Bioresource Technology 343 (2022) 126099

Contents lists available at ScienceDirect

Bioresource Technology
journal homepage: www.elsevier.com/locate/biortech

Review

The role of machine learning to boost the bioenergy and

biofuels conversion
Zhengxin Wang a, b, 1, Xinggan Peng c, 1, Ao Xia a, b, *, Akeel A. Shah a, b, Yun Huang a, b,
Xianqing Zhu a, b, Xun Zhu a, b, Qiang Liao a, b
a
Key Laboratory of Low-grade Energy Utilization Technologies and Systems, Chongqing University, Ministry of Education, Chongqing 400044, PR China
b
Institute of Engineering Thermophysics, School of Energy and Power Engineering, Chongqing University, Chongqing 400044, PR China
c
School of Electrical and Electronic Engineering, Nanyang Technological University, 639798, Singapore

H I G H L I G H T S G R A P H I C A L A B S T R A C T

• Complexity of bioenergy system limits

accurate prediction by experience or
theory.
• Machine learning (ML) opens a new
opportunity in prediction of bioenergy
system.
• Classification, regression, and optimiza­
tion are involved in bioenergy problems.
• ML boosts the research in lignocellulosic
biofuels and microalgae cultivation.
• Novel ML algorithms (such as deep
learning) with large databases are
expected.

A R T I C L E I N F O A B S T R A C T

Keywords: The development and application of bioenergy and biofuels conversion technology can play a significant role for
Bioenergy the production of renewable and sustainable energy sources in the future. However, the complexity of bioenergy
Biofuels systems and the limitations of human understanding make it difficult to build models based on experience or
Machine learning
theory for accurate predictions. Recent developments in data science and machine learning (ML), can provide
Lignocellulosic biomass
new opportunities. Accordingly, this critical review provides a deep insight into the application of ML in the
Algae
bioenergy context. The latest advances in ML assisted bioenergy technology, including energy utilization of
lignocellulosic biomass, microalgae cultivation, biofuels conversion and application, are reviewed in detail. The
strengths and limitations of ML in bioenergy systems are comprehensively analysed. Moreover, we highlight the
capabilities and potential of advanced ML methods when encountering multifarious tasks in the future prospects
to advance a new generation of bioenergy and biofuels conversion technologies.

1. Introduction fossil fuels, the burning of which released over 32 billion tons of carbon
dioxide, causing serious environmental pollution (BP, 2021). In
In 2020, nearly 83.1% of global energy consumption came from contrast, the abundant and diverse biomass waste resources, such as

* Corresponding author.
E-mail address: aoxia@cqu.edu.cn (A. Xia).
1
These authors contributed equally to this work.

