrate the advantages of this framework, experiments were conducted using a deep learning architecture, showing improvements in model performance when pre-trained on bearing vibration data and fine-tuned on a smaller, domain-specific dataset. These findings highlight the potential to parallel the success of ImageNet in visual computing but for vibration analysis. For future work, this research will include a broader range of vibration signals from multiple types of machinery, emphasizing spectrogram-based representations of the data. Each sample will be labeled according to machinery type, operational status, and the presence or type of faults, ensuring its utility for supervised and unsupervised learning tasks. Additionally, a framework for data preprocessing, feature extraction, and model training specific to vibration data will be developed. This framework will standardize methodologies across the research community, allowing for collaboration and accelerating progress in predictive maintenance, structural health monitoring, and related fields. By mirroring the success of ImageNet in visual computing, this dataset has the potential to improve the development of intelligent systems in industrial applications.

Recent accelerations in multi-modal applications have been made possible with the plethora of image and text data available online. However, the scarcity of analogous data in the medical field, specifically in histopathology, has halted comparable progress. To enable similar representation learning for histopathology, we turn to YouTube, an untapped resource of videos, offering 1,087 hours of valuable educational histopathology videos from expert clinicians. From YouTube, we curate Quilt: a large-scale vision-language dataset consisting of 768,826 image and text pairs. Quilt was automatically curated using a mixture of models, including large language models, handcrafted algorithms, human knowledge databases, and automatic speech recognition. In comparison, the most comprehensive datasets curated for histopathology amass only around 200K samples. We combine Quilt with datasets from other sources, including Twitter, research papers, and the internet in general, to create an even larger dataset: Quilt-1M, with 1M paired image-text samples, marking it as the largest vision-language histopathology dataset to date. We demonstrate the value of Quilt-1M by fine-tuning a pre-trained CLIP model. Our model outperforms state-of-the-art models on both zero-shot and linear probing tasks for classifying new histopathology images across 13 diverse patch-level datasets of 8 different sub-pathologies and cross-modal retrieval tasks.

Magnetic resonance imaging (MRI) is a cornerstone of modern medical imaging. However, long image acquisition times, the need for qualitative expert analysis, and the lack of (and difficulty extracting) quantitative indicators that are sensitive to tissue health have curtailed widespread clinical and research studies. While recent machine learning methods for MRI reconstruction and analysis have shown promise for reducing this burden, these techniques are primarily validated with imperfect image quality metrics, which are discordant with clinically-relevant measures that ultimately hamper clinical deployment and clinician trust. To mitigate this challenge, we present the Stanford Knee MRI with Multi-Task Evaluation (SKM-TEA) dataset, a collection of quantitative knee MRI (qMRI) scans that enables end-to-end, clinically-relevant evaluation of MRI reconstruction and analysis tools. This 1.6TB dataset consists of raw-data measurements of ~25,000 slices (155 patients) of anonymized patient MRI scans, the corresponding scanner-generated DICOM images, manual segmentations of four tissues, and bounding box annotations for sixteen clinically relevant pathologies. We provide a framework for using qMRI parameter maps, along with image reconstructions and dense image labels, for measuring the quality of qMRI biomarker estimates extracted from MRI reconstruction, segmentation, and detection techniques. Finally, we use this framework to benchmark state-of-the-art baselines on this dataset. We hope our SKM-TEA dataset and code can enable a broad spectrum of research for modular image reconstruction and image analysis in a clinically informed manner. Dataset access, code, and benchmarks are available at https://github.com/StanfordMIMI/skm-tea.

Deep Learning (DL) in neuroimaging has become increasingly relevant for detecting neurological conditions and neurodegenerative disorders. One of the most predominant biomarkers in neuroimaging is represented by brain age, which has been shown to be a good indicator for different conditions, such as Alzheimer's Disease. Using brain age for weakly supervised pre-training of DL models in transfer learning settings has also recently shown promising results, especially when dealing with data scarcity of different conditions. On the other hand, anatomical information of brain MRIs (e.g. cortical thickness) can provide important information for learning good representations that can be transferred to many downstream tasks. In this work, we propose AnatCL, an anatomical foundation model for brain MRIs that i.) leverages anatomical information in a weakly contrastive learning approach, and ii.) achieves state-of-the-art performances across many different downstream tasks. To validate our approach we consider 12 different downstream tasks for the diagnosis of different conditions such as Alzheimer's Disease, autism spectrum disorder, and schizophrenia. Furthermore, we also target the prediction of 10 different clinical assessment scores using structural MRI data. Our findings show that incorporating anatomical information during pre-training leads to more robust and generalizable representations. Pre-trained models can be found at: https://github.com/EIDOSLAB/AnatCL.

Previous research on retinal vessel segmentation is targeted at a specific image domain, mostly color fundus photography (CFP). In this paper we make a brave attempt to attack a more challenging task of broad-domain retinal vessel segmentation (BD-RVS), which is to develop a unified model applicable to varied domains including CFP, SLO, UWF, OCTA and FFA. To that end, we propose Dual Convoltuional Prompting (DCP) that learns to extract domain-specific features by localized prompting along both position and channel dimensions. DCP is designed as a plug-in module that can effectively turn a R2AU-Net based vessel segmentation network to a unified model, yet without the need of modifying its network structure. For evaluation we build a broad-domain set using five public domain-specific datasets including ROSSA, FIVES, IOSTAR, PRIME-FP20 and VAMPIRE. In order to benchmark BD-RVS on the broad-domain dataset, we re-purpose a number of existing methods originally developed in other contexts, producing eight baseline methods in total. Extensive experiments show the the proposed method compares favorably against the baselines for BD-RVS.

Face detection is one of the most studied topics in the computer vision community. Much of the progresses have been made by the availability of face detection benchmark datasets. We show that there is a gap between current face detection performance and the real world requirements. To facilitate future face detection research, we introduce the WIDER FACE dataset, which is 10 times larger than existing datasets. The dataset contains rich annotations, including occlusions, poses, event categories, and face bounding boxes. Faces in the proposed dataset are extremely challenging due to large variations in scale, pose and occlusion, as shown in Fig. 1. Furthermore, we show that WIDER FACE dataset is an effective training source for face detection. We benchmark several representative detection systems, providing an overview of state-of-the-art performance and propose a solution to deal with large scale variation. Finally, we discuss common failure cases that worth to be further investigated. Dataset can be downloaded at: mmlab.ie.cuhk.edu.hk/projects/WIDERFace

We present a deep learning segmentation model that can automatically and robustly segment all major anatomical structures in body CT images. In this retrospective study, 1204 CT examinations (from the years 2012, 2016, and 2020) were used to segment 104 anatomical structures (27 organs, 59 bones, 10 muscles, 8 vessels) relevant for use cases such as organ volumetry, disease characterization, and surgical or radiotherapy planning. The CT images were randomly sampled from routine clinical studies and thus represent a real-world dataset (different ages, pathologies, scanners, body parts, sequences, and sites). The authors trained an nnU-Net segmentation algorithm on this dataset and calculated Dice similarity coefficients (Dice) to evaluate the model's performance. The trained algorithm was applied to a second dataset of 4004 whole-body CT examinations to investigate age dependent volume and attenuation changes. The proposed model showed a high Dice score (0.943) on the test set, which included a wide range of clinical data with major pathologies. The model significantly outperformed another publicly available segmentation model on a separate dataset (Dice score, 0.932 versus 0.871, respectively). The aging study demonstrated significant correlations between age and volume and mean attenuation for a variety of organ groups (e.g., age and aortic volume; age and mean attenuation of the autochthonous dorsal musculature). The developed model enables robust and accurate segmentation of 104 anatomical structures. The annotated dataset (https://doi.org/10.5281/zenodo.6802613) and toolkit (https://www.github.com/wasserth/TotalSegmentator) are publicly available.

