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Cogno N, Axenie C, Bauer R, Vavourakis V. Agent-based modeling in cancer biomedicine: applications and tools for calibration and validation. Cancer Biol Ther 2024; 25:2344600. [PMID: 38678381 PMCID: PMC11057625 DOI: 10.1080/15384047.2024.2344600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 04/15/2024] [Indexed: 04/29/2024] Open
Abstract
Computational models are not just appealing because they can simulate and predict the development of biological phenomena across multiple spatial and temporal scales, but also because they can integrate information from well-established in vitro and in vivo models and test new hypotheses in cancer biomedicine. Agent-based models and simulations are especially interesting candidates among computational modeling procedures in cancer research due to the capability to, for instance, recapitulate the dynamics of neoplasia and tumor - host interactions. Yet, the absence of methods to validate the consistency of the results across scales can hinder adoption by turning fine-tuned models into black boxes. This review compiles relevant literature that explores strategies to leverage high-fidelity simulations of multi-scale, or multi-level, cancer models with a focus on verification approached as simulation calibration. We consolidate our review with an outline of modern approaches for agent-based models' validation and provide an ambitious outlook toward rigorous and reliable calibration.
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Affiliation(s)
- Nicolò Cogno
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Institute for Condensed Matter Physics, Technische Universit¨at Darmstadt, Darmstadt, Germany
| | - Cristian Axenie
- Computer Science Department and Center for Artificial Intelligence, Technische Hochschule Nürnberg Georg Simon Ohm, Nuremberg, Germany
| | - Roman Bauer
- Nature Inspired Computing and Engineering Research Group, Computer Science Research Centre, University of Surrey, Guildford, UK
| | - Vasileios Vavourakis
- Department of Medical Physics and Biomedical Engineering, University College London, London, UK
- Department of Mechanical and Manufacturing Engineering, University of Cyprus, Nicosia, Cyprus
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Ramos MC, Gomes DF, Mello NFD, Silva END, Barreto JOM, Shimizu HE. Big Data e Inteligência Artificial para pesquisa translacional na Covid-19: revisão rápida. SAÚDE EM DEBATE 2022. [DOI: 10.1590/0103-1104202213518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
RESUMO O objetivo deste estudo foi identificar como a Inteligência Artificial (IA) vem sendo utilizada para a pesquisa translacional no contexto da Covid-19. Foi realizada uma revisão rápida para identificar o uso de técnicas de IA na translação de tecnologias para o enfrentamento da Covid-19. Empregou-se estratégia de busca com base em termos MeSH e seus respectivos sinônimos em sete bases de dados. Dos 59 artigos identificados, oito foram incluídos. Foram identificadas 11 experiências que usaram IA para a pesquisa translacional em Covid-19: predição de eficácia medicamentosa; predição de patogenicidade do Sars-CoV-2; diagnóstico de imagem para Covid-19; predição de incidência de Covid-19; estimativas de impacto da Covid-19 na sociedade; automatização de sanitização de ambientes hospitalares e clínicos; rastreio de pessoas infectadas e possivelmente infectadas; monitoramento do uso de máscaras; predição de gravidade de pacientes; estratificação de risco do paciente; e predição de recursos hospitalares. A pesquisa translacional pode ajudar no desenvolvimento produtivo e industrial em saúde, especialmente quando apoiada em métodos de IA, uma ferramenta cada vez mais importante, sobretudo quando se discute a Quarta Revolução Industrial e suas aplicações na saúde.
