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We develop and evaluate neural architectures to model the user behavior in recommender systems (RS) inspired by click models for Web search but going beyond standard click models. Proposed architectures include recurrent networks, Transformer-based models that alleviate the quadratic complexity of self-attention, adversarial and hierarchical architectures. Our models outperform baselines on the ContentWise and RL4RS datasets and can be used in RS simulators to model user response for RS evaluation and pretraining.

Image compression is a critical tool in decreasing the cost of storage and improving the speed of transmission over the internet. While deep learning applications for natural images widely adopts the usage of lossy compression techniques, it is not widespread for 3D medical images. Using three CT datasets (17 tasks) and one MRI dataset (3 tasks) we demonstrate that lossy compression up to 20 times have no negative impact on segmentation quality with deep neural networks (DNN). In addition, we demonstrate the ability of DNN models trained on compressed data to predict on uncompressed data and vice versa with no quality deterioration., Comment: 12 pages, 5 figures, 2 tables; accepted on MICCAI Workshop on Advancing Data Solutions in Medical Imaging AI

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 .

Methods of computational quantum chemistry provide accurate approximations of molecular properties crucial for computer-aided drug discovery and other areas of chemical science. However, high computational complexity limits the scalability of their applications. Neural network potentials (NNPs) are a promising alternative to quantum chemistry methods, but they require large and diverse datasets for training. This work presents a new dataset and benchmark called $\nabla^2$DFT that is based on the nablaDFT. It contains twice as much molecular structures, three times more conformations, new data types and tasks, and state-of-the-art models. The dataset includes energies, forces, 17 molecular properties, Hamiltonian and overlap matrices, and a wavefunction object. All calculations were performed at the DFT level ($\omega$B97X-D/def2-SVP) for each conformation. Moreover, $\nabla^2$DFT is the first dataset that contains relaxation trajectories for a substantial number of drug-like molecules. We also introduce a novel benchmark for evaluating NNPs in molecular property prediction, Hamiltonian prediction, and conformational optimization tasks. Finally, we propose an extendable framework for training NNPs and implement 10 models within it.

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%., Comment: 17 pages, 6 figures, 8 tables

Detecting out-of-distribution (OOD) samples for trusted medical image segmentation remains a significant challenge. The critical issue here is the lack of a strict definition of abnormal data, which often results in artificial problem settings without measurable clinical impact. In this paper, we redesign the OOD detection problem according to the specifics of volumetric medical imaging and related downstream tasks (e.g., segmentation). We propose using the downstream model's performance as a pseudometric between images to define abnormal samples. This approach enables us to weigh different samples based on their performance impact without an explicit ID/OOD distinction. We incorporate this weighting in a new metric called Expected Performance Drop (EPD). EPD is our core contribution to the new problem design, allowing us to rank methods based on their clinical impact. We demonstrate the effectiveness of EPD-based evaluation in 11 CT and MRI OOD detection challenges.

Boolean satisfiability (SAT) is a fundamental NP-complete problem with many applications, including automated planning and scheduling. To solve large instances, SAT solvers have to rely on heuristics, e.g., choosing a branching variable in DPLL and CDCL solvers. Such heuristics can be improved with machine learning (ML) models; they can reduce the number of steps but usually hinder the running time because useful models are relatively large and slow. We suggest the strategy of making a few initial steps with a trained ML model and then releasing control to classical heuristics; this simplifies cold start for SAT solving and can decrease both the number of steps and overall runtime, but requires a separate decision of when to release control to the solver. Moreover, we introduce a modification of Graph-Q-SAT tailored to SAT problems converted from other domains, e.g., open shop scheduling problems. We validate the feasibility of our approach with random and industrial SAT problems.

