Concept
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Role of Artificial Intelligence and Machine Learning
in Nanosafety
David A. Winkler
Robotics and automation provide potentially paradigm shifting improvements
in the way materials are synthesized and characterized, generating large,
complex data sets that are ideal for modeling and analysis by modern
machine learning (ML) methods. Nanomaterials have not yet fully captured
the benefits of automation, so lag behind in the application of ML methods
of data analysis. Here, some key developments in, and roadblocks to the
application of ML methods are reviewed to model and predict potentially
adverse biological and environmental effects of nanomaterials. This work
focuses on the diverse ways a range of ML algorithms are applied to
understand and predict nanomaterials properties, provides examples of the
application of traditional ML and deep learning methods to nanosafety, and
provides context and future perspectives on developments that are likely to
occur, or need to occur in the near future that allow artificial intelligence to
make a deeper contribution to nanosafety.
1. Introduction
Most areas of science and technology have been impacted
greatly by developments in automation, robotics, data science,
and modeling over the past decade, or soon will be. Automa-
tion and robotics have made it possible to synthesize and char-
acterize materials much faster than traditional one-at-a-time
Prof. D. A. Winkler
La Trobe Institute for Molecular Science
La Trobe University
Kingsbury Drive, Bundoora 3042, Australia
E-mail: d.winkler@latrobe.edu.au
Prof. D. A. Winkler
CSIRO Data61
1 Technology Court
Pullenvale 4069, Australia
Prof. D. A. Winkler
School of Pharmacy
University of Nottingham
Nottingham NG7 2QL, UK
Prof. D. A. Winkler
Monash Institute of Pharmaceutical Sciences
Monash University
392 Royal Parade, Parkville 3052, Australia
The ORCID identification number(s) for the author(s) of this article
can be found under https://doi.org/10.1002/smll.202001883.
© 2020 The Authors. Published by WILEY-VCH Verlag GmbH & Co. KGaA,
Weinheim. This is an open access article under the terms of the Creative
Commons Attribution License, which permits use, distribution and re-
production in any medium, provided the original work is properly cited.
DOI: 10.1002/smll.202001883
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experiments and are also the driver of
the spectacular growth in omics tech-
nologies (including materiomics). These
developments have not only seen massive
growth in the number of materials that can
be synthesized and studied but also in the
complexity of the information collected, for
example, from high content imaging and
various omics technologies. This has led to
an exponential increase in data being accu-
mulated, the formation of “data lakes,” and
urgent need for computational methods for
processing and extracting useful scientific
meaning from often highly multidimen-
sional data sets generated for large libraries
of diverse materials. Data driven modeling
techniques based on machine learning
(ML) have concurrently risen in impor-
tance, sophistication and utility, driven
largely by the availability of these massive
data sets.[1] Larger training data sets usually result in models with
high prediction accuracies and large domains of applicability.
These exciting developments of course impact on nanotech-
nologies and nanomaterials. Surprisingly, high throughput
synthesis and characterization of nanomaterials have been less
widely adopted than in other areas of materials science, and ML
methods to interpret nanomaterials data sets have consequently
not been adopted strongly. Undoubtedly these enabling technol-
ogies will be applied more broadly in the next few years, lever-
aging the high throughput synthesis and characterization and
ML modeling methods developed for bulk materials (Figure 1).[2]
This Concept report provides a limited review of develop-
ments in ML that have been adopted by scientists interested in
developing safer nanomaterials, or that are particularly useful
and should be adopted by researchers in this field in the near
future. Our aim is to provide some contextual background on
the application of ML to nanosafety and to explore current
roadblocks, possible solutions, and to introduce artificial intelli-
gence (AI) methods not yet widely used that allow exploration of
larger regions of nanomaterials physicochemical, provenance,
and biological response spaces. There are recent reviews dis-
cussing the application of ML to nanosafety to which we refer
readers interested in more in-depth summaries of that field.[4]
For example, the comprehensive review by Furxhi et  al.[4c]
concluded that the use of nonlinear modeling was gaining pop-
ularity, although linear regression is commonly used. There is a
clear shift away from models trained on theoretical descriptors
toward those trained on more physicochemically interpretable
nanospecific features, but little consensus on data preproc-
essing techniques and general lack of justification in choice of
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Figure 1.  The scope of machine learning methods to progress “safe-by-design” nanotechnology. Reproduced with permission.[3] Copyright 2019,
American Chemical Society.
modeling algorithm and model validation method, although in
quantitative structure–activity relationships (QSARs) generally
such validation methods have converged.[5] Lamon et al.[4a] pro-
pose model reporting templates for systematic and transparent
specification of models used to support regulatory risk assess-
ments of engineered nanomaterials. The templates included
a QSAR model reporting format and a model reporting tem-
plate for PBK and environmental exposure models for nano-
materials. They demonstrated the utility of these templates for
reporting diverse models and for generating an overview of
the computational model landscape for nanomaterials that is
a useful aid for risk assessment. They also identified a lack of
analytical techniques hinders model validation, application, and
acceptance in risk assessment. A recent EU report[4b] reviewed
the state of the art of computational methods for predicting
the properties of engineered nanomaterials and assessed their
applicability in order to provide guidance in REACH regulation.
The review focused on the use of QSAR methods for modeling
and predicting nanomaterials properties and on a range of
compartment-based mathematical models for toxicokinetic, tox-
icodynamic, in vitro and in vivo dosimetry, and environmental
fate models. While this paper was being reviewed, Shatkin pub-
lished another brief perspective on the future of nanosafety.[6]
She identified that interdisciplinary collaborations as one clear
key benefit of international investments in nanosafety. She
described the current pressing issues: evaluating health/and
environmental risks across the product life cycle; a need for
future safety evaluation of more advanced (e.g., active rather
than passive) materials; development of reliable and relevant
new methods for evaluating safety with reduced mammalian
testing. She advocated development of faster and more efficient
screening methods to advance concepts of safety by design.
Here, we do not address developments in partial or full auto-
mation that are relevant to nanotechnology as these have been
reviewed recently elsewhere (e.g., Jensen et al.,[7] Li et al.,[2] Chan
et al.[8]) and by other authors in this special issue of Small. These
technologies aim to automate experimental aspects of nanoscience
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and, ultimately, to generate autonomous experimental systems.