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Gondal MN, Chaudhary SU. Navigating Multi-Scale Cancer Systems Biology Towards Model-Driven Clinical Oncology and Its Applications in Personalized Therapeutics. Front Oncol 2021; 11:712505. [PMID: 34900668 PMCID: PMC8652070 DOI: 10.3389/fonc.2021.712505] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 10/26/2021] [Indexed: 12/19/2022] Open
Abstract
Rapid advancements in high-throughput omics technologies and experimental protocols have led to the generation of vast amounts of scale-specific biomolecular data on cancer that now populates several online databases and resources. Cancer systems biology models built using this data have the potential to provide specific insights into complex multifactorial aberrations underpinning tumor initiation, development, and metastasis. Furthermore, the annotation of these single- and multi-scale models with patient data can additionally assist in designing personalized therapeutic interventions as well as aid in clinical decision-making. Here, we have systematically reviewed the emergence and evolution of (i) repositories with scale-specific and multi-scale biomolecular cancer data, (ii) systems biology models developed using this data, (iii) associated simulation software for the development of personalized cancer therapeutics, and (iv) translational attempts to pipeline multi-scale panomics data for data-driven in silico clinical oncology. The review concludes that the absence of a generic, zero-code, panomics-based multi-scale modeling pipeline and associated software framework, impedes the development and seamless deployment of personalized in silico multi-scale models in clinical settings.
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Affiliation(s)
- Mahnoor Naseer Gondal
- Biomedical Informatics Research Laboratory, Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, United States
| | - Safee Ullah Chaudhary
- Biomedical Informatics Research Laboratory, Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
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Ouzounoglou E, Kolokotroni E, Stanulla M, Stamatakos GS. A study on the predictability of acute lymphoblastic leukaemia response to treatment using a hybrid oncosimulator. Interface Focus 2018; 8:20160163. [PMID: 29285342 PMCID: PMC5740218 DOI: 10.1098/rsfs.2016.0163] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Efficient use of Virtual Physiological Human (VPH)-type models for personalized treatment response prediction purposes requires a precise model parameterization. In the case where the available personalized data are not sufficient to fully determine the parameter values, an appropriate prediction task may be followed. This study, a hybrid combination of computational optimization and machine learning methods with an already developed mechanistic model called the acute lymphoblastic leukaemia (ALL) Oncosimulator which simulates ALL progression and treatment response is presented. These methods are used in order for the parameters of the model to be estimated for retrospective cases and to be predicted for prospective ones. The parameter value prediction is based on a regression model trained on retrospective cases. The proposed Hybrid ALL Oncosimulator system has been evaluated when predicting the pre-phase treatment outcome in ALL. This has been correctly achieved for a significant percentage of patient cases tested (approx. 70% of patients). Moreover, the system is capable of denying the classification of cases for which the results are not trustworthy enough. In that case, potentially misleading predictions for a number of patients are avoided, while the classification accuracy for the remaining patient cases further increases. The results obtained are particularly encouraging regarding the soundness of the proposed methodologies and their relevance to the process of achieving clinical applicability of the proposed Hybrid ALL Oncosimulator system and VPH models in general.
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Affiliation(s)
- Eleftherios Ouzounoglou
- In Silico Oncology and In Silico Medicine Group, Institute of Communication and Computer Systems, National Technical University of Athens, Athens, Greece
| | - Eleni Kolokotroni
- In Silico Oncology and In Silico Medicine Group, Institute of Communication and Computer Systems, National Technical University of Athens, Athens, Greece
| | - Martin Stanulla
- Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Georgios S Stamatakos
- In Silico Oncology and In Silico Medicine Group, Institute of Communication and Computer Systems, National Technical University of Athens, Athens, Greece
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Ouzounoglou E, Dionysiou D, Stamatakos GS. Differentiation resistance through altered retinoblastoma protein function in acute lymphoblastic leukemia: in silico modeling of the deregulations in the G1/S restriction point pathway. BMC SYSTEMS BIOLOGY 2016; 10:23. [PMID: 26932523 PMCID: PMC4774111 DOI: 10.1186/s12918-016-0264-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 01/31/2016] [Indexed: 12/13/2022]
Abstract
BACKGROUND As in many cancer types, the G1/S restriction point (RP) is deregulated in Acute Lymphoblastic Leukemia (ALL). Hyper-phosphorylated retinoblastoma protein (hyper-pRb) is found in high levels in ALL cells. Nevertheless, the ALL lymphocyte proliferation rate for the average patient is surprisingly low compared to its normal counterpart of the same maturation level. Additionally, as stated in literature, ALL cells possibly reside at or beyond the RP which is located in the late-G1 phase. This state may favor their differentiation resistant phenotype. A major phenomenon contributing to this fact is thought to be the observed limited redundancy in the phosphorylation of retinoblastoma protein (pRb) by the various Cyclin Dependent Kinases (Cdks). The latter may result in partial loss of pRb functions despite hyper-phosphorylation. RESULTS To test this hypothesis, an in silico model aiming at simulating the biochemical regulation of the RP in ALL is introduced. By exploiting experimental findings derived from leukemic cells and following a semi-quantitative calibration procedure, the model has been shown to satisfactorily reproduce such a behavior for the RP pathway. At the same time, the calibrated model has been proved to be in agreement with the observed variation in the ALL cell cycle duration. CONCLUSIONS The proposed model aims to contribute to a better understanding of the complex phenomena governing the leukemic cell cycle. At the same time it constitutes a significant first step in the creation of a personalized proliferation rate predictor that can be used in the context of multiscale cancer modeling. Such an approach is expected to play an important role in the refinement and the advancement of mechanistic modeling of ALL in the context of the emergent and promising scientific domains of In Silico Oncology and more generally In Silico Medicine.
