In this work, we present LesionLocator, a framework for zero-shot longitudinal lesion tracking and segmentation in 3D medical imaging, establishing the first end-to-end model capable of 4D tracking with dense spatial prompts. Our model leverages an extensive dataset of 23,262 annotated medical scans, as well as synthesized longitudinal data across diverse lesion types. The diversity and scale of our dataset significantly enhances model generalizability to real-world medical imaging challenges and addresses key limitations in longitudinal data availability. LesionLocator outperforms all existing promptable models in lesion segmentation by nearly 10 dice points, reaching human-level performance, and achieves state-of-the-art results in lesion tracking, with superior lesion retrieval and segmentation accuracy. LesionLocator not only sets a new benchmark in universal promptable lesion segmentation and automated longitudinal lesion tracking but also provides the first open-access solution of its kind, releasing our synthetic 4D dataset and model to the community, empowering future advancements in medical imaging. Code is available at: www.github.com/MIC-DKFZ/LesionLocator

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.

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.

Measuring the similarity of different representations of neural architectures is a fundamental task and an open research challenge for the machine learning community. This paper presents the first comprehensive benchmark for evaluating representational similarity measures based on well-defined groundings of similarity. The representational similarity (ReSi) benchmark consists of (i) six carefully designed tests for similarity measures, (ii) 24 similarity measures, (iii) 14 neural network architectures, and (iv) seven datasets, spanning over the graph, language, and vision domains. The benchmark opens up several important avenues of research on representational similarity that enable novel explorations and applications of neural architectures. We demonstrate the utility of the ReSi benchmark by conducting experiments on various neural network architectures, real world datasets and similarity measures. All components of the benchmark are publicly available and thereby facilitate systematic reproduction and production of research results. The benchmark is extensible, future research can build on and further expand it. We believe that the ReSi benchmark can serve as a sound platform catalyzing future research that aims to systematically evaluate existing and explore novel ways of comparing representations of neural architectures. ReSi is available at https://github.com/mklabunde/resi.

How can we test AI performance? This question seems trivial, but it isn't. Standard benchmarks often have problems such as in-distribution and small-size test sets, oversimplified metrics, unfair comparisons, and short-term outcome pressure. As a consequence, good performance on standard benchmarks does not guarantee success in real-world scenarios. To address these problems, we present Touchstone, a large-scale collaborative segmentation benchmark of 9 types of abdominal organs. This benchmark is based on 5,195 training CT scans from 76 hospitals around the world and 5,903 testing CT scans from 11 additional hospitals. This diverse test set enhances the statistical significance of benchmark results and rigorously evaluates AI algorithms across various out-of-distribution scenarios. We invited 14 inventors of 19 AI algorithms to train their algorithms, while our team, as a third party, independently evaluated these algorithms on three test sets. In addition, we also evaluated pre-existing AI frameworks---which, differing from algorithms, are more flexible and can support different algorithms—including MONAI from NVIDIA, nnU-Net from DKFZ, and numerous other open-source frameworks. We are committed to expanding this benchmark to encourage more innovation of AI algorithms for the medical domain.

What representation do deep neural networks learn? How similar are images to each other for neural networks? Despite the overwhelming success of deep learning methods key questions about their internal workings still remain largely unanswered, due to their internal high dimensionality and complexity. To address this, one approach is to measure the similarity of activation responses to various inputs. Representational Similarity Matrices (RSMs) distill this similarity into scalar values for each input pair. These matrices encapsulate the entire similarity structure of a system, indicating which input lead to similar responses. While the similarity between images is ambiguous, we argue that the spatial location of semantic objects does neither influence human perception nor deep learning classifiers. Thus this should be reflected in the definition of similarity between image responses for computer vision systems. Revisiting the established similarity calculations for RSMs we expose their sensitivity to spatial alignment. In this paper we propose to solve this through _semantic RSMs_, which are invariant to spatial permutation. We measure semantic similarity between input responses by formulating it as a set-matching problem. Further, we quantify the superiority of _semantic_ RSMs over _spatio-semantic_ RSMs through image retrieval and by comparing the similarity between representations to the similarity between predicted class probabilities.

Despite the remarkable success of deep learning systems over the last decade, a key difference still remains between neural network and human decision-making: As humans, we can not only form a decision on the spot, but also ponder, revisiting an initial guess from different angles, distilling relevant information, arriving at a better decision. Here, we propose RecycleNet, a latent feature recycling method, instilling the pondering capability for neural networks to refine initial decisions over a number of recycling steps, where outputs are fed back into earlier network layers in an iterative fashion. This approach makes minimal assumptions about the neural network architecture and thus can be implemented in a wide variety of contexts. Using medical image segmentation as the evaluation environment, we show that latent feature recycling enables the network to iteratively refine initial predictions even beyond the iterations seen during training, converging towards an improved decision. We evaluate this across a variety of segmentation benchmarks and show consistent improvements even compared with top-performing segmentation methods. This allows trading increased computation time for improved performance, which can be beneficial, especially for safety-critical applications.

For reliable environment perception, the use of temporal information is essential in some situations. Especially for object detection, sometimes a situation can only be understood in the right perspective through temporal information. Since image-based object detectors are currently based almost exclusively on CNN architectures, an extension of their feature extraction with temporal features seems promising. Within this work we investigate different architectural components for a CNN-based temporal information extraction. We present a Temporal Feature Network which is based on the insights gained from our architectural investigations. This network is trained from scratch without any ImageNet information based pre-training as these images are not available with temporal information. The object detector based on this network is evaluated against the non-temporal counterpart as baseline and achieves competitive results in an evaluation on the KITTI object detection dataset.