Automated or semi-automated synthesis of inorganic nanomate-
rials has been achieved heterogeneously on substrates via pulsed
laser deposition,[9] electrodeposition,[10] chemical vapor deposi-
tion,[11] and biomolecular templating.[12] Solution-phase syntheses
of colloidal nanomaterials have also been automated using flow
chemistry.[13] We also have not addressed the use of automation,
informatics, or ML modeling for nanomaterials developed for
medicine, where they are deliberately introduced into the body
for diagnostic or therapeutic purposes, or the very active research
area of text mining of nanomaterials data.[14] Our focus is on the
use of ML to model nanomaterials datasets relevant to their pos-
sible adverse biological or ecological impacts, the use of these
data to progress the “safe-by-design” paradigm,[15] and their use
by regulators of nanomaterials.[16]
2. AI and Machine Learning Methods
and Why They Are Important
Modeling of biological properties of nanomaterials (indeed any
materials) involves several unit operations. Materials are syn-
thesized and tested in relevant biological assays to generate a
data set for training ML models. The physicochemical proper-
ties of nanomaterials must be encoded as mathematical entities
called descriptors, suitable relevant features selected from the
pool of descriptors, and ML methods used to generate a predic-
tive model of the desired property. The models must be vali-
dated by prediction of an independent set of materials not used
to build the models, or by cross-validation methods that involve
withholding one or more materials from the model, with the
withheld material being predicted by the model derived from
the remaining materials (Figure 2).
Here we distinguish between AI and ML in the following way.
AI is the superset of tasks that demonstrate characteristics of
human intelligence, while ML is a subset of AI, which accesses
data, analyzes trends, and generates intelligent, actionable
© 2020 The Authors. Published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
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Figure 2.  The process of developing a nanomaterials neural network-based ML model. Reproduced with permission.[17] Copyright 2013, Elsevier.
insights. The excitement about ML methods is their generality
and platform technology functionality. In the past, when soft-
ware was required to perform a particular function, each step
required to calculate the outcome needed to explicitly and pre-
cisely encoded into the program. Machine learning methods
removed this restriction as the same algorithm and software
code can be applied to a wide variety of modeling applica-
tions, encompassing a vast array of materials and endpoints.
ML algorithms learn patterns in data in a similar way to that
in which humans learn, by repetition and example. However,
ML methods are vastly quicker and can handle much higher
dimensional data than human researchers can.
A comprehensive description of the different types of
machine learning and neural network methods is beyond the
scope of this Concept report. Recent reviews provide this infor-
mation for interested readers, e.g.,[18] and only a brief summary
is provided here.
2.1. Traditional Machine Learning Methods
Traditional ML methods include linear and nonlinear regres-
sion, artificial neural networks, various types of decision
trees,[19] Bayesian networks,[20] support and relevance vector
machines,[21] and genetic algorithms.[22] They have been used to
generate the majority of useful models of the biological prop-
erties of nanomaterials in the literature, selected examples of
which are discussed below. These methods have been exten-
sively used and are widely known so are not described again
here. The abovementioned recent reviews and references cited
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for each ML method listed above provide in depth description
of these ML methods.
Almost all of the published computational models map-
ping nanomaterials properties to biological endpoints have
used simple statistical methods like regression, and conven-
tional ML methods, principally neural networks with simple
architectures.[23] Given the increased awareness of neural net-
works in science and technology generally, the use of ANNs in
nanosafety and other areas such as drug discovery, is under-
going a renaissance.[24]
2.2. Deep Learning Methods
Deep learning methods consist of neural networks with a larger
number of hidden layers and complex architectures. They have
revolutionized some fields of science and technology by their
ability the recognize features in images, in speech recognition,
and complex decision making.[18c] An important advantage that
the newer deep learning methods have over earlier “shallow”
methods is not their ability to generate superior models, but
their ability to automatically generate useful descriptors without
the need for expert input to the modeling process (Figure  3).
Indeed, the universal approximation theorem states that both
deep and shallow neural networks, for example, will generate
models of similar quality given the same training data, shown
to be the case in several published studies.[25] Three of the most
commonly used deep learning algorithms are convolutional
neural networks (CNNs), autoencoders, and generative adver-
sarial networks (GANs).
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Figure 3.  Conventional “shallow” ML methods require a skilled researcher to define relevant descriptors for the materials (top) while deep learning
methods automatically generate complex features from simple representations of materials and use these to generate quantitative models of endpoints
(bottom). Reproduced with permission.[26] Copyright 2019, Royal Society of Chemistry.
CNNs are supervised ML methods that are particularly
useful in identify image features resulting from spatial corre-
lations. These ANNs learn primarily local correlations within
the data, and models are invariant to small translations.[3]
Cascading deep neural networks (DNNs) consist of two net-
works, one that maps each material to an outcome and one that
maps the outcome to one or more material. This architecture is
also known as an autoencoder, also used to reduce the dimen-
sionality of datasets and to predict materials that have a specific
property based on the trained ML model. This inverse mapping
(materials design) problem has also been tackled by GANs, an
unsupervised learning method. GAN consists of a generator
that generates trial structure–property models and a discrimi-
nator that evaluates the quality of trial models by comparing
it to existing unlabeled data. GANs were initially developed
as a way to designed structures without input from an expert
scientist. Another approach, active learning, uses ML to select
experiments that most efficiently achieve a goal. This approach
is similar to directed evolution, where candidate structures are
selected, modified, and tested in sequential generations.[3]
3. Computational Nanosafety Roadblocks,
Milestones, and Context
The first comprehensive list of milestones was developed by the
participants of the COST (European Cooperation in Science and
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Technology)-sponsored exploratory workshop on Quantitative
Nanostructure Toxicity Relationships held at Vaeshartelt Castle,
Maastricht in 2011.[17] The milestones needed to be met for 2-,
5-, and 10-year timeframes to progress the use of ML methods
in nanosafety research and for the design of effective but safe
nanomaterials for commercial applications. This was driven by
concern that many nanomaterials were being incorporated into
products currently on the market and complete safety data were
not available for many of them. The two-year timeframe listed
the establishment of well characterized materials for experi-
ments, development of specific nanoparticle descriptors, and
development of high throughput in vitro assays for toxicologi-
cally relevant endpoints. In vivo studies in laboratory animals
that are inconsistently predictive of human biology and patho-
physiology and are increasingly difficult because of animal eth-
ical concerns. The use of in vitro assays that correlate with in
vivo outcomes are required to provide reliable information of
immediate use by regulators and allow construction of in vivo
ML models. For example, the US National Institutes of Health
and Environmental Protection Agency developed a suite of
cell-based assays to profile the toxicity of chemical compounds
in a variety of cell types. A similar approach, coupled with
ML modeling methods, could yield useful in vivo predictions
for nanomaterials. The ambitious two-year milestones also
included development of high throughput methods for meas-
uring the interactions of commercially relevant nanoparticles
with plasma proteins (so that the protein corona can be better
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understood and predicted), and better methods for tracking
nanoparticles in the body. It was also important to develop
mechanisms for information sharing and close collaboration
between experimentalists and computational scientists, with
input from regulators and industry. Tools for data storage and
sharing, toxicity mark-up languages and informatics tools (like
ToxML, a toxicology database language; DSSTox, a distributed
toxicity database network; and ACToR, an online warehouse of
all publicly available chemical toxicity data), and development
of ontologies (formal representations of knowledge as a set of
concepts, and the relationships between those concepts) for
nanomaterials)[27] needed to be developed.
