Expertise

Dr. Bittremieux's research deals with developing advanced machine learning techniques to uncover novel knowledge from mass spectrometry-based proteomics and metabolomics data. While his current research mainly focuses on how deep learning can be used to analyze mass spectrometry data he is interested in a wide variety of bioinformatics problems. An important part of his work involves developing insights and computational approaches for quality control in biological mass spectrometry.

Technique

bioinformatics machine learning deep learning mass spectrometry proteomics metabolomics

Users

bioinformatics researchers computational biology researchers

Keywords

Machine learning

Analysis of dynamic network data Most works in network analysis concentrate on static graphs and find patterns such as the most in influential nodes in the network. Very few existing methods are able to deal with repeated interactions between nodes in a network. The main goal of the research in this topic is hence to fill this gap by developing methods to identify patterns in interactions between network nodes. We studied so-called information channels that indicate information flows. Process Mining In process mining the object of study are logs generated by business processes. Consider for instance a log generated by a leave request system, recording activities such as users logging in, opening a new request, managers approving requests, emails being sent by the system, etc. In process mining such logs are analyzed to better understand, monitor, and improve the business processes. One tasks in this context is detecting complex events. Complex events can be used to find pre-defined security problems or abnormalities. Often, however, anomalies may occur that are not foreseen in the systems. In order to be able to handle such cases, anomaly detection techniques are necessary. With the following work on model-based anomaly detection using dynamic Bayesian networks, we won the Business Process Intelligence challenge at the BPM 2018 conference: S. Pauwels and T. Calders. Detecting and Explaining Drifts in Yearly Grant Applications. In BPM Workshop Business Process Intelligence (BPI), 2018. Fairness-Aware Machine Learning In contemporary society we are continuously being profiled; banks have profiles to divide up people according to credit risk, insurance companies profile clients for accident risk, telephone companies profile users on their calling behavior, web corporations profile users according to their interests and preferences based on web activity and visitation patterns. These profiles are more and more built automatically by machine learning methods trained on historical data. Within society there are growing concerns that these machine learning methods do not have ethical or moral restrictions. Recent studies show indeed that in circumstances where historical data is biased, or when there is omitted variable bias, automatically learned methods may take decisions that could be considered discriminatory. Apart from ethical considerations, there are also legal restrictions to the use of profiling methods that blindly optimize accuracy without taking unwanted discriminatory effects into account. The recent General Data Protection Regulation (GDPR; Regulation (EU) 2016/679) explicitly mentions profiling (Art. 22 GDPR Automated individual decision-making, including profiling) as an activity in which decisions should not be based on personal data and suitable measures should be in place to safeguard the data subjects rights and freedoms and legitimate interests. Most profiling techniques, however, do not consider anti-discrimination legislation and may unintentionally produce models that are unfair and hence do not safeguard the data subjects freedoms. A further complication is that often detecting whether a model is unfair, is highly non-trivial.

Technique

- Formalizing research problems mathematically; - Development of algorithmic solutions; - Study of computational properties of algorithms; - Case studies: application of developed techniques in real-life contexts.

Users

All sectors in which machine learning is applied, including: - default prediction in the financial sector; - risk assessment in insurance; - outlier detection from log files for security monitoring; - predictive modelling. There are existing collaborations with insurance companies (fairness in machine leanring - building fair score models), bankin sector (default prediction), scientific institutes (BIRA: analysis of spectrograms for meteor detection),...

