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Bayesian and deep-learning models applied to the early detection of ovarian cancer using multiple longitudinal biomarkers

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CANCER MEDICINE 2024年第7期13卷 e7163页

作者： Abrego, Luis Zaikin, Alexey Marino, Ines P. Krivonosov, Mikhail I. Jacobs, Ian Menon, Usha Gentry-Maharaj, Aleksandra Blyuss, Oleg UCL EGA Inst Womens Hlth Dept Womens Canc London England UCL Dept Math London WC1E 6BT England Univ Rey Juan Carlos Dept Biol Geol Phys & Inorgan Chem Madrid Spain Russian Acad Sci Ivannikov Inst Syst Programming Res Ctr Trusted Artificial Intelligence Moscow Russia Lobachevsky State Univ Inst Biogerontol Nizhnii Novgorod Russia UCL MRC Clin Trials Unit London England Queen Mary Univ London Wolfson Inst Populat Hlth London England Sechenov First Moscow State Med Univ Sechenov Univ Inst Childs Hlth Dept Paediat & Paediat Infect Dis Moscow Russia Queen Mary Univ London Wolfson Inst Populat Hlth Ctr Canc Screening Prevent & Early Detect Charterhouse Sq London EC1M 6BQ England

BackgroundOvarian cancer is the most lethal of all gynecological cancers. Cancer Antigen 125 (CA125) is the best-performing ovarian cancer biomarker which however is still not effective as a screening test in the general population. Recent literature reports additional biomarkers with the potential to improve on CA125 for early detection when using longitudinal multimarker *** data comprised 180 controls and 44 cases with serum samples sourced from the multimodal arm of UK Collaborative Trial of Ovarian Cancer Screening (UKCTOCS). Our models were based on Bayesian change-point detection and recurrent neural *** obtained a significantly higher performance for CA125-HE4 model using both methodologies (AUC 0.971, sensitivity 96.7% and AUC 0.987, sensitivity 96.7%) with respect to CA125 (AUC 0.949, sensitivity 90.8% and AUC 0.953, sensitivity 92.1%) for Bayesian change-point model (BCP) and recurrent neural networks (RNN) approaches, respectively. One year before diagnosis, the CA125-HE4 model also ranked as the best, whereas at 2 years before diagnosis no multimarker model outperformed *** study identified and tested different combination of biomarkers using longitudinal multivariable models that outperformed CA125 alone. We showed the potential of multivariable models and candidate biomarkers to increase the detection rate of ovarian cancer. Using the data from largest prospective ovarian cancer clinical trial, we assessed, for the first time, the performance of deep and statistical learning approaches in evaluating of the panel longitudinal biomarkers. Our results demonstrate that these models outperform CA125, the single best ovarian cancer biomarker. These findings underscore the potential of multimarker models in improving the detection rate of ovarian cancer and have significant implications for the field of cancer screening and early ***

关键词： CA125 change-point detection longitudinal biomarkers ovarian cancer recurrent neural networks

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Random Graph Modeling: A Survey of the Concepts

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ACM COMPUTING SURVEYS 2020年第6期52卷 131-131页

作者： Drobyshevskiy, Mikhail Turdakov, Denis Russian Acad Sci Ivannikov Inst Syst Programming Alexander Solzhenitsyn St 25 Moscow 109004 Russia Moscow Inst Phys & Technol Alexander Solzhenitsyn St 25 Moscow 109004 Russia

Random graph (RG) models play a central role in complex networks analysis. They help us to understand, control, and predict phenomena occurring, for instance, in social networks, biological networks, the Internet, and so on. Despite a large number of RG models presented in the literature, there are few concepts underlying them. instead of trying to classify awide variety of very dispersedmodels, we capture and describe concepts they exploit considering preferential attachment, copying principle, hyperbolic geometry, recursively defined structure, edge switching, Monte Carlo sampling, and so on. We analyze RG models, extract their basic principles, and build a taxonomy of concepts they are based on. We also discuss how these concepts are combined in RG models and how they work in typical applications like benchmarks, null models, and data anonymization.

关键词： Random graph models patterns

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Experimental Evaluation of Timed Finite State Machine Based Test Derivation 20

Experimental Evaluation of Timed Finite State Machine Based ...