The five-year timeframe specified a significant increase in
the volume of in vivo data on the effects of nanoparticles, devel-
opment of data storage and sharing methods, development of
reliable in vitro models of in vivo endpoints , generation of the
first models of nanoparticle corona in different environments,
elucidation of mechanisms of entry of nanoparticles into cells
and toxicity such as free-radical production, genotoxicity, and
apoptosis.
The ten-year plan specified milestones that should have been
completed by 2020: creation of ML models of in vitro and in
vivo effects of nanoparticles sufficiently reliable for regula-
tory purposes; development of models that can reliably predict
nanoparticle corona in diverse environments, and development
of nanomaterials classification fingerprints (physicochemical,
genomic, and/or biological profiles of nanomaterials that group
materials with similar in vivo effects) that allow regulators to
classify nanomaterials into hazard classes in a similar way to
that currently adopted for industrial chemicals.
Achieving these milestones in this roadmap required the
maintenance of a network of experimental and computational
researchers, regulators, and policymakers. This was done
through a series of EU Projects and Actions (e.g., MODENA,
MARINA, NANOSOLUTIONS) and more recently by the
funding of at least three EU Horizon 2020 projects, Nano-
SolveIT (https://nanosolveit.eu/),[28] SABYDOMA (https://
www.bnn.at/projects/sabydoma), and NanoCommons (https://
www.nanocommons.eu/). The milestones also assumed that
high throughput experimentation methods for synthesis and
characterization of nanomaterials would arise to provide data
to train ML models, Achieving this ambitious set of milestones
would provide the tools for the development of nanomaterials
that were both functional and safe using rational “safe-by-
design” principles.
4. Unresolved Roadblocks Impeding the Progress
of ML in Nanosafety
In the ensuing seven years these ambitious milestones have
only partially been achieved, largely because the automated
nanomaterials synthesis and characterization methods have not
been adopted as quickly as expected, limiting the availability
of data for training models. High throughput nanomaterials
synthesis and characterization methods are now being adopted
more widely to address this deficiency. Additionally, the par-
ticipants of the Maastricht conference could not have foreseen
the spectacular developments in ML such as deep learning and
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image processing neural networks that have appeared over
the past 5 years in particular. A new set of nanoinformatics
milestones for 2030 has recently been defined,[29] essentially
echoing, extending, and elaborating the important milestones
identified previously. The Nanoinformatics Roadmap 2030, to
which the author was a contributor, summarizes the state-of-
the-art in diverse research areas relevant to NM risk assessment
and governance. The new Roadmap identified additional sig-
nificant challenges: limited access to data; the need to validate
computational models in a way that is acceptable to regulatory
agencies; a need to connect and harmonize data sets, e.g., by
employing read across and other methods of filling data gaps.
Machine learning methods are critically dependent on suffi-
cient data for training and validation, the generation of relevant
descriptors that represent properties of nanomaterials, context-
dependent selection of the most useful subsets of descriptors,
robust training of models, validation of the predictive power of
models, and use of the models to predict properties of new and
improved materials often not yet synthesized.
One of the most important aspects of this process is
descriptor generation. With good descriptors, almost any ML
algorithm will generate a useful model, whereas descriptors
that are poor representatives of materials will always generate
very poor models.
4.1. Paucity of Data Sets to Train ML Models
As machine learning methods are highly dependent on the
quantity and quality of the data used to train them, the larger
and more diverse the data set used to train the models, the
more reliably they can predict the properties of new mate-
rials not used to train the models. The current focus on high
throughput methods for synthesis and characterization of
nanomaterials and increased use of toxicogenomic data will sig-
nificantly address this deficiency.
Unfortunately, most of the ML studies in the nanomaterial lit-
erature have been trained on small data sets with limited diver-
sity. Models derived from small data sets can more easily be over-
fitted, as the number of descriptors that can be used is limited by
the size of the data set. This limited set of descriptors may not
contain sufficient information on the molecular, physicochem-
ical, and structural characteristics of the nanomaterial to allow
a robust and predictive model to be generated. Models derived
from such small data sets also necessarily have small domains
of applicability so are not very useful for predicting properties
of new nanomaterials more broadly. Nanosafety researchers are
now employing a number of methods to address these issues
of data set size including experimental design and “read-across”
methods. Read-across methods are a nonexperimental method for
filling data gaps based on properties of close analogues or similar
chemical category.[30] Design of experiments is a technique for
designing a minimal number of experiments that covers as much
of parameter space as possible, albeit sparsely. The expectation is
that ML methods can model this activity landscape and provide
accurate interpolation or imputation of data gaps.
