| 1. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 2. |
- An, Li, et al.
(author)
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Challenges, tasks, and opportunities in modeling agent-based complex systems
- 2021
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In: Ecological Modelling. - : Elsevier BV. - 0304-3800 .- 1872-7026. ; 457
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Research review (peer-reviewed)abstract
- Humanity is facing many grand challenges at unprecedented rates, nearly everywhere, and at all levels. Yet virtually all these challenges can be traced back to the decision and behavior of autonomous agents that constitute the complex systems under such challenges. Agent-based modeling has been developed and employed to address such challenges for a few decades with great achievements and caveats. This article reviews the advances of ABM in social, ecological, and socio-ecological systems, compare ABM with other traditional, equation-based models, provide guidelines for ABM novice, modelers, and reviewers, and point out the challenges and impending tasks that need to be addressed for the ABM community. We further point out great opportunities arising from new forms of data, data science and artificial intelligence, showing that agent behavioral rules can be derived through data mining and machine learning. Towards the end, we call for a new science of Agent-based Complex Systems (ACS) that can pave an effective way to tackle the grand challenges.
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| 3. |
- An, Li, et al.
(author)
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Modeling agent decision and behavior in the light of data science and artificial intelligence
- 2023
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In: Environmental Modelling & Software. - 1364-8152 .- 1873-6726. ; 166
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Journal article (peer-reviewed)abstract
- Agent-based modeling (ABM) has been widely used in numerous disciplines and practice domains, subject to many eulogies and criticisms. This article presents key advances and challenges in agent-based modeling over the last two decades and shows that understanding agents' behaviors is a major priority for various research fields. We demonstrate that artificial intelligence and data science will likely generate revolutionary impacts for science and technology towards understanding agent decisions and behaviors in complex systems. We propose an innovative approach that leverages reinforcement learning and convolutional neural networks to equip agents with the intelligence of self-learning their behavior rules directly from data. We call for further developments of ABM, especially modeling agent behaviors, in the light of data science and artificial intelligence.
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