Un-Mixing Test-Time Normalization Statistics: Combatting Label Temporal Correlation

In an era where test-time adaptation methods increasingly rely on the nuanced manipulation of batch normalization (BN) parameters, one critical assumption often goes overlooked: that of independently and identically distributed (i.i.d.) test batches with respect to unknown labels. This assumption culminates in biased estimates of BN statistics and jeopardizes system stability under non-i.i.d. conditions. This paper pioneers a departure from the i.i.d. paradigm by introducing a groundbreaking strategy termed "Un-Mixing Test-Time Normalization Statistics" (UnMix-TNS). UnMix-TNS re-calibrates the instance-wise statistics used to normalize each instance in a batch by mixing it with multiple unmixed statistics components, thus inherently simulating the i.i.d. environment. The key lies in our innovative online unmixing procedure, which persistently refines these statistics components by drawing upon the closest instances from an incoming test batch. Remarkably generic in its design, UnMix-TNS seamlessly integrates with an array of state-of-the-art test-time adaptation methods and pre-trained architectures equipped with BN layers. Empirical evaluations corroborate the robustness of UnMix-TNS under varied scenarios ranging from single to continual and mixed domain shifts. UnMix-TNS stands out when handling test data streams with temporal correlation, including those with corrupted real-world non-i.i.d. streams, sustaining its efficacy even with minimal batch sizes and individual samples. Our results set a new standard for test-time adaptation, demonstrating significant improvements in both stability and performance across multiple benchmarks.

Cross-Age and Cross-Site Domain Shift Impacts on Deep Learning-Based White Matter Fiber Estimation in Newborn and Baby Brains

Deep learning models have shown great promise in estimating tissue microstructure from limited diffusion magnetic resonance imaging data. However, these models face domain shift challenges when test and train data are from different scanners and protocols, or when the models are applied to data with inherent variations such as the developing brains of infants and children scanned at various ages. Several techniques have been proposed to address some of these challenges, such as data harmonization or domain adaptation in the adult brain. However, those techniques remain unexplored for the estimation of fiber orientation distribution functions in the rapidly developing brains of infants. In this work, we extensively investigate the age effect and domain shift within and across two different cohorts of 201 newborns and 165 babies using the Method of Moments and fine-tuning strategies. Our results show that reduced variations in the microstructural development of babies in comparison to newborns directly impact the deep learning models' cross-age performance. We also demonstrate that a small number of target domain samples can significantly mitigate domain shift problems.

CrIBo: Self-Supervised Learning via Cross-Image Object-Level Bootstrapping

Leveraging nearest neighbor retrieval for self-supervised representation learning has proven beneficial with object-centric images. However, this approach faces limitations when applied to scene-centric datasets, where multiple objects within an image are only implicitly captured in the global representation. Such global bootstrapping can lead to undesirable entanglement of object representations. Furthermore, even object-centric datasets stand to benefit from a finer-grained bootstrapping approach. In response to these challenges, we introduce a novel Cross-Image Object-Level Bootstrapping method tailored to enhance dense visual representation learning. By employing object-level nearest neighbor bootstrapping throughout the training, CrIBo emerges as a notably strong and adequate candidate for in-context learning, leveraging nearest neighbor retrieval at test time. CrIBo shows state-of-the-art performance on the latter task while being highly competitive in more standard downstream segmentation tasks. Our code and pretrained models will be publicly available upon acceptance.

AMAE: Adaptation of Pre-Trained Masked Autoencoder for Dual-Distribution Anomaly Detection in Chest X-Rays

Unsupervised anomaly detection in medical images such as chest radiographs is stepping into the spotlight as it mitigates the scarcity of the labor-intensive and costly expert annotation of anomaly data. However, nearly all existing methods are formulated as a one-class classification trained only on representations from the normal class and discard a potentially significant portion of the unlabeled data. This paper focuses on a more practical setting, dual distribution anomaly detection for chest X-rays, using the entire training data, including both normal and unlabeled images. Inspired by a modern self-supervised vision transformer model trained using partial image inputs to reconstruct missing image regions -- we propose AMAE, a two-stage algorithm for adaptation of the pre-trained masked autoencoder (MAE). Starting from MAE initialization, AMAE first creates synthetic anomalies from only normal training images and trains a lightweight classifier on frozen transformer features. Subsequently, we propose an adaptation strategy to leverage unlabeled images containing anomalies. The adaptation scheme is accomplished by assigning pseudo-labels to unlabeled images and using two separate MAE based modules to model the normative and anomalous distributions of pseudo-labeled images. The effectiveness of the proposed adaptation strategy is evaluated with different anomaly ratios in an unlabeled training set. AMAE leads to consistent performance gains over competing self-supervised and dual distribution anomaly detection methods, setting the new state-of-the-art on three public chest X-ray benchmarks: RSNA, NIH-CXR, and VinDr-CXR.