Sisochenko et  al. recently reported a multi-nano-read-
across modeling technique that also employed self-organizing
maps.[31] They predicted toxicity of 184 metal oxide and silica
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(30 unique chemical types) nanoparticles from 15 datasets to
bacteria, algae, protozoa, and mammalian cell lines. They com-
bined interspecies correlation analysis with a self-organizing
map to identify the factors underlying toxicity. Nanoparti-
cles were categorized into four classes of action. Using these
classes, they estimated the cytotoxicity for untested nanosized
metal oxides, providing both qualitative and quantitative predic-
tion of effects of nanoparticles on different cells and bacteria,
and revealing different mechanisms of metal oxide nanopar-
ticle toxicity for prokaryotes and eukaryotes. In a related study,
Gajewicz also sought to overcome the paucity of data roadblock
to ML modeling of adverse effects of nanomaterials.[32] She
employed read-across methods in models to backfill data voids.
Similarity of a target nanomaterial to a reference material in
N-dimensional chemical property space can be used to predict
the activity of target nanomaterial based on the activity of its
nearest neighbors.
4.2. Inadequacy of Nanospecific Descriptors to Represent
Nanomaterials
Generation of mathematical entities to represent properties of
nanomaterials in a context dependent way (descriptors or fea-
tures) is critical to creation of robust, predictive ML models
of nanomaterials properties. It has been shown in a number
of studies that descriptors have a much larger impact on the
quality and predictivity of ML models than does the specific
ML algorithm used to build the model.[33] Nanomaterials have
particular issues that make finding useful descriptors more dif-
ficult than for single molecules or bulk materials. Largely these
revolve around the distribution of sizes and shapes adopted
by nanoparticles, their propensity to agglomerate, and their
interaction with biological macromolecules that create a sur-
face coating (corona) that modulates the biological properties
of these materials. Commonly used nanoparticle descriptors
are obtained from the whole particle and include diameter,
surface area, aspect ratio, constitutional properties number of
atoms, number of metal atoms, number of surface atoms, etc.),
energy-related properties such as potential energy of surface
atoms and of metal atoms, descriptors for any surface coat-
ings, zeta potential, aqueous solubility, etc. Earlier published
nano-QSAR studies also employed 1-hot descriptors (indicator
variables) that distinguished between different types of nano-
particle cores, dopants, coatings, etc. Although very simple
and often effective descriptors, they do not provide mecha-
nistic insight, but are useful for finding an optimal combina-
tion of complex nanoparticle attributes.[23a] The state-of-the-art
in nanospecific descriptor generation was reviewed recently by
Wyrzykowska and Jagiello.[34] They described the difficulties
in defining effective descriptors for distributions of nanoma-
terials and in accounting for environmental dynamic changes
to the surface of nanomaterials due to corona formation. Sur-
face modified nanomaterials have traditionally been encoded
using descriptors developed for small organic molecules
(DRAGON and SMILES) but SMILES-based descriptors have
been recently improved (SMILES-based optimal descriptors)
that consider correlations between SMILES attributes. This
concept was extended to include physicochemical properties
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such as molecular weight, charge, elemental composition, etc.
They also discussed the development of periodic table descrip-
tors for metal and metal oxide nanomaterials.[35] These include
electronegativity, charge, valence, ionic radius, etc. Significant
progress in this important area has been reported recently.[36]
They described Sizochenko et  al.’s development of simplex
representation of molecular structure, liquid drop models, and
metal ligand binding descriptors, some of which can be derived
using quantum chemical methods.[37] They also discussed the
utility of descriptors derived from images of nanoparticles,
such as sphericity. Image-based approaches (TEM and struc-
tural representations such as SMILES) are likely to become
increasingly important because of the ease of descriptor gen-
eration using convolutional neural networks. Interpretability,
removal of human bias in descriptor selection and exploiting
deep ML objectivity for descriptor generation were seen to be
increasingly important. For example, very recently Varsou
et  al. described how image-based descriptors can be used to
predict the zeta potential of nanoparticles.[38] They developed
NanoXtract, an automated online tool for the extraction of NM
image descriptors from TEM images of nanoparticles. These
descriptors encode the geometric properties of distributions
of nanoparticles and zeta potential models trained on them
could predict zeta potential with r2 values > 0.9. A very similar
image processing approach to calculate geometric descriptors
was reported by Odziomek et  al.[39] Mac Fhionnlaoich and
Guldin used information entropy to characterize distributions
of nanoparticles, providing a better estimate of the properties
of distributions.[40]
Novel “universal” descriptors for nanoparticles were also
reported by Yan et al. and used to generate ML models of gold
nanoparticle properties using random forest and k-nearest
neighbor (kNN) algorithms.[41] The descriptors were generated
by Delaunay tessellation of the surface of the nanoparticles
(a particular way of joining a set of points to make a triangular
mesh) and summing Pauling electronegativity of atoms in each
tessellation cell to represent the nanostructures (to simulate
the nanomaterial’s surface properties). The efficacy of these
nanodescriptors was verified by modeling six gold nanoparticle
datasets. The properties modeled were both physicochemical
(e.g., logP, zeta potential) and biological (e.g., enzyme binding,
ROS, cellular uptake). A consensus of prediction of the two ML
methods could predict properties of external test sets with r2
values between 0.76 and 0.95.
4.3. In Vitro Models, Model Systems, Translation to In Vivo
Systems
Ultimately, ML models need to predict potential adverse biolog-
ical effects on humans, animals, and the environment. Clearly,
ethical and cost considerations mean that the amount of in vivo
data in higher animals is very limited, thus most in vivo data
relates to fish and other aquatic organisms. Consequently, it
is essential that model systems capable of generating substan-
tial data for training ML models have a relationship to in vivo
effects of nanomaterials.
The use of in vitro data combined with nanomaterials
descriptors has been shown to model in vivo responses better
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than descriptors alone.[17,42] Extending this concept, this sug-
gests that predicted in vitro responses may be used in this way
to better predict in vivo properties.