In the realm of computer vision and graphics, accurately establishing correspondences between geometric 3D shapes is pivotal for applications like object tracking, registration, texture transfer, and statistical shape analysis. Moving beyond traditional hand-crafted and data-driven feature learning methods, we incorporate spectral methods with deep learning, focusing on functional maps (FMs) and optimal transport (OT). Traditional OT-based approaches, often reliant on entropy regularization OT in learning-based framework, face computational challenges due to their quadratic cost. Our key contribution is to employ the sliced Wasserstein distance (SWD) for OT, which is a valid fast optimal transport metric in an unsupervised shape matching framework. This unsupervised framework integrates functional map regularizers with a novel OT-based loss derived from SWD, enhancing feature alignment between shapes treated as discrete probability measures. We also introduce an adaptive refinement process utilizing entropy regularized OT, further refining feature alignments for accurate point-to-point correspondences. Our method demonstrates superior performance in non-rigid shape matching, including near-isometric and non-isometric scenarios, and excels in downstream tasks like segmentation transfer. The empirical results on diverse datasets highlight our framework's effectiveness and generalization capabilities, setting new standards in non-rigid shape matching with efficient OT metrics and an adaptive refinement module.

Star-convex shapes arise across bio-microscopy and radiology in the form of nuclei, nodules, metastases, and other units. Existing instance segmentation networks for such structures train on densely labeled instances for each dataset, which requires substantial and often impractical manual annotation effort. Further, significant reengineering or finetuning is needed when presented with new datasets and imaging modalities due to changes in contrast, shape, orientation, resolution, and density. We present AnyStar, a domain-randomized generative model that simulates synthetic training data of blob-like objects with randomized appearance, environments, and imaging physics to train general-purpose star-convex instance segmentation networks. As a result, networks trained using our generative model do not require annotated images from unseen datasets. A single network trained on our synthesized data accurately 3D segments C. elegans and P. dumerilii nuclei in fluorescence microscopy, mouse cortical nuclei in micro-CT, zebrafish brain nuclei in EM, and placental cotyledons in human fetal MRI, all without any retraining, finetuning, transfer learning, or domain adaptation. Code is available at https://github.com/neel-dey/AnyStar.

In the current deep learning paradigm, the amount and quality of training data are as critical as the network architecture and its training details. However, collecting, processing, and annotating real data at scale is difficult, expensive, and time-consuming, particularly for tasks such as 3D object registration. While synthetic datasets can be created, they require expertise to design and include a limited number of categories. In this paper, we introduce a new approach called AutoSynth, which automatically generates 3D training data for point cloud registration. Specifically, AutoSynth automatically curates an optimal dataset by exploring a search space encompassing millions of potential datasets with diverse 3D shapes at a low cost.To achieve this, we generate synthetic 3D datasets by assembling shape primitives, and develop a meta-learning strategy to search for the best training data for 3D registration on real point clouds. For this search to remain tractable, we replace the point cloud registration network with a much smaller surrogate network, leading to a 4056.43 times speedup. We demonstrate the generality of our approach by implementing it with two different point cloud registration networks, BPNet and IDAM. Our results on TUD-L, LINEMOD and Occluded-LINEMOD evidence that a neural network trained on our searched dataset yields consistently better performance than the same one trained on the widely used ModelNet40 dataset.

Learning 3D shape representation with dense correspondence for deformable objects is a fundamental problem in computer vision. Existing approaches often need additional annotations of specific semantic domain, e.g., skeleton poses for human bodies or animals, which require extra annotation effort and suffer from error accumulation, and they are limited to specific domain. In this paper, we propose a novel self-supervised approach to learn neural implicit shape representation for deformable objects, which can represent shapes with a template shape and dense correspondence in 3D. Our method does not require the priors of skeleton and skinning weight, and only requires a collection of shapes represented in signed distance fields. To handle the large deformation, we constrain the learned template shape in the same latent space with the training shapes, design a new formulation of local rigid constraint that enforces rigid transformation in local region and addresses local reflection issue, and present a new hierarchical rigid constraint to reduce the ambiguity due to the joint learning of template shape and correspondences. Extensive experiments show that our model can represent shapes with large deformations. We also show that our shape representation can support two typical applications, such as texture transfer and shape editing, with competitive performance. The code and models are available at https://iscas3dv.github.io/deformshape

Emerging from low-level vision theory, steerable filters found their counterpart in prior work on steerable convolutional neural networks equivariant to rigid transformations. In our work, we propose a steerable feed-forward learning-based approach that consists of neurons with spherical decision surfaces and operates on point clouds. Such spherical neurons are obtained by conformal embedding of Euclidean space and have recently been revisited in the context of learning representations of point sets. Focusing on 3D geometry, we exploit the isometry property of spherical neurons and derive a 3D steerability constraint. After training spherical neurons to classify point clouds in a canonical orientation, we use a tetrahedron basis to quadruplicate the neurons and construct rotation-equivariant spherical filter banks. We then apply the derived constraint to interpolate the filter bank outputs and, thus, obtain a rotation-invariant network. Finally, we use a synthetic point set and real-world 3D skeleton data to verify our theoretical findings. The code is available at https://github.com/pavlo-melnyk/steerable-3d-neurons.

The success of deep learning in vision can be attributed to: (a) models with high capacity; (b) increased computational power; and (c) availability of large-scale labeled data. Since 2012, there have been significant advances in representation capabilities of the models and computational capabilities of GPUs. But the size of the biggest dataset has surprisingly remained constant. What will happen if we increase the dataset size by 10x or 100x? This paper takes a step towards clearing the clouds of mystery surrounding the relationship between `enormous data' and visual deep learning. By exploiting the JFT-300M dataset which has more than 375M noisy labels for 300M images, we investigate how the performance of current vision tasks would change if this data was used for representation learning. Our paper delivers some surprising (and some expected) findings. First, we find that the performance on vision tasks increases logarithmically based on volume of training data size. Second, we show that representation learning (or pre-training) still holds a lot of promise. One can improve performance on many vision tasks by just training a better base model. Finally, as expected, we present new state-of-the-art results for different vision tasks including image classification, object detection, semantic segmentation and human pose estimation. Our sincere hope is that this inspires vision community to not undervalue the data and develop collective efforts in building larger datasets.

Learning similarity is a key aspect in medical image analysis, particularly in recommendation systems or in uncovering the interpretation of anatomical data in images. Most existing methods learn such similarities in the embedding space over image sets using a single metric learner. Images, however, have a variety of object attributes such as color, shape, or artifacts. Encoding such attributes using a single metric learner is inadequate and may fail to generalize. Instead, multiple learners could focus on separate aspects of these attributes in subspaces of an overarching embedding. This, however, implies the number of learners to be found empirically for each new dataset. This work, Dynamic Subspace Learners, proposes to dynamically exploit multiple learners by removing the need of knowing apriori the number of learners and aggregating new subspace learners during training. Furthermore, the visual interpretability of such subspace learning is enforced by integrating an attention module into our method. This integrated attention mechanism provides a visual insight of discriminative image features that contribute to the clustering of image sets and a visual explanation of the embedding features. The benefits of our attention-based dynamic subspace learners are evaluated in the application of image clustering, image retrieval, and weakly supervised segmentation. Our method achieves competitive results with the performances of multiple learners baselines and significantly outperforms the classification network in terms of clustering and retrieval scores on three different public benchmark datasets. Moreover, our attention maps offer a proxy-labels, which improves the segmentation accuracy up to 15% in Dice scores when compared to state-of-the-art interpretation techniques.

Psychological research results have confirmed that people can have different emotional reactions to different visual stimuli. Several papers have been published on the problem of visual emotion analysis. In particular, attempts have been made to analyze and predict people's emotional reaction towards images. To this end, different kinds of hand-tuned features are proposed. The results reported on several carefully selected and labeled small image data sets have confirmed the promise of such features. While the recent successes of many computer vision related tasks are due to the adoption of Convolutional Neural Networks (CNNs), visual emotion analysis has not achieved the same level of success. This may be primarily due to the unavailability of confidently labeled and relatively large image data sets for visual emotion analysis. In this work, we introduce a new data set, which started from 3+ million weakly labeled images of different emotions and ended up 30 times as large as the current largest publicly available visual emotion data set. We hope that this data set encourages further research on visual emotion analysis. We also perform extensive benchmarking analyses on this large data set using the state of the art methods including CNNs.

