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Mechanistic Modeling and Multiscale Applications for Precision Medicine: Theory and Practice

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Network and Systems Medicine

Network and Systems Medicine 2020年第1期3卷 36-56页

作者： Stalidzans, Egils Zanin, Massimiliano Tieri, Paolo Castiglione, Filippo Polster, Annikka Scheiner, Stefan Pahle, Jürgen Stres, Blaž List, Markus Baumbach, Jan Lautizi, Manuela Van Steen, Kristel Schmidt, Harald H.H.W. Computational Systems Biology Group University of Latvia Riga Latvia Latvian Biomedical Reasearch and Study Centre Riga Latvia Centro de Tecnología Biomédica Universidad Politécnica de Madrid Pozuelo de Alarcón Spain CNR National Research Council IAC Institute for Applied Computing Rome Italy Oslo Norway Institute for Mechanics of Materials and Structures Vienna University of Technology Vienna Austria BioQuant Heidelberg University Heidelberg Germany Department of Animal Science University of Ljubljana Ljubljana Slovenia Faculty of Civil and Geodetic Engineering University of Ljubljana Ljubljana Slovenia Department of Automation Biocybernetics and Robotics Jozef Stefan Institute Ljubljana Slovenia Big Data in BioMedicine Research Group Chair of Experimental Bioinformatics TUM School of Weihenstephan Technical University of Munich Freising Germany Chair of Experimental Bioinformatics TUM School of Weihenstephan Technical University of Munich Freising Germany Computational Systems Medicine Research Group Chair of Experimental Bioinformatics TUM School of Weihenstephan Technical University of Munich Freising Germany BIO-Systems Genetics GIGA-R University of Liège Liège Belgium BIO3 - Systems Medicine Department of Human Genetics KU Leuven Leuven Belgium Department of Pharmacology and Personalised Medicine Faculty of Health Medicine and Life Science Maastricht University Maastricht Netherlands

Drug research, therapy development, and other areas of pharmacology and medicine can benefit from simulations and optimization of mathematical models that contain a mathematical description of interactions between systems elements at the cellular, tissue, organ, body, and population level. This approach is the foundation of systems medicine and precision medicine. Here, simulated experiments are performed with computers (in silico) first, and they are then replicated through lab experiments (in vivo or in vitro) or clinical studies. In turn, these experiments and studies can be used to validate or improve the models. This iterative loop of dry and wet lab work is successful when biomedical researchers tightly collaborate with data scientists and modelers. From an educational point of view, the interdisciplinary research in systems biology can be sustained most effectively when specialists have been trained to have both a strong background in the disciplines of biology or modeling and strong communication skills, which make them able to communicate with other specialists. This overview addresses possible interdisciplinary communication gaps. Focusing our attention on biomedical researchers, we describe the reasons for using modeling and ways to collaborate with modelers, including their needs for specific biological expertise and data. This review includes an introduction to the principles of several widely used mechanistic modeling methods, focusing on their areas of applicability as well as their limitations. A potential complementary role of machine-learning methods in the development of mechanistic models is also discussed. The descriptions of the methods also include links to corresponding modeling software tools as well as practical examples of their application. Finally, we also explicitly address different aspects of multiscale modeling approaches that allow a more complete and holistic perspective of the human body. © Egils Stalidzans et al. 2020 Published b

关键词： Iterative methods

Complete mitochondrial genome sequences of two ground crickets,Dianemobius fascipes nigrofasciatusandPolionemobius taprobanensis(Orthoptera: Grylloidea: trigonidiidae)

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Mitochondrial DNA Part B 2023年第12期8卷

