Received: 16 May 2023 | Revised: 9 July 2023 | Accepted: 10 July 2023

DOI: 10.1002/bit.28503

REVIEW

Hybrid modeling in bioprocess dynamics: Structural

variabilities, implementation strategies, and
practical challenges

Biswanath Mahanty

Department of Biotechnology, Krunya

Institute of Technology and Sciences,
Coimbatore, Tamil Nadu, India
Correspondence
Biswanath Mahanty, Department of
Biotechnology, Karunya Institute of
Technology and Sciences, Coimbatore
‐641114, Tamil Nadu, India.
Email: bmahanty@karunya.edu
Abstract
Hybrid modeling, with an appropriate blend of the mechanistic and data‐driven
framework, is increasingly being adopted in bioprocess modeling, model‐based
experimental design (digital‐twin), identification of critical process parameters, and
optimization. However, the development of a hybrid model from experimental data
is an inherently complex workflow, involving designed experiments, selection of the
data‐driven process, identification of model parameters, assessment fitness, and
generalization capability. Depending on the complexity of the process system and
purpose, each piece of these modules can flexibly be incorporated into the puzzle.
However, this extra flexibility can be a cause of concern to trace an “optimal” model
structure. In this paper, the development of hybrid models in a common bioprocess
system, selection of data‐driven components and their mapping to states, choice of
parameter identification techniques, and model quality assurance are revisited. The
challenges associated with hybrid‐model development, and corrective actions have
also been reviewed. The review also suggests the lack of data, and code sharing in
communal repositories can be a hurdle in the exploration, and expansion of those
tools in a bioprocess system.

KEYWORDS
ANN, black‐box, experimental design, generalization, sensitivity

1 | INTRODUCTION
Bioprocess models are widely adopted to understand the process
dynamics and to predict the temporal change of biomass, substrate,
product, or other state variables under consideration in a reproduc-
ible manner. Incorporation of fundamental knowledge about the
process, and interdependency of the variables through mathematical
formalization in the form of algebraic, ordinary differential, or partial
differential equations, is the core of the process modeling exercise
(Luo et al., 2021). Though the use of parametric expressions, e.g.,
Monod's kinetics for biomass growth, Luedeking‐Piret kinetics for
product formation, or yield coefficient tagged substrate utilization
does not reveal any “mechanistic” insight but are certainly convincing
and logical (Tsopanoglou & Jiménez del Val, 2021). When embedded
into the first‐principles architecture of material, charge, or energy
balance from process‐level understanding of the system, such
parametric “white‐box” models have great potential for extrapolation,
and offer a robust option in process engineering. Incorporation of
charge balance through the differential‐algebraic equation in a
bioprocess model is essential when carbonate chemistry, speciation
of weak acids, or pH dynamics are mapped to the system (Kresnowati
et al., 2008; Nayak et al., 2015).
However, model identification (i.e., selection of appropriate
kinetics) requires a tedious trial‐and‐error approach, even in the
presence of reasonable process knowledge (Moser et al., 2020). A
single kinetic model may not be capable of simulating the entire

Biotechnol Bioeng. 2023;1–20. wileyonlinelibrary.com/journal/bit © 2023 Wiley Periodicals LLC. | 1