https://doi.org/10.1016/j.biortech.2021.126099
Received 9 August 2021; Received in revised form 4 October 2021; Accepted 5 October 2021
Available online 7 October 2021
0960-8524/© 2021 Elsevier Ltd. All rights reserved.
Z. Wang et al.
lignocellulose, algae, food wastes, livestock and poultry manure (Deng
et al., 2019; Xia & Murphy, 2016), are widely distributed on the earth’s
surface, can offer an alternative solution for sustainable and carbon
neutral energy supply. For example, the annual production of terrestrial
biomass (dominated by lignocellulose) is estimated 130 billion metric
tons based on dry weight (Potter et al., 2012), which is equal to
approximate 65 billion metric tons of standard coal. These biomass re­
sources have the potential to be converted into fuels and value-added
chemicals in bioenergy systems (Leong et al., 2020; Liao et al., 2020),
which may play a significant role for future development to alleviate and
deal with the energy crisis and environmental issues.
Nevertheless, bioenergy systems basically involve complex, high-
dimensional, and multi-scale conversion processes across temporal
and spatial variation, which are the result of the interaction of many
factors. For example, a more successful case is anaerobic digestion (AD),
with the significant factors of raw materials (components, structure,
characteristics, pretreatment etc.), operational parameters (tempera­
ture, hydraulic retention time, volume loading, pH, stir, reactor
configuration, nutrients, inhibitors etc.), and inoculum (inoculum ratio,
microbial community and activity etc.) (Feng et al., 2021). Therefore,
repeated trial-and-error is carried out in traditional research, and a se­
ries of experience-based hypotheses or conjectures are derived by
empirical judgment, contributing to the establishment of theory-driven
(also known as model-driven or hypothesis-driven) models. With these
models, the rationality and feasibility of a task can be predicted first,
thereby greatly reducing the workload. The Anaerobic Digestion Model
No. 1 (ADM1) was developed to simulate the AD process (Batstone et al.,
2002; Weinrich & Nelles, 2021; Zhao et al., 2019). Although ADM1
performed well in laboratory-scale AD, it had limited applications on the
industrial scale by virtue of the complexity of the AD system and a lack
of detailed substrate characterization (Derbal et al., 2009; Maharaj et al.,
2019; Weinrich et al., 2021). Therefore, on the one hand, the con­
struction of a successful theory-driven model for a bioenergy system is a
challenge. On the other hand, when it meets with the data collected from
complex phenomena, it is difficult to develop comprehensive knowledge
based on physical principles, especially in processing the big data sets
from bioenergy systems. The potential of such data can only be exploited
based on high-level data analysis methods.
In the 21st century, artificial intelligence (AI) has been hailed as the
fourth industrial revolution (Diez-Olivan et al., 2019). As a vital data
analysis technique, machine learning (ML) has gained explosive growth
in the past ten years, which greatly extends AI, extending its problem-
solving scope and ability. ML is a collection of advanced data analysis
methods based on the principles of mathematics and probability/sta­
tistics, identifying the patterns between features in a data set and
allowing for predictions in the case of new inputs. ML has been suc­
cessfully applied to business, medicine (Stokes et al., 2020), biology
(Kim et al., 2018), physical sciences (Mehta et al., 2019), chemistry
(Dral, 2020)) and geoscience (Reichstein et al., 2019), with new appli­
cations areas emerging continually. The complex mechanisms of bio­
logical systems can be captured through multi-modal learning from
different views (Li et al., 2018). Advances in optics and imaging tech­
nology have enabled ML to analyse and monitor the trace of cells (Moen
et al., 2019), and even achieve automatic control of atomic force mi­
croscopes at the nanometre scale (DePristo, 2018). With regard to
human tasks, ML can serve as an auxiliary tool to achieve more efficient
or reliable outcomes. Furthermore, ML can be theoretically competent
for tasks involving the attribution of causality or discovering connec­
tions between variables, which is advantageous for solving tasks that
cannot be solved through traditional modelling or experiment, and for
making new discoveries.
Notably, ML has attracted increasing attention in the bioenergy field.
Del Rio-Chanona et al. (2019b) proposed a deep learning (DL) model
based on a convolutional neural network (CNN) to optimise a photo­
bioreactor and microalgal production, which greatly reduced the time
spent compared with traditional simulation calculations. Mujtaba et al.
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Bioresource Technology 343 (2022) 126099
(2020) combined an extreme learning machine (ELM) and a cuckoo
search algorithm to predict optimal P50S50 biodiesel yield, and the
error between the predicted and experimental values was less than
0.26%. Phromphithak et al. (2021) used a random forest (RF) to predict
the cellulose enrichment factor and solid recovery of lignocellulosic
biomass pre-treated with ionic liquid solvents, which included 23 vari­
ables. The regression coefficients (R2) were 0.94 and 0.84, respectively.
More specifically, when it aims at a microbial metabolic production
process, it focuses on how to maximise the yield of the desired products,
and ML models can provide guidance on different scales, whether it is
gene-annotated strain planning to change metabolic pathways (Hanni­
gan et al., 2019; Kumar et al., 2019; Oyetunde et al., 2018) or fermen­
tation operation parameter optimisation to improve production of
metabolites (Gopakumar et al., 2018; Zhang et al., 2020).
As a consequence, the intersection between ML and bioenergy covers
a wide range in the last five years, including the cultivation and moni­
toring of microalgae, the extraction and optimisation of energy mate­
rials, the interaction analysis of microbial communities, and the
prediction of industrial production. To our best, a comprehensive review
of ML in bioenergy is still lacking. Therefore, this work reviews the
recent applications of ML in bioenergy for the first time, to provide some
useful guidelines for bioenergy research. The review aims to:
• Analyse the adaptability and flexibility of ML in the bioenergy
context;
• Assess the recent applications of ML in bioenergy and biofuel
conversion;
• Identify the future direction of ML in bioenergy and biofuel
conversion.
2. Machine learning flexibility in bioenergy research
Although ML algorithms have been applied to bioenergy utilization
with increasing regularity, ML-assisted predictions are still in the initial
stage of development. The current main barriers to employing ML
techniques for bioenergy research are the lack of sufficient knowledge
for how the subject incorporates with ML methods to accomplish
specialized tasks. In this section, we discuss the differences between
traditional theory-driven models and data-driven models, and analyze
the available data sources and their characteristics in the bioenergy
field.
2.1. Data-driven and theory-driven modelling
A great deal of effort has been directed towards making theoretical
predictions in order to facilitate the deployment of bioenergy technol­
ogy and to decrease the time and energy costs. Theory-driven (or hy­
pothesis based) models have been built to understand the natural
mechanisms using known natural laws, specialized knowledge and
sometimes intuition (Carleo et al., 2019). The construction of a theory-
driven model requires an adequate understanding of the behaviour of a
system. With the consideration of specific goals, a mathematical (or
empirical) model can be derived from first principles or hypotheses, and
the parameters of the model will have physical interpretations. In
contrast, data-driven methods extract patterns from the given data
without the need of any insight into the physical mechanisms. Theory-
driven methods impose pre-existing knowledge of the system, pre­
supposing that it is correct, whereas data-driven methods extract such
knowledge from data using ML algorithms, but face the issue of
interpretability.
The differences between theory-driven methods and data-driven
methods are listed in Table 1. Generally, theory-driven methods
require enough domain knowledge along with cogent hypotheses.
Nevertheless, many theory-driven models are underdeveloped due to
the incomplete knowledge of certain phenomena, which restricts their
accuracy and applicability. An example is ADM1, which was not
Z. Wang et al. Bioresource Technology 343 (2022) 126099

Table 1
Differences between theory-driven methods and data-driven methods.
Class Specialized Hypothesis Process Origin Interpretability Inductive learning Complexity Resource
knowledge characteristic ability from limited cost e
samples
a,b
Theory- Much Yes a,b Data fit model Experience, first High Strong d
Decided by the Experts and
driven principles b brain b time e
methods
a,b
Data-driven Little No a,b Model fit data Mathematics and Low c Weak d
Decided by data Data e
methods probability / statistics and algorithms
b

a
(Toyao et al., 2020)
b
(Reichstein et al., 2019)
c
(NOE et al., 2020)
d
(Lake et al., 2015)
e
(Feffer, 2017)

