Machine learning for biochemical engineering: A review

Applications of machine learning algorithms for biological wastewater treatment: Updates and perspectives

(2021) Batsuren Sundui et al.   Clean Technologies and Environmental Policy

Using process data to generate an optimal control policy via apprenticeship and reinforcement learning

(2021) Max Mowbray et al.   AICHE JOURNAL

Improved protein structure prediction using potentials from deep learning

(2020) Andrew W. Senior et al.   NATURE

An artificial neural network approach to recognise kinetic models from experimental data

(2020) Marco Quaglio et al.   COMPUTERS & CHEMICAL ENGINEERING

A Review on Reinforcement Learning: Introduction and Applications in Industrial Process Control

(2020) Rui Nian et al.   COMPUTERS & CHEMICAL ENGINEERING

Mitigating Scattering Effects in Light-Based Three-Dimensional Printing Using Machine Learning

(2020) Shangting You et al.   JOURNAL OF MANUFACTURING SCIENCE AND ENGINEERING-TRANSACTIONS OF THE ASME

Modern Soft-Sensing Modeling Methods for Fermentation Processes

(2020) Xianglin Zhu et al.   SENSORS

Model-driven generation of artificial yeast promoters

(2020) Benjamin J. Kotopka et al.   Nature Communications

SDN2GO: An Integrated Deep Learning Model for Protein Function Prediction

(2020) Yideng Cai et al.   Frontiers in Bioengineering and Biotechnology

From inverse optimal control to inverse reinforcement learning: A historical review

(2020) Nematollah Ab Azar et al.   ANNUAL REVIEWS IN CONTROL

Combining model structure identification and hybrid modelling for photo‐production process predictive simulation and optimisation

(2020) Dongda Zhang et al.   BIOTECHNOLOGY AND BIOENGINEERING

A robust soft sensor to monitor 1,3‐propanediol fermentation process by Clostridium butyricum based on artificial neural network

(2020) Ai‐Hui Zhang et al.   BIOTECHNOLOGY AND BIOENGINEERING

Biomass soft sensor for a Pichia pastoris fed‐batch process based on phase detection and hybrid modeling

(2020) Vincent Brunner et al.   BIOTECHNOLOGY AND BIOENGINEERING

Stochastic data-driven model predictive control using gaussian processes

(2020) Eric Bradford et al.   COMPUTERS & CHEMICAL ENGINEERING

Transfer learning for process fault diagnosis: Knowledge transfer from simulation to physical processes

(2020) Weijun Li et al.   COMPUTERS & CHEMICAL ENGINEERING

Modeling, design, and machine learning-based framework for optimal injectability of microparticle-based drug formulations

(2020) Morteza Sarmadi et al.   Science Advances

Knowledge Graph Approach to Combustion Chemistry and Interoperability

(2020) Feroz Farazi et al.   ACS Omega

Spectroscopic detection of traumatic brain injury severity and biochemistry from the retina

(2020) Carl Banbury et al.   Biomedical Optics Express

The Era of Big Data: Genome-scale Modelling meets Machine Learning

(2020) Athanasios Antonakoudis et al.   Computational and Structural Biotechnology Journal

Machine learning for metabolic engineering: A review

(2020) Christopher E. Lawson et al.   METABOLIC ENGINEERING

Exploring the critical factors of algal biomass and lipid production for renewable fuel production by machine learning

(2020) Ahmet Coşgun et al.   RENEWABLE ENERGY

Reinforcement learning based optimization of process chromatography for continuous processing of biopharmaceuticals

(2020) Saxena Nikita et al.   CHEMICAL ENGINEERING SCIENCE

Online deep neural network-based feedback control of a Lutein bioprocess

(2020) Pappa Natarajan et al.   JOURNAL OF PROCESS CONTROL

Single-cell RNA-seq denoising using a deep count autoencoder

(2019) Gökcen Eraslan et al.   Nature Communications

Machine learning metrology of cell confinement in melt electrowritten three-dimensional biomaterial substrates