Establishing visual correspondences under large intra-class variations, which is often referred to as semantic correspondence or semantic matching, remains a challenging problem in computer vision. Despite its significance, however, most of the datasets for semantic correspondence are limited to a small amount of image pairs with similar viewpoints and scales. In this paper, we present a new large-scale benchmark dataset of semantically paired images, SPair-71k, which contains 70,958 image pairs with diverse variations in viewpoint and scale. Compared to previous datasets, it is significantly larger in number and contains more accurate and richer annotations. We believe this dataset will provide a reliable testbed to study the problem of semantic correspondence and will help to advance research in this area. We provide the results of recent methods on our new dataset as baselines for further research. Our benchmark is available online at http://cvlab.postech.ac.kr/research/SPair-71k/.

Accurate detection and segmentation of cell nuclei in volumetric (3D) fluorescence microscopy datasets is an important step in many biomedical research projects. Although many automated methods for these tasks exist, they often struggle for images with low signal-to-noise ratios and/or dense packing of nuclei. It was recently shown for 2D microscopy images that these issues can be alleviated by training a neural network to directly predict a suitable shape representation (star-convex polygon) for cell nuclei. In this paper, we adopt and extend this approach to 3D volumes by using star-convex polyhedra to represent cell nuclei and similar shapes. To that end, we overcome the challenges of 1) finding parameter-efficient star-convex polyhedra representations that can faithfully describe cell nuclei shapes, 2) adapting to anisotropic voxel sizes often found in fluorescence microscopy datasets, and 3) efficiently computing intersections between pairs of star-convex polyhedra (required for non-maximum suppression). Although our approach is quite general, since star-convex polyhedra include common shapes like bounding boxes and spheres as special cases, our focus is on accurate detection and segmentation of cell nuclei. Finally, we demonstrate on two challenging datasets that our approach (StarDist-3D) leads to superior results when compared to classical and deep learning based methods.

We propose a novel zero-shot approach to computing correspondences between 3D shapes. Existing approaches mainly focus on isometric and near-isometric shape pairs (e.g., human vs. human), but less attention has been given to strongly non-isometric and inter-class shape matching (e.g., human vs. cow). To this end, we introduce a fully automatic method that exploits the exceptional reasoning capabilities of recent foundation models in language and vision to tackle difficult shape correspondence problems. Our approach comprises multiple stages. First, we classify the 3D shapes in a zero-shot manner by feeding rendered shape views to a language-vision model (e.g., BLIP2) to generate a list of class proposals per shape. These proposals are unified into a single class per shape by employing the reasoning capabilities of ChatGPT. Second, we attempt to segment the two shapes in a zero-shot manner, but in contrast to the co-segmentation problem, we do not require a mutual set of semantic regions. Instead, we propose to exploit the in-context learning capabilities of ChatGPT to generate two different sets of semantic regions for each shape and a semantic mapping between them. This enables our approach to match strongly non-isometric shapes with significant differences in geometric structure. Finally, we employ the generated semantic mapping to produce coarse correspondences that can further be refined by the functional maps framework to produce dense point-to-point maps. Our approach, despite its simplicity, produces highly plausible results in a zero-shot manner, especially between strongly non-isometric shapes.

In this study, we examine the efficacy of post-hoc local attribution methods in identifying features with predictive power from irrelevant ones in domains characterized by a low signal-to-noise ratio (SNR), a common scenario in real-world machine learning applications. We developed synthetic datasets encompassing symbolic functional, image, and audio data, incorporating a benchmark on the {\it (Model \(\times\) Attribution\(\times\) Noise Condition)} triplet. By rigorously testing various classic models trained from scratch, we gained valuable insights into the performance of these attribution methods in multiple conditions. Based on these findings, we introduce a novel extension to the notable recursive feature elimination (RFE) algorithm, enhancing its applicability for neural networks. Our experiments highlight its strengths in prediction and feature selection, alongside limitations in scalability. Further details and additional minor findings are included in the appendix, with extensive discussions. The codes and resources are available at https://github.com/geshijoker/ChaosMining/{URL}.

This paper presents a data-driven, task-specific paradigm for experimental design, to shorten acquisition time, reduce costs, and accelerate the deployment of imaging devices. Current approaches in experimental design focus on model-parameter estimation and require specification of a particular model, whereas in imaging, other tasks may drive the design. Furthermore, such approaches often lead to intractable optimization problems in real-world imaging applications. Here we present a new paradigm for experimental design that simultaneously optimizes the design (set of image channels) and trains a machine-learning model to execute a user-specified image-analysis task. The approach obtains data densely-sampled over the measurement space (many image channels) for a small number of acquisitions, then identifies a subset of channels of prespecified size that best supports the task. We propose a method: TADRED for TAsk-DRiven Experimental Design in imaging, to identify the most informative channel-subset whilst simultaneously training a network to execute the task given the subset. Experiments demonstrate the potential of TADRED in diverse imaging applications: several clinically-relevant tasks in magnetic resonance imaging; and remote sensing and physiological applications of hyperspectral imaging. Results show substantial improvement over classical experimental design, two recent application-specific methods within the new paradigm, and state-of-the-art approaches in supervised feature selection. We anticipate further applications of our approach. Code is available: https://github.com/sbb-gh/experimental-design-multichannel

Contrastive pretraining on parallel image-text data has attained great success in vision-language processing (VLP), as exemplified by CLIP and related methods. However, prior explorations tend to focus on general domains in the web. Biomedical images and text are rather different, but publicly available datasets are small and skew toward chest X-ray, thus severely limiting progress. In this paper, we conducted by far the largest study on biomedical VLP, using 15 million figure-caption pairs extracted from biomedical research articles in PubMed Central. Our dataset (PMC-15M) is two orders of magnitude larger than existing biomedical image-text datasets such as MIMIC-CXR, and spans a diverse range of biomedical images. The standard CLIP method is suboptimal for the biomedical domain. We propose BiomedCLIP with domain-specific adaptations tailored to biomedical VLP. We conducted extensive experiments and ablation studies on standard biomedical imaging tasks from retrieval to classification to visual question-answering (VQA). BiomedCLIP established new state of the art in a wide range of standard datasets, substantially outperformed prior VLP approaches. Surprisingly, BiomedCLIP even outperformed radiology-specific state-of-the-art models such as BioViL on radiology-specific tasks such as RSNA pneumonia detection, thus highlighting the utility in large-scale pretraining across all biomedical image types. We will release our models at https://aka.ms/biomedclip to facilitate future research in biomedical VLP.

This paper introduces MedTrinity-25M, a comprehensive, large-scale multimodal dataset for medicine, covering over 25 million images across 10 modalities, with multigranular annotations for more than 65 diseases. These enriched annotations encompass both global textual information, such as disease/lesion type, modality, region-specific descriptions, and inter-regional relationships, as well as detailed local annotations for regions of interest (ROIs), including bounding boxes, segmentation masks. Unlike existing approach which is limited by the availability of image-text pairs, we have developed the first automated pipeline that scales up multimodal data by generating multigranular visual and texual annotations (in the form of image-ROI-description triplets) without the need for any paired text descriptions. Specifically, data from over 90 different sources have been collected, preprocessed, and grounded using domain-specific expert models to identify ROIs related to abnormal regions. We then build a comprehensive knowledge base and prompt multimodal large language models to perform retrieval-augmented generation with the identified ROIs as guidance, resulting in multigranular texual descriptions. Compared to existing datasets, MedTrinity-25M provides the most enriched annotations, supporting a comprehensive range of multimodal tasks such as captioning and report generation, as well as vision-centric tasks like classification and segmentation. Pretraining on MedTrinity-25M, our model achieves state-of-the-art performance on VQA-RAD and PathVQA, surpassing both multimodal large language models and other representative SoTA approaches. This dataset can also be utilized to support large-scale pre-training of multimodal medical AI models, contributing to the development of future foundation models in the medical domain.