4.4. Identifying and Modeling the Biologically Relevant Entity
Nanomaterials almost always undergo significant modification
in biological or environmentally relevant fluids such as serum,
plasma, and waterways. Initially, the most abundant macro-
molecules in the fluid (protein, humic substances, etc.) bind
to the material in processes modulated by the surface chem-
istry and shape of the particles. Over time, these macromole-
cules are replaced by less abundant macromolecules that bind
more strongly to the nanomaterial. A hard corona is formed
from these proteins that are very tightly adsorbed on nanopar-
ticles. It is the affinity of the proteins toward the nanoparticles
that determines the hard corona composition. Subsequently,
there is exchange of population of proteins, which constitute
the dynamic structure called a soft corona. Apart from affinity,
the nanoparticle curvature has a significant effect on corona
composition, with larger particles generally binding a more
diverse population of proteins.[43] Thus, the nanomaterial plus
the corona defines the “biologically relevant entity” that inter-
acts with biology. Fortunately, QSAR-based ML models act as
“top down” rather than bottom up approaches. That is, models
of in vivo (or more complex in vitro) systems are still ame-
nable to ML modeling because these universal approximation
methods can encapsulate a large number of complex receptor
interactions, signalling, and downstream processes triggered
by exposure to nanomaterials into a complex nonlinear func-
tion inside the model. The surface chemistry of nanoparticles
determines the composition of the corona, and the corona
determines how the particles interact with cells. Essentially,
ML models can accommodate these transformations of nano-
materials on exposure to biological fluids within the model,
capturing the emergent biological responses due to a large
number of interacting smaller biological processes.[44] Findlay
et  al. tackled this important problem of predicting the protein
corona around silver nanoparticles using an ML approach.[45]
They training a random forest model using biophysicochemical
characteristics of proteins, ENMs, and solution conditions. The
area under the receiver operating characteristic curve was 0.83
indicating strong predictive performance. Their model pro-
vided insight into how the corona is influenced by particle sizes
and surface curvature and coatings, and into mechanisms of
protein enrichment. Very recently, Ban et al. also used machine
learning to predict the corona composition surrounding
nanoparticles.[46]
5. Examples of the Application of AI and ML
to Nanosafety
There have been a number of reviews of the use of ML in
nanotoxicology in the past decade,[4d,17,23e,47] and we provide
some key examples of published research below. These were
chosen to highlight the diversity of ML approaches in modeling
nanomaterials properties across a range of applications. We
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summarize selected literature applications of ML to nanoma-
terials hazard prediction and “safe-by-design” project outcomes
and highlight technologies that are likely to lead to achieving
unmet milestones defined above.
One of the first examples of the use of ML or statistical mod-
eling to predict the adverse properties of nanomaterials was pub-
lished by Puzyn et al.[48] These researchers discovered a simple,
one parameter linear regression model that predicted the cyto-
toxicity of 17 different metal oxide nanoparticles to Escherichia
coli using descriptors derived from quantum chemical calcu-
lations. At a similar time Epa et  al. reported the use of linear
regression and Bayesian regularized neural networks to predict
the biological effects of 51 metal oxide nanoparticles with diverse
metal cores and 109 metal oxide nanoparticles with similar cores
but diverse surface modifiers.[23a] The models could make quan-
titative predictions of the smooth muscle cell apoptosis and
uptake of nanoparticles by human umbilical vein epithelial cells
and pancreatic cancer cells from in vitro assays. These models
could predict apoptosis in an independent test set of nanomate-
rials with a standard error of <3 and uptake in the two cells lines
within a factor of 2. Fourches et al. used support vector machine-
based classification and kNNs-based regression to model the
same data set. The external prediction accuracy of these models
was up to 73% for classification modeling and regression models
had an r2 of 0.72 for predicting the same properties.[49]
Liu et al. subsequently reported classification ML models of
the effect of 44 iron oxide core nanoparticles (used in molecular
imaging) on four cell types (aortic endothelial, vascular smooth
muscle, hepatocyte, and monocyte/macrophage), using four
different biological assays and four concentrations of nanoparti-
cles.[50] They employed self-organizing map-based clustering to
define the classes and a Bayesian classifier, logistic regression,
linear discriminate analysis, and nearest neighbor classifiers
trained on size, spin-lattice, and spin–spin relaxivity, and zeta
potential descriptors. Their two-class models had relatively high
accuracies >78%.
Gernand and Casman reported the application of classifica-
tion and regression trees and random forest methods to pre-
dicting the pulmonary toxicity of 17 types carbon nanotubes.[51]
Descriptors used to train the model related to the types and
dimensions of the nanotubes, the concentration of metallic
impurities in the materials, the exposure time and dose, and
characteristics of the exposed rodents. The pulmonary toxicity
endpoints were the number of polymorphonuclear neutrophils,
number of macrophages, and lactate dehydrogenase and total
protein concentrations. Their models could predict the four
pulmonary endpoints with r2 values between 0.88 and 0.96.
CNT attributes that contributed most to carbon nanotube pul-
monary toxicity were amount and identities of metallic impuri-
ties, nanotube length and diameter, surface area, and aggregate
size. Nanoparticle agglomeration is very important modulator
of the biological effects of nanomaterials. It strongly depends
on the surface charge that stabilizes dispersed nanoparticles,
preventing them cohering. Mikolajczyk et  al. reported ML
models of zeta potential, a measure of surface charge on nano-
materials, for 15 metal oxide nanoparticles characterized by 11
image-based and 17 computed descriptors.[52] They used only
linear regression methods but could predict zeta potentials with
an RMSE error in a test set of 1.25 mV and an r2 value of 0.87.
© 2020 The Authors. Published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
www.advancedsciencenews.com
Papa et  al. reported linear and nonlinear modeling of
the cytotoxicity of TiO2 and ZnO nanoparticles by empirical
descriptors.[53] The nanoparticles were tested at different con-
centrations for their ability to disrupt the lipid membrane
in cells, assessed using lactate dehydrogenase levels. Data
were measured for 42 different nanoparticle sizes and shapes
(24 nanoforms of TiO2 and 18 of ZnO). The models were devel-
oped using multiple linear regression, two types of neural
network, and support vector machines. The models could pre-
dict the LDH levels for nanoparticles in the test set with errors
of between 8% and 17% relative to intreated control cells. They
found the nonlinear ML methods clearly outperformed the
linear regression models.
As mentioned above, machine learning models of nanosafety-
relevant properties of nanomaterials are still severely limited
by the paucity of available toxicity data, due to cost, time, and
ethical issues. To address this paucity, Chen et  al. developed
ML models for classifying the ecotoxicity of nanomaterials.[54]
They used read-across properties derived from multisource
ecotoxicity data to build individual species-specific models and
a single model predicting toxicity for multiple species. They
employed four types of tree algorithms to generate across-
species and species-specific models with significant predictive
power. For LC50 global models the functional tree, C4.5 deci-
sion tree, and random tree models all correctly classified more
than 70% of the samples in training (320 nanomaterials) and
test sets (80 nanomaterials). The functional tree predicted the
toxicity of metallic nanoparticles to Danio rerio with accura-
cies of 93% and 100% on training (76 materials) and test sets
(18 materials), respectively.