Keywords

Pattern mining

Dr. Bart Cuypers (Msc. 2013, PhD 2018) is FWO post-doc and a bioinformatics scientist who uses multi 'omic and machine learning methods to unravel the molecular biology and drug-resistance mechanisms of pathogens, as well as their host responses. Currently, his post-doctoral at the interface the Adrem Data Lab (University of Antwerp, Antwerp, Belgium). Bart Cuypers has a background in biology (BSc) and cell- and systems biology (MSc). During his PhD, he studied the functional impact and adaptive role of aneuploidy and gene copy number variation in the protozoan parasite Leishmania, a pathogen of which the molecular biology is still elusive. As such, he worked on the collection, analysis, integration and interpretation of (epi-) genomics, transcriptomics, proteomics and metabolomics data over a wide array of genetic backgrounds, life stages and resistance profiles. As such, he has both wet-lab and computational experience. His post-doc focussed on unravelling the (poorly characterised) post-transcriptional regulatory chain of Leishmania by integration of third generation sequencing data (PacBio) with ribosome profiling and proteomics. Bart Cuypers has obtained several competitive grants and fellowships. Firstly, he has started his career with an FWO Aspirant fellowship (2013) and later continued with and FWO post-doc fellowship (2018). To strengthen his post-doc project, he has obtained additional BOF funding (BOF KP, 2019) as well as an FWO credit for post-docs (2020) and a credit for a long research stay abroad at the Notredame Lab (7 months, 2019-2020). He is co-promotor the SB fellowship of Katlijn de Meulenaere (2019) that investigates Plasmodium vivax reticulocyte invasion pathways and ligand candidates using a multi-omic approach. Finally, he obtained an award from the UA research council for promising young researchers (2015). In total this accounts to more than 660 000 euro in acquired funding. As a bioinformatics enthusiast and strong supporter of interdisciplinary research Bart Cuypers has a leading role in the International Society for Computational Biology Student Council (Executive team, treasurer) a global network of more than 2000 master students, PhD students and young post-docs that are passionate about computational biology. He is one of the main organisers of the International Society for Computational Biology Student Council webinar programme (ISCB Academy). Further, Bart is involved in several research consortia, such as BIOMINA (Biomedical Informatics Research Network, Antwerp, steering committee member) and the Tuberculosis ‘Omics Research Consortium (TORCH). He also represents the Institute of Tropical Medicine (ITM) in the CalcUA Supercomputer User Board, is member of the academic council at ITM and Faculty of Science Faculty Board at UA. Keywords: Systems Biology, Multi 'omics, Data Mining, Molecular Biology, Molecular Parasitology.

Technique

From sample prep to data analysis for genomics, transcriptomics, proteomics, metabolomics, as well as integrated multi-omics solutions, particularly in the context of infectious diseases. Computationele immunologie (inc. epitope prioritisation) of infectious diseases.

Users

Academic and industrial researchers interested in: (1) (integrated) multi-omics, genomics, transcriptomics, proteomics or metabolomics of infectious diseases, (2) the molecular interactions of pathogens with the human immune system.

Keywords

Data mining, Infectious diseases, Immunology, Machine learning, Transcriptomics, Metabolomics, Genomics, Proteomics

Dr. Wim Cuypers is a postdoctoral researcher at the Adrem Data Lab at the University of Antwerp. With a strong background in microbial genomics, transcriptomics and general bioinformatics, his research focuses on employing cutting-edge techniques to understand and combat infectious diseases. Within the branch of the Adrem Data Lab headed by prof. Kris Laukens, Dr. Cuypers' principal objective centers around harnessing the revolutionary capabilities inherent to nanopore sequencing technology for the purpose of pathogen monitoring. After securing a competitive FWO-SB research grant, Wim conducted extensive investigations into microbial genomics, antimicrobial resistance and transcriptomics for his PhD research from 2018 onwards. Key contributions he made during his PhD include a review on fluoroquinolone resistance in Salmonella which has been cited over 100 times after publication in Microbial Genomics, and a large collaborative study on Salmonella Concord, which was published in Nature Communications. In 2023, he defended his PhD thesis entitled: “Genomic adaptation of Salmonella to antimicrobials and the human host”. In addition to his computational expertise, Wim is also proficient in various wet-lab techniques, including cultivating bacteria, performing DNA extractions, and performing library preps fof sequencing. This practical knowledge allows him to seamlessly integrate benchwork experiments with computational analyses, facilitating a holistic and comprehensive approach to research. Through a strong connection with the Institute of Tropical Medicine in Antwerp were he performed part of his doctoral studies, Wim has established a robust partnership that greatly enriches his academic pursuits. His diverse background and scientific network allows him to actively engage with interdisciplinary teams, fostering an environment conducive to inclusive research. Driven by a passion for effective communication, he can explain difficult scientific concepts to audiences with varying levels of technical expertise. As a true evangelist for the field of bioinformatics and computational biology, Wim holds the position of Vice Chair in the Executive Team of the International Society for Computational Biology (ISCB) Student Council. He plays a crucial role in fostering connections and building bridges within a diverse global network of more than 2000 master's students, PhD students, and early-career researchers who share a profound dedication to advancing the frontiers of computational biology. Driven by a strong sense of social responsibility, and through his active involvement in the ISCB Student Council and his current research position, Wim is dedicated to providing equitable access to sequencing capacity and high-quality bioinformatics training, particularly for individuals in low- and middle-income countries who face limited opportunities in this field.