Self-Supervised Learning (SSL) presents an exciting opportunity to unlock the potential of vast, untapped clinical datasets, for various downstream applications that suffer from the scarcity of labeled data. While SSL has revolutionized fields like natural language processing and computer vision, its adoption in 3D medical image computing has been limited by three key pitfalls: Small pre-training dataset sizes, architectures inadequate for 3D medical image analysis, and insufficient evaluation practices. In this paper, we address these issues by i) leveraging a large-scale dataset of 39k 3D brain MRI volumes and ii) using a Residual Encoder U-Net architecture within the state-of-the-art nnU-Net framework. iii) A robust development framework, incorporating 5 development and 8 testing brain MRI segmentation datasets, allowed performance-driven design decisions to optimize the simple concept of Masked Auto Encoders (MAEs) for 3D CNNs. The resulting model not only surpasses previous SSL methods but also outperforms the strong nnU-Net baseline by an average of approximately 3 Dice points setting a new state-of-the-art. Our code and models are made available here.

We introduce Brain-JEPA, a brain dynamics foundation model with the Joint-Embedding Predictive Architecture (JEPA). This pioneering model achieves state-of-the-art performance in demographic prediction, disease diagnosis/prognosis, and trait prediction through fine-tuning. Furthermore, it excels in off-the-shelf evaluations (e.g., linear probing) and demonstrates superior generalizability across different ethnic groups, surpassing the previous large model for brain activity significantly. Brain-JEPA incorporates two innovative techniques: Brain Gradient Positioning and Spatiotemporal Masking. Brain Gradient Positioning introduces a functional coordinate system for brain functional parcellation, enhancing the positional encoding of different Regions of Interest (ROIs). Spatiotemporal Masking, tailored to the unique characteristics of fMRI data, addresses the challenge of heterogeneous time-series patches. These methodologies enhance model performance and advance our understanding of the neural circuits underlying cognition. Overall, Brain-JEPA is paving the way to address pivotal questions of building brain functional coordinate system and masking brain activity at the AI-neuroscience interface, and setting a potentially new paradigm in brain activity analysis through downstream adaptation.

Deep neural representations of 3D shapes as implicit functions have been shown to produce high fidelity models surpassing the resolution-memory trade-off faced by the explicit representations using meshes and point clouds. However, most such approaches focus on representing closed shapes. Unsigned distance function (UDF) based approaches have been proposed recently as a promising alternative to represent both open and closed shapes. However, since the gradients of UDFs vanish on the surface, it is challenging to estimate local (differential) geometric properties like the normals and tangent planes which are needed for many downstream applications in vision and graphics. There are additional challenges in computing these properties efficiently with a low-memory footprint. This paper presents a novel approach that models such surfaces using a new class of implicit representations called the closest surface-point (CSP) representation. We show that CSP allows us to represent complex surfaces of any topology (open or closed) with high fidelity. It also allows for accurate and efficient computation of local geometric properties. We further demonstrate that it leads to efficient implementation of downstream algorithms like sphere-tracing for rendering the 3D surface as well as to create explicit mesh-based representations. Extensive experimental evaluation on the ShapeNet dataset validate the above contributions with results surpassing the state-of-the-art.

In recent years, the application of machine learning to minimally invasive surgery (MIS) has attracted considerable interest. Datasets are critical to the use of such techniques. This paper presents a unique dataset recorded during ex vivo pseudo-cholecystectomy procedures on pig livers using the da Vinci Research Kit (dVRK). Unlike existing datasets, it addresses a critical gap by providing comprehensive kinematic data, recordings of all pedal inputs, and offers a time-stamped record of the endoscope's movements. This expanded version also includes segmentation and keypoint annotations of images, enhancing its utility for computer vision applications. Contributed by seven surgeons with varied backgrounds and experience levels that are provided as a part of this expanded version, the dataset is an important new resource for surgical robotics research. It enables the development of advanced methods for evaluating surgeon skills, tools for providing better context awareness, and automation of surgical tasks. Our work overcomes the limitations of incomplete recordings and imprecise kinematic data found in other datasets. To demonstrate the potential of the dataset for advancing automation in surgical robotics, we introduce two models that predict clutch usage and camera activation, a 3D scene reconstruction example, and the results from our keypoint and segmentation models.

Formula-driven supervised learning (FDSL) has been shown to be an effective method for pre-training vision transformers, where ExFractalDB-21k was shown to exceed the pre-training effect of ImageNet-21k. These studies also indicate that contours mattered more than textures when pre-training vision transformers. However, the lack of a systematic investigation as to why these contour-oriented synthetic datasets can achieve the same accuracy as real datasets leaves much room for skepticism. In the present work, we develop a novel methodology based on circular harmonics for systematically investigating the design space of contour-oriented synthetic datasets. This allows us to efficiently search the optimal range of FDSL parameters and maximize the variety of synthetic images in the dataset, which we found to be a critical factor. When the resulting new dataset VisualAtom-21k is used for pre-training ViT-Base, the top-1 accuracy reached 83.7% when fine-tuning on ImageNet-1k. This is close to the top-1 accuracy (84.2%) achieved by JFT-300M pre-training, while the number of images is 1/14. Unlike JFT-300M which is a static dataset, the quality of synthetic datasets will continue to improve, and the current work is a testament to this possibility. FDSL is also free of the common issues associated with real images, e.g. privacy/copyright issues, labeling costs/errors, and ethical biases.

Recent work has investigated the distributions of learned convolution filters through a large-scale study containing hundreds of heterogeneous image models. Surprisingly, on average, the distributions only show minor drifts in comparisons of various studied dimensions including the learned task, image domain, or dataset. However, among the studied image domains, medical imaging models appeared to show significant outliers through "spikey" distributions, and, therefore, learn clusters of highly specific filters different from other domains. Following this observation, we study the collected medical imaging models in more detail. We show that instead of fundamental differences, the outliers are due to specific processing in some architectures. Quite the contrary, for standardized architectures, we find that models trained on medical data do not significantly differ in their filter distributions from similar architectures trained on data from other domains. Our conclusions reinforce previous hypotheses stating that pre-training of imaging models can be done with any kind of diverse image data.

Instance shape reconstruction from a 3D scene involves recovering the full geometries of multiple objects at the semantic instance level. Many methods leverage data-driven learning due to the intricacies of scene complexity and significant indoor occlusions. Training these methods often requires a large-scale, high-quality dataset with aligned and paired shape annotations with real-world scans. Existing datasets are either synthetic or misaligned, restricting the performance of data-driven methods on real data. To this end, we introduce LASA, a Large-scale Aligned Shape Annotation Dataset comprising 10,412 high-quality CAD annotations aligned with 920 real-world scene scans from ArkitScenes, created manually by professional artists. On this top, we propose a novel Diffusion-based Cross-Modal Shape Reconstruction (DisCo) method. It is empowered by a hybrid feature aggregation design to fuse multi-modal inputs and recover high-fidelity object geometries. Besides, we present an Occupancy-Guided 3D Object Detection (OccGOD) method and demonstrate that our shape annotations provide scene occupancy clues that can further improve 3D object detection. Supported by LASA, extensive experiments show that our methods achieve state-of-the-art performance in both instance-level scene reconstruction and 3D object detection tasks.

We present a novel approach for recovering 3D shape and view dependent appearance from a few colored images, enabling efficient 3D reconstruction and novel view synthesis. Our method learns an implicit neural representation in the form of a Signed Distance Function (SDF) and a radiance field. The model is trained progressively through ray marching enabled volumetric rendering, and regularized with learning-free multi-view stereo (MVS) cues. Key to our contribution is a novel implicit neural shape function learning strategy that encourages our SDF field to be as linear as possible near the level-set, hence robustifying the training against noise emanating from the supervision and regularization signals. Without using any pretrained priors, our method, called SparseCraft, achieves state-of-the-art performances both in novel-view synthesis and reconstruction from sparse views in standard benchmarks, while requiring less than 10 minutes for training.