(2019) Filippos Tourlomousis et al.   Microsystems & Nanoengineering

Machine-learning phase prediction of high-entropy alloys

(2019) Wenjiang Huang et al.   ACTA MATERIALIA

Microfluidic block copolymer membrane arrays for nanopore DNA sequencing

(2019) Justin Rofeh et al.   APPLIED PHYSICS LETTERS

Reinforcement Learning – Overview of Recent Progress and Implications for Process Control

(2019) Joohyun Shin et al.   COMPUTERS & CHEMICAL ENGINEERING

DeePromoter: Robust Promoter Predictor Using Deep Learning

(2019) Mhaned Oubounyt et al.   Frontiers in Genetics

Hybrid physics‐based and data‐driven modeling for bioprocess online simulation and optimization

(2019) Dongda Zhang et al.   BIOTECHNOLOGY AND BIOENGINEERING

Machine-learning-guided directed evolution for protein engineering

(2019) Kevin K. Yang et al.   NATURE METHODS

Development of the Self Optimising Kohonen Index Network (SKiNET) for Raman Spectroscopy Based Detection of Anatomical Eye Tissue

(2019) Carl Banbury et al.   Scientific Reports

A bootstrap-aggregated hybrid semi-parametric modeling framework for bioprocess development

(2019) José Pinto et al.   BIOPROCESS AND BIOSYSTEMS ENGINEERING

Unified rational protein engineering with sequence-based deep representation learning

(2019) Ethan C. Alley et al.   NATURE METHODS

Protein structure prediction using multiple deep neural networks in the 13th Critical Assessment of Protein Structure Prediction (CASP13)

(2019) Andrew W. Senior et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Analytical solution for a hybrid Logistic‐Monod cell growth model in batch and continuous stirred tank reactor culture

(2019) Peng Xu   BIOTECHNOLOGY AND BIOENGINEERING

Multivariate statistical process control of an industrial-scale fed-batch simulator

(2019) Carlos A. Duran-Villalobos et al.   COMPUTERS & CHEMICAL ENGINEERING

Effects of corn straw on dissipation of polycyclic aromatic hydrocarbons and potential application of backpropagation artificial neural network prediction model for PAHs bioremediation

(2019) Huanyu Bao et al.   ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY

Advances in industrial biopharmaceutical batch process monitoring: Machine-learning methods for small data problems

(2018) Aditya Tulsyan et al.   BIOTECHNOLOGY AND BIOENGINEERING

Machine learning: Overview of the recent progresses and implications for the process systems engineering field

(2018) Jay H. Lee et al.   COMPUTERS & CHEMICAL ENGINEERING

Photocatalytic Production of Bisabolene from Green Microalgae Mutant: Process Analysis and Kinetic Modeling

(2018) Irina Harun et al.   INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH

Assessment of producer gas composition in air gasification of biomass using artificial neural network model

(2018) Joel George et al.   INTERNATIONAL JOURNAL OF HYDROGEN ENERGY

A machine learning approach towards the prediction of protein–ligand binding affinity based on fundamental molecular properties

(2018) Indra Kundu et al.   RSC Advances

Dynamic modeling and optimization of sustainable algal production with uncertainty using multivariate Gaussian processes

(2018) Eric Bradford et al.   COMPUTERS & CHEMICAL ENGINEERING

Design of metalloproteins and novel protein folds using variational autoencoders

(2018) Joe G. Greener et al.   Scientific Reports

Deep reinforcement learning for de novo drug design

(2018) Mariya Popova et al.   Science Advances

Deep learning‐Based surrogate modeling and optimization for microalgal biofuel production and photobioreactor design

(2018) Ehecatl Antonio Rio‐Chanona et al.   AICHE JOURNAL

GSAE: an autoencoder with embedded gene-set nodes for genomics functional characterization

