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Balraadjsing, S.; Peijnenburg, W.J.G.M.; Vijver, M.G. 2022

Exploring the potential of in silico machine learning tools for the prediction of acute Daphnia magna nanotoxicity

Article / Letter to editor

open access

Engineered nanomaterials (ENMs) are ubiquitous nowadays, finding their application in different fields of technology and various consumer products. Virtually any chemical can be manipulated at the... Show moreEngineered nanomaterials (ENMs) are ubiquitous nowadays, finding their application in different fields of technology and various consumer products. Virtually any chemical can be manipulated at the nano-scale to display unique characteristics which makes them appealing over larger sized materials. As the production and development of ENMs have increased considerably over time, so too have concerns regarding their adverse effects and environmental impacts. It is unfeasible to assess the risks associated with every single ENM through in vivo or in vitro experiments. As an alternative, in silico methods can be employed to evaluate ENMs. To perform such an evaluation, we collected data from databases and literature to create classification models based on machine learning algorithms in accordance with the principles laid out by the OECD for the creation of QSARs. The aim was to investigate the performance of various machine learning algorithms towards predicting a well-defined in vivo toxicity endpoint (Daphnia magna immobilization) and also to identify which features are important drivers of D. magna in vivo nanotoxicity. Results indicated highly comparable model performance between all algorithms and predictive performance exceeding ∼0.7 for all evaluated metrics (e.g. accuracy, sensitivity, specificity, balanced accuracy, Matthews correlation coefficient, area under the receiver operator characteristic curve). The random forest, artificial neural network, and k-nearest neighbor models displayed the best performance but this was only marginally better compared to the other models. Furthermore, the variable importance analysis indicated that molecular descriptors and physicochemical properties were generally important within most models, while features related to the exposure conditions produced slightly conflicting results. Lastly, results also indicate that reliable and robust machine learning models can be generated for in vivo endpoints with smaller datasets. Show less

Barrientos, A.; Holdship, J.R.; Solar, M.; Martín, S.; Rivilla, V.M.; Viti, S.; ... ; Humire, P. 2021

Towards the prediction of molecular parameters from astronomical emission lines using Neural Networks

Article / Letter to editor

open access

Brandsen, A. 2022

Digging in documents: using text mining to access the hidden knowledge in Dutch archaeological excavation reports

Doctoral Thesis

open access

The archaeology domain produces large amounts of texts, too much to effectively read or manually search through for research. To alleviate this problem, we created a search system (called AGNES),... Show moreThe archaeology domain produces large amounts of texts, too much to effectively read or manually search through for research. To alleviate this problem, we created a search system (called AGNES), which combines full text search with entity and geographical search. We first created a manually labelled data set to train a Named Entity Recognition model, which is used to extract entities from text. We also did a user requirement study, and usability evaluation on the system, to make sure it is suitable for archaeological research. In a case study on Early Medieval cremations, we show that using AGNES leads to a knowledge increase when compared to the knowledge of experts, gathered using previously available search engines. This shows that this kind of intelligent search system can help with literature research, find more relevant data, and lead to a better understanding of the past. Show less

Brandsen, A.; Lambers, K.; Verberne, S.; Wansleeben, M. 2019

User Requirement Solicitation for an Information Retrieval System Applied to Dutch Grey Literature in the Archaeology Domain

Article / Letter to editor

open access

In this paper, we present the results of user requirement solicitation for a search system of grey literature in archaeology, specifically Dutch excavation reports. This search system uses Named... Show moreIn this paper, we present the results of user requirement solicitation for a search system of grey literature in archaeology, specifically Dutch excavation reports. This search system uses Named Entity Recognition and Information Retrieval techniques to create an effective and effortless search experience. Specifically, we used Conditional Random Fields to identify entities, with an average accuracy of 56%. This is a baseline result, and we identified many possibilities for improvement. These entities were indexed in ElasticSearch and a user interface was developed on top of the index. This proof of concept was used in user requirement solicitation and evaluation with a group of end users. Feedback from this group indicated that there is a dire need for such a system, and that the first results are promising. Show less