作者： Kohyoh Murata Kosuke Kataoka Ryuto Sanno Kazuhiro Satomura Atsushi Ogura Toru Asahi Kei Yura Takeshi Suzuki a Graduate School of Bio-Applications and Systems Engineering Tokyo University of Agriculture and Technology Tokyo Japan b Comprehensive Research Organization Waseda University Tokyo Japan c Graduate School of Advanced Science and Engineering Waseda University Tokyo Japan d Department of Bioscience Nagahama Institute of Bio-Science and Technology Shiga Japan b Comprehensive Research Organization Waseda University Tokyo Japanc Graduate School of Advanced Science and Engineering Waseda University Tokyo Japane Global Consolidated Research Institute for Science Wisdom Waseda University Tokyo Japanf Institute for Advanced Research of Biosystem Dynamics Waseda Research Institute for Science and Engineering Waseda University Tokyo Japang Research Organization for Nano & Life Innovation Waseda University Tokyo Japan c Graduate School of Advanced Science and Engineering Waseda University Tokyo Japanh Graduate School of Humanities and Sciences Ochanomizu University Tokyo Japani Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL) National Institute of Advanced Industrial Science and Technology Tokyo Japan

The authors sequenced the complete mitochondrial (mt) genomes of the band-legged ground cricket (Dianemobius fascipes nigrofasciatusMatsumura, 1904) and a temperate form of the lawn ground cricket (Polionemobius taprobanensisWalker, 1869), collected in Japan. The length of the mt genome sequences was 15,354 bp inD. fascipes nigrofasciatusand 16,063 bp inP. taprobanensis. Annotation of the mt genome sequences revealed 13 protein-coding genes, two rRNA genes, and 22 tRNA genes. The orientation of the genes was the same as in other Grylloidea species, and the order was the same as in other Trigonidiidae species. In our phylogenetic analysis,D. fascipes nigrofasciatusformed a clade withD. fascipescollected in China, and the temperate form ofP. taprobanensisformed a clade withP. taprobanensiscollected in China. Comparison of the numbers of positions with different amino acid residues encoded by the protein-coding genes implied the separate species status of each member of each of the two pairs of ground crickets. The mt genome sequences ofD. fascipes nigrofasciatusandP. taprobanensiswill contribute to phylogenetic and taxonomic studies of the Trigonidiidae.

关键词： Complete mitogenome crickets phylogenetic analysis speciation

Deep learning in video multi-object tracking: A survey

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arXiv 2019年

作者： Ciaparrone, Gioele Sánchez, Francisco Luque Tabik, Siham Troiano, Luigi Tagliaferri, Roberto Herrera, Francisco 84084 Italy Andalusian Research Institute in Data Science and Computational Intelligence University of Granada Granada18071 Spain Department of Engineering University of Sannio Benevento82100 Italy

The problem of Multiple Object Tracking (MOT) consists in following the trajectory of different objects in a sequence, usually a video. In recent years, with the rise of Deep Learning, the algorithms that provide a solution to this problem have benefited from the representational power of deep models. This paper provides a comprehensive survey on works that employ Deep Learning models to solve the task of MOT on single-camera videos. Four main steps in MOT algorithms are identified, and an in-depth review of how Deep Learning was employed in each one of these stages is presented. A complete experimental comparison of the presented works on the three MOTChallenge datasets is also provided, identifying a number of similarities among the top-performing methods and presenting some possible future research directions. Copyright © 2019, The Authors. All rights reserved.

关键词： Surveys

Vaccinations or Non-Pharmaceutical Interventions: Safe Reopening of Schools in England

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Research Square

Research Square 2021年

作者： Cuesta-Lazaro, Carolina Quera-Bofarull, Arnau Aylett-Bullock, Joseph Lawrence, Bryan N. Fong, Kevin Icaza-Lizaola, Miguel Sedgewick, Aidan Truong, Henry Vernon, Ian Williams, Julian Pagel, Christina Krauss, Frank Institute for Data Science Durham University Durham United Kingdom Institute for Computational Cosmology Durham University Durham United Kingdom Institute for Particle Physics Phenomenology Durham University Durham United Kingdom National Centre for Atmospheric Science University of Reading Reading United Kingdom Departments of Meteorology and Computer Science University of Reading Reading United Kingdom Department of Science Technology Engineering and Public Policy University College London London United Kingdom Department of Anaesthesia University College London Hospital London United Kingdom Centre for Extragalactic Astronomy Durham University Durham United Kingdom Department of Mathematical Sciences Durham University DurhamDH1 3LE United Kingdom Institute for Hazard Risk & Resilience Durham University DurhamDH1 3LE United Kingdom Clinical Operational Research Unit University College London United Kingdom

