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Object-Attribute Biclustering for Elimination of Missing Genotypes in Ischemic Stroke Genome-Wide Data
Springer
,
2020.
Ignatov D. I., Khvorykh G. V., Khrunin A. V., Nikolic S., Shaban M., Petrova E. A., Koltsova E. A., Fouzi T., Egurnov D.
In press
Missing genotypes can affect the effcacy of machine learning approaches to identify the risk genetic variants of common diseases and traits. The problem occurs when genotypic data are collected from different experiments with different DNA microarrays, each being characterised by its pattern of uncalled (missing) genotypes. This can prevent the machine learning classifier from assigning the classes correctly. To tackle this issue, we used well-developed notions of object-attribute biclusters and formal concepts that correspond to dense subrelations in the binary relation patients x SNPs. The paper contains experimental results on applying a biclustering algorithm to a large real-world dataset collected for studying the genetic bases of ischemic stroke. The algorithm could identify large dense biclusters in the genotypic matrix for further processing, which in return significantly improved the quality of machine learning classifiers. The proposed algorithm was also able to generate biclusters for the whole dataset without size constraints in comparison to the In-Close4 algorithm for generation of formal concepts.
Egurnov D., Ignatov D. I., Точилкин Д. С., / Springer. Series LNCS "Lecture Notes in Computer Science". 2020.
In this paper, we describe versions of triclustering algorithms adapted for efficient calculations in distributed environments with MapReduce model or parallelisation mechanism provided by modern programming languages. OAC-family of triclustering algorithms shows good parallelisation capabilities due to the independent processing of triples of a triadic formal context. We provide the time and space complexity of ...
Added: November 10, 2020
Ignatov D. I., Khvorykh G., Khrunin A. et al., , in : Recent Trends in Analysis of Images, Social Networks and Texts. 9th International Conference, AIST 2020, Skolkovo, Moscow, Russia, October 15–16, 2020 Revised Supplementary Proceedings. Vol. 12602.: Springer, 2021. P. 185-204.
© 2021, Springer Nature Switzerland AG.Missing genotypes can affect the efficacy of machine learning approaches to identify the risk genetic variants of common diseases and traits. The problem occurs when genotypic data are collected from different experiments with different DNA microarrays, each being characterised by its pattern of uncalled (missing) genotypes. This can prevent the ...
Added: November 1, 2022
CEUR Workshop Proceedings, 2019
Added: October 31, 2019
M. : Higher School of Economics Publishing House, 2011
Concept discovery is a Knowledge Discovery in Databases (KDD) research field that uses human-centered techniques such as Formal Concept Analysis (FCA), Biclustering, Triclustering, Conceptual Graphs etc. for gaining insight into the underlying conceptual structure of the data. Traditional machine learning techniques are mainly focusing on structured data whereas most data available resides in unstructured, often ...
Added: December 3, 2012
Ignatov D. I., Kuznetsov S., Zhukov L. E. et al., International Journal of General Systems 2013 Vol. 42 No. 6 P. 572-593
formal concept analysis,
data mining,
triclustering,
three-way data,
folksonomy,
spectral triclustering ...
Added: October 16, 2013
Irina E. Utkina, Mikhail V. Batsyn, Ekaterina K. Batsyna, International Journal of Production Research 2018 Vol. 56 No. 9 P. 3262-3273
The Cell Formation Problem (CFP) is an important optimisation problem in manufacturing. It has been introduced in the Group Technology (GT) and its goal is to group machines and parts processed on them into production cells minimising the movement of parts to other cells for processing and maximising for each cell the loading of its ...
Added: March 11, 2018
Ignatov D. I., Kuznetsov S., В кн. : Двенадцатая национальная конференция по искусственному интеллекту с международным участием КИИ-2010 (20-24 сентября 2010 г., г. Тверь, Россия). Труды конференции. Том 1. Т. 1.: М. : Физматлит, 2010. С. 175-182.
