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Addressing the Data Scarcity Problem in Ecotoxicology via Small Data Machine Learning Methods

ENVIRONMENTAL SCIENCE & TECHNOLOGY 2025年第12期59卷 5867-5871页

作者： Wang, Ying Dong, Jinchu Zhou, Yunchi Cheng, Yinghao Zhao, Xiaoli Peijnenburg, Willie J. G. M. Vijver, Martina G. Leung, Kenneth M. Y. Fan, Wenhong Wu, Fengchang Beihang Univ Sch Mat Sci & Engn Beijing 100191 Peoples R China Nucl & Radiat Safety Ctr Beijing 100082 Peoples R China Chinese Res Inst Environm Sci State Key Lab Environm Criteria & Risk Assessment Beijing 100012 Peoples R China Leiden Univ Inst Environm Sci NL-2300 RA Leiden Netherlands Natl Inst Publ Hlth & Environm Ctr Safety Prod & Subst NL-3720 BA Bilthoven Netherlands City Univ Hong Kong Dept Chem State Key Lab Marine Pollut Hong Kong 999077 Peoples R China City Univ Hong Kong Sch Energy & Environm Hong Kong 999077 Peoples R China

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workflow to set up substantial target-oriented mechanistic process models in bioprocess engineering

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PROCESS BIOCHEMISTRY 2017年第Nov.期62卷 24-36页

作者： Kroll, Paul Hofer, Alexandra Stelzer, Ines V. Herwig, Christoph TU Wien Inst Chem Engn Res Area Biochem Engn Gumpendorfer Str 1A A-1060 Vienna Austria TU Wien Christian Doppler Lab Mechanist & Physiol Methods Vienna Austria

A multitude of new applications in bioprocess technology strongly depend on model-based methods as they feature prediction and control capabilities. The critical path is usually the availability of suitable models. In this work a workflow for the generation of substantial target-oriented mechanistic process models is presented. This workflow is based on backpropagation starting from a material balance for a certain target variable. Iteratively, necessary states as well as mechanistic links are included in the model using a model library reducing the computational effort. The parameters of these links are estimated using a simplex algorithm whose objective function depends on the target variable only. Practical identifiability analysis is used for the assessment of the need of further iterations and for validating the mechanistic model. To demonstrate the workflow, a model describing a mammalian cell culture process aiming at modeling viable cell count is used as an example. The generated model satisfies the predefined requirements and is very simple, consisting of three states and seven model parameters only. The presented workflow is simple, generic, transparent, so that also applications in a regulatory environment should be possible. It also provides additional process knowledge that can be used in bioprocess development and optimization.

关键词： modeling workflow Substantial target-oriented mechanistic models Mechanistic links Practical identifiability Bioprocess engineering

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Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information

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JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN 2011年第6期25卷 533-554页

作者： Sushko, Iurii Novotarskyi, Sergii Koerner, Robert Pandey, Anil Kumar Rupp, Matthias Teetz, Wolfram Brandmaier, Stefan Abdelaziz, Ahmed Prokopenko, Volodymyr V. Tanchuk, Vsevolod Y. Todeschini, Roberto Varnek, Alexandre Marcou, Gilles Ertl, Peter Potemkin, Vladimir Grishina, Maria Gasteiger, Johann Schwab, Christof Baskin, Igor I. Palyulin, Vladimir A. Radchenko, Eugene V. Welsh, William J. Kholodovych, Vladyslav Chekmarev, Dmitriy Cherkasov, Artem Aires-de-Sousa, Joao Zhang, Qing-You Bender, Andreas Nigsch, Florian Patiny, Luc Williams, Antony Tkachenko, Valery Tetko, Igor V. eADMET GmbH D-85764 Neuherberg Germany German Res Ctr Environm Hlth GmbH Helmholtz Zentrum Munchen D-85764 Neuherberg Germany Inst Bioorgan & Petrochem UA-253660 Kiev Ukraine Univ Milano Bicocca Milano Chemometr & QSAR Res Grp Dept Environm Sci I-20126 Milan Italy Univ Strasbourg Lab Infochim CNRS UMR 7177 F-67000 Strasbourg France Novartis Inst BioMed Res CH-4056 Basel Switzerland Chelyabinsk State Med Acad Chelyabinsk Russia Mol Networks GmbH D-91052 Erlangen Germany Moscow MV Lomonosov State Univ Dept Chem Moscow 119991 Russia UMDNJ Robert Wood Johnson Med Sch Dept Pharmacol Piscataway NJ 08854 USA UMDNJ Robert Wood Johnson Med Sch ebCTC Piscataway NJ 08854 USA Univ British Columbia Vancouver Prostate Ctr Fac Med Vancouver BC V6H 3Z6 Canada Univ Nova Lisboa CQFB REQUIMTE Dept QuimFac Ciencias & Tecnol P-2829516 Caparica Portugal Henan Univ Inst Environm & Analyt Sci Coll Chem & Chem Engn Kaifeng 475004 Peoples R China Univ Cambridge Unilever Ctr Mol Sci Informat Cambridge CB2 1EW England Novartis Inst BioMed Res Inc Cambridge MA 02139 USA Ecole Polytech Fed Lausanne CH-1015 Lausanne Switzerland Royal Soc Chem Wake Forest NC 27587 USA