We present a method for estimating neural scenes representations of objects given only a single image. The core of our method is the estimation of a geometric scaffold for the object and its use as a guide for the reconstruction of the underlying radiance field. Our formulation is based on a generative process that first maps a latent code to a voxelized shape, and then renders it to an image, with the object appearance being controlled by a second latent code. During inference, we optimize both the latent codes and the networks to fit a test image of a new object. The explicit disentanglement of shape and appearance allows our model to be fine-tuned given a single image. We can then render new views in a geometrically consistent manner and they represent faithfully the input object. Additionally, our method is able to generalize to images outside of the training domain (more realistic renderings and even real photographs). Finally, the inferred geometric scaffold is itself an accurate estimate of the object's 3D shape. We demonstrate in several experiments the effectiveness of our approach in both synthetic and real images.

To endow machines with the ability to perceive the real-world in a three dimensional representation as we do as humans is a fundamental and long-standing topic in Artificial Intelligence. Given different types of visual inputs such as images or point clouds acquired by 2D/3D sensors, one important goal is to understand the geometric structure and semantics of the 3D environment. Traditional approaches usually leverage hand-crafted features to estimate the shape and semantics of objects or scenes. However, they are difficult to generalize to novel objects and scenarios, and struggle to overcome critical issues caused by visual occlusions. By contrast, we aim to understand scenes and the objects within them by learning general and robust representations using deep neural networks, trained on large-scale real-world 3D data. To achieve these aims, this thesis makes three core contributions from object-level 3D shape estimation from single or multiple views to scene-level semantic understanding.

A major goal of neuroscience is to understand brain computations during visual processing in naturalistic settings. A dominant approach is to use image-computable deep neural networks trained with different task objectives as a basis for linear encoding models. However, in addition to requiring tuning a large number of parameters, the linear encoding approach ignores the structure of the feature maps both in the brain and the models. Recently proposed alternatives have focused on decomposing the linear mapping to spatial and feature components but focus on finding static receptive fields for units that are applicable only in early visual areas. In this work, we employ the attention mechanism used in the transformer architecture to study how retinotopic visual features can be dynamically routed to category-selective areas in high-level visual processing. We show that this computational motif is significantly more powerful than alternative methods in predicting brain activity during natural scene viewing, across different feature basis models and modalities. We also show that this approach is inherently more interpretable, without the need to create importance maps, by interpreting the attention routing signal for different high-level categorical areas. Our approach proposes a mechanistic model of how visual information from retinotopic maps can be routed based on the relevance of the input content to different category-selective regions.

Datasets have gained an enormous amount of popularity in the computer vision community, from training and evaluation of Deep Learning-based methods to benchmarking Simultaneous Localization and Mapping (SLAM). Without a doubt, synthetic imagery bears a vast potential due to scalability in terms of amounts of data obtainable without tedious manual ground truth annotations or measurements. Here, we present a dataset with the aim of providing a higher degree of photo-realism, larger scale, more variability as well as serving a wider range of purposes compared to existing datasets. Our dataset leverages the availability of millions of professional interior designs and millions of production-level furniture and object assets -- all coming with fine geometric details and high-resolution texture. We render high-resolution and high frame-rate video sequences following realistic trajectories while supporting various camera types as well as providing inertial measurements. Together with the release of the dataset, we will make executable program of our interactive simulator software as well as our renderer available at https://interiornetdataset.github.io. To showcase the usability and uniqueness of our dataset, we show benchmarking results of both sparse and dense SLAM algorithms.

Existing public face datasets are strongly biased toward Caucasian faces, and other races (e.g., Latino) are significantly underrepresented. This can lead to inconsistent model accuracy, limit the applicability of face analytic systems to non-White race groups, and adversely affect research findings based on such skewed data. To mitigate the race bias in these datasets, we construct a novel face image dataset, containing 108,501 images, with an emphasis of balanced race composition in the dataset. We define 7 race groups: White, Black, Indian, East Asian, Southeast Asian, Middle East, and Latino. Images were collected from the YFCC-100M Flickr dataset and labeled with race, gender, and age groups. Evaluations were performed on existing face attribute datasets as well as novel image datasets to measure generalization performance. We find that the model trained from our dataset is substantially more accurate on novel datasets and the accuracy is consistent between race and gender groups.

The burgeoning integration of 3D medical imaging into healthcare has led to a substantial increase in the workload of medical professionals. To assist clinicians in their diagnostic processes and alleviate their workload, the development of a robust system for retrieving similar case studies presents a viable solution. While the concept holds great promise, the field of 3D medical text-image retrieval is currently limited by the absence of robust evaluation benchmarks and curated datasets. To remedy this, our study presents a groundbreaking dataset, BIMCV-R (This dataset will be released upon acceptance.), which includes an extensive collection of 8,069 3D CT volumes, encompassing over 2 million slices, paired with their respective radiological reports. Expanding upon the foundational work of our dataset, we craft a retrieval strategy, MedFinder. This approach employs a dual-stream network architecture, harnessing the potential of large language models to advance the field of medical image retrieval beyond existing text-image retrieval solutions. It marks our preliminary step towards developing a system capable of facilitating text-to-image, image-to-text, and keyword-based retrieval tasks.

Human perception of 3D shapes goes beyond reconstructing them as a set of points or a composition of geometric primitives: we also effortlessly understand higher-level shape structure such as the repetition and reflective symmetry of object parts. In contrast, recent advances in 3D shape sensing focus more on low-level geometry but less on these higher-level relationships. In this paper, we propose 3D shape programs, integrating bottom-up recognition systems with top-down, symbolic program structure to capture both low-level geometry and high-level structural priors for 3D shapes. Because there are no annotations of shape programs for real shapes, we develop neural modules that not only learn to infer 3D shape programs from raw, unannotated shapes, but also to execute these programs for shape reconstruction. After initial bootstrapping, our end-to-end differentiable model learns 3D shape programs by reconstructing shapes in a self-supervised manner. Experiments demonstrate that our model accurately infers and executes 3D shape programs for highly complex shapes from various categories. It can also be integrated with an image-to-shape module to infer 3D shape programs directly from an RGB image, leading to 3D shape reconstructions that are both more accurate and more physically plausible.

We propose a novel 3D morphable model for complete human heads based on hybrid neural fields. At the core of our model lies a neural parametric representation that disentangles identity and expressions in disjoint latent spaces. To this end, we capture a person's identity in a canonical space as a signed distance field (SDF), and model facial expressions with a neural deformation field. In addition, our representation achieves high-fidelity local detail by introducing an ensemble of local fields centered around facial anchor points. To facilitate generalization, we train our model on a newly-captured dataset of over 5200 head scans from 255 different identities using a custom high-end 3D scanning setup. Our dataset significantly exceeds comparable existing datasets, both with respect to quality and completeness of geometry, averaging around 3.5M mesh faces per scan. Finally, we demonstrate that our approach outperforms state-of-the-art methods in terms of fitting error and reconstruction quality.

Medical image segmentation has recently demonstrated impressive progress with deep neural networks, yet the heterogeneous modalities and scarcity of mask annotations limit the development of segmentation models on unannotated modalities. This paper investigates a new paradigm for leveraging generative models in medical applications: controllably synthesizing data for unannotated modalities, without requiring registered data pairs. Specifically, we make the following contributions in this paper: (i) we collect and curate a large-scale radiology image-text dataset, MedGen-1M, comprising modality labels, attributes, region, and organ information, along with a subset of organ mask annotations, to support research in controllable medical image generation; (ii) we propose a diffusion-based data engine, termed MRGen, which enables generation conditioned on text prompts and masks, synthesizing MR images for diverse modalities lacking mask annotations, to train segmentation models on unannotated modalities; (iii) we conduct extensive experiments across various modalities, illustrating that our data engine can effectively synthesize training samples and extend MRI segmentation towards unannotated modalities.

