Maxim Sharaev

Marina Pominova, Ekaterina Kondrateva, Maxim Sharaev et al.

ABIDE is the largest open-source autism spectrum disorder database with both fMRI data and full phenotype description. These data were extensively studied based on functional connectivity analysis as well as with deep learning on raw data, with top models accuracy close to 75\% for separate scanning sites. Yet there is still a problem of models transferability between different scanning sites within ABIDE. In the current paper, we for the first time perform domain adaptation for brain pathology classification problem on raw neuroimaging data. We use 3D convolutional autoencoders to build the domain irrelevant latent space image representation and demonstrate this method to outperform existing approaches on ABIDE data.

Maxim Kan, Ruslan Aliev, Anna Rudenko et al.

Deep learning shows high potential for many medical image analysis tasks. Neural networks can work with full-size data without extensive preprocessing and feature generation and, thus, information loss. Recent work has shown that the morphological difference in specific brain regions can be found on MRI with the means of Convolution Neural Networks (CNN). However, interpretation of the existing models is based on a region of interest and can not be extended to voxel-wise image interpretation on a whole image. In the current work, we consider the classification task on a large-scale open-source dataset of young healthy subjects -- an exploration of brain differences between men and women. In this paper, we extend the previous findings in gender differences from diffusion-tensor imaging on T1 brain MRI scans. We provide the voxel-wise 3D CNN interpretation comparing the results of three interpretation methods: Meaningful Perturbations, Grad CAM and Guided Backpropagation, and contribute with the open-source library.

Rinat Prochii, Elizaveta Dakhova, Pavel Birulin et al.

Accurate classification of second-trimester fetal ultrasound images remains challenging due to low image quality, high intra-class variability, and significant class imbalance. In this work, we introduce a simple yet powerful, biologically inspired deep learning ensemble framework that-unlike prior studies focused on only a handful of anatomical targets-simultaneously distinguishes 16 fetal structures. Drawing on the hierarchical, modular organization of biological vision systems, our model stacks two complementary branches (a "shallow" path for coarse, low-resolution cues and a "detailed" path for fine, high-resolution features), concatenating their outputs for final prediction. To our knowledge, no existing method has addressed such a large number of classes with a comparably lightweight architecture. We trained and evaluated on 5,298 routinely acquired clinical images (annotated by three experts and reconciled via Dawid-Skene), reflecting real-world noise and variability rather than a "cleaned" dataset. Despite this complexity, our ensemble (EfficientNet-B0 + EfficientNet-B6 with LDAM-Focal loss) identifies 90% of organs with accuracy > 0.75 and 75% of organs with accuracy > 0.85-performance competitive with more elaborate models applied to far fewer categories. These results demonstrate that biologically inspired modular stacking can yield robust, scalable fetal anatomy recognition in challenging clinical settings.

Ruslan Aliev, Ekaterina Kondrateva, Maxim Sharaev et al.

Focal cortical dysplasia (FCD) is one of the most common epileptogenic lesions associated with cortical development malformations. However, the accurate detection of the FCD relies on the radiologist professionalism, and in many cases, the lesion could be missed. In this work, we solve the problem of automatic identification of FCD on magnetic resonance images (MRI). For this task, we improve recent methods of Deep Learning-based FCD detection and apply it for a dataset of 15 labeled FCD patients. The model results in the successful detection of FCD on 11 out of 15 subjects.

Ekaterina Kondrateva, Marina Pominova, Elena Popova et al.

Machine learning and computer vision methods are showing good performance in medical imagery analysis. Yetonly a few applications are now in clinical use and one of the reasons for that is poor transferability of themodels to data from different sources or acquisition domains. Development of new methods and algorithms forthe transfer of training and adaptation of the domain in multi-modal medical imaging data is crucial for thedevelopment of accurate models and their use in clinics. In present work, we overview methods used to tackle thedomain shift problem in machine learning and computer vision. The algorithms discussed in this survey includeadvanced data processing, model architecture enhancing and featured training, as well as predicting in domaininvariant latent space. The application of the autoencoding neural networks and their domain-invariant variationsare heavily discussed in a survey. We observe the latest methods applied to the magnetic resonance imaging(MRI) data analysis and conclude on their performance as well as propose directions for further research.