The Online Chemical modeling Environment is a web-based platform that aims to automate and simplify the typical steps required for QSAR modeling. The platform consists of two major subsystems: the database of experimental measurements and the modeling framework. A user-contributed database contains a set of tools for easy input, search and modification of thousands of records. The OCHEM database is based on the wiki principle and focuses primarily on the quality and verifiability of the data. The database is tightly integrated with the modeling framework, which supports all the steps required to create a predictive model: data search, calculation and selection of a vast variety of molecular descriptors, application of machine learning methods, validation, analysis of the model and assessment of the applicability domain. As compared to other similar systems, OCHEM is not intended to re-implement the existing tools or models but rather to invite the original authors to contribute their results, make them publicly available, share them with other users and to become members of the growing research community. Our intention is to make OCHEM a widely used platform to perform the QSPR/QSAR studies online and share it with other users on the Web. The ultimate goal of OCHEM is collecting all possible chemoinformatics tools within one simple, reliable and user-friendly resource. The OCHEM is free for web users and it is available online at http://***.

关键词： On-line web platform modeling workflow Estimation of accuracy of predictions Applicability domain Data sharing Open access

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3D Geological modeling under Extremely Complex Geological Conditions

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JOURNAL OF COMPUTERS 2012年第3期7卷 699-705页

作者： Shao, Yanlin Zheng, Ailing He, Youbin Xiao, Keyan Yangtze Univ Sch Geosci Jingzhou Peoples R China Yangtze Univ Sch Petr Engn Jingzhou Peoples R China

3D modeling method is divided into geospatial modeling and 3D geological modeling. 3D geological modeling technique has become a favorable tool for people to observe and analyze the geological body enriched in mineral resources. Unlike geospatial modeling, 3D geological modeling must consider various geological conditions affecting spatial shape and petrophysical distribution of geological body for its complexity. This article analyzes the uncertainty, complexity and diversity of geological body, and lists complex geological conditions controlling spatial shape and petrophysical distributions of geological body. And then 3D geological modeling method under the control of complex geological conditions is proposed, and corresponding modeling workflow is set up. Finally, taking 3D geological modeling of petroleum exploration and development for example, 3D geological model of Shu II district in the Liaohe oil-field is built. Based on this model, some applications are realized, such as 3D visualization of structural model and petrophysical model, reserves calculation and drilling design, etc.

关键词： geological body complex geological conditions 3D geological modeling modeling workflow

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A workflow for Building Computationally Rational Models of Human Behavior

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Computational Brain and Behavior 2024年第3期7卷 399-419页

作者： Chandramouli, Suyog Shi, Danqing Putkonen, Aini De Peuter, Sebastiaan Zhang, Shanshan Jokinen, Jussi Howes, Andrew Oulasvirta, Antti Aalto University Espoo Finland University of Helsinki Helsinki Finland University of Jyväskylä Jyväskylä Finland University of Exeter Exeter United Kingdom

Computational rationality explains human behavior as arising due to the maximization of expected utility under the constraints imposed by the environment and limited cognitive resources. This simple assumption, when instantiated via partially observable Markov decision processes (POMDPs), gives rise to a powerful approach for modeling human adaptive behavior, within which a variety of internal models of cognition can be embedded. In particular, such an instantiation enables the use of methods from reinforcement learning (RL) to approximate the optimal policy solution to the sequential decision-making problems posed to the cognitive system in any given setting;this stands in contrast to requiring ad hoc hand-crafted rules for capturing adaptive behavior in more traditional cognitive architectures. However, despite their successes and promise for modeling human adaptive behavior across everyday tasks, computationally rational models that use RL are not easy to build. Being a hybrid of theoretical cognitive models and machine learning (ML) necessitates that model building take into account appropriate practices from both cognitive science and ML. The design of psychological assumptions and machine learning decisions concerning reward specification, policy optimization, parameter inference, and model selection are all tangled processes rife with pitfalls that can hinder the development of valid and effective models. Drawing from a decade of work on this approach, a workflow is outlined for tackling this challenge and is accompanied by a detailed discussion of the pros and cons at key decision points. © The Author(s) 2024.

