=Paper=
{{Paper
|id=Vol-2790/paper09
|storemode=property
|title=
An Information System for Inorganic Substances Physical Properties Prediction Based on Machine Learning Methods
|pdfUrl=https://ceur-ws.org/Vol-2790/paper09.pdf
|volume=Vol-2790
|authors=Victor A. Dudarev,Nadezhda N. Kiselyova,Andrei V. Stolyarenko,Alexander A. Dokukin,Oleg V. Senko,Vladimir V. Ryazanov,Elena A. Vashchenko,Mikhail A. Vitushko,Vyacheslav S. Pereverzev-Orlov
|dblpUrl=https://dblp.org/rec/conf/rcdl/DudarevKSDSRVVP20
}}
==
An Information System for Inorganic Substances Physical Properties Prediction Based on Machine Learning Methods
==
https://ceur-ws.org/Vol-2790/paper09.pdf
An Information System for Inorganic Substances
Physical Properties Prediction Based on Machine
Learning Methods
V.A. Dudarev1,2[0000-0001-7243-9096], N.N. Kiselyova1[0000-0002-3583-0704], A.V. Stolyarenko1,
A.A. Dokukin3, O.V. Senko3, V.V. Ryazanov3, E.A. Vashchenko4, M.A. Vitushko4
and V.S. Pereverzev-Orlov4
1 A.A. Baikov Institute of Metallurgy and Materials Science of RAS (IMET RAS), Moscow,
119334, Russia
2 HSE University, Moscow, 109028, Russia
3 Federal Research Center "Computer Science and Control" of RAS (FRC CSC RAS), Mos-
cow, 119333, Russia
4 A.A. Kharkevich Institute for Information Transmission Problems of RAS (IITP RAS), Mos-
cow, 127051, Russia
kis@imet.ac.ru
Abstract. ParIS (Parameters of Inorganic Substances) system was developed for
predicting inorganic substances physical properties. It is based on the use of ma-
chine learning methods to find the relationships between inorganic substances
parameters and the properties of chemical elements. The main components of the
system are an integrated database system on inorganic substances and materials
properties, a subsystem of machine learning and prediction results analysis, a
knowledge base and a prediction database. The machine learning subsystem in-
cludes programs based on the algorithms developed by the authors of this paper
and the algorithms included in the scikit-learn package. The results of the ParIS
system application are illustrated by an example of predicting chalcospinels crys-
tal lattice parameter. To get prediction results, only the properties of chemical
elements included in the composition of not yet synthesized chalcospinels were
used. Moreover, the prediction accuracy was within ± 0.1 Å.
Keywords: Machine Learning, Databases, Prediction of Inorganic Substances
Physical Properties.
1 Introduction
Machine learning methods are widely used in chemistry. Object classification and qual-
itative (categorical) characteristics prediction tasks are among the most successfully
solved problems. In inorganic chemistry machine learning methods made it possible to
make predictions knowing only the parameters of chemical elements. For example, it’s
possible to predict compound formation of a certain composition and / or with a given
crystal structure type under certain external conditions with an average accuracy of
Copyright © 2020 for this paper by its authors. Use permitted under Creative
Commons License Attribution 4.0 International (CC BY 4.0).
89
more than 80% (according to the results of predictions comparison with new experi-
mental data) [1-3]. However, categorical properties prediction is only a small part of
the practical problems in chemistry. The vast majority of problems are associated with
the quantitative objects characteristics prediction (for example, crystal lattice parame-
ters, melting and boiling points, impact strength, elasticity, electrical conductivity, etc.).
Despite the great importance of such tasks of predicting the quantitative (numerical,
scalar, vector) objects properties, machine learning methods, which in this case are of-
ten connected with regression problems, are used to solve them much less frequently.