adopted for large-scale industrial applications (De Clercq et al., 2020). In
contrast, data-driven methods require only a sufficient number of data
samples covering the full variation of phenomena (in terms of the pa­
rameters, operating conditions or evolutionary stages associated with
the problem).
Supervised ML models take input–output pairs as the data set and use
the data set to ‘train’ the model for making predictions at new inputs, for
either classification or regression tasks. Such models use explicitly
(parametric) or implicitly (non-parametric) defined functions to learn
relationships between variables in the data. Training is the process by
which the parameters of the models are estimated from the data, either
by minimising a loss function (error between predictions and data) or
maximising a likelihood (probability of generating the data from the
assumed ML model). In parametric approaches, the parameters are those
appearing in the explicitly defined function, which take the form a basis
expansion with a specified basis and undetermined coefficients (the
parameters, also called weights). In non-parametric approaches the
function does not have an explicit form (e.g., a neural network or
Gaussian process (GP) model) and is characterised by certain ‘hyper­
parameters’ (learned during training) that control the specification of
the model, e.g., parameters appearing in the mean and covariance
functions in a GP model. One of the main criticisms of ML approaches is
their lack of interpretability, i.e., the ability to relate the results to the
underlying physical mechanisms in order to gain further insights. The
specific and often complicated equations given by theory can be difficult
to solve with a major expenditure of time (NOE et al., 2020), whereas
ML methods are able to bypass the direct solution altogether (with
experimental data) or use only a limited number of full numerical so­
lutions as the data set (Brockherde et al., 2017).
2.2. Data sources
Particular emphasis is placed on the quality and quantity of data,
which are paramount considerations for developing the robust and ac­
curate ML prediction models (Toyao et al., 2020). A clear understanding
of data sources is necessary for the selection of suitable approaches. Data
in the bioenergy conversion context could be generated from laboratory
scale experiments (Yew et al., 2020), simulations (Del Rio-Chanona
et al., 2019b), and industrial operations (De Clercq et al., 2020)
(Fig. 1). According to the types of problems, existing studies at the
intersection between bioenergy conversion and ML include tabular data
(the most common type in current papers), images (usually associated
with DL approaches, and applied to the analysis of microalgae), struc­
ture data (a handful of relevant reports, such as molecular descriptors
for chemical formulae (Kessler et al., 2017)), sensor signals (Cramer
et al., 2018), and texts (Benites-Lazaro et al., 2018). Although raw data
is available, data is usually required to be transformed to the format that
the computer is able to understand. With a more appropriate
input–output format after data pre-processing and bias-variance trade-
off (such as data cleaning and feature engineering), the final model
would have better performances.
Of particular note is that many phenomena (such as biological pro­
cesses) are dynamic rather than static as in most applications of ML in
physical science (Mehta et al., 2019) or molecular and materials science

Fig. 1. Application of machine learning in bioenergy.