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20th International Conference of Young Specialists on Micro/Nanotechnologies and Electron Devices (EDM)

作者： Tvardovskii, Aleksandr S. Vinarskii, Evgenii M. Yevtushenko, Nina, V Tomsk State Univ Tomsk Russia Lomonosov Moscow State Univ Moscow Russia Ivannikov Inst Syst Programming Moscow Russia

ISBN: (纸本)9781728117539

Finite State Machines (FSMs) are widely used for deriving tests with guaranteed fault coverage for various kinds of discrete and hybrid systems such as telecommunication protocols and services. A Timed FSM (TFSM) seems to be a natural extension of an FSM annotated with timed variables that allows to adequately describe a system under test for which time aspects are important. However, most of existing test derivation methods for timed automata with several clocks return very long test suites. We propose to consider FSMs with a single clock for deriving test suites with guaranteed fault coverage and this can be a compromise between the model complexity and adequacy. A test is derived based on FSM abstraction of a given TFSM and is complete with respect to an established fault model. The experiments were performed for randomly generated TFSMs as well as for TFSMs which are used for service description and they clearly show that a proposed method returns high quality tests with the length that is close to those returned by classical FSM based methods. For service TFSMs we also evaluate the test suite length for different fault domains, the length of preset distinguishing and homing sequences which are widely used for minimizing FSM based test suites with guaranteed fault coverage.

关键词： Finite State Machine (FSM) Timed FSM test derivation

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EndoNuke: Nuclei Detection Dataset for Estrogen and Progesterone Stained IHC Endometrium Scans

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DATA 2022年第6期7卷 75页

作者： Naumov, Anton Ushakov, Egor Ivanov, Andrey Midiber, Konstantin Khovanskaya, Tatyana Vishnyakova, Polina Nora, Sergei Mikhaleva, Liudmila Fatkhudinov, Timur Karpulevich, Evgeny Russian Acad Sci ISP RAS Ivannikov Inst Syst Programming Informat Syst Dept Moscow 109004 Russia AP Avtsyn Sci Res Inst Human Morphol Moscow 117418 Russia City Clin Hosp 31 Moscow Healthcare Dept Moscow 119415 Russia RUDN Univ Peoples Friendship Univ Russia Med Inst Moscow 117198 Russia Minist Healthcare Russian Federat Natl Med Res Ctr Obstet Gynecol & Perinatol Lab Regenerat Med Moscow 117997 Russia Yaroslav The Wise Novgorod State Univ Dept Microbiol Immunol & Infect Dis Veliky Novgorod 173003 Russia

We present EndoNuke, an open dataset consisting of tiles from endometrium immunohistochemistry slides with the nuclei annotated as keypoints. Several experts with various experience have annotated the dataset. Apart from gathering the data and creating the annotation, we have performed an agreement study and analyzed the distribution of nuclei staining intensity.

关键词： digital pathology endometrium nuclei detection dataset whole-slide imaging

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Approaching natural conversation chatbots by interactive dialogue modelling & Microsoft LUIS 1

Approaching natural conversation chatbots by interactive dia...

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1st IEEE International Conference on Conversational Data and Knowledge Engineering (CDKE)

作者： Wachtel, Alexander Fuchss, Dominik Schulz, Sophie Tichy, Walter F. Educ Support Ctr Deutschland GmbH AI Res Lab Karlsruhe Germany Karlsruhe Inst Technol Chair Programming Syst Karlsruhe Germany

ISBN: (纸本)9781728160887

In this paper, we preset guidelines on how to model a dialogue-based conversation with a chatbot build on Microsoft conversational services. Therefore, we created a free framework which manages dialogues and user sessions. For this purpose, we use a systematic classification of the input and intents. Especially, we used Microsoft Language Understanding Intelligent Service (LUIS) for intent extraction. LUIS provides a platform to extract the user need by calculating the intent probability. Unfortunately, LUIS does not provide dialogue management. For that reason, developers need to create own dialogue behavior in Visual Studio project. Therefore, we extracted and use it as a free guideline for the community and other platform developers.