In applications to inorganic chemistry, this paradox is associated, in particular, with the
classical regression analysis limitations: multicollinearity problems (and as a result in
poor conditionality of feature description matrices), the approximated dependencies
non-smoothness, the large feature description dimension combined with a small num-
ber of precedents, presence of erroneous outliers in data etc. The above-mentioned
problems are task’s peculiarities in inorganic chemistry. The use of regularization
(ridge regression methods, LASSO, LARS, elastic networks, regularized neural net-
works, etc.), various methods of the most important features selecting, filtering of er-
roneous outliers, in many cases allows to circumvent some of these limitations. How-
ever, the task of developing combined methods that would overcome most of the limi-
tations in solving the problems of reconstructing multivariate regression cannot be con-
sidered as completely solved. One of the common ways to develop such methods is to
consider problem domain (inorganic chemistry) peculiarities. The development of
methods and systems for predicting inorganic substances quantitative parameters based
on machine learning (ML) methods allows to speed up the search, research and intro-
duction of new materials with specified functional properties. We have developed such
an information system for searching for relationships that connect physical and chemi-
cal properties of inorganic compounds with the properties of chemical elements that
form compound. The developed system allows a solution of various tasks in inorganic
chemistry.
2 Selection of Machine Learning Methods for Prediction of
Inorganic Compounds Physical Properties
Let’s define some terms that we use. In this study, an object is a chemical system (in-
organic compound, solid solution, heterogeneous mixture, etc.) formed by components
(chemical elements or simpler inorganic compounds), represented in computer’s
memory as a set of attribute values (component properties) with indication of the value
of a given physical or chemical property. A quantitative property is an object parameter
expressed as a numeric-scaled (scalar, vector) variable.
Let’s consider the various most commonly used methods and their limitations in
solving the problem, specified by the characteristics of inorganic chemistry.
The most widely-spread method for predicting the quantitative properties of objects
is multivariate regression analysis (multiple regression) [4]. It is designed to analyze
90
the relationship between several independent variables (also called regressors or pre-
dictors – in our case, the properties of components) and the dependent variable (com-
pound property). Limitations (taking into account the problem domain peculiarities):
it is assumed that the residuals (the dependent variable calculated values minus ex-
perimental values) are distributed normally, while the independent variables do not
contain errors in values. However, any experimental data are not error-free, and
moreover the normality of corresponding distributions is always a moot point;
the assumption of the absence of property multicollinearity, which leads to poor con-
ditionality of the feature description matrix and the instability of the regression co-
efficients estimates. It should be noted that the chemical compounds properties de-
scription is strongly correlated due to the dependences of chemical elements proper-
ties on their atomic number;
the approximated function smooth character requirement. It must be taken into ac-
count, that the dependences of inorganic compounds properties on chemical ele-
ments parameters often take the “saw” form with different tooth sizes (due to the
Periodic Law).
Support vector regression (SVR) [5, 6] is widely used in chemistry to predict the quan-
titative properties of substances [7]. In its implementation the regression model param-
eters are determined by the quadratic programming problem solution, which has a
unique solution. The problems of using SVR are connected with the lack of recommen-
dations for choosing the kernel function parameters that are most suitable for solving a
specific problem, as well as other effective algorithm parameters (for example, the pen-
alty coefficient). In addition, the algorithm is very sensitive to data outliers while chem-
ical problems, as a rule, contain erroneous and out-of-date experimental values. One of
the ways to solve the last problem is outliers detection and filtering, for example, using
a system developed and used by us in chemistry [8, 9]. The overfitting problem can be
solved by means of regularization.
Artificial neural networks learning can be used both for calculating functions of
qualitative and quantitative parameters. In the latter case (for example, for training net-
works with radial basis functions (RBF) [10] or generalized regression neural network
(GRNN) [11]) for the network stability to measurement errors of input vectors, it’s
required continuity of the conduction functions of edges and functions of neurons acti-
vation, and for the network learning using gradient methods, their differentiability is
required also. Recent requirements limit the opportunity of using these methods in in-
organic chemistry. The overfitting problem can be solved by means of regularization
also. It should be noted that neural networks are weak in properties extrapolation. The
method disadvantages include the lack of modeling transparency, which does not allow
a physical interpretation of the results obtained, the complexity of choosing a network
architecture, high requirements for measurement errors, the complexity of choosing a
learning algorithm, and high resource consumption of neural networks learning process.
It should be noted that all the above methods, as well as many others, are included
in many free distributed and widely used software packages: the scikit-learn package
[12], which contains a number of ML-algorithms based on the Python programming
language, and packages for statistical data processing in R language [13].