关键词： Computational rationality modeling workflow POMDPs Resource rationality

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An Open-Source Toolchain for Simulation and Optimization of Aquifer-Wide CO₂ Storage 8

An Open-Source Toolchain for Simulation and Optimization of ...

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8th Trondheim Conference on CO2 Capture, Transport and Storage (TCCS)

作者： Andersen, Odd Lie, Knut-Andreas Nilsen, Halvor Moll SINTEF ICT Dept Appl Math POB 124 Blindern N-0314 Oslo Norway

Planning and execution of large-scale, aquifer-wide CO2 storage operations will require extensive use of computer modelling and simulations. The required computational tools will vary depending on the physical characteristics of the targeted aquifer, the stage of the project, and the questions asked, which may not always be anticipated in advance. In this paper, we argue that a one-size-fits-all simulation tool for the modelling CO2 storage does not exist. Instead, we propose an integrated toolchain of computational methods that can be used in a flexible way to set up adaptive workflows. Although a complete toolchain will require computational methods at all levels of complexity, we further argue that lightweight methods play a particularly important role in addressing many of the relevant questions. We have implemented a number of such simplified methods in MRST-co2lab, a separate module to the open-source MATLAB Reservoir Simulation Toolbox (MRST). In particular, MRST-co2lab contains percolation-type methods that within seconds can identify structural traps and their catchment areas and compute spill paths and rough estimates of trapping capacity. The software also offers two-phase simulators based on vertical-equilibrium assumptions that can forecast structural, residual, and solubility trapping in a thousand-year perspective and are orders of magnitude faster than traditional 3D simulators. Herein, we apply these methods on realistic, large-scale datasets to demonstrate their capabilities and show how they can be used in combination to address optimal use of open aquifers for large-scale storage. (C) 2015 The Authors. Published by Elsevier Ltd.

关键词： CO2 storage modeling workflow open-source software simulation vertical equilibrium spill-point analysis nonlinear optimization migration Bravo Dome thermal effects

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Developing a coupled geo-hydrostratigraphic model for a complex lithologic reservoir: a case study of Dakhla Basin, Southwestern Morocco

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modeling EARTH SYSTEMS AND ENVIRONMENT 2024年第6期10卷 7173-7184页

作者： Afquir, Ayoub Saad, Aicha Rotz, Rachel Hssaissoune, Mohammed El Kanti, Sidi Mokhtar Ez-zaouy, Yassine Hydraul Agcy Sakia Elhmara & Oued Eddahab Bassin Laayoune 70000 Morocco Ibn Zohr Univ Lab Geobioenvironm Engn & Innovat 2GBEI POB 271 Taroudant 83000 Morocco Dept Marine & Earth Sci 10501 FGCU Blvd S Off Seidler Hall 435 Ft Myers FL 33965 USA Ibn Zohr Univ Lab Appl Geol & Geoenvironm Agadir 80035 Morocco Univ Mohammed VI Polytech UM6P Int Water Res Inst Ben Guerir 43150 Morocco

Geological modeling has become a valuable tool for characterizing reservoir architecture. It is only possible with a fundamental conceptual model, which is, in turn, based on hypotheses about geological evolutionary processes. This study aims to develop the first 3D geological and hydrostratigraphic model of the Dakhla Basin in the southwestern Moroccan Sahara, addressing the challenges its complex lithology poses. Geological maps and borehole log-derived cross-sections were employed by the Groundwater modeling System (GMS) to create a detailed 3D model, with a corresponding modeling workflow established. Finally, our findings classify the basin into ten geological and five stratigraphic units, revealing a monocline structure oriented east-west. Notably, the model identifies a deep aquifer within SU3 (Paleogene), primarily composed of fine to medium sand and sandstone, with an estimated volume of 1.71 x 10(12) m(3), representing a vital water resource for the region. Additionally, the model uncovers east-to-west groundwater flow patterns and recharge areas in the northeast and eastern parts of the basin. These results provide new insights into the region's geology and hydrostratigraphy, advancing research and practical applications in groundwater resource management.

关键词： 3D geological modeling GMS modeling workflow Coastal aquifer Dakhla

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Physics-Based Forward modeling of Multistage Hydraulic Fracturing in Unconventional Plays

Physics-Based Forward Modeling of Multistage Hydraulic Fract...

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作者： Parsegov, Sergei Texas A&M University

学位级别：Ph.D.