Recent advances in neural reconstruction enable high-quality 3D object reconstruction from casually captured image collections. Current techniques mostly analyze their progress on relatively simple image collections where Structure-from-Motion (SfM) techniques can provide ground-truth (GT) camera poses. We note that SfM techniques tend to fail on in-the-wild image collections such as image search results with varying backgrounds and illuminations. To enable systematic research progress on 3D reconstruction from casual image captures, we propose NAVI: a new dataset of category-agnostic image collections of objects with high-quality 3D scans along with per-image 2D-3D alignments providing near-perfect GT camera parameters. These 2D-3D alignments allow us to extract accurate derivative annotations such as dense pixel correspondences, depth and segmentation maps. We demonstrate the use of NAVI image collections on different problem settings and show that NAVI enables more thorough evaluations that were not possible with existing datasets. We believe NAVI is beneficial for systematic research progress on 3D reconstruction and correspondence estimation. Project page: https://navidataset.github.io

Automatic identification of brain lesions from magnetic resonance imaging (MRI) scans of stroke survivors would be a useful aid in patient diagnosis and treatment planning. We propose a multi-modal multi-path convolutional neural network system for automating stroke lesion segmentation. Our system has nine end-to-end UNets that take as input 2-dimensional (2D) slices and examines all three planes with three different normalizations. Outputs from these nine total paths are concatenated into a 3D volume that is then passed to a 3D convolutional neural network to output a final lesion mask. We trained and tested our method on datasets from three sources: Medical College of Wisconsin (MCW), Kessler Foundation (KF), and the publicly available Anatomical Tracings of Lesions After Stroke (ATLAS) dataset. Cross-study validation results (with independent training and validation datasets) were obtained to compare with previous methods based on naive Bayes, random forests, and three recently published convolutional neural networks. Model performance was quantified in terms of the Dice coefficient. Training on the KF and MCW images and testing on the ATLAS images yielded a mean Dice coefficient of 0.54. This was reliably better than the next best previous model, UNet, at 0.47. Reversing the train and test datasets yields a mean Dice of 0.47 on KF and MCW images, whereas the next best UNet reaches 0.45. With all three datasets combined, the current system compared to previous methods also attained a reliably higher cross-validation accuracy. It also achieved high Dice values for many smaller lesions that existing methods have difficulty identifying. Overall, our system is a clear improvement over previous methods for automating stroke lesion segmentation, bringing us an important step closer to the inter-rater accuracy level of human experts.

The large abundance of perspective camera datasets facilitated the emergence of novel learning-based strategies for various tasks, such as camera localization, single image depth estimation, or view synthesis. However, panoramic or omnidirectional image datasets, including essential information, such as pose and depth, are mostly made with synthetic scenes. In this work, we introduce a large scale 360^{circ} videos dataset in the wild. This dataset has been carefully scraped from the Internet and has been captured from various locations worldwide. Hence, this dataset exhibits very diversified environments (e.g., indoor and outdoor) and contexts (e.g., with and without moving objects). Each of the 25K images constituting our dataset is provided with its respective camera's pose and depth map. We illustrate the relevance of our dataset for two main tasks, namely, single image depth estimation and view synthesis.

Foundation vision-language models are currently transforming computer vision, and are on the rise in medical imaging fueled by their very promising generalization capabilities. However, the initial attempts to transfer this new paradigm to medical imaging have shown less impressive performances than those observed in other domains, due to the significant domain shift and the complex, expert domain knowledge inherent to medical-imaging tasks. Motivated by the need for domain-expert foundation models, we present FLAIR, a pre-trained vision-language model for universal retinal fundus image understanding. To this end, we compiled 37 open-access, mostly categorical fundus imaging datasets from various sources, with up to 97 different target conditions and 284,660 images. We integrate the expert's domain knowledge in the form of descriptive textual prompts, during both pre-training and zero-shot inference, enhancing the less-informative categorical supervision of the data. Such a textual expert's knowledge, which we compiled from the relevant clinical literature and community standards, describes the fine-grained features of the pathologies as well as the hierarchies and dependencies between them. We report comprehensive evaluations, which illustrate the benefit of integrating expert knowledge and the strong generalization capabilities of FLAIR under difficult scenarios with domain shifts or unseen categories. When adapted with a lightweight linear probe, FLAIR outperforms fully-trained, dataset-focused models, more so in the few-shot regimes. Interestingly, FLAIR outperforms by a large margin more generalist, larger-scale image-language models, which emphasizes the potential of embedding experts' domain knowledge and the limitations of generalist models in medical imaging.

Despite the remarkable success of deep neural networks in a myriad of settings, several works have demonstrated their overwhelming sensitivity to near-imperceptible perturbations, known as adversarial attacks. On the other hand, prior works have also observed that deep networks can be under-sensitive, wherein large-magnitude perturbations in input space do not induce appreciable changes to network activations. In this work, we study in detail the phenomenon of under-sensitivity in vision models such as CNNs and Transformers, and present techniques to study the geometry and extent of "equi-confidence" level sets of such networks. We propose a Level Set Traversal algorithm that iteratively explores regions of high confidence with respect to the input space using orthogonal components of the local gradients. Given a source image, we use this algorithm to identify inputs that lie in the same equi-confidence level set as the source image despite being perceptually similar to arbitrary images from other classes. We further observe that the source image is linearly connected by a high-confidence path to these inputs, uncovering a star-like structure for level sets of deep networks. Furthermore, we attempt to identify and estimate the extent of these connected higher-dimensional regions over which the model maintains a high degree of confidence. The code for this project is publicly available at https://github.com/SriramB-98/blindspots-neurips-sub

We propose an experimental method for measuring bias in face recognition systems. Existing methods to measure bias depend on benchmark datasets that are collected in the wild and annotated for protected (e.g., race, gender) and non-protected (e.g., pose, lighting) attributes. Such observational datasets only permit correlational conclusions, e.g., "Algorithm A's accuracy is different on female and male faces in dataset X.". By contrast, experimental methods manipulate attributes individually and thus permit causal conclusions, e.g., "Algorithm A's accuracy is affected by gender and skin color." Our method is based on generating synthetic faces using a neural face generator, where each attribute of interest is modified independently while leaving all other attributes constant. Human observers crucially provide the ground truth on perceptual identity similarity between synthetic image pairs. We validate our method quantitatively by evaluating race and gender biases of three research-grade face recognition models. Our synthetic pipeline reveals that for these algorithms, accuracy is lower for Black and East Asian population subgroups. Our method can also quantify how perceptual changes in attributes affect face identity distances reported by these models. Our large synthetic dataset, consisting of 48,000 synthetic face image pairs (10,200 unique synthetic faces) and 555,000 human annotations (individual attributes and pairwise identity comparisons) is available to researchers in this important area.

The ImageNet Large Scale Visual Recognition Challenge is a benchmark in object category classification and detection on hundreds of object categories and millions of images. The challenge has been run annually from 2010 to present, attracting participation from more than fifty institutions. This paper describes the creation of this benchmark dataset and the advances in object recognition that have been possible as a result. We discuss the challenges of collecting large-scale ground truth annotation, highlight key breakthroughs in categorical object recognition, provide a detailed analysis of the current state of the field of large-scale image classification and object detection, and compare the state-of-the-art computer vision accuracy with human accuracy. We conclude with lessons learned in the five years of the challenge, and propose future directions and improvements.

With the increasing number of new neural architecture designs and substantial existing neural architectures, it becomes difficult for the researchers to situate their contributions compared with existing neural architectures or establish the connections between their designs and other relevant ones. To discover similar neural architectures in an efficient and automatic manner, we define a new problem Neural Architecture Retrieval which retrieves a set of existing neural architectures which have similar designs to the query neural architecture. Existing graph pre-training strategies cannot address the computational graph in neural architectures due to the graph size and motifs. To fulfill this potential, we propose to divide the graph into motifs which are used to rebuild the macro graph to tackle these issues, and introduce multi-level contrastive learning to achieve accurate graph representation learning. Extensive evaluations on both human-designed and synthesized neural architectures demonstrate the superiority of our algorithm. Such a dataset which contains 12k real-world network architectures, as well as their embedding, is built for neural architecture retrieval.