(2018) Hung-I Harry Chen et al.   BMC Systems Biology

Prediction of bioavailability and toxicity of complex chemical mixtures through machine learning models

(2018) S. Cipullo et al.   CHEMOSPHERE

Deep Learning with Microfluidics for Biotechnology

(2018) Jason Riordon et al.   TRENDS IN BIOTECHNOLOGY

Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models

(2018) David Heckmann et al.   Nature Communications

An integrative machine learning strategy for improved prediction of essential genes in Escherichia coli metabolism using flux-coupled features

(2017) Sutanu Nandi et al.   Molecular BioSystems

Prediction of organic carbon and total nitrogen contents in organic wastes and their composts by Infrared spectroscopy and partial least square regression

(2017) M. Sisouane et al.   TALANTA

Mechanistic Fermentation Models for Process Design, Monitoring, and Control

(2017) Lisa Mears et al.   TRENDS IN BIOTECHNOLOGY

Learning a Health Knowledge Graph from Electronic Medical Records

(2017) Maya Rotmensch et al.   Scientific Reports

Interactive effects of PAHs and heavy metal mixtures on oxidative stress in Chlorella sp. MM3 as determined by artificial neural network and genetic algorithm

(2017) Suresh R. Subashchandrabose et al.   Algal Research-Biomass Biofuels and Bioproducts

Scale-up/Scale-down of microbial bioprocesses: a modern light on an old issue

(2017) Frank Delvigne et al.   Microbial Biotechnology

Artificial neural network based modeling to evaluate methane yield from biogas in a laboratory-scale anaerobic bioreactor

(2016) Vijay V. Nair et al.   BIORESOURCE TECHNOLOGY

Fatty Acid Methyl Ester (FAME) composition used for estimation of biodiesel cetane number employing random forest and artificial neural networks: A new approach

(2016) Seyed MohammadReza Miraboutalebi et al.   FUEL

Estimation of in-situ bioremediation system cost using a hybrid Extreme Learning Machine (ELM)-particle swarm optimization approach

(2016) Basant Yadav et al.   JOURNAL OF HYDROLOGY

Principal component analysis: a review and recent developments

(2016) Ian T. Jolliffe et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Semisupervised Gaussian Process for Automated Enzyme Search

(2016) Joseph Mellor et al.   ACS Synthetic Biology

Rapid Prediction of Bacterial Heterotrophic Fluxomics Using Machine Learning and Constraint Programming

(2016) Stephen Gang Wu et al.   PLoS Computational Biology

Dynamic modeling and optimization of cyanobacterial C-phycocyanin production process by artificial neural network

(2016) Ehecatl Antonio del Rio-Chanona et al.   Algal Research-Biomass Biofuels and Bioproducts

Corrigendum: Predicting Essential Genes and Proteins Based on Machine Learning and Network Topological Features: A Comprehensive Review

(2016) Xue Zhang et al.   Frontiers in Physiology

Robust and efficient parameter estimation in dynamic models of biological systems

(2015) Attila Gábor et al.   BMC Systems Biology

Methods and advances in metabolic flux analysis: a mini-review

(2015) Maciek R. Antoniewicz   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Principal component analysis of proteomics (PCAP) as a tool to direct metabolic engineering

(2015) Jorge Alonso-Gutierrez et al.   METABOLIC ENGINEERING

Deep learning

(2015) Yann LeCun et al.   NATURE

Sparse Bayesian extreme learning machine and its application to biofuel engine performance prediction

(2015) Ka In Wong et al.   NEUROCOMPUTING

Modeling and optimization of biodiesel engine performance using kernel-based extreme learning machine and cuckoo search

(2015) Pak Kin Wong et al.   RENEWABLE ENERGY

Artificial neural network model for predicting methane percentage in biogas recovered from a landfill upon injection of liquid organic waste

