Mikhail Belyaev

Mikhail Goncharov, Vera Soboleva, Anvar Kurmukov et al.

This paper introduces vox2vec - a contrastive method for self-supervised learning (SSL) of voxel-level representations. vox2vec representations are modeled by a Feature Pyramid Network (FPN): a voxel representation is a concatenation of the corresponding feature vectors from different pyramid levels. The FPN is pre-trained to produce similar representations for the same voxel in different augmented contexts and distinctive representations for different voxels. This results in unified multi-scale representations that capture both global semantics (e.g., body part) and local semantics (e.g., different small organs or healthy versus tumor tissue). We use vox2vec to pre-train a FPN on more than 6500 publicly available computed tomography images. We evaluate the pre-trained representations by attaching simple heads on top of them and training the resulting models for 22 segmentation tasks. We show that vox2vec outperforms existing medical imaging SSL techniques in three evaluation setups: linear and non-linear probing and end-to-end fine-tuning. Moreover, a non-linear head trained on top of the frozen vox2vec representations achieves competitive performance with the FPN trained from scratch while having 50 times fewer trainable parameters. The code is available at https://github.com/mishgon/vox2vec .

Mikhail Goncharov, Valentin Samokhin, Eugenia Soboleva et al.

We propose a self-supervised model producing 3D anatomical positional embeddings (APE) of individual medical image voxels. APE encodes voxels' anatomical closeness, i.e., voxels of the same organ or nearby organs always have closer positional embeddings than the voxels of more distant body parts. In contrast to the existing models of anatomical positional embeddings, our method is able to efficiently produce a map of voxel-wise embeddings for a whole volumetric input image, which makes it an optimal choice for different downstream applications. We train our APE model on 8400 publicly available CT images of abdomen and chest regions. We demonstrate its superior performance compared with the existing models on anatomical landmark retrieval and weakly-supervised few-shot localization of 13 abdominal organs. As a practical application, we show how to cheaply train APE to crop raw CT images to different anatomical regions of interest with 0.99 recall, while reducing the image volume by 10-100 times. The code and the pre-trained APE model are available at https://github.com/mishgon/ape .

Farukh Yaushev, Daria Nogina, Valentin Samokhin et al.

Understanding body part geometry is crucial for precise medical diagnostics. Curves effectively describe anatomical structures and are widely used in medical imaging applications related to cardiovascular, respiratory, and skeletal diseases. Traditional curve detection methods are often task-specific, relying heavily on domain-specific features, limiting their broader applicability. This paper introduces a novel approach for detecting non-branching curves, which does not require prior knowledge of the object's orientation, shape, or position. Our method uses neural networks to predict (1) an attraction field, which offers subpixel accuracy, and (2) a closeness map, which limits the region of interest and essentially eliminates outliers far from the desired curve. We tested our curve detector on several clinically relevant tasks with diverse morphologies and achieved impressive subpixel-level accuracy results that surpass existing methods, highlighting its versatility and robustness. Additionally, to support further advancements in this field, we provide our private annotations of aortic centerlines and masks, which can serve as a benchmark for future research. The dataset can be found at https://github.com/neuro-ml/curve-detection.

David Li, Anvar Kurmukov, Mikhail Goncharov et al.

Recent advances in deep learning have shown that learning robust feature representations is critical for the success of many computer vision tasks, including medical image segmentation. In particular, both transformer and convolutional-based architectures have benefit from leveraging pretext tasks for pretraining. However, the adoption of pretext tasks in 3D medical imaging has been less explored and remains a challenge, especially in the context of learning generalizable feature representations. We propose a novel pretraining strategy using diffusion models with anatomical guidance, tailored to the intricacies of 3D medical image data. We introduce an auxiliary diffusion process to pretrain a model that produce generalizable feature representations, useful for a variety of downstream segmentation tasks. We employ an additional model that predicts 3D universal body-part coordinates, providing guidance during the diffusion process and improving spatial awareness in generated representations. This approach not only aids in resolving localization inaccuracies but also enriches the model's ability to understand complex anatomical structures. Empirical validation on a 13-class organ segmentation task demonstrate the effectiveness of our pretraining technique. It surpasses existing restorative pretraining methods in 3D medical image segmentation by $7.5\%$, and is competitive with the state-of-the-art contrastive pretraining approach, achieving an average Dice coefficient of 67.8 in a non-linear evaluation scenario.

Anvar Kurmukov, Valeria Chernina, Regina Gareeva et al.

Interpretation of chest computed tomography (CT) is time-consuming. Previous studies have measured the time-saving effect of using a deep-learning-based aid (DLA) for CT interpretation. We evaluated the joint impact of a multi-pathology DLA on the time and accuracy of radiologists' reading. 40 radiologists were randomly split into three experimental arms: control (10), who interpret studies without assistance; informed group (10), who were briefed about DLA pathologies, but performed readings without it; and the experimental group (20), who interpreted half studies with DLA, and half without. Every arm used the same 200 CT studies retrospectively collected from BIMCV-COVID19 dataset; each radiologist provided readings for 20 CT studies. We compared interpretation time, and accuracy of participants diagnostic report with respect to 12 pathological findings. Mean reading time per study was 15.6 minutes [SD 8.5] in the control arm, 13.2 minutes [SD 8.7] in the informed arm, 14.4 [SD 10.3] in the experimental arm without DLA, and 11.4 minutes [SD 7.8] in the experimental arm with DLA. Mean sensitivity and specificity were 41.5 [SD 30.4], 86.8 [SD 28.3] in the control arm; 53.5 [SD 22.7], 92.3 [SD 9.4] in the informed non-assisted arm; 63.2 [SD 16.4], 92.3 [SD 8.2] in the experimental arm without DLA; and 91.6 [SD 7.2], 89.9 [SD 6.0] in the experimental arm with DLA. DLA speed up interpretation time per study by 2.9 minutes (CI95 [1.7, 4.3], p<0.0005), increased sensitivity by 28.4 (CI95 [23.4, 33.4], p<0.0005), and decreased specificity by 2.4 (CI95 [0.6, 4.3], p=0.13). Of 20 radiologists in the experimental arm, 16 have improved reading time and sensitivity, two improved their time with a marginal drop in sensitivity, and two participants improved sensitivity with increased time. Overall, DLA introduction decreased reading time by 20.6%.