We present the HANDAL dataset for category-level object pose estimation and affordance prediction. Unlike previous datasets, ours is focused on robotics-ready manipulable objects that are of the proper size and shape for functional grasping by robot manipulators, such as pliers, utensils, and screwdrivers. Our annotation process is streamlined, requiring only a single off-the-shelf camera and semi-automated processing, allowing us to produce high-quality 3D annotations without crowd-sourcing. The dataset consists of 308k annotated image frames from 2.2k videos of 212 real-world objects in 17 categories. We focus on hardware and kitchen tool objects to facilitate research in practical scenarios in which a robot manipulator needs to interact with the environment beyond simple pushing or indiscriminate grasping. We outline the usefulness of our dataset for 6-DoF category-level pose+scale estimation and related tasks. We also provide 3D reconstructed meshes of all objects, and we outline some of the bottlenecks to be addressed for democratizing the collection of datasets like this one.

Learning long-term spatial-temporal features are critical for many video analysis tasks. However, existing video segmentation methods predominantly rely on static image segmentation techniques, and methods capturing temporal dependency for segmentation have to depend on pretrained optical flow models, leading to suboptimal solutions for the problem. End-to-end sequential learning to explore spatialtemporal features for video segmentation is largely limited by the scale of available video segmentation datasets, i.e., even the largest video segmentation dataset only contains 90 short video clips. To solve this problem, we build a new large-scale video object segmentation dataset called YouTube Video Object Segmentation dataset (YouTube-VOS). Our dataset contains 4,453 YouTube video clips and 94 object categories. This is by far the largest video object segmentation dataset to our knowledge and has been released at http://youtube-vos.org. We further evaluate several existing state-of-the-art video object segmentation algorithms on this dataset which aims to establish baselines for the development of new algorithms in the future.

The integration of deep learning and neuroscience has been advancing rapidly, which has led to improvements in the analysis of brain activity and the understanding of deep learning models from a neuroscientific perspective. The reconstruction of visual experience from human brain activity is an area that has particularly benefited: the use of deep learning models trained on large amounts of natural images has greatly improved its quality, and approaches that combine the diverse information contained in visual experiences have proliferated rapidly in recent years. In this technical paper, by taking advantage of the simple and generic framework that we proposed (Takagi and Nishimoto, CVPR 2023), we examine the extent to which various additional decoding techniques affect the performance of visual experience reconstruction. Specifically, we combined our earlier work with the following three techniques: using decoded text from brain activity, nonlinear optimization for structural image reconstruction, and using decoded depth information from brain activity. We confirmed that these techniques contributed to improving accuracy over the baseline. We also discuss what researchers should consider when performing visual reconstruction using deep generative models trained on large datasets. Please check our webpage at https://sites.google.com/view/stablediffusion-with-brain/. Code is also available at https://github.com/yu-takagi/StableDiffusionReconstruction.

Due to the lack of paired samples and the low signal-to-noise ratio of functional MRI (fMRI) signals, reconstructing perceived natural images or decoding their semantic contents from fMRI data are challenging tasks. In this work, we propose, for the first time, a task-agnostic fMRI-based brain decoding model, BrainCLIP, which leverages CLIP's cross-modal generalization ability to bridge the modality gap between brain activity, image, and text. Our experiments demonstrate that CLIP can act as a pivot for generic brain decoding tasks, including zero-shot visual categories decoding, fMRI-image/text matching, and fMRI-to-image generation. Specifically, BrainCLIP aims to train a mapping network that transforms fMRI patterns into a well-aligned CLIP embedding space by combining visual and textual supervision. Our experiments show that this combination can boost the decoding model's performance on certain tasks like fMRI-text matching and fMRI-to-image generation. On the zero-shot visual category decoding task, BrainCLIP achieves significantly better performance than BraVL, a recently proposed multi-modal method specifically designed for this task. BrainCLIP can also reconstruct visual stimuli with high semantic fidelity and establishes a new state-of-the-art for fMRI-based natural image reconstruction in terms of high-level semantic features.

Distribution shifts are a major source of failure of deployed machine learning models. However, evaluating a model's reliability under distribution shifts can be challenging, especially since it may be difficult to acquire counterfactual examples that exhibit a specified shift. In this work, we introduce dataset interfaces: a framework which allows users to scalably synthesize such counterfactual examples from a given dataset. Specifically, we represent each class from the input dataset as a custom token within the text space of a text-to-image diffusion model. By incorporating these tokens into natural language prompts, we can then generate instantiations of objects in that dataset under desired distribution shifts. We demonstrate how applying our framework to the ImageNet dataset enables us to study model behavior across a diverse array of shifts, including variations in background, lighting, and attributes of the objects themselves. Code available at https://github.com/MadryLab/dataset-interfaces.

Recent advancements in multimodal pre-training methods have shown promising efficacy in 3D representation learning by aligning features across 3D modality, their 2D counterpart modality, and corresponding language modality. However, the methods used by existing multimodal pre-training frameworks to gather multimodal data for 3D applications lack scalability and comprehensiveness, potentially constraining the full potential of multimodal learning. The main bottleneck lies in the language modality's scalability and comprehensiveness. To address this bottleneck, we introduce ULIP-2, a multimodal pre-training framework that leverages state-of-the-art multimodal large language models (LLMs) pre-trained on extensive knowledge to automatically generate holistic language counterparts for 3D objects. We conduct experiments on two large-scale datasets, Objaverse and ShapeNet55, and release our generated three-modality triplet datasets (3D Point Cloud - Image - Language), named "ULIP-Objaverse Triplets" and "ULIP-ShapeNet Triplets". ULIP-2 requires only 3D data itself and eliminates the need for any manual annotation effort, demonstrating its scalability; and ULIP-2 achieves remarkable improvements on downstream zero-shot classification on ModelNet40 (74% Top1 Accuracy). Moreover, ULIP-2 sets a new record on the real-world ScanObjectNN benchmark (91.5% Overall Accuracy) while utilizing only 1.4 million parameters(~10x fewer than current SOTA), signifying a breakthrough in scalable multimodal 3D representation learning without human annotations. The code and datasets are available at https://github.com/salesforce/ULIP.

This paper introduces the first public large-scale, long-span dataset with sea turtle photographs captured in the wild -- SeaTurtleID2022 (https://www.kaggle.com/datasets/wildlifedatasets/seaturtleid2022). The dataset contains 8729 photographs of 438 unique individuals collected within 13 years, making it the longest-spanned dataset for animal re-identification. All photographs include various annotations, e.g., identity, encounter timestamp, and body parts segmentation masks. Instead of standard "random" splits, the dataset allows for two realistic and ecologically motivated splits: (i) a time-aware closed-set with training, validation, and test data from different days/years, and (ii) a time-aware open-set with new unknown individuals in test and validation sets. We show that time-aware splits are essential for benchmarking re-identification methods, as random splits lead to performance overestimation. Furthermore, a baseline instance segmentation and re-identification performance over various body parts is provided. Finally, an end-to-end system for sea turtle re-identification is proposed and evaluated. The proposed system based on Hybrid Task Cascade for head instance segmentation and ArcFace-trained feature-extractor achieved an accuracy of 86.8%.

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.

