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Aghayev Z, Szafran AT, Tran A, Ganesh HS, Stossi F, Zhou L, Mancini MA, Pistikopoulos EN, Beykal B. Machine Learning Methods for Endocrine Disrupting Potential Identification Based on Single-Cell Data. Chem Eng Sci 2023; 281:119086. [PMID: 37637227 PMCID: PMC10448728 DOI: 10.1016/j.ces.2023.119086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Abstract
Humans are continuously exposed to a variety of toxicants and chemicals which is exacerbated during and after environmental catastrophes such as floods, earthquakes, and hurricanes. The hazardous chemical mixtures generated during these events threaten the health and safety of humans and other living organisms. This necessitates the development of rapid decision-making tools to facilitate mitigating the adverse effects of exposure on the key modulators of the endocrine system, such as the estrogen receptor alpha (ERα), for example. The mechanistic stages of the estrogenic transcriptional activity can be measured with high content/high throughput microscopy-based biosensor assays at the single-cell level, which generates millions of object-based minable data points. By combining computational modeling and experimental analysis, we built a highly accurate data-driven classification framework to assess the endocrine disrupting potential of environmental compounds. The effects of these compounds on the ERα pathway are predicted as being receptor agonists or antagonists using the principal component analysis (PCA) projections of high throughput, high content image analysis descriptors. The framework also combines rigorous preprocessing steps and nonlinear machine learning algorithms, such as the Support Vector Machines and Random Forest classifiers, to develop highly accurate mathematical representations of the separation between ERα agonists and antagonists. The results show that Support Vector Machines classify the unseen chemicals correctly with more than 96% accuracy using the proposed framework, where the preprocessing and the PCA steps play a key role in suppressing experimental noise and unraveling hidden patterns in the dataset.
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Affiliation(s)
- Zahir Aghayev
- Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, CT
- Center for Clean Energy Engineering, University of Connecticut, Storrs, CT
| | - Adam T. Szafran
- Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
| | - Anh Tran
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX
- Texas A&M Energy Institute, Texas A&M University, College Station, TX
| | - Hari S. Ganesh
- Discipline of Chemical Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat - 382055, India
| | - Fabio Stossi
- Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
- GCC Center for Advanced Microscopy and Image Informatics, Houston, TX
| | - Lan Zhou
- Department of Statistics, Texas A&M University, College Station, TX
| | - Michael A. Mancini
- Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
- GCC Center for Advanced Microscopy and Image Informatics, Houston, TX
| | - Efstratios N. Pistikopoulos
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX
- Texas A&M Energy Institute, Texas A&M University, College Station, TX
| | - Burcu Beykal
- Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, CT
- Center for Clean Energy Engineering, University of Connecticut, Storrs, CT
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Zinare T, Di Pretoro A, Chiari V, Montastruc L, Negny S. Benefits of feasibility constrained sampling on unit operations surrogate model accuracy. Comput Chem Eng 2023. [DOI: 10.1016/j.compchemeng.2023.108210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
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3
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Kim SH, Landa HOR, Ravutla S, Realff MJ, Boukouvala F. Data-Driven Simultaneous Process Optimization and Adsorbent Selection for Vacuum Pressure Swing Adsorption. Chem Eng Res Des 2022. [DOI: 10.1016/j.cherd.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Li T, Long J, Zhao L, Du W, Qian F. A bilevel data-driven framework for robust optimization under uncertainty – applied to fluid catalytic cracking unit. Comput Chem Eng 2022. [DOI: 10.1016/j.compchemeng.2022.107989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Miao G, Zhuo K, Li G, Xiao J. An advanced optimization strategy for enhancing the performance of a hybrid pressure-swing distillation process in effective binary-azeotrope separation. Sep Purif Technol 2022. [DOI: 10.1016/j.seppur.2021.120130] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Di Pretoro A, Bruns B, Negny S, Grünewald M, Riese J. Demand Response Scheduling Using Derivative-Based Dynamic Surrogate Models. Comput Chem Eng 2022. [DOI: 10.1016/j.compchemeng.2022.107711] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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7
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An α-Model Parametrization Algorithm for Optimization with Differential-Algebraic Equations. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12020890] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
An optimization task with nonlinear differential-algebraic equations (DAEs) was approached. In special cases in heat and mass transfer engineering, a classical direct shooting approach cannot provide a solution of the DAE system, even in a relatively small range. Moreover, available computational procedures for numerical optimization, as well as differential- algebraic systems solvers are characterized by their limitations, such as the problem scale, for which the algorithms can work efficiently, and requirements for appropriate initial conditions. Therefore, an αDAE model optimization algorithm based on an α-model parametrization approach was designed and implemented. The main steps of the proposed methodology are: (1) task discretization by a multiple-shooting approach, (2) the design of an α-parametrized system of the differential-algebraic model, and (3) the numerical optimization of the α-parametrized system. The computations can be performed by a chosen iterative optimization algorithm, which can cooperate with an outer numerical procedure for solving DAE systems. The implemented algorithm was applied to solve a counter-flow exchanger design task, which was modeled by the highly nonlinear differential-algebraic equations. Finally, the new approach enabled the numerical simulations for the higher values of parameters denoting the rate of changes in the state variables of the system. The new approach can carry out accurate simulation tests for systems operating in a wide range of configurations and created from new materials.