This dissertation proposes a workflow for modeling of multistage hydraulic fracturing stimulation in unconventional formations. Based on the field case of a horizontal well targeted lower Wolfcamp formation in Midland Basin, this study identifies main gaps of publicly available data and provides estimations for critically important inputs: elastic properties, horizontal stress anisotropy, and pressure dependent leakoff. Breakdown and shut-in pressure are used to constrain horizontal stress anisotropy to a narrow range of 7.6-11.0% and avoid misleading published data for the Midland Basin. The developed model shows that oilfield operators can significantly, up to two times, reduce the size of the pad and associated cost without risk of streenout. From the estimation of friction losses and modeling in planar-3D model this work shows how to overcome adverse effects of stress shadowing by perforation redesign and reduce cluster spacing. Finally, fracture conductivity and production history are used to model fluid flow in two reservoir simulators. History match demonstrates that effective permeability should be several orders of magnitude higher than measured from the pressure pulse decay method. This dissertation will be useful for completion and reservoir *** though theories of fracture growth in elastic medium are known for decades, multiple field observations show limitations in their predictive power. Therefore operators tend to use descriptive, data-driven models, to further optimize completion design. This dissertation identifies gaps and misconceptions in hydraulic fracturing design and shows both the benefits and limitations of grid-based fracturing models. More importantly, it demonstrates a workflow for fracture modeling based on a limited amount of publicly available data and practical recommendations for completion redesign coming from observation from physics-driven modeling. This dissertation will be useful for completion engineers and geomechan

关键词： Stress anisotropy Hydraulic fracturing Unconventionals Permian Basin Liquid Rich Reservoirs Wolfcamp Pressure Dependent Leakoff, Stress Shadowing modeling workflow Perforation Design

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A review of rock physical models for elastic properties characterization of gas hydrate bearing sediments

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JOURNAL OF PETROLEUM SCIENCE AND ENGINEERING 2022年第0期218卷

作者： Yuan, Hemin Han, De-hua Wang, Yang China Univ Geosci Beijing Sch Geophys & Informat Technol Beijing 100083 Peoples R China Univ Houston Dept Earth & Atmospher Sci Houston TX 77204 USA SINOPEC Geophys Res Inst Nanjing 211103 Peoples R China

Gas hydrate is mainly explored through seismic methods, which, however, are bedeviled by the problem of uncertainty due to lack of constraints. Rock physics model links the physical parameters with elastic properties and can serve as constraint for seismic methods. A number of models were proposed to simulate the elastic properties of gas hydrate bearing sediments, addressing different mechanisms and applications. However, they are generally miscellaneous, making it difficult to choose the proper model in a specific scenario. Besides, since the simulation usually involves multiple sub-models and steps, determining the uncertainty sources is trouble-some. We summarize the previous models and classify them into five categories according to different principles, which include hydrate morphology, frame structure, research purpose, hydrate generation stage, and lithology. We also analyze the advantages and disadvantages of different models and explain the application scenarios. Moreover, we also generalize the modeling workflow, enumerate the feasible models in each step, and indicate the possible uncertainty sources. In the end, we summarize the problems in the current modeling and suggest multiple research directions. This work provides a clear perspective of the models, related uncertainties, and simulation workflow of gas hydrate bearing sediments;it also offers some implications for future research, which may be helpful for seismic characterization of hydrate reservoirs.

关键词： Gas hydrate Model category modeling workflow Challenges in modeling

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Watershed workflow: A toolset for parameterizing data-intensive, integrated hydrologic models

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ENVIRONMENTAL MODELLING & SOFTWARE 2022年 157卷

作者： Coon, Ethan T. Shuai, Pin Climate Change Sci Inst Oak Ridge Natl Lab 1 Bethel Valley Rd Oak Ridge TN 37830 USA Oak Ridge Natl Lab Environm Sci Div 1 Bethel Valley Rd Oak Ridge TN 37830 USA Pacific Northwest Natl Lab Richland WA 99352 USA Utah State Univ Logan UT 84322 USA

Integrated, distributed hydrologic models leverage advances in computational power and data accessibility to improve predictive understanding of the water cycle. While impressive advances in this area of environmental modeling have been accomplished, such models are still rarely used, partially because of difficulty integrating model and data. This research describes the release of Watershed workflow version 1.2, a new library aiming to automate and enable complex workflows defining inputs to high resolution, integrated, distributed hydrologic models. Watershed workflow provides tools enabling the discovery, acquisition, mapping, and coordination of watershed geometry, land cover, soil properties, and meteorological data. It enables the construction of unstructured meshes that incorporate this data, and provides tools for automating a "first'' simulation on any watershed in the United States. We present the design of the workflow tool, and describe best practices for its usage, culminating in a final example from watershed specification to simulation at the Coweeta Hydrologic Laboratory.

关键词： Integrated hydrologic modeling modeling workflow Model parameterization and setup

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