关键词： Dialogue systems Interactive Conversation Dialogue Modeling Dialogue Framework Bot Framework

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Using an SMT Solver for Checking the Completeness of FSM-Based Tests 1

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32nd IFIP WG 6.1 International Conference on Testing Software and systems (ICTSS)

作者： Vinarskii, Evgenii Laputenko, Andrey Yevtushenko, Nina Lomonosov Moscow State Univ 1 Leninskiye Gory St Moscow 119991 Russia Natl Res Tomsk State Univ 36 Lenin Ave Tomsk 634050 Russia Russian Acad Sci Ivannikov Inst Syst Programming 25 Alexander Solzhenitsyn St Moscow 109004 Russia

ISBN: (数字)9783030648817

ISBN: (纸本)9783030648817;9783030648800

Deriving tests with guaranteed fault coverage by FSM-based test methods is rather complex for systems with a large number of states. At the same time, formal verification methods allow to effectively process large transition systems;in particular, SMT solvers are widely used to solve analysis problems for finite transition systems. In this paper, we describe the known necessary and sufficient conditions of completeness of test suites derived by FSM-based test methods via the first-order logic formulas and use an SMT solver in order to check them. In addition, we suggest a new sufficient condition for test suite completeness and check the corresponding first-order logic formula via the SMT solver. The results of computer experiments with randomly generated finite state machines confirm the correctness and efficiency of a proposed approach.

关键词： FSM based testing SMT solver Fist order logic formulas

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Modulating glucocorticoid receptor actions in physiology and pathology: Insights from coregulators

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PHARMACOLOGY & THERAPEUTICS 2023年 251卷 108531页

作者： Fadel, Lina Dacic, Marija Fonda, Vlera Sokolsky, Baila A. Quagliarini, Fabiana Rogatsky, Inez Uhlenhaut, N. Henriette Helmholtz Munich Inst Diabet & Endocrinol IDE Ingolstaedter Landstr 1 D-857649 Neuherberg Germany Hosp Special Surg Res Inst David Rosenzweig Genom Ctr New York NY USA Weill Cornell Grad Sch Med Sci Grad Program Physiol Biophys & Syst Biol New York NY USA Weill Cornell Grad Sch Med Sci Grad Program Immunol & Microbial Pathogenesis New York NY USA TUM Sch Life Sci Metab Programming D-85354 Freising Weihenstephan Germany ZIEL Inst Food & Hlth Gregor11 Mendel Str 2 D-85354 Freising Weihenstephan Germany

Glucocorticoids (GCs) are a class of steroid hormones that regulate key physiological processes such as metabolism, immune function, and stress responses. The effects of GCs are mediated by the glucocorticoid receptor (GR), a ligand-dependent transcription factor that activates or represses the expression of hundreds to thousands of genes in a tissue-and physiological state-specific manner. The activity of GR is modulated by numerous coregulator proteins that interact with GR in response to different stimuli assembling into a multitude of DNA-protein complexes and facilitate the integration of these signals, helping GR to communicate with basal transcriptional machinery and chromatin. Here, we provide a brief overview of the physiological and molecular functions of GR, and discuss the roles of GR coregulators in the immune system, key metabolic tissues and the central nervous system. We also present an analysis of the GR interactome in different cells and tissues, which suggests tissue-specific utilization of GR coregulators, despite widespread functions shared by some of them.(c) 2023 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY-NC license (http:// ***/licenses/by-nc/4.0/).

关键词： Glucocorticoid receptor Coregulators Transcription

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Smart wearable system for safety-related medical IoT application: case of epileptic patient working in industrial environment

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HEALTH AND TECHNOLOGY 2020年第1期10卷 363-372页

作者： Hayek, Ali Telawi, Samer Boercsoek, Josef Daou, Roy Abi Zeid Halabi, Nashaat Univ Kassel Inst Comp Architecture & Syst Programming Wilhelmshoeher Allee 71 D-34121 Kassel Germany Lebanese German Univ Dept Biomed Engn Sahel Alma Lebanon Mart Learning Educ & Res Ctr Chananiir Lebanon Amer Univ Sci & Technol Fac Engn Achrafieh Lebanon