Bruin, G.J. de; Veenman, C.J.; Herik, H.J. van den; Takes, F.W. 2021

Experimental evaluation of train and test split strategies in link prediction

Article in monograph or in proceedings

open access

In link prediction, the goal is to predict which links will appear in the future of an evolving network. To estimate the performance of these models in a supervised machine learning model, disjoint... Show moreIn link prediction, the goal is to predict which links will appear in the future of an evolving network. To estimate the performance of these models in a supervised machine learning model, disjoint and independent train and test sets are needed. However, objects in a real-world network are inherently related to each other. Therefore, it is far from trivial to separate candidate links into these disjoint sets.Here we characterize and empirically investigate the two dominant approaches from the literature for creating separate train and test sets in link prediction, referred to as random and temporal splits. Comparing the performance of these two approaches on several large temporal network datasets, we find evidence that random splits may result in too optimistic results, whereas a temporal split may give a more fair and realistic indication of performance. Results appear robust to the selection of temporal intervals. These findings will be of interest to researchers that employ link prediction or other machine learning tasks in networks. Show less

De Gouveia da Costa Cachucho, R.E. 2018

Methods and tools for mining multivariate time series

Doctoral Thesis

open access

Mining time series is a machine learning subfield that focuses on a particular data structure, where variables are measured over (short or long) periods of time. In this thesis we focus on... Show moreMining time series is a machine learning subfield that focuses on a particular data structure, where variables are measured over (short or long) periods of time. In this thesis we focus on multivariate time series, with multiple vari- ables measured over the same period of time. In most cases, such variables are collected at different sampling rates. When combined, these variables can be explored with machine learning methods for multiple purposes.Firstly, we consider the possibility of unsupervised learning. In this case, we propose a pattern recognition method that discovers subsets of variables that show consistent behavior in a number of shared time segments. Fur- thermore, when in a supervised setting, given a dependent variable (target),we propose a method that aggregates independent variables into meaningful features.Additionally to the methods above, we provide two tools in the form of Software as a Service, where users without programming background can intuitively follow the learning and testing methodologies for both methods.Finally, we present an applied study of machine learning to improve speed skating athletes performance. Here, we make a deep analysis of historical data, in order to help optimize performance results. Show less

Echtenbruck, M.M. 2020

Optimally weighted ensembles of surrogate models for sequential parameter optimization

Doctoral Thesis

open access

It is a common technique in global optimization with expensive black-box functions to learn a surrogate-model of the response function from past evaluations and use it to decide on the location of... Show moreIt is a common technique in global optimization with expensive black-box functions to learn a surrogate-model of the response function from past evaluations and use it to decide on the location of future evaluations.In surrogate-model-assisted optimization, selecting the right modeling technique without preliminary knowledge about the objective function can be challenging. It might be beneficial if the algorithm trains many different surrogate models and selects the model with the smallest training error. This approach is known as model selection.In this thesis, a generalization of this approach is developed. Instead of choosing a single model, the optimal convex combinations of model predictions is used to combine surrogate models into one more accurate ensemble surrogate model.This approach is studied in a fundamental way, by first evaluating minimalistic ensembles of only two surrogate models in detail and then proceeding to ensembles with more surrogate models.Finally, the approach is adopted and evaluated in the context of sequential parameter optimization. Besides discussing the general strategy, the optimal frequency of learning the convex combination of weights is investigated.The results provide insights into the performance, scalability, and robustness of the approach. Show less

Goedmakers, C.M.W. 2023

Outcome after anterior cervical discectomy: from inferential statistics to Machine Learning