3
Z. Wang et al.
(Butler et al., 2018). Data of inherent structure–property relationships
with suitable descriptors can be used for the discovery of new materials,
such as catalysts (Toyao et al., 2020) and organic photovoltaic materials
(Sun et al., 2019), or even the antibiotic discovery (Stokes et al., 2020).
In the bioenergy context, ML models may result in poor performance due
to lack of data, poor coverage of the range of operation or the presence of
random noise in the data, but these limitations can be broken through
with promising and advanced ML methods (Reichstein et al., 2019).
Table 2 assesses the different data sources for ML applications in
bioenergy technology. Whether the data is designed or recycled will
result in different levels of data quality and quantity, especially for
biotechnology. Another way to obtain data is from published papers.
These data seem to be highly correlated, but a lot of random noise will be
generated from the different experimental equipment, researchers, and
operation protocols in time-consuming experiments. The performance of
models learning from simulated data will not surpass the accuracy of
fully simulated results. The source of errors in industrial data is different
from that in simulated data, which are due to measurement errors and
missing data. Additionally, industrial data have more redundant fea­
tures. As a typical linear method, principal component analysis (PCA)
have better performance than discriminant analysis (LDA) in all mea­
sures, as well as ML algorithms with PCA performed better results in
high dimensional datasets, while ML algorithms without dimensionality
reduction techniques performed better results in low dimensional
datasets (Reddy et al., 2020).
3. Machine learning in bioenergy conversion technology and
system
Many experiments are long-term trials and may need highly so­
phisticated equipment for monitoring. To avoid trial-and-error or
expensive operations and summarize the inner mechanism to achieve
the purpose of predictions or optimisation, data-driven models have
been tried when theory-driven models meet with major challenges on
account of the complexity of bioenergy conversion processes. Further­
more, ML models can complete tasks that theory-driven models cannot
accomplish, such as image-activated cell sorting (Isozaki et al., 2019;
Nitta et al., 2018). In this section, specific examples of ML predictive
models are discussed mainly in bioproduction processes and bioenergy
conversion and applications.
3.1. Machine learning in physicochemical characteristics of bioresources
In fact, ML can not only make good predictions, but also allows for
attribution of phenomena. Bioresources have various correlated physi­
cochemical attributes. Some important attributes are difficult to mea­
sure, and ML can capture the correlation between these attributes and
make predictions, such as the photo-property estimation (Yew et al.,
2020).
Among various scientific tasks that use ML methods (see Table 3),
some predictive results based on the correlated attributes. Xing et al.
(2019b) predicted higher heating values of biomass from proximate or
ultimate analysis, and the R2 (>0.90) of ML models were better than
empirical correlations (less than 0.70). Uzun et al. (2017) reported
Table 2
Comparison of different data sources in bioenergy.
Data source Size Accessibility Reliability Significance of preprocessing
Experimental data – – ++ high
Simulated data ++ ++ ++ low
Collected from published papers + ++ + very high
Industrial data + ++ + very high
-: Weak performance for different data sources;
+: Medium performance for different data sources;
++: High performance for different data sources.
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Bioresource Technology 343 (2022) 126099
similar results (R2 = 0.963) when using an ANN to forecast higher
heating values. Further improvement in the model accuracy may depend
on the descriptions of the biomass composition and structure.
Daassi-Gnaba et al. (2017) predicted wood moisture content from
reflection coefficient measurements, and the SVM models performed a
slightly better than ANN models, possibly due to the regularization
mechanism of SVM. Compared with the frequent overfitting of ANN, the
SVM method was able to reduce the structured risk in the training
process. The study of Cao et al. (2016) also showed that a SVM model
had a more robust performance compared to an ANN model. Kessler
et al. (2017) predicted the cetane number of furan biofuel additives from
compound structures (molecular descriptors), and the predicted values
were the average of the output of five ANN models using ensemble
learning.
3.2. Machine learning in biofuels production and application
3.2.1. Biological process
Biofuels can be produced via biological conversion approaches at a
mild environment. The principles underlying the predictions from AD
based on operational parameters appear to be correct, but there are
other entrenched factors that will seriously affect the performance of the
model. In the long-term AD process, the evolution of the microbial
community is elusive, bringing significant changes in microbial meta­
bolism. Even with the same operation, equipment, and environment, the
final results have a certain variability, such as the microbial structure,
which may change seasonally (Gruszka Vendruscolo et al., 2020).
As shown in Table 4, the generalization ability of models was poor
when data was generated from biological process (Antwi et al., 2017;
Lesnik et al., 2020; Sydney et al., 2020; Wang et al., 2020), which was
possibly caused by the complexity of biological systems and the limi­
tations and variation in the data variables. Wang et al. (2020) predicted
methane production values from operational parameters, and the
dataset was collected from published papers. These data were generated
from the same configuration of AD reactor. However, the limited num­
ber of data points may reduce the accuracy of such ML models. Antwi
et al. (2017) estimated methane yields in an upflow anaerobic sludge
blanket reactor, and the performance of an ANN model (R2 = 0.9793)
was better than a nonlinear regression model (R2 = 0.9262). Meanwhile,
the data kept stability at some stages, because the experiment was
continuous. The results showed the potential of simulating wastewater
treatment systems through ML.
Hosseinzadeh et al. (2020) combined ANN and FL to model elec­
trochemical performance in a microbial electrolysis cell, and the adap­
tive network based on the fuzzy inference system performed better than
the ANN, which was consistent with the report of Rego et al. (2018).
Calero et al. (2018) also indicated the potential of neural fuzzy models
for breakthrough curve prediction. Lesnik et al. (2020) evaluated the
functional resistance and resilience of microbial fuel cells. Though the
performance of the model was limited by the quantity of data, it pro­
vided an insight into the biological conversion process based on genomic
data. In contrast, Gruszka Vendruscolo et al. (2020) investigated the
importance of each function group of a microbial community to the
electrochemical performance of a microbial electrolysis cell using PCA
Complexity of robust models Accuracy of model Applied range
+ ++ –
++ ++ +
+ + +
++ + ++
Z. Wang et al.
Table 3
Machine learning for attribute connection of biomass resources.
Scientific task Methods Number/Type of
features
Estimating higher heating values of ANN, SVM, 7/Continuous
biomass RF
Predicting wood moisture content SVM, ANN ≤8/Continuous
Predicting cetane number for furanic ANN 15/Molecular
biofuel additives descriptors
Predicting compost maturity CNN, ResNet 300 × 300 pixels
Estimating biomass major chemical RF 3/Continuous
constituents
ANN: Artificial Neural Network; CNN: Convolutional Neural Network; RF: Random Forest; SVM: Support Vector Machine.
-: Low accuracy; +: Medium accuracy; ++: High accuracy.
and RF algorithms.
Besides the problem of insufficient data caused by experimental
difficulties, there are challenges in obtaining data in a valid domain.
More efforts should be focused on adaptability, complementarity, and
constraints between them, which would improve the performance of ML
models. Last but not least, more rigorous experimental design would be
conducive to the generation of high-quality data and coverage of the
valid domain.
3.2.2. Thermochemical process
The thermochemical conversion rate is much faster than biological
conversion, though it requires a significant devotion of energy. In the
case of the same configuration conditions and no interference in the
thermochemical reaction process, the numerical result is relatively sta­
ble and only based on the reaction conditions. As a consequence, the
trained ML models can achieve high-accuracy predictions and guide the
design of new plans (Table 4). The combination of ML models and
optimisation algorithms had shown great potential. Mujtaba et al.
(2020) designed a P50S50 with improved cold flow and lower friction
(reduced by 12.37% compared to B10 commercial diesel) when they
combined an extreme learning machine (ELM) model with a cuckoo
search algorithm. Li et al. (2020) used waste peanut shells to produce
methyl levulinate and achieved efficient catalytic conversion when the
combined an ANN model with a genetic algorithm (GA). Both of them
found the performance of such hybrid models was superior to a response
surface methodology (RSM). Analogously, Patil et al. (2017) found that
an ANN performed better than RSM and SVM in the release of arginine
deiminase through ultrasonic disruption.
Zhu et al. (2019) modeled the yield and carbon contents of biochar
from published data, which indicated that structural information led to a
higher R2 (by 5%) compared to elemental information. On the other
hand, Xing et al. (2019a) used RF to reveal a strong correlation (R2 >
0.93) between chemical constituents and elemental analysis. Ullah et al.
(2021) used RF with the help of genetic algorithm-based feature selec­
tion to predict bio-oil yield (R2 > 0.98). These authors suggested
biomass characteristics and pyrolysis conditions were important
features.
Engines shows different levels of adaptability to biofuels under
different operating conditions, and it is possible to achieve the best
engine performance by tuning the ratio of biofuel blends. ML can
automatically search for the optimal solution to help overcome the
shortcomings of traditional trial-and-error based calibration. The opti­
mised engine tends to achieve a higher biofuel utilization efficiency as
well as lower exhaust emission parameters (Silitonga et al., 2018). An
air–fuel ratio controller based on a ELM model outperformed the engine
built-in controller in the work of Wong and Wong (2018). Moreover, a
kernel-based ELM model could further improve prediction accuracy
(Wong & Wong, 2017; Zhao et al., 2021).
As a consequence, biological conversion approaches are time-
Bioresource Technology 343 (2022) 126099
Samples Accuracy Remark Reference
495 and + Slightly better performance of RF (Xing et al., 2019b)
190 Optimisation of hyper-parameter
was vital
32 ++ Inaccessible directed variables (Daassi-Gnaba et al.,
Finding out associated factors 2017)
291 + Reflecting the ideology of ensemble (Kessler et al., 2017)
learning
~30000 ++ Just for classification (Xue et al., 2019)
Data augmentation could be useful
144 + Better than empirical correlation (Xing et al., 2019a)
consuming, and the action of microorganisms or enzymes is highly
nonlinear and complex, making the performance of ML in biological
conversion weaker than in thermochemical conversion (as shown in
Table 4). While ML led to ideal results in thermochemical optimisation
processes, overshadowing the predictions for biological conversion.
3.3. Machine learning in microalgae cultivation
The cultivation and bioproduction of microalgae are affected by
many factors such as light, carbon source and nutrient composition, pH,
mixing conditions, etc. More subtle control and insight into microalgae
production can be acquired through ML. While traditional methods
depend on extensive of characterization analysis and expert knowledge,
ML methods provide a more effective approach to accommodate the
intricacies of the metabolism and production of microalgae. Various ML
approaches have been applied to predict, control, and design a variety of
scientific tasks (Table 5). Despite some drawbacks or limitations, these
studies provided notable approaches for applying ML to the respective
topics and have opened up new ideas.
One obvious application of ML is to predict the occurrence of results
based on important factors (so called causality), such as the evaluation
of the toxicity of micrometre scale plastics on marine microalgae (Guo
et al., 2020) and the combination of variables contributing to high algal
biomass productivity and lipid content (Cosgun et al., 2021). Yew et al.
(2020) performed an interesting study to find correlations between
images of microalgae cultivated in molasses wastewater and experi­
mental outcomes, predicting the changes in biomass concentration, ni­
trogen concentration, and pH. However, the model was not entirely
successful, which may be due to inability of the KNN method to identify
image features well. As an alternative to extracting features from im­
ages, Reimann et al. (2020) applied bioimage informatics (FastFluoScan
software) to obtain the features of microalgae (such as size) for the
identification of dead and living microalgae cells or their distribution.
Such image feature extraction methods are quite different from ML
approaches.
In comparison to advanced image analysis methods, the major
reason why a different approach has to be taken is the scarcity of
datasets. Biological science is benefitting developments in ML, such as
DL techniques (Camacho et al., 2018). DL has enabled the application of
computer vision to process problems, and progress in optics has enabled
dynamic measurements of single molecules or even living systems
(Moen et al., 2019). Recent advances, such as image classification
(Isozaki et al., 2019; Nitta et al., 2018), image segmentation (Bai et al.,
2017), object tracking (Newby et al., 2018), and augmented microscopy
(Ounkomol et al., 2018) may provide innovative approaches.
Simulations can be used to generate large amounts of data if the
time–cost is reasonable. Established ML models greatly reduce the cost
of time-consuming simulations (Del Rio-Chanona et al., 2019b), as well
as time-consuming experiments (Lopez-Exposito et al., 2019), especially
5
Z. Wang et al. Bioresource Technology 343 (2022) 126099

