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AnnotatorJ combines single-cell identification with deep learning and manual annotation. Cellular analysis quality depends on accurate and reliable detection and segmentation of cells so that the subsequent steps of analyses e.g. expression measurements may be carried out precisely and without bias. Deep learning has recently become a popular way of segmenting cells, performing unimaginably better than conventional methods. However, such deep learning applications may be trained on a large amount of annotated data to be able to match the highest expectations. High-quality annotations are unfortunately expensive as they require field experts to create them, and often cannot be shared outside the lab due to medical regulations.
We propose AnnotatorJ, an ImageJ plugin for the semi-automatic annotation of cells (or generally, objects of interest) on (not only) microscopy images in 2D that helps find the true contour of individual objects by applying U-Net-based pre-segmentation. The manual labour of hand-annotating cells can be significantly accelerated by using our tool. Thus, it enables users to create such datasets that could potentially increase the accuracy of state-of-the-art solutions, deep learning or otherwise, when used as training data.
Nowadays, a lot of scientists’ works aim to improve the quality of people’s life but it could be quite complicated without building a successful collaboration. Productive partnerships can increase research efficiency in many cases and make a huge impact on society. However, today there is no clear way to find such collaborators. In this paper, we propose a recommender system for the scientists from the Higher School of Economics university to help them find co-authors for their prospective studies.
In this paper, we study the problem of learning graph embeddings for dynamic networks and the ability to generalize to unseen nodes called inductive learning. Firstly, we overview the state-of-the-art methods and techniques for constructing graph embeddings and learning algorithms for both transductive and inductive approaches. Secondly, we propose an improved GSM based on GraphSAGE algorithm and set up the experiments on datasets CORA, Reddit, and HSEcite, which is collected from Scopus citation database across the authors with affiliation to NRU HSE in 2011–2017. The results show that our three-layer model with attention-based aggregation function, added normalization layers, regularization (dropout) outperforms suggested by the respective authors’ GraphSAGE models with mean, LSTM, and pool aggregation functions, thus giving more insight into possible ways to improve inducting learning model based on GraphSAGE model.