Fourches et  al. published a study that reduced to practice
the concepts of “safe-by-design” using ML models of biological
endpoints.[23b] They studied a small library of 83 surface modi-
fied carbon nanotubes with relatively constant dimensions.
They assessed their bovine serum albumin, carbonic anhydrase,
chymotrypsin, and hemoglobin activity together with acute tox-
icity and immune toxicity in vitro assays. Traditional k-nearest
neighbors, random forest, and support vector machine ML
models could predict the properties of an external test set with
accuracies up to 75% and 77% for protein binding and acute
toxicity endpoints, respectively. They discovered chemical sur-
face features that correlated with particular biological activities.
The models were used to virtually screen a library of 240  000
potential surface ligands for carbon nanotubes. Experimental
measurement of nanotubes whose biological properties had
been predicted by ML models showed good agreement.
Systematic modification of physicochemical properties of
nanoparticles, combined with comprehensive biological evalu-
ation and computational analysis, is an important goal for
predictive nanotoxicology and the “safe-by-design” paradigm.
This provides better mechanistic understanding of nano–bio
interactions and facilitates generation of quantitatively predic-
tive and robust models of the properties of nanomaterials that
have useful domains of applicability.[55] Le et al. reported such a
study of 45 ZnO nanoparticles in which the particle size, aspect
ratio, doping type, doping concentration, and surface coating of
the nanoparticles was varied systematically, and the resulting
biological response data modeled using linear regression and
Bayesian regularized neural network ML methods.[56] Biological
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assays for cell viability, membrane integrity, and oxidative stress
were performed that reflected cellular damage by ZnO nano-
particles to human umbilical vein endothelial cells or human
hepatocellular liver carcinoma cells (HepG2). The nonlinear
ML models were superior to the linear models, with predictions
for an external test set of nanoparticles having an r2 value of
0.89 and a standard error of prediction of 12% for cell viability,
r2 of 0.86 and standard error of 80 RFU for LDH level (mem-
brane integrity), and r2 of 0.67 and standard error of 2.4-fold for
the luciferase assay characterizing oxidative stress. Apart from
being one of the first studies where the physicochemical prop-
erties of inorganic nanoparticles were varied systematically, the
study also showed that nonlinear ML methods were capable of
modeling the entire nanoparticle dose–response curve.
While ML methods with computed descriptors usually gen-
erate relatively robust and predictive models of nanoparticle
structure–property relationships, molecular or mechanistic
interpretation of these models is often difficult or impossible.
Oksel et al. described the use of a genetic programming-based
decision tree (GPTree) in modeling nanomaterials properties.[57]
GPTree is a robust, automatic method for generation of accu-
rate nanoSAR models that works with small datasets, automati-
cally selects descriptors, and provides significantly improved
interpretability of models. The generality of the method was
exemplified by the training of accurate nanoSAR models for
four diverse exemplar datasets. The models were quite sparse,
employing only 13 predictors selected from a large pool of
descriptors and exhibited accuracies between 98–100% and
86–100% on training and test data, respectively. The decision
trees provided a clear graphical representation of the decision
thresholds for each descriptor, providing much needed clarity
of interpretation of NP structure–activity models.
Concu et  al. conducted a large study of set of 260 metal,
metal oxide, and silica nanoparticles with 31 chemical composi-
tions from literature sources.[58] They also measured ecotoxicity
and cytotoxicity in algae, bacteria, fungi, crustaceans, plants,
fishes, other species, and mammalian cell lines. These 260 nan-
oparticles were uniformly randomly combined to produce 54371
pairs (≈80% of all possible pairs). For each pair one nanopar-
ticle, along with its data, was used as reference state while the
other was used as a new state. The 54371 pairs were randomly
split into training (40804 pairs, 26131 nontoxic, and 14673 toxic)
and test sets (13567 pairs, 8613 nontoxic, and 4954 toxic). The
models were generated by a linear neural network, radial basis
function, multilayer perceptron, and probabilistic neural net-
work. These models generated prediction accuracies scored by
the area under the receiver operator characteristic (ROC) curve
of 0.999 for the training set and 0.998 and a two-class accu-
racy of 98% for the test set. The model also provided insight
into which descriptors influenced the nanoparticle adverse
biological responses. The authors used Y-scrambling to check
for overfitting of the model, but the unrealistically high ROC
and accuracy values coupled with the large number of neural
network weights, and repeated trials to optimize the network
architecture, suggests chance correlations or other potential
methodological issues with the models.
Wang et al. reported a combinatorial study of gold nanoparticles
of differing sizes, surface modifications, and surface coverage.[59]
They generated a small library of 34 nanoparticles and, using 29
© 2020 The Authors. Published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
www.advancedsciencenews.com
descriptors and the kNN algorithm, developed models for cellular
uptake in human lung and kidney cells, ability to induce oxidative
stress, and hydrophobicity (logP values). Each model employed
11 or fewer descriptors and the model performance was assessed
using tenfold cross-validation. The four models had high cross
validated predictivity, with r2 values of 1.0, 0.99, 0.97, and 0.99,
respectively.
Kovalishyn et al. collected data from 128 literature sources to
assemble a set of 964 data points for inorganic nanomaterials.[60]
They analysed both toxicological/ecotoxicological properties
(EC50, LC50, MIC, and mortality rate) and physicochemical
properties for metal and metal oxide nanoparticles ranging
from 1 to 90  000  nm. They generated models for these four
endpoints across multiple species using kNN, random forest,
and neural network methods. Cross-validation and test sets
were used to assess model predictive power, giving q2 values
between 0.58 and 0.80 for cross-validated regression models
and r2 between 0.49 and 0.78 for test sets. It is not clear how
they encoded the species into the models.
Recently, Hataminia et  al. used a neural network to model
the toxicity of iron oxide nanoparticles to kidney cells.[61] The
model was trained using particle size, concentration, incuba-
tion time, and the surface charge of the nanoparticles to pre-
dict the percent kidney cell viability. Their model appeared to
be highly predictive (no statistics given in graphs but extensive
analysis of the effect of the four input parameters to the model
on kidney cell viability was presented).