Table 4
Machine learning for biofuels production and application.
Analytical task Scientific task Methods Number/Type Samples Accuracy Remark Reference
of features

Regression Predicting methane production PCA, ANN, DT, 8/Continuous 3 datasets + Effective PCA (Xiao et al., 2021)
from in-situ biogas upgrading SVM, MLR, GPR, Microbes might become
Ensemble important variable
Predicting pyrolytic gas yield and RF, SVM 11/Continuous 120 and 194 + Biomass characteristics (Tang et al., 2021)
compositions contributed more
Other ML models can be
tried
Predicting bio-oil yield DT, MLR, RF, SVM 11/Continuous 263 ++ Features selection based (Ullah et al., 2021)
on a genetic algorithm
Better performance of RF
Evaluating electrochemical ANN, FL 3/Continuous 24 ++ ANN combined with FL (Hosseinzadeh et al.,
performance performed better 2020)
Predicting methane yield from KNN, RF, LR, SVM 8/Continuous 15 – Insufficient data points (Wang et al., 2020)
operational parameters
Predicting the yield and content RF 12/Continuous 128 and 245 + Structural information (Zhu et al., 2019)
of biochar performed better
More regression
algorithms (ANN) could
be tried
Understanding the pyrolytic SVR, PCA 2/Continuous NA ++ Few inputs and strong (Shahbeig & Nosrati,
behaviour pertinence 2020)
Predicting the production of ANN 5/Continuous NA ++ Only one continuous (Sydney et al., 2020)
biohydrogen experiment
Application limitation
Predicting the engine ELM 2/Continuous 60 ++ Reliable kernel-based (Silitonga et al.,
performance. ELM 2018)
Fitting delignification process ANN, FL 2/Continuous 12 ++ No test set (Rego et al., 2018)
Predicting product distribution ANN, SVM 9/Continuous 175 and 71 + Some search conditions (Chen et al., 2018)
and bio-oil heating value of remained consistent
pyrolysis Data pre-processing
could be attempted
Estimating methane yield in an ANN 8/Continuous 112 ++ Continuous experiments (Antwi et al., 2017)
upflow anaerobic sludge blanket
Classification Analysing the interaction of PCA, RF 22/Discrete 22 NA No validation data point (Gruszka
microbial community Reasonable hypothesis Vendruscolo et al.,
2020)
Predicting resistance and PLR, RF, KNN, ANN 1810/ 17 – Positive idea (Lesnik et al., 2020)
resilience of microbial fuel cell Continuous Results were at the mercy
of data size
State Improving cold flow and lubricity ELM 4/Continuous 30 ++ Better performance of (Mujtaba et al.,
optimisation of biodiesel ELM than RSM 2020)
Optimising methyl levulinate ANN 4/Continuous 29 ++ ANN could capture more (Li et al., 2020)
yield complex process
More accurate of ANN
than RSM
Enhancing the production of FL 4/Continuous 46 ++ Randomness and (Rezk et al., 2019)
hydrogen and syngas fuzziness of process
parameters
Optimal engine calibration for ELM 5/Continuous 130 ++ Aiming to adjust fuel (Wong & Wong,
dual-fuel engine mixture ratio 2017)
dynamically
Optimising alkaline-catalysed ELM, ANN 5/Continuous 46 ++ Kernel-based ELM model (Kusumo et al.,
transesterification was more reliable 2017)
Optimising ethanol production ANN 3/Continuous 20 ++ Data imbalanced (Althuri et al., 2017)