91
The creation of combined algorithms is one of the promising modern trends in the
development of methods for predicting quantitative properties. This approach makes it
possible to compensate the shortcomings of some algorithms at the expense of the ad-
vantages of others and is aimed at improving the prediction accuracy of quantitative
parameters, as one of the main criteria for methods effectiveness. Possible approaches
are a combination of classification algorithms, an elastic network, combinations of SVR
and multidimensional regression, etc. The following algorithms and programs that im-
plement this approach are included in the system for predicting inorganic compounds
physical properties.
2.1 Locally Optimal Convex Combinations (LOCC)
The multilevel method and algorithm for constructing a multidimensional regression
model based on convex combinations of predictors has some similarities with deep
learning technology. For example, in [14], when solving the problem of predicting the
halides melting points at the first level, a family of optimal convex combinations of
simple one-dimensional LSM-regressions was generated. To achieve this an approach
was used [15], which makes it possible to generate families of locally optimal convex
combinations (LOCC) of one-dimensional regressions. Selected regressions were con-
sidered as new properties for the initial task. An elastic network was the second level
of the proposed learning method. It was shown that the use of a two-level scheme based
on weighted collective decisions over near-optimal sets of LOCCs allows one to
achieve a higher generalization ability compared to the simple elastic network method.
It is also possible to use arbitrary methods for organizing ensembles from other regres-
sion algorithms, (for example, combinations of “random forest”, LOCC and “elastic
network” or “random forest” and “elastic network”).
2.2 Gluing Classifications for Regression (GCR)
Another approach to creating combined algorithms was proposed based on the method
of gluing classifications for regression (GCR). Unlike the previous approach, the de-
veloped method allows to work with substances descriptions that contain various at-
tributes types (quantitative, qualitative, ordinal and more complex). The developed al-
gorithm introduces the degree of objects relevance to each class in the “linear corrector”
regression model [16, 17]. To obtain the metric of objects relevance to each class during
recognition, algorithms for calculating estimating (ACE) are used.
Two ACE models were considered in which the proximity functions were: (1) the
metric function, (2) the function for arbitrary ordinal features. On an example of solving
the melilite crystal lattice parameters estimation problem using the program, we com-
pared two different methods for determining the proximity function in algorithms for
calculating estimating as linear corrector classifiers. It was shown that the first model
works slightly better than the second one [17].
92
2.3 Soft Voting Clique-Based Solvers
A peculiarity of the most prediction tasks in inorganic chemistry is the small volume of
learning sets in relation to the description space dimension. To solve such problems,
versions of soft voting programs of clique-based solvers modified for use in chemistry
were used [18]. As a basis for research, two variants of cliques were chosen: «Syndrome
Analysis» [19] and «Fragment-Potential» [20], which have a wide range of properties
and capabilities for solving such kind of problems.
The first program was based on the version of the syndrome analysis algorithm
(SAND). The basic idea of the algorithm: for a classified object a search is made in a
learning set in a sense for the closest properties values (one or more) on the basis of
which the predicted value is calculated. Proximity is determined using the aggregate
set of syndromic rules (syndromes), constructed individually for each object of the
learning set on the principle of "one against all the others". The syndrome rule has many
symptoms at input, each of which corresponds to one of the properties.
The second program was based on the version of the voting piecewise-linear rules
algorithm (FRAGMENT). The basic idea of the algorithm, as in the first program, is
for a predicted object in the learning set to search in a sense for the closest values in
properties (one or more) based on which the predicted value is built. Proximity is de-
termined by voting of an aggregate set of small piecewise-linear rules, constructed in-
dividually for each object of the learning set on the principle of "one against all others".
A piecewise-linear rule at the input has many initial features and is a collection of hy-
perplanes dividing objects into two classes in all a priori given pairs of classes. The
results of applying these rules are accumulated in the “voting matrix” of size K * K,
where K is the number of classes in the original data classification. Votes are summa-
rized over the rows and columns of this matrix, allowing us to determine the integrated
measures of similarity and dissimilarity of the tested object with the classes, and their
relations are then used to form the final decisions about the similarity with specific ones
from K classes.
The ParIS (Parameters of Inorganic Substances) system, that we developed for pre-
dicting inorganic substances physical properties, includes the above-mentioned pro-
grams developed by us and the scikit-learn software package [12].