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Beykal B, Diangelakis NA, Pistikopoulos EN. Continuous-Time Surrogate Models for Data-Driven Dynamic Optimization. ESCAPE. EUROPEAN SYMPOSIUM ON COMPUTER AIDED PROCESS ENGINEERING 2022; 51:205-210. [PMID: 36622647 PMCID: PMC9823268 DOI: 10.1016/b978-0-323-95879-0.50035-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
This work addresses the control optimization of time-varying systems without the full discretization of the underlying high-fidelity models and derives optimal control trajectories using surrogate modeling and data-driven optimization. Time-varying systems are ubiquitous in the chemical process industry and their systematic control is essential for ensuring each system to be operated at the desired settings. To this end, we postulate nonlinear continuous-time control action trajectories using time-varying surrogate models and derive the parameters of these functional forms using data-driven optimization. Data-driven optimization allows us to collect data from the high-fidelity model without pursuing any discretization and fine-tune candidate control trajectories based on the retrieved input-output information from the nonlinear system. We test exponential and polynomial surrogate forms for the control trajectories and explore various data-driven optimization strategies (local vs. global and sample-based vs. model-based) to test the consistency of each approach for controlling dynamic systems. The applicability of our approach is demonstrated on a motivating example and a CSTR control case study with favorable results.
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Affiliation(s)
- Burcu Beykal
- Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, CT 06269, USA
- Center for Clean Energy Engineering, University of Connecticut, Storrs, CT 06269, USA
| | - Nikolaos A Diangelakis
- Texas A&M Energy Institute, Texas A&M University, College Station, TX 77843, USA
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Efstratios N Pistikopoulos
- Texas A&M Energy Institute, Texas A&M University, College Station, TX 77843, USA
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, USA
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Beykal B, Avraamidou S, Pistikopoulos EN. Data-Driven Optimization of Mixed-integer Bi-level Multi-follower Integrated Planning and Scheduling Problems Under Demand Uncertainty. Comput Chem Eng 2022; 156:107551. [PMID: 34720250 PMCID: PMC8553017 DOI: 10.1016/j.compchemeng.2021.107551] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The coordination of interconnected elements across the different layers of the supply chain is essential for all industrial processes and the key to optimal decision-making. Yet, the modeling and optimization of such interdependent systems are still burdensome. In this paper, we address the simultaneous modeling and optimization of medium-term planning and short-term scheduling problems under demand uncertainty using mixed-integer bi-level multi-follower programming and data-driven optimization. Bi-level multi-follower programs model the natural hierarchy between different layers of supply chain management holistically, while scenario analysis and data-driven optimization allow us to retrieve the guaranteed feasible solutions of the integrated formulation under various demand considerations. We address the data-driven optimization of this challenging class of problems using the DOMINO framework, which was initially developed to solve single-leader single-follower bi-level optimization problems to guaranteed feasibility. This framework is extended to solve single-leader multi-follower stochastic formulations and its performance is characterized by well-known single and multi-product process scheduling case studies. Through our data-driven algorithmic approach, we present guaranteed feasible solutions to linear and nonlinear mixed-integer bi-level formulations of simultaneous planning and scheduling problems and further characterize the effects of the scheduling level complexity on the solution performance, which spans over several hundred continuous and binary variables, and thousands of constraints.