ANN: Artificial Neural Network; DT: Decision Tree; ELM: Extreme Learning Machine; FL: Fuzzy Logic; GPR: Gaussian Process Regression; KNN: K-Nearest Neighbour;
LR: Logistic Regression; MLR: Multiple Linear Regression; NA: Not Available; PCA: Principal Component Analysis; PLR: Partial Least-squares; RF: Random Forest; RSM:
Response Surface Methodology; SVM: Support Vector Machine; SVR: Support Vector Regression.
-: Low accuracy; +: Medium accuracy; ++: High accuracy.

in applications such as optimisation, sensitivity analysis and control. optimisation).

The approach consists of replacing the full simulations with an ML
model (called a surrogate model) trained on a selected number of data
points (inputs and outputs) obtained from the full model. It should be
emphasized that the errors in simulated results due to uncertain as­
sumptions and the numerical approximations of the equations, domain
and initial-boundary conditions (collectively called modelling error)
will also be integrated into the predictions of ML models. Although such
errors can be accounted for, it leads to more complex ML approaches
with more hyperparameters and higher predictive variances. ML sur­
rogate models can replace full simulations as objective functions in state
optimisation (Nayak et al., 2018) and process optimisation (online
Optimising bioproduction progress to gain effective metabolite
production is a good example of process optimisation using ML. Two
recent studies involve how to optimise microalgae lutein production
with innovative ideas. In the first study, Del Rio-Chanona et al. (2019a)
achieved a>40% increase of total lutein production, and the results of an
ANN were better than those of a kinetic model. In the second study,
Zhang et al. (2020) combined physical knowledge (a known dynamic
model) with an automatic structure identification framework that con­
sisted of a data-driven approach to identify the mismatch between the
dynamic model and data. This approach adopted a simple polynomial
model rather than an ANN in order to avoid overfitting.

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Table 5
Machine learning for microalgae cultivation and bioproduction.
Analytical task Scientific task Methods Number/Type of Samples Accuracy Remark Reference
features

Regression Photo-to-property estimation for KNN Image was converted 2100 – Plenty of experiments (Yew et al.,
microalgae growth 198 × 146 RGB array Noticing the quality of 2020)
pictures
Predicting the average fractal RF 200/Continuous 3240 – Virtual flocs (Lopez-Exposito
dimension of floc suspensions Synthetic virtual chord et al., 2019)
length distribution
Correlation between growth and FL 3/Continuous 3 datasets ++ Multiobjective tasks (Bhola et al.,
metabolism of Chlorella sp. 2017)
Classification Determining critical factors for DT, AR 17/Discrete and 4670 ++ Low accuracy in regression (Cosgun et al.,
algal biomass production continuous task 2021)
Some variables were
discretized up
Classifying pellet spectra from SVM, DT, RF, 261/Continuous 90 + Different algorithms were (Mancini et al.,
near-infrared spectrophotometer MLP, NB, KNN tried out 2020)
Dimension reduction
technology might be useful
Classifying the living/dead NB, KNN, QDA, 14 Features were NA + Not binary but actually (Reimann et al.,
microalgae population ANN, DT, AB, RF extracted from image gradual viability status 2020)
Extracting functional DT 4/Discrete 32 – Appling few relevant (Zitnik et al.,
dependencies in blackwater features 2019)
treatment
State Improving cell biomass and ANN 4/Continuous 30 ++ Multi-objective (Saini et al.,
optimisation phycobiliproteins yield optimisation 2021)
Strict experimental design
and high-precision model
Optimising microalgae CNN 7/Continuous 360,000 ++ Different outputs showed (Del Rio-
production different deviations Chanona et al.,
Learning from a physical 2019b)
model
Accuracy subjected to
physical model
Online optimisation for fed-batch ANN 4/Continuous 3 datasets + Data was pre-processed by (Zhang et al.,
microalgae lutein production kinetic model 2019)
Artificial datasets were
created
No predicted process in
optimisation result
Dynamic optimisation of the ANN 5/Continuous 5 datasets + Data-driven model (Del Rio-
efficiency for open-loop control outperformed the kinetic Chanona et al.,
model 2019a)
Developing a hybrid model for PR NA/Continuous 3 datasets + Combining with physical (Zhang et al.,
microalgae lutein production model 2020)
Simple ML model was more
suitable
Enhancing microalgae ANN 4/Continuous 30 ++ Combining with genetic (Nayak et al.,
production algorithm 2018)

AB: Adaptive Boosting; ANN: Artificial Neural Network; AR: Association Rule; CNN: Convolutional Neural Network; DT: Decision Tree; FL: Fuzzy Logic; KNN: K-
Nearest Neighbour; MLP: Multilayer Perceptron; NA, Not Available; NB: Naive Bayes; PR: Polynomial Regression; QDA: Quadratic Discriminant Analysis; RF: Random
Forest; SVM: Support Vector Machine.
-: Low accuracy; +: Medium accuracy; ++: High accuracy.