With high levels of the Delta variant of COVID-19 circulating in England during September 2021, schools are set to reopen with few school-based non-pharmaceutical interventions (NPIs). In this paper, we present simulation results obtained from the individual-based model, JUNE, for English school opening after a prior vaccination campaign using an optimistic set of assumptions about vaccine efficacy and the likelihood of prior-reinfection. We take a scenario-based approach to modelling potential interventions to assess relative changes rather than real-world forecasts. Specifically, we assess the effects of vaccinating those aged 16-17, those aged 12-17, and not vaccinating children at all relative to only vaccinating the adult population, addressing what might have happened had the UK began teenage vaccinations earlier. Vaccinating children in the 12-15 age group would have had a significant impact on the course of the epidemic, saving thousands of lives overall in these simulations. In the absence of such a vaccination campaign our simulations show there could still be a significant positive impact on the epidemic (fewer cases, fewer deaths) by continuing NPI strategies in schools. Our analysis suggests that the best results in terms of lives saved are likely derived from a combination of the now planned vaccination campaign and NPIs in schools. © 2021, CC BY.

关键词： COVID-19

Uplink-downlink duality between multiple-access and broadcast channels with compressing relays

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arXiv 2020年

作者： Liu, Liang Liu, Ya-Feng Patil, Pratik Yu, Wei the Department of Electronic and Information Engineering The Hong Kong Polytechnic University Hong Kong the State Key Laboratory of Scientific and Engineering Computing Institute of Computational Mathematics and Scientific/Engineering Computing Academy of Mathematics and Systems Science Chinese Academy of Sciences Beijing100190 China The Edward S. Rogers Sr. Department of Electrical and Computer Engineering the University of Toronto the Department of Statistics and Data Science and the Machine Learning Department Carnegie Mellon University PittsburghPA15213 United States The Edward S. Rogers Sr. Department of Electrical and Computer Engineering University of Toronto 10 King’s College Road TorontoONM5S3G4 Canada

—Uplink-downlink duality refers to the fact that under a sum-power constraint, the capacity regions of a Gaussian multiple-access channel and a Gaussian broadcast channel with Hermitian transposed channel matrices are identical. This paper generalizes this result to a cooperative cellular network, in which remote access-points are deployed as relays in serving the users under the coordination of a central processor (CP). In this model, the users and the relays are connected over noisy wireless links, while the relays and the CP are connected over noiseless but rate-limited fronthaul links. Based on a Lagrangian technique, this paper establishes a duality relationship between such a multiple-access relay channel and broadcast relay channel, under the assumption that the relays use compression-based strategies. Specifically, we show that under the same total transmit power constraint and individual fronthaul rate constraints, the achievable rate regions of the Gaussian multiple-access and broadcast relay channels are identical, when either independent compression or Wyner-Ziv and multivariate compression strategies are used. The key observations are that if the beamforming vectors at the relays are fixed, the sum-power minimization problems under the achievable rate and fronthaul constraints in both the uplink and the downlink can be transformed into either a linear programming or a semidefinite programming problem depending on the compression technique, and that the uplink and downlink problems are Lagrangian duals of each other. Moreover, the dual variables corresponding to the downlink rate constraints become the uplink powers;the dual variables corresponding to the downlink fronthaul constraints become the uplink quantization noises. This duality relationship enables an efficient algorithm for optimizing the downlink transmission and relaying strategies based on the uplink. Copyright © 2020, The Authors. All rights reserved.