Deep Learning models perform unreliably when the data comes from a distribution different from the training one. In critical applications such as medical imaging, out-of-distribution (OOD) detection methods help to identify such data samples, preventing erroneous predictions. In this paper, we further investigate the OOD detection effectiveness when applied to 3D medical image segmentation. We design several OOD challenges representing clinically occurring cases and show that none of these methods achieve acceptable performance. Methods not dedicated to segmentation severely fail to perform in the designed setups; their best mean false positive rate at 95% true positive rate (FPR) is 0.59. Segmentation-dedicated ones still achieve suboptimal performance, with the best mean FPR of 0.31 (lower is better). To indicate this suboptimality, we develop a simple method called Intensity Histogram Features (IHF), which performs comparable or better in the same challenges, with a mean FPR of 0.25. Our findings highlight the limitations of the existing OOD detection methods on 3D medical images and present a promising avenue for improving them. To facilitate research in this area, we release the designed challenges as a publicly available benchmark and formulate practical criteria to test the OOD detection generalization beyond the suggested benchmark. We also propose IHF as a solid baseline to contest the emerging methods., Comment: This work has been submitted to the IEEE for possible publication. 10 pages, 5 figures, 5 tables

Deep Learning (DL) models tend to perform poorly when the data comes from a distribution different from the training one. In critical applications such as medical imaging, out-of-distribution (OOD) detection helps to identify such data samples, increasing the model's reliability. Recent works have developed DL-based OOD detection that achieves promising results on 2D medical images. However, scaling most of these approaches on 3D images is computationally intractable. Furthermore, the current 3D solutions struggle to achieve acceptable results in detecting even synthetic OOD samples. Such limited performance might indicate that DL often inefficiently embeds large volumetric images. We argue that using the intensity histogram of the original CT or MRI scan as embedding is descriptive enough to run OOD detection. Therefore, we propose a histogram-based method that requires no DL and achieves almost perfect results in this domain. Our proposal is supported two-fold. We evaluate the performance on the publicly available datasets, where our method scores 1.0 AUROC in most setups. And we score second in the Medical Out-of-Distribution challenge without fine-tuning and exploiting task-specific knowledge. Carefully discussing the limitations, we conclude that our method solves the sample-level OOD detection on 3D medical images in the current setting., Comment: We had made a mistake in the proposed algorithm's code (IHF), which led to a biased evaluation -- the reported AUROC scores (Tab. 1) are higher than they should be. It led to a false conclusion and the primary paper's message

When applying a Deep Learning model to medical images, it is crucial to estimate the model uncertainty. Voxel-wise uncertainty is a useful visual marker for human experts and could be used to improve the model's voxel-wise output, such as segmentation. Moreover, uncertainty provides a solid foundation for out-of-distribution (OOD) detection, improving the model performance on the image-wise level. However, one of the frequent tasks in medical imaging is the segmentation of distinct, local structures such as tumors or lesions. Here, the structure-wise uncertainty allows more precise operations than image-wise and more semantic-aware than voxel-wise. The way to produce uncertainty for individual structures remains poorly explored. We propose a framework to measure the structure-wise uncertainty and evaluate the impact of OOD data on the model performance. Thus, we identify the best UE method to improve the segmentation quality. The proposed framework is tested on three datasets with the tumor segmentation task: LIDC-IDRI, LiTS, and a private one with multiple brain metastases cases.

Magnetic resonance imaging (MRI) data is heterogeneous due to differences in device manufacturers, scanning protocols, and inter-subject variability. A conventional way to mitigate MR image heterogeneity is to apply preprocessing transformations such as anatomy alignment, voxel resampling, signal intensity equalization, image denoising, and localization of regions of interest. Although a preprocessing pipeline standardizes image appearance, its influence on the quality of image segmentation and on other downstream tasks in deep neural networks has never been rigorously studied. We conduct experiments on three publicly available datasets and evaluate the effect of different preprocessing steps in intra- and inter-dataset training scenarios. Our results demonstrate that most popular standardization steps add no value to the network performance; moreover, preprocessing can hamper model performance. We suggest that image intensity normalization approaches do not contribute to model accuracy because of the reduction of signal variance with image standardization. Finally, we show that the contribution of skull-stripping in data preprocessing is almost negligible if measured in terms of estimated tumor volume. We show that the only essential transformation for accurate deep learning analysis is the unification of voxel spacing across the dataset. In contrast, inter-subjects anatomy alignment in the form of non-rigid atlas registration is not necessary and intensity equalization steps (denoising, bias-field correction and histogram matching) do not improve models' performance. The study code is accessible online https://github.com/MedImAIR/brain-mri-processing-pipeline