3.4. Full-scale applications of machine learning
By concentrating on specific experimental situations, ML methods
have been used successfully to predict a restricted number of variables.
There is significant room for more ambitious applications of ML models
to full-scale processes.
Full-scale studies can provide holistic and comprehensive informa­
tion, insight and guidance. Prediction can be employed for the timely
adjustment of related industrial operations, helping in detection, opti­
misation and automatic control. In this regard (see Table 6), De Clercq
et al. (2019) designed a graphical user interface to assist the enhance­
ment of biogas production by trained ML models from the data of two
biogas facilities. The authors predicted daily biomethane production in a
subsequent research (De Clercq et al., 2020). Based on a combination of
an ANN and a particle swarm optimisation (PSO) algorithm, Pereira
et al. (2020) achieved an increase of 10% in industrial bioethanol pro­
duction and concentration.
Furthermore, the fusion of ML methods and traditional life cycle
assessment was used to evaluate the feasibility of hydrothermal treat­
ment aimed at different raw materials (Cheng et al., 2020). Vondra et al.
(2019) developed a techno-economic model based on ML to evaluate the
economics of the evaporation system in biogas plants and the authors
provided a heuristic method for stakeholders and decision makers.
Occasionally, a trained ML model may not satisfactorily achieve the
desired goal. In such cases, an examination of both the data and the
algorithm is required to identify the source of the problem. The choice of
ML algorithm, the quality and volume of data, as well as expert
knowledge together contribute to the final performance of the model.
Simple models such as linear regression are often more accurate
(Camacho et al., 2018). High model complexity (involving more
hyperparameters) leads to overfitting if insufficient data is available to
learn the hyperparameters accurately (such models are said to have a
low bias and a high variance in the bias-variance trade-off).

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Z. Wang et al. Bioresource Technology 343 (2022) 126099

Table 6
Machine learning for industrial forecast and system assessment.
Object Scientific task Methods Number/Type of features Samples Accuracy Remark Reference

Industrial Predicting daily biomethane RF, EN, 17/Discrete and ≤1398 + No need for detailed substrate (De Clercq
forecast production XGBoost continuous characterization et al., 2020)
Predicting biogas output SVM, RF, LR, 14 and 20/Discrete and NA + Noise data (De Clercq
KNN, XGBoost continuous et al., 2019)
Optimising industrial bioethanol ANN 7/Continuous 3400 ++ Seven vital inputs were select by (Pereira et al.,
production cross-correlation analysis 2020)
Predicting the concentration of RF 10/Continuous 280 – Suitable for algae bloom event (Asnaghi et al.,
toxic algae prediction 2017)
System Analysing the techno-economics MC, ANN, DT 23/Continuous and ≥20000 ++ A heuristic method (Vondra et al.,
assessment of evaporation technology combination of variables ANN selected vital variables 2019)
Predicting yields and MLR, DT, RF 6/Continuous 800 + Fusion of ML and conventional (Cheng et al.,
characteristics of hydrothermal LCA 2020)
treatment Other nonlinear regression can
be tried

ANN: Artificial Neural Network; DT: Decision Tree; EN: Elastic Net; KNN: K-Nearest Neighbour; LCA: Life-Cycle Assessment; LR: Logistic Regression; MC: Monte Carlo;
MLR: Multiple Linear Regression; NA: Not Available; RF: Random Forest; SVM: Support Vector Machine; XGBoost: Extreme Gradient Boosting.
-: Low accuracy; +: Medium accuracy; ++: High accuracy.

4. Future perspectives with advanced machine learning
With the continuous development in ML and the explosion in interest
and applications that it has generated, there are currently a plethora of
approaches. The differences in learners can be exploited for ensemble
learning. The difference in views leads to the development of multi-view
learning or multi-modal learning. The intersection of ML and bioenergy
still involves some grand challenges. Overcoming these challenges can
boost the progress of bioenergy technology. In this section, we make
some recommendations.
process is also an important topic.
Notwithstanding that DL can accomplish more complex tasks across
temporal and spatial scales, it usually requires an enormous amount of
data, which is frequently unavailable or difficult (expensive and time
consuming) to obtain. More cooperation to obtain and complement
large datasets is required between researchers in the community,
creating a database for testing new algorithms. In addition, attention
should be paid to include more variables in datasets, in order to com­
plete more tasks. When the variables directly related to the problem at
hand are difficult to measure, alternative variables that are easily
available and implicitly relevant to the outputs could be sought.