Source-Free Open-Set Domain Adaptation for Histopathological Images via Distilling Self-Supervised Vision Transformer

There is a strong incentive to develop computational pathology models to i) ease the burden of tissue typology annotation from whole slide histological images; ii) transfer knowledge, e.g., tissue class separability from the withheld source domain to the distributionally shifted unlabeled target domain, and simultaneously iii) detect Open Set samples, i.e., unseen novel categories not present in the training source domain. This paper proposes a highly practical setting by addressing the abovementioned challenges in one fell swoop, i.e., source-free Open Set domain adaptation (SF-OSDA), which addresses the situation where a model pre-trained on the inaccessible source dataset can be adapted on the unlabeled target dataset containing Open Set samples. The central tenet of our proposed method is distilling knowledge from a self-supervised vision transformer trained in the target domain. We propose a novel style-based data augmentation used as hard positives for self-training a vision transformer in the target domain, yielding strongly contextualized embedding. Subsequently, semantically similar target images are clustered while the source model provides their corresponding weak pseudo-labels with unreliable confidence. Furthermore, we propose cluster relative maximum logit score (CRMLS) to rectify the confidence of the weak pseudo-labels and compute weighted class prototypes in the contextualized embedding space that are utilized for adapting the source model on the target domain. Our method significantly outperforms the previous methods, including open set detection, test-time adaptation, and SF-OSDA methods, setting the new state-of-the-art on three public histopathological datasets of colorectal cancer (CRC) assessment- Kather-16, Kather-19, and CRCTP. Our code is available at https://github.com/LTS5/Proto-SF-OSDA.

Fast refacing of MR images with a generative neural network lowers re-identification risk and preserves volumetric consistency

With the rise of open data, identifiability of individuals based on 3D renderings obtained from routine structural magnetic resonance imaging (MRI) scans of the head has become a growing privacy concern. To protect subject privacy, several algorithms have been developed to de-identify imaging data using blurring, defacing or refacing. Completely removing facial structures provides the best re-identification protection but can significantly impact post-processing steps, like brain morphometry. As an alternative, refacing methods that replace individual facial structures with generic templates have a lower effect on the geometry and intensity distribution of original scans, and are able to provide more consistent post-processing results by the price of higher re-identification risk and computational complexity. In the current study, we propose a novel method for anonymised face generation for defaced 3D T1-weighted scans based on a 3D conditional generative adversarial network. To evaluate the performance of the proposed de-identification tool, a comparative study was conducted between several existing defacing and refacing tools, with two different segmentation algorithms (FAST and Morphobox). The aim was to evaluate (i) impact on brain morphometry reproducibility, (ii) re-identification risk, (iii) balance between (i) and (ii), and (iv) the processing time. The proposed method takes 9 seconds for face generation and is suitable for recovering consistent post-processing results after defacing.

Neural Implicit Dense Semantic SLAM

Visual Simultaneous Localization and Mapping (vSLAM) is a widely used technique in robotics and computer vision that enables a robot to create a map of an unfamiliar environment using a camera sensor while simultaneously tracking its position over time. In this paper, we propose a novel RGBD vSLAM algorithm that can learn a memory-efficient, dense 3D geometry, and semantic segmentation of an indoor scene in an online manner. Our pipeline combines classical 3D vision-based tracking and loop closing with neural fields-based mapping. The mapping network learns the SDF of the scene as well as RGB, depth, and semantic maps of any novel view using only a set of keyframes. Additionally, we extend our pipeline to large scenes by using multiple local mapping networks. Extensive experiments on well-known benchmark datasets confirm that our approach provides robust tracking, mapping, and semantic labeling even with noisy, sparse, or no input depth. Overall, our proposed algorithm can greatly enhance scene perception and assist with a range of robot control problems.

Cellular EXchange Imaging (CEXI): Evaluation of a diffusion model including water exchange in cells using numerical phantoms of permeable spheres

Purpose: Biophysical models of diffusion MRI have been developed to characterize microstructure in various tissues, but existing models are not suitable for tissue composed of permeable spherical cells. In this study we introduce Cellular Exchange Imaging (CEXI), a model tailored for permeable spherical cells, and compares its performance to a related Ball \& Sphere (BS) model that neglects permeability. Methods: We generated DW-MRI signals using Monte-Carlo simulations with a PGSE sequence in numerical substrates made of spherical cells and their extracellular space for a range of membrane permeability. From these signals, the properties of the substrates were inferred using both BS and CEXI models. Results: CEXI outperformed the impermeable model by providing more stable estimates cell size and intracellular volume fraction that were diffusion time-independent. Notably, CEXI accurately estimated the exchange time for low to moderate permeability levels previously reported in other studies ($\kappa<25\mu m/s$). However, in highly permeable substrates ($\kappa=50\mu m/s$), the estimated parameters were less stable, particularly the diffusion coefficients. Conclusion: This study highlights the importance of modeling the exchange time to accurately quantify microstructure properties in permeable cellular substrates. Future studies should evaluate CEXI in clinical applications such as lymph nodes, investigate exchange time as a potential biomarker of tumor severity, and develop more appropriate tissue models that account for anisotropic diffusion and highly permeable membranes.