Deep learning methods provide significant assistance in analyzing coronavirus disease (COVID-19) in chest computed tomography (CT) images, including identification, severity assessment, and segmentation. Although the earlier developed methods address the lack of data and specific annotations, the current goal is to build a robust algorithm for clinical use, having a larger pool of available data. With the larger datasets, the domain shift problem arises, affecting the performance of methods on the unseen data. One of the critical sources of domain shift in CT images is the difference in reconstruction kernels used to generate images from the raw data (sinograms). In this paper, we show a decrease in the COVID-19 segmentation quality of the model trained on the smooth and tested on the sharp reconstruction kernels. Furthermore, we compare several domain adaptation approaches to tackle the problem, such as task-specific augmentation and unsupervised adversarial learning. Finally, we propose the unsupervised adaptation method, called F-Consistency, that outperforms the previous approaches. Our method exploits a set of unlabeled CT image pairs which differ only in reconstruction kernels within every pair. It enforces the similarity of the network hidden representations (feature maps) by minimizing mean squared error (MSE) between paired feature maps. We show our method achieving 0.64 Dice Score on the test dataset with unseen sharp kernels, compared to the 0.56 Dice Score of the baseline model. Moreover, F-Consistency scores 0.80 Dice Score between predictions on the paired images, which almost doubles the baseline score of 0.46 and surpasses the other methods. We also show F-Consistency to better generalize on the unseen kernels and without the specific semantic content, e.g., presence of the COVID-19 lesions.

Domain Adaptation (DA) has recently raised strong interests in the medical imaging community. While a large variety of DA techniques has been proposed for image segmentation, most of these techniques have been validated either on private datasets or on small publicly available datasets. Moreover, these datasets mostly addressed single-class problems. To tackle these limitations, the Cross-Modality Domain Adaptation (crossMoDA) challenge was organised in conjunction with the 24th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2021). CrossMoDA is the first large and multi-class benchmark for unsupervised cross-modality DA. The challenge's goal is to segment two key brain structures involved in the follow-up and treatment planning of vestibular schwannoma (VS): the VS and the cochleas. Currently, the diagnosis and surveillance in patients with VS are performed using contrast-enhanced T1 (ceT1) MRI. However, there is growing interest in using non-contrast sequences such as high-resolution T2 (hrT2) MRI. Therefore, we created an unsupervised cross-modality segmentation benchmark. The training set provides annotated ceT1 (N=105) and unpaired non-annotated hrT2 (N=105). The aim was to automatically perform unilateral VS and bilateral cochlea segmentation on hrT2 as provided in the testing set (N=137). A total of 16 teams submitted their algorithm for the evaluation phase. The level of performance reached by the top-performing teams is strikingly high (best median Dice - VS:88.4%; Cochleas:85.7%) and close to full supervision (median Dice - VS:92.5%; Cochleas:87.7%). All top-performing methods made use of an image-to-image translation approach to transform the source-domain images into pseudo-target-domain images. A segmentation network was then trained using these generated images and the manual annotations provided for the source image., Comment: In Medical Image Analysis

We systematically evaluate a Deep Learning (DL) method in a 3D medical image segmentation task. Our segmentation method is integrated into the radiosurgery treatment process and directly impacts the clinical workflow. With our method, we address the relative drawbacks of manual segmentation: high inter-rater contouring variability and high time consumption of the contouring process. The main extension over the existing evaluations is the careful and detailed analysis that could be further generalized on other medical image segmentation tasks. Firstly, we analyze the changes in the inter-rater detection agreement. We show that the segmentation model reduces the ratio of detection disagreements from 0.162 to 0.085 (p < 0.05). Secondly, we show that the model improves the inter-rater contouring agreement from 0.845 to 0.871 surface Dice Score (p < 0.05). Thirdly, we show that the model accelerates the delineation process in between 1.6 and 2.0 times (p < 0.05). Finally, we design the setup of the clinical experiment to either exclude or estimate the evaluation biases, thus preserve the significance of the results. Besides the clinical evaluation, we also summarize the intuitions and practical ideas for building an efficient DL-based model for 3D medical image segmentation.