Deep learning algorithms are having enormous impact in
many areas of science and technology,[18b,c,62] including mate-
rials science. As stated previously, the main advantage of deep
neural networks is their ability to automatically generate useful
higher order feature for ML models. It is therefore surprising
that they have not yet been widely applied to modeling nanoma-
terials properties relevant to nanosafety, given that the dearth of
nanospecific descriptors is one of the factors limiting progress
in predictive nanotoxicology.
Most applications have employed DNNs image recognition
capabilities to extract useful data from microscopy images of
nanoparticles and cells. For example, Coquelin et  al. reported
the use of CNNs to estimation of particle size distribution on
SEM images of aggregated TiO2 particles.[63] Their aim was
automation of SEM measurements to estimate individual par-
ticle diameters. Aggregated nanoparticles are often partially
or fully omitted from estimates of particle size distribution or
from ML models of biological responses to nanoparticles. They
reported a method called “context encoding” to predict missing
parts of aggregated nanoparticles. Likewise, Horwath et al. used
CNNs to segment TEM images of nanoparticles to more reli-
ably calculate size distributions.[62] Image profiling using open
source CellProfiler and a CNN-based algorithm ilastik,[64] were
employed by Ilet et al. to study nanoparticle distributions.[65]
A particularly impressive use of ML in nanosafety was pub-
lished recently by Lazerovits et  al.[66] They conducted experi-
ments aimed at understanding the adsorption of blood proteins
on nanoparticles immediately after intravenous injection, how
this interface changes during circulation, and how it alters to
distribution of nanoparticles in vivo. They showed that the
evolution of proteins on nanoparticle surfaces predicts the
biological fate of nanoparticles in vivo. They employed protein
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mass spectrometry protein data as inputs, and blood clearance
and organ accumulation as outputs to train a supervised deep
neural network that predicted nanoparticle spleen and liver
accumulation ≥94% accuracy. This showed that the complex
pattern or fingerprint of nanoparticle surface adsorbed pro-
teins modulates liver and spleen uptake. Using these models,
they designed nanoparticles with 50% and 70% lower liver and
spleen uptake, respectively.
6. Perspective
Clearly the remaining roadblocks to the application of ML to
nanosafety need to be removed or reduced. Increased automa-
tion of synthesis and characterization of nanomaterials, and
improved descriptors from deep learning methods should help
resolve some of these roadblocks. By extending the developments
in ML methods in other areas of science and technology to
nanomaterials and identifying where these overlap with current
areas of need, we can postulate areas where ML methods will
generate impact in the short to medium term.
6.1. Multiobjective ML Models and Evolutionary Methods
Most ML models reported in the literature can predict a single
biological property for nanomaterials. Clearly, “safe-by-design”
implies that nanomaterials should meet a number of key
design criteria, some taking advantage of important new and
useful properties shown by nanoscale forms of materials, some
eliminating or at least reducing adverse human and ecological
properties so that the products incorporating nanomaterials
can be manufactured, used, and disposed of safely. Some ML
methods are general, not restricted to a single dependent vari-
able. For example, neural networks can have multiple outputs,
each representing a different property. Although multiobjective
ML models are becoming more widely used in the pharmaceu-
tical field for example, there is only very limited proof-of-con-
cept studies reported for nanomaterials. For example, Ambure
et  al. reported the development of a specific software package,
QSAR-Co, to tackle the modeling of nanomaterials properties
simultaneously.[67]
Evolutionary methods are the usual approach to find the
best balance between multiple requirements for nanomaterials,
e.g., functional performance, lack of toxicity, cost. ML models,
particularly those than can predict more than one property
simultaneously, can be used as surrogate fitness functions in
such evolutionary optimization methods, reducing the need for
experimental evaluation of fitness of materials. Encoding rele-
vant physicochemical, structural, and processing parameters of
nanomaterials as a vector defines essentially their “genome.”[22]
By generating a relatively small number of different nano-
materials, ideally using design of experiments to systemi-
cally explore nano–bio interactions,[55] these materials can
be assessed against one or more utility and safety endpoints
that represent fitness functions in an evolutionary algorithm.
Selecting the nanomaterials that best match the desired proper-
ties and mutating their nanomaterials genome generates a new
population of materials for synthesis and testing. By iterating
© 2020 The Authors. Published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
www.advancedsciencenews.com
around this evolutionary cycle a number of times, new mate-
rials with superior properties can be discovered in a similar
way to how niche species evolve in natural selection. Single
point mutations (changing one element in the genome) usually
explore local regions of nanomaterials space, while crossover
operations (splitting two genomes and combining the pieces
in new ways) allow jumps into new areas of nanomaterials
space.[22] As the evolutionary cycle progresses, it is possible to
use the experimental data on nanomaterials and their proper-
ties to generate ML models as surrogate fitness functions later
in the cycle, reducing the number of experiments required.
Multiple objective fitness functions, e.g., a favorable strength
coupled with low adverse biological effects, can be defined by
a Pareto surface, the curve of solutions of equal fitness but
that involve different tradeoffs between the multiple objectives.
To our knowledge, evolutionary algorithms have not yet been
used to generate new optimal nanomaterials, although there is
ample evidence in other areas of materials science of the value
of this approach.[22]
6.2. Inverse Design
One of the important aims of ML models is the ability to have to
model predict new materials with better properties than those
in the training set, essentially inverting the model to generate
new materials structures. Given the nature of the descriptors
used in these models and the complexity of the response sur-
faces that constitute the nonlinear models, it has been almost
impossible until recently to achieve this highly desirable out-
come. Consequently, the main way models achieve this is by
predicting the properties of a large number of real or virtual
materials in databases. However, care must be taken to ensure
that the materials lie within or close to the domains of applica-
bility of the models (the multidimensional space defined by the
ranges of the descriptor variables and the dependent variable
that is modeled).