4.1. Start-of-the-art deep learning methods

Although classical ML methods have been applied to problems in
bioenergy conversion, there is room to expand the scope of the models
and improve their performance. The success of DL in the complex game
of Go is underlines its potential to solve complex scientific problems. DL
has had notable success in other fields with remarkable results when
facing complex tasks. DL is based on the expanding the size (model ca­
pacity) of traditional 3-layer neural networks by incorporating more
layers and more complex interactions between nodes in layers. Different
types of layers (beyond fully connected layers) can be introduced,
notably convolutional and recurrent layers, together with additional
pooling operations for pruning the network size. Such layers can be
interpreted in the classical node-activation framework but result in
greater flexibility in terms of the tasks that can be performed (regression,
detection, classification) and the types of data that can be processed. For
example, a convolutional layer (defined by kernels or windows) can
extract features to find a more meaningful or compact interpretation of
inputs. Recurrent layer networks are powerful for tasks involving
sequential data, such as natural language processing, or time series
analysis. There is a vast number of possibilities for the architecture of a
DL network and one of the greatest challenges is in finding a systematic
method for their design. Currently, it is largely done through trial-and-
error as well as prior knowledge. Transfer learning allows for networks
to be pre-trained on similar data before being applied to a specific task,
and can greatly enhance the performance of DL networks.
The diversity of DL networks makes them suitable for many complex
bioenergy conversion processes compared to classical ML methods.
Many DL algorithms have been applied to characterize morphological
changes or object trace at cellular level (Isozaki et al., 2020; Moen et al.,
2019; Nitta et al., 2018). The method feeds imaging data to a DL model
when using biotechnology to intelligently identify microalgae cells or
produce biofuel, as in image segmentation for dead or living microalgae
cell analysis and the augmented microscopy for more distinct image
information. The modelling of time series in bioenergy conversion
4.2. Smaller datasets
ML models usually perform better with increasing data, but in the
actual bioenergy context, the cost of acquiring data tends to be high in
terms of time and finances. In the case of limited datasets, it will be a
wise choice to improve the quality of the data. Data pre-processing is a
promising, but it is more effective to control the overall quality of the
data from the source. More systematic experimental design and data
collection operation specification should be followed. Data augmenta­
tion can artificially expand datasets based on the principle of known
invariances, so that the trained model can learn these invariances with
improved generalization. It needs to be emphasized that unreasonable
data augmentation will direct to potentially poor predictions. Other
solutions to the latter are the adoption of expert knowledge to design the
algorithm structure (such as the addition of physical constraints),
whereby the search space size is reduced, or more advanced ML methods
such as imitation learning (Bonardi et al., 2020). Moreover, based on a
Bayesian criterion, a report stated that the realization of human-level
performance becomes possible in sparse data (Lake et al., 2015).
The selection of learners tends to be a prominent problem when
dealing with small datasets. ELM can avoid the problems caused by
gradient decent, and has a short learning time with excellent general­
ization performance. Notably, ELM models showed higher prediction
accuracy for biofuels applications (Kusumo et al., 2017; Mujtaba et al.,
2020; Silitonga et al., 2018; Wong & Wong, 2017). The adjustment of
algorithms, comparison between different models, and construction of
ensemble learning models may help to find a robust model suitable for
some scientific tasks. More importantly, the context of the data and the
relationships between the variables need to be adequately recognized.
4.3. Integration with theory-driven model
Theory-driven models are simpler to interpret but involve fixed as­
sumptions are structures related to the physical process. ML models can

8
Z. Wang et al.
implicitly discover hidden patterns that have eluded consideration. The
two approaches are generally considered to have no intersection, but in
fact they can complement each other. For example, some theory-driven
models have parameters that cannot be inferred from first principles.
Recent work has predicted and optimised the photo-production process
by using a hybrid theory and data driven model, learning the parameters
of a kinetic model (Zhang et al., 2020). Interestingly, a simple dynamic
model can effectively handle the noise in datasets (Zhang et al., 2019).
In particular, for an integrated model formed by many theory-driven
sub-models, the ML models can replace the weak theoretical sub-
models. Also, the deviation between the ML model and the theory-
driven model can help correct the inadequate theory of the theory-
driven approach. In systems biology, the identifications of key gene
transcripts and fluxes by ML tools can furnish critical mechanistic details
and improve genome-scale metabolic models to fit the metabolism of
cyanobacteria (Vijayakumar et al., 2020).
4.4. Machine learning for multi-view data
In bioinformatics, the integration of different omics data offers a
more detailed understanding and better predictions for complex phe­
nomena (Joshi et al., 2020; Kristensen et al., 2014; Ritchie et al., 2015).
On the one hand, the performance of the data-driven model is limited by
the data, and a model learned from a single view data has a certain
degree of one-sidedness. On the other hand, the diversification of
characterization methods allows the same observation object to have
different characteristic morphological representations, and the collected
data comes from multiple sources and may have different types. Multi-
view learning can realize the complementation and integration of in­
formation from different views and levels, avoid the limitations of a
single-view model, and obtain more comprehensive information. An ML
model that combines gene expression with flux data provided a more
complete picture of cyanobacteria metabolism than single view data
(Vijayakumar et al., 2020). In the context of bioenergy, the expansion of
task scale and the improvement of accuracy are also likely to provide
ground-breaking progress via the contribution of multi-view learning,
such as the combination of imaging data and sensor data to achieve
target monitoring (cultivation of microalgae, biological and thermo­
chemical conversion of biomass, etc.).
5. Conclusion
ML has the potential to predict and optimise the highly complicated
nonlinear bioenergy systems, which are usually difficult to build models
based on experience or theory for accurate predictions. However, the
prediction accuracy and the coverage of the data valid domain of bio­
energy systems by using ML were still not satisfactory. More research
work should be carried out to create high quality databases to test and
apply new algorithms, to promote the application of advanced ML al­
gorithms (such as deep learning and multi-view learning), and to inte­
grate theory-driven models into ML models for a better interpretability
and predictability.
CRediT authorship contribution statement
Zhengxin Wang: Methodology, Writing – original draft, Writing –
review & editing. Xinggan Peng: Writing – original draft, Writing –
review & editing. Ao Xia: Conceptualization, Writing – review & edit­
ing, Project administration. : . Akeel A. Shah: Writing – review &
editing. Yun Huang: Writing – review & editing. Xianqing Zhu:
Methodology. Xun Zhu: Project administration. Qiang Liao:
Supervision.
Declaration of Competing Interest
The authors declare that they have no known competing financial
9
Bioresource Technology 343 (2022) 126099
interests or personal relationships that could have appeared to influence
the work reported in this paper.
Acknowledgments
This work was supported by the National Natural Science Foundation
of China (Nos. 52022015, 51876016), the Fundamental Research Funds
for Central Universities (2020CDJQY-A054), the State Key Program of
National Natural Science of China (No. 51836001), and the Creative
Research Groups of the National Natural Science Foundation of China
(52021004).
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