Domain shift is one of the most salient challenges in medical computer vision. Due to immense variability in scanners' parameters and imaging protocols, even images obtained from the same person and the same scanner could differ significantly. We address variability in computed tomography (CT) images caused by different convolution kernels used in the reconstruction process, the critical domain shift factor in CT. The choice of a convolution kernel affects pixels' granularity, image smoothness, and noise level. We analyze a dataset of paired CT images, where smooth and sharp images were reconstructed from the same sinograms with different kernels, thus providing identical anatomy but different style. Though identical predictions are desired, we show that the consistency, measured as the average Dice between predictions on pairs, is just 0.54. We propose Filtered Back-Projection Augmentation (FBPAug), a simple and surprisingly efficient approach to augment CT images in sinogram space emulating reconstruction with different kernels. We apply the proposed method in a zero-shot domain adaptation setup and show that the consistency boosts from 0.54 to 0.92 outperforming other augmentation approaches. Neither specific preparation of source domain data nor target domain data is required, so our publicly released FBPAug can be used as a plug-and-play module for zero-shot domain adaptation in any CT-based task., Comment: table fixed

Domain Adaptation (DA) methods are widely used in medical image segmentation tasks to tackle the problem of differently distributed train (source) and test (target) data. We consider the supervised DA task with a limited number of annotated samples from the target domain. It corresponds to one of the most relevant clinical setups: building a sufficiently accurate model on the minimum possible amount of annotated data. Existing methods mostly fine-tune specific layers of the pretrained Convolutional Neural Network (CNN). However, there is no consensus on which layers are better to fine-tune, e.g. the first layers for images with low-level domain shift or the deeper layers for images with high-level domain shift. To this end, we propose SpotTUnet - a CNN architecture that automatically chooses the layers which should be optimally fine-tuned. More specifically, on the target domain, our method additionally learns the policy that indicates whether a specific layer should be fine-tuned or reused from the pretrained network. We show that our method performs at the same level as the best of the nonflexible fine-tuning methods even under the extreme scarcity of annotated data. Secondly, we show that SpotTUnet policy provides a layer-wise visualization of the domain shift impact on the network, which could be further used to develop robust domain generalization methods. In order to extensively evaluate SpotTUnet performance, we use a publicly available dataset of brain MR images (CC359), characterized by explicit domain shift. We release a reproducible experimental pipeline., Comment: Accepted for MICCAI-2021 conference

MRI scans appearance significantly depends on scanning protocols and, consequently, the data-collection institution. These variations between clinical sites result in dramatic drops of CNN segmentation quality on unseen domains. Many of the recently proposed MRI domain adaptation methods operate with the last CNN layers to suppress domain shift. At the same time, the core manifestation of MRI variability is a considerable diversity of image intensities. We hypothesize that these differences can be eliminated by modifying the first layers rather than the last ones. To validate this simple idea, we conducted a set of experiments with brain MRI scans from six domains. Our results demonstrate that 1) domain-shift may deteriorate the quality even for a simple brain extraction segmentation task (surface Dice Score drops from 0.85-0.89 even to 0.09); 2) fine-tuning of the first layers significantly outperforms fine-tuning of the last layers in almost all supervised domain adaptation setups. Moreover, fine-tuning of the first layers is a better strategy than fine-tuning of the whole network, if the amount of annotated data from the new domain is strictly limited., Comment: Accepted to DART workshop at MICCAI-2020

Target imbalance affects the performance of recent deep learning methods in many medical image segmentation tasks. It is a twofold problem: class imbalance - positive class (lesion) size compared to negative class (non-lesion) size; lesion size imbalance - large lesions overshadows small ones (in the case of multiple lesions per image). While the former was addressed in multiple works, the latter lacks investigation. We propose a loss reweighting approach to increase the ability of the network to detect small lesions. During the learning process, we assign a weight to every image voxel. The assigned weights are inversely proportional to the lesion volume, thus smaller lesions get larger weights. We report the benefit from our method for well-known loss functions, including Dice Loss, Focal Loss, and Asymmetric Similarity Loss. Additionally, we compare our results with other reweighting techniques: Weighted Cross-Entropy and Generalized Dice Loss. Our experiments show that inverse weighting considerably increases the detection quality, while preserves the delineation quality on a state-of-the-art level. We publish a complete experimental pipeline for two publicly available datasets of CT images: LiTS and LUNA16 (https://github.com/neuro-ml/inverse_weighting). We also show results on a private database of MR images for the task of multiple brain metastases delineation., Comment: Accepted to MICCAI 2020