2 |
process, hence combining more than one kinetic model or shifting to
a different kinetic model depending on growth phases may be
warranted (Zhang et al., 2015). Fully mechanistic models are often
over‐parametrized to capture complex dynamics and require an
exorbitantly high volume of data to estimate parameters to any
degree of confidence. Bioprocesses models are often associated with
partially nonidentifiable parameters due to the lack of sufficient
quality experimental data. However, the removal of such nonidentifi-
able but physically interpretable terms makes the model over-
simplified, poor in fitting and predictability, leaving no choice but
inevitable use of mildly overfitted models as a trade‐off between
physical insight and mathematical accuracy (Lee et al., 2018). Ignoring
structured‐segregated biomass populations in a highly dynamic
process results in unsatisfactory prediction capabilities. In addition
to generalization and overfitting problems, ensuring data adequacy
for an accurate representation of inherent process variability, that is,
change in feedstock, nonlinearity of processes, or altered product
specification, are unique deployment challenges in industrial settings
(Fisher et al., 2020; Tsopanoglou & Jiménez del Val, 2021). Limited
data in batch production with frequent changes to manufacturing
practices, and implementation of new technologies complicates the
situation further.
Even if a perfect model could be formulated, the kinetic
constants may not be time‐invariant during bioprocess operation.
On the contrary, data‐driven nonparametric models (referred to as
black‐box models) are formulated exclusively from process data
without the incorporation of knowledge, or mechanistic obligations
(Härdle et al., 2004). Though different data‐driven modeling
subvariants, such as multiple linear regression (MLR), principal
component analysis (PCA), or partial least squares (PLS) regression
do exist to map functional dependency of process rates on state
variables, the artificial neural network (ANN)‐based approaches are
by far more widely adopted in the literature (del Rio‐Chanona
et al., 2017a; Dong et al., 2014; Mowbray et al., 2023; Narayanan
et al., 2019; Pinto et al., 2022). ANN‐based black‐box model,
adopting either shallow or deep networks, is a universal function
approximator and can offer excellent training performance in
supervised learning on a large raw data set. These nonparametric
models also have parameters (e.g., weight, bias), but are flexible in
dimension and not fixed in priori. The data‐driven model captures the
process dynamics without mechanistic preview but relies on the
quantity and quality of process data (Sansana et al., 2021). Pure
“black‐box” models completely disregard the first‐principles informa-
tion (e.g., mass balances) (Zorzetto et al., 2000), and even though they
offer an excellent fit on trained data, their extrapolation or
generalization capability for inputs beyond the training constellations
are very poor (Bardow & Marquardt, 2004; Bhadriraju et al., 2020).
Between the two extreme paradigms with their pros and cons, a
synergy referred to as gray‐box or hybrid models, has emerged as an
invaluable tool for process modeling (Rogers et al., 2023). Hybrid
models still adopt a mechanistic first‐principle framework for the
biological process but unidentified parts of the dynamics (i.e., specific
growth, product formation rates) are represented through a flexible
MAHANTY
data‐driven component, thereby improving robustness, extrapolation,
and reducing overfitting (Solle et al., 2017). Data‐driven information
is a valuable supplement (not an alternative) to mechanistic
knowledge, increasing transparency and cost‐effectiveness of the
modeling approach (Sansana et al., 2021). The constraints imposed by
conservation equations ensure the robustness (Tsopanoglou &
Jiménez del Val, 2021), and prediction accuracy of hybrid models in
an identified valid domain (Bae et al., 2020). Automated identification
of data‐driven architecture reduces the expertise required for the
parametric representation of the mechanistic part (Lopes Dias
et al., 2007; Luna et al., 2021). Increased process knowledge from
hybrid modeling when combined with the design of experiments
(DoE), can reduce the experimental burden and accelerate process
development (Bayer et al., 2020b).
A hybrid modeling framework, incorporating ANNs‐based reaction
kinetics in mass balance equations, has successfully been adopted in
different bioprocess systems (Bangi et al., 2022; Bayer et al., 2021b;
Oliveira, 2004; Vega‐Ramon et al., 2021). Parameters from existing
kinetic models can also be reformulated as probabilistic Gaussian
processes, reducing prediction errors from uncertainty propagation
(Vega‐Ramon et al., 2021). Hybrid model‐based framework has been
adopted to develop soft sensors to predict bioprocess trajectories and
identify critical process parameters (CPP) relevant to specific critical
quality attributes (Rathinavelu et al., 2023). Model predictive control-
lers (MPCs) use either a mechanistic, data‐driven, or hybrid dynamic
model to adapt real‐time process control using online measurements
of CPP (i.e., temperature, dissolved oxygen, and pH) or spectroscopic
soft sensor‐based measurements of additional variables (Brunner
et al., 2020; Narayanan et al., 2020b). Optimal control actions are
regularly re‐calculated by minimizing a global objective function based
on the prediction of future model outputs over a limited time horizon
and current process information (Caramihai & Severi, 2013). The data‐
driven module can embed multivariate data analysis to identify CPP,
without focusing on the mechanistic insight of the relationships
(Sokolov et al., 2017). The hybrid modeling approach not only offers
better time‐resolved process characterization in comparison to pure
data‐driven or response surface methodology on process endpoints
but have the potential for soft‐sensing and MPCs (Bayer et al., 2020a).
Mechanistic model prediction of total organic carbon (TOC) generation
rate, and base federate in Pichia pastoris culture, has been integrated
into an MLR‐based data‐driven approach to develop an adaptive soft
sensor for biomass measurement (Brunner et al., 2020). The TOC
change rate in the reactor, calculated by subtracting the online
measured CO2 emission rate from the inline measured methanol
reaction rate, is numerically integrated to get cumulative TOC
accumulation in biomass. The cumulative TOC and base feed serve
as predictors to model the measured biomass concentration
using MLR.
Though, the superiority of the hybrid‐modeling approach is well
recognized, their expansion into bioprocess systems is not very
exciting. A bibliometric search in the Scopus database for “hybrid
model” AND (“bioprocess” OR “fermentation”) in TITLE‐ABS‐KEY
returns just 150 documents, published over the past three decades
MAHANTY
(Figure S1). The association strength of keywords across those
articles suggests contextual relevancy of “neural network,” “optimi-
zation,” “mathematical model,” “bioreactors,” and “kinetic parame-
ters” with hybrid modeling. However, keywords relevant to the
modeling approach, and model quality (i.e., training, parameter
estimation, model identification, cross‐validation, and bootstrapping)
are nearly nonexistent.
In recent times, a couple of reviews on the advantages, and
disadvantages hybrid of models (Tsopanoglou & Jiménez del
Val, 2021), the use of machine learning algorithms in bioprocess
optimization, and process monitoring (Mondal et al., 2023), and
recent trends on hybrid modeling considering bigdata and Industry
4.0 (Sansana et al., 2021) have been published. The utility of
statistical and hybrid modeling approaches has been reviewed
considering upstream pharmaceutical bioprocesses (Tsopanoglou &
Jiménez del Val, 2021). The structural arrangement, information
integration strategy in hybrid modeling, and their application in
chemical bioprocess have also been reviewed in the recent past (von
Stosch et al., 2014). However, the practical challenges associated
with the arrangement of black‐box white‐box model components,
selection of black‐box architecture, training, and assembling the
entire puzzle altogether into an optimization framework from a
researcher's perspective have not been well documented.
In this review, following this introduction, important machine
learning tools have been presented in Section 2. In Section 3, the
structural arrangement of hybrid models and their difference from
mechanistic or data‐driven counterparts has been clarified. The
formalization of the black‐box model part and different approaches
for training has been elaborated in Section 4. Assessment of
generalization capability through designed experiments, cross‐
validation, and boot‐strapping is presented in Section 5. Finally, the
application of the hybrid model, challenges, and future directions has
been discussed.
2 | M A C H I N E LE A R N I N G TO O L S I N
H YB R I D M O D E L I N G
Bioprocess involves a complex dynamic interaction of different
biochemical species. High time scale variability in bioprocess makes it
difficult to determine and implement effective control unless the
process could be reliably modeled by incorporating CPPs (Rathore
et al., 2021). Mechanistic models are inefficient with nonlinear
problems, rely on an accurate understanding of the mechanism, and
are not suitable for optimal control strategy (del Rio‐Chanona
et al., 2017b). On the other hand, hybrid modeling of bioprocess
incorporates a data‐driven approach to map the specific rates in
mechanistic models, without advocating any explicit functional
relationship with process variables. Artificial intelligence has been
introduced as a facilitating approach to build a data‐driven model by
learning the relationship between input and output using a training
data set, creating a rule on trained structure for future predictions
(Cheng et al., 2023).
| 3
2.1 | ANN‐based models
ANNs consisting of an input layer, one or more interconnected
hidden layers, and an output layer for information processing, are
widely adopted tools good at mapping complex nonlinear problems.
Each neuron in the hidden or output layer adds ups the inputs (i.e.,
weight) from all neurons in the previous layer, combines with
adjustable bias. Subsequently, each neuron processes the input
through nonlinear “Activation functions” (linear, hyperbolic tangent,
logistic function, or a rectified linear unit) before passing it over to
neurons in the next layer. The weight and bias of the ANN model are
estimated through iterative training with experimental data. How-
ever, the selection of the number of neurons can be critical as an
increase in the number always results in better fitness but with
deteriorated generalization capability (Alrashed et al., 2018).
ANN has evolved from a single hidden layer to multiple fully
connected hidden layers of deep neural network (DNN) architecture
requiring a smaller number of neurons for specific functions
(Schmidhuber, 2015). Hybrid models with a DNN have been utilized
in different process operations (Bangi & Kwon, 2020) and industrial‐
scale bioreactor system modeling (Shah et al., 2022). Though DNN
can offer excellent model fitting to observations, their prediction can
be inconsistent or implausible due to extrapolation or observational
biases. The incorporation of any physical laws correlating predictors
and responses during ANN training is referred to as physics‐informed
neural networks (PINNs) (Karniadakis et al., 2021). PINNs add up the
unsupervised loss from partial differential equations (PDEs) using
automatic differentiation of ANN along with supervised loss of data
measurements in the training process (Figure 1). The utility of PINNs
is essentially a data‐driven model, with albeit better predictability, but
should not be confused with a hybrid model built on a mechanistic
framework. Biologically‐informed neural networks (BINNs) as an
extension of has been used in approximate in vitro experiments while
respecting governing reaction‐diffusion partial differential equations
(Lagergren et al., 2020). The author used a BINN to model cell density
as a function of space, and time. The network output is further used
to approximate diffusivity and growth functions imbibed in governing
dynamic systems.
Long short‐term memory (LSTM)‐ANN models are another
variant of machine learning (ML) algorithm useful for multiscale
models with time‐varying and time‐invariant inputs. LSTMs are
known for learning temporal dependencies in sequence data through
the use of input, output, and forget gates (Jeon & Kim, 2021). These
networks take the current input value, previous output, and the
previous unit state as inputs to generate the current output and unit
state (Schwedersky et al., 2019).
2.2 | Support vector machine (SVM)
SVM as a supervised statistical ML algorithm maps the input into
multi‐dimensional feature space based on a nonlinear mapping kernel
function (Raghavendra & Deka, 2014). The optimal hyperplane that
4 |
F I G U R E 1 A typical physics‐informed neural network (PINN). Network input (x, t) are processed through multiple hidden layer neurons, with
weight and bias, activation (σ) to prediction (u). Loss from partial differentials ∂u/∂t, ∂u/∂x, ∂2u/∂x2 calculated through automatic differentiation
of the network is added with loss from the prediction (u). The combined loss is minimized below a threshold (ε) during the training process.
maximizes the margin between the nearest data points and the
hyperplane is located, and the most “important” training points
defining the hyperplane are support vectors. Linear, polynomial,
radial basis, and sigmoid kernels in SVM allow modeling complicated
separating hyperplanes. Nonlinear kernel processed input multiplied
with a weight vector of dimension same as feature‐space, added with
bias, is the SVM prediction (Wang et al., 2010). Unlike ANN, SVM
uses structural risk minimization and is less likely to be overfitted
from a small data set. Prediction of SVM heavily depends on kernel
function selection (Andrade Cruz et al., 2022) and the computational
burden increases as the kernel matrix grows with data size (Cervantes
et al., 2020). Support vector regression (SVR) model with radial bases
kernel functions was adopted as data‐driven component (cumulative
oxygen uptake and carbon dioxide production rates) as nonlinear
functions of the biomass concentration in hybrid modeling of
recombinant therapeutic protein production process in Escherichia
coli (Simutis & Lübbert, 2017).
2.3 | Fuzzy logic (FL)
Fuzzy logic incorporates the idea that all biological information
(e.g., a transition from lag phase to exponential and stationary
phase) cannot be identified precisely and operates similarly to
human thinking defined by membership functions with different
probabilities for each value and “If–then” rules (Patnaik, 2006).
FL‐based algorithms are robust and perform well in small sample
datasets. Neuro‐fuzzy estimator has been used in penicillin
fermentation pilot plant, an adaptation of bacteria to inhibitor in
acetic acid fermentation (Araúzo‐Bravo et al., 2004; Arnold
et al., 2002). FL model has been adopted to predict metabolic
flow in Chlorella sp. utilizing a synthetic flue gas mixture correlating
to growth performance (Bhola et al., 2017), to determine nutrient
composition for phycobiliproteins production from cyanobacteria
(Kumar Saini et al., 2020).
MAHANTY
2.4 | Latent variable methods
Latent variable (LV) approaches project high‐dimensional correlated
predictors into a few uncorrelated orthogonal LVs, as linear
combinations of the original variables, while preserving the variability
in original predictors and response spaces (Liu et al., 2022a). Principal
component regression (PCR), and PLS regression are the most
popular. In PCR, principal components scores extracted from the
covariance matrix (arranged based on the original variability they
explain) are associated with the response adopting an ordinary least
squares approach (Artigue & Smith, 2019). PLS, on the other hand,
finds the linear combinations of predictors (latent vectors) through
the simultaneous decomposition of predictors and response so that
maximal covariance between them (Mehmood et al., 2012).
PLS‐based MPC has been proposed to account for variability in yield
as a result of random variations in raw material properties and in‐
batch process fluctuations (Duran‐Villalobos et al., 2020). The data‐
driven soft sensor has been utilized to control glucose concentration
in mammalian cell cultures based on online cumulative oxygen uptake
rates (DOc) (Goldrick et al., 2018). The DOc values are calculated from
agitator speed, online dissolved oxygen (DO) measurements, satura-
tion DO concentration, and inlet gas flow rate. On the other hand,
cumulative glucose consumption rates (Glc) are calculated from
glucose feed and off‐line measured glucose concentrations. A least
square regression (R2 > 0.99) between DOc and Glc serves as a data‐
driven component to predict glucose measurement and control.
3 | H Y B R I D M O D E L ST R U C T U R A L
FRAME WORK
3.1 | General model structure
Dynamic model provides temporal evolution of key biological or
chemical species (e.g., biomass, substrate, product, off‐gas
MAHANTY
composition, and pH) in a complex interacting environment. The
mathematical representation of the model depends on the availability
of data, inherent complexity, and our understanding of the process.
The dynamics of substrate, biomass, or product when governed by
fundamental laws of physics, for example, material, energy balance,
and chemical equilibrium are termed first principles models, as shown
in Figure 2a. The material balance of substrate accounts for the
portions utilized toward biomass growth, product formation, and
cellular maintenance mapped through respective yield (YX / S, YP / S ), or
maintenance coefficients (m). In the mechanistic model, ordinary
differential equations (ODEs) representing biomass growth (dX /dt) or
product formation (dP /dt) rates are explicit functions of biomass (X),
substrate (S), product (P), and time‐invariant parameters (θ , ϕ). In
contrast, the data‐driven model (Figure 2b) represents growth rate µ
(.), substrate consumption rate g(.), and product formation rate h(.), as
implicit functions (e.g., ANN) of state variables. There are no material
balance constraints in the data‐driven modeling approach. Hybrid
model, though respects the material balance, some of the poorly
understood rates or terms are modeled through data‐driven
functions (Figure 2c).
Though ODEs are part of dynamic models irrespective of the
white box or hybrid architecture, process informative state vectors or
(a) (b)
(c)
F I G U R E 2 General structure of (a) mechanistic first‐principal
model, (b) data‐driven model, and (c) hybrid model involving biomass
(X) growth, substrate (S) consumption, and product (P) formation. In
the mechanistic model each rate is explicitly represented in a formal
algebraic expression (e.g., Monod's growth model), and material
balance is incorporated in substrate consumption rate through
biomass yield (YX/S), product yield (YP/S), or maintenance (m)
coefficient. In a data‐driven model, all specific rates (µ, g, h) are
represented as black‐box functions (e.g., ANN) of state variables.
Hybrid model, though respects the material balance, some of the
poorly understood rates or terms are modeled through a data‐driven
backbox function. Either a function (e.g., μ), term (e.g., μX), parameter
(i.e., α, β), or even an entire rate (dX /dt, dP /dt) can be mapped using
the black box approach. The rate equation of a state may entirely be
omitted in a hybrid modeling exercise.
| 5
those having significant influence on the same, and can be measured
in bioprocess are generally included (Simutis & Lübbert, 2017). Some
of the complex mechanistic insight can however be dropped or
simplified from hybrid model ODEs (Dong et al., 2014).
3.2 | Hybrid modeling—Serial or parallel
The black‐box and white‐box modules can be arranged in three
different ways, that is, parallel to each other or one of the two serial
structures depending on their order (von Stosch et al., 2014), as
shown in Figure 3. In parallel structure, the black box model can map
the residuals between experimental and white box model predictions
so that mechanistic model outputs can be corrected for future
prediction (Bhutani et al., 2006) or to account for the unknown
dynamics in numerical integration (Zhang et al., 2020). Very similar
framework with some differences in objective, ML algorithm has
been adopted in different studies (see Table 1). Blackbox model
prediction from real‐time measurements can be used to reconcile the
kinetic model output (Cabaneros Lopez et al., 2021). The parallel
structure hybrid model offers an exceptionally good fit without
consideration of specific reasons for mismatch. It only uses the
deviation between the actual process and mechanistic model output,
referred to as residual model (RM), to describe the dynamics that
mechanism models cannot describe. The semi−supervised hybrid
modeling approach has been adopted in continuous ethanol produc-
tion with Saccharomyces cerevisiae (Zhao et al., 2023). The RM was
trained using a feed−forward neural network built on selected
bioreactor input and output of the kinetic model. PLS regression has
been used to predict the real‐time concentration of glucose, xylose,
and ethanol from attenuated total reflectance spectra in ligno-
cellulosic ethanol fermentation (Cabaneros Lopez et al., 2021). The
reconciled predictions of data‐driven and kinetic models, with
F I G U R E 3 General scheme for mechanistic and serial/parallel
hybrid model in bioprocess. In the mechanistic model, the initial value
of the state vector ζ ∈ [X , S]T along with parameters θ ∈ [μm, KS, kd ] is
used for prediction ζˆ ∈ [Xˆ , Sˆ]T . In a hybrid serial structure, the
data‐driven component of the model (μ) is computed from the state
either before or during the integration of the ordinary differential
equations (ODEs). In parallel hybrid structure, the residuals (EX) from
the mechanistic model are mapped as a black box function and added
back to mechanistic output for final prediction.
6 | MAHANTY

TABLE 1 A representative list of data‐driven hybrid models and their structure.

Data‐driven model Hybrid model structure Bioprocess References

ANN Serial/parallel Industrial hydrocracking Bhutani et al. (2006)

Polynomial regression Parallel Algal biomass growth and lutein synthesis Zhang et al. (2020)

PLS regression Parallel Cellulose‐to‐ethanol fermentations Cabaneros Lopez et al. (2021)

Feed−forward ANN Parallel Continuous yeast fermentation for ethanol production Zhao et al. (2023)

PLS Parallel Mammalian cell culture Narayanan et al. (2020a)

PLS Parallel Lignocellulosic fermentation Lopez et al. (2020)

DNN Parallel β‐carotene production using Saccharomyces cerevisiae Bangi et al. (2022)

ANN Serial Viral capsid protein production by Escherichia coli von Stosch et al. (2012)

ANN Serial Sodium gluconate fermentation by Aspergillus niger Dong et al. (2014)

Reinforcement learning Serial In silico fermentation with biomass, substrate, and product Mowbray et al. (2023)

ANN Serial Fed‐batch fermentation Zuo & Wu (2000)

ANN Serial Cell culture Narayanan et al. (2019)

Abbreviations: ANN, artificial neural network; DNN, deep neural network; PLS, partial least squares.

