Tony Xu

Tony Xu, Sarah Klamt, Katherine Turner et al.

GPU-accelerated Self-Organizing Map (SOM) implementations are among the most competitive options for large-scale SOM analysis, but growing dataset sizes increasingly challenge their practical use because workloads no longer fit cleanly within device-memory limits. We introduce FloatSOM, a SOM framework for scalable training and deployment that supports multi-GPU execution, out-of-memory disk-backed streaming, and novel topologies beyond regular lattices. We evaluate FloatSOM on 14 synthetic and real benchmark datasets together with controlled speed scaling benchmarks, and show that these improved topologies, combined with topology-aware hyperparameter fine-tuning, yield lower quantization error than current state-of-the-art SOM baselines. FloatSOM also sustains this performance at large scale with high-throughput distributed execution; in the largest benchmark, it trains a 1024-node SOM network on 1,000,000,000 samples with 50 features in 6.16 minutes on 8 GPUs across two separate high-performance-computing nodes.

Lidia Garrucho, Smriti Joshi, Kaisar Kushibar et al.

Breast cancer is the most frequently diagnosed malignancy among women worldwide and a leading cause of cancer-related mortality. Dynamic contrast-enhanced magnetic resonance imaging plays a central role in tumor characterization and treatment monitoring, particularly in patients receiving neoadjuvant chemotherapy. However, existing artificial intelligence models for breast magnetic resonance imaging are often developed using single-center data and evaluated using aggregate performance metrics, limiting their generalizability and obscuring potential performance disparities across demographic subgroups. The MAMA-MIA Challenge was designed to address these limitations by introducing a large-scale benchmark that jointly evaluates primary tumor segmentation and prediction of pathologic complete response using pre-treatment magnetic resonance imaging only. The training cohort comprised 1,506 patients from multiple institutions in the United States, while evaluation was conducted on an external test set of 574 patients from three independent European centers to assess cross-continental and cross-institutional generalization. A unified scoring framework combined predictive performance with subgroup consistency across age, menopausal status, and breast density. Twenty-six international teams participated in the final evaluation phase. Results demonstrate substantial performance variability under external testing and reveal trade-offs between overall accuracy and subgroup fairness. The challenge provides standardized datasets, evaluation protocols, and public resources to promote the development of robust and equitable artificial intelligence systems for breast cancer imaging.

Ozan Ciga, Tony Xu, Anne L. Martel

Unsupervised learning has been a long-standing goal of machine learning and is especially important for medical image analysis, where the learning can compensate for the scarcity of labeled datasets. A promising subclass of unsupervised learning is self-supervised learning, which aims to learn salient features using the raw input as the learning signal. In this paper, we use a contrastive self-supervised learning method called SimCLR that achieved state-of-the-art results on natural-scene images and apply this method to digital histopathology by collecting and pretraining on 57 histopathology datasets without any labels. We find that combining multiple multi-organ datasets with different types of staining and resolution properties improves the quality of the learned features. Furthermore, we find using more images for pretraining leads to a better performance in multiple downstream tasks. Linear classifiers trained on top of the learned features show that networks pretrained on digital histopathology datasets perform better than ImageNet pretrained networks, boosting task performances by more than 28% in F1 scores on average. These findings may also be useful when applying newer contrastive techniques to histopathology data. Pretrained PyTorch models are made publicly available at https://github.com/ozanciga/self-supervised-histopathology.

Tony Xu, Sepehr Hosseini, Chris Anderson et al.

Current self-supervised learning methods for 3D medical imaging rely on simple pretext formulations and organ- or modality-specific datasets, limiting their generalizability and scalability. We present 3DINO, a cutting-edge SSL method adapted to 3D datasets, and use it to pretrain 3DINO-ViT: a general-purpose medical imaging model, on an exceptionally large, multimodal, and multi-organ dataset of ~100,000 3D medical imaging scans from over 10 organs. We validate 3DINO-ViT using extensive experiments on numerous medical imaging segmentation and classification tasks. Our results demonstrate that 3DINO-ViT generalizes across modalities and organs, including out-of-distribution tasks and datasets, outperforming state-of-the-art methods on the majority of evaluation metrics and labeled dataset sizes. Our 3DINO framework and 3DINO-ViT will be made available to enable research on 3D foundation models or further finetuning for a wide range of medical imaging applications.