Doctoral Thesis

some documents under embargo until 2025-09-21

After standard surgery for neck hernias, about 25% of patients report low satisfaction. This thesis applied inferential statistics to clinical data and Machine Learning to medical imaging, with the... Show moreAfter standard surgery for neck hernias, about 25% of patients report low satisfaction. This thesis applied inferential statistics to clinical data and Machine Learning to medical imaging, with the goal of finding out where differences in functional outcomes after surgery come from and how artificial intelligence can improve the diagnostic and prognostic process. The initial idea that differences in functional recovery were due to surgical technique was refuted by an RCT from this dissertation. The differences in functional recovery between three different surgical groups (removal of the intervertebral disc without artificial material, placement of intervertebral disc prosthesis, and fusion of vertebrae with a cage) were found to be minimal. It was striking that not surgical technique, but patients' mental health and preoperative, radiological imaging were found to be predictive of clinical recovery after surgery. Although the intervertebral disc prosthesis did not deliver on the promise of preserving mobility and thus could not prevent degeneration at adjacent levels, using Deep Learning based solely on the preoperative MRI of the neck, researchers were able to predict, among other things, which patients would require reoperation after surgery for that adjacent degeneration. The Deep Learning model did that significantly better than an experienced neuroradiologist and neurosurgeon. Such Deep Learning models eliminate the need for time-consuming questionnaires and are thus more cost-effective and less stressful for the patient, while they can be used to identify radiological features important for predicting the postoperative course. After validation with larger radiological datasets, these models can support clinical decision-making and help physicians develop personalized treatment strategies. Challenges within image analysis research for the spine lies in integrating different models into one automated process, preferably built into the electronic health record. Show less

Gorostiola Gonzalez, M.; Janssen, A.P.A.; IJzerman, A.P.; Heitman, L.H.; Westen, G.J.P. van 2022

Oncological drug discovery: AI meets structure-based computational research

Article / Letter to editor

open access

The integration of machine learning and structure-based methods has proven valuable in the past as a way to prioritize targets and compounds in early drug discovery. In oncological research, these... Show moreThe integration of machine learning and structure-based methods has proven valuable in the past as a way to prioritize targets and compounds in early drug discovery. In oncological research, these methods can be highly beneficial in addressing the diversity of neoplastic diseases portrayed by the different hallmarks of cancer. Here, we review six use case scenarios for integrated computational methods, namely driver prediction, computational mutagenesis, (off)-target prediction, binding site prediction, virtual screening, and allosteric modulation analysis. We address the heterogeneity of integration approaches and individual methods, while acknowledging their current limitations and highlighting their potential to bring drugs for personalized oncological therapies to the market faster. Show less

Kurchaba, S.; Vliet, J. van; Verbeek, F.J.; Veenman, C.J. 2023

Anomalous NO2 emitting ship detection with TROPOMI satellite data and machine learning

Article / Letter to editor

open access

Starting from 2021, more demanding NOx emission restrictions were introduced for ships operating in the North and Baltic Sea waters. Since all methods currently used for ship compliance monitoring are financially and time demanding, it is important to prioritize the inspection of ships that have high chances of being non-compliant. The current state-of-the-art approach for a large-scale ship NO2 estimation is a supervised machine learning-based segmentation of ship plumes on TROPOMI/S5P images. However, challenging data annotation and insufficiently complex ship emission proxy used for the validation limit the applicability of the model for ship compliance monitoring. In this study, we present a methodology towards the automated and scalable selection of potentially non-compliant ships using a combination of machine learning models on TROPOMI satellite data. It is based on a proposed regression model predicting the amount of NO2 that is expected to be produced by a ship with certain properties operating in the given atmospheric conditions. The model does not require manual labeling and is validated with TROPOMI data directly. The differences between the predicted and actual amount of produced NO2 are integrated over observations of the ship in time and are used as a measure of the inspection worthiness of a ship. To add further evidence, we compare the obtained results with the results of the previously developed segmentation-based method. Ships that are also highly deviating in accordance with the segmentation method require further attention. If no other explanations can be found by checking the TROPOMI data, the respective ships are advised to be the candidates for inspection.