continuous‐discrete extended Kalman filter, have been resilient to
measurement disturbances. A PLS‐based hybrid model with an
extended Kalman filter has also been adopted for real‐time
monitoring and control of mammalian cell culture (Narayanan
et al., 2020a). A soft‐sensor hybrid modeling approach has been
adopted to monitor the progress of batch cellulose‐to‐ethanol
fermentation, where a spectroscopic data‐driven PLS module
measures real‐time glucose concentration that is recursively fitted
to update mechanistic model parameters, and long‐horizon predic-
tions (Lopez et al., 2020). The supervised learning‐based parallel‐
hybrid approach only considers the correlation between residuals and
process inputs but does not account for oversimplification of the
mechanism model, or model parameter inaccuracies. Studies have
suggested that the use of ANNs in a hybrid dynamic model can
impede numerical accuracy in parameter estimation, particularly if
multiple ANNs are involved (Zhang et al., 2020). Hybrid models can
also incorporate neural ordinary differential equations, that is,
derivatives of unknown dynamics along with kinetic model ODEs to
have increased the overall prediction accuracy (Bangi et al., 2022).
Neural ODE assumes continuous variation of hidden state and is
parameterized using an ODE specified by a neural network, and the
output layer can be computed using an ODE solver. A detailed
theoretical treatment and implementational strategy of a neural
ODE‐based system can be found elsewhere (Bangi et al., 2022; Chen
et al., 2018).
The black box‐white box serial combination is most popular in
bioprocess modeling, where the former usually represents the
“imprecise” part of underlying kinetics in the latter, derived from
first principles, that is, material, or energy balances for the process
(von Stosch et al., 2012). The black‐box module is used to map the
kinetic part of the model (e.g., specific growth rate) taking current
state measurements and/or reaction conditions as input (Figure 3).
The black‐box part can independently be trained if the kinetic terms
(e.g., specific rates) can precisely be measured/calculated from
experimental data, before integrating it into mechanistic model
framework. However, parameters from both black‐box (e.g., weights
of feed‐forward ANN, or coefficients of multiple linear regression)
and mechanistic model are combinedly estimated while minimizing
residuals between measured and modeled states.
A serial hybrid structure with two independent ANN, one to map
mycelium growth rate, and the other to map growth‐associated and
nongrowth‐associated parameters relevant to substrate consumption
and product formation kinetics has been adopted to model sodium
gluconate fermentation by Aspergillus niger (Dong et al., 2014).
Reinforcement learning‐based identification of hybrid model struc-
ture has been adopted to model silico experiment data to quantify
time‐varying and history‐dependent kinetic behavior for typical
fermentation processes involving biomass, substrate, and product
(Mowbray et al., 2023). Production of thuringiensin using Bacillus
thuringiensis in a fed‐batch system has been modeled using a hybrid
unstructured model, where specific growth, substrate consumption
and production rates were mapped to state variables using ANN (Zuo
& Wu, 2000). Similarly, a feed‐forward single hidden layer ANN was
adopted to project‐specific rates for biochemical species while
modeling the fed‐batch cell culture process data set using a serial
hybrid model (Narayanan et al., 2019). The author reported robust
prediction of titer when compared to statistical predictive models.
4 | HYBRID MODELING STRATEGIES
4.1 | Selection of model terms into a black box
Dynamic bioprocess models involving structured kinetics are typically
represented by a set of coupled differential equations as a function of
the current state and time‐invariant model parameters. The kinetic
MAHANTY
expressions are often improvised, before conversion to a hybrid
model, based on specific knowledge about the bioprocess. In serial
architecture, either the existing rate terms (i.e., specific growth rate,
product formation rates) can be substituted with black‐box, or
corrective terms can be added to the state dynamics (Lee
et al., 2020b).
The subset of kinetic parameters or rate expression to be
mapped as a black‐box function is not straightforward for multi-
parametric, multi‐state industrial scale fermentation. Ideally, key
sensitive and uncertain model parameters, having considerable
influence on prediction, are identified through local and global
sensitivity analysis and wrapped into a black box framework (Shah
et al., 2022). Time‐varying parameters identified through the
clustering approach from the short‐listed subset can further be
considered for the hybrid model (Shah et al., 2022). In such a
situation, global sensitivity analysis is performed to identify the most
important parameters, and a clustering technique is adopted to locate
temporal subdomains where the parameter differs (Lee
et al., 2019, 2020a). As the functional relation of biochemical
reaction rates with biomass, and substrate/product concentrations
are not known in sufficient detail, such terms are often defined as a
flexible mixture of parametric (i.e., specific substrate utilization rate)
and nonparametric functions (i.e., specific growth and product
formation rates) (Pinto et al., 2019). There is no consciousness across
literature on the selection of model terms to be formulated as black
box components. Different combinations of parametric and non-
parametric variants may be considered, as schematically shown for an
empirical model (Figure 2c).
However, the reason for selecting or not selecting one/more
rates, functions, or parameters in the black box model are not always
obvious (Table 2). It is also necessary to identify whose dynamics
should be corrected by the black‐box intervention, by examining the
correlation between each state and outputs through relative order.
For example, specific growth, and product formation rates in the fed‐
batch bioreactor were modeled using a feedforward neural network,
while specific substrate consumption rates maintained original kinetic
expression relating to biomass yield coefficient and maintenance
coefficient (Pinto et al., 2019). In the referred study, biomass (X), the
feeding rate (F), and cultivation temperature (T) were used as input
for the ANN models.
Unlike their mechanistic counterparts, a hybrid model only
requires capturing a data‐driven approximation of standard kinetics
to reduce the nonlinearity of the problem. Rogers et al. (2023)
adopted a hybrid modeling approach in γ‐linolenic acid (GLA)
fermentation via Cunninghamella echinulata X‐15 in bioreactors under
three different temperatures. The authors modified the original
kinetic expression and referred to specific growth rate as an ANN
function of temperature, biomass, and substrate concentration.
A hybrid modeling strategy can be formulated, even without any
prior knowledge of the functional relationship of specific rates. This is
more common than the exception as evident in the literature (Pinto
et al., 2022; von Stosch et al., 2016a; Zuo & Wu, 2000). Though,
specific rates (growth, product formation) are generally modeled into
| 7
backbox function, encapsulating the growth rate itself into a neural
network is also evident (Dong et al., 2014). Rate expression for all the
states, as in structured models, need not be replicated in hybrid
modeling. For example, fungal cell mass classification (i.e., primary
mycelia, secondary mycelia, and spores) in structured kinetics for
Trichoderma reesei RL‐P37 in cellulase production was re‐assigned
into single biomass while adopting a hybrid modeling strategy
(Tholudur et al., 1999). The amount of “greyness” to be incorporated
in a hybrid model without inductive bias can be important for
performance.
4.2 | Sensitivity analysis
Restructuring the kinetic model into a hybrid model involves
assigning a few existing model parameters into flexible, time‐
varying data‐driven functions that are appropriate to map changing
bioprocess environments (Duan et al., 2020). Critical parameters
having a significant influence on outputs need to be identified and
reformulated into a data‐driven function for a hybrid model (Chu &
Hahn, 2007). Identification of such critical parameters is performed
through sensitivity analysis, where insensitive parameters can be
dropped from optimization and fixed at their baseline values (O'Brien
et al., 2021).
Local sensitivity analysis involves the assessment of parametric
perturbation (around the nominal values) on different model outputs.
A sensitivity matrix is first derived and the Fisher information matrix
is calculated to assess the effect of parameters, one at a time, on the
outputs (Shah et al., 2022). Local sensitivity analysis of model
structure has been performed with a finite‐difference approach in the
biopharmaceutical process (Möller et al., 2020). The sensitivity of the
process outputs, on a wide range of parameter settings, is reflected in
the global sensitivity analysis (GSA). The range of parameters for GSA
analysis is first determined from repeated parameter estimation, each
time using slightly different datasets. For GSA, lain hypercube
sampling of a parametric range is considered, where sensitivity
analysis values are averaged at the end. Other approaches for GSA,
such as Sobol's sensitivity indices can be used with a surrogate model
minimizing the repeated solution of the hybrid model (Abbiati
et al., 2021). Parameter significance can be measured based on
sensitivity indices ranging from 0 to 1 (Tsipa et al., 2018).
4.3 | Mapping the black‐box component and
architecture
4.3.1 | ANN‐based hybrid models
Though there is a range of data‐driven modeling approaches to map
the black‐box part of a hybrid model, ANNs are most widely adopted
for nonlinear, complex systems to predict multiple responses
simultaneously, whilst taking multiple independent predictors as
input (Noll & Henkel, 2020). Moreover, ANN can be adapted to have
 8

TABLE 2 Model terms considered for the black box approach and their justification.
|

Time invariant Time invariant

Number of parameters in parameters after
System description state variable original kinetics the hybrid model Justification References

Production of viral capsid protein by a 3a 12 0 Specific rates of growth and product formation are Pinto et al. (2019)
recombinant Escherichia coli strain in a fed‐ difficult to establish
batch bioreactor

Biomass‐specific productivity rates, base addition 3 0b 0 Rates and correlation coefficients depend von Stosch et al.
correlation coefficient with biomass on process conditions, not directly measurable. (2016a)

Industrial fermentation for biomass growth on 6 32 29 Three time‐varying parameters using the clustering Shah et al. (2022)
two substrates, and intermediate, product approach were selected to avoid overfitting
formation

γ‐linolenic acid (GLA) fermentation via 4 24 0, 5,11c Parameters directly related to biomass growth, Rogers
Cunninghamella echinulata X‐15 ‐batch substrate consumption, and production were et al. (2023)
experiment replaced

Growth and protein production by Trichoderma 6 14d 0 Four specific rate terms are included in artificial Tholudur
reesei on lactose, and xylose neural network (ANN) modeling et al. (1999)

Sodium gluconate fermentation by Aspergillus 3 6 0 Growth rate modeled through back propagation Dong et al. (2014)
niger lack of knowledge of mycelium growth neural network (BPNN), kinetic parameters for
substrate and product through ANN

Fermentation system to cultivate Bacillus 3 0b 0 Specific growth, substrate consumption, and Zuo and
thuringiensis for thuringiensin production production rates Wu (2000)

Recombinant E. coli fed‐batch process 7 0b 0b Specific growth, substrate consumption, and Pinto et al. (2022)
production rates, and recovery rate constant

Fed‐batch cell culture therapeutic protein 8e 0b 0b Lack of knowledge of specific rates and metabolism. Narayanan
production. Included viable cells, concentration of glucose, et al. (2019)
lactate, glutamine, glutamate, ammonia,
osmolality, and titer.

Fed‐batch data on interleukin‐8 antibody 7 12 0 Specific rate of growth (total, viable cell), four (Bayer et al. (2023)
production by Chinese hamster ovary (CHO) substrate consumption, product formation
DP‐12 cells. modeled

Simulated batch production of monoclonal 6 6 0 Specific rate of glucose, glutamine, lactate, Botton
antibodies ammonia, and mAbs titer modeled from et al. (2022)
simulated experiments
MAHANTY
MAHANTY | 9

a different number of fully or partially connected hidden layers, a

Luna et al. (2021)

variety of transfer functions (Apicella et al., 2021), and learning

et al. (2021)
Vega‐Ramon
algorithms which can be optimized for the complexity of a given
References problem (Karimi Alavijeh et al., 2022). In ANN‐based hybrid models,
however, a time‐intensive optimization approach must be integrated
to refine hyperparameters and network topology (Lancashire
et al., 2008).
(biomass/substrate, product/biomass) mapped as

Specific rates of growth, substrates, and product Identification of the most likely combination of kinetic model
structures with their time‐varying parameter through reinforcement
Specific growth rate, and two yield coefficients

learning (RL) has been proposed in hybrid modeling for typical in silico
formation mapped using a single ANN

fermentation measuring biomass, substrate, and product concentration

(Mowbray et al., 2023). ANN has been adopted as parameterized
control policy in RL, mapping optimal parameters from input state
function biomass, substrate

variables, through maximization of the expected sum of rewards over

the time domain. A simple feed‐forward ANN can be effective to model
specific rates of multiple bioprocess variables in a hybrid modeling
approach (Narayanan et al., 2019). A two‐norm regularized objective
function and cross‐validation can be adopted to avoid overfitting and
Justification

identify the optimal number of neurons and regularization parameters.

Similarly, a single hidden layer ANN (with hyperbolic tangent and linear
transfer functions) was chosen to model specific rates of biomass,
viable cell, substrate and product formation in fed‐batch production of
interleukin‐8 antibody by Chinese hamster ovary (CHO) DP‐12 cell
the hybrid model
parameters after
Time invariant

(Bayer et al., 2023). Adopting a serial hybrid structure, the ANN models
the specific rates utilizing four operating parameters and predictions of
the previous time step of each response variable as input. Bayer et al.
0

(2021b) adopted an ANN‐based hybrid model for fed‐batch cultivation

of CHO cells. Standardized input (z‐score) cultivation temperature,
glucose, glutamine, asparagine, alanine, and aspartate to glutamate ratio
original kinetics
Time invariant
parameters in

were used to model specific growth and product formation rates. The
author adopted in‐depth knowledge, correlation analysis, and PCA to
select appropriate inputs for the ANN model.
7

10

Out of three process variables, substrate profile is dropped from hybrid model.

The rate of production/consumption of culture variables (i.e.,

biomass, substrate, product) can be modeled as a product of
maximum specific rates, stoichiometric coefficients (reaction rates
state variable

on the cell concentration), and specific production/consumption rates

Number of

estimated by the ANN from reduced concentration vector as input

(Botton et al., 2022). A single hidden layer containing 10 neurons,
f

4
3

hyperbolic‐tangent activation function, linear output transfer func-

Dynamically changing, noncontrolled process variables.

tion, and minimization of the normalized sum of squared errors with

regularization term in training convergence was adopted. Separate
PHA production by Pseudomonas putida GPo1
Astaxanthin production by Xanthophyllomyces

Parametric white box models not described.

ANN submodels for each of the data‐driven model terms/parameters

dendrorhous in batch culture – glucose

(i.e., specific rates), with independent input space mapping, can also
The different hybrid model considered.

be formulated in a hybrid model (Yang et al., 2016). Though, such a

using ammonia and octanoate

strategy improves the flexibility of the network design, the number of

In a structured kinetic model.

hyperparameters to be identified increases proportionally.

&/sucrose as substrate

For single sugar utilization.