关键词： Linear programming

Small inter-event times govern epidemic spreading on networks

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Physical Review Research 2020年第2期2卷 023163-023163页

作者： Naoki Masuda Petter Holme Department of Mathematics University at Buffalo State University of New York Buffalo New York 14260-2900 USA Computational and Data-Enabled Science and Engineering Program University at Buffalo State University of New York Buffalo New York 14260-5030 USA Tokyo Tech World Research Hub Initiative (WRHI) Institute of Innovative Research Tokyo Institute of Technology Yokohama 226-8503 Japan

Many aspects of human and animal interaction, such as the frequency of contacts of an individual, the number of interaction partners, and the time between the contacts of two individuals, are characterized by heavy-tailed distributions. These distributions affect the spreading of, e.g., infectious diseases or rumors, often because of impacts of the right tail of the distributions (i.e., the large values). In this paper we show that when it comes to inter-event time distributions, it is not the tail but the small values that control spreading dynamics. We investigate this effect both analytically and numerically for different versions of the susceptible-infected-recovered model on different types of networks.

关键词： Epidemic Epidemic evolution Epidemic growth Epidemic prevalence

A "Black Hole Star" Reveals the Remarkable Gas-Enshrouded Hearts of the Little Red Dots

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arXiv 2025年

作者： Naidu, Rohan P. Matthee, Jorryt Katz, Harley de Graaff, Anna Oesch, Pascal Smith, Aaron Greene, Jenny E. Brammer, Gabriel Weibel, Andrea Hviding, Raphael Chisholm, John Labbé, Ivo Simcoe, Robert A. Witten, Callum Atek, Hakim Baggen, Josephine F.W. Belli, Sirio Bezanson, Rachel Boogaard, Leindert A. Bose, Sownak Covelo-Paz, Alba Dayal, Pratika Fudamoto, Yoshinobu Furtak, Lukas J. Giovinazzo, Emma Goulding, Andy Gronke, Max Heintz, Kasper E. Hirschmann, Michaela Illingworth, Garth Inoue, Akio K. Johnson, Benjamin D. Leja, Joel Leonova, Ecaterina McConachie, Ian Maseda, Michael V. Natarajan, Priyamvada Nelson, Erica Setton, David J. Shivaei, Irene Sobral, David Stefanon, Mauro Tacchella, Sandro Toft, Sune Torralba, Alberto van Dokkum, Pieter van der Wel, Arjen Volonteri, Marta Walter, Fabian Wang, Bingjie Watson, Darach MIT Kavli Institute for Astrophysics and Space Research 70 Vassar Street CambridgeMA02139 United States Am Campus 1 Klosterneuburg3400 Austria Department of Astronomy & Astrophysics University of Chicago 5640 S Ellis Avenue ChicagoIL60637 United States Max-Planck-Institut f"ur Astronomie K"onigstuhl 17 HeidelbergD-69117 Germany Department of Astronomy University of Geneva Chemin Pegasi 51 Versoix1290 Switzerland Copenhagen Denmark Niels Bohr Institute University of Copenhagen Jagtvej 128 Copenhagen Denmark Department of Physics The University of Texas at Dallas RichardsonTX75080 United States Department of Astrophysical Sciences Princeton University PrincetonNJ08544 United States Department of Astronomy The University of Texas at Austin AustinTX78712 United States Centre for Astrophysics and Supercomputing Swinburne University of Technology MelbourneVIC3122 Australia Institut d’Astrophysique de Paris CNRS Sorbonne Universit’e 98bis Boulevard Arago Paris75014 France Department of Astronomy Yale University New HavenCT06511 United States Dipartimento di Fisica e Astronomia Università di Bologna Bologna Italy Department of Physics and Astronomy PITT PACC University of Pittsburgh PittsburghPA15260 United States Leiden Observatory Leiden University PO Box 9513 Leiden2300 RA Netherlands Institute for Computational Cosmology Department of Physics Durham University South Road DurhamDH1 3LE United Kingdom Kapteyn Astronomical Institute University of Groningen P.O. Box 800 Groningen9700 AV Netherlands Center for Frontier Science Chiba University 1-33 Yayoi-cho Inage-ku Chiba263-8522 Japan Department of Physics Ben-Gurion University of the Negev P.O. Box 653 Be’er-Sheva84105 Israel Max Planck Institute for Astrophysics Karl-Schwarzschild-Str. 1 Garching85748 Germany Institute of Physics Lab for Galaxy Evolution and Spectral Modelling EPFL Observatory of Sauverny Chemin Pegasi 51 Versoix1290 Switzerland Department of