Technique

DNA isolation Whole-genome sequencing Nanopore sequencing Sequencing QC Genome assembly Variant calling Phylogenetics Identification of resistance markers Bioinformatics pipeline development Antimicrobial susceptibility testing Cultivation of bacteria

Users

Fundamental and applied researchers and clinicians

Keywords

Sequencing, Salmonella, Microbial genetics, Computational biology, Nanopore sequencing, Bacterial resistance, Microbiology, Bioinformatics

Development and study of advanced data mining and machine learning methods. In particular, we investigate: (i) new methods to efficiently discover interesting patterns in sequential data; (ii) new methods to detect contextual anomalies in heterogeneous sequential data; (iii) and new methods for multi-label classification in extremely large datasets. In addition, we investigate applications of these methods in areas such as the monitoring of wind farms and anomaly detection in an Industrial Internet of Things context.

Technique

Development of algorithmic solutions to (un)supervised machine learning problems; Formalizing research problems mathematically; Development of algorithmic solutions; Analysis of properties of algorithms; Case studies: application of developed techniques in real-life contexts.

Users

All sectors in which data mining or machine learning is applied. More specifically, anomaly detection, prediction and/or discovering patterns in sequential data, such as event log data and time series. There are existing collaborations for: (i) predicting labels for federal police; (ii) condition monitoring in wind turbine farms (using pattern mining); (iii) anomaly detection in water consumption of supermarket chains; (iv) data cleaning and entity resolution to combine different databases.

Keywords

Pattern mining, Data mining, Machine learning, Data science

Development and study of advanced methods for data storage, cleaning, processing and querying of vast amounts of data.

Technique

Database Systems, Data Cleaning Methods, Provenance techniques, Indexing methods.

Users

Big data analysts and users of data managements systems.

Keywords

Data providers, Information technology, Theoretical study

Development and study of advanced methods for Data Mining, Big Data Analytics, Recommender Systems, Data Cleaning, and other technologies related to the management and analysis of large amounts of data.

Technique

Data Mining, Big Data Analytics, Recommender Systems, Data Cleaning

Users

Analysts and managers of large amounts of data

Keywords

Mathematics, Data mining, Informatics, Data quality, Pattern mining, Data analysis

Both biological sciences and clinical medicine are currently overwhelmed by vast amounts of complex data and are becoming increasingly dependent on information technology for data analysis, interpretation and organisation. Although powerful data mining techniques are being developed within and outside the University, they are still underutilized in the life sciences. We aim to bring state-of-the-art data mining techniques to life science applications by setting up interdisciplinary collaborations between computer scientists, life scientists and clinicians. Core activities are: 1) the introduction, adaptation and application of innovative pattern mining and machine learning techniques to heterogeneous 'omics data (genome, transcriptome, proteome and metabolome) and to clinical information; 2) using these techniques to generate computational (network) models for biological systems and diseases; and 3) the development of interactive and intuitive visualizations of complex life science data and pattern mining results.

Technique

Various bioinformatics, data mining and artificial intelligence techniques: analysis, interpretation, pattern mining, integration of heterogeneous 'omics data (genome, transcriptome, proteome, metabolome), sequence and structure analysis, spectrum analysis and interpretation, functional analysis of molecular data, multivariate statistics, network theory, algorithmic modeling, advanced machine learning, deep learning, advanced data visualization, prototyping

Users

Life scientists, biomedical researchers, clinicians, molecular biologists

Keywords

Computational biology, Data mining, Pattern mining, Bioinformatics, Artificial intelligence (ai), Systems medicine, Systems biology

My current research interest is the development of automated methods for pharmaceutical compounds identification, i.e. structure elucidation of drug impurities and degradation products. Major research activities include building large spectral library from historical pharmaceutical data and developing advanced machine learning models for compound substructure recommendation. Data used in this study are massive high-resolution mass spectrometry data accumalated in Janssen Pharmaceuticals.

Technique

Mass spectrometry, Machine learning, Network and Graphs, Web server development

Users

Life scientists, biomedical researchers, clinicians, molecular biologists, microbiologist

Keywords

Metabolomics, Bioinformatics

Dr. Meysman specializes in the application of data mining and artificial intelligence techniques on biomedical data. He has worked on molecular 'omics data, genetic data, medical data and immunological data. He has experience with several common bioinformatics pipelines and has aided in the development of bioinformatics databases.

Technique

The data mining expertise includes a wide range of techniques from unsupervised methods (e.g. principle component analysis, frequent item set mining) to supervised methods (e.g. lasso regression, random forest, convolutional neural networks).

Users

Dr. Meysman has collaborated in the past with research hospitals, general practitioners, biotech and pharma companies.

Keywords

Computational biology, Immunogenicity, Bioinformatics