(Continued)

System description

4.3.2 | Non‐ANN hybrid models

TABLE 2

Due to the perceived risk of overfitting from the ANN‐integrated

kinetic model, polynomial regression has been elected as a data‐
driven component in the hybrid modeling exercise (Zhang et al., 2020).
b

e
a

f
10 | MAHANTY
In serial hybrid structure, the author adopted a mixed integer
nonlinear programming (MINLP) for the automatic identification of
kinetic model alternatives and polynomial model reduction in
conjunction with the parameter estimation approach.
Hybrid Gaussian process state spaces models (GPSSM) with fully
discretized numerical solution has been used to model viable cell
density, glucose, glutamine, ammonia, lactate, and product titer in cell
culture (Cruz‐Bournazou et al., 2022). Following a quadratic
polynomial to fit the experimental data, the polynomial derivatives
were used to train the GPM for each finite element adopting
penalized least‐square approach. Vega‐Ramon (Vega‐Ramon
et al., 2021) adopted a mechanistic model in astaxanthin production
in Xanthophyllomyces dendrorhous batch culture. Following the
estimation of model parameters, the calculated specific growth rate,
substrate consumption rate, and product accumulation rate at each
time step for each data set were used to build three Gaussian process
models, using an exponential kernel function. The author observed
lower uncertainty associated with the hybrid model in comparison to
its kinetic variant, a better representation of the process dynamics.
4.4 | Difficulties in implementation of black‐box
component
The mechanistic model of a dynamic bioprocess system is repre-
sented by a system of coupled differential equations of the states as a
known function of state variables and time‐invariant parameters as
shown in Equation (1).
dξ
= f (ξ , t, θ), (1)
dt
where ξ is the state vector, that is, ξ = [X , S, P ]T and θ is a set of
time‐invariant parameters. As the functional form of f(.) is explicitly
known, the differential can be calculated at each time step without
difficulty. Model fitting exercise can take either differentiation of
time series data to calculate the rate, or integration of the model to
predict the concentrations. However, the former is not considered
due to noise amplification. With a specified initial state vector (ξ(t =0) )
and guess the value of θ, the system of ODEs is numerically
integrated while iteratively changing the parameter vector to
minimize the weighted sum of squared error (Ew) between
experimental and modeled states inside an optimization framework
(Wang et al., 2018).
1 n m
(ξij − ξˆij )2
Ew = ∑ ∑
n × m i =1 j =1 σ 2ξi
, (2)
where, i = 1, 2, …, n denotes the ith state variable, j = 1,2, …, m is a
different time point of measurement, and ξij, ξˆij, ξ¯i are the measured,
predicted, and measured average value of the ith state, respectively.
In hybrid modeling, the representation of rate equations can be
different depending on whether one/more specific rates, terms, or
some time‐invariant coefficients of the mechanistic model (i.e.,
maintenance, yield coefficients) are encapsulated into a black box
architecture, as shown in Equation (3).
dξ
= f (g (ξ , t, w ), ξ , t, θ), (3)
dt
where the rate expression f (g (.), ξ , t, θ) is well defined a parametric
function, however, g (ξ , t, w ) is the prediction (e.g., specific growth
rate) from the data‐driven model (i.e., ANN, polynomial regression),
with hyperparameter w (network weight, bias, or polynomial coeffi-
cients), using states, and/or time input predictors. Selection of
predictors for the black‐box models, though remains heuristic, may
be guided based on fundamental knowledge about the process. As
the data‐driven components lack the direct measurements of specific
rates, they are not pre‐trained on any independent data set and
cannot even have a finalized topology, or weights and biases
(Oliveira, 2004).
4.5 | Parameter estimation approaches
Parameter estimation for a mechanistic model is often directed
through a least‐square regression approach incorporated into the
optimization framework. Developing the data‐driven model part is
certainly the most challenging aspect of the hybrid model. However,
the output of the data‐driven component is often a specific rate and
the explicit relationship between the network trainable variables and
the concentrations is unknown (lack of target outputs). Two different
strategies have been proposed to train the hybrid model (Karimi
Alavijeh et al., 2022) with the data set, i.e., (i) approximation of
bioreaction rates, followed by minimization of the deviation from the
predicted specific rates; and (ii) minimization of error between
experimental and predicted state concentrations through sensitivity
approach.
4.5.1 | Direct approach
Existing hybrid modeling approaches take a multi‐step strategy to
develop the empirical models of unknown variables (Yang et al., 2016),
as briefed below. The simplest approach would take an appropriate
interpolation function for the data set, and calculation of derivatives
of state variables ( ) at different time points (Figure 4a). If the
dξ
dt
proposed hybrid model does not have any time‐invariant parameter
(to estimate), the data‐driven target output g(.) can be calculated at
each time point by plugging the value of ( ) in Equation (3). The
dξ
dt
empirical data‐driven model can now be formalized as both ξ and g(.)
are available at each time point. The length of an interpolated data
set can be much higher than experimental data points, which can be
advantageous for the data‐driven model. Once the data‐driven model
parameters (weight, bias, coefficients) are determined, the hybrid
model can be integrated using a numerical approach. Experimental
design, for example, central composite design, or full‐factorial design
MAHANTY | 11

(a) (b)

F I G U R E 4 Direct approach of hybrid modeling (a) dimension of experimental data is increased through interpolation, and the specific rates
at different times g (ξ , t, w ) are approximated from differences between adjacent data points. The data‐driven part is trained and then
incorporated into the ordinary differential equations (ODEs) of the hybrid model. In the optimization‐based approach (b) data‐driven prediction,
that is, the output g (ξ , t, w ) is guessed for all sampling points and the midpoint of each interval. The system of ODEs is numerically integrated
using discretized RK4 algorithm, and the objective function is calculated. Once the objective (Ewr) stops decreasing, the optimization terminates,
and the data‐driven model is trained with the optimized set g (ξ , t, w ), and reintegrated into a hybrid model.

is used to generate different combinations of process factors or
settings for batch or fed‐batch experiments to be executed in
laboratory conditions (Pinto et al., 2022). Intra‐experimental shifts of
CPP from one to another set point during fed‐batch fermentation
reduce experimental burden (Bayer et al., 2020b). Data sets (time‐
series transient or steady state) from such designed experiments are
smoothed and interpolated over time to create a large training
pattern for the neural network, that maps the input state variables to
output (i.e., specific rates) (Zuo & Wu, 2000).
A pre‐existing mechanistic bioprocess model can be used to
generate the necessary training data for a neural network. First,
multiple experimental data sets are simultaneously fitted to the
mechanistic model. In a refitting exercise, the parameters related to
growth, uptake, and product formation rates are independently
estimated for each data set while leaving other parameters at their
global estimates (Luna et al., 2021). The simulated states can be used
to calculate the specific rates using the model equations, and this
appears to be a major challenge. This inevitably has a detrimental
influence on the unknown variable estimation values, leading to
compromised reliability and accuracy, and eventually impacting the
generalization capability of the hybrid model (Karimi Alavijeh
et al., 2022).
The hybrid models can also be constructed by first dividing the
time domain into equally spaced intervals (Figure 4b). For example, if
experimental measurements are available at m different time points,
unique values of the different specific rates g lj are assumed for each
of the m−1 intervals. In addition, if the hybrid model contains k time‐
invariant parameters, the entire set of m−1+k parameters can be
estimated (from their initial guess) by adopting a least‐squares
regression problem (Rogers et al., 2023). The objective function, that
is, weighted error with regularization (Ewr) for the optimization is
formulated as in Equation (4).
1 n m
(ξij − ξˆij )2 r m −1 2

compilation can subsequently be used to train the data‐driven

Ewr = ∑∑
n × m i =1 j =1 2
σ ξi (
l =1 j =1
)
+ λT ∑ ∑ g lj − g lj +1 , (4)

components of the hybrid model. Experimental data can also be

modeled to some typical mathematical function (i.e., logistic function)
for the estimation of time derivatives through analytical differentia-
tion (Tholudur et al., 1999). The time derivatives (rates) can be used
to train the data‐driven component of the hybrid model.
Although this procedure appears to be simple, the interpolation
itself at the very first step of modeling is the key source of the noise.
Moreover, offline data are acquired at large uneven time intervals (up
to several hours) in bioprocess. Nevertheless, state dynamics evolve
as a continuous time‐dependent function and its discretization
where, ξij and ξ̂ij are experimental and predicted values of ith state
(i = 1, 2…n) on jth time point (j = 1, 2…m), respectively. The first term
of the objective function is the normalized sum of square error, while
the second part penalizes a drastic change in specific rates (prediction
for r different black box modules) between two consecutive time
points. The λ is the penalty weight vector for state variables that
controls the “rigidity” of black‐box output with time, where larger
values will minimize rapid change in rates, and reduces the risk of
overfitting to measurement noise (Rogers et al., 2023). The choice of
12 | MAHANTY
penalty weight should balance between mean relative percentage
error and uncertainty during parameter estimation.
To estimate the model parameters, the system of ODEs needs to
be discretised into fourth‐order Runge‐Kutta algebraic form and
transformed into a nonlinear programming problem. However, the
discretization of the process to match sampling time steps would
impact the derivative approximation and accuracy of the solution
(Cruz‐Bournazou et al., 2022). However, following the minimization
of the objective function (as in Equation 4), the data‐driven model
g (ξ , t, w ) needs to be trained to fix the weight and bias (for ANN).
Finally, hybrid models need to re‐simulate the state trajectories to
check the final fitness.
4.5.2 | Indirect training approach
The training of hybrid models is essentially the identification of time‐
invariant parameters (θ), and data‐driven model parameters (w)
coefficients, weight, and bias. If w is considered as a parameter vector
(along with θ) to be identified, the training is transformed into a
simple dynamic system parameter estimation problem (Yang
et al., 2016), that is, minimizing the SSE between observed and
predicted states as in Equation (2). The specific rates (e.g., µ, qp) can
be modeled as a feed‐forward neural network in a hybrid model
system of ODEs (von Stosch et al., 2016b), as exemplified in Equation
(5).
H1 = tansig (w1*ξ + b1)
H2 = tansig (w2*H1 + b2) (5)
[μ; qp] = purelin (w3*H2 + b3)
The above example considers two hidden layers with the
network weight wi (i = 1:3), and bias bi (i = 1:3). The network takes
the input of state vector (ξ ), and tangential‐sigmoidal (tansig), linear
(purelin) transfer functions in the nodes of hidden, and output layers,
respectively. The H1 and H2 are cumulative inputs received by the
different units in the first and second hidden layers, respectively. The
μ, qp , for example, are ANN output for specific growth, and product
formation rate respectively. The dimension of wi or bi depends on the
number of inputs, hidden layer neurons, and output. This approach
has been adopted in numerous studies, particularly when the
topology of the data‐driven part is prefixed, or assumed. In this
indirect method, the loss function is not directly linked to the neural
network outputs (Pinto et al., 2022). As the data‐driven model is
trained indirectly in the optimization framework, a regularization term
can also be included in the fitness function (Ewr) to improve training
convergence (Botton et al., 2022; Yang et al., 2011) as shown in
Equation (6).
1 n m
(ξij − ξˆij )2
Ewr = ∑∑ + λ‖g‖, (6)
n × m i =1 j =1 σ 2ξi
where λ is the regularization parameter (weight), and g is the
parameter for the data‐driven component. The regularization drives
the values of those parameters that are not contributing to the model
to zero, promoting a parsimonious structure (Stosch et al., 2018). The
Levenberg–Marquardt method (LMM), is very effective in solving
indirect training and identification, to estimate the respective specific
rates (Bayer et al., 2021b; Bayer et al., 2023). The error back
propagation can be performed by calculating the gradient of the
squared errors (E) for the model state to the ANN weights, that is,
∂E
∂w
(Oliveira, 2004; Pinto et al., 2019). Evaluation of Jacobian (J) in an
ANN‐based hybrid model with sensitivities equations is shown in
Equation (7).
 dE   dξ  2 m  dξ 
= ∑     = − ∑ eTt  
m t =1  dw t
m
∂w t =1  dξ t  dw t
∂E
J= (7)
with et =ξit − ξˆit . The matrix ( )
dξ
dw t
can be computed from the
differentiation of state rates in Equation (3) to w, resulting in an
expression ( ) = ϕ( ),
d dξ
dt dw
dξ
dw
which should be simultaneously inte-
grated along with hybrid model ODEs, starting from the initial
condition ( )
dξ
dw t=0
= 0 , and Euler forward integration method with a
fixed step size (Oliveira, 2004; von Stosch et al., 2016a). The
implementation of the LMM algorithm for the estimation of data‐
driven model (particularly ANN) parameters is shown in Figure 5.
Model output and error are calculated from initialized weights and
biases, to estimate the Jacobian, and update the network parameters
for new outputs (Shah et al., 2022). This process continues in an inner
loop till the error becomes lower than a tolerance value. The network
weights are restored if weight‐updating results in the amplification of
error between model prediction and experimental observation. The
loss function can also be monitored on an independent validation set
as a stopping criterion, that is, when validation error starts to increase
(Pinto et al., 2019).
For the hybrid model, different specific rates can be modeled
using the independent feed‐forward network. The topology selection
(number of neurons in hidden layer) and parameter identification
process (i.e., weight and bias) can be performed sequentially. The
number of hidden neurons for each ANN sub‐model in the hybrid
model can be varied within a given range (expert judgment), using a
uniform experimental design. A leave‐one‐out cross‐validation
technique (using different batch experiments) can be adopted in
each of the hidden neuron combinations to find the optimal group
(Yang et al., 2016). Different network structures can be compared
based on their Bayesian information criteria (BIC) value, the one with
the highest BIC is retained (von Stosch et al., 2016a).
5 | GE NERALIZATION
CAPABILITIES —H O W T O ENS URE ?
5.1 | Experimental design to model—Digital twins
Design of experiments (DoE) is the tool to systematically investigate
the relationship between input factors and the response of interest
(product concentration). DoE suggests a series of experimental
MAHANTY | 13

F I G U R E 5 Hybrid model training scheme based on sensitivity analysis. The model outputs are calculated based on initialized weights and
biases (wk, bk). The corresponding error, Ek, is used to calculate the Jacobian matrix with respect to the neural network parameters. The weight
and bias values are updated (wk+1, bk+1) to calculate new outputs and the process continues as the error decreases. An inner loop counter (m) is
used to control the change in the combination coefficient and update the parameters. Adopted and modified from (Shah et al., 2022).