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Marchetti, T. 2019

Hunting for the fastest stars in the Milky Way

Doctoral Thesis

open access

The high velocity tail of the total velocity distribution of stars provides essential insight into fundamental properties of the Galaxy. Hypervelocity stars (HVSs), travelling on unbound orbits... Show moreThe high velocity tail of the total velocity distribution of stars provides essential insight into fundamental properties of the Galaxy. Hypervelocity stars (HVSs), travelling on unbound orbits coming from the Galactic Centre, are powerful tracers of the underlying Galactic gravitational potential, and can shed light on the stellar population in the proximity of our massive black hole. Runaway stars, ejected from the stellar disk, provide information on binary evolution and stellar clusters' dynamical processes. The advent of the data from the European Space Agency satellite Gaia has revolutionized our knowledge on high velocity stars. In my PhD thesis entitled "Hunting for the fastest stars in the Milky Way" I present my work on searching for the fastest stars in the Milky Way. I start by presenting our modelling work on predicting the HVS population expected to be contained in the Gaia catalogue. Then I illustrate the data mining techniques built and implemented to find these rare objects in the first and second data release of Gaia. Finally, I conclude discussing how HVSs can be used to constrain the Galactic dark matter halo and the binary population in the Galactic Centre. Show less

Moussa, C. 2023

Algorithm selection and configuration for Noisy Intermediate Scale Quantum methods for industrial applications

Doctoral Thesis

open access

Quantum hardware comes with a different computing paradigm and new ways to tackle applications. Much effort has to be put into understanding how to leverage this technology to give real-world... Show moreQuantum hardware comes with a different computing paradigm and new ways to tackle applications. Much effort has to be put into understanding how to leverage this technology to give real-world advantages in areas of interest for industries such as combinatorial optimization or machine learning. Variational quantum algorithms (VQAs) have been introduced as a way to work within the scope of reach of the current imperfect and unstable hardware. A VQA boils down to a parameterized quantum circuit, which is a quantum circuit with adjustable real-valued parameters. These parameters are generally tweaked by a classical optimization algorithm to optimize a quantity of interest. As VQAs are most often used as heuristics, it is not clear whether they genuinely outperform current classical state-of-the-art algorithms in relevant domains of application. Plus, a VQA can come with many components (which can also be calledhyperparameters) making it a (growing) complex system to analyze performances on many considered tasks. Consequently, we will face the issues of algorithm selection and configuration, which we tackle through this thesis on many examples relevant to industrial applications. In this thesis, VQAs for combinatorial optimization, chemistry/material science, and machine learning problems were considered. Show less

Nijssen, Siegfried Gerardus Remius 2006

Mining Structured Data

Doctoral Thesis

open access

Many databases do not consist of a single table of fixed dimensions, but of objects that are related to each other: the databases are relational, or structured. We study the discovery of patterns... Show moreMany databases do not consist of a single table of fixed dimensions, but of objects that are related to each other: the databases are relational, or structured. We study the discovery of patterns in such data. In our approach, a data analyst specifies constraints on patterns that she believes to be of interest, and the computer searches for patterns that satisfy these constraints. An important constraint on which we focus, is the constraint that a pattern should have a significant number of occurrences in the data. Constraints like this allow the search to be performed reasonably efficiently. We develop algorithms for searching ppatterns taht are represented in formal first order logic, tree data structures and graph data structures. We perform experiments in which these algorithms, and algorithms proposed by other researchers, are compared with each other, and study which properties determine the efficiency of the algorithms. As a result, we are able to develop more efficient algorithms. As application we study the discovery of fragments in molecular datasets. The aim is to discover fragments that relate the structure of molecules to their activity. Show less

Pratiwi Bunga, C.; Dusseldorp, E.; Karch, J.D.; de Rooij, M. 2023

Predictive performance of psychological tests: is it better to use items than subscales?

