To study the ways in which compounds can induce adverse effects, toxicologists have been constructing Adverse Outcome Pathways (AOPs). An AOP can be considered as a pragmatic tool to capture and visualize mechanisms underlying different types of toxicity inflicted by any kind of stressor, and describes the interactions between key entities that lead to the adverse outcome on multiple biological levels of organization. The construction or optimization of an AOP is a labor intensive process, which currently depends on the manual search, collection, reviewing and synthesis of available scientific literature. This process could however be largely facilitated using Natural Language Processing (NLP) to extract information contained in scientific literature in a systematic, objective, and rapid manner that would lead to greater accuracy and reproducibility. This would support researchers to invest their expertise in the substantive assessment of the AOPs by replacing the time spent on evidence gathering by a critical review of the data extracted by NLP. As case examples, we selected two frequent adversities observed in the liver: namely, cholestasis and steatosis denoting accumulation of bile and lipid, respectively. We used deep learning language models to recognize entities of interest in text and establish causal relationships between them. We demonstrate how an NLP pipeline combining Named Entity Recognition and a simple rules-based relationship extraction model helps screen compounds related to liver adversities in the literature, but also extract mechanistic information for how such adversities develop, from the molecular to the organismal level. Finally, we provide some perspectives opened by the recent progress in Large Language Models and how these could be used in the future. We propose this work brings two main contributions: 1) a proof-of-concept that NLP can support the extraction of information from text for modern toxicology and 2) a template open-source model for recognition of toxicological entities and extraction of their relationships. All resources are openly accessible via GitHub (https://github.com/ontox-project/en-tox).
The built environment requires energy-flexible buildings to reduce energy peak loads and to maximize the use of (decentralized) renewable energy sources. The challenge is to arrive at smart control strategies that respond to the increasing variations in both the energy demand as well as the variable energy supply. This enables grid integration in existing energy networks with limited capacity and maximises use of decentralized sustainable generation. Buildings can play a key role in the optimization of the grid capacity by applying demand-side management control. To adjust the grid energy demand profile of a building without compromising the user requirements, the building should acquire some energy flexibility capacity. The main ambition of the Brains for Buildings Work Package 2 is to develop smart control strategies that use the operational flexibility of non-residential buildings to minimize energy costs, reduce emissions and avoid spikes in power network load, without compromising comfort levels. To realise this ambition the following key components will be developed within the B4B WP2: (A) Development of open-source HVAC and electric services models, (B) development of energy demand prediction models and (C) development of flexibility management control models. This report describes the developed first two key components, (A) and (B). This report presents different prediction models covering various building components. The models are from three different types: white box models, grey-box models, and black-box models. Each model developed is presented in a different chapter. The chapters start with the goal of the prediction model, followed by the description of the model and the results obtained when applied to a case study. The models developed are two approaches based on white box models (1) White box models based on Modelica libraries for energy prediction of a building and its components and (2) Hybrid predictive digital twin based on white box building models to predict the dynamic energy response of the building and its components. (3) Using CO₂ monitoring data to derive either ventilation flow rate or occupancy. (4) Prediction of the heating demand of a building. (5) Feedforward neural network model to predict the building energy usage and its uncertainty. (6) Prediction of PV solar production. The first model aims to predict the energy use and energy production pattern of different building configurations with open-source software, OpenModelica, and open-source libraries, IBPSA libraries. The white-box model simulation results are used to produce design and control advice for increasing the building energy flexibility. The use of the libraries for making a model has first been tested in a simple residential unit, and now is being tested in a non-residential unit, the Haagse Hogeschool building. The lessons learned show that it is possible to model a building by making use of a combination of libraries, however the development of the model is very time consuming. The test also highlighted the need for defining standard scenarios to test the energy flexibility and the need for a practical visualization if the simulation results are to be used to give advice about potential increase of the energy flexibility. The goal of the hybrid model, which is based on a white based model for the building and systems and a data driven model for user behaviour, is to predict the energy demand and energy supply of a building. The model's application focuses on the use case of the TNO building at Stieltjesweg in Delft during a summer period, with a specific emphasis on cooling demand. Preliminary analysis shows that the monitoring results of the building behaviour is in line with the simulation results. Currently, development is in progress to improve the model predictions by including the solar shading from surrounding buildings, models of automatic shading devices, and model calibration including the energy use of the chiller. The goal of the third model is to derive recent and current ventilation flow rate over time based on monitoring data on CO₂ concentration and occupancy, as well as deriving recent and current occupancy over time, based on monitoring data on CO₂ concentration and ventilation flow rate. The grey-box model used is based on the GEKKO python tool. The model was tested with the data of 6 Windesheim University of Applied Sciences office rooms. The model had low precision deriving the ventilation flow rate, especially at low CO2 concentration rates. The model had a good precision deriving occupancy from CO₂ concentration and ventilation flow rate. Further research is needed to determine if these findings apply in different situations, such as meeting spaces and classrooms. The goal of the fourth chapter is to compare the working of a simplified white box model and black-box model to predict the heating energy use of a building. The aim is to integrate these prediction models in the energy management system of SME buildings. The two models have been tested with data from a residential unit since at the time of the analysis the data of a SME building was not available. The prediction models developed have a low accuracy and in their current form cannot be integrated in an energy management system. In general, black-box model prediction obtained a higher accuracy than the white box model. The goal of the fifth model is to predict the energy use in a building using a black-box model and measure the uncertainty in the prediction. The black-box model is based on a feed-forward neural network. The model has been tested with the data of two buildings: educational and commercial buildings. The strength of the model is in the ensemble prediction and the realization that uncertainty is intrinsically present in the data as an absolute deviation. Using a rolling window technique, the model can predict energy use and uncertainty, incorporating possible building-use changes. The testing in two different cases demonstrates the applicability of the model for different types of buildings. The goal of the sixth and last model developed is to predict the energy production of PV panels in a building with the use of a black-box model. The choice for developing the model of the PV panels is based on the analysis of the main contributors of the peak energy demand and peak energy delivery in the case of the DWA office building. On a fault free test set, the model meets the requirements for a calibrated model according to the FEMP and ASHRAE criteria for the error metrics. According to the IPMVP criteria the model should be improved further. The results of the performance metrics agree in range with values as found in literature. For accurate peak prediction a year of training data is recommended in the given approach without lagged variables. This report presents the results and lessons learned from implementing white-box, grey-box and black-box models to predict energy use and energy production of buildings or of variables directly related to them. Each of the models has its advantages and disadvantages. Further research in this line is needed to develop the potential of this approach.
We give a refinement of the well known business model canvas by Osterwalder and Pigneur by splitting the basic blocks into further subblocks to reduce confusion and increase its expressive power. The splitting is used in an online tool which in addition comes with a set of questions to further structure the business modelling process and help doing thought experiments.