3 System structure for inorganic substances physical properties
prediction
The information base for searching the dependences of inorganic substances parameters
on the properties of components in the ParIS system is the integrated database system
on properties of inorganic substances and materials (DB PISM) that we created [21]
(Fig. 1). It virtually unites seven databases developed in Russia and Japan, and contains
information on tens of thousands of inorganic substances and materials.
The machine learning subsystem includes three components (Fig. 1):
93
a subsystem for searching for dependencies between the substances’ properties and
components parameters (a machine learning subsystem) based on the programs we
developed and the scikit-learn software package;
prediction subsystem using the found dependencies;
a subsystem for estimating prediction accuracy, which allows one to estimate the
mean absolute and mean square errors (with cross-validation), the R2 determination
coefficient, etc., as well as construct a diagram of deviations of the calculated pa-
rameter values from the experimental ones for the substances, information about
which was used for machine learning.
The dependencies obtained during machine learning process are entered into the
knowledge base. They can be used to predict the parameters of substances not yet ob-
tained in certain composition.
The prediction database contains the prediction results for substances not yet syn-
thesized, the composition of which was set by an expert conducting machine learning.
These data are also exported to special tables in “Phases” database on inorganic com-
pounds properties [21]. This allows us to expand the functionality of the DB PISM,
allowing the user to query data not only about already experimentally studied com-
pounds, but also predictions.
The managing subsystem orchestrates the work of the information system and con-
trols access to it from the Internet for specialists.
Figure 1. ParIS system structure for inorganic substances physical properties prediction.
94
The system is designed as an ASP.Net Core 3 Web application in C#. The Web
application itself is developed using microservice architecture and it is an extensible
shell that consolidates several independent calculation modules available through a sin-
gle API followed by end-user interface. Calculation modules are responsible for prob-
lem solving using different mathematical methods.
Each module is implemented as an independent REST API microservice, that uses
common conventions for API methods and custom configuration in JSON document,
that consists of a set of mathematical algorithms parameters, suitable for a particular
module. As a short example, a couple of config.json files containing default parameters
are provided for K Nearest Neighbors and SVM methods (document format is defined
individually for a corresponding module with respect to mathematical method’s param-
eters):
{ {
"int": { "select": {
"k": { "kernel": {
"type": "int", "default": "rbf",
"min": 1, "options": [
"max": 10, "rbf", "linear",
"default": 5, "poly", "sigmoid"
"fullName": "neigh- ]
bors count" }
} },
}, "int": {
"select": { "degree": {
"method": { "default": 3,
"fullName": "K "min": 1,
Neighbors", "max": 10
"type": "select", }
"default": "auto", }
"options": [ }
"auto",
"ball_tree",
"kd_tree", "brute"
]
}
}
}
The modules are minimal and stateless to scale well. Every module implements a
single algorithm: performs calculations on input data specified by the caller and returns
a result.
The architecture allows adding modules easily to extend a set of available methods
and gives a lot of flexibility, allowing us to deploy different ParIS modules on various
hosts. This implies that modules can be written in any suitable programming language
on any software platform. The only requirement is API accessibility via HTTP(S) end-
point. Currently, all modules (written in Python, C++, C#) run on Microsoft IIS within
95
a single virtual machine, but in future, they could be relocated, if required, e.g. for load
balancing or other purposes.
The calculation results obtained from the calculation modules are processed by the
Web-application to build a report on solving the problem by various methods or by a
high-level collective solution module. Web-application contains a list of active modules
in a config file which makes it easy to add module or update its default settings (all
URIs are currently relative, illustrating a single host application, but in future, they
could be reconfigured to reside on separate hosts referred by absolute URIs):
{
"algorithms": {
"knn": {
"type": "classification",
"uri": "/algorithms/knn",
"fullName": "K Neighbors"
},
"svm": {
"type": "classification",
"uri": "/algorithms/svm",
"fullName": "SVM"
},
...
},
"combinations": {
"average": {
"uri": "/combinations/average",
"fullName": "Average value"
},
"majority": {
"uri": "/combinations/majority",
"fullName": "Voting by majority"
},
...