Article / Letter to editor

open access

Sbrollini, A.; Barocci, M.; Mancinelli, M.; Paris, M.; Raffaelli, S.; Marcantoni, I.; ... ; Burattini, L. 2023

Automatic diagnosis of newly emerged heart failure from serial electrocardiography by repeated structuring & learning procedure

Article / Letter to editor

open access

Heart failure (HF) diagnosis, typically visually performed by serial electrocardiography, may be supported by machine-learning approaches. Repeated structuring & learning procedure (RS & LP... Show moreHeart failure (HF) diagnosis, typically visually performed by serial electrocardiography, may be supported by machine-learning approaches. Repeated structuring & learning procedure (RS & LP) is a constructive algorithm able to automatically create artificial neural networks (ANN); it relies on three parameters, namely maximal number of hidden layers (MNL), initializations (MNI) and confirmations (MNC), arbitrarily set by the user. The aim of this study is to evaluate RS & LP robustness to varying values of parameters and to identify an optimized combination of parameter values for HF diagnosis. To this aim, the Leiden University Medical Center HF data-base was used. The database is constituted by 129 serial ECG pairs acquired in patients who experienced myocardial infarction; 48 patients developed HF at follow-up (cases), while 81 remained clinically stable (controls). Overall, 15 ANNs were created by considering 13 serial ECG features as inputs (extracted from each serial ECG pair), 2 classes as outputs (cases/controls), and varying values of MNL (1, 2, 3, 4 and 10), MNI (50, 250, 500, 1000 and 1500) and MNC (2, 5, 10, 20 and 50). The area under the curve (AUC) of the receiver operating characteristic did not significantly vary with varying parameter values (P >= 0.09). The optimized combination of parameter values, identified as the one showing the highest AUC, was obtained for MNL = 3, MNI = 500 and MNC = 50 (AUC = 86 %; ANN structure: 3 hidden layers of 14, 14 and 13 neurons, respectively). Thus, RS & LP is robust, and the optimized ANN represents a potentially useful clinical tool for a reliable auto-matic HF diagnosis. Show less

Sears, A.M. 2020

Algorithmic speech and freedom of expression

Article / Letter to editor

open access

Algorithms have become increasingly common, and with this development, so have algorithms that approximate human speech. This has introduced new issues with which courts and legislators will have... Show moreAlgorithms have become increasingly common, and with this development, so have algorithms that approximate human speech. This has introduced new issues with which courts and legislators will have to grapple. Courts in the United States have found that search engine results are a form of speech that is protected by the Constitution, and cases in Europe concerning liability for autocomplete suggestions have led to varied results. Beyond these instances, insight into how courts handle algorithmic speech are few and far between.By focusing on three categories of algorithmic speech, defined as curated production, interactive/responsive production, and semiautonomous production, this Article analyzes these various forms of algorithmic speech within the international framework for freedom of expression. After a brief introduction of that framework and a look towards approaches to algorithmic speech in the United States, the Article then examines whether the creators or controllers of different forms of algorithms should be considered content providers or mere intermediaries, the determination of which ultimately has implications for liability, which is also explored. The Article then looks at possible interferences with algorithmic speech, and how such interferences may be examined under the three-part test—particular attention is paid to the balancing of rights and interests at play—in order to answer the question of the extent to which algorithmic speech is worthy of protection under international standards of freedom of expression. Finally, other relevant issues surrounding algorithmic speech are discussed that will have an impact going forward, many of which involve questions of policy and societal values that accompany granting algorithmic speech protection. Show less

Shan, H. 2020

Towards high performance and efficient brain computer interface character speller : convolutional neural network based methods

Doctoral Thesis

open access

A P300-based Brain Computer Interface character speller, also known as P300 speller, has been an important communication pathway, under extensive research, for people who lose motor ability, such... Show moreA P300-based Brain Computer Interface character speller, also known as P300 speller, has been an important communication pathway, under extensive research, for people who lose motor ability, such as patients with Amyotrophic Lateral Sclerosis or spinal-cord injury because a P300 speller allows human-beings to directly spell characters using eye-gazes, thereby building communication between the human brain and a computer. Unfortunately, P300 spellers are still not used in human’s daily life and remain in an experimental stage at research labs. The reason for this situation is that the performance and the efficiency of current P300 spellers are unacceptably low for BCI users in their daily life. Therefore, in this thesis, we have focused our attention on developing high performance and efficient P300 spellers in order to bring P300 spellers into practical use. More specifically, in order to increase the performance of a P300 speller, we have developed methods to increase the character spelling accuracy and the Information Transfer Rate. In order to improve the efficiency of a P300 speller, we have developed methods to reduce the number of sensors needed to acquire EEG signals as well as to reduce the complexity of the classifier used in a P300 speller without losing the performance. Show less