The physical processes that led to the formation of billion solar mass black holes within the first 700 million years of cosmic time remain a puzzle1–3. Several theoretical scenarios have been proposed to seed and rapidly grow black holes4–7, but direct observations of these mechanisms remain elusive. Here we present a source 660 million years after the Big Bang that displays singular properties: among the largest Hydrogen Balmer breaks reported at any redshift, broad multi-peaked Hβ emission, and Balmer line absorption in multiple transitions. We model this source as a "black hole star" (BH*) where the Balmer break and absorption features are a result of extremely dense, turbulent gas forming a dust-free "atmosphere" around a supermassive black hole8, 9. This source may provide evidence of an early black hole embedded in dense gas – a theoretical configuration proposed to rapidly grow black holes via super-Eddington accretion10–14. Radiation from the BH* appears to dominate almost all observed light, leaving limited room for contribution from its host galaxy. We demonstrate that the recently discovered "Little Red Dots" (LRDs)15–19 with perplexing spectral energy distributions20–26 can be explained as BH*s embedded in relatively brighter host galaxies. This source provides evidence that SMBH masses in the LRDs may be over-estimated by orders of magnitude – the BH* is effectively dust-free contrary to the steep dust corrections applied while modeling LRDs9, 16, 27, 28, and the physics that gives rise to the complex line shapes and luminosities may deviate from assumptions underlying standard scaling relations. © 2025, CC BY.

关键词： Cosmology

Opinion dynamics on tie-decay networks

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arXiv 2020年

作者： Sugishita, Kashin Porter, Mason A. Beguerisse-Díaz, Mariano Masuda, Naoki Department of Mathematics State University of New York at Buffalo BuffaloNY14260-2900 United States Department of Mathematics University of California Los AngelesCA90095 United States Mathematical Institute University of Oxford OxfordOX2 6GG United Kingdom Computational and Data-Enabled Science and Engineering Program State University of New York at Buffalo BuffaloNY14260-5030 United States Faculty of Science and Engineering Waseda University Tokyo169-8555 Japan

In social networks, interaction patterns typically change over time. We study opinion dynamics on tie-decay networks in which tie strength increases instantaneously when there is an interaction and decays exponentially between interactions. Specifically, we formulate continuous-time Laplacian dynamics and a discrete-time DeGroot model of opinion dynamics on these tie-decay networks, and we carry out numerical computations for the continuous-time Laplacian dynamics. We examine the speed of convergence by studying the spectral gaps of combinatorial Laplacian matrices of tie-decay networks. First, we compare the spectral gaps of the Laplacian matrices of tie-decay networks that we construct from empirical data with the spectral gaps for corresponding randomized and aggregate networks. We find that the spectral gaps for the empirical networks tend to be smaller than those for the randomized and aggregate networks. Second, we study the spectral gap as a function of the tie-decay rate and time. Intuitively, we expect small tie-decay rates to lead to fast convergence because the influence of each interaction between two nodes lasts longer for smaller decay rates. Moreover, as time progresses and more interactions occur, we expect eventual convergence. However, we demonstrate that the spectral gap need not decrease monotonically with respect to the decay rate or increase monotonically with respect to time. Our results highlight the importance of the interplay between the times that edges strengthen and decay in temporal networks. Copyright © 2020, The Authors. All rights reserved.