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Affiliation(s)
- Eleftherios Ouzounoglou
- In Silico Oncology and In Silico Medicine Group, Laboratory of Microwaves and Fiber Optics, Institute of Communication and Computer Systems, School of Electrical and Computer Engineering, National Technical University of Athens, 9 Iroon Polytechniou, Zografou, 15780, Athens, Greece.
| | - Dimitra Dionysiou
- In Silico Oncology and In Silico Medicine Group, Laboratory of Microwaves and Fiber Optics, Institute of Communication and Computer Systems, School of Electrical and Computer Engineering, National Technical University of Athens, 9 Iroon Polytechniou, Zografou, 15780, Athens, Greece.
| | - Georgios S Stamatakos
- In Silico Oncology and In Silico Medicine Group, Laboratory of Microwaves and Fiber Optics, Institute of Communication and Computer Systems, School of Electrical and Computer Engineering, National Technical University of Athens, 9 Iroon Polytechniou, Zografou, 15780, Athens, Greece.
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Li XL, Oduola WO, Qian L, Dougherty ER. Integrating Multiscale Modeling with Drug Effects for Cancer Treatment. Cancer Inform 2016; 14:21-31. [PMID: 26792977 PMCID: PMC4712979 DOI: 10.4137/cin.s30797] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 11/08/2015] [Accepted: 11/15/2015] [Indexed: 12/12/2022] Open
Abstract
In this paper, we review multiscale modeling for cancer treatment with the incorporation of drug effects from an applied system's pharmacology perspective. Both the classical pharmacology and systems biology are inherently quantitative; however, systems biology focuses more on networks and multi factorial controls over biological processes rather than on drugs and targets in isolation, whereas systems pharmacology has a strong focus on studying drugs with regard to the pharmacokinetic (PK) and pharmacodynamic (PD) relations accompanying drug interactions with multiscale physiology as well as the prediction of dosage-exposure responses and economic potentials of drugs. Thus, it requires multiscale methods to address the need for integrating models from the molecular levels to the cellular, tissue, and organism levels. It is a common belief that tumorigenesis and tumor growth can be best understood and tackled by employing and integrating a multifaceted approach that includes in vivo and in vitro experiments, in silico models, multiscale tumor modeling, continuous/discrete modeling, agent-based modeling, and multiscale modeling with PK/PD drug effect inputs. We provide an example application of multiscale modeling employing stochastic hybrid system for a colon cancer cell line HCT-116 with the application of Lapatinib drug. It is observed that the simulation results are similar to those observed from the setup of the wet-lab experiments at the Translational Genomics Research Institute.
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Affiliation(s)
- Xiangfang L. Li
- Department of Electrical and Computer Engineering, Prairie View A&M University, Prairie View, TX, USA
| | - Wasiu O. Oduola
- Department of Electrical and Computer Engineering, Prairie View A&M University, Prairie View, TX, USA
| | - Lijun Qian
- Department of Electrical and Computer Engineering, Prairie View A&M University, Prairie View, TX, USA
| | - Edward R. Dougherty
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA
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