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Affiliation(s)
- Burcu Beykal
- Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, CT 06269, USA
- Center for Clean Energy Engineering, University of Connecticut, Storrs, CT 06269, USA
| | - Styliani Avraamidou
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Efstratios N. Pistikopoulos
- Texas A&M Energy Institute, Texas A&M University, College Station, TX 77843, USA
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, USA
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Zhang S, Li H, Qiu T. An Innovative Graph Neural Network Model for Detailed Effluent Prediction in Steam Cracking. Ind Eng Chem Res 2021. [DOI: 10.1021/acs.iecr.1c03728] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shuyuan Zhang
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
- Beijing Key Laboratory of Industrial Big Data Systems and Applications, Tsinghua University, Beijing 100084, China
| | - Haoran Li
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
- Beijing Key Laboratory of Industrial Big Data Systems and Applications, Tsinghua University, Beijing 100084, China
| | - Tong Qiu
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
- Beijing Key Laboratory of Industrial Big Data Systems and Applications, Tsinghua University, Beijing 100084, China
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Orr A, Wang M, Beykal B, Ganesh HS, Hearon SE, Pistikopoulos EN, Phillips TD, Tamamis P. Combining Experimental Isotherms, Minimalistic Simulations, and a Model to Understand and Predict Chemical Adsorption onto Montmorillonite Clays. ACS OMEGA 2021; 6:14090-14103. [PMID: 34124432 PMCID: PMC8190805 DOI: 10.1021/acsomega.1c00481] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/11/2021] [Indexed: 05/05/2023]
Abstract
An attractive approach to minimize human and animal exposures to toxic environmental contaminants is the use of safe and effective sorbent materials to sequester them. Montmorillonite clays have been shown to tightly bind diverse toxic chemicals. Due to their promise as sorbents to mitigate chemical exposures, it is important to understand their function and rapidly screen and predict optimal clay-chemical combinations for further testing. We derived adsorption free-energy values for a structurally and physicochemically diverse set of toxic chemicals using experimental adsorption isotherms performed in the current and previous studies. We studied the diverse set of chemicals using minimalistic MD simulations and showed that their interaction energies with calcium montmorillonite clays calculated using simulation snapshots in combination with their net charge and their corresponding solvent's dielectric constant can be used as inputs to a minimalistic model to predict adsorption free energies in agreement with experiments. Additionally, experiments and computations were used to reveal structural and physicochemical properties associated with chemicals that can be adsorbed to calcium montmorillonite clay. These properties include positively charged groups, phosphine groups, halide-rich moieties, hydrogen bond donor/acceptors, and large, rigid structures. The combined experimental and computational approaches used in this study highlight the importance and potential applicability of analogous methods to study and design novel advanced sorbent systems in the future, broadening their applicability for environmental contaminants.
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Affiliation(s)
- Asuka
A. Orr
- Artie
McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
- Texas
A&M Energy Institute, Texas A&M
University, College
Station, Texas 77843-3372, United States
| | - Meichen Wang
- Veterinary
Integrative Biosciences Department, College of Veterinary Medicine
and Biomedical Sciences, Texas A&M University, College Station, Texas 77843-3122, United States
| | - Burcu Beykal
- Texas
A&M Energy Institute, Texas A&M
University, College
Station, Texas 77843-3372, United States
| | - Hari S. Ganesh
- Texas
A&M Energy Institute, Texas A&M
University, College
Station, Texas 77843-3372, United States
| | - Sara E. Hearon
- Veterinary
Integrative Biosciences Department, College of Veterinary Medicine
and Biomedical Sciences, Texas A&M University, College Station, Texas 77843-3122, United States
| | - Efstratios N. Pistikopoulos
- Artie
McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
- Texas
A&M Energy Institute, Texas A&M
University, College
Station, Texas 77843-3372, United States
| | - Timothy D. Phillips
- Veterinary
Integrative Biosciences Department, College of Veterinary Medicine
and Biomedical Sciences, Texas A&M University, College Station, Texas 77843-3122, United States
| | - Phanourios Tamamis
- Artie
McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
- Texas
A&M Energy Institute, Texas A&M
University, College
Station, Texas 77843-3372, United States
- Department
of Materials Science and Engineering, Texas
A&M University, College
Station, Texas 77843-3003, United States
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12
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A Direct Optimization Algorithm for Problems with Differential-Algebraic Constraints: Application to Heat and Mass Transfer. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10249027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In this article, an optimization task with nonlinear differential-algebraic equations (DAEs) is considered. As a main result, a new solution procedure is designed. The computational procedure represents the sequential optimization approach. The proposed algorithm is based on a multiple shooting parametrization method. Two main aspects of a generalized parametrization approach are analyzed in detail: a control function and DAE model parametrization. A comparison between the original and modified DAEs is made. The new algorithm is applied to solve an optimization task in heat and mass transfer engineering.
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