В работе предлагается новый метод бикластеризации объектно-признаковых данных, опирающийся на свойства решеток замкнутых множеств. Предложено определение плотного бикластера, эффективный алгоритм для поиска таких бикластеров, исследована его сложность, проведены вычислительные эксперименты на реальных данных. Исследована на практике возможность масштабирования (распараллеливания) алгоритма. ...
Added: December 3, 2012
Naidenova X., Ignatov D. I., Hershey : IGI Global, 2012
The consideration of symbolic machine learning algorithms as an entire class will make it possible, in the future, to generate algorithms, with the aid of some parameters, depending on the initial users’ requirements and the quality of solving targeted problems in domain applications.
Diagnostic Test Approaches to Machine Learning and Commonsense Reasoning Systems surveys, analyzes, and ...
Added: December 3, 2012
Кулеш А. А., Дробаха В. Е., Sobyanin K. et al., Russian Neurological Journal 2021 Т. 26 № 3 С. 23-33
Studies over the past decade demonstrate the high potential of diff usion-weighted MRI (dMRI) as a modern technique for non-invasive quantitative assessment of the microstructural integrity of the white matter of the brain, which allows predicting some aspects of the rehabilitation potential.
Purpose of the study: to calculate the threshold values of fractional anisotropy (FA) of ...
Added: July 24, 2021
Alam M., Buzmakov A. V., Napoli A., Discrete Applied Mathematics 2018 Vol. 249 P. 2-17
With an increased interest in machine processable data and with the progress of semantic technologies, many datasets are now published in the form of RDF triples for constituting the so-called Web of Data. Data can be queried using SPARQL but there are still needs for integrating, classifying and exploring the data for data analysis and ...
Added: September 26, 2017
Ignatov D. I., Lobachevskii Journal of Mathematics 2023 No. 44 P. 137-146
We consider two ways how to compute the number of maximal antichains in the Boolean lattice on 𝑛 elements. The first one is based on full direct enumeration, while the second ones relies on concept lattices or Galois lattices (studied in Formal Concept Analysis, an applied branch of lattice theory) and the Dedekind–McNeil completion of a partial ...
Added: June 13, 2023
CEUR-WS.org, 2020
The CLA conference is an international forum for researchers, practitioners and students dedicated to the practice of Formal Concept Analysis (FCA) and areas closely related to it, including data analysis and mining, information retrieval, knowledge management, knowledge engineering, logic, algebra and lattice theory.
The 15th of CLA, CLA 2020, was going to be held in Tallinn, Estonia ...
Added: October 30, 2020
Springer, 2017
The book studies the existing and potential connections between Social Network Analysis (SNA) and Formal Concept Analysis (FCA) by showing how standard SNA techniques, usually based on graph theory, can be supplemented by FCA methods, which rely on lattice theory.
The book presents contributions to the following areas: acquisition of terminological knowledge from social networks, knowledge ...
Added: December 17, 2017
Kashnitsky Y., Ignatov D. I., Интеллектуальные системы. Теория и приложения 2015 Т. 19 № 4 С. 37-55
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 ...
Added: December 7, 2015
Buzmakov A. V., Kuznetsov S., Napoli A., Procedia Computer Science 2014 Vol. 31 P. 918-927
There is a lot of usefulness measures of patterns in data mining. This paper is focused on the measures used in Formal Concept Analysis (FCA). In particular, concept stability is a popular relevancy measure in FCA. Experimental results of this paper show that high stability of a pattern in a given dataset derived from the ...
Added: October 22, 2015
Ignatov D. I., Gnatyshak D. V., Sergei O. Kuznetsov et al., Machine Learning 2015 Vol. 101 No. 1 P. 271-302
This paper presents several definitions of “optimal patterns” in triadic data and results of experimental comparison of five triclustering algorithms on real-world and synthetic datasets. The evaluation is carried over such criteria as resource efficiency, noise tolerance and quality scores involving cardinality, density, coverage, and diversity of the patterns. An ideal triadic pattern is a totally dense ...