关键词： Laplace transforms

Chemical identification and indexing in full-text articles: an overview of the NLM-Chem track at BioCreative VII

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database 2023年第2023期2023卷 baad005-baad005页

作者： Leaman, Robert Islamaj, Rezarta Adams, Virginia Alliheedi, Mohammed A. Almeida, João Rafael Antunes, Rui Bevan, Robert Chang, Yung-Chun Erdengasileng, Arslan Hodgskiss, Matthew Ida, Ryuki Kim, Hyunjae Li, Keqiao Mercer, Robert E. Mertová, Lukrécia Mobasher, Ghadeer Shin, Hoo-Chang Sung, Mujeen Tsujimura, Tomoki Yeh, Wen-Chao Lu, Zhiyong National Center for Biotechnology Information (NCBI) National Library of Medicine National Institutes of Health 8600 Rockville Pike Bethesda 20894 MD United States Nvidia 2788 San Tomas Expressway Santa Clara 95051 CA United States Department of Computer Science Al Baha University 4781 King Fahd Rd Al Aqiq 65779 Saudi Arabia Department of Electronics Telecommunications and Informatics (DETI) Institute of Electronics and Informatics Engineering of Aveiro (IEETA) University of Aveiro Campus Universitário de Santiago Aveiro 3810-193 Portugal Department of Information and Communications Technologies University of A Coruña Camiño Do Lagar de Castro A Coruña 15008 Spain Informatics Department Medicines Discovery Catapult Alderley Park Block 35 Mereside Macclesfield SK10 4ZF United Kingdom Graduate Institute of Data Science Taipei Medical University No. 172-1 Section 2 Keelung Rd Da’an District Taipei City 106 Taiwan Department of Statistics Florida State University 117 N. Woodward Ave Tallahassee 32306 FL United States Computational Intelligence Laboratory Toyota Technological Institute 2-12-1 Hisakata Tempaku-ku Nagoya Aichi 468-8511 Japan Department of Computer Science and Engineering Korea University 145 Anam-ro Seongbuk-gu Seoul 02841 South Korea Department of Computer Science The University of Western Ontario Middlesex College Room 355 London N6A 5B7 ON Canada Scientific Databases and Visualization Group Heidelberg Institute for Theoretical Studies (HITS GGmbH) Schloss-Wolfsbrunnenweg 35 Heidelberg 69118 Germany Institute of Computer Science Heidelberg University Im Neuenheimer Feld 205 Heidelberg 69120 Germany Institute of Information Systems and Applications National Tsing Hua University No. 101 Section 2 Kuang-Fu Road Hsinchu 30013 Taiwan

The BioCreative National Library of Medicine (NLM)-Chem track calls for a community effort to fine-tune automated recognition of chemical names in the biomedical literature. Chemicals are one of the most searched biomedical entities in PubMed, and - as highlighted during the coronavirus disease 2019 pandemic - their identification may significantly advance research in multiple biomedical subfields. While previous community challenges focused on identifying chemical names mentioned in titles and abstracts, the full text contains valuable additional detail. We, therefore, organized the BioCreative NLM-Chem track as a community effort to address automated chemical entity recognition in full-text articles. The track consisted of two tasks: (i) chemical identification and (ii) chemical indexing. The chemical identification task required predicting all chemicals mentioned in recently published full-text articles, both span [i.e. named entity recognition (NER)] and normalization (i.e. entity linking), using Medical Subject Headings (MeSH). The chemical indexing task required identifying which chemicals reflect topics for each article and should therefore appear in the listing of MeSH terms for the document in the MEDLINE article indexing. This manuscript summarizes the BioCreative NLM-Chem track and post-challenge experiments. We received a total of 85 submissions from 17 teams worldwide. The highest performance achieved for the chemical identification task was 0.8672 F-score (0.8759 precision and 0.8587 recall) for strict NER performance and 0.8136 F-score (0.8621 precision and 0.7702 recall) for strict normalization performance. The highest performance achieved for the chemical indexing task was 0.6073 F-score (0.7417 precision and 0.5141 recall). This community challenge demonstrated that (i) the current substantial achievements in deep learning technologies can be utilized to improve automated prediction accuracy further and (ii) the chemical indexing task is substanti

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