Medical/Industrial IoT is being implemented currently in several domains due to the autonomy it offers to patients, as well as the productivity efficiency that it could enhance. Additionally, the ease of monitoring of the patient, and of action taking in case of sudden medical problems has highlighted the use of such system. The IoT application presented in this paper will target epileptic patients working in an industrial environment. A smart wearable jacket will capture continuously the vital signs of the patient. In case of problem detection, some control signals will be sent to nearby machines to disable them and to alert the medical entities in the working environment. As industrial environments are often safety-critical, the proposed approach is based on basic safety and reliability concepts, which will be enhanced in future works. For this aim, a set of various sensors is used in this work. Although none of the sensors are redundant, all of them give complementary data about the patient health and will insert diversity to the system. A further safety issue consists on using a safety-related processor architecture for processing the sensor data and providing safe outputs.

关键词： Medical internet-of-things Safety systems Vital signs Smart wearable Industrial environment Epileptic patient

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Fine-Grained Address Space Layout Randomization on Program Load

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programming AND COMPUTER SOFTWARE 2018年第5期44卷 363-370页

作者： Nurmukhametov, A. R. Zhabotinskiy, E. A. Kurmangaleev, Sh F. Gaissaryan, S. S. Vishnyakov, A. V. Russian Acad Sci Ivannikov Inst Syst Programming Moscow 109004 Russia

Software vulnerabilities are a serious security threat. It is important to develop protection mechanisms preventing their exploitation, especially with a rapid increase of ROP attacks. State of the art protection mechanisms have some drawbacks that can be used by attackers. In this paper, we propose fine-grained address space layout randomization on program load that is able to protect from such kind of attacks. During the static linking stage, the executable and library files are supplemented with information about function boundaries and relocations. A system dynamic linker/loader uses this information to perform permutation of functions. The proposed method was implemented for 64-bit programs on CentOS 7 operating system. The implemented method has shown good resistance to ROP attacks evaluated by two metrics: the number of survived gadgets and the exploitability estimation of ROP chain examples. The implementation presented in this article is applicable across the entire operating system and has no compatibility problems affecting the program performance. The working capacity of proposed approach was demonstrated on real programs. The further research can cover forking randomization and finer granularity than on the function level. It also makes sense to implement the randomization of short functions placement taking into account the relationships between them. The close arrangement of functions that often call each other can improve the performance of individual programs.

关键词： address space layout randomization diversification ASLR ROP

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Parallel multigrid method for solving inverse problems

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METHODSX 2022年 9卷 101887页

作者： Al-Mahdawi, H. K. Sidikova, A., I Alkattan, Hussein Abotaleb, Mostafa Kadi, Ammar El-kenawy, El-Sayed M. Univ Diyala Elect Comp Ctr Diyala 32001 Iraq South Ural State Univ Dept Syst Programming Chelyabinsk 454080 Russia South Ural State Univ Dept Food & Biotechnol Chelyabinsk 454080 Russia Delta Higher Inst Engn & Technol Dept Commun & Elect Mansoura 35111 Egypt

We considered in this work the linear operator equation and used the Landweber iterative method as an iterative solver. After that, we used the multigrid method as an optimization method for obtaining an approximation solution with a highly accurate and fast process. A new parallel algorithm for the multigrid process has been developed. The proposed algorithm is based on a V-cycle mixed with the two-grid method. This modification of the V-cycle provides for parallel computing for each level. A coarse grid operator with a residual right-hand side vector for each coarse grid is provided. This parallel algorithm is used to accelerate and enhance computation for the solution of the iteration method in solving the inverse ill-posed problems. The necessary cost-time computation for all stages and processes for the parallel V-cycle algorithm has been done. A numerical experiment on solving the IVP (initial value problem) for the heat equation showed that the new parallel algorithm is much more efficient than the sequential *** dot The study of iteration algorithms and mathematical experiments reveals a slow rate of *** dot The Multigrid method is often used to speed up the rate of convergence of iterative methods, which is an effective method of solving large systems of linear algebra *** dot The approximation solution for the linear algebra equations was found by using the parallel method with the multigrid method.(c) 2022 The Author(s). Published by Elsevier *** is an open access article under the CC BY license ( http://***/licenses/by/4.0/ )

关键词： Multigrid Inverse problem Iteration method Parallel

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