SpheroidPicker for automated 3D cell culture manipulation using deep learning
Recent statistics report that more than 3.7 million new cases of cancer occur in Europe yearly, and the disease accounts for approximately 20% of all deaths. High-throughput screening of cancer cell cultures has dominated the search for novel, effective anticancer therapies in the past decades. Recently, functional assays with patient-derived ex vivo 3D cell culture have gained importance for drug discovery and precision medicine. We recently evaluated the major advancements and needs for the 3D cell culture screening, and concluded that strictly standardized and robust sample preparation is the most desired development. Here we propose an artificial intelligence-guided low-cost 3D cell culture delivery system. It consists of a light microscope, a micromanipulator, a syringe pump, and a controller computer. The system performs morphology-based feature analysis on spheroids and can select uniform sized or shaped spheroids to transfer them between various sample holders. It can select the samples from standard sample holders, including Petri dishes and microwell plates, and then transfer them to a variety of holders up to 384 well plates. The device performs reliable semi- and fully automated spheroid transfer. This results in highly controlled experimental conditions and eliminates non-trivial side effects of sample variability that is a key aspect towards next-generation precision medicine.
Graph-based approaches are empirically shown to be very successful for the nearest neighbor search (NNS). However, there has been very little research on their theoretical guarantees. We fill this gap and rigorously analyze the performance of graph-based NNS algorithms, specifically focusing on the low-dimensional (d << log n) regime. In addition to the basic greedy algorithm on nearest neighbor graphs, we also analyze the most successful heuristics commonly used in practice: speeding up via adding shortcut edges and improving accuracy via maintaining a dynamic list of candidates. We believe that our theoretical insights supported by experimental analysis are an important step towards understanding the limits and benefits of graph-based NNS algorithms.
The paper makes a brief introduction into multiple classifier systems and describes a particular algorithm which improves classification accuracy by making a recommendation of an algorithm to an object. This recommendation is done under a hypothesis that a classifier is likely to predict the label of the object correctly if it has correctly classified its neighbors. The process of assigning a classifier to each object involves here the apparatus of Formal Concept Analysis. We explain the principle of the algorithm on a toy example and describe experiments with real-world datasets.
The volume contains the abstracts of the 12th International Conference "Intelligent Data Processing: Theory and Applications". The conference is organized by the Russian Academy of Sciences, the Federal Research Center "Informatics and Control" of the Russian Academy of Sciences and the Scientific and Coordination Center "Digital Methods of Data Mining". The conference has being held biennially since 1989. It is one of the most recognizable scientific forums on data mining, machine learning, pattern recognition, image analysis, signal processing, and discrete analysis. The Organizing Committee of IDP-2018 is grateful to Forecsys Co. and CFRS Co. for providing assistance in the conference preparation and execution. The conference is funded by RFBR, grant 18-07-20075. The conference website http://mmro.ru/en/.
Data management and analysis is one of the fastest growing and most challenging areas of research and development in both academia and industry. Numerous types of applications and services have been studied and re-examined in this field resulting in this edited volume which includes chapters on effective approaches for dealing with the inherent complexity within data management and analysis. This edited volume contains practical case studies, and will appeal to students, researchers and professionals working in data management and analysis in the business, education, healthcare, and bioinformatics areas.
This paper is an overview of the current issues and tendencies in Computational linguistics. The overview is based on the materials of the conference on computational linguistics COLING’2012. The modern approaches to the traditional NLP domains such as pos-tagging, syntactic parsing, machine translation are discussed. The highlights of automated information extraction, such as fact extraction, opinion mining are also in focus. The main tendency of modern technologies in Computational linguistics is to accumulate the higher level of linguistic analysis (discourse analysis, cognitive modeling) in the models and to combine machine learning technologies with the algorithmic methods on the basis of deep expert linguistic knowledge.
The article is devoted to improving the quality of education in prospective interdisciplinary areas of knowledge such as biomedical engineering. The experience of universities in the U.S.A. and Western Europe is described. Particular attention is paid to the content formation and certification of educating and training programs.
A model for organizing cargo transportation between two node stations connected by a railway line which contains a certain number of intermediate stations is considered. The movement of cargo is in one direction. Such a situation may occur, for example, if one of the node stations is located in a region which produce raw material for manufacturing industry located in another region, and there is another node station. The organization of freight traﬃc is performed by means of a number of technologies. These technologies determine the rules for taking on cargo at the initial node station, the rules of interaction between neighboring stations, as well as the rule of distribution of cargo to the ﬁnal node stations. The process of cargo transportation is followed by the set rule of control. For such a model, one must determine possible modes of cargo transportation and describe their properties. This model is described by a ﬁnite-dimensional system of diﬀerential equations with nonlocal linear restrictions. The class of the solution satisfying nonlocal linear restrictions is extremely narrow. It results in the need for the “correct” extension of solutions of a system of diﬀerential equations to a class of quasi-solutions having the distinctive feature of gaps in a countable number of points. It was possible numerically using the Runge–Kutta method of the fourth order to build these quasi-solutions and determine their rate of growth. Let us note that in the technical plan the main complexity consisted in obtaining quasi-solutions satisfying the nonlocal linear restrictions. Furthermore, we investigated the dependence of quasi-solutions and, in particular, sizes of gaps (jumps) of solutions on a number of parameters of the model characterizing a rule of control, technologies for transportation of cargo and intensity of giving of cargo on a node station.
Event logs collected by modern information and technical systems usually contain enough data for automated process models discovery. A variety of algorithms was developed for process models discovery, conformance checking, log to model alignment, comparison of process models, etc., nevertheless a quick analysis of ad-hoc selected parts of a journal still have not get a full-fledged implementation. This paper describes an ROLAP-based method of multidimensional event logs storage for process mining. The result of the analysis of the journal is visualized as directed graph representing the union of all possible event sequences, ranked by their occurrence probability. Our implementation allows the analyst to discover process models for sublogs defined by ad-hoc selection of criteria and value of occurrence probability