Ying Chen, Rami Al-Maskari, Izabela Horvath et al.

Recent innovations in light sheet microscopy, paired with developments in tissue clearing techniques, enable the 3D imaging of large mammalian tissues with cellular resolution. Combined with the progress in large-scale data analysis, driven by deep learning, these innovations empower researchers to rapidly investigate the morphological and functional properties of diverse biological samples. Segmentation, a crucial preliminary step in the analysis process, can be automated using domain-specific deep learning models with expert-level performance. However, these models exhibit high sensitivity to domain shifts, leading to a significant drop in accuracy when applied to data outside their training distribution. To address this limitation, and inspired by the recent success of self-supervised learning in training generalizable models, we organized the SELMA3D Challenge during the MICCAI 2024 conference. SELMA3D provides a vast collection of light-sheet images from cleared mice and human brains, comprising 35 large 3D images-each with over 1000^3 voxels-and 315 annotated small patches for finetuning, preliminary testing and final testing. The dataset encompasses diverse biological structures, including vessel-like and spot-like structures. Five teams participated in all phases of the challenge, and their proposed methods are reviewed in this paper. Quantitative and qualitative results from most participating teams demonstrate that self-supervised learning on large datasets improves segmentation model performance and generalization. We will continue to support and extend SELMA3D as an inaugural MICCAI challenge focused on self-supervised learning for 3D microscopy image segmentation.

Ozan Ciga, Tony Xu, Sharon Nofech-Mozes et al.

Whole slide images (WSIs) pose unique challenges when training deep learning models. They are very large which makes it necessary to break each image down into smaller patches for analysis, image features have to be extracted at multiple scales in order to capture both detail and context, and extreme class imbalances may exist. Significant progress has been made in the analysis of these images, thanks largely due to the availability of public annotated datasets. We postulate, however, that even if a method scores well on a challenge task, this success may not translate to good performance in a more clinically relevant workflow. Many datasets consist of image patches which may suffer from data curation bias; other datasets are only labelled at the whole slide level and the lack of annotations across an image may mask erroneous local predictions so long as the final decision is correct. In this paper, we outline the differences between patch or slide-level classification versus methods that need to localize or segment cancer accurately across the whole slide, and we experimentally verify that best practices differ in both cases. We apply a binary cancer detection network on post neoadjuvant therapy breast cancer WSIs to find the tumor bed outlining the extent of cancer, a task which requires sensitivity and precision across the whole slide. We extensively study multiple design choices and their effects on the outcome, including architectures and augmentations. Furthermore, we propose a negative data sampling strategy, which drastically reduces the false positive rate (7% on slide level) and improves each metric pertinent to our problem, with a 15% reduction in the error of tumor extent.

Ademola Oladosu, Tony Xu, Philip Ekfeldt et al.

This paper presents a meta-learning framework for few-shots One-Class Classification (OCC) at test-time, a setting where labeled examples are only available for the positive class, and no supervision is given for the negative example. We consider that we have a set of `one-class classification' objective-tasks with only a small set of positive examples available for each task, and a set of training tasks with full supervision (i.e. highly imbalanced classification). We propose an approach using order-equivariant networks to learn a 'meta' binary-classifier. The model will take as input an example to classify from a given task, as well as the corresponding supervised set of positive examples for this OCC task. Thus, the output of the model will be 'conditioned' on the available positive example of a given task, allowing to predict on new tasks and new examples without labeled negative examples. In this paper, we are motivated by an astronomy application. Our goal is to identify if stars belong to a specific stellar group (the 'one-class' for a given task), called \textit{stellar streams}, where each stellar stream is a different OCC-task. We show that our method transfers well on unseen (test) synthetic streams, and outperforms the baselines even though it is not retrained and accesses a much smaller part of the data per task to predict (only positive supervision). We see however that it doesn't transfer as well on the real stream GD-1. This could come from intrinsic differences from the synthetic and real stream, highlighting the need for consistency in the 'nature' of the task for this method. However, light fine-tuning improve performances and outperform our baselines. Our experiments show encouraging results to further explore meta-learning methods for OCC tasks.