F I G U R E 6 Hybrid model‐based prediction of optimal process conditions adopting digital twins. Hybrid model developed from an initial data
set is used to simulate optimal process conditions. If the recommended conditions are not reflected in existing data, experiments are carried out
under laboratory conditions and added to the initial data set for re‐training the hybrid model. The procedure is repeated until the best process
conditions are ascertained.

conditions combining different levels of each process factor for
effective exploration of response space (Mandenius & Brundin, 2008).
DoE considering critical process parameters is the most widely
adopted approach to ensure quality by design target in a hybrid
modeling paradigm. A hybrid model‐based experimental design can
be adopted to explore the design space more effectively and identify
the optimum process conditions in bioprocess (Bayer et al., 2020b;
Bayer et al., 2021b; Sommeregger et al., 2017). A hybrid model
developed from a small initial data set is used to predict
recommended optimal experiments, and once carried out the same
can be added to the existing data set for re‐training the hybrid model
(Bayer et al., 2021a). This exercise can be repeated unless the
projected best process conditions get stabilized (Figure 6). In silico
generation of simulated batch experiments with a semi‐parametric
hybrid has been shown to improve product titer, while deciphering
the correlation between critical process parameters and critical
quality attributes (Botton et al., 2022).
The pattern of process operation space in the data set, used to
train the data‐driven module, should, however, cover the expected
process region in prediction sets, for all practical purposes (Zhang &
14 | MAHANTY
Mao, 2017). The generation of high‐quality experimental data can be
laborious and time‐consuming. Intensified DOE (iDoE) that adopts
intra‐experimental set‐point changes in fed‐batch experiments can
be used to train hybrid models, with good prediction performance
across multiple test batches, while substantially reducing the
experimental burden (Bayer et al., 2020b; von Stosch et al., 2016b).
Experimental design for iDOE adds several stages (typically three or
four) in each experiment, but requires no information on the process
model in priori (von Stosch & Willis, 2017). The process response
information gathered from iDoE can be managed through hybrid
modeling, as a tool to have the best possible description of process
behavior. Studies have suggested low errors in model transfer from
shaker to reactor scale and between the DoE and the iDoE approach
(Bayer et al., 2021b).
Experimental conditions for fed‐batch cultivations can be
formulated with model‐assisted DoE of feeding strategies for
seamless integration into a hybrid model development routine. For
example, Bayer et al., (Bayer et al., 2023) performed four initial
experiments, and a full DoE with 29 experiments varying the glucose,
and glutamine concentration in the feed, the bolus feed rate, and the
feed start. The author adopted different data set labels in the training
and validation exercise, using combinations of the initial four and fill
DoE sets.
A moderate number of experimental batch/fed‐batch studies
can be performed in laboratories, where the generated data set can
randomly be distributed (in a defined proportion) into training and
testing subsets (Dong et al., 2014; Narayanan et al., 2019) to build
the hybrid model. However, the dimension of the data set used to
train and test the hybrid model can vary depending on the model
complexity, data availability, and at the discretion of the modeler.
For example, Rogers (Rogers et al., 2023) chose three batch
experiments (13 measurement points in each set) to train, and
two batches to test the performance of hybrid models of different
“grayness.” Entire experimental data sets can also be used to train a
hybrid model while reusing the same data set following Gaussian
noise addition as a validation set to stop overfitting (Pinto
et al., 2022). The incorporation of random noise increases the
dimension of an existing experimental data set, which is likely to
improve the predictive power of ANN models with biological
systems (del Rio‐Chanona et al., 2017a). However, the authors have
not explicitly compared the effectiveness of the strategy. Smooth-
ing and interpolation of experimental data in time dimension
facilitate data‐driven modeling, though the consequence on the
model's generalization capability remains questionable (Zuo &
Wu, 2000). The existing parametric kinetic model can mimic a
“true” experimental system to generate in‐silico experimental data
to evaluate the hybrid model's performance (Pinto et al., 2019;
Zhang et al., 2020). The size of generated data is maintained to
match the real experimental implementations. Gaussian measure-
ment noise can also be added to in‐silico data before hybrid
modeling (Mowbray et al., 2023). Raw experimental data collected
from process plants can initially be modeled using simple kinetic to
correct and generate missing values, which can further be processed
through the top‐level data‐driven model to incorporate different
process behaviors (Zhang et al., 2019).
5.2 | Cross‐validation
Predictability and interpretability of any bioprocess models, whether
mechanistic, data‐driven or hybrid, need to be evaluated to decide on
the usability of the model. Over‐fitting is a well‐known identification
problem, where the model fits the training data exceptionally well but
shows poor performance on a new data set. Cross‐validation is an
internal re‐sampling method to ensure the quality of the mathemati-
cal model formulated, where the original data is split into training and
validation subsets, and simultaneously used for model building and
validation (Rajamanickam et al., 2021). Partitioning is typically
performed batch‐wise with the amount of data allocated in each
partition depending on data availability (Pinto et al., 2022). In hybrid
modeling, hyper‐parameter selection (i.e., number of neurons in
hidden layer) can be conducted through a k‐fold fashion, where a
subset of experimental batches is used for training and the remaining
data set is used to obtain a normalized error estimate across all states
along the trajectory (del Rio‐Chanona et al., 2017a). This procedure is
repeated until the chosen network configuration has been tested
against all the sets. The cross‐validation error can be used to choose
the optimal topology in hybrid modeling.
To fix an optimal number of neurons for three different empirical
submodels in a hybrid modeling structure, Yang et al. (2016) adopted
a uniform design table for the combination of hidden neuron
numbers and performed leave‐one‐out cross‐validation with 12
batches of modeling data. The random data partitioning in the
cross‐validation process (except for the leave‐one‐out) can be
repeated multiple times to average the cross‐validation error (Bayer
et al., 2023).
5.3 | Bootstrap‑aggregation
Bootstrap aggregation, also known as bagging, is a machine‐learning
approach designed to improve the stability and accuracy of models in
statistical regression (Baron & Zhang, 2020). The bootstrap aggrega-
tion approach is particularly preferred for a smaller data set, where
prefixing validation and training fold may not offer sufficient variation
in the model development. Experimental sets (not data points) from
the combined training‐validation pool are randomly re‐sampled into
training/validation partitions n number of times (Pinto et al., 2019).
Each time, a different hybrid model is generated and identified using
the weighted least squares approach. During training, the loss of the
validation set is also measured as a stopping criterion. Finally,
predictions from best k hybrid models (k«n) are averaged for the
process states (i.e., biomass, substrate concentration), or data‐driven
function (i.e., specific rates). Different hybrid models can have better
performance in different regions of input space, and combining
multiple models can offer better prediction accuracy.
MAHANTY
6 | H Y B R I D M O D E L AP P L I C A T I O N S ,
P R A C T I C A L CH A L L E N G E S , A N D F U T U R E
RESEARCH DIRECTIONS
6.1 | Application in model predictive control (MPC)
Hybrid model offers better extrapolation capabilities in comparison
to the data‐driven model and is useful for process control and
optimization. In MPC, the optimal future control actions are predicted
based on the current horizon and control actions are delivered for
execution for the next time step. To account for future disturbances,
MPC requires a robust dynamic process model where online
measurements from the ongoing processes are used to fine‐tune
the dynamic model parameters for future control actions (Zhang
et al., 2019). Though MPC can also be formulated with any model
variants, the hybrid models generally with fewer parameters are
easier to adopt, interpret, and control strategies can be reviewed
(Cubillos et al., 2001). Control Lyapunov–Barrier function (CLBF)
based MPC, which offers constrained input stabilization of nonlinear
systems, was developed that utilizes a DNN combined with a first‐
principles model (Bangi & Kwon, 2023). A hybrid model‐based MPC
strategy has been adopted to increase the profitability of an industry‐
scale fermentation process that utilizes multi‐rate state observers
(Shah et al., 2023). Open‐loop MPC with a predetermined optimal
control action sequence has been adopted to minimize inter‐batch
variability in recombinant protein production (Jenzsch et al., 2006).
Poor system‐to‐system transferability of ML‐based algorithms
necessitates finetuning of a digital twin for MPC even in related
systems, where large‐language models (e.g., ChatGPT) inspired
transfer learning‐enhanced model development can be promising
(Sitapure & Kwon, 2023a). Cutting‐edge first‐generation time‐series
transformers models, with the potential for multivariate time‐series
prediction, have also been integrated into process modeling and
control (Sitapure & Kwon, 2023b).
6.2 | Challenges with hybrid modeling
Hybrid models are of great potential for efficient use of available
experimental data, adopting digital twins in process development,
and validation of model transferability into a different scale.
However, hybrid models should be considered as an augmentation
tool, not a magic bullet to cover up poor‐experimental design,
erroneous measurements, or lack of knowledge in the concerned
bioprocess. A hybrid model must be well‐trained on a wider process
space data set to have accurate predictions on unseen data (Walsh
et al., 2022). Each modeling exercise is unique to available data
(offline, online measurement), the complexity of the bioprocess, and
cannot be replicated in a different process system. Though a general
framework for a hybrid model development pipeline can be laid
down, the mapping of data‐driven components (process terms,
specific rates, or parameters as a function of state variables, external
inputs), their architecture, and hyperparameters remains largely
| 15
heuristic. The hybrid model should be considered with prior domain
knowledge of the underlying process (Zhang et al., 2020). Accurate
modeling of the kinetic part to account for primary process
mechanisms simplifies the data‐driven modeling of the secondary
process. Such formalization or distinction may not always be
apparent in complex bioprocess systems. Implementation of a hybrid
model from experimental data could be a significant hurdle for
researchers, who may not be well‐versed in complex mathematical
formalization of sensitivity equations involved in hybrid‐model
identification, and parameter estimation exercises. Sharing experi-