Added: April 15, 2015
Springer, 2014
This book constitutes the proceedings of the 21st International Conference on Conceptual Structures, ICCS 2014, held in Iaşi, Romania, in July 2014. The 17 regular papers and 6 short papers presented in this volume were carefully reviewed and selected from 40 and 10 submissions, respectively. The topics covered are: conceptual structures, knowledge representation, reasoning, conceptual ...
Added: June 9, 2014
Kashnitsky Y., Труды Московского физико-технического института 2014 Т. 6 № 3 С. 43-56
Triclustering is an outgrowth of Formal Concept Analysis intented to detect groups of objects with similar properties (clusters) in a context of three sets of entities. In case of social network analysis, for instance, these sets might be users, their interests and events they take part in. Triclustering here can help to detect users with ...
Added: November 8, 2013
Ignatov D. I., Kaminskaya A. Y., Konstantinova N. et al., , in : Proceedings of The 2014 IEEE/WIC/ACM International Joint Conference on Web Intelligence and Intelligent Agent Technology, WI-IAT 2014, 11-14 August 2014 Warsaw, Poland. : Los Alamitos, Washington, Tokyo : IEEE Computer Society, 2014. P. 327-335.
This paper discusses the recommender models and methods for crowdsourcing platforms. These models are based on modern methods of data analysis of object-attribute data, such as Formal Concept Analysis and biclustering. In particular, the paper is focused on the solution of two tasks – idea and antagonists recommendation – on the example of crowdsourcing platform ...
Added: June 9, 2014
Buzmakov A. V., Egho E., Jay N. et al., International Journal of General Systems 2016 Vol. 45 No. 2 P. 135-159
Nowadays data-sets are available in very complex and heterogeneous ways. Mining of such data collections is essential to support many real-world applications ranging from healthcare to marketing. In this work, we focus on the analysis of “complex” sequential data by means of interesting sequential patterns. We approach the problem using the elegant mathematical framework of ...
Added: February 25, 2016
Aachen : CEUR Workshop Proceedings, 2013
Formal Concept Analysis (FCA) is a mathematically well-founded theory aimed at data analysis and classication, introduced and detailed in the book of Bernhard Ganter and Rudolf Wille, \Formal Concept Analysis", Springer 1999. The area came into being in the early 1980s and has since then spawned over 10000 scientic publications and a variety of practically ...
Added: October 10, 2013
Poelmans J., Ignatov D. I., Kuznetsov S. et al., International Journal of General Systems 2014 Vol. 43 No. 2 P. 105-134
Formal Concept Analysis (FCA) is a mathematical technique that has been extensively applied to Boolean data in knowledge discovery, information retrieval, web mining, etc. applications. During the past years, the research on extending FCA theory to cope with imprecise and incomplete information made significant progress. In this paper, we give a systematic overview of the ...
Added: June 9, 2014
Springer, 2021
This book constitutes the proceedings of the 16th International Conference on Formal Concept Analysis, ICFCA 2021, held in Strasbourg, France, in June/July 2021.
The 14 full papers and 5 short papers presented in this volume were carefully reviewed and selected from 32 submissions. The book also contains four invited contributions in full paper length.
The research part ...
Added: July 10, 2021
Ignatov D. I., Kaminskaya A. Y., Malioukov A. et al., , in : Proceedings of International Conference on Conceptual Structures 2014. Vol. 8577: Graph-Based Representation and Reasoning.: Springer, 2014. P. 287-292.
This paper considers a recommender part of the data anal- ysis system for the collaborative platform Witology. It was developed by the joint research team of the National Research University Higher School of Economics and the Witology company. This recommender sys- tem is able to recommend ideas, like-minded users and antagonists at the respective phases ...
Added: June 9, 2014