Recent advances in machine learning methods have changed
this landscape allowing for the first time, de novo predictions
of new structures that are predicted to have improved proper-
ties. Autoencoders and GANs convert nanomaterials structural,
physicochemical, and processing variables into latent variable/
descriptors that can be used to generate ML models of proper-
ties relevant to nanomaterials utility and safety. The advantage
of these methods is that they allow the latent descriptions to be
“inverted” to generate structures and processing conditions for
new nanomaterials with improved properties. There are so far
no clear examples of the application of this approach to nano-
materials. In related fields, Kim et al. recently reported the use
of GANs in the inverse design of porous materials[68] and So
and Rho used deep convolutional GANs to generate new nano-
photonic structures by inverse design.[69] Gomez-Bombarelli
et  al. showed how a DNN and a recurrent neural network
(RNN) can be used as an encoder and the decoder, respectively,
for inverse design. The DNN models structure–property rela-
tionships between molecule structures and material proper-
ties and encodes the materials into latent molecule descriptors
encoding molecule information. The RNN allows decoding of
the latent molecule information corresponding to improved
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materials to map encoded molecular descriptors into a mate-
rials structure.[70] Given the potentially large advantages of these
inverse design approaches it is likely that the nanoscience com-
munity will adopt these novel learning approaches to reduce to
practice inverse design of “safe-by-design” nanomaterials.
6.3. Autonomous Methods
Inverse design and evolutionary methods make possible a new
paradigm for the design, synthesis, and optimization of mate-
rials that is clearly applicable to nanomaterials. Fully autono-
mous researchers or robot scientists that select and carry out
experiments without a human in the loop are an exciting and
potentially accessible development in chemical and materials,
science.[7,71] Such systems can be achieved in several ways.
Active learning can be combined with automated experimenta-
tion to generate a closed loop system, or ML models of nano-
materials fitness landscapes can be used with evolutionary
algorithms to select the fittest materials and “mutate” them for
input into the next set of optimization experiments.[22] The first
proof of concept in nanoscience was exemplified by a system
for automated growth and characterization of carbon nano-
tubes on the surface of micropillars.[72] An automated experi-
mental system was combined with logistic regression analysis
to autonomously select new experimental conditions to achieve
an experimental goal. This fully autonomous system was able
to generate information and useful materials faster than nonau-
tonomous methods by automating water-assisted CVD growth
experiments, using in situ spectroscopy, that conducted over
100 experiments per day. Regression modeling mapped regions
of selectivity toward single-wall and multiwall carbon nanotube
growth in a complex parameter space.
6.4. Use of Web Cloud Services
Data and model disposition and sharing is being recognized
as essential to improve efficiency and transparency of research
into nanosafety. Making these accessible using the FAIR princi-
ples (Findable, Accessible, Interoperable, and Reusable) that is
a cornerstone of the Open Science.[73] Making data and models
available to all researchers increases the robustness of the sci-
ence, allows reuse of models, and expands the pool of data on
nanoparticles that can be used to train new models. Expanding
the use of automation to accelerate synthesis and testing, the
application of omics technologies to probe the biological effects
of nanomaterials, and collecting, curating, and making widely
accessible the data collected so far are the best ways to over-
come the paucity of data identified earlier in this paper. Most
database activities are now cloud based and this trend will
surely increase. Nanosafety has established a number of initia-
tives that aim to make data and models accessible via cloud ser-
vices. For example, Afantitis et  al. reported the Enalos Cloud
Platform (http://enalos.insilicotox.com/NanoProteinCorona/)
developed under an EU 7th Framework project NanoMILE, that
can be used for regulatory or NP safe-by-design projects.[15d,74]
It allows the virtual screening of NPs, based on a list of the
significant NP descriptors, identifying those NPs that would
© 2020 The Authors. Published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
www.advancedsciencenews.com
warrant further toxicity testing on the basis of predicted NP cel-
lular association. This work is being extended by the develop-
ment of cloud services under a new EU Horizon 2020 project,
NanoSolveIT, in which the author is a member.[28]
6.5. Toxicogenomics
The use of genomic data to predict and understand the mech-
anisms by which nanomaterials generate adverse biological
effects has been growing rapidly over the past decade and now
represents a substantial field of research in its own right. Charac-
teristic gene expression profiles (or fingerprints) of toxicological
responses to exposure to nanoparticles can identify biomarkers
that are predictive of nanomaterials toxicity.[75] Gene expression
profiles provide a rich data set that can be linked to specific path-
ways being modulated by exposure to nanomaterials. Such data
are amenable to analysis by sparse feature selection methods and
machine learning. Fortunately, this large research area has been
comprehensively reviewed by the Greco group in Finland.[76] In
particular they discussed in detail the synergistic combination
of transcriptomic data and machine learning for understanding
and predicting adverse biological effects of nanomaterials for
regulatory purposes and potential SbD applications.[76b] The
question still remains as to how well changes in the geno-
type translate to the observed phenotype. Microarray data have
serious limitations when it comes to showing associations using
biological inference because these data rarely indicate cause and
effect. One of the greatest limitations of microarray data is that
expression of mRNAs does not always translate into proteins
because siRNAs and other mechanisms can block the transla-
tion process.[77] Nonetheless gene expression fingerprints cou-
pled with modern ML methods can provide valuable insight into
the mechanisms of nanoparticle interactions with biology, as has
been found in other areas of science.[78]
7. Conclusions
Machine learning has enormous potential to accelerate the
development and use of safer nanomaterials for industrial
applications. The main issues holding the field back are still the
relative paucity of high-quality data that can be used to train and
validate models, the need for better mathematical descriptors to
encode nanomaterials properties, and ways of incorporating the
heterogeneity and dynamic nature of the “biologically relevant
entity” when nanomaterials transit particular biological envi-
ronments and compartments. Capturing this complexity with
robust mathematical descriptors is of prime importance, as
descriptor quality is the most important element for robust and
predictive ML model generation. Advances in automated syn-
thesis and characterization, high content screening, predictive
modeling of the nanoparticle corona for a given environment,
understanding of how to mathematically encode the biophys-
icochemical surface properties of nanoparticle, and advances in
deep and shallow ML methods on the horizon should remove
these roadblocks and catalyze a rapid expansion in the power
and usefulness of these computational methods in design of
safer nanomaterials.
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Conflict of Interest
The author declares no conflict of interest.
Keywords
adverse biological effects, artificial intelligence, deep learning, machine
learning, nanomaterials, safe-by-design
Received: March 22, 2020
Revised: May 7, 2020
Published online: June 15, 2020
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