Stel, W. van der; Yang, H.; Le Dévédec, S.E.; Water, B. van de; Beltman, J.B.; Danen, E.H.J. 2022

High-content high-throughput imaging reveals distinct connections between mitochondrial morphology and functionality for oxphos complex I, III, and V inhibitors

Article / Letter to editor

open access

Cells can adjust their mitochondrial morphology by altering the balance between mitochondrial fission and fusion to adapt to stressful conditions. The connection between a chemical perturbation,... Show moreCells can adjust their mitochondrial morphology by altering the balance between mitochondrial fission and fusion to adapt to stressful conditions. The connection between a chemical perturbation, changes in mitochondrial function, and altered mitochondrial morphology is not well understood. Here, we made use of high-throughput high-content confocal microscopy to assess the effects of distinct classes of oxidative phosphorylation (OXPHOS) complex inhibitors on mitochondrial parameters in a concentration and time resolved manner. Mitochondrial morphology phenotypes were clustered based on machine learning algorithms and mitochondrial integrity patterns were mapped. In parallel, changes in mitochondrial membrane potential (MMP), mitochondrial and cellular ATP levels, and viability were microscopically assessed. We found that inhibition of MMP, mitochondrial ATP production, and oxygen consumption rate (OCR) using sublethal concentrations of complex I and III inhibitors did not trigger mitochondrial fragmentation. Instead, complex V inhibitors that suppressed ATP and OCR but increased MMP provoked a more fragmented mitochondrial morphology. In agreement, complex V but not complex I or III inhibitors triggered proteolytic cleavage of the mitochondrial fusion protein, OPA1. The relation between increased MMP and fragmentation did not extend beyond OXPHOS complex inhibitors: increasing MMP by blocking the mPTP pore did not lead to OPA1 cleavage or mitochondrial fragmentation and the OXPHOS uncoupler FCCP was associated with OPA1 cleavage and MMP reduction. Altogether, our findings connect vital mitochondrial functions and phenotypes in a high-throughput high-content confocal microscopy approach that help understanding of chemical-induced toxicity caused by OXPHOS complex perturbing chemicals. Show less

Thill, M. 2022

Machine learning and deep learning approaches for multivariate time series prediction and anomaly detection

Doctoral Thesis

open access

In many real-world applications today, it is critical to continuously record and monitor certain machine or system health indicators to discover malfunctions or other abnormal behavior at an early... Show moreIn many real-world applications today, it is critical to continuously record and monitor certain machine or system health indicators to discover malfunctions or other abnormal behavior at an early stage and prevent potential harm. The demand for such reliable monitoring systems is expected to increase in the coming years. Particularly in the industrial context, in the course of ongoing digitization, it is becoming increasingly important to analyze growing volumes of data in an automated manner using state-of-the-art algorithms. In many practical applications, one has to deal with temporal data in the form of data streams or time series. The problem of detecting unusual (or anomalous) behavior in time series is commonly referred to as time series anomaly detection. Anomalies are events observed in the data that do not conform to the normal or expected behavior when viewed in their temporal context.This thesis focuses on unsupervised machine learning algorithms for anomaly detection in time series. In an unsupervised learning setup, a model attempts to learn the normal behavior in a time series — which might already be contaminated with anomalies — without any external assistance. The model can then use its learned notion of normality to detect anomalous events. Show less

Thomson, S.L.; Stein, N. van; Berg, D. van den; Leeuwen, C. van 2023

The opaque nature of intelligence and the pursuit of explainable AI

Article in monograph or in proceedings

open access

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