Ekaterina Artemova, Amir Bakarov, Aleksey Artemov et al.

In this paper, our focus is the connection and influence of language technologies on the research in neurolinguistics. We present a review of brain imaging-based neurolinguistic studies with a focus on the natural language representations, such as word embeddings and pre-trained language models. Mutual enrichment of neurolinguistics and language technologies leads to development of brain-aware natural language representations. The importance of this research area is emphasized by medical applications.

Marina Pominova, Ekaterina Kondrateva, Maksim Sharaev et al.

Deep learning convolutional neural networks have proved to be a powerful tool for MRI analysis. In current work, we explore the potential of the deformable convolutional deep neural network layers for MRI data classification. We propose new 3D deformable convolutions(d-convolutions), implement them in VoxResNet architecture and apply for structural MRI data classification. We show that 3D d-convolutions outperform standard ones and are effective for unprocessed 3D MR images being robust to particular geometrical properties of the data. Firstly proposed dVoxResNet architecture exhibits high potential for the use in MRI data classification.

Sergey Pavlov, Alexey Artemov, Maksim Sharaev et al.

Segmentation of tumors in brain MRI images is a challenging task, where most recent methods demand large volumes of data with pixel-level annotations, which are generally costly to obtain. In contrast, image-level annotations, where only the presence of lesion is marked, are generally cheap, generated in far larger volumes compared to pixel-level labels, and contain less labeling noise. In the context of brain tumor segmentation, both pixel-level and image-level annotations are commonly available; thus, a natural question arises whether a segmentation procedure could take advantage of both. In the present work we: 1) propose a learning-based framework that allows simultaneous usage of both pixel- and image-level annotations in MRI images to learn a segmentation model for brain tumor; 2) study the influence of comparative amounts of pixel- and image-level annotations on the quality of brain tumor segmentation; 3) compare our approach to the traditional fully-supervised approach and show that the performance of our method in terms of segmentation quality may be competitive.

Marina Pominova, Anna Kuzina, Ekaterina Kondrateva et al.

In this work, we aim at predicting children's fluid intelligence scores based on structural T1-weighted MR images from the largest long-term study of brain development and child health. The target variable was regressed on a data collection site, socio-demographic variables and brain volume, thus being independent to the potentially informative factors, which are not directly related to the brain functioning. We investigate both feature extraction and deep learning approaches as well as different deep CNN architectures and their ensembles. We propose an advanced architecture of VoxCNNs ensemble, which yield MSE (92.838) on blind test.

Maxim Sharaev, Alexander Andreev, Alexey Artemov et al.

As machine learning continues to gain momentum in the neuroscience community, we witness the emergence of novel applications such as diagnostics, characterization, and treatment outcome prediction for psychiatric and neurological disorders, for instance, epilepsy and depression. Systematic research into these mental disorders increasingly involves drawing clinical conclusions on the basis of data-driven approaches; to this end, structural and functional neuroimaging serve as key source modalities. Identification of informative neuroimaging markers requires establishing a comprehensive preparation pipeline for data which may be severely corrupted by artifactual signal fluctuations. In this work, we review a large body of literature to provide ample evidence for the advantages of pattern recognition approaches in clinical applications, overview advanced graph-based pattern recognition approaches, and propose a noise-aware neuroimaging data processing pipeline. To demonstrate the effectiveness of our approach, we provide results from a pilot study, which show a significant improvement in classification accuracy, indicating a promising research direction.

Alexander Bernstein, Evgeny Burnaev, Ekaterina Kondratyeva et al.

We consider a problem of diagnostic pattern recognition/classification from neuroimaging data. We propose a common data analysis pipeline for neuroimaging-based diagnostic classification problems using various ML algorithms and processing toolboxes for brain imaging. We illustrate the pipeline application by discovering new biomarkers for diagnostics of epilepsy and depression based on clinical and MRI/fMRI data for patients and healthy volunteers.