We present Point2SSM, a novel unsupervised learning approach for constructing correspondence-based statistical shape models (SSMs) directly from raw point clouds. SSM is crucial in clinical research, enabling population-level analysis of morphological variation in bones and organs. Traditional methods of SSM construction have limitations, including the requirement of noise-free surface meshes or binary volumes, reliance on assumptions or templates, and prolonged inference times due to simultaneous optimization of the entire cohort. Point2SSM overcomes these barriers by providing a data-driven solution that infers SSMs directly from raw point clouds, reducing inference burdens and increasing applicability as point clouds are more easily acquired. While deep learning on 3D point clouds has seen success in unsupervised representation learning and shape correspondence, its application to anatomical SSM construction is largely unexplored. We conduct a benchmark of state-of-the-art point cloud deep networks on the SSM task, revealing their limited robustness to clinical challenges such as noisy, sparse, or incomplete input and limited training data. Point2SSM addresses these issues through an attention-based module, providing effective correspondence mappings from learned point features. Our results demonstrate that the proposed method significantly outperforms existing networks in terms of accurate surface sampling and correspondence, better capturing population-level statistics.

Clinical routine and retrospective cohorts commonly include multi-parametric Magnetic Resonance Imaging; however, they are mostly acquired in different anisotropic 2D views due to signal-to-noise-ratio and scan-time constraints. Thus acquired views suffer from poor out-of-plane resolution and affect downstream volumetric image analysis that typically requires isotropic 3D scans. Combining different views of multi-contrast scans into high-resolution isotropic 3D scans is challenging due to the lack of a large training cohort, which calls for a subject-specific framework. This work proposes a novel solution to this problem leveraging Implicit Neural Representations (INR). Our proposed INR jointly learns two different contrasts of complementary views in a continuous spatial function and benefits from exchanging anatomical information between them. Trained within minutes on a single commodity GPU, our model provides realistic super-resolution across different pairs of contrasts in our experiments with three datasets. Using Mutual Information (MI) as a metric, we find that our model converges to an optimum MI amongst sequences, achieving anatomically faithful reconstruction. Code is available at: https://github.com/jqmcginnis/multi_contrast_inr/

The advancements in neural rendering have increased the need for techniques that enable intuitive editing of 3D objects represented as neural implicit surfaces. This paper introduces a novel neural algorithm for parameterizing neural implicit surfaces to simple parametric domains like spheres and polycubes. Our method allows users to specify the number of cubes in the parametric domain, learning a configuration that closely resembles the target 3D object's geometry. It computes bi-directional deformation between the object and the domain using a forward mapping from the object's zero level set and an inverse deformation for backward mapping. We ensure nearly bijective mapping with a cycle loss and optimize deformation smoothness. The parameterization quality, assessed by angle and area distortions, is guaranteed using a Laplacian regularizer and an optimized learned parametric domain. Our framework integrates with existing neural rendering pipelines, using multi-view images of a single object or multiple objects of similar geometries to reconstruct 3D geometry and compute texture maps automatically, eliminating the need for any prior information. We demonstrate the method's effectiveness on images of human heads and man-made objects.

Obtaining large pre-trained models that can be fine-tuned to new tasks with limited annotated samples has remained an open challenge for medical imaging data. While pre-trained deep networks on ImageNet and vision-language foundation models trained on web-scale data are prevailing approaches, their effectiveness on medical tasks is limited due to the significant domain shift between natural and medical images. To bridge this gap, we introduce LVM-Med, the first family of deep networks trained on large-scale medical datasets. We have collected approximately 1.3 million medical images from 55 publicly available datasets, covering a large number of organs and modalities such as CT, MRI, X-ray, and Ultrasound. We benchmark several state-of-the-art self-supervised algorithms on this dataset and propose a novel self-supervised contrastive learning algorithm using a graph-matching formulation. The proposed approach makes three contributions: (i) it integrates prior pair-wise image similarity metrics based on local and global information; (ii) it captures the structural constraints of feature embeddings through a loss function constructed via a combinatorial graph-matching objective; and (iii) it can be trained efficiently end-to-end using modern gradient-estimation techniques for black-box solvers. We thoroughly evaluate the proposed LVM-Med on 15 downstream medical tasks ranging from segmentation and classification to object detection, and both for the in and out-of-distribution settings. LVM-Med empirically outperforms a number of state-of-the-art supervised, self-supervised, and foundation models. For challenging tasks such as Brain Tumor Classification or Diabetic Retinopathy Grading, LVM-Med improves previous vision-language models trained on 1 billion masks by 6-7% while using only a ResNet-50.

Identification of vessel structures of different sizes in biomedical images is crucial in the diagnosis of many neurodegenerative diseases. However, the sparsity of good-quality annotations of such images makes the task of vessel segmentation challenging. Deep learning offers an efficient way to segment vessels of different sizes by learning their high-level feature representations and the spatial continuity of such features across dimensions. Semi-supervised patch-based approaches have been effective in identifying small vessels of one to two voxels in diameter. This study focuses on improving the segmentation quality by considering the spatial correlation of the features using the Maximum Intensity Projection~(MIP) as an additional loss criterion. Two methods are proposed with the incorporation of MIPs of label segmentation on the single~(z-axis) and multiple perceivable axes of the 3D volume. The proposed MIP-based methods produce segmentations with improved vessel continuity, which is evident in visual examinations of ROIs. Patch-based training is improved by introducing an additional loss term, MIP loss, to penalise the predicted discontinuity of vessels. A training set of 14 volumes is selected from the StudyForrest dataset comprising of 18 7-Tesla 3D Time-of-Flight~(ToF) Magnetic Resonance Angiography (MRA) images. The generalisation performance of the method is evaluated using the other unseen volumes in the dataset. It is observed that the proposed method with multi-axes MIP loss produces better quality segmentations with a median Dice of 80.245 pm 0.129. Also, the method with single-axis MIP loss produces segmentations with a median Dice of 79.749 pm 0.109. Furthermore, a visual comparison of the ROIs in the predicted segmentation reveals a significant improvement in the continuity of the vessels when MIP loss is incorporated into training.

The Open Images Dataset contains approximately 9 million images and is a widely accepted dataset for computer vision research. As is common practice for large datasets, the annotations are not exhaustive, with bounding boxes and attribute labels for only a subset of the classes in each image. In this paper, we present a new set of annotations on a subset of the Open Images dataset called the MIAP (More Inclusive Annotations for People) subset, containing bounding boxes and attributes for all of the people visible in those images. The attributes and labeling methodology for the MIAP subset were designed to enable research into model fairness. In addition, we analyze the original annotation methodology for the person class and its subclasses, discussing the resulting patterns in order to inform future annotation efforts. By considering both the original and exhaustive annotation sets, researchers can also now study how systematic patterns in training annotations affect modeling.

Despite the progress in automatic detection of radiologic findings from chest X-ray (CXR) images in recent years, a quantitative evaluation of the explainability of these models is hampered by the lack of locally labeled datasets for different findings. With the exception of a few expert-labeled small-scale datasets for specific findings, such as pneumonia and pneumothorax, most of the CXR deep learning models to date are trained on global "weak" labels extracted from text reports, or trained via a joint image and unstructured text learning strategy. Inspired by the Visual Genome effort in the computer vision community, we constructed the first Chest ImaGenome dataset with a scene graph data structure to describe 242,072 images. Local annotations are automatically produced using a joint rule-based natural language processing (NLP) and atlas-based bounding box detection pipeline. Through a radiologist constructed CXR ontology, the annotations for each CXR are connected as an anatomy-centered scene graph, useful for image-level reasoning and multimodal fusion applications. Overall, we provide: i) 1,256 combinations of relation annotations between 29 CXR anatomical locations (objects with bounding box coordinates) and their attributes, structured as a scene graph per image, ii) over 670,000 localized comparison relations (for improved, worsened, or no change) between the anatomical locations across sequential exams, as well as ii) a manually annotated gold standard scene graph dataset from 500 unique patients.

Deep learning algorithms, in particular convolutional networks, have rapidly become a methodology of choice for analyzing medical images. This paper reviews the major deep learning concepts pertinent to medical image analysis and summarizes over 300 contributions to the field, most of which appeared in the last year. We survey the use of deep learning for image classification, object detection, segmentation, registration, and other tasks and provide concise overviews of studies per application area. Open challenges and directions for future research are discussed.