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readme.txt
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Deep hybrid modeling of a HEK293 process: combining Long Short-Term Memory (LSTM) networks with first principles equations
https://doi.org/10.1002/bit.28668
João R. C. Ramos1, #, José Pinto1, #, Gil Poiares-Oliveira1, Ludovic Peeters2, Patrick Dumas2, Rui Oliveira1
1 LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
2 GSK, 89 rue de l'Institut, 1330 Rixensart, Belgium
*Correspondence:
Rui Oliveira
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To run hybrid model training or simulation of two previously trained hybrid model
use the code "hybnet_train_main.m"
This codes shows how to define model structures and which parameter to use to run the
training process. Furthemore, several ways to plot and analyse the results
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This code "hybnet_train_main.m" comes with two predefined hybrid model structures one FFNN and
one LSTM. Both structures were pre-trained and the data saved in "hybrid_FFNN_1.mat"
and "hybrid_LSTM_1.mat". It asks if the user wants to train these model structures again
or simulate from saved files. Different plots are generated and a excel file
"structures_fit_results.xlsx" with the overall results.
The folder ~/data contains data.xlsx with the feed DoE details and the simulations of
concentrations over time generated using a dynamic model. This is a synthetic dataset,
the model was created based on the metabolic model proposed by Robitaille et al. (2015).
It also contains "data.mat" which is the import the concentrations, feed and other relevant
informations. This file is generated using "/data/main_data_processing.m". When imported into
matlab data(i).accum is the total amount of a metabolite that should be in the bioreactor over
time, it is the "sum of all added concentrations × volume added - sample volume × reactor concentration".
The file also contains data(i).m_r which are the reacted amounts over time.
The calculation of data(i).accum is made during the process of data(i).m_r calculation.
The latter is described in the supplementary material of this paper or the file "/data/read_me_data_processing.doc"
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DoE for experiment Br1 - Br9 (see data.xlsx):
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Br5
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Br1 -------------- Br2
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Br7 ----| Br9 |---- Br8
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Br3 -------------- Br4
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Br6
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