(2014) Shishir Kumar Behera et al.   Clean Technologies and Environmental Policy

Modelling and predicting the biological effects of nanomaterials

(2014) D.A. Winkler et al.   SAR AND QSAR IN ENVIRONMENTAL RESEARCH

Optimizing multi-variables of microbial fuel cell for electricity generation with an integrated modeling and experimental approach

(2013) Fang Fang et al.   APPLIED ENERGY

Machine learning models for predicting PAHs bioavailability in compost amended soils

(2013) Guozhong Wu et al.   CHEMICAL ENGINEERING JOURNAL

Hybrid semi-parametric modeling in process systems engineering: Past, present and future

(2013) Moritz von Stosch et al.   COMPUTERS & CHEMICAL ENGINEERING

Performance evaluation of microbial fuel cell by artificial intelligence methods

(2013) A. Garg et al.   EXPERT SYSTEMS WITH APPLICATIONS

Use of artificial neural network for the prediction of bioelectricity production in a membrane less microbial fuel cell

(2013) Ali Tardast et al.   FUEL

Optimal design of an in-situ bioremediation system using support vector machine and particle swarm optimization

(2013) Sudheer ch et al.   JOURNAL OF CONTAMINANT HYDROLOGY

Development of Ann-Based Models to Predict Biogas and Methane Productions in Anaerobic Treatment of Molasses Wastewater

(2012) Kaan Yetilmezsoy et al.   International Journal of Green Energy

Prediction of methane production in wastewater treatment facility: a data-mining approach

(2011) Andrew Kusiak et al.   ANNALS OF OPERATIONS RESEARCH

Coping with complexity: Machine learning optimization of cell-free protein synthesis

(2011) Filippo Caschera et al.   BIOTECHNOLOGY AND BIOENGINEERING

Hybrid metabolic flux analysis: combining stoichiometric and statistical constraints to model the formation of complex recombinant products

(2011) Nuno Carinhas et al.   BMC Systems Biology

Machine learning methods for metabolic pathway prediction

(2010) Joseph M Dale et al.   BMC BIOINFORMATICS

Sequence feature-based prediction of protein stability changes upon amino acid substitutions

(2010) Shaolei Teng et al.   BMC GENOMICS

Prediction of diesel engine performance using biofuels with artificial neural network

(2010) Hidayet Oğuz et al.   EXPERT SYSTEMS WITH APPLICATIONS

Using the Concept of Chous Pseudo Amino Acid Composition to Predict Enzyme Family Classes: An Approach with Support Vector Machine Based on Discrete Wavelet Transform

(2010) Jian-Ding Qiu et al.   PROTEIN AND PEPTIDE LETTERS

Applications of genome-scale metabolic reconstructions

(2009) Matthew A Oberhardt et al.   Molecular Systems Biology

Comparison of artificial neural network (ANN) and response surface methodology (RSM) in fermentation media optimization: Case study of fermentative production of scleroglucan

(2008) Kiran M. Desai et al.   BIOCHEMICAL ENGINEERING JOURNAL

A modeling study by response surface methodology and artificial neural network on culture parameters optimization for thermostable lipase production from a newly isolated thermophilic Geobacillus sp. strain ARM

(2008) Afshin Ebrahimpour et al.   BMC BIOTECHNOLOGY

Prediction of effluent quality of an anaerobic treatment plant under unsteady state through ANFIS modeling with on-line input variables

(2008) A PERENDECI et al.   CHEMICAL ENGINEERING JOURNAL

Biomass estimation in batch biotechnological processes by Bayesian Gaussian process regression

(2008) Fernando di Sciascio et al.   COMPUTERS & CHEMICAL ENGINEERING

Microfluidics-based electrospray ionization enhances the intrasource separation of lipid classes and extends identification of individual molecular species through multi-dimensional mass spectrometry: development of an automated high-throughput platform for shotgun lipidomics

(2008) Xianlin Han et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY

Diesel engine performance and exhaust emission analysis using waste cooking biodiesel fuel with an artificial neural network

(2008) B. Ghobadian et al.   RENEWABLE ENERGY