}
}
4 The ParIS System Application for Inorganic Compounds
Physical Properties Prediction
The developed system was used to predict the crystal lattice parameter of not yet ob-
tained chalcospinels – promising materials for creating magneto-optical memory ele-
ments and sensors [22]. Predicting of crystal lattice parameters of compounds is of great
interest for both chemical research and materials science investigations. Machine learn-
ing methods are widely used to solve this problem. For example, in [23-26], the crystal
96
lattice parameters of orthorhombic perovskites with ABO3 composition not yet ob-
tained were predicted using the methods of neural network training and support vector
machine. Using the neural network training and regression on support vectors, it was
possible to predict the crystal lattice parameters of cubic and monoclinic perovskites
with ABX3 composition (X is halogen or oxygen) [27]. The same methods and random
forest learning were used to predict the crystal lattice parameters of cubic perovskites
of A2+2BCO6 composition [28, 29] and apatites [30-32]. The lattice parameters and band
gap were predicted for compounds of ABX2 composition with chalcopyrite structure
using neural network training and various statistical methods (discriminate analysis,
principal component analysis, etc.) [33].
First, using the information-analytical system developed by us for the computer-
aided inorganic compounds design [34], new chalcospinels with AIBIIICIVX4 composi-
tions (A, B and C – hereinafter, various chemical elements, and X – S or Se) and
AIIBIIICIIIS4 were predicted. In the first case, the sample for machine learning included
information on 20 known chalcospinels of AIBIIICIVX4 composition, 103 compounds
with a crystal structure different from spinel under ambient conditions, and 10 A2X –
B2X3 – CX2 systems in which compounds of ABCX4 composition are not formed. For
the second composition, information on 13 chalcospinels with AIIBIIICIIIS4 composition
and on 20 compounds with a crystal structure different from spinel under normal con-
ditions were selected for the learning set. This learning set was extended by examples
of 48 spinels with AIIBIII2S4 composition, 90 compounds of this composition having a
crystal structure different from spinel, and 18 AS - B2S3 systems in which compounds
of AB2S4 composition are not formed. When predicting new chalcospinels, only data
on the chemical elements’ properties were used. According to examination prediction
using cross-validation, the accuracy of new chalcospinels prediction was not lower than
80%.
Chalcospinels have a cubic crystal lattice; therefore, the only one parameter was
predicted further – “a”. Because of this parameter value is not known for all obtained
chalcospinels, two learning samples for various compositions were prepared. The first
one included 19 examples of the “a” parameter values for AIBIIICIVX4 (X – S or Se)
chalcospinels composition and the second one included 53 examples for AIIBIIICIIIS4
composition, including information on AIIBIII2S4 spinels composition. The feature de-
scription included 11 property values for each element that is a part of the chalcospinel,
i.e. 44 features values for AIBIIICIVX4 composition, and 33 property values for
AIIBIIICIIIS4 composition. Prediction accuracy was determined by calculating the mean
absolute percentage error (MAPE) and a standard mean squared error (MSE) (in the
leave-one-out cross-validation mode).
To illustrate the developed information system capabilities we used, the prediction
results of the crystal lattice parameter for known chalcospinels are presented in the Ta-
ble 1 (for a part of the methods with the smallest error rate values). In fig. 2, the pre-
diction results using a multilevel approach, which is a combination of Random Forest
and Elastic Net machine learning methods, are presented in graphical form. It should
be noted that such a multilevel method provided the smallest prediction errors (see Ta-
bles 1 and 2). The prediction results using this method for AIBIIICIVX4 composition is
shown in Table 3.
97
Table 1. Crystal lattice parameter examination prediction results for AIBIIICIVX4 composition
chalcospinels.