mental data, code (or at least pseudocode) in a communal repository
or as supplementary material to publications, is rarely reflected.
6.3 | Future research directions
Hybrid modeling approach has been a key enabler for industrial
bioprocess for estimation of the unknown‐specific uptake/secretion
rates, predictions for key nutrient/metabolite and product concen-
trations (Kotidis & Kontoravdi, 2020), accelerate process develop-
ment through DoE with reduced experimental effort (Möller
et al., 2019). As an assembly of hybrid models can be readily
automated, smart manufacturing with safer, and more cost‐effective
could be accessible for biopharmaceuticals processes (Tsopanoglou &
Jiménez del Val, 2021). Even though the data requirements are
certainly reduced in hybrid modeling, the quality of data should be
reasonable to model multivariate interactions. In addition, active
learning coupled with iterative experimental design approaches will
be required to probe the poorly understood part of the model
(Narayanan et al., 2023). In addition, there is no specific guideline on
the choice of ML algorithm, or the proportion of greyness to be
inscribed in model development. The next generation of hybrid
models has to be flexible enough to support different modeling
formalisms and available powerful tools with user interfaces (Liu
et al., 2022b). The development of software tools with the option to
integrate various sources of knowledge to formulate the best hybrid
model for a given application is warranted (Sansana et al., 2021).
Transformation of nonlinear dynamics into linear ones and the close‐
loop stabilization through Lyapunov‐based model predictive control
(LMPC) or feed‐back control design can be realized in a bioprocess
system (Narasingam & Kwon, 2019, 2020). The use of hybrid‐model
based digital‐twins (DTs) to manage process data to derive novel
insights, near‐real‐time process characterization (identification of
future disturbances), and as a part of industry 4.0 standards in diverse
biomanufacturing process would require features for adaptability and
transferability (Sokolov et al., 2021).
7 | CONCLUSIONS
Hybrid modeling is certainly a useful tool to explore, control, and
predict complex bioprocess system behavior. Integration of data‐
driven components into the first‐principal model offers many
16 | MAHANTY
flexibilities, starting from the selection of the data set, the process to
be mapped as a black‐box function and their topology, hyperpara-
meters, training algorithm, and validation. A review of literature from
the last two decades, however, does not suggest a profound
expansion of hybrid modeling into bioprocess/biotechnology. This
is not because of the unavailability of resources (i.e., reviews,
textbooks, and commercial software packages), but because the
complex mathematical concepts presented in them are usually
beyond the formal academic training of researchers in biotechnology.
Furthermore, methodological descriptions in research articles are not
always in sufficient detail that enables the readers to grasp the
intricate implementation strategy. There are many methods at
different levels of complexity so it is very easy to get lost in the
search for a simple, reliable strategy for model identification.
A U T H O R C O N TR I B U T I O N S
Biswanath Mahanty as sole author contributed to conceptualization,
project administration, writing‐original draft, writing review, and
editing.
A C KN O W L E D G M E N T S
Biswanath Mahanty acknowledge the support from Karunya Institute
of Technology and Sciences. The author also appreciates the “lesson”
learned from Ms Pema, when decided to explore the hybrid modeling
avenue.
CO NFL I CT OF INTERES T S T ATEME NT
The author declares no conflict of interest.
D A TA A V A I L A B I L I T Y S T A T E M E N T
Data sharing is not applicable to this article as no new data were
created or analyzed in this study.
ORCID
Biswanath Mahanty http://orcid.org/0000-0002-5815-2440
REFERENCES
Abbiati, G., Marelli, S., Tsokanas, N., Sudret, B., & Stojadinović, B. (2021). A
global sensitivity analysis framework for hybrid simulation.
Mechanical Systems and Signal Processing, 146, 106997. https://
linkinghub.elsevier.com/retrieve/pii/S0888327020303836
Alrashed, A. A. A. A., Karimipour, A., Bagherzadeh, S. A., Safaei, M. R., &
Afrand, M. (2018). Electro‐ and thermophysical properties of water‐
based nanofluids containing copper ferrite nanoparticles coated with
silica: Experimental data, modeling through enhanced ANN and curve
fitting. International Journal of Heat and Mass Transfer, 127, 925–935.
https://linkinghub.elsevier.com/retrieve/pii/S0017931018324876
Andrade Cruz, I., Chuenchart, W., Long, F., Surendra, K. C.,
Renata Santos Andrade, L., Bilal, M., Liu, H., Tavares Figueiredo, R.,
Khanal, S. K., & Fernando Romanholo Ferreira, L. (2022). Application
of machine learning in anaerobic digestion: Perspectives and
challenges. Bioresource Technology, 345, 126433. https://
linkinghub.elsevier.com/retrieve/pii/S0960852421017752
Apicella, A., Donnarumma, F., Isgrò, F., & Prevete, R. (2021). A survey on
modern trainable activation functions. Neural Networks, 138, 14–32.
https://linkinghub.elsevier.com/retrieve/pii/S0893608021000344
Araúzo‐Bravo, M. J., Cano‐Izquierdo, J. M., Gómez‐Sánchez, E., López‐
Nieto, M. J., Dimitriadis, Y. A., & López‐Coronado, J. (2004).
Automatization of a penicillin production process with soft sensors
and an adaptive controller based on neuro fuzzy systems. Control
Engineering Practice, 12, 1073–1090. https://linkinghub.elsevier.
com/retrieve/pii/S0967066103002508
Arnold, S., Becker, T., Delgado, A., Emde, F., & Enenkel, A. (2002).
Optimizing high strength acetic acid bioprocess by cognitive
methods in an unsteady state cultivation. Journal of Biotechnology,
97, 133–145. https://linkinghub.elsevier.com/retrieve/pii/
S0168165602000652
Artigue, H., & Smith, G. (2019). The principal problem with principal
components regression. Cogent Mathematics & Statistics, 6,
1622190. https://doi.org/10.1080/25742558.2019.1622190
Bae, J., Lee, H., Jeong, D. H., & Lee, J. M. (2020). Construction of a valid
domain for a hybrid model and its application to dynamic
optimization with controlled exploration. Industrial & Engineering
Chemistry Research, 59, 16380–16395. https://doi.org/10.1021/acs.
iecr.0c02720
Bangi, M. S. F., Kao, K., & Kwon, J. S.‐I. (2022). Physics‐informed neural
networks for hybrid modeling of lab‐scale batch fermentation for β‐
carotene production using Saccharomyces cerevisiae. Chemical
Engineering Research and Design, 179, 415–423. https://linkinghub.
elsevier.com/retrieve/pii/S0263876222000491
Bangi, M. S. F., & Kwon, J. S.‐I. (2020). Deep hybrid modeling of chemical
process: Application to hydraulic fracturing. Computers & Chemical
Engineering, 134, 106696. https://linkinghub.elsevier.com/retrieve/
pii/S0098135419311019
Bangi, M. S. F., & Kwon, J. S. I. (2023). Deep hybrid model‐based
predictive control with guarantees on domain of applicability. AIChE
Journal, 69(5):e18012. https://doi.org/10.1002/aic.18012
Bardow, A., & Marquardt, W. (2004). Incremental and simultaneous
identification of reaction kinetics: Methods and comparison.
Chemical Engineering Science, 59, 2673–2684. https://linkinghub.
elsevier.com/retrieve/pii/S0009250904002015
Baron, C. M. C., & Zhang, J. (2020). Reliable on‐line re‐optimization
control of a fed‐batch fermentation process using bootstrap
aggregated extreme learning machine. In O. Gusikhin, & K. Madani
(Eds.), Informatics in control, automation and robotics. ICINCO 2017.
Lecture Notes in Electrical Engineering (Vol. 495, pp. 272–294).
Springer. https://doi.org/10.1007/978-3-030-11292-9_14
Bayer, B., Dalmau Diaz, R., Melcher, M., Striedner, G., & Duerkop, M.
(2021a). Digital twin application for model‐based DoE to rapidly
identify ideal process conditions for space‐time yield optimization.
Processes, 9, 1109. https://www.mdpi.com/2227-9717/9/7/1109
Bayer, B., Duerkop, M., Pörtner, R., & Möller, J. (2023). Comparison of
mechanistic and hybrid modeling approaches for characterization of
a CHO cultivation process: Requirements, pitfalls and solution paths.
Biotechnology Journal, 18, 2200381. https://doi.org/10.1002/biot.
202200381
Bayer, B., Duerkop, M., Striedner, G., & Sissolak, B. (2021b). Model
transferability and reduced experimental burden in cell culture
process development facilitated by hybrid modeling and intensified
design of experiments. Frontiers in Bioengineering and Biotechnology,
9, 740215. https://doi.org/10.3389/fbioe.2021.740215/full
Bayer, B., Stosch, M., Striedner, G., & Duerkop, M. (2020a). Comparison of
modeling methods for DoE‐based holistic upstream process charac-
terization. Biotechnology Journal, 15, 1900551. https://doi.org/10.
1002/biot.201900551
Bayer, B., Striedner, G., & Duerkop, M. (2020b). Hybrid modeling and
intensified DoE: An approach to accelerate upstream process
characterization. Biotechnology Journal, 15, 2000121. https://doi.
org/10.1002/biot.202000121
Bhadriraju, B., Bangi, M. S. F., Narasingam, A., & Kwon, J. S. I. (2020).
Operable adaptive sparse identification of systems: Application to
MAHANTY
chemical processes. AIChE Journal, 66(11):e16980. https://doi.org/
10.1002/aic.16980
Bhola, V., Swalaha, F. M., Nasr, M., & Bux, F. (2017). Fuzzy intelligence for
investigating the correlation between growth performance and
metabolic yields of a Chlorella sp. exposed to various flue gas
schemes. Bioresource Technology, 243, 1078–1086. https://
linkinghub.elsevier.com/retrieve/pii/S0960852417311252
Bhutani, N., Rangaiah, G. P., & Ray, A. K. (2006). First‐principles, data‐
based, and hybrid modeling and optimization of an industrial
hydrocracking unit. Industrial & Engineering Chemistry Research, 45,
7807–7816. https://doi.org/10.1021/ie060247q
Botton, A., Barberi, G., & Facco, P. (2022). Data augmentation to support
biopharmaceutical process development through digital models—A
proof of concept. Processes, 10, 1796. https://www.mdpi.com/
2227-9717/10/9/1796
Brunner, V., Siegl, M., Geier, D., & Becker, T. (2020). Biomass soft sensor
for a Pichia pastoris fed‐batch process based on phase detection and
hybrid modeling. Biotechnology and Bioengineering, 117, 2749–2759.
https://doi.org/10.1002/bit.27454
Cabaneros Lopez, P., Udugama, I. A., Thomsen, S. T., Roslander, C.,
Junicke, H., Iglesias, M. M., & Gernaey, K. V. (2021). Transforming
data to information: A parallel hybrid model for real‐time state
estimation in lignocellulosic ethanol fermentation. Biotechnology and
Bioengineering, 118, 579–591. https://doi.org/10.1002/bit.27586
Caramihai, M., & Severi, I. (2013). Bioprocess modeling and control. In M.
D. Matovic, Biomass now ‐ Sustainable growth use. InTech Open.
http://www.intechopen.com/books/biomass-now-sustainable-
growth-and-use/bioprocess-modeling-and-control
Cervantes, J., Garcia‐Lamont, F., Rodríguez‐Mazahua, L., & Lopez, A.
(2020). A comprehensive survey on support vector machine
classification: Applications, challenges and trends. Neurocomputing,
408, 189–215. https://linkinghub.elsevier.com/retrieve/pii/
S0925231220307153
Chen, T. Q., Rubanova, Y., Bettencourt, J., & Duvenaud, D. K. (2018).
Neural ordinary differential equations. In: 32nd Conference on Neural
Information Processing Systems (NeurIPS 2018), Montréal, Canada
(pp. 6571–6583).
Cheng, Y., Bi, X., Xu, Y., Liu, Y., Li, J., Du, G., Lv, X., & Liu, L. (2023).
Artificial intelligence technologies in bioprocess: Opportunities and
challenges. Bioresource Technology, 369, 128451. https://linkinghub.
elsevier.com/retrieve/pii/S0960852422017849
Chu, Y., & Hahn, J. (2007). Parameter set selection for estimation of
nonlinear dynamic systems. AIChE Journal, 53, 2858–2870. https://
doi.org/10.1002/aic.11295
Cruz‐Bournazou, M. N., Narayanan, H., Fagnani, A., & Butté, A. (2022).
Hybrid Gaussian process models for continuous time series in bolus
fed‐batch cultures. IFAC‐PapersOnLine, 55, 204–209. https://
linkinghub.elsevier.com/retrieve/pii/S2405896322008461
Cubillos, F., Callejas, H., Lima, E. L., & Vega, M. P. (2001). Adaptive control
using a hybrid‐neural model: Application to a polymerisation reactor.
Brazilian Journal of Chemical Engineering, 18, 113–120. http://www.
scielo.br/scielo.php?script=sci_arttext&pid=S0104-
66322001000100010&lng=en&tlng=en
Dong, Y., Fan, Q., Yan, X., Guo, M., & Lu, F. (2014). Development of a
hybrid model for sodium gluconate fermentation by Aspergillus niger.
Journal of Chemical Technology & Biotechnology, 89, 1875–1882.
https://doi.org/10.1002/jctb.4270
Duan, Z., Wilms, T., Neubauer, P., Kravaris, C., & Cruz Bournazou, M. N.
(2020). Model reduction of aerobic bioprocess models for efficient
simulation. Chemical Engineering Science, 217, 115512. https://
linkinghub.elsevier.com/retrieve/pii/S0009250920300440
Duran‐Villalobos, C. A., Goldrick, S., & Lennox, B. (2020). Multivariate
statistical process control of an industrial‐scale fed‐batch simulator.
Computers & Chemical Engineering, 132, 106620. https://linkinghub.
elsevier.com/retrieve/pii/S0098135419304375
| 17
Fisher, O. J., Watson, N. J., Escrig, J. E., Witt, R., Porcu, L., Bacon, D.,
Rigley, M., & Gomes, R. L. (2020). Considerations, challenges and
opportunities when developing data‐driven models for process
manufacturing systems. Computers & Chemical Engineering, 140,
106881. https://linkinghub.elsevier.com/retrieve/pii/
S0098135419308373
Goldrick, S., Lee, K., Spencer, C., Holmes, W., Kuiper, M., Turner, R., &
Farid, S. S. (2018). On‐line control of glucose concentration in high‐
yielding mammalian cell cultures enabled through oxygen transfer
rate measurements. Biotechnology Journal, 13, 1700607. https://doi.
org/10.1002/biot.201700607
Härdle, W., Werwatz, A., Müller, M., & Sperlich, S. (2004). Nonparametric
and semiparametric models. Springer series in statistics. Springer.
https://doi.org/10.1007/978-3-642-17146-8
Jenzsch, M., Gnoth, S., Beck, M., Kleinschmidt, M., Simutis, R., &
Lübbert, A. (2006). Open‐loop control of the biomass concentration
within the growth phase of recombinant protein production
processes. Journal of Biotechnology, 127, 84–94. https://linkinghub.
elsevier.com/retrieve/pii/S0168165606004780
Jeon, B.‐K., & Kim, E.‐J. (2021). LSTM‐based model predictive control for
optimal temperature set‐point planning. Sustainability, 13, 894.
https://www.mdpi.com/2071-1050/13/2/894
Karimi Alavijeh, M., Baker, I., Lee, Y. Y., & Gras, S. L. (2022). Digitally
enabled approaches for the scale up of mammalian cell bioreactors.
Digital Chemical Engineering, 4, 100040. https://linkinghub.elsevier.
com/retrieve/pii/S277250812200031X
Karniadakis, G. E., Kevrekidis, I. G., Lu, L., Perdikaris, P., Wang, S., &
Yang, L. (2021). Physics‐informed machine learning. Nature Reviews
Physics, 3, 422–440. https://www.nature.com/articles/s42254-021-
00314-5
Kotidis, P., & Kontoravdi, C. (2020). Harnessing the potential of artificial
neural networks for predicting protein glycosylation. Metabolic
Engineering Communications, 10, e00131. https://linkinghub.
elsevier.com/retrieve/pii/S2214030120300067
Kresnowati, M. T. A. P., Suarez‐Mendez, C. M., van Winden, W. A.,
van Gulik, W. M., & Heijnen, J. J. (2008). Quantitative physiological
study of the fast dynamics in the intracellular pH of Saccharomyces
cerevisiae in response to glucose and ethanol pulses. Metabolic
Engineering, 10, 39–54. https://linkinghub.elsevier.com/retrieve/pii/
S1096717607000651
Kumar Saini, D., Yadav, D., Pabbi, S., Chhabra, D., & Shukla, P. (2020).
Phycobiliproteins from Anabaena variabilis CCC421 and its produc-
tion enhancement strategies using combinatory evolutionary algo-
rithm approach. Bioresource Technology, 309, 123347. https://
linkinghub.elsevier.com/retrieve/pii/S0960852420306192
Lagergren, J. H., Nardini, J. T., Baker, R. E., Simpson, M. J., & Flores, K. B.
(2020). Biologically‐informed neural networks guide mechanistic
modeling from sparse experimental data. PLoS Computational
Biology, 16, e1008462. https://doi.org/10.1371/journal.pcbi.
1008462
Lancashire, L. J., Lemetre, C., & Ball, G. R. (2008). An introduction to
artificial neural networks in bioinformatics: Application to complex
microarray and mass spectrometry datasets in cancer studies.
Briefings in Bioinformatics, 10, 315–329. https://doi.org/10.1093/
bib/bbp012012
Lee, D., Ding, Y., Jayaraman, A., & Kwon, J. (2018). Mathematical modeling
and parameter estimation of intracellular signaling pathway: Appli-
cation to LPS‐induced NFκB activation and TNFα production in
macrophages. Processes, 6, 21. http://www.mdpi.com/2227-9717/
6/3/21
Lee, D., Jayaraman, A., & Kwon, J. S. (2020b). Development of a hybrid
model for a partially known intracellular signaling pathway through
correction term estimation and neural network modeling. PLoS
Computational Biology, 16, e1008472. https://doi.org/10.1371/
journal.pcbi.1008472
18 | MAHANTY
Lee, D., Jayaraman, A., & Kwon, J. S.‐I. (2020a). Identification of cell‐to‐
cell heterogeneity through systems engineering approaches. AIChE
Journal, 66(5), e16925. https://doi.org/10.1002/aic.16925
Lee, D., Jayaraman, A., & Sang‐Il Kwon, J. (2019). Identification of a time‐
varying intracellular signalling model through data clustering and
parameter selection: application to NF‐B signalling pathway induced
by LPS in the presence of BFA. IET Systems Biology, 13(4), 169–179.
https://doi.org/10.1049/iet-syb.2018.5079
Liu, C., Zhang, X., Nguyen, T. T., Liu, J., Wu, T., Lee, E., & Tu, X. M. (2022a).
Partial least squares regression and principal component analysis:
Similarity and differences between two popular variable reduction
approaches. Gen. Psychiatry, 35, e100662. https://doi.org/10.1136/
gpsych-2021-100662
Liu, F., Heiner, M., & Gilbert, D. (2022b). Hybrid modelling of biological
systems: current progress and future prospects. Briefings in
Bioinformatics, 23, 00. https://doi.org/10.1093/bib/bbac081/
6555400
Lopes Dias, J. M., Lemos, P., Serafim, L., Oehmen, A., Reis, M. A. M., &
Oliveira, R. (2007). Development and implementation of a non‐
parametric/metabolic model in the process optimisation of PHA
production by mixed microbial cultures. Computer Aided Chemical
Engineering 24, 995–1000. https://linkinghub.elsevier.com/retrieve/
pii/S1570794607801908
Lopez, P. C., Udugama, I. A., Thomsen, S. T., Roslander, C., Junicke, H.,
Mauricio‐Iglesias, M., & Gernaey, K. V. (2020). Towards a digital
twin: A hybrid data‐driven and mechanistic digital shadow to
forecast the evolution of lignocellulosic fermentation. Biofuels,
Bioproducts and Biorefining, 14, 1046–1060. https://doi.org/10.
1002/bbb.2108
Luna, M. F., Ochsner, A. M., Amstutz, V., von Blarer, D., Sokolov, M.,
Arosio, P., & Zinn, M. (2021). Modeling of continuous PHA
production by a hybrid approach based on first principles and
machine learning. Processes, 9, 1560. https://www.mdpi.com/2227-
9717/9/9/1560
Luo, Y., Kurian, V., & Ogunnaike, B. A. (2021). Bioprocess systems analysis,
modeling, estimation, and control. Current Opinion in Chemical
Engineering, 33, 100705. https://linkinghub.elsevier.com/retrieve/
pii/S221133982100037X
Mandenius, C.‐F., & Brundin, A. (2008). Bioprocess optimization using
design‐of‐experiments methodology. Biotechnology Progress, 24,
1191–1203. https://doi.org/10.1002/btpr.67
Mehmood, T., Liland, K. H., Snipen, L., & Sæbø, S. (2012). A review of
variable selection methods in partial least squares regression.
Chemometrics and Intelligent Laboratory Systems, 118, 62–69.
https://linkinghub.elsevier.com/retrieve/pii/S0169743912001542
Möller, J., Hernández Rodríguez, T., Müller, J., Arndt, L.,
Kuchemüller, K. B., Frahm, B., Eibl, R., Eibl, D., & Pörtner, R.
(2020). Model uncertainty‐based evaluation of process strategies
during scale‐up of biopharmaceutical processes. Computers &
Chemical Engineering, 134, 106693. https://linkinghub.elsevier.
com/retrieve/pii/S009813541930821X
Möller, J., Kuchemüller, K. B., Steinmetz, T., Koopmann, K. S., & Pörtner, R.
(2019). Model‐assisted design of experiments as a concept for
knowledge‐based bioprocess development. Bioprocess and
Biosystems Engineering, 42, 867–882. https://doi.org/10.1007/
s00449-019-02089-7
Mondal, P. P., Galodha, A., Verma, V. K., Singh, V., Show, P. L.,
Awasthi, M. K., Lall, B., Anees, S., Pollmann, K., & Jain, R. (2023).
Review on machine learning‐based bioprocess optimization, mon-
itoring, and control systems. Bioresource Technology, 370, 128523.
https://linkinghub.elsevier.com/retrieve/pii/S0960852422018569
Moser, A., Appl, C., Brüning, S., & Hass, V. C. (2020). Mechanistic
mathematical models as a basis for digital twins. In C. Herwig, R.
Pörtner, & J. Möller (Eds.), Digital twins: Advances in biochemical
engineering/biotechnology (Vol. 176, pp. 133–180). Springer. https://
doi.org/10.1007/10_2020_152
Mowbray, M. R., Wu, C., Rogers, A. W., Rio‐Chanona, E. A. D., & Zhang, D.
(2023). A reinforcement learning‐based hybrid modeling framework
for bioprocess kinetics identification. Biotechnology and
Bioengineering, 120, 154–168. https://doi.org/10.1002/bit.28262
Narasingam, A., & Kwon, J. S. I. (2019). Koopman Lyapunov‐based model
predictive control of nonlinear chemical process systems. AIChE
Journal, 65(1):e16743. https://doi.org/10.1002/aic.16743
Narasingam, A., & Kwon, J. S.‐I. (2020). Closed‐loop stabilization of
nonlinear systems using Koopman Lyapunov‐based model predictive
control. In: 2020 59th IEEE Conference on Decision and Control
(CDC) Jeju Island, Republic of Korea, December 14‐18 (pp. 704–709).
https://ieeexplore.ieee.org/document/9304259/
Narayanan, H., Behle, L., Luna, M. F., Sokolov, M., Guillén‐Gosálbez, G.,
Morbidelli, M., & Butté, A. (2020a). Hybrid‐EKF: Hybrid model
coupled with extended Kalman filter for real‐time monitoring and
control of mammalian cell culture. Biotechnology and Bioengineering,
117, 2703–2714. https://doi.org/10.1002/bit.27437
Narayanan, H., Luna, M. F., Stosch, M., Cruz Bournazou, M. N., Polotti, G.,
Morbidelli, M., Butté, A., & Sokolov, M. (2020b). Bioprocessing in the
digital age: The role of process models. Biotechnology Journal, 15,
1900172. https://doi.org/10.1002/biot.201900172
Narayanan, H., Sokolov, M., Morbidelli, M., & Butté, A. (2019). A new
generation of predictive models: The added value of hybrid models
for manufacturing processes of therapeutic proteins. Biotechnology
and Bioengineering, 116, 2540–2549. https://doi.org/10.1002/bit.
27097
Narayanan, H., von Stosch, M., Feidl, F., Sokolov, M., Morbidelli, M., &
Butté, A. (2023). Hybrid modeling for biopharmaceutical processes:
Advantages, opportunities, and implementation. Frontiers in Chemical
Engineering, 5, 1157889. https://doi.org/10.3389/fceng.2023.
1157889/full
Nayak, J., Pal, M., & Pal, P. (2015). Modeling and simulation of direct
production of acetic acid from cheese whey in a multi‐stage
membrane‐integrated bioreactor. Biochemical Engineering Journal,
93, 179–195. https://linkinghub.elsevier.com/retrieve/pii/
S1369703X14002861
Noll, P., & Henkel, M. (2020). History and evolution of modeling in
biotechnology: Modeling & simulation, application and hardware
performance. Computational and Structural Biotechnology Journal, 18,
3309–3323. https://linkinghub.elsevier.com/retrieve/pii/
S2001037020304402
O'Brien, C. M., Zhang, Q., Daoutidis, P., & Hu, W.‐S. (2021). A hybrid
mechanistic‐empirical model for in silico mammalian cell bioprocess
simulation. Metabolic Engineering, 66, 31–40. https://linkinghub.
elsevier.com/retrieve/pii/S1096717621000525
Oliveira, R. (2004). Combining first principles modelling and artificial