Composition MAPE 0.10 0.10 0.11 0.09
MSE 0.02 0.02 0.02 0.01
Method Ridge Re- Bayesian ARD Re- Random
gression Ridge gression Forest +
Regres- Elastic Net
sion
a, Å (ex-
peri- a, Å (prediction)
mental)
LiInSnS4 10.629 10.63 10.63 10.61 10.63
CuVTiS4 9.902 9.91 9.91 9.91 9.91
CuCrSnS4 10.2 10.17 10.17 10.17 10.21
CuCrTiS4 9.9 9.90 9.90 9.90 9.89
CuCoTiS4 9.744 9.75 9.75 9.75 9.750
CuTiZrS4 10.236 10.22 10.22 10.21 10.24
CuTiSnS4 10.244 10.25 10.25 10.24 10.24
CuVZrS4 10.209 10.15 10.15 10.15 10.19
CuVSnS4 10.124 10.19 10.19 10.19 10.14
CuCrZrS4 10.1 10.13 10.13 10.14 10.11
CuCrHfS4 10.1 10.10 10.10 10.10 10.10
CuInSnS4 10.4938 10.48 10.48 10.49 10.48
CuCrSnSe4 10.7 10.67 10.67 10.68 10.71
CuCrTiSe4 10.4 10.40 10.40 10.40 10.40
CuCrZrSe4 10.6 10.64 10.64 10.64 10.60
CuCrHfSe4 10.6 10.60 10.60 10.60 10.60
AgCrSnS4 10.44 10.44 10.44 10.44 10.43
AgInSnS4 10.74 10.75 10.75 10.76 10.75
AgCrSnSe4 10.97 10.95 10.95 10.95 10.96
98
Table 2. Crystal lattice parameter examination prediction results for AIIBIIICIIIS4 composition
chalcospinels.
Composition MAPE 0.18 0.17 0.18 0.10
MSE 0.05 0.04 0.05 0.02
Method Ridge Re- Bayesian ARD Re- Random
gression Ridge Re- gression Forest
gression + Elas-
tic Net
a, Å (ex- a, Å (prediction)
peri-
mental)
MnCrInS4 10.4297 10.42 10.42 10.42 10.41
FeCrInS4 10.323 10.30 10.30 10.30 10.31
CoCrInS4 10.31 10.26 10.25 10.29 10.31
NiCrInS4 10.22 10.15 10.16 10.20 10.31
CdCrGaS4 10.1784 10.22 10.24 10.24 10.18
CuCoRhS4 9.64 9.65 9.66 9.67 9.66
CdSbInS4 10.8 10.78 10.77 10.783 10.77
CdCrInS4 10.54 10.51 10.51 10.49 10.44
A b
Fig. 2. Comparison of the values predicted using multilevel predicting (random forest + elastic
network) of the chalcospinel crystal lattice parameter with experimental values for AIBIIICIVX4
(a) and AIIBIIICIIIS4 (b) compositions.
99
Table 3. Crystal lattice parameter prediction results for AIBIIICIVX4 composition
chalcospinels.
Composition a, Å Composition a, Å Composition a, Å
CuInTiS4 10.10 AgCoZrS4 10.19 CuCoZrSe4 10.46
CuCoZrS4 9.99 AgInZrS4 10.62 CuVSnSe4 10.48
CuInZrS4 10.41 AgVSnS4 10.40 CuCoSnSe4 10.43
CuCoSnS4 9.95 AgCoSnS4 10.22 CuVHfSe4 10.52
CuTiHfS4 10.23 AgVHfS4 10.37 CuCoHfSe4 10.46
CuVHfS4 10.17 AgCrHfS4 10.25 AgCoZrSe4 10.71
CuCoHfS4 9.98 AgCoHfS4 10.17 AgCrHfSe4 10.79
CuInHfS4 10.39 AgInHfS4 10.59 AgCoHfSe4 10.70
AgInTiS4 10.35 CuCoTiSe4 10.26
AgVZrS4 10.40 CuVZrSe4 10.53
5 Conclusion
The ParIS system was developed for inorganic substances physical properties predic-
tion. It allows a search for the relationships between inorganic compounds physical
properties and chemical elements parameters by means of machine learning analysis of
information contained in databases on inorganic substances properties. The main com-
ponents of the system are an integrated system of databases on inorganic substances
and materials properties developed in Russia and abroad, a machine learning-based data
analysis subsystem for making predictions and a knowledge base for prediction results.
The ML-subsystem includes programs based on the original algorithms developed by
the authors of this paper together with methods implemented in the scikit-learn pack-
age. Using the developed system, “a” crystal lattice parameter values have been suc-
cessfully predicted for not yet obtained chalcospinels with ABCX4 composition (A, B
and C are various chemical elements, and X is S or Se). During prediction chemical
elements properties values were used only. Moreover, the prediction accuracy was ±
0.1 Å. Thus, it is shown that the original multilevel method developed by the authors
provided the smallest predicting errors.
This work was supported in part by the Russian Foundation for Basic Research, pro-
ject nos. 18-07-00080 and 20-01-00609. The study was carried out as part of the state
assignment (project no. 075-00947-20-00).
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