neural networks: A general framework. Computers & Chemical
Engineering, 28, 755–766. https://linkinghub.elsevier.com/retrieve/
pii/S0098135404000432
Patnaik, P. R. (2006). Synthesizing cellular intelligence and artificial
intelligence for bioprocesses. Biotechnology Advances, 24,
1 2 9 – 1 3 3 . h t t p s : / / l i n k i n g h u b . e l s e v i er . c o m / r e t r i e v e / p i i /
S0734975005001011
Pinto, J., de Azevedo, C. R., Oliveira, R., & von Stosch, M. (2019). A
bootstrap‐aggregated hybrid semi‐parametric modeling framework
for bioprocess development. Bioprocess and Biosystems Engineering,
42, 1853–1865. https://doi.org/10.1007/s00449-019-02181-y
Pinto, J., Mestre, M., Ramos, J., Costa, R. S., Striedner, G., & Oliveira, R.
(2022). A general deep hybrid model for bioreactor systems:
Combining first principles with deep neural networks. Computers &
Chemical Engineering, 165, 107952. https://linkinghub.elsevier.com/
retrieve/pii/S0098135422002897
MAHANTY
Raghavendra. N, S., & Deka, P. C. (2014). Support vector machine
applications in the field of hydrology: A review. Applied Soft
Computing, 19, 372–386. https://linkinghub.elsevier.com/retrieve/
pii/S1568494614000611
Rajamanickam, V., Babel, H., Montano‐Herrera, L., Ehsani, A., Stiefel, F.,
Haider, S., Presser, B., & Knapp, B. (2021). About model validation in
bioprocessing. Processes, 9, 961. https://www.mdpi.com/2227-
9717/9/6/961
Rathinavelu, S., Pavan, S. S., & Sivaprakasam, S. (2023). Hybrid model‐
based framework for soft sensing and forecasting key process
variables in the production of hyaluronic acid by Streptococcus
zooepidemicus. Biotechnology and Bioprocess Engineering, 28,
203–214.
Rathore, A. S., Mishra, S., Nikita, S., & Priyanka, P. (2021). Bioprocess
control: Current progress and future perspectives. Life, 11, 557.
https://www.mdpi.com/2075-1729/11/6/557
del Rio‐Chanona, E. A., Ahmed, N. rashid, Zhang, D., Lu, Y., & Jing, K.
(2017b). Kinetic modeling and process analysis for Desmodesmus sp.
lutein photo‐production. AIChE Journal, 63, 2546–2554. https://doi.
org/10.1002/aic.15667
del Rio‐Chanona, E. A., Fiorelli, F., Zhang, D., Ahmed, N. R., Jing, K., &
Shah, N. (2017a). An efficient model construction strategy to
simulate microalgal lutein photo‐production dynamic process.
Biotechnology and Bioengineering, 114, 2518–2527. https://doi.org/
10.1002/bit.26373
Rogers, A. W., Song, Z., Ramon, F. V., Jing, K., & Zhang, D. (2023).
Investigating ‘greyness’ of hybrid model for bioprocess predictive
modelling. Biochemical Engineering Journal, 190, 108761. https://
linkinghub.elsevier.com/retrieve/pii/S1369703X22004302
Sansana, J., Joswiak, M. N., Castillo, I., Wang, Z., Rendall, R., Chiang, L. H.,
& Reis, M. S. (2021). Recent trends on hybrid modeling for Industry
4.0. Computers & Chemical Engineering, 151, 107365. https://
linkinghub.elsevier.com/retrieve/pii/S0098135421001435
Schmidhuber, J. (2015). Deep learning in neural networks: An overview.
Neural Networks, 61, 85–117. https://linkinghub.elsevier.com/
retrieve/pii/S0893608014002135
Schwedersky, B. B., Flesch, R. C. C., & Dangui, H. A. S. (2019). Practical
nonlinear model predictive control algorithm for long short‐term
memory networks. IFAC‐PapersOnLine, 52, 468–473. https://
linkinghub.elsevier.com/retrieve/pii/S2405896319301922
Shah, P., Sheriff, M. Z., Bangi, M. S. F., Kravaris, C., Kwon, J. S., Botre, C., &
Hirota, J. (2023). Multi‐rate observer design and optimal control to
maximize productivity of an industry‐scale fermentation process.
AIChE Journal, 69(2):e17946. https://doi.org/10.1002/aic.17946
Shah, P., Sheriff, M. Z., Bangi, M. S. F., Kravaris, C., Kwon, J. S.‐I., Botre, C.,
& Hirota, J. (2022). Deep neural network‐based hybrid modeling and
experimental validation for an industry‐scale fermentation process:
Identification of time‐varying dependencies among parameters.
Chemical Engineering Journal, 441, 135643. https://linkinghub.
elsevier.com/retrieve/pii/S1385894722011433
Simutis, R., & Lübbert, A. (2017). Hybrid approach to state estimation for
bioprocess control. Bioengineering, 4, 21. http://www.mdpi.com/
2306-5354/4/1/21
Sitapure, N., & Kwon, J. S. (2023a). CrystalGPT: Enhancing system‐to‐
system transferability in crystallization prediction and control using
time‐series‐transformers. Computers & Chemical Engineering.
Advance online publication. http://arxiv.org/abs/2306.03099
Sitapure, N., & Kwon, J. S.‐I. (2023b). Exploring the potential of time‐
series transformers for process modeling and control in chemical
systems: An inevitable paradigm shift? Chemical Engineering Research
and Design, 194, 461–477. https://linkinghub.elsevier.com/retrieve/
pii/S026387622300240X
Sokolov, M., Ritscher, J., MacKinnon, N., Souquet, J., Broly, H.,
Morbidelli, M., & Butté, A. (2017). Enhanced process understanding
and multivariate prediction of the relationship between cell culture
| 19
process and monoclonal antibody quality. Biotechnology Progress, 33,
1368–1380. https://doi.org/10.1002/btpr.2502
Sokolov, M., von Stosch, M., Narayanan, H., Feidl, F., & Butté, A. (2021).
Hybrid modeling — A key enabler towards realizing digital twins in
biopharma? Current Opinion in Chemical Engineering, 34, 100715.
https://linkinghub.elsevier.com/retrieve/pii/S2211339821000472
Solle, D., Hitzmann, B., Herwig, C., Pereira Remelhe, M., Ulonska, S.,
Wuerth, L., Prata, A., & Steckenreiter, T. (2017). Between the poles
of data‐driven and mechanistic modeling for process operation.
Chemie Ingenieur Technik, 89, 542–561. https://doi.org/10.1002/
cite.201600175
Sommeregger, W., Sissolak, B., Kandra, K., von Stosch, M., Mayer, M., &
Striedner, G. (2017). Quality by control: Towards model predictive
control of mammalian cell culture bioprocesses. Biotechnology
Journal, 12, 1600546. https://doi.org/10.1002/biot.201600546
von Stosch, M., Hamelink, J.‐M., & Oliveira, R. (2016a). Hybrid modeling as
a QbD/PAT tool in process development: an industrial E. coli case
study. Bioprocess and Biosystems Engineering, 39, 773–784. https://
doi.org/10.1007/s00449-016-1557-1
von Stosch, M., Hamelink, J.‐M., & Oliveira, R. (2016b). Toward
intensifying design of experiments in upstream bioprocess develop-
ment: An industrial Escherichia coli feasibility study. Biotechnology
Progress, 32, 1343–1352. https://doi.org/10.1002/btpr.2295
von Stosch, M., Oliveira, R., Peres, J., & Feyo de Azevedo, S. (2014).
Hybrid semi‐parametric modeling in process systems engineering:
Past, present and future. Computers & Chemical Engineering, 60,
86–101. https://linkinghub.elsevier.com/retrieve/pii/
S0098135413002639
von Stosch, M., Oliveria, R., Peres, J., & de Azevedo, S. F. (2012). Hybrid
modeling framework for process analytical technology: Application
to Bordetella pertussis cultures. Biotechnology Progress, 28, 284–291.
https://doi.org/10.1002/btpr.706
von Stosch, M., Portela, R. M. C., & Oliveira, R. (2018). Hybrid model
structures for knowledge integration. In J. Glassey, M. Stosch, & Von
(Eds.), Hybrid Modeling in Process Industries (1st ed., pp. 13–35). CRC,
Taylor & Francis.
von Stosch, M., & Willis, M. J. (2017). Intensified design of experiments for
upstream bioreactors. Engineering in Life Sciences, 17, 1173–1184.
https://doi.org/10.1002/elsc.201600037
Tholudur, A., Ramirez, W. F., & McMillan, J. D. (1999). Mathematical
modeling and optimization of cellulase protein production using
Trichoderma reesei RL‐P37. Biotechnology and Bioengineering, 66,
1–16. https://doi.org/10.1002/(SICI)1097-0290(1999)66:1%
3C1::AID-BIT1%3E3.0.CO;2-K
Tsipa, A., Koutinas, M., Usaku, C., & Mantalaris, A. (2018). Optimal
bioprocess design through a gene regulatory network – growth
kinetic hybrid model: Towards replacing Monod kinetics. Metabolic
Engineering, 48, 129–137. https://linkinghub.elsevier.com/retrieve/
pii/S1096717617304718
Tsopanoglou, A., & Jiménez del Val, I. (2021). Moving towards an era of
hybrid modelling: Advantages and challenges of coupling mechanis-
tic and data‐driven models for upstream pharmaceutical biopro-
cesses. Current Opinion in Chemical Engineering, 32, 100691. https://
linkinghub.elsevier.com/retrieve/pii/S221133982100023X
Vega‐Ramon, F., Zhu, X., Savage, T. R., Petsagkourakis, P., Jing, K., &
Zhang, D. (2021). Kinetic and hybrid modeling for yeast astaxanthin
production under uncertainty. Biotechnology and Bioengineering, 118,
4854–4866. https://doi.org/10.1002/bit.27950
Walsh, I., Myint, M., Nguyen‐Khuong, T., Ho, Y. S., Ng, S. K., &
Lakshmanan, M. (2022). Harnessing the potential of machine
learning for advancing “quality by design” in biomanufacturing.
mAbs, 14(1):e2013593. https://doi.org/10.1080/19420862.2021.
2013593
Wang, X., Chen, J., Liu, C., & Pan, F. (2010). Hybrid modeling of penicillin
fermentation process based on least square support vector machine.
20 | MAHANTY
Chemical Engineering Research and Design, 88, 415–420. https://
linkinghub.elsevier.com/retrieve/pii/S0263876209002160
Wang, Z., Sheikh, H., Lee, K., & Georgakis, C. (2018). Sequential parameter
estimation for mammalian cell model based on in silico design of
experiments. Processes, 6, 100. http://www.mdpi.com/2227-9717/
6/8/100
Yang, A., Martin, E., & Morris, J. (2011). Identification of semi‐parametric
hybrid process models. Computers & Chemical Engineering, 35,
63–70. https://linkinghub.elsevier.com/retrieve/pii/
S0098135410001626
Yang, Q., Gao, H., Zhang, W., & Li, H. (2016). Simultaneous hybrid
modeling of a nosiheptide fermentation process using particle
swarm optimization. Chinese Journal of Chemical Engineering, 24,
1631–1639. https://linkinghub.elsevier.com/retrieve/pii/
S1004954116304128
Zhang, D., Del Rio‐Chanona, E. A., Petsagkourakis, P., & Wagner, J. (2019).
Hybrid physics‐based and data‐driven modeling for bioprocess
online simulation and optimization. Biotechnology and
Bioengineering, 116, 2919–2930. https://doi.org/10.1002/bit.27120
Zhang, D., Savage, T. R., & Cho, B. A. (2020). Combining model structure
identification and hybrid modelling for photo‐production process
predictive simulation and optimisation. Biotechnology and
Bioengineering, 117, 3356–3367. https://doi.org/10.1002/bit.27512
Zhang, D., Xiao, N., Mahbubani, K. T., del Rio‐Chanona, E. A.,
Slater, N. K. H., & Vassiliadis, V. S. (2015). Bioprocess modelling of
biohydrogen production by Rhodopseudomonas palustris: Model
development and effects of operating conditions on hydrogen yield
and glycerol conversion efficiency. Chemical Engineering Science,
130, 68–78. https://linkinghub.elsevier.com/retrieve/pii/
S0009250915001815
Zhang, L., & Mao, S. (2017). Application of quality by design in the current
drug development. Asian Journal of Pharmaceutical Sciences, 12, 1–8.
https://linkinghub.elsevier.com/retrieve/pii/S1818087616300575
Zhao, M., Zhao, S., & Liu, F. (2023). Semi−supervised hybrid modeling of
the yeast fermentation process. Machines, 11, 63. https://www.
mdpi.com/2075-1702/11/1/63
Zorzetto, L. F. M., Filho, R. M., & Wolf‐Maciel, M. R. (2000). Processing
modelling development through artificial neural networks and hybrid
models. Computers & Chemical Engineering, 24, 1355–1360. https://
linkinghub.elsevier.com/retrieve/pii/S0098135400004191
Zuo K., Wu W. T. 2000. Semi‐realtime optimization and control of a fed‐
batch fermentation system. Computers & Chemical Engineering 24:
1105–1109. https://linkinghub.elsevier.com/retrieve/pii/
S0098135400004907
SUPP ORTING INFO RM ATION
Additional supporting information can be found online in the
Supporting Information section at the end of this article.
How to cite this article: Mahanty, B. (2023). Hybrid modelling
in bioprocess dynamics: Structural variabilities,
implementation strategies, and practical challenges.
Biotechnology and Bioengineering, 1–20.
https://doi.org/10.1002/bit.28503